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11,177 results for “identify”
Identifying the fitness consequences of sex in complex natural environments
In the natural world, sex prevails, despite its costs. While much effort has been dedicated to identifying the intrinsic costs of sex (e.g. the cost of males), few studies have identified the ecological fitness consequences of sex. Furthermore, correlated biological traits that differ between sexuals and asexuals may alter these costs, or even render the typical costs of sex irrelevant. We conducted a large-scale multi-site reciprocal transplant using multiple sexual and asexual genotypes of a native North American wildflower to show that sexual genotypes have reduced lifetime fitness, despite lower herbivory. We separated the effects of sex from those of hybridity, finding that over-winter survival is elevated in asexuals regardless of hybridity, but herbivores target hybrid asexuals more than non-hybrid asexual or sexual genotypes. Survival is lowest in homozygous sexual lineages, implicating inbreeding depression as a cost of sex. Our results show that the consequences of sex are shaped not just by sex itself, but by complex natural environments, correlated traits, and the identity and availability of mates.
A novel method for using RNA-seq data to identify imprinted genes in social Hymenoptera with multiply mated queens
<p>Genomic imprinting results in parent-of-origin dependent gene expression biased towards either the maternally- or paternally-derived allele at the imprinted locus. The kinship theory of genomic imprinting argues that this unusual expression pattern is a manifestation of intra-genomic conflict between the maternally- and paternally-derived halves of the genome that arises because they are not equally related to the genomes of social partners. The theory thus predicts that imprinting may evolve wherever there are close interactions among asymmetrically related kin. The social Hymenoptera with permanent caste differentiation are suitable candidates for testing the kinship theory because haplodiploid sex determination creates strong relatedness asymmetries and nursing workers interact closely with kin. However, progress in the search for imprinted genes in the social Hymenoptera has been slow, in part because tests for imprinting rely on reciprocal crosses that are impossible in most species. Here, we develop a method to systematically search for imprinting in haplodiploid social insects without crosses, using instead samples of pooled individuals collected from natural colonies. We tested this protocol using data available for the leaf-cutting ant <i>Acromyrmex echinatior</i>, providing the first genome-wide search for imprinting in any ant. While we identified several genes as potentially imprinted, none of the four genes tested could be verified as imprinted using digital droplet PCR, highlighting the need for higher quality genomic assemblies that accurately map duplicated genes.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Hayley Lanier, <a href="https://orcid.org/0000-0001-9337-4017">https://orcid.org/0000-0001-9337-4017</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Geometric morphometric wing analysis represents a robust tool to identify female mosquitoes (Diptera: Culicidae) in Germany
<p>Accurate species identification is the prerequisite to assess the relevance of mosquito specimens, but is often hindered by missing or damaged morphological features. The present study analyses the applicability of wing geometric morphometrics as a low-cost and practical alternative to identify native mosquitoes in Germany. Wing pictures were collected for 502 female mosquitoes of five genera and 19 species from 80 sampling sites. The reliable species identification based on interspecific wing geometry of 18 landmarks per specimen was tested. Leave-one-out cross validation revealed an overall accuracy of 99% for the genus and 90% for the species identification. Misidentifications were mainly due to three pairings of <i>Aedes</i> species: <i>Aedes annulipes</i> vs. <i>Aedes cantans</i>, <i>Aedes cinereus</i> vs. <i>Aedes rossicus</i> and <i>Aedes communis </i>vs. <i>Aedes punctor.</i> Cytochrome oxidase subunit I (COI) gene region was sequenced to validate the morphological and morphometric identification. Similar to the results of the morphometric analysis, the same problematic three <i>Aedes</i>-pairs clustered, but most other species could be well separated. Overall, our study underpins that morphometric wing analysis is a robust tool for reliable mosquito identification, which reach the accuracy of COI barcoding.</p>
Challenges identified during inDemand in the pilot regions
<p>inDemand is a new co-creation model where Healthcare organizations (Challengers) and companies (Solvers) co-develop Digital Health solutions, with the economic support of public regional funds managed by Regional funding organisations (Funders). inDemand targets to solve Challenges identified by the Healthcare organizations.</p> <p>The first phase focuses on the need identification by the Challenger (Healthcare organisation), who launches an internal call for challenges (i.e.needs) among the professionals in the organisation.</p> <p>During the inDemand project challenges were identified in three pilot regions (Murcia, Oulu and Paris) in two different iterations:</p> <ul> <li>Paris 1<sup>st</sup> call: 05/01/2018 to 31/01/2018</li> <li>Oulu 1<sup>st</sup> call: 09/01/2018 to 28/01/2018</li> <li>Murcia 1<sup>st</sup> call: 06/11/2017 to 20/11/2017</li> <li>Paris 2<sup>nd</sup> call: 15/11/2018 to 31/12/2018</li> <li>Oulu 2<sup>nd</sup> call: 20/09/2018 to 06/10/2018</li> <li>Murcia 2<sup>nd</sup> call: 15/10/2018 to 09/11/2018</li> </ul> <p>In prevision of the Call for Challenges, a questionnaire (common for the 3 pilot regions) was created to collect the most important information necessary to assess and select the challenges in each region:</p> <ul> <li>Responsible of the challenge (name, position, department, email, etc.): anonymised for publication in Zenodo.</li> <li>Title and acronym of the challenge</li> <li>Definition of the challenge (description of the problem, overview of the current way or working, etc.)</li> <li>Potential scalability of the challenge to other areas/hospitals</li> <li>Expected functional requirements of an ICT solution that could tackle the need</li> <li>Feasibility to implement ICT solutions to address the challenge</li> <li>The commitment of the team to be involved in the inDemand model</li> </ul> <p>The data collected was of a qualitative nature. It was received via electronic tool and downloaded into .docx and .pdf formats. </p>
Data From: Conservation planning in an uncertain climate: identifying projects that remain valuable and feasible across future scenarios
<p>Conservation actors face the challenge of allocating limited resources despite uncertainty about future climate. A key goal is to minimize the potential for negative outcomes under future scenarios. Thus, we address a global conservation challenge: how to allocate conservation investments given high uncertainty about future climate conditions. To that end, we present a method for identifying projects that remain valuable and feasible across climate scenarios and apply our framework to freshwater biodiversity conservation in the South-Central USA. We combine data from a recent high-resolution hydrologic planning tool and species distribution models to estimate the conservation feasibility and biodiversity value of river reaches below 38 major reservoirs in the Red River basin.We find that only 13% of sites have high conservation priority across all future climate scenarios and that spatial patterns of conservation priority largely reflect patterns of water availability and fish biodiversity.</p>
ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs
<p>Genomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test.</p>
Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by Andrea A. Cabrera, <a href="https://orcid.org/0000-0001-5385-1114">https://orcid.org/0000-0001-5385-1114</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Wikidata: Persistent identifiers as the basis for multilingual and human-machine collaboration
<p>This repository hosts a video recording of a dry-run of the PIDapalooza 2021 <a href="https://www.pidapalooza.org/schedule">https://www.pidapalooza.org/schedule</a> session</p> <p><strong>"Wikidata: Persistent identifiers as the basis for multilingual and human-machine collaboration"</strong><strong> </strong></p> <p>taking place Thursday January 28, 2021 00:00 - 00:30 UTC on Stage 1, as per <a href="https://sched.co/gD2n">https://sched.co/gD2n</a> .</p> <p>The video is also available on YouTube via <a href="https://youtu.be/g5VCr--Q1Ig">https://youtu.be/g5VCr--Q1Ig</a> .</p> <p>See <a href="https://etherpad.wikimedia.org/p/zenodo.4253308">https://etherpad.wikimedia.org/p/zenodo.4253308</a> for notes and <a href="https://github.com/Daniel-Mietchen/events/blob/master/PIDapalooza-2021.md">https://github.com/Daniel-Mietchen/events/blob/master/PIDapalooza-2021.md</a> for background on the session.</p> <p>Resources demoed in the recording:</p> <ul> <li>Wikidata: <a href="https://www.wikidata.org/wiki/Q420330">https://www.wikidata.org/wiki/Q420330</a> - persistent identifier</li> <li>Scholia: <a href="https://scholia.toolforge.org/event/Q47486859">https://scholia.toolforge.org/event/Q47486859</a> - PIDapalooza 2018 </li> <li>Ordia: <a href="https://ordia.toolforge.org/">https://ordia.toolforge.org/</a> <ul> <li><a href="https://ordia.toolforge.org/text-to-languages">https://ordia.toolforge.org/text-to-languages</a> </li> <li><a href="https://ordia.toolforge.org/text-to-lexemes">https://ordia.toolforge.org/text-to-lexemes</a> <ul> <li><a href="https://www.wikidata.org/wiki/Lexeme:L407266">https://www.wikidata.org/wiki/Lexeme:L407266</a> - biocapacity</li> </ul> </li> </ul> </li> </ul> <ul> <li>Lingua Libre: <a href="https://lingualibre.org/">https://lingualibre.org/</a> <ul> <li><a href="https://w.wiki/wBL">https://w.wiki/wBL</a> - audio recording example</li> </ul> </li> <li>Sample content: <ul> <li><a href="https://doi.org/10.3389/fcosc.2020.615419">https://doi.org/10.3389/fcosc.2020.615419</a> - Underestimating the Challenges of Avoiding a Ghastly Future</li> <li><a href="https://en.wikipedia.org/wiki/Persistent_identifier">https://en.wikipedia.org/wiki/Persistent_identifier</a> </li> </ul> </li> <li>Testing: <a href="https://www.wikidata.org/wiki/Q13406268">https://www.wikidata.org/wiki/Q13406268</a> - Wikidata Sandbox 2</li> </ul> <p>Also relevant:</p> <ul> <li><a href="https://w.wiki/hmb">https://w.wiki/hmb</a> - Items with Disease Ontology ID and MeSH Descriptor ID and optional descriptions in multiple languages</li> <li><a href="https://en.wikiquote.org/wiki/Identity">https://en.wikiquote.org/wiki/Identity</a> - quotes around "identity"</li> </ul> <ul> </ul>
Identifying Energy Efficiency Patterns in Sorting Algorithms via Abstract Syntax Tree Mining
<p>Replication package for Submission "Identifying Energy Efficiency Patterns in Sorting Algorithms via Abstract Syntax Tree Mining".</p> <p>Authors kept anonymous for review.</p>
bachelor-thesis: Rapid Review - Identified Tools to Support SLR Including Features and Supported Stages
<p>This item presents the identified tools to support SLR and the supported stages and features of these tools.</p>
Natural history specimens collected and/or identified and deposited.
Natural history specimen data collected and/or identified by John Dumbacher, <a href="https://orcid.org/0000-0001-8942-1554">https://orcid.org/0000-0001-8942-1554</a>. Claims were made on Bionomia, <a href="http://bionomia.net">https://bionomia.net</a> using specimen data from the Global Biodiversity Information Facility, <a href="https://gbif.org">https://gbif.org</a>.
Combining GWAS and FST-based approaches to identify targets of Borrelia-mediated selection in natural rodent hosts
Recent advances in high-throughput sequencing technologies provide opportunities to gain novel insights into the genetic basis of phenotypic trait variation. Yet to date, progress in our understanding of genotype-phenotype associations in non-model organisms in general and natural vertebrate populations in particular has been hampered by small sample sizes typically available for wildlife populations and a resulting lack of statistical power, as well as a limited ability to control for false positive signals. Here we propose to combine a genome-wide association (GWAS) and FST-based approach with population-level replication to partly overcome these limitations. We present a case study in which we used this approach in combination with Genotyping-by-Sequencing (GBS) SNP data to identify genomic regions associated with Borrelia afzelii resistance or susceptibility in the natural rodent host of this Lyme disease-causing spirochete, the bank vole (Myodes glareolus). Using this combined approach we identified four consensus SNPs located in exonic regions of the genes Slc26a4, Tns3, Wscd1 and Espnl, which were significantly associated with the voles' Borrelia infectious status within and across populations. Functional links between host responses to bacterial infections and most of these genes have previously been demonstrated in other rodent systems, making them promising new candidates for the study of evolutionary host responses to Borrelia emergence. Our approach is applicable to other systems and may facilitate the identification of genetic variants underlying disease resistance or susceptibility, as well as other ecologically relevant traits, in wildlife populations.
Genome-wide association mapping to identify genetic loci for cold tolerance and cold recovery during germination in rice
<p>To investigate the genetic architecture underlying cold tolerance during germination in rice (<i>Oryza sativa</i>), we conducted a genome-wide association study (GWAS) using a novel diversity panel of 257 rice accessions from around the world and 5,185 SNP markers from a 7K SNP marker array. Genotyping was performed using a 7K Illumina iSelect custom-designed array by following the Infinium HD Array Ultra Protocol. The 7K array, called the C7AIR, was designed by Dr. Susan McCouch's Lab at Cornell University and consists of 7,098 SNPs (Morales et al. 2020, under review). After genotyping 257 rice accessions with the 7K array (C7AIR), poor-performing SNP markers (SNPs of call rate <90%; minor allele frequency <5%; or heterozygosity >20%) were removed from the dataset. For our study, a subset of 5,185 high-quality SNP markers obtained after filtering was used to perform the genome-wide association analysis. The dataset representing the genotype data of 5,185 SNP markers by 257 rice accessions is presented here.</p>
Characterisation of protease activity duringSARS-CoV-2 infection identifies novel viralcleavage sites and cellular targets withtherapeutic potential
<p><strong>Virus infections in siRNA-based cellular protein knockdowns - imaging dataset for cell viability</strong><br> Host proteins were knocked-down in A549-Ace2 cells using specific dsiRNAs from IDT. Briefly, A549-Ace2 cells seeded at 1x10$^{4}$ cells/well in 96-well plates. After 24 hours, each well was transfected with 5 pmol of individual dsiRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific) according to the manufacturer’s instructions. 24 hours post transfection, the cell culture supernatant was removed and replaced with virus inoculum (MOI of 0.1 PFU/cell). Following a 1 hour adsorption at 37°C, the virus inoculum was removed and replaced with fresh 2\% FBS/DMEM media. Cells were incubated at 37°C for 3 days before supernatants were harvested. Samples were either heat-inactivated at 80°C for 20 min and viral RNA was quantified by RT-qPCR, using previously published SARS-CoV-2 specific primers targeting the N gene \cite{ChuClinChem}. RT-qPCR was performed using the Luna Universal One-Step RT-qPCR Kit (NEB) in an Applied Biosystems QuantStudio 7 thermocycler, using the following cycling conditions: 55 °C for 10 min, 95 °C for 1 min, and 40 cycles of 95 °C for 10 sec, followed by 60 °C for 1 min. The quantity of viral genomes is expressed as PFU equivalents, and was calculated by performing a standard curve with RNA derived from a viral stock with a known viral titer. Alternatively, infectious virus titers were quantified using plaque assays as described above.</p> <p>To quantify siRNA-based cellular protein knockdowns, A549-Ace2 cells were seeded and transfected with individual dsiRNAs as described above. After 24 hours incubation at 37 °C cells were lysed and RNA was extracted using Trizol (ThermoFisher Scientific) followed by purification using the Direct-zol-96 RNA extraction kit (Zymo) following the manufacturer’s instructions. RNA levels of target proteins were subsequently quantified by using RT-with the Luna Universal One-Step RT-qPCR Kit (NEB) in an Applied Biosystems QuantStudio 7 thermocycler using gene-specific primers. Expression levels were compared to scrambled dsiRNA-transfected cells und normalized to expression of human beta-actin. Knockdown efficiencies were calculated using ΔΔCt in Matlab. </p> <p>To assess cell viability after siRNA knockdowns, cells were seeded and transfected as described above. 24 hours after transfection cell viability was measured using alamarBlue reagent (ThermoFisher Scientific), media was removed and replaced with alamarBlue and incubated for 1h at 37 °C and fluorescence measured in a Tecan Infinite M200 Pro plate reader. Percentage viability was calculated relative to untreated cells (100\% viability) and cells lysed with 20\% ethanol (0\% viability), included in each plate.</p> <p>For cell counting to determine cell numbers, cells were fixed in formalin to deactivate virus. The fixed cells were stained with 5µg/ml of Hoechst 33258 (Sigma). The assay plates were imaged on an IX-83 automated inverted microscope (Olympus) using a 10x objective. The DAPI settings (Ex UV 377/50, Em 415–480) were used to image Hoechst 33258. The acquisition setup was configured to image 4 sites per well. The nuclei were identified using the object detection module in the ScanR analysis software.</p> <p> </p> <p>Data provided in two zip files. Sample layout/key within the plates is provided within the zip files.</p>
Data from: Long-lived metabolic enzymes in the crystalline lens identified by pulse-labeling of mice and mass spectrometry
<p>The lenticular fiber cells are comprised of extremely long-lived proteins while still maintaining an active biochemical state. Dysregulation of these activities has been implicated in age-related cataracts, and other lens diseases. However, the lenticular protein dynamics underlying health and disease is unclear. We sought to measure the global protein turnover rates in the eye using dietary nitrogen-15 (15N)-labeling of mice between 3 and 15 weeks of age. By performing mass spectrometry we measured the 14N- to 15N-peptide ratios of 248 lens proteins, including Crystallin, Aquaporin, Collagen and Laminin of the lens capsule, and enzymes that catalyze glycolysis as well as oxidation and reduction reactions. Unexpectedly, like the crystallin proteins, many of these enzymes are also exceedingly long-lived. The slow replacement of these enzymes in spite of young age of the mice suggests their potential roles in age-related metabolic changes in the lens.</p>
Data from: DNA barcoding identifies cryptic animal tool materials
<p>Some animals fashion tools and other constructions out of plant materials to aid foraging, reproduction, self-maintenance, and protection. The choice of raw materials can affect the structure and mechanical properties of the resulting artefacts, with significant fitness consequences. Documenting animals' material preferences is challenging, however, as manufacture behaviour is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding techniques to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (<em>Corvus moneduloides</em>) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using conventional approaches had failed, including targeted observations, radio-tracking, bird-mounted video-cameras, and behavioural experiments with wild and temporarily captive subjects. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviours, helping to unlock significant research potential across a wide range of study systems.</p>
Dataset from 'Size Distribution of Sperm Whales Acoustically Identified During Long Term Deep-Sea Monitoring in the Ionian Sea'
<p>This dataset is from the study:</p> <p>Caruso Francesco, Virginia Sciacca, Giorgio Bellia, Emilio De Domenico, Giuseppina Larosa, Elena Papale, Carmelo Pellegrino, Sara Pulvirenti, Giorgio Riccobene, Francesco Simeone, Fabrizio Speziale, Salvatore Viola and Gianni Pavan. “Size Distribution of Sperm Whales Acoustically Identified During Long Term Deep-Sea Monitoring in the Ionian Sea.”</p> <p>The archive named NEMO-OvDE Dataset.zip contains the results of an automatic analysis developed and applied to the data acquired by the Ocean noise Detection Experiment. In detail, a subsample of the large dataset was processed to assess the size of the recorded sperm whales, by measuring the structure of their acoustic signals. The dataset consists in several plots generated by the algorithm described in the cited research article. The files are in PNG format. These data were used to study the size distribution of the sperm whale recorded during the OvDE Passive Acoustic Monitoring.</p> <p>For further information: riccobene@lns.infn.it (Principal Investigator of the Ocean noise Detection Experiment)</p>
Catalogue of identified flood peaks from GRDC dataset (FLOOD TYPE experiment)
This dataset provides flood peaks identified from GRDC dataset for gaugung stations in Europe.
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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.