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7,378 results for “case”
Cantemist Silver Standard: Participant predictions in SEPLN IberLEF2020 - Spanish oncology clinical cases coded in ICD-O
<p><strong>Introduction</strong></p> <p>Predictions in the background set of Cantemist participants.</p> <p> </p> <p><strong>Zip structure</strong></p> <p>One directory per Cantemist subtask. Within each Cantemist subtask directory, there is one directory per team that contains the prediction runs.</p> <p> </p> <p><strong>Format</strong></p> <p>The text documents are distributed in plain text files, UTF-8 encoding.<br> The CodiEsp Silver Standard annotations have the following format:</p> <p>For the sub-tracks Cantemist-NER and Cantemist-Norm, the files are in Brat format.</p> <p>For the sub-track Cantemist-Coding files have the following fields:</p> <pre>articleID ICDO-code </pre> <p> </p> <p><strong>Resources:</strong></p> <ul> <li><strong><a href="https://temu.bsc.es/cantemist/">Web</a></strong></li> <li><strong>Citation: </strong>Miranda-Escalada, A., Farré, E., & Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In <em>Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings</em>.</li> <li><a href="https://doi.org/10.5281/zenodo.3773228"><strong>Gold Standard corpus</strong></a></li> <li><strong><a href="https://doi.org/10.5281/zenodo.3878178">Annotation guidelines</a></strong></li> <li><a href="https://www.youtube.com/playlist?list=PL5uSCzf1azhC24g5dsp5eVMp8BZFWCraX"><strong>YouTube presentations</strong></a></li> <li><a href="https://temu.bsc.es/cantemist/?p=4606"><strong>Participant codes</strong></a></li> </ul> <p> </p> <p>All credit to Cantemist participants. </p> <p> </p> <p>For more information, visit the track webpage: <a href="http://temu.bsc.es/cantemist/">http://temu.bsc.es/cantemist/</a> or email us at encargo-pln-life@bsc.es</p>
Integrating functional connectivity in designing networks of protected areas under climate change: a caribou case-study
<p>Land-use change and climate change are recognized as two main drivers of the current biodiversity decline. Protected areas help safeguard the landscape from additional anthropogenic disturbances and, when properly designed, can help species cope with climate change impacts. When designed to protect the regional biodiversity rather than to conserve focal species or landscape elements, protected areas need to cover a representative sample of the regional biodiversity and be functionally connected, facilitating individual movements among protected areas in a network to maximize their effectiveness. We developed a methodology to define effective protected areas to implement in a regional network using ecological representativeness and functional connectivity as criteria. We illustrated this methodology in the Gaspésie region of Québec, Canada. We simulated movements for the endangered Atlantic-Gaspésie caribou population (<i>Rangifer tarandus caribou</i>), using an individual-based model, to determine functional connectivity based on this large mammal. We created multiple protected areas network scenarios and evaluated their ecological representativeness and functional connectivity for the current and future conditions. We selected a subset of the most effective network scenarios and extracted the protected areas included in them. There was a tradeoff between ecological representativeness and functional connectivity for the created networks. Only a few protected areas among those available were repeatedly chosen in the most effective networks. Protected areas maximizing both ecological representativeness and functional connectivity represented suitable areas to implement in an effective protected areas network. These areas ensured that a representative sample of the regional biodiversity was covered by the network, as well as maximizing the movement over time between and inside the protected areas for the focal population.</p>
Expanding Search-Based Software Modularization to Enterprise-Level Projects: A Case Study at Adyen (Master's Thesis)
<p>The zip file uploaded contains the interactive 3d graphs shown in chapter 6 in the thesis. The thesis can be found on the TU Delft repository.</p>
Data from: Exploring patterns of beta-diversity to test the consistency of biogeographical boundaries: a case study across forest plant communities of Italy
Aim. To date, despite their great potential biogeographical regionalization models have been mostly developed on descriptive and empirical bases. This paper aims at applying the beta-diversity framework on a statistically representative data set to analytically test the consistency of the biogeographical regionalization of Italian forests. Location. Italy Taxon. Vascular plants Methods. Forest plant communities were surveyed in 804 plots made in a statistically representative sample of forest communities, made by 201 sites of Italian forests across the three biogeographical regions of the country: Alpine, Continental, and Mediterranean. We conducted an ordination analysis and an analysis of beta diversity, decomposing it into its turnover and nestedness components. Results. Our results provide only partial support to the consistency of the biogeographical regionalization of Italy. While the differences in forest plant communities support the distinction between the Alpine and the other two regions, differences between Continental and Mediterranean regions had lower statistical support. Pairwise beta-diversity and its turnover component are higher between- than within biogeographical regions. This suggests that different regional species pools contribute to assembly of local communities and that spatial distance between-regions has a stronger effect than that within-regions. Main conclusions. Our findings confirm a biogeographical structure of the species pools that is captured by the biogeographical regionalization. However, non-significant differences between the Mediterranean and Continental biogeographical regions suggest that this biogeographical regionalization is not consistent for forest plant communities. Our results demonstrate that an analytical evaluation of species composition differences among regions using beta-diversity analysis is a promising approach for testing the consistency of biogeographical regionalization models. This approach is recommended to provide support to the biogeographic regionalization used in some environmental conservation polices adopted by EU.
FIG. 4 in Tyrannosaur cannibalism: A case of a tooth-traced tyrannosaurid bone in the Lance Formation (Maastrichtian), Wyoming
FIG. 4.—Histology of a Tyrannosaurus rex metatarsal (SWAU HRS13997) in cross section under different light regimes. A) Section of cortical bone from the medullary cavity (left) to the subperiosteal surface (right) under regularly transmitted light. Boxes show where areas of this bone are shown in higher detail under regularly transmitted light (B, F, J), cross-polarized light (C, G, K), cross-polarized light with a waveplate (D, H, L), and reflected light (E, I, M). Scale bar for A = 5 mm, all other scale bars = 1 mm.
Data from: Weighing homoplasy against alternative scenarios with the help of macroevolutionary modeling: a case study on limb bones of fossorial sciuromorph rodents
Homoplasy is a strong indicator of a phenotypic trait's adaptive significance when it can be linked to a similar function. We assessed homoplasy in functionally relevant scapular and femoral traits of Marmotini and Xerini, two sciuromorph rodent clades that independently acquired a fossorial lifestyle from an arboreal ancestor. We studied 125 species in the scapular dataset and 123 species in the femoral dataset. Pairwise evolutionary model comparison was used to evaluate whether homoplasy of trait optima is more likely than other plausible scenarios. The most likely trend of trait evolution among all traits was assessed via likelihood scoring of all considered models. The homoplasy hypothesis could never be confirmed as the single most likely model. Regarding likelihood scoring, scapular traits most frequently did not differ among Marmotini, Xerini, and arboreal species. For the majority of femoral traits, results indicate that Marmotini, but not Xerini, evolved away from the ancestral arboreal condition. We conclude on the basis of the scapular results that the forelimbs of fossorial and arboreal sciuromorphs share mostly similar functional demands, whereas the results on the femur indicate that the hind limb morphology is less constraint, perhaps depending on the specific fossorial habitat.
Geostatistical Analysis of SARS-CoV-2 Positive Cases in the United States
<p>Geostatistics analyzes and predicts the values associated with spatial or spatial-temporal phenomena. It incorporates the spatial (and in some cases temporal) coordinates of the data within the analyses. It is a practical means of describing spatial patterns and interpolating values for locations where samples were not taken (and measures the uncertainty of those values, which is critical to informed decision making). This archive contains results of geostatistical analysis of COVID-19 case counts for all available US counties. Test results were obtained with ArcGIS Pro (ESRI). Sources are state health departments, which are scraped and aggregated by the Johns Hopkins Coronavirus Resource Center and then pre-processed by MappingSupport.com.</p> <p>This update of the Zenodo dataset (version 6) consists of three compressed archives containing geostatistical analyses of SARS-CoV-2 testing data. This dataset utilizes many of the geostatistical techniques used in previous versions of this Zenodo archive, but has been significantly expanded to include analyses of up-to-date U.S. COVID-19 case data (from March 24th to September 8<sup>th</sup>, 2020):</p> <p><strong>Archive #1: “1.Geostat. Space-Time analysis of SARS-CoV-2 in the US (Mar24-Sept6).zip” </strong>– results of a geostatistical analysis of COVID-19 cases incorporating spatially-weighted hotspots that are conserved over one-week timespans. Results are reported starting from when U.S. COVID-19 case data first became available (March 24<sup>th</sup>, 2020) for 25 consecutive 1-week intervals (March 24th through to September 6th, 2020). Hotspots, where found, are reported in each individual state, rather than the entire continental United States.</p> <p><strong>Archive #2: "2.Geostat. Spatial analysis of SARS-CoV-2 in the US (Mar24-Sept8).zip" </strong>– the results from geostatistical spatial analyses only of corrected COVID-19 case data for the continental United States, spanning the period from March 24<sup>th</sup> through September 8th, 2020. The geostatistical techniques utilized in this archive includes ‘Hot Spot’ analysis and ‘Cluster and Outlier’ analysis.</p> <p><strong>Archive #3: "3.Kriging and Densification of SARS-CoV-2 in LA and MA.zip" </strong>– this dataset provides preliminary kriging and densification analysis of COVID-19 case data for certain dates within the U.S. states of Louisiana and Massachusetts.</p> <p>These archives consist of map files (as both static images and as animations) and data files (including text files which contain the underlying data of said map files [where applicable]) which were generated when performing the following Geostatistical analyses: Hot Spot analysis (Getis-Ord Gi*) [‘Archive #1’: consecutive weeklong Space-Time Hot Spot analysis; ‘Archive #2’: daily Hot Spot Analysis], Cluster and Outlier analysis (Anselin Local Moran's I) [‘Archive #2’], Spatial Autocorrelation (Global Moran's I) [‘Archive #2’], and point-to-point comparisons with Kriging and Densification analysis [‘Archive #3’].</p> <p>The Word document provided ("Description-of-Archive.Updated-Geostatistical-Analysis-of-SARS-CoV-2 (version 6).docx") details the contents of each file and folder within these three archives and gives general interpretations of these results.</p>
Datasets in 'Methodologies in the Identification, Analysis, and Measurement of Visual Pollution: The Case Study of Intramuros'
<p>Dataset tabulated in all the methods and procedures done in the study 'Methodologies in the Identification, Analysis, and Measurement of Visual Pollution: The Case Study of Intramuros'.</p>
English 3450: Introduction to Old English. Inflectional Paradigms, Cases, Gender, and Agreement (Week 4 lecture). Video
<p>Lecture for Week 4 introducing inflectional paradigms, cases, and agreement in Old English</p>
Data from: The effects of climate warming on the migratory status of early summer populations of Mythimna separata(Walker) moths: a case-study of enhanced corn damage in central-northern China, 1980 - 2016
Mythimna separata (Walker) moths captured in light-traps were monitored in Luohe, central-northern China, from 1980 to 2016. Annual average temperature recorded an increase of 0.298 oC/10 years in this region in the period. Our results indicate that a rising Apr and May avarage temprature and earlier occurrences of days recording the highest day temperature (30℃) caused an advanced peak and increasing proportion of high ovarian development levels of first generation females in earlier summers. Results using Johnson's formulation of 'oogenesis-flight syndrome' indicate that increasing sexual maturity proportion has resulted in more emigrant individuals in the local first generaton moth becoming residents, and then increased individuls repidly in the local second generation moth since 2006. Consequences of this action have a boom in corn damage since 2007 in this region. Advanced peak dates of the first and second generation moth revealed the same response to increasing average monthly temperatures in the monitoring period. Increasing temperatures, the avarage May temperature exceeds or equal to 22℃, during the early 2000's may represent a physiological threshold for M. separata development. Our results suggest that climate warming may impact M. separata migratory status and cause a problem of crop production in this region.
Data from: Terrestrial contributions to Afrotropical aquatic food webs: the Congo River case
1. Understanding the degree to which aquatic and terrestrial primary production fuel tropical aquatic food webs remains poorly understood, and quantifying the relative contributions of autochthonous and allochthonous inputs is methodologically challenging. Carbon and nitrogen stable isotope ratios (δ13C, δ15N) can provide valuable insights about contributions of terrestrial resources and trophic position respectively, but this approach has caveats when applied in typical complex natural food webs. 2. Here, we used a combination of C, N, and H (δ2H) stable isotope measurements and Bayesian mixing models to estimate the contribution of terrestrial (allochthonous) and aquatic (autochthonous) inputs to fish and invertebrate communities in the Congo River (and some tributaries). 3. Overall, our results show that we gained power to distinguish sources by using a multiple tracer approach and we were able to discriminate aquatic vs. terrestrial sources (esp. including hydrogen isotopes). Fish δ2H values were clearly correlated with their food preferences and revealed a high level of variation in the degree of allochthony in these tropical aquatic communities. 4. At the community level, it is clear that terrestrial C3 plants are an important source fueling the Congo River food web. However, in order to better constrain source contribution in these complex environments will require more robust constraints on stable isotope values of algal and methane-derived C sources.
Data from: Finding clarity in ecological outcomes using empirical integrated social-ecological systems: a case study of agriculture-dependent grassland birds
<p>1. Efforts to monitor and conserve populations and ecosystems in human-dominated landscapes can benefit from an empirical social-ecological systems approach.<br> 2. Here we illustrate how latent variable structural equation modelling of regional time series data can effectively describe interconnected drivers of population fluctuations in dynamic landscapes and can help to reveal previously unknown system drivers.<br> 3. Using a declining farmland-dependent bird species (Ammodramus savannarum) in the eastern United States (1994-2015) as a case study, our analysis reveals how farm management decisions drive population fluctuations (R<sup>2</sup> = 20%), while management is in turn highly influenced by climate (R<sup>2</sup> = 23-51%), but not by regional conservation spending.<br> 4. Synthesis and applications. Structural equation modelling revealed potential social-ecological pathways for halting regional population declines in a grassland bird, the Grasshopper Sparrow. Lower population growth rates followed years of higher hay yields (~4 percentage points per metric ton increase in hay yield) and later harvests (~2 percentage points per 10-day delay in harvest). Thus, one pathway for stabilising regional populations could involve compensating farmers for reducing hay harvests, potentially requiring a six-fold increase in current annual agri-environmental conservation spending.</p>
Incremental Development of Safety Cases: a Mapping Study
<p>Video presentation for Research Track article "Incremental Development of Safety Cases: a Mapping Study"</p>
On the impact of release policies on bug handing activity: A case study of Eclipse
<p>This repository contains the data used in our paper entitled ["On the impact of release policies on bug handing activity: A case study of Eclipse"]</p> <p># Structure</p> <p>The repository contains :</p> <p>1. `raw_data`: a repository containing all the raw data of our study before processing.<br> 2. `data_processing`: a repository containing all the raw data of our study during processing.<br> 3. `data`: a repository containing all the data of our study after all processing steps.<br> 4. `figs`: The generated figures from the notebooks for the paper.<br> 5. The various Jupyter notebooks containing all the scripts used to gather the data and answer each research question.</p>
Assembly and origin of the flora of the Chihuahuan Desert: the case of sclerophyllous Rosaceae
<p><span><b>Aim</b></span> To test hypotheses on the origin and assembly of the flora of the Chihuahuan Desert using as a system the hard-leaved shrubby lineages of the Rosaceae distributed in North American Deserts.</p> <p><span><b>Location</b></span><span> North American Deserts, Chihuahuan Desert, Mexican Plateau, Tehuacán Valley. </span></p> <p><span><b>Methods</b></span> Phylogenetic analyses were conducted based on nine chloroplast and nuclear molecular markers of eleven newly sequenced species of Rosaceae distributed in the Chihuahuan Desert along with previous sequences of 41 species in 25 genera representative of the major clades in the family. Based on phylogeny, divergence times, migration, vicariance events and ancestral biogeographic areas were determined. Ecological niche-based modeling will predict changes in distribution during Pleistocene climate oscillations. Traitgrams were constructted to visualize departure among lineages in the most significant climate variables.</p> <div><span><b>Results</b> The lineages studied diverged during the Eocene-Oligocene (53 – 33Mya). The ancestral area for most of the taxa was in the Mojave and Chihuahuan Deserts. Most dispersal events occurred from the Mojave Desert to the central area of the Chihuahuan Desert on the Mexican Plateau. Ecological niche-based modeling suggests a contraction of suitable habitat during the Last Interglacial period (~120,000 - 140,000 years), followed by expansion during the Last Glacial Maximum (~ 22,000 years) and the Middle Holocene (~ 6000 years). </span></div> <p><span><b>Main conclusions </b></span><span>Our results confirm the Axelrod's hypothesis of an origin of the flora of the Chihuahuan Desert in SW North America migrating to occupy North American arid lands. Vicariance and the expansion of arid lands allowed divergence, migration and permanence of the lineages studied on the Mexican Plateau. Divergence occurred prior to the onset of aridification. The Mexican Plateau acted as a refuge for hard-leaved lineages during the Miocene. Shifts in ecological niches of related species allowed them to colonize new areas with different temperatures and precipitation. Current distribution of lineages is the most limited. </span></p>
Supplementary material 1 from: Brock KC, Daehler CC (2020) Applying an invasion and risk framework to track non-native island floras: a case study of challenges and solutions in Hawai'i. In: Wilson JR, Bacher S, Daehler CC, Groom QJ, Kumschick S, Lockwood JL, Robinson TB, Zengeya TA, Richardson DM. NeoBiota 62: 55-79. https://doi.org/10.3897/neobiota.62.52764
Guidance on the status confidence rating and adapting a regional checklist to track invasion statuses
Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation
<p>Database of the ODYM-RECC v2.4 model, used for the Germany case study on material efficiency and climate change mitigation. For the model code, see https://github.com/YaleCIE/RECC-ODYM. The model results archived here were calculated by running the ODYM-RECC scripts of commit no. cb3a388 with the data in this archive.</p>
Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels
<p>Dataset accompanying "Ryan Brate, Paul Groth and Marieke van Erp (2020) Towards Olfactory Information Extraction from Text: A Case Study on Detecting Smell Experiences in Novels. LaTeCH-CLfL 2020. Barcelona, December 2020."</p> <p>Abstract:</p> <p>Environmental factors determine the smells we perceive, but societal factors factors shape the importance, sentiment and biases we give to them. Descriptions of smells in text, or as we call them `smell experiences', offer a window into these factors, but they must first be identified. To the best of our knowledge, no tool exists to extract references to smell experiences from text. In this paper, we present two variations on a semi-supervised approach to identify smell experiences in English literature. The combined set of patterns from both implementations offer significantly better performance than a keyword-based baseline.</p>
Smart Energy Use Case Clustering Dataset - II
<p>Cluster data set for multilayered and contextualized smart energy blockchain traces</p>
Data from: Exceptional preservation requires fast biodegradation: the case study of thylacocephalan specimens from La Voulte-sur-Rhône (Callovian, Jurassic, France)
<p>Konservat-Lagerstätten are seen as snapshots of past biodiversity for a given location and time. Yet, processes leading to the exceptional morphological preservation of fossils in these deposits remain incompletely understood. This results in the deficient assessment of taphonomic biases and limits the robustness/relevance of palaeobiological reconstructions. Here, we report the mineralogical characterization of crustacean fossils preserved within carbonate-rich concretions from the Jurassic Konservat-Lagerstätte of La Voulte-sur-Rhône (Ardèche, France). The combination of SEM-EDS, TEM, synchrotron-based XRF, XRD and XANES allows identifying the mineralogical phases composing these fossils (i.e. fluorapatite, Fe-sulfides (pyrite, pyrrhotite) and Mg-calcite) and the surrounding matrix (i.e. Mg-calcite, clays and detrital silicates). Fluorapatite and pyrite (and pyrrhotite) precipitated during decay under anoxic conditions, replacing delicate organic structures and preserving anatomical details. These mineral structures were subsequently consolidated by a Mg-calcite cement. Of note, histologically similar tissues were replaced by the same mineral phases, confirming that 'fossilization [in La Voulte] occurred rapidly enough to be influenced by tissue composition'. Altogether, the present study shows that exceptional preservation requires fast biodegradation, thereby confirming recent experimental evidence.</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.