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Bibliography on: Ecological Informatics

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ESP: PubMed Auto Bibliography 01 Jun 2023 at 01:43 Created: 

Ecological Informatics

Wikipedia: Ecological Informatics Ecoinformatics, or ecological informatics, is the science of information (Informatics) in Ecology and Environmental science. It integrates environmental and information sciences to define entities and natural processes with language common to both humans and computers. However, this is a rapidly developing area in ecology and there are alternative perspectives on what constitutes ecoinformatics. A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as Knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web. Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like Ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE and Data Conservancy.

Created with PubMed® Query: ( "ecology OR ecological" AND ("data management" OR informatics) NOT "assays for monitoring autophagy" ) NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

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RevDate: 2023-05-30

Borg JM, Buskell A, Kapitany R, et al (2023)

Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research.

Artificial life pii:116175 [Epub ahead of print].

The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.

RevDate: 2023-05-31

Hassard F, Vu M, Rahimzadeh S, et al (2023)

Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.

PloS one, 18(5):e0286259.

BACKGROUND: Schools are high-risk settings for infectious disease transmission. Wastewater monitoring for infectious diseases has been used to identify and mitigate outbreaks in many near-source settings during the COVID-19 pandemic, including universities and hospitals but less is known about the technology when applied for school health protection. This study aimed to implement a wastewater surveillance system to detect SARS-CoV-2 and other public health markers from wastewater in schools in England.

METHODS: A total of 855 wastewater samples were collected from 16 schools (10 primary, 5 secondary and 1 post-16 and further education) over 10 months of school term time. Wastewater was analysed for SARS-CoV-2 genomic copies of N1 and E genes by RT-qPCR. A subset of wastewater samples was sent for genomic sequencing, enabling determination of the presence of SARS-CoV-2 and emergence of variant(s) contributing to COVID-19 infections within schools. In total, >280 microbial pathogens and >1200 AMR genes were screened using RT-qPCR and metagenomics to consider the utility of these additional targets to further inform on health threats within the schools.

RESULTS: We report on wastewater-based surveillance for COVID-19 within English primary, secondary and further education schools over a full academic year (October 2020 to July 2021). The highest positivity rate (80.4%) was observed in the week commencing 30th November 2020 during the emergence of the Alpha variant, indicating most schools contained people who were shedding the virus. There was high SARS-CoV-2 amplicon concentration (up to 9.2x106 GC/L) detected over the summer term (8th June - 6th July 2021) during Delta variant prevalence. The summer increase of SARS-CoV-2 in school wastewater was reflected in age-specific clinical COVID-19 cases. Alpha variant and Delta variant were identified in the wastewater by sequencing of samples collected from December to March and June to July, respectively. Lead/lag analysis between SARS-CoV-2 concentrations in school and WWTP data sets show a maximum correlation between the two-time series when school data are lagged by two weeks. Furthermore, wastewater sample enrichment coupled with metagenomic sequencing and rapid informatics enabled the detection of other clinically relevant viral and bacterial pathogens and AMR.

CONCLUSIONS: Passive wastewater monitoring surveillance in schools can identify cases of COVID-19. Samples can be sequenced to monitor for emerging and current variants of concern at the resolution of school catchments. Wastewater based monitoring for SARS-CoV-2 is a useful tool for SARS-CoV-2 passive surveillance and could be applied for case identification and containment, and mitigation in schools and other congregate settings with high risks of transmission. Wastewater monitoring enables public health authorities to develop targeted prevention and education programmes for hygiene measures within undertested communities across a broad range of use cases.

RevDate: 2023-05-31
CmpDate: 2023-05-31

Wang Y, Lin C, Wang H, et al (2023)

Implementation of pollution source assessment and treatment strategy for plateau railway construction in China: an AHP-cloud model approach.

Environmental monitoring and assessment, 195(6):749.

During the construction process of railways in the plateau region, various types of pollution sources can have serious or even irreversible impacts on the plateau ecology. To address pollution source treatment during the construction process, protect the ecological environment along the railway, and maintain the ecological balance, we collected geological and environmental data and analyzed the influencing factors of pollution sources. Taking sewage as the main research subject, we propose a new method based on the Analytic Hierarchy Process (AHP)-cloud model to classify the pollution source treatment level, establish an index system, and select the ecological environment level, sewage rate, and pollutant characteristics as the three main influencing factors. Finally, we divide the pollution source treatment level into I, II, and III, corresponding to V1 = {I-level} = {high impact}, V2 = {II-level} = {moderate impact}, and V3 = {III-level} = {low impact}. Based on the comprehensive factor weight analysis and the field engineering conditions of the studied railway in the western plateau of China, we classify the pollution source treatment level of six tunnels and propose treatment suggestions for each level. To advance the efficient implementation of environmental protection during the construction of the plateau railway, we propose three policy recommendations that can positively contribute to environmental protection and green development. This work provides theoretical and technical guidance for the treatment of pollution sources in the construction of the plateau railway, which also serves as a significant reference for other similar projects.

RevDate: 2023-05-30

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2023)

The genome sequence of the long-horned flat-body, Carcina quercana (Fabricius, 1775).

Wellcome open research, 8:16.

We present a genome assembly from an individual male Carcina quercana (the long-horned flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 409 megabases in span. Most of the assembly (99.96%) is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,108 protein coding genes.

RevDate: 2023-05-30

Dhellemmes F, Aspillaga E, CT Monk (2023)

ATfiltR: A solution for managing and filtering detections from passive acoustic telemetry data.

MethodsX, 10:102222.

Acoustic telemetry is a popular and cost-efficient method for tracking the movements of animals in the aquatic ecosystem. But data acquired via acoustic telemetry often contains spurious detections that must be identified and excluded by researchers to ensure valid results. Such data management is difficult as the amount of data collected often surpasses the capabilities of simple spreadsheet applications. ATfiltR is an open-source package programmed in R that allows users to integrate all telemetry data collected into a single file, to conditionally attribute animal data and location data to detections and to filter spurious detections based on customizable rules. Such tool will likely be useful to new researchers in acoustic telemetry and enhance results reproducibility.•ATfiltR compiles telemetry files and identifies and stores all data that was collected outside of your study period (e.g. when your receivers were on land for servicing) elsewhere.•As spurious detections are unlikely to appear sequentially in the data, ATfiltR finds all detections that occurred only once (per receiver or in the whole array) within a user-designated time period and stores them elsewhere.•ATfiltR identifies detections that are impossible given the animals' swimming speeds and the receivers detection range and stores them elsewhere.

RevDate: 2023-05-30
CmpDate: 2023-05-29

Mattalia G, Svanberg I, Ståhlberg S, et al (2023)

Outdoor activities foster local plant knowledge in Karelia, NE Europe.

Scientific reports, 13(1):8627.

Wild edible plants, particularly berries, are relevant nutritional elements in the Nordic countries. In contrast to decreasing global trends, approximately 60% of the Finnish population is actively involved in (berry) foraging. We conducted 67 interviews with Finns and Karelians living in Finnish Karelia to: (a) detect the use of wild edible plants, (b) compare those results with the published data about neighbouring Russian Karelians, and (c) document the sources of local plant knowledge. The results revealed three main findings. First, we observed a similarity in wild food plant knowledge among Karelians and Finns from Karelia. Second, we detected divergences in wild food plant knowledge among Karelians living on both sides of the Finnish-Russian border. Third, the sources of local plant knowledge include vertical transmission, acquisition through literary sources, acquisition from "green" nature shops promoting healthy lifestyles, childhood foraging activities performed during the famine period following WWII, and outdoor recreational activities. We argue that the last two types of activities in particular may have influenced knowledge and connectedness with the surrounding environment and its resources at a stage of life that is crucial for shaping adult environmental behaviours. Future research should address the role of outdoor activities in maintaining (and possibly enhancing) local ecological knowledge in the Nordic countries.

RevDate: 2023-05-30
CmpDate: 2023-05-29

Tokito T, Kido T, Muramatsu K, et al (2023)

Impact of Administering Intravenous Azithromycin within 7 Days of Hospitalization for Influenza Virus Pneumonia: A Propensity Score Analysis Using a Nationwide Administrative Database.

Viruses, 15(5):.

The potential antimicrobial and anti-inflammatory effectiveness of azithromycin against severe influenza is yet unclear. We retrospectively investigated the effect of intravenous azithromycin administration within 7 days of hospitalization in patients with influenza virus pneumonia and respiratory failure. Using Japan's national administrative database, we enrolled and classified 5066 patients with influenza virus pneumonia into severe, moderate, and mild groups based on their respiratory status within 7 days of hospitalization. The primary endpoints were total, 30-day, and 90-day mortality rates. The secondary endpoints were the duration of intensive-care unit management, invasive mechanical ventilation, and hospital stay. The inverse probability of the treatment weighting method with estimated propensity scores was used to minimize data collection bias. Use of intravenous azithromycin was proportional to the severity of respiratory failure (mild: 1.0%, moderate: 3.1%, severe: 14.8%). In the severe group, the 30-day mortality rate was significantly lower with azithromycin (26.49% vs. 36.65%, p = 0.038). In the moderate group, the mean duration of invasive mechanical ventilation after day 8 was shorter with azithromycin; there were no significant differences in other endpoints between the severe and moderate groups. These results suggest that intravenous azithromycin has favorable effects in patients with influenza virus pneumonia using mechanical ventilation or oxygen.

RevDate: 2023-05-29
CmpDate: 2023-05-29

Lafleur S, Bodein A, Mbuya Malaïka Mutombo J, et al (2023)

Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.

International journal of molecular sciences, 24(10):.

Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.

RevDate: 2023-05-30
CmpDate: 2023-05-30

Zerouali B, Santos CAG, do Nascimento TVM, et al (2023)

A cloud-integrated GIS for forest cover loss and land use change monitoring using statistical methods and geospatial technology over northern Algeria.

Journal of environmental management, 341:118029.

Over the last two decades, forest cover has experienced significant impacts from fires and deforestation worldwide due to direct human activities and climate change. This paper assesses trends in forest cover loss and land use and land cover changes in northern Algeria between 2000 and 2020 using datasets extracted from Google Earth Engine (GEE), such as the Hanssen Global Forest Change and MODIS Land Cover Type products (MCD12Q1). Classification was performed using the pixel-based supervised machine-learning algorithm called Random Forest (RF). Trends were analyzed using methods such as Mann-Kendall and Sen. The study area comprises 17 basins with high rainfall variability. The results indicated that the forest area decreased by 64.96%, from 3718 to 1266 km[2], during the 2000-2020 period, while the barren area increased by 40%, from 134,777 to 188,748 km[2]. The findings revealed that the Constantinois-Seybousse-Mellegue hydrographic basin was the most affected by deforestation and cover loss, exceeding 50% (with an area of 1018 km[2]), while the Seybouse River basin experienced the highest percentage of cover loss at 40%. Nonparametric tests showed that seven river basins (41%) had significantly increasing trends of forest cover loss. According to the obtained results, the forest loss situation in Algeria, especially in the northeastern part, is very alarming and requires an exceptional and urgent plan to protect forests and the ecological system against wildfires and climate change. The study provides a diagnosis that should encourage better protection and management of forest cover in Algeria.

RevDate: 2023-05-26

Watson SJ, Aguirre BA, AJ Wright (2023)

Soil versus atmospheric drought: A test case of plant functional trait responses.

Ecology [Epub ahead of print].

Climate change alters mean global surface temperatures, precipitation regimes, and atmospheric moisture. Resultant drought affects the composition and diversity of terrestrial ecosystems worldwide. To date, there are no assessments of the combined impacts of reduced precipitation and atmospheric drying on functional trait distributions of any species in an outdoor experiment. Here, we examined whether soil and atmospheric drought affect the functional traits of a focal grass species (Poa secunda) growing in monoculture and 8-species grass communities in outdoor mesocosms. We focused on specific leaf area (SLA), leaf area, stomatal density, root:shoot ratio, and fine root:coarse root ratio responses. Leaf area and overall growth were reduced with soil drying. Root:shoot ratio only increased for P. secunda growing in monoculture under combined atmospheric and soil drought. Plant energy allocation strategy (measured using principal components) differed when P. secunda was grown in combined soil and atmospheric drought conditions compared with soil drought alone. Given a lack of outdoor manipulations of this kind, our results emphasize the importance of atmospheric drying on functional trait responses more broadly. We suggest that drought methods focused purely on soil water inputs may be imprecisely predicting drought effects on other terrestrial organisms as well (other plants, arthropods, and higher trophic levels). This article is protected by copyright. All rights reserved.

RevDate: 2023-05-25

Bizzotto E, Bonetto A, Marcomini A, et al (2023)

Environmental exposure and ecotoxicological properties of a new generation fluorosurfactant (cC6O4): A comparison with selected legacy perfluoroalkyl acids (PFAA).

Integrated environmental assessment and management [Epub ahead of print].

Cyclic C6O4 (cC6O4, CAS number 1190931-27-1) is a new generation polyfluorinated alkyl substance (PFAS) used as polymerisation aid in the synthesis of fluoropolymers, produced in Italy since 2011. A review of the properties of cC6O4, focused on environmental distribution and ecotoxicology, was conducted. EQC model was applied, using default environmental scenarios, to estimate environmental distribution and fate. In a situation of static thermodynamic equilibrium in a closed system (level I) cC6O4 distributes mainly to water (97.6%) and in a minor amount to soil (2.3%). In a more realistic scenario (level III), with dynamic condition in an open system, with advection in air and water and with equal emissions in air and water, the major amount of the compound is transported through water advection. Monitoring data, mainly referred to surface and groundwater, are available for water bodies close to the production sites (maximum measured concentration 52 μg/L) as well as for a wider area in the river Po watershed with concentrations generally lower than 1 μg/L. Few values are also available for concentration in biota. Effect data indicate low toxicity on all tested organisms with NOEC values always higher than the maximum concentrations tested (100 mg/L for acute tests). Bioaccumulation potential is also very low. A comparison with selected widely used PFAS with five to eight C atoms indicate that cC6O4 is substantially less dangerous to aquatic organisms. At the time being, an ecological risk for the aquatic ecosystem may be excluded even in directly exposed ecosystems. However, for a complete assessment of the suitability of cC6O4 as substitute of other PFAS (namely PFOA), more comprehensive chronic experiments are necessary, to produce realistic NOECs, as well as higher tier experiments (e.g., mesocosms) capable to provide ecologically relevant endpoints. Moreover, a more accurate evaluation of the environmental persistence would be necessary.

RevDate: 2023-05-26
CmpDate: 2023-05-26

Bakó C, Balázs VL, Kerekes E, et al (2023)

Flowering phenophases influence the antibacterial and anti-biofilm effects of Thymus vulgaris L. essential oil.

BMC complementary medicine and therapies, 23(1):168.

BACKGROUND: Essential oils are becoming increasingly popular in medicinal applications because of their antimicrobial effect. Thymus vulgaris L. (Lamiaceae) is a well-known and widely cultivated medicinal plant, which is used as a remedy for cold, cough and gastrointestinal symptoms. Essential oil content of thyme is responsible for its antimicrobial activity, however, it has been reported that the chemical composition of essential oils influences its biological activity. In order to explore flowering phenophases influence on the chemical composition of thyme essential oil and its antibacterial and anti-biofilm activity, plant materials were collected at the beginning of flowering, in full bloom and at the end of flowering periods in 2019.

METHODS: Essential oils from fresh and dried plant materials were distilled and analyzed with gas chromatography-mass spectrometry (GC-MS) and gas chromatography-flame ionization detection (GC-FID). The antibacterial activity was performed by broth microdilution and thin layer chromatography-direct bioautography (TLC-DB) assays and the anti-biofilm effect by crystal violet assay, respectively. Scanning electron microscopy was applied to illustrate the cellular changes of bacterial cells after essential oil treatment.

RESULTS: Thymol (52.33-62.46%) was the main component in the thyme essential oils. Thyme oil distilled from fresh plant material and collected at the beginning of flowering period exerted the highest antibacterial and anti-biofilm activity against Haemophilus influenzae, H. parainfluenzae and Pseudomonas aeruginosa.

CONCLUSION: The different flowering periods of Thymus vulgaris influence the antibacterial and anti-biofilm activity of its essential oils, therefore, the collection time has to be taken into consideration and not only the full bloom, but the beginning of flowering period may provide biological active thyme essential oil.

RevDate: 2023-05-24

Tao F, Huang Y, Hungate BA, et al (2023)

Microbial carbon use efficiency promotes global soil carbon storage.

Nature [Epub ahead of print].

Soils store more carbon than other terrestrial ecosystems[1,2]. How soil organic carbon (SOC) forms and persists remains uncertain[1,3], which makes it challenging to understand how it will respond to climatic change[3,4]. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss[5-7]. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways[4,6,8-11], microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes[12,13]. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved[7,14,15]. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.

RevDate: 2023-05-26
CmpDate: 2023-05-26

Przybylska MS, Violle C, Vile D, et al (2023)

AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana.

Scientific data, 10(1):314.

Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.

RevDate: 2023-05-26
CmpDate: 2023-05-26

Passmore S, Barth W, Greenhill SJ, et al (2023)

Kinbank: A global database of kinship terminology.

PloS one, 18(5):e0283218.

For a single species, human kinship organization is both remarkably diverse and strikingly organized. Kinship terminology is the structured vocabulary used to classify, refer to, and address relatives and family. Diversity in kinship terminology has been analyzed by anthropologists for over 150 years, although recurrent patterning across cultures remains incompletely explained. Despite the wealth of kinship data in the anthropological record, comparative studies of kinship terminology are hindered by data accessibility. Here we present Kinbank, a new database of 210,903 kinterms from a global sample of 1,229 spoken languages. Using open-access and transparent data provenance, Kinbank offers an extensible resource for kinship terminology, enabling researchers to explore the rich diversity of human family organization and to test longstanding hypotheses about the origins and drivers of recurrent patterns. We illustrate our contribution with two examples. We demonstrate strong gender bias in the phonological structure of parent terms across 1,022 languages, and we show that there is no evidence for a coevolutionary relationship between cross-cousin marriage and bifurcate-merging terminology in Bantu languages. Analysing kinship data is notoriously challenging; Kinbank aims to eliminate data accessibility issues from that challenge and provide a platform to build an interdisciplinary understanding of kinship.

RevDate: 2023-05-24

Lohse K, Vila R, Hayward A, et al (2022)

The genome sequence of the high brown fritillary, Fabriciana adippe (Dennis & Schiffermüller, 1775).

Wellcome open research, 7:298.

We present a genome assembly from an individual female Fabriciana adippe (the high brown fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 485 megabases in span. Most of the assembly (99.98%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.1 kilobases in length. Gene annotation of this assembly in Ensembl identified 13,536 protein coding genes.

RevDate: 2023-05-25
CmpDate: 2023-05-25

Chaudhary S, Wu Y, Strongman D, et al (2023)

CIGAF-a database and interactive platform for insect-associated trichomycete fungi.

Database : the journal of biological databases and curation, 2023:.

Trichomycete fungi are gut symbionts of arthropods living in aquatic habitats. The lack of a central platform with accessible collection records and associated ecological metadata has limited ecological investigations of trichomycetes. We present CIGAF (short for Collections of Insect Gut-Associated Fungi), a trichomycetes-focused digital database with interactive visualization functions enabled by the R Shiny web application. CIGAF curated 3120 collection records of trichomycetes across the globe, spanning from 1929 to 2022. CIGAF allows the exploration of nearly 100 years of field collection data through the web interface, including primary published data such as insect host information, collection site coordinates, descriptions and date of collection. When possible, specimen records are supplemented with climatic measures at collection sites. As a central platform of field collection records, multiple interactive tools allow users to analyze and plot data at various levels. CIGAF provides a comprehensive resource hub to the research community for further studies in mycology, entomology, symbiosis and biogeography.

RevDate: 2023-05-22
CmpDate: 2023-05-22

Jiang WJ, Wang MT, Du ZY, et al (2023)

Bioinformatic and functional analysis of OsDHN2 under cadmium stress.

Functional & integrative genomics, 23(2):170.

As a toxic heavy metal, cadmium (Cd) is one of the principal pollutants influencing rice productivity and food security. Despite several studies, the underlying mechanism of Cd response in plants remains largely unclear. Dehydrins are part of the late embryogenesis abundant (LEA) family which protect plants against abiotic stresses. In this study, a Cd-responsive LEA gene, OsDHN2, was functionally characterized. The chromosome localization results indicated that OsDHN2 was located on chromosome 2 of rice. Meanwhile, cis-acting elements, such as MBS (MYB binding site involved in drought-inducibility), ARE (anaerobic induction), and ABRE (abscisic acid), were present in the OsDHN2 promoter region. Expression pattern analysis also showed that OsDHN2 expression was induced in both roots and shoots under Cd stress. Overexpression of OsDHN2 improved Cd tolerance and reduced Cd concentration in yeast. Moreover, increased expression levels of SOD1, CTA1, GSH1, or CTT1 were found in transgenic yeast under Cd stress, suggesting the increased antioxidant enzymatic activities. These results suggested that OsDHN2 is a Cd-responsive gene that has the potential to improve resistance to Cd in rice.

RevDate: 2023-05-19

Girardi P, Lupo A, Mastromatteo LY, et al (2023)

Behavioral outcomes and exposure to perfluoroalkyl substances among children aged 6-13 years: The TEDDY child study.

Environmental research pii:S0013-9351(23)00841-1 [Epub ahead of print].

BACKGROUND: Although some studies report that exposure to per- and polyfluoroalkyl substances (PFAS) during pregnancy and early life stages of a child could adversely impact neurodevelopment, literature shows mixed evidence.

OBJECTIVES: Using an ecological framework for human development, we assessed the association of risk factors for environmental PFAS exposure and childhood PFAS concentrations with behavioral difficulties among school-age children exposed to PFAS from birth, while also controlling for the important influence of the parenting and familial environment.

METHODS: The study participants included 331 school-age children (6-13 years) born in a PFAS-contaminated area in the Veneto Region (Italy). We study the associations between environmental risk factors of maternal PFAS exposure (residential time, consumption of tap water, residence in Red zone A or B), and breastfeeding duration with parent assessments of children's behavioral problems (using the Strengths and Difficulties Questionnaire [SDQ]), adjusting for socio-demographic, parenting and familial variables. The direct relationships between serum blood PFAS concentrations and SDQ scores was evaluated in a subset of children (n = 79), both with single PFAS and weighted quantile sum (WQS) regressions.

RESULTS: Poisson regression models reported positive associations between high consumption of tap water and externalizing SDQ scores (Incidence Rate Ratio [IRR]: 1.18; 95% confidence interval [CI]: 1.04-1.32) and total difficulty scores (IRR: 1.14; 95% CI: 1.02-1.26). Childhood perfluorooctane sulfonate (PFOS) and perfluorohexane sulfonate (PFHxS) were associated with higher internalizing SDQ scores (4th vs. 1st quartile, PFOS IRR: 1.54, 95% CI: 1.06-2.25), externalizing scores (4th vs. 1st quartile, PFHxS IRR: 1.59, 95% CI: 1.09-2.32), and total difficulty scores (4th vs. 1st quartile, PFOS IRR: 1.37, 95% CI: 1.05-1.71; PFHxS IRR: 1.54, 95% CI: 1.09-1.90). The WQS regressions confirmed the associations reported by single-PFAS analyses.

CONCLUSIONS: We observed cross-sectional associations of tap water consumption and childhood PFOS, and PFHxS concentrations with greater behavioral difficulties.

RevDate: 2023-05-19

Cocker D, Chidziwisano K, Mphasa M, et al (2023)

Investigating One Health risks for human colonisation with extended spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae in Malawian households: a longitudinal cohort study.

The Lancet. Microbe pii:S2666-5247(23)00062-9 [Epub ahead of print].

BACKGROUND: Low-income countries have high morbidity and mortality from drug-resistant infections, especially from enteric bacteria such as Escherichia coli. In these settings, sanitation infrastructure is of variable and often inadequate quality, creating risks of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales transmission. We aimed to describe the prevalence, distribution, and risks of ESBL-producing Enterobacterales colonisation in sub-Saharan Africa using a One Health approach.

METHODS: Between April 29, 2019, and Dec 3, 2020, we recruited 300 households in Malawi for this longitudinal cohort study: 100 each in urban, peri-urban, and rural settings. All households underwent a baseline visit and 195 were selected for longitudinal follow-up, comprising up to three additional visits over a 6 month period. Data on human health, antibiotic usage, health-seeking behaviours, structural and behavioural environmental health practices, and animal husbandry were captured alongside human, animal, and environmental samples. Microbiological processing determined the presence of ESBL-producing E coli and Klebsiella pneumoniae, and hierarchical logistic regression was performed to evaluate the risks of human ESBL-producing Enterobacterales colonisation.

FINDINGS: A paucity of environmental health infrastructure and materials for safe sanitation was identified across all sites. A total of 11 975 samples were cultured, and ESBL-producing Enterobacterales were isolated from 1190 (41·8%) of 2845 samples of human stool, 290 (29·8%) of 973 samples of animal stool, 339 (66·2%) of 512 samples of river water, and 138 (46·0%) of 300 samples of drain water. Multivariable models illustrated that human ESBL-producing E coli colonisation was associated with the wet season (adjusted odds ratio 1·66, 95% credible interval 1·38-2·00), living in urban areas (2·01, 1·26-3·24), advanced age (1·14, 1·05-1·25), and living in households where animals were observed interacting with food (1·62, 1·17-2·28) or kept inside (1·58, 1·00-2·43). Human ESBL-producing K pneumoniae colonisation was associated with the wet season (2·12, 1·63-2·76).

INTERPRETATION: There are extremely high levels of ESBL-producing Enterobacterales colonisation in humans and animals and extensive contamination of the wider environment in southern Malawi. Urbanisation and seasonality are key risks for ESBL-producing Enterobacterales colonisation, probably reflecting environmental drivers. Without adequate efforts to improve environmental health, ESBL-producing Enterobacterales transmission is likely to persist in this setting.

FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.

TRANSLATION: For the Chichewa translation of the abstract see Supplementary Materials section.

RevDate: 2023-05-24
CmpDate: 2023-05-24

Amato S, Benson JS, Stewart B, et al (2023)

Current patterns of trauma center proliferation have not led to proportionate improvements in access to care or mortality after injury: An ecologic study.

The journal of trauma and acute care surgery, 94(6):755-764.

BACKGROUND: Timely access to high-level (I/II) trauma centers (HLTCs) is essential to minimize mortality after injury. Over the last 15 years, there has been a proliferation of HLTC nationally. The current study evaluates the impact of additional HLTC on population access and injury mortality.

METHODS: A geocoded list of HLTC, with year designated, was obtained from the American Trauma Society, and 60-minute travel time polygons were created using OpenStreetMap data. Census block group population centroids, county population centroids, and American Communities Survey data from 2005 and 2020 were integrated. Age-adjusted nonoverdose injury mortality was obtained from CDC Wide-ranging Online Data for Epidemiologic Research and the Robert Wood Johnson Foundation. Geographically weighted regression models were used to identify independent predictors of HLTC access and injury mortality.

RESULTS: Over the 15-year (2005-2020) study period, the number of HLTC increased by 31.0% (445 to 583), while population access to HLTC increased by 6.9% (77.5-84.4%). Despite this increase, access was unchanged in 83.1% of counties, with a median change in access of 0.0% (interquartile range, 0.0-1.1%). Population-level age-adjusted injury mortality rates increased by 5.39 per 100,000 population during this time (60.72 to 66.11 per 100,000). Geographically weighted regression controlling for population demography and health indicators found higher median income and higher population density to be positively associated with majority (≥50%) HLTC population coverage and negatively associated with county-level nonoverdose mortality.

CONCLUSION: Over the past 15 years, the number of HLTC increased 31%, while population access to HLTC increased only 6.9%. High-level (I/II) trauma center designation is likely driven by factors other than population need. To optimize efficiency and decrease potential oversupply, the designation process should include population level metrics. Geographic information system methodology can be an effective tool to assess optimal placement.

LEVEL OF EVIDENCE: Prognostic and Epidemiological; Level IV.

RevDate: 2023-05-23

Rokhsar JL, Raynor B, Sheen J, et al (2023)

Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.

medRxiv : the preprint server for health sciences.

BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi , affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.

OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.

DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.

RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.

CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.

AUTHOR SUMMARY: Chagas disease, caused by the parasite Trypanosoma cruzi , is transmitted via triatomine insect vectors. In Latin America, dogs are a common feeding source for triatomine vectors and subsequently an important reservoir of T. cruzi . One proposed intervention to reduce T. cruzi transmission is xenointoxication: treating dogs with oral insecticide to kill triatomine vectors in order to decrease overall T. cruzi transmission. Fluralaner, commonly administered to prevent ectoparasites such as fleas and ticks, is effective under laboratory conditions against the triatomine vectors. One concern with fluralaner treatment is that rapid death of the insect vectors may make the insects more available to oral ingestion by dogs; a more effective transmission pathway than stercorarian, the usual route for T. cruzi transmission. Using a mathematical model, we explored 3 different epidemiologic scenarios: high prevalence endemic disease within a domestic T. cruzi cycle, low prevalence endemic disease within a domestic T. cruzi cycle, and low prevalence endemic disease within a semi-sylvatic T. cruzi cycle. We found a range of beneficial to detrimental effects of fluralaner xenointoxication depending on the epidemiologic scenario. Our results suggest that careful field trials should be designed and carried out before wide scale implementation of fluralaner xenointoxication to reduce T. cruzi transmission.

RevDate: 2023-05-17

Pairo-Castineira E, Rawlik K, Bretherick AD, et al (2023)

GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.

Nature [Epub ahead of print].

Critical illness in COVID-19 is an extreme and clinically homogeneous disease phenotype that we have previously shown[1] to be highly efficient for discovery of genetic associations[2]. Despite the advanced stage of illness at presentation, we have shown that host genetics in patients who are critically ill with COVID-19 can identify immunomodulatory therapies with strong beneficial effects in this group[3]. Here we analyse 24,202 cases of COVID-19 with critical illness comprising a combination of microarray genotype and whole-genome sequencing data from cases of critical illness in the international GenOMICC (11,440 cases) study, combined with other studies recruiting hospitalized patients with a strong focus on severe and critical disease: ISARIC4C (676 cases) and the SCOURGE consortium (5,934 cases). To put these results in the context of existing work, we conduct a meta-analysis of the new GenOMICC genome-wide association study (GWAS) results with previously published data. We find 49 genome-wide significant associations, of which 16 have not been reported previously. To investigate the therapeutic implications of these findings, we infer the structural consequences of protein-coding variants, and combine our GWAS results with gene expression data using a monocyte transcriptome-wide association study (TWAS) model, as well as gene and protein expression using Mendelian randomization. We identify potentially druggable targets in multiple systems, including inflammatory signalling (JAK1), monocyte-macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).

RevDate: 2023-05-22
CmpDate: 2023-05-22

Osmanski AB, Paulat NS, Korstian J, et al (2023)

Insights into mammalian TE diversity through the curation of 248 genome assemblies.

Science (New York, N.Y.), 380(6643):eabn1430.

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.

RevDate: 2023-05-17

Yang P, Yang W, Wei Z, et al (2023)

Novel targets for gastric cancer: The tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis and cuproptosis.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 163:114883 pii:S0753-3322(23)00673-X [Epub ahead of print].

Gastric cancer (GC) is a fatal illness, and its mortality rate is very high all over the world. At present, it is a serious health problem for any country. It is a multifactorial disease due to the rising drug resistance and the increasing global cancer burden, the treatment of GC still faces many obstacles and problems. In recent years, research on GC is being carried out continuously, and we hope to address the new targets of GC treatment through this review. At the same time, we also hope to discover new ways to fight GC and create more gospel for clinical patients. First, we discuss the descriptive tumor microenvironment (TME), N6-methyladenosine (m6A), pyroptosis, autophagy, ferroptosis, and cuproptosis. Finally, we expounded on the new or potential targets of GC treatment.

RevDate: 2023-05-19

Mollicone DJ, Kan K, Coats S, et al (2023)

Use of the psychomotor vigilance test to aid in the selection of risk controls in an air medical transport operation.

Sleep advances : a journal of the Sleep Research Society, 4(1):zpad003.

STUDY OBJECTIVES: This study evaluated the utility and ecological validity of the 3-minute psychomotor vigilance test (PVT) completed by safety-critical personnel in an air medical transport operation as part of a fatigue risk management program.

METHODS: Crewmembers in an air medical transport operation self-administered an alertness assessment incorporating a 3-minute PVT at different time points during their duty schedule. The prevalence of alertness deficits was evaluated based on a failure threshold of 12 errors considering both lapses and false starts. To evaluate the ecological validity of the PVT, the relative frequency of failed assessments was evaluated relative to crewmember position, timing of the assessment within the duty schedule, time of day, and sleep quantity in the last 24 h.

RESULTS: 2.1% of assessments were associated with a failing PVT score. Crewmember position, timing of assessment within the duty shift, time of day, and sleep quantity in the last 24 h were found to affect the relative frequency of failed assessments. Obtaining less than 7-9 h of sleep was associated with systematic increases in the failure rate (F[1, 54 612] = 168.1, p < .001). Obtaining less than 4 h of sleep was associated with a frequency of a failed assessment 2.99 times higher than the frequency of a failed assessment when obtaining 7-9 h of sleep.

CONCLUSIONS: Results provide evidence for the utility and ecological validity of the PVT as well as the suitability of the PVT failure threshold to support fatigue risk management in safety-critical operations.

RevDate: 2023-05-19
CmpDate: 2023-05-19

Tang Y, Hardy TJ, JY Yoon (2023)

Receptor-based detection of microplastics and nanoplastics: Current and future.

Biosensors & bioelectronics, 234:115361.

Plastic pollution is an emerging environmental concern, gaining significant attention worldwide. They are classified into microplastics (MP; defined from 1 μm to 5 mm) and smaller nanoplastics (NP; <1 μm). NPs may pose higher ecological risks than MPs. Various microscopic and spectroscopic techniques have been used to detect MPs, and the same methods have occasionally been used for NPs. However, they are not based on receptors, which provide high specificity in most biosensing applications. Receptor-based micro/nanoplastics (MNP) detection can provide high specificity, distinguishing MNPs from the environmental samples and, more importantly, identifying the plastic types. It can also offer a low limit of detection (LOD) required for environmental screening. Such receptors are expected to detect NPs specifically at the molecular level. This review categorizes the receptors into cells, proteins, peptides, fluorescent dyes, polymers, and micro/nanostructures. Detection techniques used with these receptors are also summarized and categorized. There is plenty of room for future research to test for broader classes of environmental samples and many plastic types, to lower the LOD, and to apply the current techniques for NPs. Portable and handheld MNP detection should also be demonstrated for field use since the current demonstrations primarily utilized laboratory instruments. Detection on microfluidic platforms will also be crucial in miniaturizing and automating the assay and, eventually, collecting an extensive database to support machine learning-based classification of MNP types.

RevDate: 2023-05-16
CmpDate: 2023-05-12

Liao WW, Asri M, Ebler J, et al (2023)

A draft human pangenome reference.

Nature, 617(7960):312-324.

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals[1]. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.

RevDate: 2023-05-13
CmpDate: 2023-05-13

Santana BEF, Andrade ACS, AP Muraro (2023)

Trend of incompleteness of maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System, 2012-2020.

Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil, 32(1):e2022725.

OBJECTIVE: to analyze the trend of incompleteness of the maternal schooling and race/skin color variables held on the Brazilian Live Birth Information System (SINASC) between 2012 and 2020.

METHODS: this was an ecological time series study of the incompleteness of maternal schooling and race/skin color data for Brazil, its regions and Federative Units, by means of joinpoint regression and calculation of annual percentage change (APC) and average annual percentage change.

RESULTS: a total of 26,112,301 births were registered in Brazil in the period; incompleteness of maternal schooling data decreased for Brazil (APC = -8.1%) and the Southeast (APC = -19.5%) and Midwest (APC = -17.6%) regions; as for race/skin color, there was a downward trend for Brazil (APC = -8.2%) and all regions, except the Northeast region, while nine Federative Units and the Federal District showed a stationary trend.

CONCLUSION: there was an improvement in filling out these variables on the SINASC, but with regional disparities, mainly for race/skin color.

RevDate: 2023-05-17
CmpDate: 2023-05-17

Alam N, Saha S, Gupta S, et al (2023)

Settlement suitability analysis of a riverine floodplain in the perspective of GIS-based multicriteria decision analysis.

Environmental science and pollution research international, 30(24):66002-66020.

Riverine floodplains are highly dynamic and the most vulnerable space on Earth particularly in flat alluvial plains of major river systems. Suitable site selection for sustainable human settlements in active floodplain areas is a critical task for decision-makers in terms of quality of lithology, ecologically fragile landmass, climate-induced hazards, immense population pressure, and environmental conservation issues. This research introduces a methodology for settlement suitability zone (SSZ) that employs GIS-based multi-criteria decision-making (MCDM) techniques. As a case study, an altered hydrological regime of the lower Ganga riparian zone was chosen to identify the SSZ as these areas are the most susceptible to riverine hazards. Twelve significant variables reflecting on topography, climate, landscape, and environment have been selected in the multi-criteria evaluation platform. The CRiteria Importance Through Intercriteria Correlation (CRITIC) method is adopted to specify the weights of the criteria and utilize an inverse distance-weighted (IDW) spatial interpolation technique to generate an SSZ map in a GIS environment. The study zone is spatially quantified into five categories, from unsuitable to high-suitable with a natural breaks (Jenks) classification method. Subsequently, the final results are validated through a receiver operating characteristics (ROC) curve using randomly selected 56 hazard-exposed location points. The outcome revealed that 8.45% of the riparian area falls under unsuitable, 21.87% under low-suitable, and 33.27% under moderate-suitable for locating human settlements. The generally suitable and high-suitable categories account for 36.40% of the total study zone. A spatial sensitivity analysis is also applied to gauge the influence of each parameter on the MCDM outcomes. The SSZ mapping results from this study can help local authorities to plan for sustainable settlement development in environmentally fragile areas.

RevDate: 2023-05-13
CmpDate: 2023-05-11

Kortz AR, Moyes F, Pivello VR, et al (2023)

Elevated compositional change in plant assemblages linked to invasion.

Proceedings. Biological sciences, 290(1998):20222450.

Alien species are widely linked to biodiversity change, but the extent to which they are associated with the reshaping of ecological communities is not well understood. One possible mechanism is that assemblages where alien species are found exhibit elevated temporal turnover. To test this, we identified assemblages of vascular plants in the BioTIME database for those assemblages in which alien species are either present or absent and used the Jaccard measure to compute compositional dissimilarity between consecutive censuses. We found that, although alien species are typically rare in invaded assemblages, their presence is associated with an increase in the average rate of compositional change. These differences in compositional change between invaded and uninvaded assemblages are not linked to differences in species richness but rather to species replacement (turnover). Rapid compositional restructuring of assemblages is a major contributor to biodiversity change, and as such, our results suggest a role for alien species in bringing this about.

RevDate: 2023-05-15
CmpDate: 2023-05-15

Klein B, Ogbunugafor CB, Schafer BJ, et al (2023)

COVID-19 amplified racial disparities in the US criminal legal system.

Nature, 617(7960):344-350.

The criminal legal system in the USA drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features[1-3]. During the first year of the coronavirus disease 2019 (COVID-19) pandemic, the number of incarcerated people in the USA decreased by at least 17%-the largest, fastest reduction in prison population in American history[4]. Here we ask how this reduction influenced the racial composition of US prisons and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the US prison population and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decade-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people[5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacerbated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration. To advance opportunities for data-driven social science, we publicly released the data associated with this study at Zenodo[6].

RevDate: 2023-05-08

Rokhsar JL, Raynor B, Sheen J, et al (2023)

Modeling the impact of xenointoxication in dogs to halt Trypanosoma cruzi transmission.

PLoS computational biology, 19(5):e1011115 pii:PCOMPBIOL-D-22-00771 [Epub ahead of print].

BACKGROUND: Chagas disease, a vector-borne parasitic disease caused by Trypanosoma cruzi, affects millions in the Americas. Dogs are important reservoirs of the parasite. Under laboratory conditions, canine treatment with the systemic insecticide fluralaner demonstrated efficacy in killing Triatoma infestans and T. brasiliensis, T. cruzi vectors, when they feed on dogs. This form of pest control is called xenointoxication. However, T. cruzi can also be transmitted orally when mammals ingest infected bugs, so there is potential for dogs to become infected upon consuming infected bugs killed by the treatment. Xenointoxication thereby has two contrasting effects on dogs: decreasing the number of insects feeding on the dogs but increasing opportunities for exposure to T. cruzi via oral transmission to dogs ingesting infected insects.

OBJECTIVE: Examine the potential for increased infection rates of T. cruzi in dogs following xenointoxication.

DESIGN/METHODS: We built a deterministic mathematical model, based on the Ross-MacDonald malaria model, to investigate the net effect of fluralaner treatment on the prevalence of T. cruzi infection in dogs in different epidemiologic scenarios. We drew upon published data on the change in percentage of bugs killed that fed on treated dogs over days post treatment. Parameters were adjusted to mimic three scenarios of T. cruzi transmission: high and low disease prevalence and domestic vectors, and low disease prevalence and sylvatic vectors.

RESULTS: In regions with high endemic disease prevalence in dogs and domestic vectors, prevalence of infected dogs initially increases but subsequently declines before eventually rising back to the initial equilibrium following one fluralaner treatment. In regions of low prevalence and domestic or sylvatic vectors, however, treatment seems to be detrimental. In these regions our models suggest a potential for a rise in dog prevalence, due to oral transmission from dead infected bugs.

CONCLUSION: Xenointoxication could be a beneficial and novel One Health intervention in regions with high prevalence of T. cruzi and domestic vectors. In regions with low prevalence and domestic or sylvatic vectors, there is potential harm. Field trials should be carefully designed to closely follow treated dogs and include early stopping rules if incidence among treated dogs exceeds that of controls.

RevDate: 2023-05-10
CmpDate: 2023-05-10

Ondrikova N, Harris JP, Douglas A, et al (2023)

Predicting Norovirus in England Using Existing and Emerging Syndromic Data: Infodemiology Study.

Journal of medical Internet research, 25:e37540 pii:v25i1e37540.

BACKGROUND: Norovirus is associated with approximately 18% of the global burden of gastroenteritis and affects all age groups. There is currently no licensed vaccine or available antiviral treatment. However, well-designed early warning systems and forecasting can guide nonpharmaceutical approaches to norovirus infection prevention and control.

OBJECTIVE: This study evaluates the predictive power of existing syndromic surveillance data and emerging data sources, such as internet searches and Wikipedia page views, to predict norovirus activity across a range of age groups across England.

METHODS: We used existing syndromic surveillance and emerging syndromic data to predict laboratory data indicating norovirus activity. Two methods are used to evaluate the predictive potential of syndromic variables. First, the Granger causality framework was used to assess whether individual variables precede changes in norovirus laboratory reports in a given region or an age group. Then, we used random forest modeling to estimate the importance of each variable in the context of others with two methods: (1) change in the mean square error and (2) node purity. Finally, these results were combined into a visualization indicating the most influential predictors for norovirus laboratory reports in a specific age group and region.

RESULTS: Our results suggest that syndromic surveillance data include valuable predictors for norovirus laboratory reports in England. However, Wikipedia page views are less likely to provide prediction improvements on top of Google Trends and Existing Syndromic Data. Predictors displayed varying relevance across age groups and regions. For example, the random forest modeling based on selected existing and emerging syndromic variables explained 60% variance in the ≥65 years age group, 42% in the East of England, but only 13% in the South West region. Emerging data sets highlighted relative search volumes, including "flu symptoms," "norovirus in pregnancy," and norovirus activity in specific years, such as "norovirus 2016." Symptoms of vomiting and gastroenteritis in multiple age groups were identified as important predictors within existing data sources.

CONCLUSIONS: Existing and emerging data sources can help predict norovirus activity in England in some age groups and geographic regions, particularly, predictors concerning vomiting, gastroenteritis, and norovirus in the vulnerable populations and historical terms such as stomach flu. However, syndromic predictors were less relevant in some age groups and regions likely due to contrasting public health practices between regions and health information-seeking behavior between age groups. Additionally, predictors relevant to one norovirus season may not contribute to other seasons. Data biases, such as low spatial granularity in Google Trends and especially in Wikipedia data, also play a role in the results. Moreover, internet searches can provide insight into mental models, that is, an individual's conceptual understanding of norovirus infection and transmission, which could be used in public health communication strategies.

RevDate: 2023-05-11
CmpDate: 2023-05-11

Lee HE, Kim YG, Jeong JY, et al (2023)

Data resource profile: the Korean Community Health Status Indicators (K-CHSI) database.

Epidemiology and health, 45:e2023016.

Korean Community Health Status Indicators (K-CHSI) is a model-based database containing annual data on health outcomes and determinants at the municipal level (si/gun/gu-level regions, including mid-sized cities, counties, and districts). K-CHSI's health outcomes include overall mortality, disease incidence, prevalence rates, and self-reported health. Health determinants were measured in 5 domains: socio-demographic factors, health behaviors, social environment, physical environment, and the healthcare system. The data sources are 71 public databases, including Causes of Death Statistics, Cancer Registration Statistics, Community Health Survey, Population Census, and Census on Establishments and Statistics of Urban Plans. This dataset covers Korea's 17 metropolitan cities and provinces, with data from approximately 250 municipal regions (si/gun/gu). The current version of the database (DB version 1.3) was built using 12 years of data from 2008 to 2019. All data included in K-CHSI may be downloaded via the Korea Community Health Survey site, with no login requirement (https://chs.kdca.go.kr/chs/recsRoom/dataBaseMain.do). K-CHSI covers extensive health outcomes and health determinants at the municipal level over a period of more than 10 years, which enables ecological and time-series analyses of the relationships among various health outcomes and related factors.

RevDate: 2023-05-08

Chen D, Zhang Y, Q Feng (2023)

Hydrochemical characteristics and microbial community evolution of Pinglu River affected by regional abandoned coal mine drainage, Guizhou Province, China.

Environmental science and pollution research international [Epub ahead of print].

Pinglu River in southwestern China was continuously polluted by acid mine drainage (AMD) from abandoned coal mines, and AMD has become a major source of recharge to the river (43.26% of total flow), resulting in structural changes in the physicochemical properties and microbial communities of river water and sediments. In this study, we collected abandoned coal mine drainage, river water, and river sediment samples for comprehensive analysis. Results indicated that the hydrochemical types of AMD from abandoned coal mines were mainly SO4-Ca·Mg. The pH of river water in Pinglu River decreased from upstream to downstream due to AMD, with the hydrochemical type gradually changing from SO4·HCO3-Ca·Mg to SO4-Ca·Mg. The variation of pH along the river sediments was less than that of water samples, which remained weakly alkaline. However, high-throughput sequencing revealed a gradual decrease in microbial diversity in river sediments from upstream to downstream. The core bacteria groups in the upstream sediments were mainly attributed to the phylum Proteobacteria and Actinobacteriota, mainly including Geobacter, Anaeromyxobacter, Marmoricola, and Phycicoccus. The relative abundance of Gaiella, MND1, and Pseudolabrys in sediment samples gradually increased with the confluence of AMD, and the differences in microbial communities may be attributed to pH, TOC, and TP. Results of phenotype prediction demonstrated that the relative abundance of anaerobic microorganisms in river sediment gradually decreased from upstream to downstream (from 24.77 to 12.46%), presumably due to the large amount of oligotrophic AMD converge.

RevDate: 2023-05-08

Lin F, Kennelly EJ, Linington RG, et al (2023)

Comprehensive Metabolite Profiling of Two Edible Garcinia Species Based on UPLC-ESI-QTOF-MS[E] Coupled with Bioactivity Assays.

Journal of agricultural and food chemistry [Epub ahead of print].

In China, the endemic species Garcinia yunnanensis and native Garcinia xanthochymus are known as edible and medicinal plants. However, a systematic metabolomic and bioactivity evaluation of different plant parts from both species is lacking. In this study, comprehensive investigations of 11 plant parts of G. yunnanensis and 10 of G. xanthochymus employing UPLC-ESI-QTOF-MS[E]-based metabolomic analysis in conjunction with three bioactivity assays were undertaken. A customized chemotaxonomic-based in-house library containing 6456 compounds was constructed and coupled to the Progenesis QI informatic platform for metabolite annotations. From these two species, a total of 235 constituents were characterized using multiple criteria. Differences in metabolite profiles between the plant parts within each species were uncovered using multivariate analysis. Based on orthogonal partial least-squares discriminant analysis (OPLS-DA), 23 markers were identified as highly differential metabolites from G. xanthochymus and 20 from G. yunnanensis. Comparative assessment of the biological assays revealed the activity variations among different plant parts. The seeds of both species and G. yunnanensis latex exhibited excellent cytotoxic and antibacterial activities, while G. xanthochymus roots and G. yunnanensis arils showed strong anti-inflammatory effects. S-plot analysis identified 26 potential biomarkers for the observed activities, including the known cytotoxic agent cycloxanthochymol and the anti-inflammatory compound garcimultiflorone B, which likely explains some of the potent observed bioactivity.

RevDate: 2023-05-08

Mori Y, Okawara M, Shibao K, et al (2023)

Changes in operative trends and short-term outcomes of surgery for congenital biliary dilatation in adults using real-world data: A multilevel analysis based on a nationwide administrative database in Japan.

Annals of gastroenterological surgery, 7(3):471-478.

AIM: We aimed to evaluate the operative trends and compare the short-term outcomes between open and laparoscopic surgery for congenital biliary dilatation (CBD) in adults using real-world data from Japan.

METHODS: Data from the Japanese Diagnosis Procedure Combination database on 941 patients undergoing surgery for CBD at 357 hospitals from April 1, 2016, to March 31, 2021, were analyzed. The patients were divided into two groups: open surgery (n = 764) and laparoscopic surgery (n = 177). We performed a retrospective analysis via a multilevel analysis of the short-term surgical outcomes and costs between open and laparoscopic surgery.

RESULTS: The rate of laparoscopic surgery has been increasing annually and had almost doubled to 25% by 2021. There were no significant differences in the in-hospital mortality rate or postoperative morbidity between the two groups. The length of anesthesia was significantly longer in the laparoscopic than open surgery group (8.80 vs 6.16 hours, p < .001). The time to removal of the abdominal drain and length of hospital stay were significantly shorter in the laparoscopic than open surgery group (6.12 vs 8.35 days, p = .001 and 13.57 vs 15.79 days, p < .001, respectively). The coefficient for cost was 463 235 yen (95% confidence interval, 289 679-636 792) higher in laparoscopic than open surgery (p < .001).

CONCLUSION: The short-term results were comparable between laparoscopic and open surgery for CBD. Further investigation is needed to validate our findings and long-term outcomes.

RevDate: 2023-05-07

Wieczorek P, Pruc M, Krajsman M, et al (2023)

Comparison of the bébé VieScope™ and direct laryngoscope for pediatric tongue oedema scenario: A simulation study.

RevDate: 2023-05-03

Schuler T, King C, Matsveru T, et al (2023)

Wearable-Triggered Ecological Momentary Assessments Are Feasible in People With Advanced Cancer and Their Family Caregivers: Feasibility Study from an Outpatient Palliative Care Clinic at a Cancer Center.

Journal of palliative medicine [Epub ahead of print].

Background: Emerging digital health approaches could play a role in better personalized palliative care. Aim: We conducted a feasibility study testing wearable sensor (WS)-triggered ecological momentary assessments (EMAs) and electronic patient-reported outcomes in community palliative care with patient-caregiver dyads. Design: All wore consumer-grade WS for five weeks. Sensor-detected "stress" (heart rate variability algorithm) that passed individualized thresholds triggered a short smartphone survey. Daily sleep surveys, weekly symptom surveys (Integrated Palliative care Outcome Scale), and a poststudy experience survey were conducted. Setting/Participants: Fifteen dyads (n = 30) were recruited from an outpatient palliative care clinic for people with cancer. Results: Daytime sensor wear-time had 73% adherence. Participants perceived value in this support. Quantity and severity of "stress" events were higher in patients. Sleep disturbance was similar but for different reasons: patients (physical symptoms) and caregivers (worrying about the patient). Conclusions: EMAs are feasible and valued in community palliative care.

RevDate: 2023-05-02
CmpDate: 2023-05-01

Minhas BF, Beck EA, Cheng CC, et al (2023)

Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes.

Scientific reports, 13(1):6939.

Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.

RevDate: 2023-05-01

Maimone G, Azzaro M, Placenti F, et al (2023)

A Morphometric Approach to Understand Prokaryoplankton: A Study in the Sicily Channel (Central Mediterranean Sea).

Microorganisms, 11(4):.

A new understanding of plankton ecology has been obtained by studying the phenotypic traits of free-living prokaryotes in the Sicily Channel (Central Mediterranean Sea), an area characterised by oligotrophic conditions. During three cruises carried out in July 2012, January 2013 and July 2013, the volume and morphology of prokaryotic cells were assessed microscopically using image analysis in relation to environmental conditions. The study found significant differences in cell morphologies among cruises. The largest cell volumes were observed in the July 2012 cruise (0.170 ± 0.156 µm[3]), and the smallest in the January 2013 cruise (0.060 ± 0.052 µm[3]). Cell volume was negatively limited by nutrients and positively by salinity. Seven cellular morphotypes were observed among which cocci, rods and coccobacilli were the most abundant. Cocci, although they prevailed numerically, always showed the smallest volumes. Elongated shapes were positively related to temperature. Relationships between cell morphologies and environmental drivers indicated a bottom-up control of the prokaryotic community. The morphology/morphometry-based approach is a useful tool for studying the prokaryotic community in microbial ecology and should be widely applied to marine microbial populations in nature.

RevDate: 2023-05-04
CmpDate: 2023-05-04

Wu Z, Jiang Z, Li Z, et al (2023)

Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves in Populus.

Plant physiology, 192(1):188-204.

Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.

RevDate: 2023-05-01
CmpDate: 2023-05-01

Schütt EM, Hundsdörfer MAJ, von Hoyningen-Huene AJE, et al (2023)

First Steps towards a near Real-Time Modelling System of Vibrio vulnificus in the Baltic Sea.

International journal of environmental research and public health, 20(8):.

Over the last two decades, Vibrio vulnificus infections have emerged as an increasingly serious public health threat along the German Baltic coast. To manage related risks, near real-time (NRT) modelling of V. vulnificus quantities has often been proposed. Such models require spatially explicit input data, for example, from remote sensing or numerical model products. We tested if data from a hydrodynamic, a meteorological, and a biogeochemical model are suitable as input for an NRT model system by coupling it with field samples and assessing the models' ability to capture known ecological parameters of V. vulnificus. We also identify the most important predictors for V. vulnificus in the Baltic Sea by leveraging the St. Nicolas House Analysis. Using a 27-year time series of sea surface temperature, we have investigated trends of V. vulnificus season length, which pinpoint hotspots mainly in the east of our study region. Our results underline the importance of water temperature and salinity on V. vulnificus abundance but also highlight the potential of air temperature, oxygen, and precipitation to serve as predictors in a statistical model, albeit their relationship with V. vulnificus may not be causal. The evaluated models cannot be used in an NRT model system due to data availability constraints, but promising alternatives are presented. The results provide a valuable basis for a future NRT model for V. vulnificus in the Baltic Sea.

RevDate: 2023-04-28

Olivieri R, Vannini P, Corzani A, et al (2023)

Rapid Decrease in Fluoroquinolones Consumption following Implementation of a Simple Antimicrobial Stewardship Bundled Intervention in a University Hospital during the COVID-19 Pandemic.

Antibiotics (Basel, Switzerland), 12(4):.

Fluoroquinolones (FQs) represent an class of antibiotics of medical importance, but their use has been restricted due to their ecologic impact and associated side effects. The reduction of FQs use is an important goal of antimicrobial stewardship programs (ASP). This work describes an ASP focused on overall antibiotics and FQs consumption reduction. From January 2021, an ASP was implemented in a 700-bed teaching hospital. The ASP was based on: (i) antibiotics consumption monitoring system (DDD/100 bed days); (ii) mandatory antibiotic prescription-motivation (using a dedicated informatic format) with the goal of >75% of motivated prescriptions; and (iii) data feedback and training on FQs use indications. We evaluated the impact of the intervention on overall systemic antibiotics and FQs consumption according to the objectives posed by Italian PNCAR (National Action Plan on Antimicrobial Resistance). A decrease of 6.6% in antibiotic use was observed (2019 vs. 2021). Notably, the FQs consumption fell by 48.3% from 7.1 DDD/100 bd in 2019 to 3.7 DDD/100 bd in 2021 (p < 0.001). After six months of mandatory antibiotic prescription-indication, all units achieved the target set. The study suggests that a simple, bundled ASP intervention can be rapidly effective obtaining the objectives of PNCAR on the reduction of overall antibiotics and FQs consumption.

RevDate: 2023-04-28

Prakofjewa J, Sartori M, Šarka P, et al (2023)

Boundaries Are Blurred: Wild Food Plant Knowledge Circulation across the Polish-Lithuanian-Belarusian Borderland.

Biology, 12(4): pii:biology12040571.

The circulation of local ecological knowledge (LEK) is a promising avenue of research for wild plant studies. To encourage the acceptance, celebration, and appreciation of biocultural diversity, which is rapidly disappearing nowadays, we need to estimate and assess multifaceted local ecological knowledge. It has direct application for local communities in informing effective policies for improving food security and building community-specific responses to environmental and social transitions. The present study draws on data collected among two ethnic groups-Lithuanians and Poles-via 200 semi-structured in-depth interviews and participant observation conducted in 2018 and 2019 in Podlasie Voivodeship (Poland), the Vilnius Region (Lithuania), and the Hrodna Region (Belarus). We aimed to observe LEK circulation in the border area through cross-ethnic and cross-country comparisons. A total of 2812 detailed use reports of wild plants were recorded. In total, 72 wild plant taxa belonging to 33 plant families were used across the food domain. Our findings show that cross-country differences were minimal, while there was some variation between the ethnic groups selected as case studies. We emphasize the need, in future studies, to combine quantitative research with qualitative approaches in order to more thoroughly identify peculiarities of cross-border circulation as a reservoir for community food resilience and biocultural diversity.

RevDate: 2023-04-27

Green SJ, Torok T, Allen JE, et al (2023)

Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.

Astrobiology [Epub ahead of print].

Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.

RevDate: 2023-04-28
CmpDate: 2023-04-28

Mosquera KD, Martínez Villegas LE, Rocha Fernandes G, et al (2023)

Egg-laying by female Aedes aegypti shapes the bacterial communities of breeding sites.

BMC biology, 21(1):97.

BACKGROUND: Aedes aegypti, the main arboviral mosquito vector, is attracted to human dwellings and makes use of human-generated breeding sites. Past research has shown that bacterial communities associated with such sites undergo compositional shifts as larvae develop and that exposure to different bacteria during larval stages can have an impact on mosquito development and life-history traits. Based on these facts, we hypothesized that female Ae. aegypti shape the bacteria communities of breeding sites during oviposition as a form of niche construction to favor offspring fitness.

RESULTS: To test this hypothesis, we first verified that gravid females can act as mechanical vectors of bacteria. We then elaborated an experimental scheme to test the impact of oviposition on breeding site microbiota. Five different groups of experimental breeding sites were set up with a sterile aqueous solution of larval food, and subsequently exposed to (1) the environment alone, (2) surface-sterilized eggs, (3) unsterilized eggs, (4) a non-egg laying female, or (5) oviposition by a gravid female. The microbiota of these differently treated sites was assessed by amplicon-oriented DNA sequencing once the larvae from the sites with eggs had completed development and formed pupae. Microbial ecology analyses revealed significant differences between the five treatments in terms of diversity. In particular, between-treatment shifts in abundance profiles were detected, showing that females induce a significant decrease in microbial alpha diversity through oviposition. In addition, indicator species analysis pinpointed bacterial taxa with significant predicting values and fidelity coefficients for the samples in which single females laid eggs. Furthermore, we provide evidence regarding how one of these indicator taxa, Elizabethkingia, exerts a positive effect on the development and fitness of mosquito larvae.

CONCLUSIONS: Ovipositing females impact the composition of the microbial community associated with a breeding site, promoting certain bacterial taxa over those prevailing in the environment. Among these bacteria, we found known mosquito symbionts and showed that they can improve offspring fitness if present in the water where eggs are laid. We deem this oviposition-mediated bacterial community shaping as a form of niche construction initiated by the gravid female.

RevDate: 2023-04-28
CmpDate: 2023-04-28

Stocco A, F Pranovi (2023)

The paradoxical need for human intervention in the conservation of natural environments in Venice lagoon.

Scientific reports, 13(1):6798.

The Venice lagoon-the largest Mediterranean coastal lagoon-is characterized by the presence at its edges of 31 "valli da pesca", types of artificial ecosystems that mime the ecological processes of a transitional aquatic ecosystem. Constituted by a series of regulated lakes bounded by artificial embankments, the valli da pesca were established centuries ago to maximize provisioning Ecosystem Services (ESs), such as fishing and hunting. As time passed, the valli da pesca underwent an intentional isolation process leading to private management. Nonetheless, the valli da pesca are still exchanging energy and matter with the "open' lagoon and today represent an essential element within the context of lagoon conservation. This study aimed to analyze the possible effects of artificial management on both ESs supply and landscape arrangements by assessing 9 ESs (climate regulation, water purification, lifecycle support, aquaculture, waterfowl hunting, wild food, tourism, information for cognitive development, and birdwatching), along with eight landscape indicators. Obtained results suggested that the valli da pesca are today ruled under five different management strategies, according to the maximized ES. Management conditions influence the landscape pattern and achieve a series of "side effects" on the other ESs. The comparison between the managed and abandoned valli da pesca highlights the importance of anthropogenic interventions for conserving these ecosystems, as the abandoned valli da pesca show a loss of ecological gradients, landscape heterogeneity, and provisioning ESs. Nevertheless, the persistence of intrinsic geographical and morphological characteristics still prevails regardless of intentional landscape molding. The result is that the provisioning ESs capacity per unit area is higher in the abandoned valli da pesca than in the open lagoon, emphasizing the importance of these confined areas of the lagoon ecosystem. Considering the spatial distribution of multiple ESs, the provisioning ESs flow that does not occur in the abandoned valli da pesca seems to be replaced by the flow of cultural ESs. Thus, the ESs spatial pattern highlights a balancing effect between different ESs categories. The results are discussed considering the trade-offs generated by private land conservation, anthropogenic interventions, and their relevance for the ecosystem-based management of Venice lagoon.

RevDate: 2023-04-26

Sutton C, Prowse J, McVey L, et al (2023)

Strategic workforce planning in health and social care - an international perspective: A scoping review.

Health policy (Amsterdam, Netherlands), 132:104827 pii:S0168-8510(23)00112-4 [Epub ahead of print].

Effective strategic workforce planning for integrated and co-ordinated health and social care is essential if future services are to be resourced such that skill mix, clinical practice and productivity meet population health and social care needs in timely, safe and accessible ways globally. This review presents international literature to illustrate how strategic workforce planning in health and social care has been undertaken around the world with examples of planning frameworks, models and modelling approaches. The databases Business Source Premier, CINAHL, Embase, Health Management Information Consortium, Medline and Scopus were searched for full texts, from 2005 to 2022, detailing empirical research, models or methodologies to explain how strategic workforce planning (with at least a one-year horizon) in health and/or social care has been undertaken, yielding ultimately 101 included references. The supply/demand of a differentiated medical workforce was discussed in 25 references. Nursing and midwifery were characterised as undifferentiated labour, requiring urgent growth to meet demand. Unregistered workers were poorly represented as was the social care workforce. One reference considered planning for health and social care workers. Workforce modelling was illustrated in 66 references with predilection for quantifiable projections. Increasingly needs-based approaches were called for to better consider demography and epidemiological impacts. This review's findings advocate for whole-system needs-based approaches that consider the ecology of a co-produced health and social care workforce.

RevDate: 2023-04-26

Shea K, Borchering RK, Probert WJM, et al (2023)

Multiple models for outbreak decision support in the face of uncertainty.

Proceedings of the National Academy of Sciences of the United States of America, 120(18):e2207537120.

Policymakers must make management decisions despite incomplete knowledge and conflicting model projections. Little guidance exists for the rapid, representative, and unbiased collection of policy-relevant scientific input from independent modeling teams. Integrating approaches from decision analysis, expert judgment, and model aggregation, we convened multiple modeling teams to evaluate COVID-19 reopening strategies for a mid-sized United States county early in the pandemic. Projections from seventeen distinct models were inconsistent in magnitude but highly consistent in ranking interventions. The 6-mo-ahead aggregate projections were well in line with observed outbreaks in mid-sized US counties. The aggregate results showed that up to half the population could be infected with full workplace reopening, while workplace restrictions reduced median cumulative infections by 82%. Rankings of interventions were consistent across public health objectives, but there was a strong trade-off between public health outcomes and duration of workplace closures, and no win-win intermediate reopening strategies were identified. Between-model variation was high; the aggregate results thus provide valuable risk quantification for decision making. This approach can be applied to the evaluation of management interventions in any setting where models are used to inform decision making. This case study demonstrated the utility of our approach and was one of several multimodel efforts that laid the groundwork for the COVID-19 Scenario Modeling Hub, which has provided multiple rounds of real-time scenario projections for situational awareness and decision making to the Centers for Disease Control and Prevention since December 2020.

RevDate: 2023-04-25

Carrol ED, Ranjit S, Menon K, et al (2023)

Operationalizing Appropriate Sepsis Definitions in Children Worldwide: Considerations for the Pediatric Sepsis Definition Taskforce.

Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies pii:00130478-990000000-00179 [Epub ahead of print].

Sepsis is a leading cause of global mortality in children, yet definitions for pediatric sepsis are outdated and lack global applicability and validity. In adults, the Sepsis-3 Definition Taskforce queried databases from high-income countries to develop and validate the criteria. The merit of this definition has been widely acknowledged; however, important considerations about less-resourced and more diverse settings pose challenges to its use globally. To improve applicability and relevance globally, the Pediatric Sepsis Definition Taskforce sought to develop a conceptual framework and rationale of the critical aspects and context-specific factors that must be considered for the optimal operationalization of future pediatric sepsis definitions. It is important to address challenges in developing a set of pediatric sepsis criteria which capture manifestations of illnesses with vastly different etiologies and underlying mechanisms. Ideal criteria need to be unambiguous, and capable of adapting to the different contexts in which children with suspected infections are present around the globe. Additionally, criteria need to facilitate early recognition and timely escalation of treatment to prevent progression and limit life-threatening organ dysfunction. To address these challenges, locally adaptable solutions are required, which permit individualized care based on available resources and the pretest probability of sepsis. This should facilitate affordable diagnostics which support risk stratification and prediction of likely treatment responses, and solutions for locally relevant outcome measures. For this purpose, global collaborative databases need to be established, using minimum variable datasets from routinely collected data. In summary, a "Think globally, act locally" approach is required.

RevDate: 2023-04-26
CmpDate: 2023-04-26

Demidova EV, Serebriiskii IG, Vlasenkova R, et al (2023)

Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing.

BMC genomics, 24(1):212.

BACKGROUND: Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined.

METHODS: Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes.

RESULTS: Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities.

CONCLUSIONS: Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.

RevDate: 2023-04-24

Girón JC, Tarasov S, González Montaña LA, et al (2023)

Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.

Systematic biology pii:7140370 [Epub ahead of print].

The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multi-species anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to (1) use controlled vocabularies and create semi-automated computer-parsable insect morphological descriptions; (2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and (3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.

RevDate: 2023-04-22

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2023)

The genome sequence of the Birch Marble, Apotomis betuletana (Haworth, 1811).

Wellcome open research, 8:66.

We present a genome assembly from an individual male Apotomis betuletana (the Birch Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 684 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The mitochondrial genome has also been assembled and is 15.8 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,717 protein coding genes.

RevDate: 2023-04-25
CmpDate: 2023-04-25

Yilanci V, Candan G, MI Shah (2023)

Identifying the roles of energy and economic factors on environmental degradation in MINT economies: a hesitant fuzzy analytic hierarchy process.

Environmental science and pollution research international, 30(19):55768-55781.

Globally, research communities have been studying the different determinants of environmental degradation or pollution using different contexts and methods. In this study, we identify several energy and economic factors, such as energy consumption (EC), gross domestic product (GDP), energy production (EP), urbanization (URB), and foreign direct investment (FDI) as the most effective factors of environmental degradation by obtaining several environmental researchers' opinions and using the hesitant fuzzy analytic hierarchy process. In the later stage of the analysis, we use these variables as regressors of the ecological footprint (EF) as a proxy for environmental degradation. Since we find evidence of cross-sectional dependence among the members of the variables, we use second-generational panel tests. First, we test the stationarity of the variables using the cross-sectionally augmented IPS (CIPS) panel unit test. The results show that the regressors have different orders of integration. So, we employ the Durbin-Hausman panel cointegration test to test the existence of a long-run relationship between the variables. Having found a long-run relationship, we estimate the long-run coefficients using the common correlated effects mean group estimator, which reveals that energy consumption has an increasing effect on the EF in Indonesia and Turkey, while energy production has a negative impact in Mexico and Turkey. While GDP has an increasing effect in all countries, FDI has a similar effect in only Indonesia. Moreover, URB decreases the ecological footprint in Nigeria, while it increases in Turkey. Our approach to the evaluation of environmental degradation can be generalized to other regions as well as where there is a significant need to understand the roles of different drivers on environmental degradation or pollution.

RevDate: 2023-04-21
CmpDate: 2023-04-21

Shu CB, Shen YL, Liu G, et al (2023)

Impacts of Eucalyptus plantation on soil and water losses in a typical small watershed in mountainous area of southern China.

Ying yong sheng tai xue bao = The journal of applied ecology, 34(4):1015-1023.

Unreasonable exploitation of artificial forest causes severe soil erosion in the mountainous areas of sou-thern China. The spatial-temporal variations of soil erosion in typical small watershed with artificial forest has signifi-cant implications for artificial forest exploitation and sustainable development of mountainous ecological environment. In this study, we used revised universal soil loss equation (RUSLE) and geographic information system (GIS) to evaluate the spatial and temporal variations of soil erosion and its key drivers of Dadingshan watershed in mountainous area of western Guangdong. The results showed that the erosion modulus was 1948.1 t·km[-2]·a[-1] (belonging to light erosion) in the Dadingshan watershed. However, the spatial variation of soil erosion was substantial, with variation coefficient of 5.12. The maximal soil erosion modulus was 191127 t·km[-2]·a[-1]. Slight erosion (<500 t·km[-2]·a[-1]) accounted for 80.6% of the total watershed area. The moderate erosion and above (>2500 t·km[-2]·a[-1]) were mainly distributed in young Eucalyptus forest area with less than 30% of the vegetation coverage, which contributed nearly 75.7% of total soil erosion. During 2014-2019, the interannual variations of mean erosion of Dadingshan catchment was modest, but the spatial variation of soil erosion was large. Vegetation cover, slope, and rainfall were key drivers of such variation. The destruction of natural vegetation resulted by plantation exploitation was the primary cause of soil erosion in afforestation areas. Soil erosion significantly increased with the increases of slope gradient in the young forest area, which was aggravated by extreme rainfall. However, soil erosion gradually decreased with the increases of the age of Eucalypt plantation. Therefore, the hot spot of soil erosion was young forest areas of Eucalypt plantation with slope >25°, and the key period for soil erosion control was the first 2-3 years after Eucalyptus planting. We suggested that reasonable afforestation measures should be used in area with >25° slopes, and that the destruction of natural vegetation should be avoided on hillslope with >35° slope gradient. The road construction standards and forest management should be further improved to address the challenge of extreme rainfalls.

RevDate: 2023-04-23
CmpDate: 2023-04-21

De Wolfe TJ, ES Wright (2023)

Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis.

BMC microbiology, 23(1):107.

BACKGROUND: The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.

RESULTS: Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).

CONCLUSIONS: Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.

RevDate: 2023-04-24
CmpDate: 2023-04-24

Swerdlow BA, Sandel DB, SL Johnson (2023)

Shame on me for needing you: A multistudy examination of links between receiving interpersonal emotion regulation and experiencing shame.

Emotion (Washington, D.C.), 23(3):737-752.

Recent theory and research have drawn attention to interpersonal dimensions of emotion regulation. Yet, few empirical investigations of the outcomes of interpersonal emotion regulation have been conducted. We propose that one negative affective outcome of received interpersonal emotion regulation of conceptual and practical interest is shame. In the present series of studies, participants from six disparate samples reported on experiences of receiving interpersonal emotion regulation using autobiographical recall and ecological sampling paradigms (total analyzed n = 1,868; total analyzed k = 2,515 instances of receiving interpersonal emotion regulation). We sought to quantify the frequency and distinctiveness of shame as an outcome of receiving interpersonal emotion regulation. We used an exploratory-confirmatory approach to identify robust and generalizable correlates of shame. We considered individual (e.g., trait external shame-proneness), situational (e.g., desire for regulation), relational (e.g., perceived closeness with the provider), and interaction-specific (e.g., perceptions of provider hostility) variables. Our results indicate that it is not uncommon for people to experience receiving interpersonal emotion regulation as shame-inducing, and these perceptions are distinct from their evaluations of the overall helpfulness of the interaction. An internal mini meta-analysis showed that the strongest correlates of shame across studies and samples were individual differences in nonacceptance of negative emotions and expressive suppression and interaction-specific ratings of provider responsiveness and hostility. We discuss the conceptual, methodological, and practical implications of these findings for studying interpersonal emotion regulation and shame. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

RevDate: 2023-04-21
CmpDate: 2023-04-21

Skirgård H, Haynie HJ, Blasi DE, et al (2023)

Grambank reveals the importance of genealogical constraints on linguistic diversity and highlights the impact of language loss.

Science advances, 9(16):eadg6175.

While global patterns of human genetic diversity are increasingly well characterized, the diversity of human languages remains less systematically described. Here, we outline the Grambank database. With over 400,000 data points and 2400 languages, Grambank is the largest comparative grammatical database available. The comprehensiveness of Grambank allows us to quantify the relative effects of genealogical inheritance and geographic proximity on the structural diversity of the world's languages, evaluate constraints on linguistic diversity, and identify the world's most unusual languages. An analysis of the consequences of language loss reveals that the reduction in diversity will be strikingly uneven across the major linguistic regions of the world. Without sustained efforts to document and revitalize endangered languages, our linguistic window into human history, cognition, and culture will be seriously fragmented.

RevDate: 2023-04-18

Jackson C, Stewart ID, Plekhanova T, et al (2023)

Effects of sleep disturbance on dyspnoea and impaired lung function following hospital admission due to COVID-19 in the UK: a prospective multicentre cohort study.

The Lancet. Respiratory medicine pii:S2213-2600(23)00124-8 [Epub ahead of print].

BACKGROUND: Sleep disturbance is common following hospital admission both for COVID-19 and other causes. The clinical associations of this for recovery after hospital admission are poorly understood despite sleep disturbance contributing to morbidity in other scenarios. We aimed to investigate the prevalence and nature of sleep disturbance after discharge following hospital admission for COVID-19 and to assess whether this was associated with dyspnoea.

METHODS: CircCOVID was a prospective multicentre cohort substudy designed to investigate the effects of circadian disruption and sleep disturbance on recovery after COVID-19 in a cohort of participants aged 18 years or older, admitted to hospital for COVID-19 in the UK, and discharged between March, 2020, and October, 2021. Participants were recruited from the Post-hospitalisation COVID-19 study (PHOSP-COVID). Follow-up data were collected at two timepoints: an early time point 2-7 months after hospital discharge and a later time point 10-14 months after hospital discharge. Sleep quality was assessed subjectively using the Pittsburgh Sleep Quality Index questionnaire and a numerical rating scale. Sleep quality was also assessed with an accelerometer worn on the wrist (actigraphy) for 14 days. Participants were also clinically phenotyped, including assessment of symptoms (ie, anxiety [Generalised Anxiety Disorder 7-item scale questionnaire], muscle function [SARC-F questionnaire], dyspnoea [Dyspnoea-12 questionnaire] and measurement of lung function), at the early timepoint after discharge. Actigraphy results were also compared to a matched UK Biobank cohort (non-hospitalised individuals and recently hospitalised individuals). Multivariable linear regression was used to define associations of sleep disturbance with the primary outcome of breathlessness and the other clinical symptoms. PHOSP-COVID is registered on the ISRCTN Registry (ISRCTN10980107).

FINDINGS: 2320 of 2468 participants in the PHOSP-COVID study attended an early timepoint research visit a median of 5 months (IQR 4-6) following discharge from 83 hospitals in the UK. Data for sleep quality were assessed by subjective measures (the Pittsburgh Sleep Quality Index questionnaire and the numerical rating scale) for 638 participants at the early time point. Sleep quality was also assessed using device-based measures (actigraphy) a median of 7 months (IQR 5-8 months) after discharge from hospital for 729 participants. After discharge from hospital, the majority (396 [62%] of 638) of participants who had been admitted to hospital for COVID-19 reported poor sleep quality in response to the Pittsburgh Sleep Quality Index questionnaire. A comparable proportion (338 [53%] of 638) of participants felt their sleep quality had deteriorated following discharge after COVID-19 admission, as assessed by the numerical rating scale. Device-based measurements were compared to an age-matched, sex-matched, BMI-matched, and time from discharge-matched UK Biobank cohort who had recently been admitted to hospital. Compared to the recently hospitalised matched UK Biobank cohort, participants in our study slept on average 65 min (95% CI 59 to 71) longer, had a lower sleep regularity index (-19%; 95% CI -20 to -16), and a lower sleep efficiency (3·83 percentage points; 95% CI 3·40 to 4·26). Similar results were obtained when comparisons were made with the non-hospitalised UK Biobank cohort. Overall sleep quality (unadjusted effect estimate 3·94; 95% CI 2·78 to 5·10), deterioration in sleep quality following hospital admission (3·00; 1·82 to 4·28), and sleep regularity (4·38; 2·10 to 6·65) were associated with higher dyspnoea scores. Poor sleep quality, deterioration in sleep quality, and sleep regularity were also associated with impaired lung function, as assessed by forced vital capacity. Depending on the sleep metric, anxiety mediated 18-39% of the effect of sleep disturbance on dyspnoea, while muscle weakness mediated 27-41% of this effect.

INTERPRETATION: Sleep disturbance following hospital admission for COVID-19 is associated with dyspnoea, anxiety, and muscle weakness. Due to the association with multiple symptoms, targeting sleep disturbance might be beneficial in treating the post-COVID-19 condition.

FUNDING: UK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council.

RevDate: 2023-04-21
CmpDate: 2023-04-19

Cai P, Liu S, Zhang D, et al (2023)

SynBioTools: a one-stop facility for searching and selecting synthetic biology tools.

BMC bioinformatics, 24(1):152.

BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology.

RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system.

CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.

RevDate: 2023-04-17

Manubens-Gil L, Zhou Z, Chen H, et al (2023)

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.

Nature methods [Epub ahead of print].

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

RevDate: 2023-04-15
CmpDate: 2023-04-14

Biswas P, Bibi S, Yousafi Q, et al (2023)

Study of MDM2 as Prognostic Biomarker in Brain-LGG Cancer and Bioactive Phytochemicals Inhibit the p53-MDM2 Pathway: A Computational Drug Development Approach.

Molecules (Basel, Switzerland), 28(7):.

An evaluation of the expression and predictive significance of the MDM2 gene in brain lower-grade glioma (LGG) cancer was carried out using onco-informatics pipelines. Several transcriptome servers were used to measure the differential expression of the targeted MDM2 gene and search mutations and copy number variations. GENT2, Gene Expression Profiling Interactive Analysis, Onco-Lnc, and PrognoScan were used to figure out the survival rate of LGG cancer patients. The protein-protein interaction networks between MDM2 gene and its co-expressed genes were constructed by Gene-MANIA tool. Identified bioactive phytochemicals were evaluated through molecular docking using Schrödinger Suite Software, with the MDM2 (PDB ID: 1RV1) target. Protein-ligand interactions were observed with key residues of the macromolecular target. A molecular dynamics simulation of the novel bioactive compounds with the targeted protein was performed. Phytochemicals targeting MDM2 protein, such as Taxifolin and (-)-Epicatechin, have been shown with more highly stable results as compared to the control drug, and hence, concluded that phytochemicals with bioactive potential might be alternative therapeutic options for the management of LGG patients. Our once informatics-based designed pipeline has indicated that the MDM2 gene may have been a predictive biomarker for LGG cancer and selected phytochemicals possessed outstanding interaction results within the macromolecular target's active site after utilizing in silico approaches. In vitro and in vivo experiments are recommended to confirm these outcomes.

RevDate: 2023-04-19
CmpDate: 2023-04-19

LaVigne AW, DeWeese TL, Wright JL, et al (2023)

Radiotherapy Deserts: The Impact of Race, Poverty, and the Rural-Urban Continuum on Density of Providers and the Use of Radiation Therapy in the US.

International journal of radiation oncology, biology, physics, 116(1):17-27.

PURPOSE: Prior efforts to characterize disparities in radiation therapy access and receipt have not comprehensively investigated interplay between race, socioeconomic status, and geography relative to oncologic outcomes. This study sought to define these complex relationships at the US county level for prostate cancer (PC) and invasive breast (BC) cancer to build a tool that facilitates identification of "radiotherapy deserts"-regions with mismatch between radiation therapy resources and oncologic need.

METHODS AND MATERIALS: An ecologic study model was constructed using national databases to evaluate 3,141 US counties. Radiation therapy resources and use densities were operationalized as physicians to persons at risk (PPR) and use to persons at risk (UPR): the number of attending radiation oncologists and Medicare beneficiaries per 100,000 persons at risk, respectively. Oncologic need was defined by "hot zone" counties with ≥2 standard deviations (SDs) above mean incidence and death rates. Univariable and multivariable logistic regressions examined links between PPR and UPR densities, epidemiologic variables, and hot zones for oncologic outcomes. Statistics are reported at a significance level of P < .05.

RESULTS: The mean (SD) PPR and UPR densities were 2.1 (5.9) and 192.6 (557.6) for PC and 1.9 (5.3) and 174.4 (501.0) for BC, respectively. Counties with high PPR and UPR densities were predominately metropolitan (odds ratio [OR], 2.9-4.4), generally with a higher percentage of Black non-Hispanic constituents (OR, 1.5-2.3). Incidence and death rate hot zones were largely nonmetropolitan (OR, 0.3-0.6), generally with a higher percentage of Black non-Hispanic constituents (OR, 3.2-6.3). Lower PPR density was associated with death rate hot zones for both types of cancer (OR, 0.8-0.9); UPR density was generally not linked to oncologic outcomes on multivariable analysis.

CONCLUSIONS: The study found that mismatch between oncologic need with PPR and UPR disproportionately affects nonmetropolitan communities with a higher percentage of Black non-Hispanic constituents. An interactive web platform (bit.ly/densitymaps) was developed to visualize "radiotherapy deserts" and drive targeted investigation of underlying barriers to care in areas of highest need, with the goal of reducing health inequities in this context.

RevDate: 2023-04-15
CmpDate: 2023-04-14

Roberts M, Colley K, Currie M, et al (2023)

The Contribution of Environmental Science to Mental Health Research: A Scoping Review.

International journal of environmental research and public health, 20(7):.

Mental health is influenced by multiple complex and interacting genetic, psychological, social, and environmental factors. As such, developing state-of-the-art mental health knowledge requires collaboration across academic disciplines, including environmental science. To assess the current contribution of environmental science to this field, a scoping review of the literature on environmental influences on mental health (including conditions of cognitive development and decline) was conducted. The review protocol was developed in consultation with experts working across mental health and environmental science. The scoping review included 202 English-language papers, published between 2010 and 2020 (prior to the COVID-19 pandemic), on environmental themes that had not already been the subject of recent systematic reviews; 26 reviews on climate change, flooding, air pollution, and urban green space were additionally considered. Studies largely focused on populations in the USA, China, or Europe and involved limited environmental science input. Environmental science research methods are primarily focused on quantitative approaches utilising secondary datasets or field data. Mental health measurement was dominated by the use of self-report psychometric scales. Measures of environmental states or exposures were often lacking in specificity (e.g., limited to the presence or absence of an environmental state). Based on the scoping review findings and our synthesis of the recent reviews, a research agenda for environmental science's future contribution to mental health scholarship is set out. This includes recommendations to expand the geographical scope and broaden the representation of different environmental science areas, improve measurement of environmental exposure, prioritise experimental and longitudinal research designs, and giving greater consideration to variation between and within communities and the mediating pathways by which environment influences mental health. There is also considerable opportunity to increase interdisciplinarity within the field via the integration of conceptual models, the inclusion of mixed methods and qualitative approaches, as well as further consideration of the socio-political context and the environmental states that can help support good mental health. The findings were used to propose a conceptual model to parse contributions and connections between environmental science and mental health to inform future studies.

RevDate: 2023-04-12

Chen D, Feng Q, Y Zhang (2023)

Enrichment and response of iron-metabolizing microorganisms and metabolic genes in the contaminated area of stratified stacking coal gangue dumps, Northern China.

Environmental science and pollution research international pii:10.1007/s11356-023-26775-y [Epub ahead of print].

In the Xishan coalfield of northern China, the stratified stacking of soil and gangue was applied to limit the acid pollution from high-sulfur coal gangue. In this study, we found that stratified stacking can effectively neutralize the acidity, with the pH value of gangue-leaching water being 6.02-8.13. In contrast to the acidic contaminated area, most of the microorganisms in the study area sediment were neutrophilic, with the main genera being Arthrobacter, Pseudorhodobacter, Pseudomonas, and Rhodoferax. A variety of iron- and sulfur-metabolizing bacteria was discovered in the gangue-leaching sediment, with the total relative abundance ranging from 4.20 to 23.75%, of which the iron-reducing bacteria (FeRB) accounted for the highest percentage. The distributions of these functional microorganisms in the samples were significantly influenced by Fe and S. The co-occurrence network analysis revealed a significant positive correlation between the iron- and sulfur-metabolizing bacteria in the sediment (93.75%), indicating a strong reciprocal symbiotic relationship between these bacteria. The iron and sulfur metabolism genes in the sediment were predicted and compared based on the Tax4Fun functional prediction method. Results showed that functional genes related to iron metabolism were highly expressed in the gangue-leaching sediment. This study enhances the understanding of iron and sulfur metabolism in gangue-leaching contaminated areas.

RevDate: 2023-04-14
CmpDate: 2023-04-14

James JE, Nelson PG, J Masel (2023)

Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.

Molecular biology and evolution, 40(4):.

Protein domains that emerged more recently in evolution have a higher structural disorder and greater clustering of hydrophobic residues along the primary sequence. It is hard to explain how selection acting via descent with modification could act so slowly as not to saturate over the extraordinarily long timescales over which these trends persist. Here, we hypothesize that the trends were created by a higher level of selection that differentially affects the retention probabilities of protein domains with different properties. This hypothesis predicts that loss rates should depend on disorder and clustering trait values. To test this, we inferred loss rates via maximum likelihood for animal Pfam domains, after first performing a set of stringent quality control methods to reduce annotation errors. Intermediate trait values, matching those of ancient domains, are associated with the lowest loss rates, making our results difficult to explain with reference to previously described homology detection biases. Simulations confirm that effect sizes are of the right magnitude to produce the observed long-term trends. Our results support the hypothesis that differential domain loss slowly weeds out those protein domains that have nonoptimal levels of disorder and clustering. The same preferences also shape the differential diversification of Pfam domains, thereby further impacting proteome composition.

RevDate: 2023-04-14
CmpDate: 2023-04-14

Halder S, Ghosh S, Chattopadhyay J, et al (2021)

Bistability in cell signalling and its significance in identifying potential drug-targets.

Bioinformatics (Oxford, England), 37(22):4156-4163.

MOTIVATION: Bistability is one of the salient dynamical features in various all-or-none kinds of decision-making processes. The presence of bistability in a cell signalling network plays a key role in input-output (I/O) relation. Our study is aiming to capture and emphasize the role of motif structure influencing the I/O relation between two nodes in the context of bistability. Here, a model-based analysis is made to investigate the critical conditions responsible for the emergence of different bistable protein-protein interaction (PPI) motifs and their possible applications to find the potential drug-targets.

RESULTS: The global sensitivity analysis is used to identify sensitive parameters and their role in maintaining the bistability. Additionally, the bistable switching through hysteresis is explored to develop an understanding of the underlying mechanisms involved in the cell signalling processes, when significant motifs exhibiting bistability have emerged. Further, we elaborate the application of the results by the implication of the emerged PPI motifs to identify potential drug-targets in three cancer networks, which is validated with existing databases. The influence of stochastic perturbations that could hinder desired functionality of any signalling networks is also described here.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2023-04-12

Labbé F, Abdeladhim M, Abrudan J, et al (2023)

Genomic analysis of two phlebotomine sand fly vectors of leishmania from the new and old World.

PLoS neglected tropical diseases, 17(4):e0010862 pii:PNTD-D-22-01257 [Epub ahead of print].

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites.

RevDate: 2023-04-11

Beauchamp AM, Lehmann CU, Medford RJ, et al (2023)

Correction: The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.

Journal of medical Internet research, 25:e47896 pii:v25i1e47896.

[This corrects the article DOI: 10.2196/43623.].

RevDate: 2023-04-13
CmpDate: 2023-04-13

Sundell D, Öhrman C, Svensson D, et al (2021)

FlexTaxD: flexible modification of taxonomy databases for improved sequence classification.

Bioinformatics (Oxford, England), 37(21):3932-3933.

SUMMARY: The Flexible Taxonomy Database framework provides a method for modification and merging official and custom taxonomic databases to create improved databases. Using such databases will increase accuracy and precision of existing methods to classify sequence reads.

Source code is freely available at https://github.com/FOI-Bioinformatics/flextaxd and installable through Bioconda.

RevDate: 2023-04-11

Lohse K, Höök L, Näsvall K, et al (2022)

The genome sequence of the wood white butterfly, Leptidea sinapis (Linnaeus, 1758).

Wellcome open research, 7:254.

We present a genome assembly from an individual male Leptidea sinapis (the wood white; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 686 megabases in span. The majority (99.99%) of the assembly is scaffolded into 48 chromosomal pseudomolecules, with three Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 14,800 protein coding genes.

RevDate: 2023-04-12
CmpDate: 2023-04-10

Nartker M, Zhou Z, C Firestone (2023)

When will AI misclassify? Intuiting failures on natural images.

Journal of vision, 23(4):4.

Machine recognition systems now rival humans in their ability to classify natural images. However, their success is accompanied by a striking failure: a tendency to commit bizarre misclassifications on inputs specifically selected to fool them. What do ordinary people know about the nature and prevalence of such classification errors? Here, five experiments exploit the recent discovery of "natural adversarial examples" to ask whether naive observers can predict when and how machines will misclassify natural images. Whereas classical adversarial examples are inputs that have been minimally perturbed to induce misclassifications, natural adversarial examples are simply unmodified natural photographs that consistently fool a wide variety of machine recognition systems. For example, a bird casting a shadow might be misclassified as a sundial, or a beach umbrella made of straw might be misclassified as a broom. In Experiment 1, subjects accurately predicted which natural images machines would misclassify and which they would not. Experiments 2 through 4 extended this ability to how the images would be misclassified, showing that anticipating machine misclassifications goes beyond merely identifying an image as nonprototypical. Finally, Experiment 5 replicated these findings under more ecologically valid conditions, demonstrating that subjects can anticipate misclassifications not only under two-alternative forced-choice conditions (as in Experiments 1-4), but also when the images appear one at a time in a continuous stream-a skill that may be of value to human-machine teams. We suggest that ordinary people can intuit how easy or hard a natural image is to classify, and we discuss the implications of these results for practical and theoretical issues at the interface of biological and artificial vision.

RevDate: 2023-04-12
CmpDate: 2023-04-12

Pernet C, Svarer C, Blair R, et al (2023)

On the Long-term Archiving of Research Data.

Neuroinformatics, 21(2):243-246.

Accessing research data at any time is what FAIR (Findable Accessible Interoperable Reusable) data sharing aims to achieve at scale. Yet, we argue that it is not sustainable to keep accumulating and maintaining all datasets for rapid access, considering the monetary and ecological cost of maintaining repositories. Here, we address the issue of cold data storage: when to dispose of data for offline storage, how can this be done while maintaining FAIR principles and who should be responsible for cold archiving and long-term preservation.

RevDate: 2023-04-06

Zimmerman S, Tierney BT, Patel CJ, et al (2023)

Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.

mSystems [Epub ahead of print].

Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.

RevDate: 2023-04-11
CmpDate: 2023-04-11

Hao N, Sun P, Zhao W, et al (2023)

Application of a developed triple-classification machine learning model for carcinogenic prediction of hazardous organic chemicals to the US, EU, and WHO based on Chinese database.

Ecotoxicology and environmental safety, 255:114806.

Cancer, the second largest human disease, has become a major public health problem. The prediction of chemicals' carcinogenicity before their synthesis is crucial. In this paper, seven machine learning algorithms (i.e., Random Forest (RF), Logistic Regression (LR), Support Vector Machines (SVM), Complement Naive Bayes (CNB), K-Nearest Neighbor (KNN), XGBoost, and Multilayer Perceptron (MLP)) were used to construct the carcinogenicity triple classification prediction (TCP) model (i.e., 1A, 1B, Category 2). A total of 1444 descriptors of 118 hazardous organic chemicals were calculated by Discovery Studio 2020, Sybyl X-2.0 and PaDEL-Descriptor software. The constructed carcinogenicity TCP model was evaluated through five model evaluation indicators (i.e., Accuracy, Precision, Recall, F1 Score and AUC). The model evaluation results show that Accuracy, Precision, Recall, F1 Score and AUC evaluation indicators meet requirements (greater than 0.6). The accuracy of RF, LR, XGBoost, and MLP models for predicting carcinogenicity of Category 2 is 91.67%, 79.17%, 100%, and 100%, respectively. In addition, the constructed machine learning model in this study has potential for error correction. Taking XGBoost model as an example, the predicted carcinogenicity level of 1,2,3-Trichloropropane (96-18-4) is Category 2, but the actual carcinogenicity level is 1B. But the difference between Category 2 and 1B is only 0.004, indicating that the XGBoost is one optimum model of the seven constructed machine learning models. Besides, results showed that functional groups like chlorine and benzene ring might influence the prediction of carcinogenic classification. Therefore, considering functional group characteristics of chemicals before constructing the carcinogenicity prediction model of organic chemicals is recommended. The predicted carcinogenicity of the organic chemicals using the optimum machine leaning model (i.e., XGBoost) was also evaluated and verified by the toxicokinetics. The RF and XGBoost TCP models constructed in this paper can be used for carcinogenicity detection before synthesizing new organic substances. It also provides technical support for the subsequent management of organic chemicals.

RevDate: 2023-04-07

Keller R, Spanu A, Puhan MA, et al (2023)

Social media and internet search data to inform drug utilization: A systematic scoping review.

Frontiers in digital health, 5:1074961.

INTRODUCTION: Drug utilization is currently assessed through traditional data sources such as big electronic medical records (EMRs) databases, surveys, and medication sales. Social media and internet data have been reported to provide more accessible and more timely access to medications' utilization.

OBJECTIVE: This review aims at providing evidence comparing web data on drug utilization to other sources before the COVID-19 pandemic.

METHODS: We searched Medline, EMBASE, Web of Science, and Scopus until November 25th, 2019, using a predefined search strategy. Two independent reviewers conducted screening and data extraction.

RESULTS: Of 6,563 (64%) deduplicated publications retrieved, 14 (0.2%) were included. All studies showed positive associations between drug utilization information from web and comparison data using very different methods. A total of nine (64%) studies found positive linear correlations in drug utilization between web and comparison data. Five studies reported association using other methods: One study reported similar drug popularity rankings using both data sources. Two studies developed prediction models for future drug consumption, including both web and comparison data, and two studies conducted ecological analyses but did not quantitatively compare data sources. According to the STROBE, RECORD, and RECORD-PE checklists, overall reporting quality was mediocre. Many items were left blank as they were out of scope for the type of study investigated.

CONCLUSION: Our results demonstrate the potential of web data for assessing drug utilization, although the field is still in a nascent period of investigation. Ultimately, social media and internet search data could be used to get a quick preliminary quantification of drug use in real time. Additional studies on the topic should use more standardized methodologies on different sets of drugs in order to confirm these findings. In addition, currently available checklists for study quality of reporting would need to be adapted to these new sources of scientific information.

RevDate: 2023-04-07
CmpDate: 2023-04-07

Xavier JMA, Firmino RT, Pereira IF, et al (2023)

The impact of the COVID-19 pandemic in Brazil: a study in tertiary dental care.

Brazilian oral research, 37:025 pii:S1806-83242023000100221.

The pandemic caused by coronavirus has resonated throughout different levels of health care in Brazil and, in this context, the present research aimed to evaluate this impact on tertiary dental care provided by the Unified Health System (SUS). Therefore, an ecological study was conducted with data obtained from the Hospital Information System processed by the Portal of the Department of Informatics of SUS. The sample consisted of patients of all sexes and age groups, whose Hospital Admission Authorizations (AIHs) were approved for dental tertiary care procedures from January 2015 to December 2020. Descriptive analyses and the ANOVA test with a significance level set at p < 0.05 were used. When the annual mean numbers of AIHs approved were evaluated, findings showed that on an average, the Southeast region authorized a higher number of procedures (p-value < 0.001), however, in the pandemic year (2020), a reduction of approximately 24.5% of these hospitalizations occurred throughout Brazil, with the Midwest being the region most affected (32.12%). A percentage increase occurred in the Surgical Treatment of Oral sinus/Oral nasal Fistula (16.1%), in addition to a significant decrease in performing procedures for Resection of Mouth Lesion (33.4%). In the pandemic year, there was a reduction of 14% in expenditures related to hospital services and 23.26% related to professional services. It was concluded that the data presented demonstrated a significant reduction in AIHs for tertiary dental care in the pandemic year.

RevDate: 2023-04-05

Pandit AA, Mahashabde RV, Brown CC, et al (2023)

Association between broadband capacity and telehealth utilization among Medicare Fee-for-service beneficiaries during the COVID-19 pandemic.

Journal of telemedicine and telecare [Epub ahead of print].

BACKGROUND: Telehealth is a rapidly growing modality for expanding healthcare access, especially in the post-COVID-19 era. However, telehealth requires high-quality broadband, thus making broadband a social determinant of health. The objective of this study was to evaluate the association between broadband access and telehealth utilization across the United States during the COVID-19 pandemic.

METHODS: Using a cross-sectional, ecological study design, we merged county-level data on broadband capacity (Microsoft's Rural Broadband Initiative), telehealth utilization among Medicare Fee-for-Service beneficiaries from January through September 2020 (CareJourney), and county-level socioeconomic characteristics (Area Health Resources Files). Multivariable linear regression was used to estimate the association between broadband capacity, county-level characteristics, and telehealth utilization.

RESULTS: Among the 3107 counties, those with the greatest broadband availability (quintile 5) had 47% higher telehealth utilization compared to counties with the least broadband availability (quintile 1). In the adjusted model, a 1 standard deviation (SD) increase in broadband access was associated with a 1.54 percentage point (pp) increase in telehealth utilization (P < 0.001). Rural county designation (-1.96 pp; P < 0.001) and 1 SD increases in average Medicare beneficiary age (-1.34 pp; P = 0.001), number of nursing home beds per 1000 individuals (-0.38 pp; P = 0.002), and proportion of Native Americans/Pacific Islanders (-0.59 pp; P < 0.001) were associated with decreased telehealth utilization.

CONCLUSION: The association between broadband access and telehealth utilization and the decreased telehealth utilization in rural areas highlight the importance of broadband access for healthcare access and the need to continue investing in broadband infrastructure to promote equitable healthcare access across populations.

RevDate: 2023-04-05
CmpDate: 2023-04-05

Still CJ, Page GFM, Rastogi B, et al (2023)

Reply to Garen et al.: Within-canopy temperature data also do not support limited homeothermy.

Proceedings of the National Academy of Sciences of the United States of America, 120(15):e2302515120.

RevDate: 2023-04-06
CmpDate: 2023-04-06

Keck F, Couton M, F Altermatt (2023)

Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses.

Molecular ecology resources, 23(4):742-755.

Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved.

RevDate: 2023-04-04

Boyes D, Wright C, University of Oxford and Wytham Woods Genome Acquisition Lab, et al (2022)

The genome sequence of the peppered moth, Biston betularia Linnaeus, 1758.

Wellcome open research, 7:97.

We present a genome assembly from an individual male Biston betularia (the peppered moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 405 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.Gene annotation of this assembly on Ensembl has identified 12,251 protein coding genes.

RevDate: 2023-04-04
CmpDate: 2023-04-04

Yang W, Wei C, Cheng J, et al (2023)

BTG2 and SerpinB5, a novel gene pair to evaluate the prognosis of lung adenocarcinoma.

Frontiers in immunology, 14:1098700.

INTRODUCTION: Lung adenocarcinoma (LUAD), as the most frequent pathological subtype of non-small cell lung cancer, is often characterized by poor prognosis and low 5-year survival rate. Exploriton of new biomarkers and accurate molecular mechanisms for effectively predicting the prognosis of LUAD patients is still necessary. Presently, BTG2 and SerpinB5, which play important roles in tumors, are studied as a gene pair for the first time with the aim of exploring whether they can be used as potential prognostic markers.

METHODS: Using the bioinformatics method to explore whether BTG2 and SerpinB5 can become independent prognostic factors, and explore their clinical application value and whether they can be used as immunotherapeutic markers. In addition, we also verify the conclusions obtained from external datasets, molecular docking, and SqRT-PCR.

RESULTS: The results show that compared with normal lung tissue, BTG2 expression level was down-regulated and SerpinB5 was up-regulated in LUAD. Additionally, Kaplan-Meier survival analysis demonstrate that the prognosis of low expression level of BTG2 was poor, and that of high expression level of SerpinB5 was poor, suggesting that both of them can be used as independent prognostic factors. Moreover, the prognosis models of the two genes were constructed respectively in this study, and their prediction effect was verified by external data. Besides, ESTIMATE algorithm reveals the relationship between this gene pair and the immune microenvironment. Furthermore, patients with a high expression level of BTG2 and a low expression level of SerpinB5 have higher immunophenoscore for CTLA-4 and PD-1 inhibitors than patients with a low expression level of BTG2 and a high expression level of SerpinB5, indicating that such patients have a more obvious effect of immunotherapy.

DISCUSSION: Collectively, all the results demonstrate that BTG2 and SerpinB5 might serve as potential prognostic biomarkers and novel therapeutic targets for LUAD.

RevDate: 2023-04-03

Khan AH, Adil M, Aziz MA, et al (2023)

Traditional foraging for ecological transition? Wild food ethnobotany among three ethnic groups in the highlands of the eastern Hindukush, North Pakistan.

Journal of ethnobiology and ethnomedicine, 19(1):9.

BACKGROUND: The Patrak Valley is home to communities, which have been inextricably linked with nature for generations, and local plant knowledge (LPK) represents an important part of their local cultural diversity. In general, globalization has come at the expense of local plant knowledge among several mountain societies, and therefore the current investigation has been undertaken to record the (possibly) last remaining wild food plant/mushroom foraging practices among Pathans, Kohistanis, and Gujjars living in the highlands of the Hindukush, North Pakistan.

METHODS: Data on the uses of wild food plants and mushrooms (WFPs) were collected through 120 semi-structured interviews. The data were cross-culturally compared among the three linguistic groups. Venn diagrams were used to visualize the comparative analysis. To determine the patterns of similarities in plant use among the different ethnic groups, we used the Jaccard similarity index (JI). The recorded data were also compared with the existing Pakistani food ethnobotanical literature.

RESULTS: A total of 68 WFPs were recorded, the majority of which were used as raw snacks and as cooked vegetables. Fruit was the most frequently reported plant part among the three researched groups. Cross-cultural comparison revealed that 37% of the used plants were commonly shared by the three studied groups. Pathans have retained rich knowledge on WFPs, and they show a comparatively closer affinity with Kohistanis is the use of WFPs compared to Gujjars. While we observed some idiosyncrasies for each of the researched groups, the distinctive plant uses among Gujjars provide insight into their food ecology, their particular human-ecological system centered on mobile pastoralism and their limited exchanges of local food/ecological knowledge due to endogamic patterns. A literature survey revealed some novel or little-known ingredients within Pakistani food ethnobotany/ethnomycology, such as Aesculus indica, Agaricus campestris, Apteranthes tuberculata, Duchesnea indica, Equisetum arvense, Eremurus himalaicus, Isodon rugosus, Morella esculenta, Sophora mollis, and Drimia indica.

CONCLUSION: The researched communities have retained important plant knowledge which could be implemented through future development programs considering that most of these traditional foraging practices fulfill environmental and social sustainability standards. Further field studies are required to thoroughly investigate the patterns of foraging among highland pastoral societies in other parts of the Hindukush region and especially their potential for the ongoing ecological transition.

RevDate: 2023-04-01

Romero Starke K, Schubert M, Kaboth P, et al (2023)

Traffic noise annoyance in the LIFE-adult study in Germany: Exposure-response relationships and a comparison to the WHO curves.

Environmental research pii:S0013-9351(23)00607-2 [Epub ahead of print].

BACKGROUND: Noise annoyance is the second-highest cause of lost disability-adjusted life-years due to environmental noise in Europe. Evidence on exposure-response relationships (ERRs) for traffic noise annoyance with more accurate exposure values is still needed.

OBJECTIVES: In an analysis of the population-based LIFE-Adult study in Leipzig, Germany, we aimed to investigate the effect of road, railway (train and tram), and aircraft noise on high annoyance (HA).

METHODS: Traffic exposure data was taken for 2012 and data on noise annoyance was evaluated between 2018 and 2021. HA was defined according to international standardized norms. We calculated risk estimates using logistic regression, controlling for age, sex, and socioeconomic status, and compared our ERRs with those from the last WHO review on this topic.

RESULTS: Aircraft noise had the highest relative risk for noise-related HA (OR = 12.7, 95% CI: 9.37-17.10 per 10 dB Lden increase). The road and railway traffic risk estimates were similar to each other (road: OR = 3.55, 95% CI: 2.78-4.54; railway: OR = 3.31, 95% CI: 2.77-3.97 per 10 dB Lden increase). Compared to the WHO curves, the proportion of highly annoyed individuals was somewhat lower for road and rail traffic noise, but higher for aircraft noise.

DISCUSSION: Aircraft noise is particularly annoying. There were differences between our study's ERRs and those in the WHO review, especially for aircraft noise. These differences may be partly explained by the improved accuracy of the exposure values, as we considered secondary road networks and tram noise, and by a lack of a nighttime flight ban at the Leipzig airport. Geographical, regional and climatic variations, inconsistency in HA cut-offs, as well as temporal developments in the annoyance experience may also explain the differences. Since ERRs serve as a basis for decision making in public policies, regular updates of the curves based on new evidence is recommended.

RevDate: 2023-04-01

Boyes D, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, et al (2022)

The genome sequence of the pale mottled willow, Caradrina clavipalpis (Scopoli, 1763).

Wellcome open research, 7:225.

We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.

RevDate: 2023-04-01
CmpDate: 2023-03-31

Howison M, Gillani FS, Novitsky V, et al (2023)

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.

Viruses, 15(3):.

Molecular HIV cluster data can guide public health responses towards ending the HIV epidemic. Currently, real-time data integration, analysis, and interpretation are challenging, leading to a delayed public health response. We present a comprehensive methodology for addressing these challenges through data integration, analysis, and reporting. We integrated heterogeneous data sources across systems and developed an open-source, automatic bioinformatics pipeline that provides molecular HIV cluster data to inform public health responses to new statewide HIV-1 diagnoses, overcoming data management, computational, and analytical challenges. We demonstrate implementation of this pipeline in a statewide HIV epidemic and use it to compare the impact of specific phylogenetic and distance-only methods and datasets on molecular HIV cluster analyses. The pipeline was applied to 18 monthly datasets generated between January 2020 and June 2022 in Rhode Island, USA, that provide statewide molecular HIV data to support routine public health case management by a multi-disciplinary team. The resulting cluster analyses and near-real-time reporting guided public health actions in 37 phylogenetically clustered cases out of 57 new HIV-1 diagnoses. Of the 37, only 21 (57%) clustered by distance-only methods. Through a unique academic-public health partnership, an automated open-source pipeline was developed and applied to prospective, routine analysis of statewide molecular HIV data in near-real-time. This collaboration informed public health actions to optimize disruption of HIV transmission.

RevDate: 2023-04-01
CmpDate: 2023-03-31

Bird N, Ormond L, Awah P, et al (2023)

Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture.

Science advances, 9(13):eabq2616.

Previous studies have highlighted how African genomes have been shaped by a complex series of historical events. Despite this, genome-wide data have only been obtained from a small proportion of present-day ethnolinguistic groups. By analyzing new autosomal genetic variation data of 1333 individuals from over 150 ethnic groups from Cameroon, Republic of the Congo, Ghana, Nigeria, and Sudan, we demonstrate a previously underappreciated fine-scale level of genetic structure within these countries, for example, correlating with historical polities in western Cameroon. By comparing genetic variation patterns among populations, we infer that many northern Cameroonian and Sudanese groups share genetic links with multiple geographically disparate populations, likely resulting from long-distance migrations. In Ghana and Nigeria, we infer signatures of intermixing dated to over 2000 years ago, corresponding to reports of environmental transformations possibly related to climate change. We also infer recent intermixing signals in multiple African populations, including Congolese, that likely relate to the expansions of Bantu language-speaking peoples.

RevDate: 2023-03-31
CmpDate: 2023-03-30

Sui J, Zhang G, Lin T, et al (2023)

Quantitative Evaluation of Spatial Accessibility of Various Urban Medical Services Based on Big Data of Outpatient Appointments.

International journal of environmental research and public health, 20(6):.

Equity of urban medical services affects human health and well-being in cities and is important in building 'just' cities. We carried out a quantitative analysis of the spatial accessibility of medical services considering the diverse demands of people of different ages, using outpatient appointment big data and refining the two-step floating catchment area (2SFCA) method. We used the traditional 2SFCA method to evaluate the overall spatial accessibility of medical services of 504 communities in Xiamen city, considering the total population and the supply of medical resources. Approximately half the communities had good access to medical services. The communities with high accessibility were mainly on Xiamen Island, and those with low accessibility were further from the central city. The refined 2SFCA method showed a more diverse and complex spatial distribution of accessibility to medical services. Overall, 209 communities had high accessibility to internal medicine services, 133 to surgery services, 50 to gynecology and obstetrics services, and 18 to pediatric services. The traditional method may over-evaluate or under-evaluate the accessibility of different types of medical services for most communities compared with the refined evaluation method. Our study can provide more precise information on urban medical service spatial accessibility to support just city development and design.

RevDate: 2023-03-29

Schalli M, Platzer S, Schmutz R, et al (2023)

Dissolved Carbon Dioxide: The Lifespan of Staphylococcus aureus and Enterococcus faecalis in Bottled Carbonated Mineral Water.

Biology, 12(3):.

During the process of mineral water production, many possible contamination settings can influence the quality of bottled water. Microbial contamination can originate from different sources, for example, the ambient air, the bottles, the caps, and from the bottling machine itself. The aim of this study was to investigate the influence of three different carbon dioxide (CO2) concentrations (3.0 g/L, 5.5 g/L, and 7.0 g/L; 20 bottles each) in bottled mineral water on the bacterial growth of Staphylococcus aureus (S. aureus) and Enterococcus faecalis (Ent. faecalis). The examined mineral water was artificially contaminated before capping the bottles inside the factory. After a specific number of days, water samples were taken from freshly opened bottles and after filtration (100 mL), filters were placed on Columbia Agar with 5% Sheep blood to cultivate S. aureus and Slanetz and Bartley Agar to cultivate Ent. faecalis. The respective colony-forming units (CFU) were counted after incubation times ranging from 24 to 120 h. Colony-forming units of S. aureus were not detectable after the 16th and 27th day, whereas Ent. faecalis was not cultivable after the 5th and 13th day when stored inside the bottles. The investigation of the bottles that were stored open for a certain amount of time with CO2 bubbling out showed only single colonies for S. aureus after the 5th day and no CFUs for Ent. faecalis after the 17th day. A reduction in the two investigated bacterial strains during storage in carbonated mineral water bottles means that a proper standardized disinfection and cleaning procedure, according to valid hygiene standards of industrial bottling machines, cannot be replaced by carbonation.

RevDate: 2023-03-29

Stanic B, Milošević N, Sukur N, et al (2023)

An in silico toxicogenomic approach in constructing the aflatoxin B1-mediated regulatory network of hub genes in hepatocellular carcinoma.

Toxicology mechanisms and methods [Epub ahead of print].

Aflatoxin B1 (AFB1) can cause hepatocellular carcinoma (HCC) through a mutagenic mode of action but can also lead to global changes in gene expression; however, the AFB1 network of molecular pathways involved in HCC is not known. Here, we used toxicogenomic data from human liver cells exposed to AFB1 to infer the network of AFB1-responsive molecular pathways involved in HCC. The following computational tools: STRING, MCODE, cytoHubba, iRegulon, kinase enrichment tool KEA3, and DAVID were used to identify protein-protein interaction network, hub genes, transcription factors (TFs), upstream kinases, and biological processes (BPs). Predicted molecular events were validated with an external dataset, whereas the hub genes in HCC were validated using the UALCAN database. The results revealed an association between AFB1 and the hub genes involved in cell cycle. We identified TFs that regulate the hub genes and linked them with upstream kinases including cyclin-dependent kinases, mitogen-activated protein kinase 1, and AKT. This approach enabled the construction of the AFB1-mediated regulatory network consisting of upstream kinases, TFs, hub genes, and BPs, thus revealing the signaling hierarchy and information flow that may contribute to AFB1-induced HCC. This could be a useful tool in predicting the molecular mechanisms involved in chemical-induced diseases when available toxicogenomic data exist.

RevDate: 2023-03-30
CmpDate: 2023-03-30

Huang F, C Chen (2023)

GIS-based approach and multivariate statistical analysis for identifying sources of heavy metals in marine sediments from the coast of Hong Kong.

Environmental monitoring and assessment, 195(4):518.

Hong Kong is an urbanized coastal city which experiences substantially different metal loads from anthropogenic activities. This study was aimed at analyzing the spatial distribution and pollution evaluation of ten selected heavy metals (As, Cd, Cr, Cu, Pb, Hg, Ni, Zn, Fe, V) in the coastal sediments of Hong Kong. The distribution of heavy metal pollution in sediments has been analyzed using the geographic information system (GIS) technique, and their pollution degrees, corresponding potential ecological risks and source identifications, have been studied by applying the enrichment factor (EF) analysis, contamination factor (CF) analysis, potential ecological risk index (PEI), and integrated multivariate statistical methods, respectively. Firstly, the GIS technique was used to access the spatial distribution of the heavy metals; the result revealed that pollution trend of these metals was decreased from the inner to the outer coast sites of the studied area. Secondly, combining the EF analysis and CF analysis, we found that the pollution degree of heavy metals followed the order of Cu > Cr > Cd > Zn > Pb > Hg > Ni > Fe > As > V. Thirdly, the PERI calculations showed that Cd, Hg, and Cu were the most potential ecological risk factors compared to other metals. Finally, cluster analysis combined with principal component analysis showed that Cr, Cu, Hg, and Ni might originate from the industrial discharges and shipping activities. V, As, and Fe were mainly derived from the natural origin, whereas Cd, Pb, and Zn were identified from the municipal discharges and industrial wastewater. In conclusion, this work should be helpful in the establishment of strategies for contamination control and optimization of industrial structures in Hong Kong.

RevDate: 2023-03-28

Yang D, Zhu H, Liu J, et al (2023)

Risk Assessment of Heavy Metals in Soils from Four Different Industrial Plants in a Medium-Sized City in North China.

Toxics, 11(3): pii:toxics11030217.

Laboratory experiments were carried out to analyze 39 soil samples collected from four industrial areas in Xuzhou City using inductively coupled plasma mass spectrometry and atomic fluorescence spectrometry. The descriptive statistics of heavy metals (HMs) in the soil profiles showed that the HM content at three depths was highly variable, and most coefficients of variation (CVs) showed moderate variability. The enrichment of Cd at all depths exceeded the risk screening value, and Cd pollution occurred in four plants. The enrichment of the other HMs at three depths was mainly concentrated in the pharmaceutical plant A and chemical plant C. It was found that the different HMs had different vertical distribution characteristics. For the different industrial plants, the raw materials and products not only made the spatial distribution characteristics of the HMs different, but also caused the HM types and contents to differ. The average single pollution indices of Cd in plant A, iron-steel plant B, and plant C indicated a slight pollution level. The other seven HMs in A, B, and C and all HMs in chemical plant D belonged to the safe category. The mean values of the Nemerow pollution index in the four industrial plants belonged to the warning category. The analysis showed that none of the HMs posed potential noncarcinogenic health risks, and only the carcinogenic health risks of Cr in plants A and C were unacceptable. The carcinogenic effect of Cr through the inhalation intake of resuspended soil particulates and that of Cd, Ni, and As via direct oral ingestion were the main exposure pathways.

RevDate: 2023-03-27

Cecchetto M, Peruzza L, Giubilato E, et al (2023)

An innovative index to incorporate transcriptomic data into weight of evidence approaches for environmental risk assessment.

Environmental research pii:S0013-9351(23)00537-6 [Epub ahead of print].

The sharp decrease in the cost of RNA-sequencing and the rapid improvement in computational analysis of eco-toxicogenomic data have brought new insights into the adverse effects of chemicals on aquatic organisms. Yet, transcriptomics is generally applied qualitatively in environmental risk assessments, hampering more effective exploitation of this evidence through multidisciplinary studies. In view of this limitation, a methodology is here presented to quantitatively elaborate transcriptional data in support to environmental risk assessment. The proposed methodology makes use of results from the application of Gene Set Enrichment Analysis to recent studies investigating the response of Mytilus galloprovincialis and Ruditapes philippinarum exposed to contaminants of emerging concern. The degree of changes in gene sets and the relevance of physiological reactions are integrated in the calculation of a hazard index. The outcome is then classified according to five hazard classes (from absent to severe), providing an evaluation of whole-transcriptome effects of chemical exposure. The application to experimental and simulated datasets proved that the method can effectively discriminate different levels of altered transcriptomic responses when compared to expert judgement (Spearman correlation coefficient of 0.96). A further application to data collected in two independent studies of Salmo trutta and Xenopus tropicalis exposed to contaminants confirmed the potential extension of the methodology to other aquatic species. This methodology can serve as a proof of concept for the integration of "genomic tools" in environmental risk assessment based on multidisciplinary investigations. To this end, the proposed transcriptomic hazard index can now be incorporated into quantitative Weight of Evidence approaches and weighed, with results from other types of analysis, to elucidate the role of chemicals in adverse ecological effects.

RevDate: 2023-03-29
CmpDate: 2023-03-29

Beauchamp AM, Lehmann CU, Medford RJ, et al (2023)

The Association of a Geographically Wide Social Media Network on Depression: County-Level Ecological Analysis.

Journal of medical Internet research, 25:e43623 pii:v25i1e43623.

BACKGROUND: Social connectedness decreases human mortality, improves cancer survival, cardiovascular health, and body mass, results in better-controlled glucose levels, and strengthens mental health. However, few public health studies have leveraged large social media data sets to classify user network structure and geographic reach rather than the sole use of social media platforms.

OBJECTIVE: The objective of this study was to determine the association between population-level digital social connectedness and reach and depression in the population across geographies of the United States.

METHODS: Our study used an ecological assessment of aggregated, cross-sectional population measures of social connectedness, and self-reported depression across all counties in the United States. This study included all 3142 counties in the contiguous United States. We used measures obtained between 2018 and 2020 for adult residents in the study area. The study's main exposure of interest is the Social Connectedness Index (SCI), a pair-wise composite index describing the "strength of connectedness between 2 geographic areas as represented by Facebook friendship ties." This measure describes the density and geographical reach of average county residents' social network using Facebook friendships and can differentiate between local and long-distance Facebook connections. The study's outcome of interest is self-reported depressive disorder as published by the Centers for Disease Control and Prevention.

RESULTS: On average, 21% (21/100) of all adult residents in the United States reported a depressive disorder. Depression frequency was the lowest for counties in the Northeast (18.6%) and was highest for southern counties (22.4%). Social networks in northeastern counties involved moderately local connections (SCI 5-10 the 20th percentile for n=70, 36% of counties), whereas social networks in Midwest, southern, and western counties contained mostly local connections (SCI 1-2 the 20th percentile for n=598, 56.7%, n=401, 28.2%, and n=159, 38.4%, respectively). As the quantity and distance that social connections span (ie, SCI) increased, the prevalence of depressive disorders decreased by 0.3% (SE 0.1%) per rank.

CONCLUSIONS: Social connectedness and depression showed, after adjusting for confounding factors such as income, education, cohabitation, natural resources, employment categories, accessibility, and urbanicity, that a greater social connectedness score is associated with a decreased prevalence of depression.

RevDate: 2023-03-26

Song W, W Song (2023)

Cropland fallow reduces agricultural water consumption by 303 million tons annually in Gansu Province, China.

The Science of the total environment pii:S0048-9697(23)01631-5 [Epub ahead of print].

The high-intensity utilization of global cropland causes water shortage and food crisis, which seriously affects the realization of SDG 2 (zero hunger), SDG 6 (clean water and sanitation) and SDG 15 (life on land), and threatens the sustainable social, economic and ecological development. Cropland fallow can not only improve the quality of cropland and maintain ecosystem balance, but also have a significant water-saving effect. However, in most developing countries, such as China, cropland fallow has not yet been widely promoted, and there are few reliable fallow cropland fallow identification methods, making it even more challenging to assess the water-saving effect. To remedy this deficit, we propose a framework for mapping cropland fallow and evaluating its water savings. First, we used the Landsat series of data to interpret the annual land use/cover changes in Gansu Province, China from 1991 to 2020. Subsequently, the spatial-temporal variation of cropland fallow in Gansu province (giving up farming for one to two years) was mapped. Finally, we evaluated the water-saving effect of cropland fallow using evapotranspiration, precipitation, irrigation maps, and crop-related data, instead of actual water consumption. The results showed that the mapping accuracy of fallow land in Gansu Province was 79.50 %, which was higher than that of most known fallow mapping studies. From 1993 to 2018, the average annual fallow rate in Gansu Province, China, was 10.86 %, which was at a low level in arid/semi-arid regions worldwide. More importantly, from 2003 to 2018, cropland fallow reduces annual water consumption of 303.26 million tons in Gansu Province, accounting for 3.44 % of agricultural water use in Gansu Province and equivalent to the annual water demand of 655,000 people in Gansu Province. Based on our research, we speculate that the increasing pilot projects of cropland fallow in China can bring significant water-saving effects and help achieve China's Sustainable Development Goals.

RevDate: 2023-03-28
CmpDate: 2023-03-28

Jin H, Zhihong P, Jiaqing Z, et al (2023)

Source apportionment and quantitative risk assessment of heavy metals at an abandoned zinc smelting site based on GIS and PMF models.

Journal of environmental management, 336:117565.

The abandoned smelters have caused serious hazards to the surrounding environment and residents. Taking an abandoned zinc smelter in southern China as an example, a total of 245 soil samples were collected to study spatial heterogeneity, source apportionment, and source-derived risk assessment of heavy metal(loid)s (HMs) in the region. The results showed that the mean values of all HMs concentrations were higher than the local background values, with Zn, Cd, Pb, and As contamination being the most serious and their plume penetrating to the bottom layer. Four sources were identified by principal component analysis and positive matrix factorization, with their contributions to the HMs contents ranked as: surface runoff (F2, 63.2%) > surface solid waste (F1, 22.2%) > atmospheric deposition (F3, 8.5%) > parent material (F4, 6.1%). Among these, F1 was a determinant source of human health risk with a contribution rate of 60%. Therefore, F1 was considered to be the priority control factor, but it only accounted for 22.2% of HMs contents contribution. Hg dominated the ecological risk with a contribution of 91.1%. Pb (25.7%) and As (32.9%) accounted for the non-carcinogenic risk, while As (95%) dominated the carcinogenic effect. The spatial characteristics of human health risk values derived from F1 indicated that high-risk areas were mainly distributed in the casting finished products area, electrolysis area, leaching-concentration area, and fluidization roasting area. The findings highlight the significance of priority control factors (including HMs, pollution sources and functional areas) for consideration in the integrated management of this region, thus saving costs for effective soil remediation.

RevDate: 2023-03-28
CmpDate: 2023-03-28

Hu Y, Wang X, Xu Y, et al (2023)

Molecular mechanisms of adaptive evolution in wild animals and plants.

Science China. Life sciences, 66(3):453-495.

Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.

RevDate: 2023-03-25

Dec E, Clement J, Cheng K, et al (2023)

Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity.

GeroScience [Epub ahead of print].

Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.

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ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

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This is a must read book for anyone with an interest in invasion biology. The full title of the book lays out the author's premise — The New Wild: Why Invasive Species Will Be Nature's Salvation. Not only is species movement not bad for ecosystems, it is the way that ecosystems respond to perturbation — it is the way ecosystems heal. Even if you are one of those who is absolutely convinced that invasive species are actually "a blight, pollution, an epidemic, or a cancer on nature", you should read this book to clarify your own thinking. True scientific understanding never comes from just interacting with those with whom you already agree. R. Robbins

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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).

Timelines

ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.

Biographies

Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )