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Supplementary material 1 from: Magesh S, Jonsson V, Bengtsson-Palme J (2019) Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics 3: e36236. https://doi.org/10.3897/mbmg.3.36236
Table S1
Supplementary material 2 from: Magesh S, Jonsson V, Bengtsson-Palme J (2019) Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics 3: e36236. https://doi.org/10.3897/mbmg.3.36236
Figure S1
Data for paper "Detection of new pioneer transcription factors as cell-type specific nucleosome binders"
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Artifacts for the paper "Concretization of Abstract Traffic Scene Specifications Using Metaheuristic Search"
<p>This deposit contains measurement data and additional artifacts pertaining to the <a href="https://ieeexplore.ieee.org/abstract/document/10315708">Concretization of Abstract Traffic Scene Specifications Using Metaheuristic Search</a>" paper.</p> <p>Specifically, the artifacts are divided into 6 directories:</p> <ul> <li><em>0-config/ </em>contains configuration files use to generate input scene specifications (using Scenic) with various number of actors.</li> <li><em>1-data/</em> contains the generated input scene specifications for each map and actor size. It also contains additional scene specifications used for RQ3 (in the `zalaFullcrop/` subfolder).</li> <li><em>2-results/</em> contains measurement results (i.e. (1) visualizations of generated scenes and (2) corresponding scene specifications containing exact positions of each vehicle, as well as (3) measurement data) for each research question.</li> <li><em>3-figures/</em> contains figures derived from the contents of `results/` (including additional figures not included in the publication).</li> <li><em>4-TestingSemanticSegmentation/</em> contains artifacts related to the integration of the CARLA simulator and of three computer-vision components: <ul> <li><em> 0-sceneConfig/</em> contains configuration files used to generate scenes.</li> <li> <em>1-scenesWithExactCoordinates/ </em>contains (1) visualizations of generated scenes and (2) corresponding Scenic-compatible scene specifications containing exact positions of each vehicle.</li> <li> <em> 2-staticImages/</em> contains dashcam images for generated scenes and corresponding ground truth semantic segmentation, obtained through the CARLA integration.</li> <li> <em>3-predictions/</em> contains predicted semantic segmentation results (and their overlay on top of the corresponding dashcam image) obtained using three computer-vision components.</li> <li> <em>4-videos/</em> contains videos of generated scenes running with the default AV stack included in CARLA.</li> <li> <em>5-metrics</em> contains initial measurement data for the predicted semantic segmentation.</li> </ul> </li> <li><em>5-simulationVideos/</em> contains videos of two scenario-based test cases executed in simulation. The two scenarios are only differenciated by the initial scene, which impacts the outcome of test execution (collision vs. no-collision).</li> </ul> <p>All the code of the proposed <a href="https://github.com/ArenBabikian/Scenic">MHS-based scene concretization approach</a> is implemented as an extension to the <a href="https://github.com/BerkeleyLearnVerify/Scenic">Scenic</a> tool, which is available under the <a href="https://opensource.org/licenses/BSD-3-Clause">3-Clause BSD License</a>.</p>
UNRAVELLING CELL TYPE SPECIFIC RESPONSE TO PARKINSON'S DISEASE AT SINGLE CELL RESOLUTION
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Figure 1 from: Kim C-J, Tan J-L, Kim JK, Choi MB (2024) Confirmation of the valid specific status of Dolichovespula kuami Kim & Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence. ZooKeys 1196: 111-119. https://doi.org/10.3897/zookeys.1196.110224
Figure 1 Comparison between the pronotal rugae and carinas of D. kuami and D. flora. Pronotum of D. kuami (A) and D. flora (D); rugae and carinas in the pronotal lateral part to the pronotal pit of D. kuami (B) and D. flora (E); rugae on the pronotum of D. kuami (C) and D. flora (F). Arrows in figures A, D indicate the enlarged parts in B, C, E, F. Scale bars: 0.5 mm.
Figure 2 from: Kim C-J, Tan J-L, Kim JK, Choi MB (2024) Confirmation of the valid specific status of Dolichovespula kuami Kim & Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence. ZooKeys 1196: 111-119. https://doi.org/10.3897/zookeys.1196.110224
Figure 2 Genitalia of Dolichovespula kuami (A–C) and D. flora (D–F) A genitalic capsules, in dorsal view (truncated dorsal terminal process, arrow) B aedeagus C gonostipes and triangular parameral spine (arrow) D genitalic capsules, in dorsal view (shortly rounded terminal process, arrow) E aedeagal tip F gonostipes and slender parameral spine (arrow). Scale bars: 1 mm.
Figure 4 from: Kim C-J, Tan J-L, Kim JK, Choi MB (2024) Confirmation of the valid specific status of Dolichovespula kuami Kim & Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence. ZooKeys 1196: 111-119. https://doi.org/10.3897/zookeys.1196.110224
Figure 4 Comparison of the general habitus of Dolichovespula kuami and D. flora (A, D queen B, E worker C, F drone): D. kuami (A–C) D. flora (D–F). Scale bars: 1 cm.
Figure 3 from: Kim C-J, Tan J-L, Kim JK, Choi MB (2024) Confirmation of the valid specific status of Dolichovespula kuami Kim & Yoon, 1996 (Hymenoptera, Vespidae) based on molecular and morphological evidence. ZooKeys 1196: 111-119. https://doi.org/10.3897/zookeys.1196.110224
Figure 3 A maximum-likelihood phylogenetic tree of the successfully DNA barcoded Dolichovespula specimens. The numbers above the branches indicate bootstrap proportions.
JSS Data from Function-specific Scheduling Policies in Cloud-Edge, Multi-Region Serverless Systems
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Single-cell multi-omics analysis identifies context specific gene regulatory gates and mechanisms
<p>There is a growing interest in inferring context specific gene regulatory networks from single-cell RNA sequencing (scRNA-seq) data. This involves identifying the regulatory relationships between transcription factors (TFs) and genes in individual cells, and then characterizing these relationships at the level of specific cell types or cell states. <br>In this study, we introduce scGATE (single-cell gene regulatory gate) as a novel computational tool for inferring TF-gene interaction networks and reconstructing Boolean logic gates involving regulatory TFs using scRNA-seq data. In contrast to current Boolean models, scGATE eliminates the need for individual formulations and likelihood calculations for each Boolean rule (e.g., AND, OR, XOR). By employing a Bayesian framework, scGATE infers the Boolean rule after fitting the model to the data, resulting in significant reductions in time-complexities for logic-based studies. <br>We have applied assay for transposase-accessible chromatin with sequencing (scATAC-seq) data and TF DNA binding motifs to filter out non-relevant TFs in gene regulations. By integrating single-cell clustering with these external cues, scGATE is able to infer context specific networks. The performance of scGATE is evaluated using synthetic and real single-cell multi-omic data from mouse tissues and human blood, demonstrating its superiority over existing tools for reconstructing TF-gene networks. Additionally, scGATE provides a flexible framework for understanding the complex combinatorial and cooperative relationships among TFs regulating target genes by inferring Boolean logic gates among them.</p>
SPECIFICITY OF TREATMENT IN PATIENTS WITH PURULENT-NECROTIC COMPLICATIONS OF DIABETIC HEEL SYNDROME
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FOREIGN EXPERIENCES OF IMPROVING THE WELL-BEING OF THE POPULATION AND ITS CHARACTERISTICS SPECIFIC TO UZBEKISTAN
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F I G U R E 2 in Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments
F I G U R E 2 Schematic representation of the different capture–mark–recapture (CMR) events occurring in the Restigouche catchment in a given year. The letters C, M, and R correspond to the captured, marked, and recaptured fish, respectively. The total nonmarked smolt population Nmtot comprises four components: Kedgwick, Upsaquitch, and Matapedia abundance Nm, and the smolt abundance originating from the rest t 1:3,t of the catchment Nmrest. Note that the "rest" component can vary between years because not all rotary screw traps (RST) are operated annually. t Each year, each operating upstream RST is associated with a CMR experiment. Marked smolts in the upstream RSTs (Mt,1:3) can also be recaptured at the downstream RSTs (Rt,1:5). Each downstream RST samples an unknown fraction of the total population of smolts migrating out of the catchment. Due to the low number of recaptures at the downstream RSTs, it is not possible to estimate this fraction, and it is confounded with the catchabilities at the downstream RSTs. Variables in square boxes are known, and variables in round boxes are unknown.
Skeletonema marinoi eco-types show specific habitat-related responses to fluctuating light supporting high potential for growth under photobioreactor light regime
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Intermediate volatility organic compounds (IVOCs) emissions based on source-specific emission ratios relative to non-methane volatile organic compounds (NMVOCs) give better representation of the spatial distribution of IVOCs in China
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Source-specific Mass Absorption Efficiencies of Char-EC and Soot-EC Improve Accuracy in Black Carbon Radiative Effect Estimation
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Sustained Release of Proteins Using Region-Specific Tunable Degradability in Hydrogels Through 3D Photopatterning and Complimentary Labile Bond Chemistry
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THE SPECIFIC FEATURES OF TEACHING DRAMA IN ENGLISH LITERATURE CLASSES: CLASSIC AND MODERN PLAYS
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Stock specific isotopic composition of maturing sockeye salmon in the North Pacific
<p>The stock-specific distribution of maturing salmon in the North Pacific has been a persistent information gap that has prevented us from determining the ocean conditions experienced by individual stocks. This continues to impede understanding of the role of ocean conditions in stock-specific population dynamics. <a name="_Hlk21877970">We assessed scale archives for 17 sockeye salmon (<i>Oncorhynchus nerka</i>) stocks covering the entire North Pacific, from the Columbia River (Washington State and British Columbia) to Kamchatka Peninsula (Russia), to infer salmon locations during their last growing season before returning to their spawning grounds. The approach used, first pioneered in salmon stocks in the Atlantic, relies on the relationship between temporal changes in δ<sup>13</sup>C in salmon scales and sea surface temperature to estimate salmon distribution based on correlation </a>strength. An advantage of this approach is that it does not require fish sampling at sea, but relies on existing fishery agency collections of salmon scales. Significant correlations were found for 7 of the stocks allowing us to propose plausible feeding grounds. Complementary information from δ<sup>15</sup>N, historical tagging studies, and connectivity analysis were used to further refine distribution estimates. This study is a first step toward estimating stock-specific distributions of salmon in the North Pacific, and provides a basis for the application of the approach to other salmon scale archives. This information has the potential to improve our ability to relate stock dynamics to ocean conditions, ultimately enabling improved stock management. For example, our estimated distributions of Bristol Bay and NE Pacific stocks demonstrated that they occupy different areas with a number of the former being distributed in the high productivity shelf waters of the Aleutian Islands and Bering Sea. This may explain why these stocks seem to have responded differently to changes in ocean conditions, and the long term trend of increased productivity of Bristol Bay sockeye.</p>
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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.