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15,733 results for “article”
Phenological data for the article: Phenotypic plasticity drives phenological changes in a Mediterranean blue tit population
<p>Earlier phenology induced by climate change, such as the passerines' breeding time, is observed in many natural populations. Understanding the nature of such changes is key to predict the responses of wild populations to climate change. Genetic changes have been rarely investigated for laying date, though it has been shown to be heritable and under directional selection, suggesting that the trait could evolve. In a Corsican blue tit population, the birds' laying date has significantly advanced over 40 years, and we here determine whether this response is of plastic or evolutionary origin, by comparing the predictions of the breeder's and the Robertson-Price (STS) equations, to the observed genetic changes. We compare the results obtained for two fitness proxies (fledgling and recruitment success), using models accounting for their zero-inflation. Because the trait appears heritable and under directional selection, the breeder's equation predicts that genetic changes could drive a significant part of the phenological change observed. We however found that fitness proxies and laying date are not genetically correlated. The STS therefore predicts no evolution of the breeding time, predicting correctly the absence of trend in breeding values. Our results also emphasize that when investigating selection on a plastic trait under fluctuating selection, part of the fitness-trait phenotypic covariance can be due to within individual covariance. In the case of repeated measurements, splitting within and between individual covariance can shift our perspective on the actual intensity of selection over multiple selection episodes, shedding light on the potential for the trait to evolve.</p>
PheneBank: Processed Medline Abstracts and PMC full articles + Phenotype-Disease Associations
<p><strong>The PheneBank project:</strong></p> <p>Free text scientific literature has the potential to be an incredibly valuable source of data for uncovering the often hidden relationships between genes, diseases and phenotypes. Phenotypic descriptions cover abnormalities in anatomical structures, processes and behaviours. For example 'growth delay' and 'body weight loss'. Such descriptions form the basis for determining the existence and treatment of a disease but, because of their inherent complexity, have previously received less attention by the text mining community. In recent years, significant effort has been spent by a small number of expert curators to create coding systems for phenotypes (called "ontologies"), such as the Human Phenotype Ontology (HP) and the Mammalian Phenotype Ontology (MP). The PheneBank project proposes to support and speed up curation using terms discovered directly from the literature and to automatically integrate them with such standard ontologies. <br> <br> The project seeks to harness texts for extracting statistically significant associations between phenotypes, diseases and genes. Earlier approaches have suffered from not providing deep semantic representations of the phenotypes they tried to target. Our deep learning-based approach is an attempt to overcome this issue by reducing the uncertainty between textual and ontological forms of phenotypes. Specifically, the model treats multitoken named entities as a single token which allows more reliable handling of multiword expressions. The approach builds on ground breaking research at the European Bininformatics Institute by the PI (Nigel Collier) and the Co-investigator (Damian Smedley, Queen Mary University London), including terminology alignment of phenotypes using pairwise scoring of the conceptual elements that make up the phenotype. </p> <p><a href="http://www.phenebank.org">http://www.phenebank.org</a></p> <p><br> <strong>The dataset:</strong></p> <p>As an output of the PheneBank project, we release the set of 24 million MEDLINE abstracts as well as 3.8M open-access PMC full articles annotated with 9 classes of entity: Phenotype, Disease, Anatomy, Cell, Cell_line, GPR, Gene_variant, Molecule, and Pathway. The entities have been mapped to five major ontologies: SNOMED, HPO, MeSH, PRO, and FMA.</p> <p>In addition, we release the phenotype-disease associations that are automatically extracted based on co-occurrences statistics in Medline abstracts. Among different statistical measures we evaluated, the Fisher test best corresponded to the known tuples available from the curated associations available from the Monarch Initiative (https://monarchinitiative.org).</p> <p><br> <strong>Processing:</strong></p> <p>The NER tagging has been done using a BiLSTM-CRF neural model (<a href="https://github.com/pilehvar/phenebank">https://github.com/pilehvar/phenebank</a>) trained on expert-annotated data (to be released for research). The grounding to ontologies relies on semantic embedding of concepts and entities in a unified semantic space.</p> <p><br> <strong>Data format:</strong></p> <p><strong>PheneBank_Processed_PubMed.part[x].tar.gz </strong>contains 24,359,010 .txt files that are classified into 812 directories. Each .txt file is named with a PubMed article ID and contains the corresponding article's abstract and its annotations. The dataset is split into four (unequal) parts based on PubMed's structure:<br> part1: medline16n00* medline16n01* medline16n02* [299 directories, 2.8GB]<br> part2: medline16n03* medline16n04* [200 directories, 4.7GB]<br> part3: medline16n05* medline16n06* [200 directories, 5.3GB]<br> part4: medline16n07* medline16n08* [113 directories, 3.1GB]</p> <p>The <strong>PheneBank_Processed_PMC.tar.gz</strong> files has 6,180 directories which are named after the journal titles from which the articles have been drawn. There are three files per each article (i.e., 3 .txt files for the 3,751,770 distinct articles), containing text from different parts of the article: .title.txt, .abstract.txt, and .body.txt. </p> <p>Each line starts with a word; for those words that are identified as entities, entity type and mapping information are followed in the same line (tab separated), with the following format:</p> <p>word <TAB> ::: <TAB> entity_type <TAB> entity_concept_ID_1##confidence_score_1 entity_concept_ID_2##confidence_score_2 ...</p> <p>Note that the concepts are sorted according to their mapping confidence scores.</p> <p><br> As for the <strong>PheneBank_Associations.tsv</strong> file, there are ten columns that correspond to the following (left to right):</p> <p>- Disease Name<br> - Disease (MONDO) ID<br> - Phenotype Name<br> - Phenotype (HPO) ID<br> - Co-occurrence Frequency<br> - Disease Frequency<br> - Phenotype Frequency<br> - Fisher (log)<br> - Dice<br> - Normalized PMI</p> <p> </p> <p> </p>
List of ID articles
<p>List of 35 ID articles resulted from a Systematic Literature Review.</p>
Dataset related to article "Defective cyclophilin A induces TDP-43 proteinopathy: implications for amyotrophic lateral sclerosis and frontotemporal dementia"
<p>Dataset related to the article 10.1093/brain/awab333</p>
Wikipedia Articles with Quality label FA, GA, A, B and C
<p>This dataset contains a filtered collection of good quality Wikipedia Articles:</p> <p>* FA: Featured Articles</p> <p>* GA: Good Articles</p> <p>* Quality lables A, B and C</p>
Research data supporting "article test"
<p>Research data supporting "article test"</p>
Data Used for Article "Imaging and spectroscopyof domains of the cellular membrane by photothermal-induced resonance"
<p>PTIR data collected from buccal cells.</p> <p>Used in article by L. Quaroni "Imaging and spectroscopy of domains of the cellular membrane by photothermal-induced resonance"</p> <p><em><strong>Analyst</strong></em>, 2020,<strong>145</strong>, 5940-5950 ; doi.org/10.1039/D0AN00696C</p>
Article experimental infection TB foxes
<p>supplementary data article Experimental infection of captive red foxes (<em>Vulpes vulpes</em>) with <em>Mycobacterium bovis</em></p>
Raw data for the article "Tosyloxybenziodoxolone: A Platform for Performing the Umpolung of Alkynes in One-pot Transformations"
<p>Raw NMR and MS data for the article "Tosyloxybenziodoxolone: A Platform for Performing the Umpolung of Alkynes in One-pot Transformations" published in Organic Letters, DOI: </p> <p><a href="https://doi.org/10.1021/acs.orglett.1c03771">https://doi.org/10.1021/acs.orglett.1c03771</a></p> <p>The number of the folders correspond to compounds numbers in the article. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Raw data used for the preparation of the article Sci. Rep. 9 (2019), 11328. DOI: 10.1038/s41598-019-47547-0.
<p>Raw data (SEM, XRD, magnetotransport measurements) used for the preparation of the article</p> <p>G. Kunakova, R. Meija, J. Andzane, U. Malinovskis, G. Petersons, M. Baitimirova, M. Bechelany, T. Bauch, F. Lombardi, D. Erts ‘Surface structure promoted high-yield growth and magnetotransport properties of Bi2Se3 nanoribbons’, Sci. Rep. 9 (2019), 11328. DOI: 10.1038/s41598-019-47547-0.</p>
Data for the article on 'Nominal and pronominal negative concord, through the lens of Belizean and Jamaican Creole' by J. van der Auwera, published in Linguistics
<p>Data for the article on 'Nominal and pronominal negative concord, through the lens of Belizean and Jamaican Creole' by J. van der Auwera, published in Linguistics</p>
Data files for the article "Bayesian hierarchical modeling of sea level extremes in the Finnish coastal region"
<p>This repository contains R data files required for reproducing the results from the article by Räty et al (2021) "Bayesian hierarchical modeling of sea level extremes in the Finnish coastal region", submitted to Nat. Hazards Earth Syst. Sci. See the README file for more details on the content of the files.</p>
Digital research materials of spectral data for the article: [3+2]-Cycloaddition of azomethine ylides to 5-methylidene-3-aryl-2-сhalcogen-imidazolones: Access to dispiro indolinone-pyrrolidine-imidazolones
<p>Digital research materials of NMR spectral data for the article "[3+2]-Cycloaddition of azomethine ylides to 5-methylidene-3-aryl-2-сhalcogen-imidazolones: access to dispiro indolinone-pyrrolidine-imidazolones" submitted to the <em>Royal Society Open Science. </em>NMR spectra were recorded on Bruker Avance 400 and Agilent MR-400 spectrometers in DMSO-d<sub>6</sub> and C<sub>6</sub>D<sub>6</sub>. Chemical shifts were measured relative to residual solvent signals and referenced in parts per million to TMS. Original fid files are presented, which can be opened, for example, using the ASD Labs software package.</p>
Supplementary materials for the article "Encouraging a sustainable adoption of autonomous vehicles for public transport in Belgium: citizen acceptance, business mod-els and policy aspects"
<p>Supplementary materials for the article "Encouraging a sustainable adoption of autonomous vehicles for public transport in Belgium: citizen acceptance, business mod-els and policy aspects". It includes:</p> <p>- The dataset excluding data subject to confidentiality due to privacy reasons</p> <p>- The consent form distributed to survey participants</p> <p>- The survey used in the study</p>
Data set for this article tiled " the relationship between product innovation and customer satisfaction
<p>my data set for this article tiled " the relationship between product innovation and customer satisfaction</p>
Data from the article "Modulation of wintertime canopy Urban Heat Island (CUHI) intensity in Beijing by synoptic weather pattern in planetary boundary layer"
<p>The link includes four datasets, "pcttype" is weather typing data, "pblh" is PBLH data, "uhii-UV" is the mean value of CUHII and wind direction UV of all urban stations, and "uhii-sws" is the value of CUHII, wind speed and wind direction of all urban stations.</p>
Dataset accompanying the article "Freedoms and free-market capitalism beyond utopias and dystopias — A World Without Money revised"
<p>The dataset in this repository provides all the data used in the charts contained in the article "Freedoms and free-market capitalism beyond utopias and dystopias — A World Without Money revised" (2022) by Fabio Ashtar Telarico published by Foundation for Economic Education.</p>
Dataset used in the assessment of the article "Basic urban services fail to neutralise environmental determinants of 'rattiness', a composite metric of rat abundance"
<p>This data was collected in four Brazilian informal settlements located in the city of Salvador - the third largest city of Brazil - in the wet season of the year 2018. The data includes the collection of three rat abundance metrics - namely, rat marks on track plates, rats caught in live traps and removed, and presence of rat signs (faecal droppings, trails and active burrows) - in a total of 529 independent sampling locations. In addition to the single rat metrics, which were also used to compose the rattiness outcome, the data contain the baseline environmental and socioeconomic (surveyed and mapped) variables and the BUS variables considered in Carvalho-Pereira et al., 2023. (the data will be available soon)</p>
Raw data repository for the article: "Spatially resolved fluorescence of caesium lead halide perovskite supercrystals reveals quasi-atomic behavior of nanocrystals"
<p>Raw data depository for the article in Nature Communications journal: <a href="https://doi.org/10.1038/s41467-022-28486-3">DOI: 10.1038/s41467-022-28486-3</a>. Details and the file description are given in the file "Lapkin_Dataset_Info.pdf"</p>
Dataset related to article CXCL1-CXCR1/2 signaling is induced in human temporal lobe epilepsy and contributes to seizures in a murine model of acquired epilepsy
<p>Raw data are organized in an excel file where for each figure (included supll. figures) data are listed in a different sheet.</p>
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.