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205 results for “long-term change”
Dataset for the intervention effects and long-term changes in physical activity and cardiometabolic outcomes among children at risk of noncommunicable diseases in South Africa
<p>Dataset used to evaluate the short-term effects of the physical and health <em>KaziKidz</em> intervention on cardiometabolic risk factors and the long-term changes thereof among school-aged children at risk of NCDs from disadvantaged communities in South Africa.</p> <p>It encompasses anonymized, unique, identification numbers, anthropometric and clinical measures, such as blood pressure, blood sugar and blood lipids, and Actigraphy-measured physical activity levels. Assigned categories to each cardiovascular risk factor and the overall classification as at risk or not is available too.</p>
Data from: Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala
<p>This dataset accompanies our publication titled: "Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala."</p> <p><strong>Files Included:</strong></p> <p><strong>1. geno.N26.vcf.gz</strong><br> - Description: Contains genotypes for 26 Heterogeneous Stock rats whose gene expression was predicted.</p> <p><strong>2. pred_expr.Brain.N26.tsv</strong><br> - Description: This tab-delimited table contains predicted relative gene expression in the brain for 26 Heterogeneous Stock rats. <br> - Details: Predictions were made for 8,997 genes from linear models based on cis-eQTLs from whole brain hemisphere tissue downloaded from the <a href="https://ratgtex.org/download/">RatGTEx Portal</a>. A gene is included in the table if it had at least one significant cis-eQTL, and if its predicted expression in these 26 animals had nonzero variance. The values in the table give the predicted log2(relative expression), where log2(2) = 1 is the baseline expression from the two haplotypes of the gene if it had only reference alleles at all its regulatory loci.<br> - Additional Info: Predictions were generated using <strong>gene_expr_pred.py</strong> available at https://github.com/PejLab/gene_expr_pred<br> An explanation of the prediction model is given in https://doi.org/10.1101/2022.01.28.478116</p> <p><strong>3. Behavioral data.xlsx</strong><br> - Description: Contains behavioral data for the Heterogeneous Stock (HS) rats.<br> - Organization: Each sheet in the file corresponds to data for a specific figure.</p> <p><strong>Additional Dataset Locations:</strong></p> <p>The primary datasets generated during this study can be found on the Gene Expression Omnibus under accession number <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212417">GSE212417</a></p> <p><strong>Publicly Available Datasets Utilized:</strong></p> <p>- Rattus norvegicus Ensembl v98 reference genome and genome assembly: <a href="http://useast.ensembl.org/Rattus_norvegicus/Info/Index">Rnor_6.0 </a><br> - JASPAR2022 transcription factor binding profiles for vertebrates: <a href="https://jaspar.genereg.net/">JASPAR</a><br> - ENCODE Honeybadger 2 ChIP-seq: <a href="https://personal.broadinstitute.org/meuleman/reg2map/">Broad Institute</a><br> - Liu et al. 2019106 GWAS for tobacco and nicotine addiction summary statistics: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6358542/">PubMed</a><br> - RatGTEx Portal tissue-specific cis-eQTLs: <a href="https://ratgtex.org/download/">RatGTEx Portal </a><br> - 1000 Genomes European reference panel: <a href="https://alkesgroup.broadinstitute.org/LDSCORE/">Alkes Group</a><br> - KEGG pathways: <a href="https://www.kegg.jp/kegg/rest/keggapi.html">KEGG API</a></p>
Data from: Long-term changes in soil carbon and nitrogen fractions in switchgrass, native grasses, and no-till corn bioenergy production systems
<p>Cellulosic bioenergy is a primary land-based climate mitigation strategy, with soil carbon (C) storage and nitrogen (N) conservation as important mitigation elements. Here, we present 13 years of soil C and N change under three cellulosic cropping systems: monoculture switchgrass (<em>Panicum virgatum</em> L.), a five native grasses polyculture, and no-till corn (<em>Zea mays</em> L.). Soil C and N fractions were measured four times over 12 years. Bulk soil C in the 0–25 cm depth at the end of the study period ranged from 28.4 (± 1.4 se) Mg C ha<sup>−1</sup> in no-till corn, to 30.8 (± 1.4) Mg C ha<sup>−1</sup> in switchgrass, and to 34.8 (± 1.4) Mg C ha<sup>−1</sup> in native grasses. Mineral-associated organic matter (MAOM) ranged from 60% to 90% and particulate organic matter (POM) from 10% to 40% of total soil C. Over 12 years, total C as well as both C fractions persisted under no-till corn and switchgrass and increased under native grasses. In contrast, POM N stocks decreased 33% to 45% across systems, whereas MAOM N decreased by less than 13% and only in no-till corn. Declining POM N stocks likely reflect pre-establishment land use, which included alfalfa and manure in earlier rotations. Root production and large soil aggregate formation explained 69% (p < 0.001) and 36% (p = 0.024) of total soil C change, respectively, and 60% (p = 0.020) and 41% (p = 0.023) of soil N change, demonstrating the importance of belowground productivity and soil aggregates for producing and protecting soil C and conserving soil N. Differences between switchgrass and native grasses also indicate a dependence on plant diversity. Soil C and N benefits of bioenergy crops depend strongly on root productivity and pre-establishment land use.</p>
Data from: Long-term changes in soil carbon and nitrogen fractions in switchgrass, native grasses, and no-till corn bioenergy production systems
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Data from: Maintaining local adaptation is key for evolutionary rescue and long-term persistence of populations experiencing habitat loss and a changing environment
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Long-term increases in wing length occur independently of changes in climate and climate-driven shifts in body size
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Data from: Long-term impacts of changed grazing regimes on the vegetation of heterogeneous upland grasslands
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Long-term change in the parasite burden of shore crabs (Hemigrapsus oregonensis and H. nudus) on the northwestern Pacific coast of North America
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Long-term data reveal widespread phenological change across major U.S. estuarine food webs
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Long-term changes in tundra carbon balance following wildfire, climate change and potential nutrient addition, a modeling analysis.
A study investigating the mechanisms that control long-term response of tussock tundra to fire and to increases in air temperature, CO2, nitrogen deposition and phosphorus weathering. The MBL MEL was used to simulate the recovery of three types of tussock tundra, unburned, moderately burned, and severely burned in response to changes in climate and nutrient additions. The simulations indicate that the recovery of nutrients lost during wildfire is difficult under a warming climate because warming increases nutrient cycles and subsequently leaching within the ecosystem. The study was published in Ecological Applications (in press, 2016). This dataset is the long term archive of the results published in the paper. The full dataset has been broken into two parts because of the number and size of the files. Part 1 contains MBL MEL executable, a model description file in word, and the input files to run the simulations. Part 2 contains the output files for all simulations. Both Part 1 and Part 2 contain several different types of files. In Part 1 the comma separated ascii file included with the dataset is one of the many driver files used for the simulations. The variable descriptions below describe the variables in that file and all the driver files. In Part 2 the comma separated ascii file included with the dataset is one of the many output files from the simulations. The variable descriptions below describe the variables in that file and all the output files. To access all the files in the dataset be sure to download the two zip files described in the Methods section below. Note that the full download is large, over 700 MB for each part. Permanent Archive of the data published in Jiang, et al., in press, Modeling long-term changes in tundra carbon balance following wildfire, climate change and potential nutrient addition, Ecological Applications.
Numerical response of predators to large variations of grassland vole abundance and long-term community change
<p>Voles can reach high densities with multi-annual population fluctuations of large amplitude, and they are at the base of predator communities in Northern Eurasia and Northern America. This status places them at the heart of management conflicts wherein crop protection and health concerns are often raised against conservation issues.<strong> Here, a 20-year survey describes the effects of large variations in grassland vole populations on the densities and the daily theoretical food intakes (TFI) of vole predators based on roadside counts.</strong> Our results show how the predator community responded to prey variations of large amplitude and how it reorganized with the increase in a dominant predator, here the red fox, which likely negatively impacted hare, European wildcat and domestic cat populations. This population increase did not lead to an increase in the average number of predators present in the study area, suggesting compensations among resident species due to intra-guild predation or competition. Large variations in vole predator number could be clearly attributed to the temporary increase in the populations of mobile birds of prey in response to grassland vole outbreaks. Our study provides empirical support for more timely and better focused actions in wildlife management and vole population control, and it supports an evidence-based and constructive dialogue about management targets and options between all stakeholders of such socio-ecosystems.</p> <p>The data set includes:</p> <p><b>S1 kml file</b>. Location of the study area (can be dropped in a Google Earth window or read from a GIS)</p> <p><b>S2 Excel file.</b> Road-side counts (sheet 1) and list of species observed (sheet 2)</p> <p><b>S3 Excel file.</b> Small mammal data</p> <p><b>S4 Excel file.</b> Data for computing theoretical daily food intakes</p> <p> </p>
Can we predict global patterns of long-term climate change from short-term simulations?
<p>Post-processed data from "Can we predict global patterns of long-term climate change from short-term simulations?". Also includes python dictionary for translating file code into the name of the run. For use with code publicly available on github.com/lm2612/Ridge_3 and github.com/lm2612/GPRegression.</p>
Long-term monitoring reveals forest tree community change driven by atmospheric sulfate pollution and contemporary climate change
Aim: Montane environments are sentinels of global change, providing unique opportunities to assess impacts on species diversity. Multiple anthropogenic stressors such as climate change and atmospheric pollution may act concurrently or synergistically in restructuring communities. Thus, a major challenge for conservation is untangling the relative importance of different stressors. Here, we combine long-term monitoring with multivariate community modeling to estimate the anthropogenic drivers shaping forest tree diversity along an elevational gradient. Location: Camels Hump Mountain, Vermont, USA Methods: We used Generalized Dissimilarity Modelling (GDM) to model spatial and temporal turnover in beta diversity along an elevational gradient over a 50-year period, and tested for spatiotemporal shifts in density and elevational distribution of individual species. GDMs were used to predict community turnover as non-linear functions of changes in elevation, climate and atmospheric pollution. Results: We observed significant shifts in elevational range and density of individual species, which contributed to an overall reduction in the elevational gradient in beta diversity through time. GDMs showed the combined effects of sulfate deposition and temperature as drivers of this temporal reduction in beta diversity. Spatiotemporal changes differed among species, with shifts observed both up and downslope. For example, in a reversal of a previous upslope range contraction, red spruce (Picea rubens Sarg.) increased in density and shifted downslope since the 1990's, occupying warmer, drier climates. Main conclusion: Our results demonstrate that global change is impacting the stratification of forest tree diversity along elevational gradients, but the responses of individual species are complex and variable in direction. We suggest abiotic drivers may directly impact individual species while also indirectly altering species interactions along elevational gradients. Our approach modelling the drivers of compositional turnover quantifies the rate and amount of change in beta diversity along environmental gradients, and serves as a powerful complement to studying species-specific responses.
Long-term movements and home range changes: rapid territory shifts in meerkats
<p>1. Territoriality and stable home ranges are a common space use pattern among animals. These ranges provide its inhabitants with important resources and thus favourable territories are associated with an increased fitness. While the role of territory quality and changes of territory ownership have often been investigated, the changes of territorial boundaries have been less studied.</p> <p>2. Here we investigated space use changes in a social mammal species, applying a novel analytical approach, calculating long-term dissimilarity in space use using distance matrices based on periodic utilization distributions. This approach makes it possible to identify different space use patterns, which cannot be distinguished by only considering changes between consecutive time periods.</p> <p>3. We analysed meerkat (Suricata suricatta) movements of a total of 24 different groups over a 16-year period, resulting in 134 group years. We then correlated the identified home range changes to life history events and possible environmental drivers.</p> <p>4. Groups had stable territories for several years before they abandoned their home range mostly to move quickly to new areas where they again remained for several years. Of 26 identified sudden shifts, 22 occurred in the summer months and often involved distances larger than the original home range size. Home-range movements that were close together in time were often also spatially clustered and moved in a similar direction. These shifts were often preceded by more frequent interactions between groups, but did not seem to be a product of direct displacements by other groups. The normalized difference vegetation index (NDVI) as a measure of food production and social factors such as dominance changes did not correlate to changes.</p> <p>5. Against our expectation space use changes were not accumulations of small changes, but more often involved long distance moves into unknown ranges. This means that the groups enter areas where they cannot profit from local knowledge. The methods used identifies episodes of long stability alternated by sudden changes in meerkats and in general provides insight into long-term space use. Our methods can be used to analyse long-term space use, either within or across species.</p>
Long-term changes in pituitary gene expression following developmental exposure to environmental contaminants (BPS, BDE-47, or TBBPA) in male mice.
<p><strong>Experimental Design</strong></p><p>In this study we evaluate the long-term gene expression changes in pituitary in male mice exposed developmentally to one of three known endocrine disrupting chemicals: bisphenol-S (BPS), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), and 3,3',5,5'-tetrabromobisphenol A (TBBPA). Male mice were exposed to chemical treatment through their mothers' during pregnancy (umbilical blood flow) and nursing, from pregnancy day 8 through weaning at postnatal day 21 (PND21). Each chemical exposure was calculated to equal 0.2mg/kg bw/day. The details of exposure protocol are described elsewhere (Kim<i> et al</i>, 2015). The male pups were allowed to grow untreated until adulthood at PND140. At PND140, male mice were euthanized, then their pituitaries removed, snap frozen in liquid nitrogen, and then stored at -80°C. </p><p>The data-files described below represent major steps of our analysis:</p><p><strong>1. FASTQ files for mouse pituitary RNA-seq data.</strong></p><p>Male mouse pituitary RNA was isolated using a Trizol protocol, checked for purity and concentration and then processed for mRNA sequencing using the Illumina TruSeq kit and protocol (TruSeq Stranded mRNA LP, Cat # 20020594 and TruSeq RNA Sg Idx SetB, Cat # 20020493, Illumina, San Diego, CA) following the manufacturer's recommended procedures. High throughput sequencing was conducted using the NextSeq500 sequencing system. cDNA libraries were single-end sequenced in 76 cycles using a NSQ 500/550 Hi Output KT v2.5 (Cat #20024906 Illumina, San-Diego, CA) in one multiplex run (N=3/exposure group). Read filtering, trimming, and de-multiplexing were performed using the BaseSpace cloud service by Illumina (<a href="https://basespace.illumina.com/home/index">https://basespace.illumina.com/home/index</a>, RRID:SCR_011881). Processed reads were mapped to the mouse reference genome (MM10) using the RNA-Seq Alignment v. 1.1.1. software with Bowtie 2. Each FASTQ file is a compressed file representing data from one sequencing flow cell lane for each sample (4 files per sample). Sample identifiers are coded for treatment: X = Vehicle control, R = TBBPA, C = BDE-47, E = BPS. </p><p><strong>2. Differential expression data.</strong></p><p>Aligned reads were used to assemble transcripts and analyze differential expression using Cufflinks Assembly & DE v. 2.1.0. package. Reads aligned to known annotated regions for both control and exposed groups were used to calculate log2 FPKM ratios. Differentially expressed genes were identified as genes altered with false discovery rate significance ≤ 0.05 (FDR, q ≤ 0.05). Data on all exposure groups are shown in different sheets of the same file - Differential_expression.xlsx.</p><p><strong>3. Enrichment of biological categories associated with DEGs induced by chemical exposures. </strong></p><p>All differentially expressed genes were uploaded to Metascape for the analysis of enriched biological categories using default settings. Results of Metascape analysis are shown in two MS Excel files per exposure group, one showing negatively enriched categories and one positively enriched categories. The title of each file consists of three parts connected via underscore sign: the name of the chemical, the direction of enrichment, and the name of analysis - metascape (e.g., BDE-47_negative_metascape.xlsx).</p><p><strong>4. Pathway analysis for chemical exposures.</strong></p><p>All differentially expressed genes were uploaded to Ingenuity Pathway Analysis and enriched canonical pathways were identified using default settings . Altered molecular or disease pathways, their p-values, and associated differentially expressed genes are provided for each exposure. Data for all exposure groups are shown in different sheets of the same file - IPA_pathway_analysis.xlsx.</p><p><strong>References:</strong></p><p>Kim B, Colon E, Chawla S, Vandenberg LN, Suvorov A. Endocrine disruptors alter social behaviors and indirectly influence social hierarchies via changes in body weight. Environ Health. 2015 Aug 5;14:64. doi: 10.1186/s12940-015-0051-6. PMID: 26242739; PMCID: PMC4524022.</p>
Fig. 2 in Long-term changes in avian relative abundances in relation to human disturbance in a tropical dry forest in central Myanmar
Fig. 2. Annual rainfall measured adjacent to Chatthin Wildlife Sanctuary 1999–2020.
Fig. 3. Forest cover within 300 in Long-term changes in avian relative abundances in relation to human disturbance in a tropical dry forest in central Myanmar
Fig. 3. Forest cover within 300 meters of bird survey points in 1999 and 2020.
Data for: Coherent long-term body-size responses across all Northwest Atlantic herring populations to warming and environmental change despite contrasting harvest and ecological factors
<p>Body size is a key component of individual fitness and an important factor in the structure and functioning of populations and ecosystems. Disentangling the effects of environmental change, harvest, and intra- and inter-specific trophic effects on body size remains challenging for populations in the wild. Herring in the Northwest Atlantic provide a strong basis for evaluating hypotheses related to these drivers given that they have experienced significant warming and harvest over the past century, while also having been exposed to a wide range of other selective constraints across their range. Using data on mean length-at-age 4 for the sixteen principal populations over a period of 53 cohorts (1962-2014), we fitted a series of empirical models for temporal and between-population variation in the response to changes in sea surface temperature. We find evidence for a unified cross-population response in the form of a parabolic function according to which populations in naturally warmer environments have responded more negatively to increasing temperature compared with those in colder locations. Temporal variation in residuals from this function was highly coherent among populations, further suggesting a common response to a large-scale environmental driver. The synchrony observed in this study system, despite strong differences in harvest and ecological histories among populations and over time, clearly indicates a dominant role of environmental change on size-at-age in wild populations, in contrast to commonly reported effects of fishing. This finding has important implications for the management of fisheries as it indicates that a key trait associated with population productivity may be under considerably less short-term management control than currently assumed. Our study, overall, illustrates the need for a comparative approach within species for inferences concerning the many possible effects on body size of natural and anthropogenic drivers in the wild.</p>
Questionnaire and interview guidelines related to Süsser et al. (2024) on how the COVID-19 pandemic changed stakeholder engagement processes in sustainability research in the long-term
<p>The survey questionnaire and the interview guidelines have been designed in the framework of the EU H2020 projects SENTINEL to study the impact of the coronavirus disease 2019 (COVID-19) on the stakeholder engagement processes in susatinability research in the longterm. We conducted interviews with researchers and engaged stakeholders, using a semi-structured interview guideline. We designed the survey as an explorative, semi-quantitative, self-completion online questionnaire, using the online tool “LimeSurvey”. The survey was reworked based on our previous survey. The study was a follow-up study on our own work (<em>Süsser, D., Ceglarz, A., Stavrakas, V., & Lilliestam, J. COVID-19 vs. stakeholder engagement: the impact of coronavirus containment measures on stakeholder involvement in European energy research projects [version 1; peer review: awaiting peer review]. Open Research Europe 2021,1:57. doi: <a href="https://doi.org/10.12688/openreseurope.13683.1">https://doi.org/10.12688/openreseurope.13683.1</a>). </em></p> <p>If you use this questionnaire or the interview guideline in an academic publication, please cite the following article:</p> <p><em>Süsser, D., Schibline, A. Ceglarz, A., Lilliestam, J., Stavrakas, V., & Schweizer, P.J. (2024), How the COVID-19 pandemic changed stakeholder engagement processes in sustainability research in the long-term, F1000 Research (to be published).</em></p> <p><em> </em></p>
Re-assessment of the climatic controls on the carbon and water fluxes of a boreal aspen forest over 1996-2016: changing sensitivity to long-term climatic conditions
<p>Recent evidence suggests that the relationships between climate and boreal tree growth are generally non-stationary; however, it remains uncertain whether the relationships between climate and carbon (C) fluxes of boreal forests are stationary or have changed over recent decades. In this study, we used continuous eddy-covariance and microclimate data over 21 years (1996-2016) from a 100-year-old trembling aspen stand in central Saskatchewan, Canada to assess the relationships between climate and ecosystem C and water fluxes. Over the study period, the most striking climatic event was a severe, 3-year drought (2001-2003). Gross ecosystem production (GEP) showed larger interannual variability than ecosystem respiration (<em>R</em><sub>e</sub>) over 1996-2016, but <em>R</em><sub>e</sub> was the dominant component contributing to the interannual variation in net ecosystem production (NEP) during post-drought years. The inter-annual variations in evapotranspiration (ET) and C fluxes were primarily driven by temperature and secondarily by water availability. Two-factor linear models combining precipitation and temperature performed well in explaining the inter-annual variation in C and water fluxes (<em>R</em><sup>2</sup>>0.5). The temperature dependence of all three C fluxes (NEP, GEP and <em>R</em><sub>e</sub>) declined over 1996-2015 (<em>p</em><0.05), and as a result, the phenological controls on annual NEP weakened. The decreasing temperature sensitivity of the C fluxes over 1996-2015 may reflect changes in forest structure, related to the over-maturity of the aspen stand at 100-years of age and exacerbated by high tree mortality following the severe 2001-2003 drought. These results may provide an early warning signal of driver shift or even an abrupt status shift of aspen forest dynamics. They may also imply a universal weakening in the relationship between temperature and GEP as forests become over-mature, associated with the structural and compositional changes that accompany forest ageing.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.