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12,662 results for “linking”
Linked Pipe: Linked Open Samian Ware
<p>A Linked Pipe for Linked Open Samian Ware</p> <p> </p>
Assessing Word Similarity Metrics for Traceability Link Recovery - Evaluation Dataset
<p>This dataset includes all data that was used for the evaluation of my bachelor's thesis:</p> <p><em>Assessing Word Similarity Metrics for Traceability Link Recovery</em></p> <p>The following files correspond to the following data sets from the evaluation:</p> <ul> <li>cc-en-300.tar.gz corresponds to fastText's cc.en.300.bin embedding</li> <li>crawl-300d-2M-subword.tar.gz corresponds to fastText's crawl-300d-2M-subword.bin embedding</li> <li>wiki-news-300d-1M-subword.tar.gz corresponds to fastText's wiki-news-300d-1M-subword.bin embedding</li> <li>wordnet.tar.gz corresponds to the WordNet 3.1 semantic network</li> <li>sewordsim.tar.gz corresponds to SEWordSimDB's vector similarity database</li> <li>glove_cc_840B_300d.tar.gz corresponds to GloVe's CC vector embedding</li> <li>glove_wikigiga_300d.tar.gz corresponds to GloVe's 300 dimensional WIGI vector embedding</li> <li>glove_wikigiga_200d.tar.gz corresponds to GloVe's 200 dimensional WIGI vector embedding</li> <li>glove_wikigiga_100d.tar.gz corresponds to GloVe's 100 dimensional WIGI vector embedding</li> <li>glove_wikigiga_50d.tar.gz corresponds to GloVe's 50 dimensional WIGI vector embedding</li> <li>glove_twitter_200d.tar.gz corresponds to GloVe's 200 dimensional TWTR vector embedding</li> <li>glove_twitter_100d.tar.gz corresponds to GloVe's 100 dimensional TWTR vector embedding</li> <li>glove_twitter_50d.tar.gz corresponds to GloVe's 50 dimensional TWTR vector embedding</li> <li>glove_twitter_25d.tar.gz corresponds to GloVe's 25 dimensional TWTR vector embedding</li> <li>eval_results.tar.gz contains the detailed evaluation results for each configuration of all measures</li> </ul> <p>The licenses of all data sets are included in their respective files.</p> <p>Some of these data sets are .sql files. To use these files to reproduce the evaluation, they need to be imported into a sqlite3 database. The version of ArDoCo used for the evaluation is only able to work with sqlite3 databases and not with sql files.</p>
Linking camera-trap data to taxonomy: Identifying photographs of morphologically similar chipmunks
<p>Remote cameras are a common method for surveying wildlife and recently have been promoted for implementing large-scale regional biodiversity monitoring programs. The use of camera-trap data depends on the correct identification of animals captured in the photographs, yet misidentification rates can be high, especially when morphologically similar species co-occur, and this can lead to faulty inferences and hinder conservation efforts. Correct identification is dependent on diagnosable taxonomic characters, photograph quality, and the experience and training of the observer. However, keys rooted in taxonomy are rarely used for the identification of camera-trap images and error rates are rarely assessed, even when morphologically similar species are present in the study area. We tested a method for ensuring high identification accuracy using two sympatric and morphologically similar chipmunk (<i>Neotamias</i>) species as a case study. We hypothesized that the identification accuracy would improve with use of the identification key, and with observer training, resulting in higher levels of observer confidence and higher levels of agreement among observers. We developed an identification key and tested identification accuracy based on photographs of verified museum specimens. Our results supported predictions for each of these hypotheses. In addition, we validated the method in the field by comparing remote camera data with live-trapping data. We recommend use of these methods to evaluate error rates and to exclude ambiguous records in camera-trap datasets. We urge that ensuring correct and scientifically defensible species identifications is incumbent on researchers and should be incorporated into the camera-trap workflow.</p>
Variations in immune parameters with age in a wild rodent population and links with survival
<p>Recent findings suggest that immune functions do not unidirectionally deteriorate with age but that a potentially adaptive remodelling, where functions of the immune system get down regulated while others get upregulated with age could also occur. Scarce in wild populations, longitudinal studies are yet necessary to properly understand the patterns and consequences of age variations of the immune system in the wild. Meanwhile, it is challenging to understand if the observed variations in immune parameters with age are due to changes at the within-individual level or to selective (dis)appearance of individuals with peculiar immune phenotypes. Thanks to a long-term and longitudinal monitoring of a wild Alpine marmot population, we aimed to understand within- and between-individual variation in the immune phenotype with age, in order to improve our knowledge about the occurrence and the evolutionary consequences of such age-variations in the wild. To do so, we recorded the age-specific leukocyte concentration and leukocyte profile in repeatedly sampled dominant individuals. We then tested whether the potential changes with age were attributable to within-individual variations and/or selective (dis)appearance. Finally, we investigated if the leukocyte concentration and profiles were correlated to the probability of death at a given age. The leukocyte concentration was stable with age, but the relative number of lymphocytes decreased, while the relative number of neutrophils increased, over the course of an individual's life. Moreover, between individuals of the same age, individuals with fewer lymphocytes but more neutrophils were more likely to die. Therefore, selective disappearance seems to play a role in the age variations of the immune parameters in this population. Further investigations linking age variations in immune phenotype to individual fitness are needed to understand whether remodelling of the immune system with age could or could not be adaptive.</p>
Dataset of "Inferring Fine-grained Traceability Links between Javadoc Comments and JUnit Test Code"
<p>Dataset of "Inferring Fine-grained Traceability Links between Javadoc Comments and JUnit Test Code"</p> <p>- study object, true link, sentence, test code snippet, experiment result</p>
Data from: A phylogenetic study to assess the link between biome specialisation and diversification in swallowtail butterflies
<p><span>The resource-use hypothesis, proposed by E.S. Vrba, states that habitat fragmentation caused by climatic oscillations would affect particularly biome specialists (species inhabiting only one biome), which might show higher speciation and extinction rates than biome generalists. If true, lineages would accumulate biome-specialist species. This effect would be particularly exacerbated for biomes located at the periphery of the global climatic conditions, namely, biomes that have high/low precipitation and high/low temperature such as rainforest (warm-humid), desert (warm-dry), steppe (cold-dry), and tundra (cold-humid). Here, we test these hypotheses in swallowtail butterflies, a clade with more than 570 species, covering all the continents but Antarctica, and all climatic conditions. Swallowtail butterflies are among the most studied insects, and they are a model group for evolutionary biology and ecology studies. Continental macroecological rules are normally tested using vertebrates, this means that there are fewer examples exploring terrestrial invertebrate patterns at global scale. Here, we compiled a large GIS database on swallowtail butterflies' distribution maps and used the most complete time-calibrated phylogeny to quantify diversification rates. In this paper we aim to answer the following questions: 1) Are there more biome-specialists swallowtail butterflies than biome-generalists? 2) Is diversification rate related to biome specialisation? 3) If so, do swallowtail butterflies inhabiting extreme biomes show higher diversification rates? 4) What is the effect of species distribution area? Our results showed that swallowtail family presents a great number of biome specialists which showed substantially higher diversification rates compared to generalists. We also found that biome-specialists are unevenly distributed across biomes. Overall, our results are consistent with the resource-use hypothesis., species climatic niche and biome fragmentation as key factors promoting isolation.</span></p>
"A link model approach to identify congestion hotspots"
<p>Congestion emerges when high demand peaks put transportation systems under stress. Understanding the interplay between the spatial organization of demand, the route choices of citizens, and the underlying infrastructures is thus crucial to locate congestion hotspots and mitigate the delay. Here we develop a model where links are responsible for the processing of vehicles, that can be solved analytically before and after the onset of congestion, and providing insights into the global and local congestion. We apply our method to synthetic and real transportation networks, observing a strong agreement between the analytical solutions and the Monte Carlo simulations, and a reasonable agreement with the travel times observed in 12~cities under congested phase. Our framework can incorporate any type of routing extracted from real trajectory data to provide a more detailed description of congestion phenomena, and could be used to dynamically adapt the capacity of road segments according to the flow of vehicles, or reduce congestion through hotspot pricing.</p>
The acclimatory response of the mayfly Neocloeon triangulifer to dilute conditions is linked to the plasticity of sodium transport
<p><span>Relative to a growing body of knowledge about the negative consequences of freshwater salinization, little is known about how aquatic insects respond to progressively ion poor conditions. Here, we examined life-history and physiological acclimation in <em>N. triangulifer</em> by rearing larvae from 1 day post egg hatch to adulthood across a gradient of decreasing salinities (15, 8, 4, 2 and 1 mg L-1 Na). We found no significant changes in survival, growth, development time and whole-body Na content across these treatments. Radiotracer data revealed that larvae acclimated to their dilute exposures by increasing their rates of Na uptake and were able to maintain a relatively narrow range of uptake rates (± SEM) of 38.5 ± 4.2 µg Na g-1 hr-1 across all treatments. In contrast, the Na uptake rates observed in naïve larvae were much more concentration dependent. This acclimatory response is partially explained by differences in ionocyte counts on the gills of larvae reared under different salinities. Acclimated larvae were surprisingly less retentive of their sodium composition when subjected to deionized water challenge. By contrasting our findings with a previous N. triangulifer salinity acclimation study, we show a physiological affinity for dilute conditions in this emerging mayfly model.</span></p>
Responses of a semiarid grassland to recurrent drought is linked to community functional composition
<p>Climate change-driven increases in the frequency of extreme droughts could negatively impact the functioning of grassland ecosystems. While several studies have documented the impact of individual droughts on grassland function, less is known about how grasslands will respond to recurrent drought. We conducted a repeated extreme drought experiment in a semiarid grassland that consisted of three stages: (1) initial drought, (2) recovery, and (3) subsequent drought. We measured aboveground net primary productivity (ANPP), species richness, plant functional traits, and functional diversity. Using structural equation modeling (SEM), we investigated the causal mechanisms of ANPP response to recurrent drought. The initial drought led to reduced ANPP, although this was driven by a differential reduction in the growth of grasses and forbs. Total ANPP completely recovered as the rapid recovery of grass productivity compensated for the slow recovery of forb productivity. The magnitude of ANPP responses to the subsequent drought was greater than the initial drought. The SEMs revealed that soil moisture influenced ANPP responses directly during the initial drought, and indirectly during the subsequent drought by altering community functional trait means and diversity during the subsequent drought. These differential mechanisms alter our fundamental understanding of ecosystem drought sensitivity, which is primarily based on single drought studies.</p>
Data from: Links across ecological scales: Plant biomass responses to elevated CO2
<p>Despite the wide agreement that increased plant biomass accumulation under <span>elevated CO2 concentrations (e[CO2]) might play a key role in climate change, the effect of e[CO2] on plant biomass levels remains a major uncertainty in climate models. In the review associated with this dataset, we discuss the evidence for increased biomass levels under e[CO2] across multiple levels of ecological organization, scaling from physiological responses to changes in population-, community-, ecosystem-, and global-scale dynamics. We find that evidence for a sustained biomass response to e[CO2] varies across ecological scales, leading to diverging conclusions about the responses of individuals, populations, communities, and ecosystems. We identify key research gaps in our understanding of the effect of e[CO2] on plant biomass and highlight the need to integrate knowledge across scales of ecological organization so that large-scale modeling can represent the finer-scale mechanisms needed to constrain our understanding of future terrestrial C storage.</span></p>
The abundance of small mammals is positively linked to survival from nest depredation but negatively linked to local recruitment of a ground nesting precocial bird
<p>Generalist predators using small mammals as their primary prey are suggested to shift hunting alternative prey such as bird nests, when small mammals are in short supply (the alternative prey hypothesis, APH). Nest survival and survival of young individuals should be positively linked to small mammal abundance and negatively linked to predator abundance, but little information exists from survival of chicks, especially until recruitment. We test these predictions of the APH using 13 years (2002-2014) of life history data from a ground nesting shorebird breeding on coastal meadows. We use small mammal abundance in the previous autumn as a proxy for spring predator abundance, mainly of mammalian predators. We examine whether small mammal abundance in the spring and previous autumn explain annual variation in nest survival from depredation and local recruitment of the southern dunlin Calidris alpina schinzii. As predicted by the APH, survival from nest predation was positively linked to spring small mammal abundance and negatively linked to autumn small mammal abundance. Importantly, local recruitment showed opposite responses. This counterintuitive result may be explained by density dependent survival. When nest depredation rates are low, predators may show stronger numerical and functional responses to high shorebird chick abundance on coastal meadows, whereas in years of high nest depredation, few hatching chicks lure fewer predators. The opposite effects on nest and local recruitment demonstrate the diverse mechanisms by which population size variation in primary prey can affect dynamics of alternative prey populations.</p>
Data from: Resolving the mesoscopic missing link: biophysical modeling of EEG from cortical columns in primates
<p class="MsoNormal"><span>Event-related potentials (ERP) are among the most widely measured indices for studying human <span>cognition. While their timing and magnitude provide valuable insights, their usefulness is limited by our understanding of their neural generators at the circuit level. Inverse source localization offers insights into such generators, but their solutions are not unique. To address this problem, scientists have assumed the source space generating such signals comprises a set of discrete equivalent current dipoles, representing the activity of small cortical regions. Based on this notion, theoretical studies have employed forward modeling of scalp potentials to understand how changes in circuit-level dynamics translate into macroscopic ERPs. However, experimental validation is lacking because it requires <em>in vivo</em> measurements of intracranial brain sources. Laminar local field potentials (LFP) offer a mechanism for estimating intracranial current sources. Yet, a theoretical link between LFPs and intracranial brain sources is missing. Here, we present a forward modeling approach for estimating mesoscopic intracranial brain sources from LFPs and predict their contribution to macroscopic ERPs. We evaluate the accuracy of this LFP-based representation of brain sources utilizing synthetic laminar neurophysiological measurements and then demonstrate the power of the approach <em>in vivo</em> to clarify the source of a representative cognitive ERP component. To that end, </span>LFP was measured across the cortical layers of visual area V4 in macaque monkeys performing an attention demanding task. <span>We show that area V4 generates dipoles through layer-specific transsynaptic currents that biophysically recapitulate the ERP component through the detailed forward modeling. The constraints imposed on EEG production by this method also revealed an important dissociation between computational and biophysical contributors. As such, this approach </span>represents an important bridge between laminar microcircuitry, through the mesoscopic activity of cortical columns to the patterns of EEG we measure at the scalp. </span></p>
Additional data for "Record-Breaking Precipitation in Indonesia's Capital of Jakarta in Early January 2020 Linked to the Northerly Surge, Equatorial Waves, and MJO" containing Cross Equatorial Northerly Surge record data
<p>Data containing the record of the daily amplitude of active Cross Equatorial Northerly Surge events on December, January, and February of 1979 to 2021. This amplitude was calculated based on the ERA5 reanalysis dataset. The rules for recording an event with the next event separated by a minimum of 1 day interval of amplitude below the threeshold.</p>
Supplemental documents for: Temperature-associated selection linked to putative chromosomal inversions in king scallop (Pecten maximus)
<p>The genomic landscape of divergence – the distribution of differences among populations or species across the genome – is increasingly characterized to understand the role that microevolutionary forces such as natural selection and recombination play in causing and maintaining genetic divergence. This line of inquiry has also revealed chromosome structure variation to be an important factor shaping the landscape of adaptive genetic variation. Due to a high prevalence of chromosome structure variation and the strong pressure for local adaptation necessitated by their sessile nature, bivalve molluscs are an ideal taxon for exploring the relationship between chromosome structure variation and local adaptation. Here, we report a population genomic survey of king scallop (<em>Pecten</em> <em>maximus</em>) across its natural range in the northeastern Atlantic Ocean, utilizing a recent chromosome-level genome assembly. We report the presence of at least three large (12-22 Mb), putative chromosomal inversions associated with sea surface temperature and whose frequencies are in contrast to neutral population structure. These results highlight a potentially large role for recombination-suppressing chromosomal inversions in local adaptation and suggest a hypothesis to explain the maintenance of differences in reproductive timing found at relatively small spatial scales across king scallop populations.</p>
GERDAT013 Dataset for literature search linked to publication "Patient Preferences for Treatment Outcomes in Oncology with a Focus on the Older Patient—A Systematic Review"
<p>Dataset of the literature search belonging to the publication "Patient preferences for treatment outcomes in oncology with a focus on the older patient- a systematic review."</p>
Neolithic House, Links of Noltland
Neolithic House, Links of Noltland, Westray, Orkney. Source: Objaverse 1.0 / Sketchfab
Neoliithic House Links of Noltland
Neoliithic House Links of Noltland Westray Orkney Islands Source: Objaverse 1.0 / Sketchfab
Supplementary Information: CHAPTER 2 - Unveiling genomic features linked to traits of plant-growth-promoting bacterial communities from sugarcane
<p>Appendix A. Summary of counts of subreads and circular consensus sequencing (CCS) sequences obtained for PacBio sequencing of SMRT libraries. (EMS_1.xlsx)</p> <p>Appendix B. Taxonomy assignment of MAGs at the higher taxonomic rank obtained from GTDB-tk and Kraken tools. (EMS_2.xlsx)</p> <p>Appendix C. Report of the classification workflow using GTDB-tk. (EMS_3.xlsx)</p> <p>Appendix D. Matrix of the KEGG Orthology (KOs) frequencies annotated by the EnrichM tool. (EMS_4.xlsx)</p> <p>Appendix E. Reconstruction and completeness of KEGG modules annotated by EnrichM. The asterisks (*) in the header represent additional values obtained by the script ‘classKEGGModules.pl’ (https://github.com/dgpinheiro/bioinfoutilities) to estimate PGPTs in KEGG modules. (EMS_5.xlsx)</p> <p>Appendix F. The secondary metabolite biosynthesis gene clusters (BGCs) identified with AntiSMASH. (EMS_6.xlsx)</p> <p>Appendix G. The raw count of plant growth-promoting traits (PGPTs) annotations, according to KEGG Orthology (KO) predictions for MAGs. (EMS_7.xlsx)</p> <p>Appendix H. The raw count of plant growth-promoting traits (PGPTs) that comprises the 39 classes (level 5 hierarchy) identified as enriched according to the results of Pearson's Chi-square test (qvalue ≤ 0.1). (EMS_8.xlsx)</p>
Bronze Age House Links of Noltland
Bronze Age House Links of Noltland, Westray, Orkney Islands Source: Objaverse 1.0 / Sketchfab
Supplementary material 1 from: DiDomenico A, Hedin M (2016) New species in the Sitalcina sura species group (Opiliones, Laniatores, Phalangodidae), with evidence for a biogeographic link between California desert canyons and Arizona sky islands. ZooKeys 586: 1-36. https://doi.org/10.3897/zookeys.586.7832
Supplementary Tables 1–3 Table S1. Voucher and locality data Table S2. PCR primer and reaction information Table S3. GenBank accession information : Explanation note:
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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.