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1,812 results for “dissection”
Dissecting the FAIR Guiding Principles - Key Categories, Core Concepts, Focus Elements, and Harmonized Indicators
<p>A comprehensive workbook created to facilitate and document the process of decomposing the FAIR Guiding Principles and mapping them to key categories, requirements, core concepts, focus elements, and harmonized indicators. It also contains a complete list of the indicators.</p>
Dissecting the smell of fear from conspecific and heterospecific prey: Investigating the processes that induce anti-predator defenses.
Prey use chemical cues from predation events to obtain information about predation risk to alter their phenotypes. Though we know how many prey respond to predators, we still have a poor understanding of the processes and chemical cues involved during a predation event. We examined how gray treefrog tadpoles (Hyla verisciolor) altered their behavior and morphology when raised with cues from different stages of predator attack, predators fed different amounts of prey, and predators consuming different combinations of treefrog tadpoles or snails (Helisoma trivolvis). We found that starved predators and predators fed snails induced no defensive responses whereas tadpoles exposed to a predator consuming gray treefrogs induced greater hiding, lower activity, and relatively deeper tails. We also found that the tadpoles did not respond to crushed, chewed, or digested conspecifics, but they did respond to consumed (i.e. chewed + digested) conspecifics. When we increased the treefrog biomass consumed by predators, tadpoles frequently increased their defenses when only tadpoles were consumed and always increased their defenses when the total diet biomass was held constant via the inclusion of snails. When predators experienced temporal variation in diet composition, including cues from snails to cause additional digestive cues or chemical noise, there was no effect on tadpole phenotypes. Our results suggest that amphibian prey rely on cues from both chewing and digestion of conspecifics and that the presence of cues from digested heterospecifics play little or no role in adding chemical noise or increased digestive enzymes and by-products that interfere with induced defenses.
PhasAGE Expert Seminar- Dissecting the contribution of motor-cargo adaptors to microtubule-based transport in neurons
<p>The PhasAGE Expert Seminars consist of a series of talks with speakers from PhasAGE partner’s institutions to promote a successful transfer of knowledge about PhasAGE topics – biomolecular phase separation, aging and age-related diseases.</p>
Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination
<p>Submissions for the Tractostorm 2 Project [1] from our collaborators (raters) are available for new analysis.<br> Contains regions of interest (ROIs) as well as resulting bundles. Segmentations were performed with MI-Brain [2] (<a href="https://github.com/imeka/mi-brain">MI-Brain</a>)</p> <p>Initial data is the same as in the initial <a href="https://zenodo.org/record/2547025#.YRV2S3VKiUk">Tractostorm Project</a> [3]<br> Contains the data as sent to collaborators and the written document containing the dissection protocol in detail.</p> <p>[1] Rheault, Francois, et al. "Tractostorm 2: Optimizing tractography dissection reproducibility with segmentation protocol dissemination." <em>Human Brain Mapping</em> (2022).<br> [2] Rheault, Francois, et al. "MI-Brain, a software to handle tractograms and perform interactive virtual dissection." <em>Proceedings of the ISMRM Diffusion study group workshop, Lisbon</em>. 2016.<br> [3] Rheault, Francois, et al. "Tractostorm: The what, why, and how of tractography dissection reproducibility." <em>Human brain mapping</em> 41.7 (2020): 1859-1874.</p> <p>Data Organization:<br> The 5 HCP subjects were duplicated 4 times each.<br> 193441 -> A111, B218, C317, D418<br> 219231 -> A127, B228, C320, D426<br> 286650 -> A136, B237, C338, D436<br> 486759 -> A149, B246, C344, D443<br> 615441 -> A156, B252, C359, D450<br> <br> Bundles can be segmented automatically using the <a href="https://github.com/scilus/scilpy">scilpy</a> toolbox.<br> scil_filter_tractogram.py ${INPUT} ${OUTPUT} ${OPTIONS}</p> <ul> <li>${INPUT} would be the whole brain tractogram of an HCP subject in data_to_segment.zip</li> <li>${OUTPUT} would be the bundle filename (preferably .trk format)</li> <li>${OPTIONS} would be the sequence of ROIs to apply, one for each bundle. <ul> <li><strong>CC</strong>: '--drawn_roi CENTRAL_CC.nii.gz any include --drawn_roi LOWER_AXIAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude --drawn_roi POST_C_R.nii.gz any exclude --drawn_roi PRE_C_R.nii.gz any exclude'</li> <li><strong>AF_L</strong>: '--drawn_roi CENTRAL_CS_L.nii.gz any include --drawn_roi MEDIAL_SAGITTAL_LIM.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any include --drawn_roi PRE_C_L.nii.gz any include --drawn_roi TEMPORAL_ENTRY.nii.gz any include --drawn_roi TEMPORAL_STEM.nii.gz any exclude'</li> <li><strong>PYT_L</strong>: '--drawn_roi IC_L.nii.gz any include --drawn_roi MO_L.nii.gz any include --drawn_roi MB_L.nii.gz any include --drawn_roi MO_L_NOT.nii.gz any exclude --drawn_roi MID_SAGITTAL_PLANE.nii.gz any exclude --drawn_roi POST_C_L.nii.gz any exclude --drawn_roi PRE_C_L.nii.gz any exclude'</li> </ul> </li> </ul>
Melon pan-genome and multi-parental framework for highresolution trait dissection
<p>Gff3 annotation files for 25 de-novo melon genomes discussed in publication.<br> These are draft annotations based on lif-over from "Harukei-3" and "HS" melon genomes.<br> Genome fasta files can be found in NCBI PRJNA726743 </p>
Online Appendix for PhD Thesis Titled "Dissecting Causal Relationships and Molecular Mechanisms in Disease using Genetic Risk Profiles"
<p>This repository contains 23 tables and two figures, which are too big to be included in the Appendix section of my thesis document.</p> <p>The second version includes additional summary statistics of metabolite-PGS associations which can be found at http://mrcieu.mrsoftware.org/metabolites_PRS_atlas/.</p>
Sensitivity Datasets - Leveraging Implicit Knowledge in Neural Networks for Functional Dissection and Engineering of Proteins
<p><strong>Leveraging Implicit Knowledge in Neural Networks for Functional Dissection and Engineering of Proteins</strong></p> <p>The Sensitivity datasets cover more than 800 proteins and are structured as follows. The sensitivity values are the mean of four DeeProtein replicates.</p> <p>It is uploaded as tar.gz. and contains one directory.</p> <p>File names contain the PDB<sup>1</sup> identifier and the respective chain identifier. </p> <p>The sequences and secondary structure information were downloaded from the RCSB Protein Databank and are available here: <a href="https://cdn.rcsb.org/etl/kabschSander/ss_dis.txt.gz">https://cdn.rcsb.org/etl/kabschSander/ss_dis.txt.gz</a> This URL can be found with some explanation at <a href="http://www.rcsb.org/pdb/static.do?p=download/http/index.html">http://www.rcsb.org/pdb/static.do?p=download/http/index.html</a></p> <p>The secondary structure annotation relies on the DSSP Algorithm by Kabsch and Sander<sup>2</sup>.</p> <p> </p> <p><strong>The files are tab-separated and contain the following columns:</strong></p> <ul> <li><strong>Pos</strong> Position in the sequence, starting from zero</li> <li><strong>AA</strong> Amino acid in that position</li> <li><strong>sec</strong> Secondary structure as annotated in the RCSB Protein Databank</li> <li><strong>dis</strong> if a region has not been experimentally observed (sometimes explains mismatches with crystal structures)</li> <li><strong>GO:_______</strong> Sensitivity for the GO term</li> </ul> <p><strong>References</strong></p> <ol> <li>The Protein Data Bank H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) Nucleic Acids Research, 28: 235-242. doi:10.1093/nar/28.1.235</li> <li>Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637, doi:10.1002/bip.360221211 (1983).</li> </ol>
Tractostorm: Rater reproducibility assessment in tractography dissection of the pyramidal tract
<p>Segmentation of the 13 experts and 11 non-experts for the Tractostorm project. Contains the original dataset each participants received to perform their tasks.</p> <p>The tractography file format is *.trk and the image file format is *.nii.gz</p>
Single cell RNA-seq Data - Dissecting the functional reprogramming of the microenvironment in bone marrow fibrosis at the single cell level
<p>We provide results regarding the bioinformatic analysis of scRNA-seq from distinct bone marrow fibrosis mouse models and human samples.</p> <p> </p> <p>These include:</p> <p>Robjects&Markdown - R markdown and R objects with QC statistics, UMAP and final scRNA-seq data sets.</p> <p>Markers - Excel tables with cluster specific marker genes.</p> <p>DE Genes - Excel table with DE genes when comparing cells in control vs. disease condition per cluster.</p> <p>GO Analysis - Gene enrichment analysis of either DE genes. These are divided by either UP or down regulated genes.</p>
РИС. 2. Дистальные отделы половой системы особей иЗ смеШанной колонии Monacha claustralis (A–D) и M. cartusiana (E–F). D, F. Вскрытый атриум у двух видов. Условные сокраЩениЯ: at – атриум; atpl – складка внутри атриума; ep – Эпифаллус; fl – бич; mg – слиЗистые желеЗы; pe – пенис; pp – папилла пениса; va – вагина; vap1 – баЗальнаЯ часть вагинального придатка; vap2 – апикальнаЯ часть вагинального придатка; vlb – латеральное выпЯчивание вагины. МасШтаб 1 мм. FIG. 2. Distal parts of the reproductive system of specimens from a mixed colony of Monacha claustralis (A–D) and M. cartusiana (E–F). D, F. Dissected atrium in two species. Abbreviations: at – atrium; atpl – pleat inside the atrium; ep – epiphallus; fl – flagellum; mg – mucus glands; pe – penis; pp – penial papilla; va – vagina; vap1 – basal part of vaginal appendage; vap2 – apical part of vaginal appendage; vlb – lateral bulge of the vagina. Scale bars 1 mm. in Monacha claustralis и M. cartusiana (Gastropoda, Hygromiidae) - два криптических вида антропохорных наЗемных моллюсков на Западе Украины
РИС. 2. Дистальные отделы половой системы особей иЗ смеШанной колонии Monacha claustralis (A–D) и M. cartusiana (E–F). D, F. Вскрытый атриум у двух видов. Условные сокраЩениЯ: at – атриум; atpl – складка внутри атриума; ep – Эпифаллус; fl – бич; mg – слиЗистые желеЗы; pe – пенис; pp – папилла пениса; va – вагина; vap1 – баЗальнаЯ часть вагинального придатка; vap2 – апикальнаЯ часть вагинального придатка; vlb – латеральное выпЯчивание вагины. МасШтаб 1 мм. FIG. 2. Distal parts of the reproductive system of specimens from a mixed colony of Monacha claustralis (A–D) and M. cartusiana (E–F). D, F. Dissected atrium in two species. Abbreviations: at – atrium; atpl – pleat inside the atrium; ep – epiphallus; fl – flagellum; mg – mucus glands; pe – penis; pp – penial papilla; va – vagina; vap1 – basal part of vaginal appendage; vap2 – apical part of vaginal appendage; vlb – lateral bulge of the vagina. Scale bars 1 mm.
Data and scripts for: Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping
<p>Plant phenotyping under field conditions plays an important role in agricultural research. Efficient and accurate high-throughput phenotyping strategies enable a better connection between genotype and phenotype. Unmanned aerial vehicle-based high-throughput phenotyping platforms (UAV-HTPPs) provide novel opportunities for large-scale proximal measurement of plant traits with high efficiency, high resolution, and low cost. The objective of this study was to use time series normalized difference vegetation index (NDVI) extracted from UAV-based multispectral imagery to characterize its pattern across development and conduct genetic dissection of NDVI in a large maize population. The time series NDVI data from the multispectral sensor were obtained at 5 time points across the growing season for 1,752 diverse maize accessions with a UAV-HTPP. Cluster analysis of the acquired measurements classified 1,752 maize accessions into 2 groups with distinct NDVI developmental trends. To capture the dynamics underlying these static observations, penalized-splines (P-splines) model was used to obtain genotype-specific curve parameters. Genome-wide association study (GWAS) using static NDVI values and curve parameters as phenotypic traits detected signals significantly associated with the traits. Additionally, GWAS using the projected NDVI values from the P-splines models revealed the dynamic change of genetic effects, indicating the role of gene-environment interplay in controlling NDVI across the growing season. Our results demonstrated the utility of ultra-high spatial resolution multispectral imagery, as that acquired using a UAV-based remote sensing, for genetic dissection of NDVI.</p>
Marine demosponge rheology / dissection microscopy
<p>Sponges are animals that inhabit many aquatic environments while filtering small particles and ejecting metabolic wastes. They are composed of cells in a bulk extracellular matrix, often with an embedded scaffolding of stiff, siliceous spicules. We hypothesize that the mechanical response of this heterogeneous tissue to hydrodynamic flow influences cell proliferation in a manner that generates the body of a sponge. Toward a more complete picture of the emergence of sponge morphology, we dissected a set of species and subjected disks of living tissue to physiological shear and uniaxial deformations on a rheometer. Various species exhibited rheological properties such as anisotropic elasticity, shear softening and compression stiffening, negative normal stress, and non-monotonic dissipation as a function of both shear strain and frequency. Erect sponges possessed aligned, spicule-reinforced fibers which endowed three times greater stiffness axially compared with orthogonally. By contrast, tissue taken from shorter sponges was more isotropic but time-dependent, suggesting higher flow sensitivity in these compared with erect forms. We explore ecological and physiological implications of our results and speculate about flow-induced mechanical signaling in sponge cells.</p>
Data from: Dissecting gene activation and chromatin remodeling dynamics in single human cells undergoing reprogramming
<p>During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent. </p>
Figure 6.- Parahololepidella greeffi. Syntype ZMH 5692. A. Anterior end, dorsal view. B. Neurochaetae from anterior region, showing damaged tips. C. Notochaetae. D. Dissected parapodia from mid-body. E in New symbiotic associations involving polynoids (Polychaeta, Polynoidae) from Atlantic waters, with redescriptions of Parahololepidella greeffi (Augener, 1918) and Gorgoniapolynoe caeciliae (Fauvel, 1913)
Figure 6.- Parahololepidella greeffi. Syntype ZMH 5692. A. Anterior end, dorsal view. B. Neurochaetae from anterior region, showing damaged tips. C. Notochaetae. D. Dissected parapodia from mid-body. E. Neurochaetae of the same (black arrow pointing at the apparently bidentate chaetae). F. Notochaetae of the same. B, C, E, F: scale bar 125 µm.
Figure. Rhynchoglossum ampliatum (C.B.Clarke) B.L.Burtt. A, Habit; B, iNfloresceNce; C, flower (froNt view); D, calyx (dissected open); E, corolla (dissected open); F, stamens; G, pistil. Photographs of Momang Taram & Ojar Taku 808: A–B and D–G, M. Taram; C, D. Borah. in A CLARIFICATION OF THE STATUS OF RHYNCHOGLOSSUM LAZULINUM (GESNERIACEAE: DIDYMOCARPOIDEAE)
Figure. Rhynchoglossum ampliatum (C.B.Clarke) B.L.Burtt. A, Habit; B, iNfloresceNce; C, flower (froNt view); D, calyx (dissected open); E, corolla (dissected open); F, stamens; G, pistil. Photographs of Momang Taram & Ojar Taku 808: A–B and D–G, M. Taram; C, D. Borah.
Imaging Data for "Ascending aortic aneurysm in angiotensin II- infused mice: formation, progression and the role of focal dissections"
<p>This dataset contains imaging files of the manuscript "Ascending aortic aneurysm in angiotensin II- infused mice: formation, progression and the role of focal dissections", published in ATVB in 2016. All .mcs files are to be opened in Mimics (Materialise, Leuven, Belgium). All files are named as follows: "technique_id_timepoint_asc.mcs". The technique can be either in vivo micro-CT, or ex-vivo synchrotron-based PCXTM. The mouse ID corresponds to the ID that was used during the experiments. Mice were distributed at random into 2 groups (G1 and G2) and sacrificed after 1 of 4 possible timepoints. TP0 corresponds to baseline (prior to Ang II infusion), TP1 corresponds to 3 days of Ang II infusion, TP2 corresponds to 10 days of Ang II infusion, TP3 corresponds to 18 days of Ang II infusion and TP4 corresponds to 28 days of Ang II infusion. Image files from PCXTM are ex vivo and always correspond to the latest timepoint available with micro-CT. Histology data are in the .zip file and have .vsi extension that can be opened with the software OlyVIA or with the BIOP extension "vsi-reader" to the open source software package fiji.</p>
Imaging dataset for "Angiotensin II infusion into ApoE-/- mice: a model for aortic dissection rather than abdominal aortic aneurysm?"
<p>This dataset contains imaging files of the manuscript "Angiotensin II infusion into ApoE-/- mice: a model for aortic dissection rather than abdominal aortic aneurysm?", published in Cardiovascular Research in 2017. All published files are to be opened in Mimics (Materialise, Leuven, Belgium). All files are named as follows: "technique_id_timepoint_abd.mcs". The technique can be either in vivo micro-CT, or ex-vivo synchrotron-based PCXTM. The mouse ID corresponds to the ID that was used during the experiments. Mice were distributed at random into 2 groups (G1 and G2) and sacrificed after 1 of 4 possible timepoints. TP0 corresponds to baseline (prior to Ang II infusion), TP1 corresponds to 3 days of Ang II infusion, TP2 corresponds to 10 days of Ang II infusion, TP3 corresponds to 18 days of Ang II infusion and TP4 corresponds to 28 days of Ang II infusion. Image files from PCXTM are ex vivo and always correspond to the latest timepoint available with micro-CT of that animal. Histology data are zipped and stored in .vsi format. They can be opened with the Olympus software package OlyVIA or with the BIOP-plugin "vsi-reader" to the open source software package fiji.</p>
Fig. 1 in Clearing and dissecting insects for internal skeletal morphological research with particular reference to bees
Fig. 1. Specimens of Scaptotrigona depilis (Moure, 1942) cleared using the protocol presented in Table 1: lateral habitus (central column, top); dorsal habitus (central column, middle); boxes show different portions of the body disarticulated, along with examples of external/internal structures made available for refined morphological inspections after the clearing procedure.
MD trajectories for "Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases"
<p>This dataset contains Amber MD trajectories for the MD simulations described in the manuscript "Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases" by Christopher D. Fage, Simone Kosol, Matthew Jenner, Carl Öster, Angelo Gallo, Milda Kaniusaite, Roman Steinbach, Michael Staniforth, Vasilios G. Stavros, Mohamed A. Marahiel, Max J. Cryle, and Józef R. Lewandowski published in ACS Catalysis (<a href="https://doi.org/10.1021/acscatal.1c02113">https://doi.org/10.1021/acscatal.1c02113</a>). If you use these data please cite the original manuscript (follow the manuscript DOI for the final citation, which was not available at the time of publishing this data set). </p> <p>To reduce their size the trajectories were stripped of water and ions. Only frames every 1 ns or 5 ns were saved. Please see the Supporting Information of the source manuscript for the conditions for the simulations. </p>
Dissecting Tiktok and social media for children and young adults
<p>This data is related to protocol for systematic literature review and the details of literatures selected for systematic review.</p>
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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.