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12,662 results for “linking”
Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)
<p>As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of genetic data indicate substantial divergence between lineages. This deep divergence with potential gene flow provides an opportunity to investigate the role of different mechanisms that shape the genomic landscape during early speciation. Here, using 184,295 SNPs and 80 populations, we investigate the genomic landscape of differentiation across the Atlantic Ocean with a focus on highly differentiated regions and processes shaping them. We found evidence of high (mean FST=0.26) and heterogeneous genomic differentiation between continents. Genomic regions associated with high trans-Atlantic differentiation ranged in size from single loci (SNPs) within important genes to large regions (1-3Mbp) on four chromosomes (Ssa06, Ssa13, Ssa16, and Ssa19). These regions showed signatures consistent with selection, including high linkage disequilibrium despite no local reduction in recombination. Genes and functional enrichment of processes associated with differentiated regions may highlight continental differences in ocean navigation and parasite resistance. Our results provide insight into potential mechanisms underlying differences between continents, and evidence of near fixed and potentially adaptive trans-Atlantic differences concurrent with a background of high genome-wide differentiation supports subspecies designation in Atlantic salmon.</p>
Bharathi - Linked Data Vocabulary for the Indian Context
<p>Bharathi is a collection of linked data vocabularies for the Indian context linking the metadata of terms and inter relationships across different entities within Government functions. In its first release, Bharathi contains information regarding Government Organisations at the Union Government and State Government level, the various Administrative Regions and its respective classifications, Sectors, Sub Sectors and common topics within the hierarchy of the Government functions</p>
Data from: Geographic patterns in colonial reproductive strategy in Myrmecina nipponica: links between biogeography and a key polymorphism in ants
<p>The ability to express different phenotypes can help define species distributions by allowing access to, and exploitation of, new environments. Social insects employ two markedly different reproductive strategies with contrasting cost/benefit characteristics: independent colony foundation (ICF), which is associated with high dispersal range and high risk, and dependent colony foundation (DCF), characterized by low risk but low dispersal. The ant <i>Myrmecina nipponica</i> employs both of these strategies, with the frequency of each apparently varying between populations. We combine molecular data with data on reproductive strategy from different populations of this species throughout Japan to explore how this polymorphism is linked to environmental factors and if this relationship can help explain the current and historical biogeography of this species. Reproductive strategy exhibited a strong geographic pattern, with ICF predominant in southern populations and DCF more common in northern and southern highland populations. Molecular analyses clearly divided populations into broad geographic regions, with the southern-lowland populations basal to (southern-highland (+ northern)) populations. Intra-population polymorphism in colony founding strategy was widespread, and polymorphism was reconstructed as the likely ancestral state. The frequency of different strategies was linked with climate, with DCF more common in colder areas. A recent inferred origin to the northern lineage suggests that colonization of northern Japan was a rapid event coincident with warming at the end of the last glacial maxima, likely facilitated by the cold-adaptive advantages of DCF. We discuss how such polymorphisms could help explain the biogeography of this and other social insects.</p>
Data from: Cu-Al mixed oxide-catalysed multicomponent synthesis of gluco- and allofuranose-linked 1,2,3-triazole derivatives
<p><span>A series of carbohydrate linked-1,2,3-triazole derivatives were synthetized in good yields from glucofuranose and allofuranose diacetonides using as key step a three-component 1,3-dipolar azide-alkyne cycloaddition catalyzed by a Cu-Al mixed oxide. In this multicomponent reaction, Cu-Al mixed oxide/sodium ascorbate system serves as highly reactive, recyclable and efficient heterogeneous catalyst for regioselective synthesis of 1,4-disubstituted 1,2,3-triazoles. The reported protocol has significant advantages over classical CuI/DIPEA or CuSO<sub>4</sub>/sodium ascorbate conditions in terms of efficiency and reduced synthetic complexity. In addition, the selective deprotection of synthesized di-<i>O</i>-isopropylidene derivatives was also carried out leading to the corresponding mono-<i>O</i>-isopropylidene products in moderate yields. Some of the synthesized triazole glycoconjugates were tested for their <em>in vitro</em> antimicrobial activity using the disk diffusion method against Gram-positive bacteria (<i>Staphylococcus aureus</i> and <i>Bacillus subtilis</i>), Gram-negative bacteria (<i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i>), as well as fungus (<i>Aspergillus niger</i>) and yeast (<i>Candida utilis</i>). The results revealed that these compounds exhibit moderate to good antimicrobial activity mainly against Gram-negative bacteria. </span></p>
Reddit Entity Linking
<p>An entity linking dataset created from the social media website, Reddit. The dataset contains 619 posts and 1,243 corresponding comments that were selected and given to human annotators. Three different human annotators were used to annotate each grouping of text. The resulting mentions and entities are included with a breakdown of the inter-annotator agreement between the various mention-entity pairs.</p> <p>The mention-entity pairs collected are broken into groups based on the level of inter-annotator agreement. </p> <p>Gold annotations - all three agree</p> <p>Silver annotations - two out of three annotators agree</p> <p>Bronze annotations - an individual annotator's annotation that the other two did not have</p> <p>In total the dataset contains 1,342 gold annotations, 2,723 silver annotations, and 7,038 bronze annotations.</p> <p>A readme file is provided that describes the structure of the files and the information within each one.</p>
Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation
Adaptation to contrasting environments occurs when advantageous alleles accumulate in each population, but it remains largely unknown whether these same advantageous alleles create genetic incompatibilities that can cause intrinsic reproductive isolation leading to speciation. Identifying alleles that underlie both adaptation and reproductive isolation is further complicated by factors such as dominance and genetic interactions among loci, which can affect both processes differently and obscure potential links between adaptation and speciation. Here, we use a combination of field and glasshouse experiments to explore the connection between adaptation and speciation while accounting for dominance and genetic interactions. We created a hybrid population with equal contributions from four contrasting ecotypes of Senecio lautus (Asteraceae), which produced hybrid genomes both before (F1 hybrid generation) and after (F4 hybrid generation) recombination among the parental ecotypes. In the glasshouse, plants in the second generation (F2 hybrid generation) showed reduced fitness as a loss of fertility, but fertility was recovered in subsequent generations suggesting that genetic variation underlying fertility reduction was lost in subsequent generations. To quantify the effects of losing genetic variation at the F2 generation on the fitness of later generation hybrids, we used a reciprocal transplant to test for fitness differences between parental ecotypes, and F1 and F4 hybrids in all four parental habitats. Compared to the parental ecotypes and F1 hybrids, variance in F4 hybrid fitness was lower, and lowest in habitats that showed stronger native-ecotype advantage, suggesting that stronger natural selection for the native ecotype reduced fitness variation in the F4 hybrids. Fitness trade-offs that were present in the parental ecotypes and F1 hybrids were absent in the F4 hybrid. Together, these results suggest that the genetic variation lost after the F2 generation was likely associated with both adaptation and intrinsic reproductive isolation among populations adapted to contrasting environments.
Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome-wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here we use low-coverage, whole-transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1,371 km of the southern section of its distribution have very low genome-wide differentiation (median FST=0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (FST>0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium blocks (LD) that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately non-synonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.
Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)
<p><span>We use genotyping by sequencing as an approach to identify sex-linked markers in the spiny frog <i>Quasipaa boulengeri</i> with 43 wild-collected adults from a single site. The GBS methodology identified 2 loci on sex differences in allele frequencies, 50 loci on sex differences in heterozygosity, and 523 loci on male-limited occurrence, altogether associated with males heterogamety, indicating an XX-XY system. The sex specificity of five markers was further validated by PCR amplification with a large number of additional individuals from 26 various populations in this species. A total of 27 sex linkage markers were matched to Dmrt1 gene, a ubiquitous role in sex determination and differentiation from flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has further been assigned to a highly potential candidate sex chromosome in anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133 individuals here, sparsely showing sex reversal detected in wild amphibian populations. </span></p>
Synthesis of Vinylene-Linked Two-Dimensional Conjugated Pol-ymers via the Horner-Wadsworth-Emmons Reaction
<p>DFTB+ // mio-0-1 optimised structures of 2D-PPQV1 and 2D-PPQV2. "Layer mismatch" structures were optimized with fixed unit cells.</p>
Linking Twitter & Survey Data [online workshop]
<p>Twitter has become an important data source for many social scientists. While using data from Twitter can help to avoid or alleviate some of the issues related to self-report data, such as social desirability or problems with recollection, Twitter data have their own sets of limitations, including the lack of information about individuals or missing outcome variables of interest. Linking data from surveys and Twitter is a way to combine the unique strengths of the two data types and overcome some of their respective limitations. The online workshop led by Luke Sloan (Cardiff University), Johannes Breuer (GESIS), and Libby Bishop (GESIS) covered the key steps in the research process of linking Twitter and survey data. Specifically, the workshop addressed the phases of study planning, (Twitter) data collection, data processing, and archiving and sharing. The workshop drew on recent experiences from different studies that the instructors were involved in and provided guidance on how to address the ethical and operational issues associated with linking Twitter and survey data in the different phases of the research process.</p> <p>The video is also available for viewing on <a href="https://youtu.be/IG1jJ3WP2h8">YouTube</a>.</p>
Domestication phenotype linked to vocal behavior in marmoset monkeys
<p>The domestication syndrome refers to a set of traits that are the incidental by-products of artificial selection for increased tolerance towards humans. One hypothesis is that some species like humans and bonobos "self domesticated", that they have been under selection for that same suite of domesticated phenotypes. However, the evidence for this has been largely circumstantial. Here, we provide evidence that in marmoset monkeys, the size of a domestication phenotype—a white facial fur patch—is linked to their degree of affiliative vocal responses. During development, the amount of parental vocal feedback experienced by influences the rate of growth of this facial white patch and this suggests a mechanistic link between the two phenotypes, possibly neural crest cells. Our study provides evidence for links between vocal behavior and the development of morphological phenotypes associated with domestication in a nonhuman primate.</p>
Evolution of Poecilimon jonicus group (Orthoptera: Tettigoniidae): A history linked to the Aegean Neogene paleogeography
<p><span>The Aegean archipelago is among the largest on Earth with astonishing biodiversity within Europe. Its territory underwent a massive geotectonic transformation in Neogene that resulted in multitude of changes in land-sea configuration and disintegrated the formerly united Aegean land to a complicated mainland-archipelago system. Therefore, it represents an excellent laboratory for studying evolution of terrestrial fauna. In the present study we use a model group of flightless bush-crickets with annual reproduction cycle – <i>Poecilimon jonicus </i>species group – to trace correlation of lineage diversification with the known paleogeographic events in the Aegean area. The group belongs to the hyperdiverse genus <i>Poecilimon </i>and has a disjunct distribution along the Hellenic arc from southwestern Anatolia through Crete to the western Balkans and the Apennines. To test our hypothesis, we inferred phylogenetic relationships of the <i>P. jonicus </i>group sensu lato using a nuclear fragment covering two spacers of the ribosomal cistron (ITS1+ITS2). To study intra-group phylogeny we compared mitochondrial phylogenies based on two matrices– (1) a concatenated ND2 and COI dataset of 1656 bp and (2) a 16S rRNA+12S rRNA dataset of 1835 bp. As a second step, we estimated divergence times applying Bayesian approach with BEAST and a relative rate framework with RelTime on the mitochondrial matrices. We compare trees calibrated based on evolutionary rates and tectonic events and discuss radiation scenarios in concordance with known paleogeographic events in the Aegean area. Our results revealed robust phylogeny of the <i>Poecilimon jonicus </i>group and confirmed a strong link between its evolution and the Aegean paleogeography. The phylogenetic relationships of the group supported</span> reconsideration of its systematics.</p>
Human DNA Cross-Link Repair 1A (DCLRE1A. SNM1A); A Target Enabling Package
<p>Cancer cells experience genomic instability, probably through a combination of excessive replicative activity and the loss of function of checkpoint and DNA repair pathways that may have contributed to the oncogenic transformation. Chemotherapy by DNA-damaging agents such as cisplatin and nitrogen mustards create DNA interstrand crosslinks (ICL), which can lead to double-strand breaks and cell death when the cells replicate their DNA. Genotoxic drugs are counteracted by the cell’s DNA damage response. Hence, it is expected that inhibiting DNA repair proteins would sensitise cells to chemotherapy.<br> Here we address an enzyme that participates in the repair of ICLs, DCLRE1A. The TEP includes expression clones and methods for producing the catalytic domain and high-throughput activity assays. Furthermore, we provide a crystallization system that generates thousands of reproducible crystals that allow soaking of small-molecule ligands. We provide crystal structures of several small molecule fragments and inhibitors, opening the way to development of more potent and selective inhibitors.</p>
Topics in Research on International Relations 2011-2015: Results from Clustering of Citation Links
<p>Supplementary information for the paper</p> <p><strong>IR Theory </strong><strong>and the Core-Periphery Structure of Global IR - Lessons from Citation Analysis</strong></p> <p>by Thomas Risse, Wiebke Wemheuer-Vogelaar, and Frank Havemann (<em>International Studies Review</em>, 2022, Vol. 4, Iss. 3, <a href="https://doi.org/10.1093/isr/viac029">doi.org/10.1093/isr/viac029</a>)</p> <p> </p> <p>Description of Files:</p> <p>File 1: Top-300 Cited Sources and Citing IR Journals<br> file name: Havemann2020top-300-sources.pdf (fourth file in list)<br> content: List of top-300 cited sources and a list of IR journals used for downloads from Web of Science</p> <p>File 2: Cited Sources in Clusters<br> file name: Havemann2020clusters.pdf (third file in list)<br> content: Lists of cited sources in link clusters and graphs of these clusters</p> <p>File 3: Citing Journals of Clusters<br> file name: citing.journals.of.clusters.pdf (second file in list)<br> content: Rank lists of publication channels with regard to numbers of papers citing papers in clusters</p> <p>File 4: Rank Lists of Cited Sources in Seven Journals Outside Web of Science<br> file name: cited-sources-in-7-journals.zip (first file in list)<br> content: Seven ASCII files</p> <p> </p> <p>A preprint of the ISR paper by Risse, Wemheuer-Vogelaar, and Havemann was published with the title "Theory Makes Global IR Hang Together. Lessons from Citation Analysis" and is available at: <a href="https://refubium.fu-berlin.de/handle/fub188/2/browse?type=affiliation&value=Otto-Suhr-Institut+f%C3%BCr+Politikwissenschaft+%2F+Arbeitsstelle+Transnationale+Beziehungen%2C+Au%C3%9Fen-+und+Sicherheitspolitik">Refubium-OSI-IR-group</a></p>
Cross-linked Mass Spectrometry (MALDI) data of GR C3 NTD and TSG101cc
<p>The zip file contains three folders from three separate datasets. The proteins were cross-linked with DST and then run on SDS-PAGE to separate unlinked protein. Bands were cut from the gels and then proteolyses overnight before conducting MS. Most of the datasets were collected using trypsin to produce protein fragments or in one case trypsin + chymotrypsin. Each folder contains a large number of control samples including: blank portions of the gel, uncross-linked protein samples, cross-linked GR without TSG101, cross-linked TSG101 without GR (four different bands because of much self-cross-linking). The files were hand curated for analysis.</p>
Data from: The presubiculum links incipient amyloid and tau pathology to memory function in older persons
Objective: To identify the hippocampal subregions linking initial amyloid and tau pathology to memory performance in clinically normal older individuals, reflecting preclinical Alzheimer's disease (AD). Methods: A total of 127 individuals from the Harvard Aging Brain Study (Mean age: 76.22 years ± 6.42, 68 females (53.5%)) with a Clinical Dementia Rating score of 0, a flortaucipir tau-PET scan, a Pittsburgh Compound B amyloid-PET scan, a structural MRI scan and cognitive testing were included. From these images, we calculated neocortical, hippocampal and entorhinal amyloid pathology, entorhinal and hippocampal tau pathology and the volumes of six hippocampal subregions and total hippocampal volume. Memory was assessed with the selective reminding test. Mediation and moderation analyses modeled associations between regional markers and memory. Analyses included covariates for age, sex and education. Results: Neocortical amyloid, entorhinal tau and presubiculum volume univariately associated with memory performance. The relationship between neocortical amyloid and memory was mediated by entorhinal tau and presubiculum volume, which was modified by hippocampal amyloid burden. With other biomarkers held constant, presubiculum volume was the only marker predicting memory performance in the total sample and in individuals with elevated hippocampal amyloid burden. Conclusions: The presubiculum captures unique AD-related biological variation that is not reflected in total hippocampal volume. Presubiculum volume may be a promising marker of imminent memory problems, and can contribute to understanding the interaction between incipient AD-related pathologies and memory performance. The modulation by hippocampal amyloid suggests that amyloid is a necessary process – but not sufficient – to drive neurodegeneration in memory-related regions.
Linked Data representation of COVID-19 data for Italy
<p>This repository includes a Linked Data representation of the <a href="https://github.com/pcm-dpc/COVID-19">covid19-ita dataset</a> provided by the Department of Civil Protection in Italy, following the <a href="https://www.w3.org/TR/vocab-data-cube/">RDF Data Cube Vocabulary</a> and the <a href="http://w3id.org/kpionto">KPIOnto</a> ontology. The dataset includes measurements of various indicators related to COVID19 spread at the province, regional, and country levels, on a daily basis from February 24th to November 20th, 2020.<br> The RDF format allows describing statistical multidimensional data as Linked Data on the Web. As such, each data point is represented as an observation of the relevant measures along two dimensions, namely time and geographical area.</p> <p>The project is also available on <a href="https://github.com/KDMG/covid19">Github</a>.</p>
Math anxiety mediates the link between number sense and math achievements in high math anxiety young adults
<p>The data are organized into three subfolders. One subfolder for each task:</p> <p><strong>MOT:</strong></p> <p>Each file contains a 3x4 matrix called “MatriceRisultati”.</p> <p>Each row of the matrix “MatriceRisultati” is a condition.</p> <p>The columns contain the following information:</p> <p>1<sup>st</sup>: Condition</p> <p>2<sup>nd</sup>: Number of response correct</p> <p>3<sup>rd</sup>: Total number of trials </p> <p>4<sup>th</sup>: proportion between column 2 and 3</p> <p> </p> <p><strong>Numerosity discrimination: </strong></p> <p>Each file contains a matrix called “a”. </p> <p>Each row of the matrix “a” is a trial.</p> <p>The columns contain the following information:</p> <p>1<sup>st</sup>: Test Numerosity</p> <p>2<sup>nd</sup>: Subject response </p> <p>3<sup>rd</sup>: Reference position: 1= left; 2=right</p> <p> </p> <p> <strong>Size discrimination:</strong> </p> <p>Each file contains a matrix called “MATR”. </p> <p>Each row of the matrix “MATR” is a trial.</p> <p>The columns contain the following information:</p> <p>1<sup>st</sup>: Delta (%) </p> <p>2<sup>nd</sup>: Subject response </p> <p>3<sup>rd</sup>: Test stimulus size (deg)</p> <p>4<sup>th</sup>: Probe stimulus size (deg)</p> <p>5<sup>th</sup>: Delta (%)</p> <p>6<sup>th</sup>: delta (deg)</p>
Increased sperm production linked to competition in the maternal social environment
<p>Maternal or early life effects may prepare offspring for similar social conditions to those experienced by their mothers. For males, the ability to achieve mating and fertilisation success is a key social challenge. Competitive conditions may therefore favour increased body size or ejaculate production in male offspring. We tested this experimentally by comparing reproductive traits of adult male bank voles (<i>Myodes glareolus</i>), whose mothers had experienced contrasting encounter regimes with female conspecifics while breeding. We found that daily sperm production rates and epididymis mass were significantly higher when dams had experienced more frequent encounters with female conspecifics. This response to maternal and early life experience was specific to sperm production and storage, with no evidence for effects on male body mass or the size of testes and accessory reproductive glands. Our findings reveal a potentially adaptive effect of maternal and early-life experience on the development of sperm production, which is worthy of wider investigation.</p>
From father Busa to Linked Data. What does Thomas Aquinas have to do with the Semantic Web
<p>5<sup>th</sup> Lecture</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.