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1,552 results for “patch”
Data from: Mean landscape-scale incidence of species in discrete habitats is patch size dependent
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Patch quality and genotype-by-environment interactions shape dispersal and post-settlement survival in a butterfly metapopulation
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Population genomic evidence that stream networks structure genetic diversity in the narrowly endemic patch-nosed salamander (Urspelerpes brucei)
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Time and matrix quality increase the relative habitat value of smaller patches in fragmented landscapes
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Effects of nurse shrubs and biochar on planted conifer seedling survival and growth in a high-severity burn patch in New Mexico, USA
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Contrasting parasite-mediated reductions in fitness within vs. between patches of a nematode host
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Identifying the proximal cue(s) for pupal color variation in the bordered patch butterfly, Chlosyne lacinia (Geyer 1837; Lepidoptera: Nymphalidae)
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Interactions outside local patches contribute to the compound topology of plant-pollinator networks in fragmented dune slacks
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Contrasting species richness in patches of alternative foundation species suggests a framework for understanding Species of Unusual Effect
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Stability of patch-turnover relationships under equilibrium and nonequilibrium metapopulation dynamics driven by biogeography
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Demographic measures of Hypericum cumulicola (Hypericaceae) in 15 populations in Florida Rosemary Scrub patches with different time-since-fire, at Archbold Biological Station, Highlands County, Florida from 1994-2015
We collected demographic data comprising 38,313 unique observations from a sample of 10,910 individuals of H. cumulicola, from 15 independent Florida rosemary scrub patches with different time-since-fire at Archbold Biological Station, Highlands County, Florida. Plants were censused during their peak of reproduction annually in July and August between 1994 and 2015.
Patch occupancy sampling of invertebrates and salamanders from Coweeta Synoptic sampling sites located in the Upper Little Tennessee River Basin, 2009 to 2012.
This research was conducted in Macon County, North Carolina, as part of the Coweeta LTER synoptic sampling program. In the summers of 2009-2012 we sampled and counted Tallaperla species, Elimia species, fish, and salamanders found in a 150meter stretch at the synoptic sites, a total of 44 sites. The 150meter stretch was divided into thirty 5meter plots that were sampled on three occasions each year of sampling; in 2009 all 44 sites were sample, in 2010 a subset of 8 sites were sampled, in 2011 a subset of 9 sites were sampled, and in 2012 a subset of 8 sites were sampled.
MCR LTER: Coral Reef: Community Dynamics: Physical Characteristics of Branching Acropora Patches and Species Richness and Abundances of Associated Fishes
Branching corals, like many in the genus Acropora, provide structurally complex habitats for reef fishes and other organisms. Fluctuations in the abundance, distribution and characteristics of staghorn Acroporid corals may contribute to changes in the abundance and species composition of reef fishes due to changes in the availability of shelter habitat and food. Farming damselfishes of the genus Stegastes occur in high abundances in staghorn thickets and actively defend food and nest space against organisms that threaten these resources. Here I examine the value of staghorn thickets as habitat for fishes, and how the presence of territorial farming damselfishes may influence the assemblage of fishes that associate with staghorn corals. Surveys of 185 Acropora pulchra thickets located in the lagoons surrounding the island of Moorea, French Polynesia revealed 85 species of fish from 25 families. Total fish abundance and species richness values ranged from no fish on a thicket to a high of 275 individuals and 26 species. Thicket area was the most important characteristic in explaining variation in attributes of the fish assemblage among staghorn thickets, with other characteristics explaining little of the species composition or trophic structure. Behavioral observations revealed that farming damselfishes were most aggressive toward corallivores, herbivores, and egg predators, while they ignored most carnivores and omnivores. Despite this pattern, I observed positive covariance between Stegastes and the group of fishes that elicited the strongest aggressive response when the effect of thicket area was removed, suggesting these fishes remain drawn to the resources produced or enhanced by Stegastes on A. pulchra thickets.
Oyster patches within 16 different 0.25 km2 regions throughout the Virginia Coast Reserve, 2015
Oyster patches were digitized based on 2015 USGS LiDAR elevation, within 16 different 0.25 km2 regions throughout the VCR.
multiple food patch collective foraging experiments
<p>This dataset contains .mp4 video files of experimental recordings for the following publication: https://doi.org/10.1101/744649.</p> <p>The .mp4 files (100x sped up) are contained within the zipped folder, and the .csv file contains the metadata for the dataset. </p> <ul> <li><strong>strains</strong> : DA609 and N2</li> <li><strong>timestamp</strong> : from 20170615 to 20170626</li> <li><strong>strain_description</strong> : DA609: npr-1(ad609)X. N2: lab reference strain.</li> <li><strong>sex</strong> : hermaphrodite</li> <li><strong>stage</strong> : adult</li> <li><strong>number_worms: </strong>40</li> <li><strong>media</strong> : NGM agar low peptone</li> <li><strong>arena</strong> : <ul> <li><strong>style</strong> : petri</li> <li><strong>size</strong> : 35 mm</li> </ul> </li> <li><strong>food</strong> : OP50, diluted OD = 0.75, freshly seeded</li> <li><strong>who</strong> : S. Serena Ding</li> <li><strong>protocol</strong> : Method in Ding, Schumacher et al. (2019) <a href="https://doi.org/10.7554/eLife.43318">https://doi.org/10.7554/eLife.43318</a>. Alternatively, visit dx.doi.org/10.17504/protocols.io.vybe7sn for a step-by-step protocol.</li> <li><strong>lab</strong> : <ul> <li><strong>name</strong> : Behavioural Genomics</li> <li><strong>location</strong> : London, United Kingdom</li> </ul> </li> <li><strong>days_of_adulthood</strong> : 1</li> <li><strong>total time (s)</strong> : 3600 per file</li> <li><strong>playback speed: </strong>100x</li> </ul>
Strong histopathological relevance patches for MSI vs. MSS classification
<p>This is a subset of dataset "Histological images for MSI vs. MSS classification in gastrointestinal cancer, FFPE samples" CRC_DX[1]. For more details, please visit [1]. After a fused distillation, a neural network based framework will vote for the candidates for the histopathological strong relevance patches. We incorporate the morphology knowledge from pathologists to sort out the most representative samples and tag them to this subdata.</p> <p>The dataset has two labels i.e., MSIMUT_strong and MSS_strong.</p> <p>MSIMUT_strong : 28 307 patches.</p> <p>MSS_strong : 27 146 patches.</p> <p>[1] Histological images for MSI vs. MSS classification in gastrointestinal cancer, FFPE samples. https://doi.org/10.5281/zenodo.2530835</p>
The dataset of the ASE'20 paper titled "Automated Patch Correctness Assessment: How Far are We?"
<p>This is the experiment result of the ASE'20 paper titled "<strong>Automated Patch Correctness Assessment: How Far are We?</strong>".</p> <p>If you use our data for academic research, please cite our paper as:</p> <pre><code class="language-html">@inproceedings{wang2020automated, title={Automated Patch Correctness Assessment: How Far are We?}, author={Wang, Shangwen and Wen, Ming and Lin, Bo and Wu, Hongjun and Qin, Yihao and Zou, Deqing and Mao, Xiaoguang and Jin, Hai}, booktitle={Proceedings of the 35th International Conference on Automated Software Engineering (ASE)}, year={2020}, organization={ACM} }</code></pre> <p>The file <strong><em>Patches.zip</em></strong> includes all the patches we take into consideration in this study. Note that 269 patches come from "<a href="http://arxiv.org/pdf/1909.13694">Automated Patch Assessment for Program Repair at Scale</a> (Ye et al.), Technical report 1909.13694, arXiv, 2019".</p> <p>The file <em><strong>Patches_for_Static</strong></em> include all the class files we used for static method.</p> <p>The file <em><strong>Tests-oracle </strong></em>includes all the test cases generated by <strong>Evosuite</strong> and <strong>Randoop</strong> on the fixed version programs.</p> <p>The file <em><strong>Tests-buggy</strong></em> includes all the test cases generated by <strong>Evosuite</strong> and <strong>Randoop</strong> on the buggy version programs.</p> <p>The file <em><strong>DiffTGen-result</strong></em> includes ingredients and output information of <strong>DiffTGen</strong>.</p> <p>The file <em><strong>Daikon-output</strong></em> includes inferred invariants of each patch and its corresponding ground-truth.</p> <p>The file <em><strong>PATCH-SIM_result</strong></em> includes the output vector files from <strong>PATCH-SIM</strong> and<strong> E-PATCH-SIM</strong>.</p> <p>The file <em><strong>Training_result</strong></em> includes the output of six ML algorithms with or without oracle.</p> <pre><code class="language-xml">Chart: 1-26; Closure: 14, 18, 31, 33, 38, 40, 57, 62, 63, 70, 73, 86, 92, 93, 115, 123, 126; Lang: 6, 7, 10, 16, 20, 21, 22, 24, 26, 27, 33, 35, 38, 39, 41, 43, 44, 45, 50, 51, 55, 57, 58, 59, 60, 61, 63; Math: 2, 3, 4, 5, 6, 8, 20, 22, 25, 28, 30, 31, 32, 33, 34, 35, 39, 41, 49, 50, 53, 56, 57, 58, 59, 60, 61, 63, 65, 68, 70, 71, 73, 74, 75, 79, 80, 81, 82, 85, 86, 88, 89, 90, 93, 97, 98, 99, 104; Time: 4, 7, 11, 14, 15, 19. </code></pre> <p>Please note that for bugs in the above table, the Evosuite tests on the fixed version programs are reused from <a href="https://arxiv.org/abs/1909.13694">a previous study</a>. We thank <strong>He Ye</strong>, <strong>Matias Martinez</strong>, and <strong>Martin Monperrus</strong> so much for sharing their data.</p> <p> </p> <p><strong>Notice!</strong> For patches under the folder <em>Patches_ICSE</em>, those under <em>Ddifferent</em> and <em>Dsame</em> folders are all correct patches. <em>Different</em> and <em>Same</em> only indicate whether the patch is syntactically identical to the ground truth patch.</p> <p>Patches generated for Mockito project (2 in total): Kali-A-Mockito-10; Arja-Mockito-10</p> <p>Patches do not pass plausibility check (6 in total): Kali-Closure-133; kPAR-Chart-12; FixMiner-Chart-12; patch1-Lang-6-SketchFix-plausible; patch2-Lang-6-SketchFix-plausible; patch1-Math-2-SOFix</p> <p>Patches that are mistakenly labeled (12 in total): patch2-Lang-51-Jaid; patch1-Lang-43-CapGen; patch2-Lang-43-CapGen; patch2-Math-53-CapGen; patch2-Math-53-Jaid; jKali-Lang-7; ACS-Lang-35; Arja-Math-35; SimFix-Math-72; SimFix-Closure-19; Arja-Math-50; SimFix-Lang-60</p> <p>Detailed reasons for the mislabeled patches: 1. the ground-truth patch modifies multiple locations while the generated patch only modifies one of them (2/12, SimFix-Math-72, SimFix-Lang-60); 2. the edit points in the generated patch are different from those in ground-truth patch (8/12, patch2-Lang-51-Jaid, patch2-Math-53-Jaid, patch1-Lang-43-CapGen, patch2-Lang-43-CapGen, patch2-Math-53-CapGen, ACS-Lang-35, SimFix-Closure-19, Arja-Math-50); 3. the generated patch doesnot fulfill the intended function in ground-truth (2/12, jKali-Lang-7, Arja-Math-35).</p> <p>Take <em>Arja-Math-50</em> as an example, this patch deletes a conditional statement which deals with an unexpected input (<em>null</em>) in the method <em><strong>verifyBracketing</strong></em>.<em><strong> </strong></em>However, in the oracle program, this conditional statement still exists. Then, <strong>Randoop</strong> generated a test case by calling <strong><em>verifyBracketing</em></strong> with a <em>null</em> argument. This test passed on the ground-truthpatch but failed on the patch generated by Arja due to the removeof the exception handling statements. As a result, this patch is actually overfitting but mistakenly labeled as correct. We have confirmed this case with Kui Liu, the first author of the recent ICSE'20 paper (Title: <em>On the Efficiency of Test Suite based Program Repair</em>) which makes up our patch benchmark.</p> <p> </p> <p>Border line Patches (3 in total): ACS-Lang-7; kPAR-Lang-7; TBar-Lang-7. Reasons for overfitting: Evosuite generates some tests that fail on those patches, e.g., test049 in Seed 1; the Java documentation above the function states that it needs to deal with the situation where the input cannot be converted. Reasons for correct: it synthesizes the correct modification; currently, in the program, <em>createBigDecimal()</em> is not called directly in other part of the production code except <em>createNumber()</em> and the test code. In our paper, we consider these three patches as correct and that's why Evosuite has 3 false positives.</p>
Data sets comparing Ca(2+) dynamics in whole-cell and β-escin-based perforated patch clamp recordings in adult mouse brain slices.
<p># Hess-et-al-beta-escin-2020<br> Data of the "Data in Brief" article concerning the added buffer approach with beta-escin perforated patch.</p> <p>A joint work by: Simon Hess (`simon.hess@uni-koeln.de`), Christophe Pouzat (`christophe.pouzat@math.unistra.fr`), and Peter Kloppenburg (`peter.kloppenburg@uni-koeln.de`).</p> <p>## Content</p> <p>This repository contains:</p> <p>- Directory `data_whole_cell` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the whole-cell configuration.<br> - Directory `data_beta_escin` contains the experimental data in [HDF5](https://en.wikipedia.org/wiki/Hierarchical_Data_Format) format. The data contains recordings of _Substantia nigra_ dopaminergic neurons recorded in the β-escin perforated patch clamp configuration.</p>
Patch size and vegetation structure drive changes to mixed-species flock diversity and composition across a gradient of fragment sizes in the Western Andes of Colombia
<p>This data set represents a series of 502 mixed-species bird flock compositions, and derived taxonomic, functional, and phylogenetic diversity indices, that were gathered along a gradient of forest fragment sizes (range = 10-173 ha) in the Colombian Western Andes. We sampled mixed-species flocks using transect surveys along 14 transects in 8 fragments and a continuous forest reference site in the same landscape and at the same elevation (~1900-2200 m.a.s.l.). We also used buffer analysis to quantify the proportion of forest cover and forest edge within 1 km of each transect, and calculated local vegetation density and complexity, as well as distance from edge, for each 100-meter transect segment (<em>n</em> = 70 segments). Flock composition data observed on a transect were used to calculate overall species richness and flock size as well as two indices of functional and phylogenetic diversity; we calculated the stadardized effect size (SES) of each measure to account for the correlation between these measures and species richness. We also provide the raw counts of each species for each flock composition. These data were used for the analyses in Jones and Robinson (2020). </p>
Data from: Influences of patch-burn grazing on headwater prairie streams and subsequent recovery
<p>1. Patch-burn grazing (PBG) can promote terrestrial heterogeneity and biodiversity, but can temporarily increase stream nutrients, ecosystem metabolism, and alter macroinvertebrate assemblages. The impacts of grazing on stream channel morphology and post-PBG recovery patterns are unclear. 2. We assessed the influence of grazing in PBG managed grassland streams in Missouri, USA, and subsequent recovery when grazing ceased for two years. We hypothesized that grazing would degrade water quality, stream biotic integrity, and channel morphology, but that riparian fencing would mitigate these effects. We predicted that biological and chemical variables in unfenced streams would return to pre-PBG levels within two years after grazing ceased, but channel morphology would not. 3. Six small headwater streams (two in ungrazed control watersheds, two in PBG watersheds with 10 m fenced riparian zones, and two in unfenced PBG) were sampled over seven years; 2 years before PBG, 3 years during PBG, and 2 years post-PBG. We sampled macroinvertebrates and water chemistry monthly when water was present and surveyed channel morphology at least once each study period. 4. During grazing, unfenced watersheds showed the greatest changes in channel width, depth, and area. During the post-PBG period, one of the two unfenced watersheds showed partial recovery of channel morphology. Although grazing increased concentrations of nutrients and chlorophyll a, concentrations returned to pre-PBG conditions after grazing ended, indicating recovery. Very fine organic sediments increased in the unfenced watersheds compared to the control during grazing but recovered afterwards. Contributions of Chironomidae to total invertebrate abundance increased in the unfenced watersheds during grazing, and then decreased during the post-PBG period. 5. Riparian fencing mostly mitigated effects of grazing on the streams. Unfenced streams were resilient to effects of grazing in a PBG managed grassland, with most metrics recovering within two years after grazing ceased, except for channel morphology. 6. Synthesis and applications: Grazing in a PBG managed grassland coupled with riparian fencing could be an effective conservation tool in prairies, with relatively modest influences on stream water quality and biotic integrity. Persistent changes in stream geomorphology and effects of longer periods of grazing deserve further research.</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.