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Fig. 5 in Efficient New Above-Ground Bucket Traps Produce Comparable Data to that of Standard Transects for the Endangered American Burying Beetle,Nicrophorus AmericanusOlivier (Coleoptera: Silphidae)
Fig. 5. Average differences in abundance estimates for Nicrophorus americanus between methods using various sample-effort conversion rates (n = 20). Normalized average differences are mean differences divided by their standard deviations to provide a standardized scale for comparisons because abundance estimates—and therefore differences between them—are inherently smaller when trap-nights are artificially increased.
Fig. 4 in Efficient New Above-Ground Bucket Traps Produce Comparable Data to that of Standard Transects for the Endangered American Burying Beetle,Nicrophorus AmericanusOlivier (Coleoptera: Silphidae)
Fig. 4. Sample site layout (n = 28) showing 800-m site buffers (open circles). The order in which trap methods were used during the two sample periods at each site included buckets then transects (circles), transects then buckets (squares), and transects during both sample periods at control sites (triangles).
Fig. 7 in Efficient New Above-Ground Bucket Traps Produce Comparable Data to that of Standard Transects for the Endangered American Burying Beetle,Nicrophorus AmericanusOlivier (Coleoptera: Silphidae)
Fig. 7. ANOVA group means showing the relationship between beetle captures and the numbers of disturbed traps. Beetle abundance values were ranked for the three sample nights at each site such that increasing rank represented increasing abundance. Precision was low in groups 4 and 5 due to small sample sizes (n = 6 and n = 4, respectively).
Fig. 1 in Efficient New Above-Ground Bucket Traps Produce Comparable Data to that of Standard Transects for the Endangered American Burying Beetle,Nicrophorus AmericanusOlivier (Coleoptera: Silphidae)
Fig. 1. Layout of a standard pitfall trap transect showing an 800-m trap sample range (USFWS estimate) and a 200-m trap sample range in comparison to 20-m trap spacing to illustrate the lack of independence among traps in a transect.
Data from: Comparison of priority rules, machine allocation, and stage allocation strategies for hybrid flow shop instances using combinatorial logic and a standard trace format
<p>datsets.zip contains benchmark data by Ruiz et al. (2008), Naderi et al.(2010), and Wittwock (1988). The according publications are listed in the related works section. The instances are publicly available under unclear license.</p><p>results.zip contains computational results for the aforementioned benchmarks using the algorithms described in "Comparison of priority rules, machine allocation, and stage allocation strategies for hybrid flow shop instances using combinatorial logic and a standard trace format". The data is licensed under Creative Commons Attribution 4.0 International license.</p>
Seasonal Standardized Precipitation Index (SPI) Data 2005-2020
Open the record for dataset details and reuse information.
Typewriter Royal Standard 5
100% Xaviere Sierra Source: Objaverse 1.0 / Sketchfab
Standard Lefkimi
Bridal Costume from North Corfu Source: Objaverse 1.0 / Sketchfab
Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags
<p><span>Microbiomes feature recurrent compositional structures under given environmental conditions. </span><span>However, these patterns may conceal diverse underlying population dynamics that require intra-strain resolution. Here, we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative PCR and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intra-strain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the <em>Arabidopsis</em> phyllosphere, both with and without microbiota context. We observed colonization resistance against late arriving strains of <em>Salmonella</em> typhimurium in the mouse gut, whereas the phyllosphere accommodated <em>Sphingomonas</em> latecomers in a proportional manner to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems. </span></p>
Mechanical test on different elastomer materials based on the ASTM D412-16 standard
<p><strong>Aim: </strong>The main goal of conducting the mechanical tensile tests was to produce non-linear stress-strain curves for input data in the Ansys Workbench software. These curves played an important role in the accurate analysis of the mechanical behavior of the Finite Element Model (FEM) of the Hybrid III 5% Female ATD lumbar spine prototype. In addition, these curves evaluated the suitability of elastomer materials for manufacturing the lumbar spine prototype.</p> <p><strong>Method:</strong> Fourty-five Mechanical tensile tests were performed on five different elastomer materials (NR60, EPDM60, NEO60, CCP60, and CCP80) based on the ASTM D412-16 standard at three different strain rates including the standard strain rate (0.32 or =8mm/s), moderate strain rate (0.64 or =16mm/s), and high strain rate (4 or =100mm/s). Samples with standard and moderate strain rates were taken to failure using the MTS Insight 2 tensile testing machine. However, samples were not taken to failure in high strain rate testing due to the limited crosshead displacement (100mm) of the tensile testing machine (MTS 858 Bionix). </p> <p><strong>Result: </strong>The EPDM60 material with a tensile strength of 9.6 MPa demonstrated minimal Strain Rate Sensitivity (SRS =-0.06) up to 100% strain. The NR60 and CCP80 materials had greater tensile strength (18.5 MPa and 14.8 MPa) than EPDM60, but medium strain rate sensitivity (SRS -0.11 and -0.15). The CCP60 and NEO60 materials had lower tensile strength (5.3 MPa and 4.8 MPa) than EPDM60, but the medium (SRS =-0.12) and maximal strain rate sensitivity (SRS=-0.3), respectively.</p> <p><strong>Conclusion:</strong> The EPDM60 and NR60 materials appeared to be suitable for manufacturing the lumbar spine prototype, as EPDM60 exhibits minimal SRS, whereas NR60, despite a slight difference with a minimal range of SRS, showed maximal strength. Results of the FEM analysis showed that the lumbar spine prototype by using NR60 performs better than EPDM60. Therefore, NR60 as a suitable material was selected for manufacturing the lumbar spine prototype.</p>
Developing a global biodiversity standard certification for tree-planting and restoration: Tutorials for standardizing species names with WorldFlora
<p>This archive provides <a href="https://rmarkdown.rstudio.com/lesson-1.html">R Markdown files (.Rmd files)</a> containing scripts used to standardize tree species names downloaded from the <a href="https://www.bgci.org/resources/bgci-databases/globaltree-portal/">GlobalTree Portal</a> for different countries with national hubs for the <a href="https://www.darwininitiative.org.uk/project/DAREX001/">Developing a global biodiversity standard certification for tree-planting and restoration</a> project.</p> <p>The R Markdown files were modified from <a href="https://rpubs.com/Roeland-KINDT/1134151">a recent Rpub</a> where I standardized tree species names from <a href="https://tools.bgci.org/global_tree_search.php">GlobalTreeSearch</a> version 1.7. One of my objectives during a training workshop held in January 2024 with national hub partners at the <a href="https://sitioduascachoeiras.org.br/">Jardim Botânico Araribá, Sítio Duas Cachoeiras</a>, site in Brazil was to show how R Markdown files can be easily modified to analyse different data sets.</p> <p> </p> <p>This publication was generated after conducting training for a <strong>Darwin Initiative project</strong> (<a href="https://www.darwininitiative.org.uk/project/DAREX001/">DAREX001</a>) that develops a <a href="https://www.biodiversitystandard.org/">Global Biodiversity Standard for tree planting</a>. Recently the <a href="https://www.nature.com/articles/s41598-023-39552-1">GlobalUsefulNativeTrees</a> and <a href="https://onlinelibrary.wiley.com/doi/10.1111/gcb.16914">Tree Globally Observed Environmental Ranges</a> databases were released from this project. With scripts such as the ones shown here, when the Global Biodiversity Standard scheme becomes operational, tree planting projects can crosscheck lists of species before applying.</p>
SympTEMIST Corpus: Gold Standard annotations for clinical symptoms, signs and findings information extraction
<p><strong>SympTEMIST</strong> stands for Symptoms TExt MIning Shared Task. It is a shared task and set of resources focused on the <strong>detection of mentions, normalization and indexing of symptoms, signs and findings in medical documents</strong> in <strong>Spanish</strong>. SympTEMIST is complementary to the DisTEMIST (https://temu.bsc.es/distemist) and MedProcNER/ProcTEMIST (https://temu.bsc.es/medprocner) corpora as they all use the same document collection.</p> <p> </p> <p><strong>Please cite if you use this dataset:</strong></p> <p>"Lima-López, S., Farré-Maduell, E., Gasco-Sánchez, L., Rodríguez-Miret, J. and Krallinger, M. (2023). Overview of SympTEMIST at BioCreative VIII: corpus, guidelines and evaluation of systems for the detection and normalization of symptoms, signs and findings from text. In: <em>Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models</em>."</p> <p> </p> <p>This repository includes the:</p> <ul> <li><strong>Train </strong>and<strong> Test Set </strong>for the three subtasks</li> <li><strong>SYMPTEMIST gazetteer </strong>of <strong>SNOMED symptoms, signs & findings </strong></li> <li><strong>Multilingual </strong>Silver Standard<strong> </strong>in <strong>9 languages:</strong> <ul> <li><em><strong>English</strong></em></li> <li><em><strong>Portuguese</strong></em></li> <li><em><strong>French</strong></em></li> <li><em><strong>Italian</strong></em></li> <li><em><strong>Romanian</strong></em></li> <li><em><strong>Catalan</strong></em></li> <li><em><strong>Swedish</strong></em></li> <li><em><strong>Dutch</strong></em></li> <li><em><strong>Czech</strong></em></li> </ul> </li> <li><strong>Background set</strong> of over 15,000 clinical cases.</li> <li><strong>Spanish</strong> Silver Standard (predictions by participants over the background set)</li> </ul> <p> </p> <p>Please read the README file attached for more information on folder structure and file format.</p> <p> </p> <p>SympTEMIST was developed by the Barcelona Supercomputing Center's NLP for Biomedical Information Analysis and used as part of BioCREATIVE 2023. For more information on the corpus, annotation scheme and task in general, please visit: https://temu.bsc.es/symptemist.</p> <p> </p> <p><strong>Resources:</strong></p> <ul> <li><a href="https://temu.bsc.es/symptemist/"><strong>Task web</strong></a></li> <li><a href="https://biocreative.bioinformatics.udel.edu/"><strong>BioCreative web</strong></a></li> <li><strong>Citation: </strong>Lima-López, S., Farré-Maduell, E., Gasco-Sánchez, L., Rodríguez-Miret, J. and Krallinger, M. (2023). Overview of SympTEMIST at BioCreative VIII: corpus, guidelines and evaluation of systems for the detection and normalization of symptoms, signs and findings from text. In: <em>Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models</em>.</li> <li><a href="../records/8246440"><strong>Annotation guidelines</strong></a></li> <li><a href="../records/10103191"><strong>BioCreative/AMIA workshop proceedings</strong></a></li> <li><a href="../doi/10.5281/zenodo.10104546"><strong>Overview paper</strong></a></li> <li><a href="https://www.youtube.com/playlist?list=PLyLDDulunoofv79Pci0-y2rGP5GOBoZhp"><strong>Youtube videos (overview & teams)</strong></a></li> <li><a href="https://www.slideshare.net/MartinKrallinger/symptemist-shared-task-on-symptoms-signs-and-findings-detection-and-normalization-task-overview-talk-at-biocreative-viii-workshop-amia-2023"><strong>SympTEMIST overview talk slides at BioCreative/AMIA workshop</strong></a></li> </ul> <p> </p> <p><strong>License</strong></p> <p>This work is licensed under a <a href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.</p> <p><strong>Contact</strong></p> <p>If you have any questions or suggestions, please contact us at:</p> <p>- Salvador Lima-López (<salvador [dot] limalopez [at] gmail [dot] com>)<br>- Martin Krallinger (<krallinger [dot] martin [at] gmail [dot] com>)</p> <p><strong>Additional resources and corpora</strong></p> <p>If you are interested in SympTEMIST, you might want to check out these corpora and resources:</p> <ul> <li><a href="../records/7614764">DisTEMIST</a> (Corpus of disease mentions and normalization to SNOMED CT, same document collection)</li> <li><a href="../records/8224056">MedProcNER </a>(Corpus of clinical procedure mentions and normalization to SNOMED CT, same document collection)</li> <li><a href="../records/4270158">PharmaCoNER</a> (Corpus of medications, drugs, chemical substances, genes, proteins and vaccine mentions and normalization, same document collection)</li> <li><a href="../records/7116201">MEDDOPROF</a> (Corpus of mentions of professions, occupations and working status and normalization, different document collection with some overlapping documents)</li> <li><a href="../records/8403498">MEDDOPLACE</a> (Corpus of mentions of place-related entity mentions, including departments, nationalities or patient movements etc.. and normalization, different document collection with some overlapping documents)</li> <li><a href="../records/4279323">MEDDOCAN</a> (Corpus of mentions of Personal Health Identifiers (PHI), modified synthetic verions of the document collection)</li> <li><a href="../records/3978041">CANTEMIST</a> (Corpus of cancer tumor morphology mentions and normalization, different document collection)</li> <li><a href="../records/3837305">CodiESp</a> (Corpus of clinical case reportes with assigned clinical codes from ICD10, Spanish version, same document collection)</li> <li><a href="../records/7684093">LivingNER</a> (Corpus of mentions of species, including human/family members, pathogens, food, etc.. and normalization to NCBI Taxonomy, different document collection with some overlapping documents)</li> <li><a href="../records/2560344">SPACCC-POS</a> (Corpus of clinical case reports in Spanish annotated with POS-tags, same document collection)</li> <li><a href="../records/2560338">SPACCC-TOKEN</a> (Corpus of clinical case reports in Spanish annotated with token-tags (word mention boundaries), same document collection)</li> <li><a href="../records/2560338">SPACCC-SPLIT</a> (Corpus of clinical case reports in Spanish annotated with sentence boundary-tags, same document collection)</li> <li><a href="../records/5602914">MESINESP-2</a> (Corpus of manually indexed records with DeCS /MeSH terms comprising scientific literature abstracts, clinical trials, and patent abstracts, different document collection)</li> </ul> <p> </p>
Research database - Regulations, Manuals and Technical Standards Professional Career Pharmaceutical Sciences and Biochemistry
<p><span>This database contains information on Regulations, Manuals and Technical Standards of the Professional Career of Pharmaceutical Sciences and Biochemistry. Inca Garcilaso de la Vega University. Lima Peru</span></p> <p><span> </span></p>
ITVC system - Terms and metadata for standardization of data collection
<p>ITVC system - Terms and metadata for standardization of data collection</p>
FIGURE 2. Campylotropis luquanensis. A. Branch. B. Quadrangular branchlet. C. Raceme and flowers. D. Standard. E. Wings. F. Keels. G in Campylotropis luquanensis (Fabaceae: Papilionoideae), a new species from Southwest China
FIGURE 2. Campylotropis luquanensis. A. Branch. B. Quadrangular branchlet. C. Raceme and flowers. D. Standard. E. Wings. F. Keels. G. Stamens, pistils, and calyx. H. Young fruit. I. Stipules. J. Bract and bracteole. Illustration by Mr. Zhen-Long Liang based on the holotype (and H is also drawn in reference to the isotypes).
FIGURE 2. Astragalus taledensis P. Yan & H. Zhang. A. Habit, B. Inflorescence, C. Fruit, D. Seed, E. Wing, F. Standard, G. Keel, H. Calyx, I. Stamens, J in Astragalus taledensis, a new species of Leguminosae from Xinjiang, China
FIGURE 2. Astragalus taledensis P. Yan & H. Zhang. A. Habit, B. Inflorescence, C. Fruit, D. Seed, E. Wing, F. Standard, G. Keel, H. Calyx, I. Stamens, J. Pistil. Drawing by Siqi Xie.
IDSL.UFA results for THSTI-IROA standards
<p>IROA standards were analyzed using the Thermo Fusion instrument. The data were processed using the IDSL.IPA and IDSL.UFA software for annotation of molecular formula. </p>
Raw mass-standardized ionomic data from seven fish species and raw transcriptome sequences for mosquitofish inhabiting the Tar Creek Superfund Site in OK, USA
<p>Our understanding of the mechanisms mediating the resilience of organisms to environmental change remains lacking. Heavy metals negatively affect processes at all biological scales, yet organisms inhabiting contaminated environments must maintain homeostasis to survive. Tar Creek in Oklahoma, USA, contains high concentrations of heavy metals and an abundance of Western mosquitofish (<em>Gambusia affinis)</em>, though several fish species persist at lower frequency. To test hypotheses about the mechanisms mediating the persistence and abundance of mosquitofish in Tar Creek, we integrated ionomic data from seven resident fish species and transcriptomic data from mosquitofish to test hypotheses about the mechanisms mediating the persistence of mosquitofish in Tar Creek. We predicted that mosquitofish minimize uptake of heavy metals more than other Tar Creek fish inhabitants and induce transcriptional responses to detoxify metals that enter the body, allowing them to persist in Tar Creek at higher density than species that may lack these responses. Tar Creek populations of all seven fish species accumulated heavy metals, suggesting mosquitofish cannot block uptake more efficiently than other species. We found population-level gene expression changes between mosquitofish in Tar Creek and nearby unpolluted sites. Gene expression differences primarily occurred in the gill, where we found upregulation of genes involved with lowering transfer of metal ions from the blood into cells and mitigating free radicals. However, many differentially expressed genes were not in known metal response pathways, suggesting multifarious selective regimes and/or previously undocumented pathways could impact tolerance in mosquitofish. Our systems-level study identified well characterized and putatively new mechanisms that enable mosquitofish to inhabit heavy metal-contaminated environments.</p>
LegacyPollen 1.0: A taxonomically harmonized global Late Quaternary pollen dataset of 2831 records with standardized chronologies
<p>This repository consists of code for downloading pollen data from the Neotoma Paleoecology Database, the harmonization of pollen taxa, and the assignment of age-depth data so that datasets for customized harmonization levels can be easily established. The input data includes a harmonization table and example data, stored in machine-readable data format (.CSV).</p>
Figure 10 in A standardized terminology of spines in the order Siluriformes (Actinopterygii: Ostariophysi)
Figure 10. Odontodes and alveoli in Loricarioid pectoralfin spines, left sides, ventral views, spine bases to left. A, odontode alveoli (odontodes removed), Hypostomus cf. wachereri (MZUSP 87480). B, Nematogenys inermis (MZUSP 75256). Scales equal 2 mm.
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.