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617 results for “base population”
Figure 1 in Microsatellite based genetic diversity of Mediterranean fruit fly (Ceratitis capitata, Diptera: Tephritidae) populations from Southwest Turkey
Figure 1. Map of Turkey with sampling sites.
FIGURE 1 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 1 | Sampling sites of Pseudoplatystoma magdaleniatum in the Magdalena-Cauca basin.
FRB Mock Catalog and Reproduction Package for "Birth and Evolution of Fast Radio Bursts: Strong Population-Based Evidence for a Neutron-Star Origin"
<h3>Quickstart: FRB Mock Catalog</h3> <p>A simulated 1-day catalog of one-off FRBs, that allows users to access the FRB population without installing the entire frbpoppy package. Download and unzip 1_Day_FRB_Sky_on_Earth.txt.zip (175 MB). This human and machine readable file contains 3.5E6 FRBs that are brighter than 0.01 Jy ms, the best limit in one-off FRB detection currently. The simulated catalog is produced by the perfect telescope in frbpoppy, free of selection effects, that observed 4pi of sky for 24 hrs, with minimum detectable fluence 0.01 Jy ms, for the best-fit no-delay SFR model. This file can be read using the accompanying jupyter notebook "starting_with_mock_catalog.ipynb".</p> <p>If you use this, please cite Wang & van Leeuwen 2024 (A&A), <a href="https://doi.org/10.1051/0004-6361/202450673">https://doi.org/10.1051/0004-6361/202450673</a></p> <h3>Reproduction package for the paper "Birth and Evolution of Fast Radio Bursts: Strong Population-Based Evidence for a Neutron-Star Origin"</h3> <p>ReproductionPackage.zip is a basic reproduction package for the paper "Birth and Evolution of Fast Radio Bursts: Strong Population-Based Evidence for a Neutron-Star Origin" by Wang & van Leeuwen (2024).</p> <p> * arXiv: [<a href="https://arxiv.org/abs/2405.06281">2405.06281</a>] <br> * DOI: [<a href="https://doi.org/10.1051/0004-6361/202450673">10.1051/0004-6361/202450673</a>] </p> <h3>Installation</h3> <p>First pull or download and `frbpoppy` from <https://github.com/TRASAL/frbpoppy>.<br>Then download `ReproductionPackage.zip` and extract it starting in the frbpoppy/ base directory.<br>The scripts to produce the Figures are found in folder `frbpoppy/tests/markov_chain_monte_carlo/`.<br>The data used for these Figures resides in folder `frbpoppy/data/populations/mcmc/`.</p> <h3>Software</h3> <p>The methods and software packages used to produce the results are listed in the paper (including links to the relevant publications and/or packages):<br> FRBPOPPY: <https://github.com/TRASAL/frbpoppy><br> TRASAL: <https://github.com/TRASAL></p> <h3>Raw Data</h3> <p>The data are publicly available at<br> https://www.wis-tns.org/</p> <p> </p>
Prevalence and Factors Associated with the Use of Traditional Medicine in Individuals with Hypercholesterolemia, Hyperglycaemia, and Arterial Hypertension in Ecuador: Results from a Population-based Study in Two Health Districts
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Data from: Population-based screening for hepatitis C antibodies and active infection using a point-of-care test in a low prevalence area
<p><span><span><span><span><span><span><span><span><span><span><span><b>Background.</b> Data on the true prevalence of hepatitis C virus (HCV) infection in the </span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>general population is essential to health policies. We evaluated a program implementing free universal HCV screening using a non-invasive point-of-care test (POCT) (OraQuick-HCV rapid test) in oral fluid in an urban area in Valencia, South-Eastern Spain. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Methods.</b> A cross-sectional study was performed during 2015-2017. Free HCV screening was offered by regular mail to 11,500 individuals aged 18 and over, randomly selected from all census residents in the Health Department. All responding participants filled in a questionnaire about HCV infection risk factors and were tested in their tertiary Hospital. In those with a positive POCT, results were confirmed by enzyme-immunoassay and HCV-RNA.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Results.</b> 1,206 persons agreed to participate (response rate: 11.16%). HCV antibodies were detected in 19 (1.60%) cases (age-sex standardized rate: 1.31%; 95%CI: 0.82-2.07), but only 8 showed positive HCV-RNA (age-sex standardized rate: 0.56%; 95%CI: 0.28-1.14). The majority (89%) of the cases were born before 1965 and 74% had at least one known risk factor for HCV infection. All anti-HCV positive individuals were already aware of their infection, and no undiagnosed cases were detected. The performance of the POCT was excellent for detecting active infection. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions.</b> These preliminary data suggest that HCV population screening with a POCT is feasible but, in our setting, mailing recruiting is not effective (11% response rate). The low prevalence of HCV antibodies and active infection in the participant population (with no new diagnoses made) suggests that, in our setting, underdiagnosis may be uncommon.</span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span><b>Files uploaded include the study database (Stata v.13) and the do.file of the study.</b></span></span></span></span></span></span></span></span></span></span></span></p>
Data from: How "simple" methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
Reduced representation (RRL) sequencing approaches (e.g., RADSeq, genotyping by sequencing) require decisions about how much to invest in genome coverage and sequencing depth (library quality), as well as choices of values for adjustable bioinformatics parameters. To empirically explore the importance of these "simple" decisions, we generated two independent sequencing libraries for the same 142 individual lake whitefish (Coregonus clupeaformis) using a nextRAD RRL approach: (1) A small number of loci and low sequencing depth (library A); and (2) more loci and higher sequencing depth (library B). The fish were selected from populations with different levels of expected genetic subdivision. Each library was analyzed using the STACKS pipeline followed by three types of population structure assessment (FST, DAPC and ADMIXTURE) with iterative increases in the stringency of sequencing depth and missing data requirements, as well as more specific a priori population maps. Library B was always able to resolve strong population differentiation in all three types of assessment regardless of the selected parameters. In contrast, library A produced more variable results; increasing the minimum sequencing depth threshold (-m) resulted in a reduced number of retained loci, and therefore lost resolution at high -m values for FST and ADMIXTURE, but not DAPC. FST and DAPC were robust to varying the population map and increasing the stringency of missing data requirements. In contrast, ADMIXTURE was unable to resolve strong population differentiation when increasing these same parameters in library A. Similarly, when examining fine scale population subdivision, library B was robust to changing parameters but library A lost resolution depending on the parameter set. We used library B to examine actual subdivision in our study populations. All three types of analysis found complete subdivision among populations in Lake Huron, ON and Dore Lake, SK, Canada using 10,640 SNP loci. Weak population subdivision was detected in Lake Huron with fish from sites in the north-west, Search Bay, North Point and Hammond Bay, showing slight differentiation. Overall, we show that apparently simple decisions about library quality and bioinformatics parameters can have potentially important impacts on the interpretation of population subdivision. Although costly, the early investment in a high-quality library and more conservative stringency settings on STACKS parameters lead to a final dataset that was more consistent and robust when examining both weak and strong population differentiation.
Raw data for the article: A commentary on "Simultaneous versus staged resection for synchronous colorectal liver metastases: A population-based cohort study". Importance of avoiding any other additional risk in selected patients with synchronous colorectal liver metastases
<p>We read with great interest the article of Dr. Bogach and Colleagues, in which they have evaluated trends of resection for synchronous colorectal cancer liver metastases (CRLM) and associated patient outcomes with a retrospective cohort study from 2006 to 2015 in the province of Ontario, Canada.</p>
Source Data: No evidence for a common blood microbiome based on a population study of 9,770 healthy humans
<p>Source data for manuscript titled: 'No evidence for a common blood microbiome based on a population study of 9,770 healthy humans' (https://www.biorxiv.org/content/10.1101/2022.07.29.502098v1)</p>
Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling
<div class="abstract"> <p>Old growth forests are declining globally, threatening dependent wildlife. Many arboreal old‐growth obligates, such as the threatened red tree vole, are difficult to monitor for changes in habitat occupancy, and abundance. Yet, conservation planning relies on this information to prevent population declines. We integrated a range of species, habitat, and landscape change information to develop a dynamic habitat‐population model. The spatial individual‐based model simulated dynamic patterns of occupancy that responded to annual habitat maps, describing 36 years of observed change. We simulated population dynamics and local movement to characterize changes in occupancy and abundance, and the capacity of remaining habitat to support red tree voles. Red tree vole redistribution patterns strongly corresponded to wildfire footprints and timber extraction locations. Population strongholds are likely to exist in clumped pockets of old‐growth forest that were unaffected by wildfire and in protected old forest reserves. However, the exact number and locations of local clusters remain uncertain. Simulated population losses occurred at different paces in different places, underscoring the need for recurring evaluation of population changes with field occupancy surveys and modeled evaluations that can anticipate potential connectivity and extirpation thresholds. This modeling approach was effective at leveraging existing information for a data‐light species to assess how historical changes to the quantity, quality, and configuration of habitat likely influenced the potential landscape capacity, species abundance, and distribution. Dynamic individual‐based modeling can benefit conservation planning for red tree vole and other reclusive forest species by providing biologically nuanced assessments of abundance and distribution. Such models can also project the long‐term benefits and impacts of spatially explicit land management plans.</p> </div> <div class="abstract"></div>
Simulated population time series used to build and test a model of accuracy for population-based global biodiversity indicators
<p class="MsoNormal">Global biodiversity is facing a crisis, which must be solved through effective policies and on-the-ground conservation. But governments, NGOs, and scientists need reliable indicators to guide research, conservation actions, and policy decisions. Developing reliable indicators is challenging because the data underlying those tools is incomplete and biased. For example, the Living Planet Index tracks the changing status of global vertebrate biodiversity, but taxonomic, geographic and temporal gaps and biases are present in the aggregated data used to calculate trends. But without a basis for real-world comparison, there is no way to directly assess an indicator's accuracy or reliability. Instead, a modelling approach can be used.</p> <p class="MsoNormal">We developed a model of trend reliability, using simulated datasets as stand-ins for the "real world", degraded samples as stand-ins for indicator datasets (e.g. the Living Planet Database), and a distance measure to quantify reliability by comparing sampled to unsampled trends. The model revealed that the proportion of species represented in the database is not always indicative of trend reliability. Important factors are the number and length of time series, as well as their mean growth rates and variance in their growth rates, both within and between time series. We found that many trends in the Living Planet Index need more data to be considered reliable, particularly trends across the global south. In general, bird trends are the most reliable, while reptile and amphibian trends are most in need of additional data. We simulated three different solutions for reducing data deficiency, and found that collating existing data (where available) is the most efficient way to improve trend reliability, and that revisiting previously-studied populations is a quick and efficient way to improve trend reliability until new long-term studies can be completed and made available.</p>
Population dynamics and seasonal migration patterns of Spodoptera exigua in northern China based on 11 years of monitoring data
<p>The beet armyworm, <em>Spodoptera exigua </em>(Hübner) is an important migratory pest worldwide that has caused serious economic losses in the main crop-producing areas of China. To effectively monitor and control this pest, it is necessary to investigate its interannual and seasonal migration patterns in northern China. In this study, we weekly monitored the population dynamics of <em>S. exigua</em> using sex pheromone traps in Shenyang, Liaoning Province from 2012 to 2022 and simulated the migration trajectories using the HYSPLIT model. Overall, the migration numbers varied significantly among years, with large migrations in 2018 and 2020 that resulted in a total catch of more than 2000 individuals. </p>
Data from: Novel methods to define invasive procedures at the end-of-life were developed to improve quality of end of life care research: A population-based cohort study in colorectal cancer
<p><strong>Background</strong></p> <p>Understanding the use of invasive procedures (IPs) at the end-of-life (EoL) is important to avoid under- and overtreatment, but epidemiologic analysis is hampered by limited methods to define treatment intent and EoL phase. This study applied novel methods to report IPs at the EoL using a colorectal cancer (CRC) case study.</p> <p><strong>Methods</strong></p> <p>An English population-based cohort of adult patients diagnosed between 2013 and 2015 was used with follow-up to 2018. Procedure intent (curative, non-curative, diagnostic) by cancer site and stage at diagnosis was classified by two surgeons independently. Joinpoint regression modelled weekly rates of IPs for 36 sub-cohorts of patients with incremental survival of 0-36 months. EoL phase was defined by a significant IP rate change before death. Zero-inflated Poisson regression explored associations between IP rates and clinical/sociodemographic variables.</p> <p><strong>Results</strong></p> <p>Of 87,731 patients included, 41,972 (48%) died. 9,492 procedures were classified by intent (interrater agreement 99.8%). Patients received 502,895 IPs (1.39 and 3.36 per person year for survivors and decedents). Joinpoint regression identified significant increases in IPs four weeks before death in those living 3-6 months, and eight weeks before death in those living 7–36 months from diagnosis. 7,908 (18.8%) patients underwent IPs at the EoL, with stoma formation the most common major procedure. Younger age, early-stage disease, men, lower comorbidity, those receiving chemotherapy and living longer from diagnosis were associated with IPs.</p> <p><strong>Conclusions</strong></p> <p>Methods to identify and classify IPs at the EoL were developed and tested within a CRC population. This approach can be now extended and validated to identify potential under- and overtreatment. </p>
I Am Able: Population Based Rehabilitation in a Family Health Team
ClinicalTrials.gov study NCT00859638. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Prognostic Impact of Increased Lymph Node Yield in Colorectal Cancer Patients With Synchronous Distant Metastasis: a Population-based Study of the US Database and a Chinese Registry
ClinicalTrials.gov study NCT05550701. IPD Sharing: NO. Countries: 1. Publications: 3.
Comprehensive Management of High-risk PopuLatIon of Stroke Based on Social Network
ClinicalTrials.gov study NCT05963828. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study
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Data from: How “simple” methodological decisions affect interpretation of population structure based on reduced representation library DNA sequencing: a case study using the lake whitefish
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Genetic diversity and population genetic structure from different host populations of <em>Spodoptera litura</em> based on microsatellite markers
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Data from: A population-based screening for hepatitis C antibodies and active infection using a point-of-care test in a low prevalence area
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Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers
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ScienceDex guides
Understand access before you commit
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.