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402 results for “ABSOLUTE”
TCGA ABSOLUTE auto-calling results with DoAbsolute
<p>The results are calculated with DoAbsolute (https://github.com/ShixiangWang/DoAbsolute) with cancer type specific and pan-cancer mode based on TCGA copy number segments data and mutation data. Take your own risk as the data are auto-processed and no manual check.</p> <p> </p> <p>array sample call status purity ploidy Genome doublings delta Coverage for 80% power Cancer DNA fraction Subclonal genome fraction tau E_CR<br> TCGA-OR-A5JO-01 TCGA-OR-A5JO-01 called 1 5 0 0.2 21 1 0.01 5.00281122783359 0<br> TCGA-OR-A5KQ-10 TCGA-OR-A5KQ-10 called 0.69 5 0 0.17 29 0.85 0 4.99022535717521 0<br> TCGA-OR-A5L8-10 TCGA-OR-A5L8-10 called 0.56 3.99 0 0.18 27 0.72 0 4.02086049427876 0<br> TCGA-OU-A5PI-10 TCGA-OU-A5PI-10 called 0.75 5 0 0.18 28 0.88 0.01 5.01366221195135 0</p> <p> </p> <p>Please cite the following paper if you use it in academic research:</p> <ul> <li>Wang, Shixiang, et al. "The predictive power of tumor mutational burden in lung cancer immunotherapy response is influenced by patients' sex." International journal of cancer (2019).</li> <li>Carter, Scott L., et al. “Absolute quantification of somatic DNA alterations in human cancer.” Nature biotechnology 30.5 (2012): 413.</li> </ul> <p> </p>
An estimation of the absolute number of axons indicates that human cortical areas are sparsely connected
<p>This is a collection of preprocessed data and standalone Matlab analysis code for the PLoS: Biology article of the same name, <a href="https://doi.org/10.1371/journal.pbio.3001575">https://doi.org/10.1371/journal.pbio.3001575</a>. The primary processed diffusion MRI connectivity data was reported and previous distributed in our eNeuro article <a href="http://doi.org/10.1523/ENEURO.0416-20.2020">https://doi.org/10.1523/ENEURO.0416-20.2020</a>. The replication dataset was reported and previous distributed by Arnatkeviciute et al. 2021, Nature Communications (<a href="http://doi.org/10.1038/s41467-021-24306-2">https://doi.org/10.1038/s41467-021-24306-2</a>). Please cite these publications when using relevant code or data. Files with the .mat extension are Matlab v7.3 data files. The raw imaging data from which these files were derived are available from <a href="https://db.humanconnectome.org/">https://db.humanconnectome.org</a>.</p>
MSDI: a geo-tagged drone imagery for absolute visual localization
<p>The MSDI (Manchester Surface Drone Imagery) is a geo-imagery registration dataset. <br> The dataset consists of <br> a. 446 downward-facing drone images.<br> b. 89 forward-facing(45-degree) drone images.<br> c. 64 forward-facing (0-degree) drone images. <br> d. parameter matrix of drone camera and transformation matrix.<br> e. checkerboard images for camera calibration.</p> <p>This dataset is collected by Mochuan Zhan for his MSC project: Registration of UAV Imagery to Aerial and Satellite Imagery<br> in the University of Manchester (2021/9 - 2022/9) which is supervised by Dr.Terence Patrick Morley. This project aims at <br> developing a system that could perform efficient UAV visual localization through image registration based on local feature <br> detectors and the technique of high-throughput computing.</p> <p>Notice:<br> The corresponding satellite image from Google Map and Bing Map could be obtained by my program, Link: </p> <pre>https://doi.org/10.5281/zenodo.6977652</pre> <p>A Ground Control Point (GCP) selector is provided for user to select GCP and create file with small effort.<br> By registrating corresponding images, users could evaluate the performance of their registration techniques.</p> <p>The Imagery contains images of 8 Areas in Manchester:<br> - Manchester Aquatics Center 80<br> - Manchester ASDA 76<br> - Manchester Bussiness School 37<br> - Manchester Energy Center 71<br> - Manchester Holy Name Church 58<br> - Manchester Hulme Park 47<br> - Manchester Hulme Part(0-degree) 64<br> - Manchester Hulme Part(45-degree) 89<br> - Manchester Metropolitan university 29 <br> - Manchester Museum 48</p> <p>Device Information:<br> - Drone brand: Parrot<br> - Drone model: Parrot Anafi</p> <p>Software Information:<br> - Pix4DCapture<br> - FreeFlight6</p> <p>Flight parameters:<br> - Height 100m<br> - Speed 5m/s<br> - overlap low</p> <p><br> </p>
Albertosaurus libratus adult and youngster? Or two species? Drawn to the same scale, note that the smaller individual's teeth, which are partly covered by the lips, are absolutely larger than the bigger one's. On the side of the lower jaw, the bulge of the surangular bone typical of tyrannosaurs can clearly be seen. in Predatory Dinosaurs of the World
Albertosaurus libratus adult and youngster? Or two species? Drawn to the same scale, note that the smaller individual's teeth, which are partly covered by the lips, are absolutely larger than the bigger one's. On the side of the lower jaw, the bulge of the surangular bone typical of tyrannosaurs can clearly be seen.
Pose Selector Workflow - Docking Poses, Absolute Binding Free Energy Estimates and Structure Input Files for Machine Learning
<p>The Pose Selector (PS) workflow calculates absolute binding free energies (ABFEs) for binding poses of protein-ligand complexes. First, it converts the binding poses (both docking poses as well as experimentally observed ligand binding poses), which are provided as a combination of protein PDB file and ligand MOL2 file, into input files for molecular dynamics (MD) simulations with GROMACS after they have passed extensive quality checks and repair steps. Next, the PS workflow post-processes and analyses the last frame of the resulting eight 100 ps trajectories per binding pose with the Generalised Born model of implicit solvation as implemented in gmx_MMPBSA to obtain the ABFE estimates. The workflow was designed for soluble proteins without post-translational modifications, co-factors and non-standard amino acids, and it has limited support for coordinated ions.</p> <p>For the dataset published here, the PS workflow was run on docking poses generated for the PDBbind 2020 dataset (http://www.pdbbind.org.cn/index.php), shared in dockingPosesPDBBind2020.tar.gz. This entry and its partner entry 10.5281/zenodo.11397486 also share the intial coordinates used in the MD simulations of >800,000 docking poses of 4022 protein-ligand complexes (structureFiles_dockingPoses1.tar.gz in this entry and structureFiles_dockingPoses2.tar.gz in 10.5281/zenodo.11397486) and of the experimental ligand binding pose of 4549 complexes (structureFiles_experimentalStructures.tar.gz) as well as the corresponding ABFE estimates (absoluteBindingFreeEnergyEstimates.tar.gz). The MD simulations were run on the LUMI and MeluXina supercomputers while the implicit-solvent calculations were carried out on Galileo (Cineca).</p> <p>The README file describes the structure of the shared data in more detail and points out how to reproduce the MD trajectories and the subsequent implicit-solvent calculations yielding the free-energy estimates as well as how to use the data provided in this entry to train a machine-learning model predicting the ABFE of binding poses of protein-ligand complexes. The workflow scripts can be downloaded from GitHub (https://github.com/LigateProject/Pose-Selector-workflow). The MD simulations were run with GROMACS 2023.2 (https://manual.gromacs.org/2023.2/index.html), and the implicit-solvent calculations were carried out with gmx_MMPBSA 1.6.1 (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/v1.6.1/).</p>
A Preisach method for estimating absolute paleofield intensity under the constraint of using only isothermal measurements: 2. Experimental testing [DATASET]
<p>Raw FORC data published in:</p> <p>Muxworthy, A.R., Heslop, D., Paterson, G.A., Michalk, D., 2011. A Preisach method for estimating absolute paleofield intensity under the constraint of using only isothermal measurements: 2. Experimental testing. J. Geophys. Res. 116, B04103, doi:04110.01029/02010JB007844.</p>
Рис. 3. Снижение чисΛенности гусениц при возΑействии разΛичных географических штаммов ВЯП. СтоΛбцы: коΛичество погибших во время эксперимента гусениц поΑ опреΑеΛенной инфекционной нагрузкой. ПоказатеΛи (в процентах) привеΑены в Λевой части табΛицы. СтреΛки: минимаΛьное и максимаΛьное коΛичество погибших во время очереΑного учета гусениц и крестообразные маркеры: среΑнее коΛичество погибших во время очереΑного учета гусениц. ПоказатеΛи (в абсоΛютных значениях) в правой части табΛицы. По горизонтаΛи: номер титра, от боΛьшего к меньшему Fig. 3. Decrease in the number of caterpillars under the influence of various geographical strains of NPV. Columns: number of caterpillars killed during the experiment under a certain infectious load. Indicators (in percent) are shown on the left side of the table. Arrows: the minimum and maximum number of deaths during the next track count and cross markers: the average number of deaths during the next track count. Indicators (in absolute values) on the right side of the table. Horizontal: titre, from highest to lowest in Sensitivity of caterpillars of the gypsy moth (Lymantria dispar, Erebidae) from the South of Khabarovsk Territory to various strains of nuclear polyhedrosis virus
Рис. 3. Снижение чисΛенности гусениц при возΑействии разΛичных географических штаммов ВЯП. СтоΛбцы: коΛичество погибших во время эксперимента гусениц поΑ опреΑеΛенной инфекционной нагрузкой. ПоказатеΛи (в процентах) привеΑены в Λевой части табΛицы. СтреΛки: минимаΛьное и максимаΛьное коΛичество погибших во время очереΑного учета гусениц и крестообразные маркеры: среΑнее коΛичество погибших во время очереΑного учета гусениц. ПоказатеΛи (в абсоΛютных значениях) в правой части табΛицы. По горизонтаΛи: номер титра, от боΛьшего к меньшему Fig. 3. Decrease in the number of caterpillars under the influence of various geographical strains of NPV. Columns: number of caterpillars killed during the experiment under a certain infectious load. Indicators (in percent) are shown on the left side of the table. Arrows: the minimum and maximum number of deaths during the next track count and cross markers: the average number of deaths during the next track count. Indicators (in absolute values) on the right side of the table. Horizontal: titre, from highest to lowest
Absolute model ages of three craters in the vicinity of the Chang'E-5 landing site and their geologic implications
<p>We used the Crater Size Frequency distribution (CSFD) method to yield the formation ages of Pythagora, Sharp B, and Harpalus crater, and the crater density values (N(1)). Here we provide the crater counting data.</p>
3D Parameter Maps of Red Clump Stars in the Milky Way -- Absolute Magnitudes and Intrinsic Colors
<p>Catalog, application and supplementary figures for the RC paper.</p> <p>1100mRC_WC2021new.fits.zip -- RC catalog</p> <p>Gaia photometric RC sample with 11 million RCs selected based on {\it Gaia}'s EDR3 parallax, our 3D parameter maps, and extinction--distance profile.</p> <p>ra, dec -- position; dm -- distance modulus; av -- V-band extinction</p> <p>dm1 -- corrected distance modulus; av1 -- corrected extinction. used for low-extinction RCs</p> <p>edm -- uncertainty of distance modulus; flag -- 1: high probability RCs, 0: low probability RCs.</p> <p> </p> <p>RC_calculator_linux.zip -- application RC2021 and installer for linux</p> <p>RC_calculator_mac.zip -- application RC2021 and installer for mac </p> <p>The application to estimate the absolute magnitudes and intrinsic colors for RCs with the APOGEE or LAMOST parameters</p> <p> </p> <p>eps -- the best applicable ranges for using application.</p> <p>pd_APOGEE.eps and pd_LAMOST.eps -- Probability densities of each parameter for absolute magnitude training set (orange) and the whole sample (blue). </p> <p>pd_APOGEE_color.eps and pd_LAMOST_color.eps -- Probability densities of each parameter for intrinsic color training set (orange) and the whole sample (blue). </p>
Text-fig. 7. Stratigraphic ranges of selected, biostratigraphically relevant taxa from Late Pennsylvanian and Early Permian of Saar-Nahe Basin. Based on data from Kerp and Fichter (1985), Lausberg et al. (2003), Schindler et al. (2004), Kerp et al. (2007a, b), Cleal (2008) and Uhl (2008). Absolute age of 300.0 ± 1.2 Ma in middle of Remigiusberg Formation based on Ar-Ar dating of sanidins published by Burger et al. (1997). in New Data On The Macroflora Of The Basal Rotliegend Group (Remigiusberg Formation; Gzhelian) In The Saar-Nahe Basin (Sw-Germany)
Text-fig. 7. Stratigraphic ranges of selected, biostratigraphically relevant taxa from Late Pennsylvanian and Early Permian of Saar-Nahe Basin. Based on data from Kerp and Fichter (1985), Lausberg et al. (2003), Schindler et al. (2004), Kerp et al. (2007a, b), Cleal (2008) and Uhl (2008). Absolute age of 300.0 ± 1.2 Ma in middle of Remigiusberg Formation based on Ar-Ar dating of sanidins published by Burger et al. (1997).
Absolute units in Arabidopsis clock models up to U2020.3
<p>The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant <em>Arabidopsis thaliana.</em> The work is published in Urquiza-Garcia and Millar, <strong>Testing the inferred transcription rates of a dynamic, gene network model in absolute units</strong>, In Silico Plants, 2021.</p> <p>Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (published as U2019.1), rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2, then reoptimises globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model.</p> <p>This project then replaces regulation of the PRRs with repression by later-expressed genes (instead of activation by earlier ones, as in P2011/P2012/U2019) in the U2019.1 model, to create the U2020.1 model, then also rescales to match the RNA levels in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3.</p> <p>The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked inside the archive structure. The DOI for the publication was not yet available but is now: 10.1093/insilicoplants/diab022.</p> <p>This version 3 replaces 10.5281/zenodo.5150823 (version 2), as model files for the earlier KF2014 models were omitted in error from versions 1 and 2. There are no other changes.</p>
Absolute reactive cross sections for the reactions of methanimine radical cation (H2CNH+) and its isomer aminomethylene (HCNH2+) with C2H2
<p>This dataset contains the data in text format (.txt files) of the experimental absolute cross sections (with error) for the various products of the reactions of H<sub>2</sub>CNH<sup>+</sup> and HCNH<sub>2</sub><sup>+</sup> with C<sub>2</sub>H<sub>2</sub>. Absolute cross sections are reported as a function of the collision (<em>E<sub>CM</sub></em>) at fixed photon energies (<em>E<sub>phot</sub></em>) and as a function of the photon energy at fixed collision energies. </p> <p>The data are published (as Fig. 2-5) in the following original research paper:</p> <p>Title: <em>Experimental and computational studies on the reactivity of methanimine radical cation (H<sub>2</sub>CNH<sup>+.</sup>) and its isomer aminomethylene (HCNH2<sup>+.</sup>) with C<sub>2</sub>H<sub>2</sub></em></p> <p>Journal: <strong>Frontiers in Astronomy and Space Science - Astrochemistry</strong></p> <p>Research Topic: <a href="http://www.frontiersin.org/Journal/SpecialTopicDetail.aspx?s=79&name=Astrochemistry&st=14997&sname=Exploring_the_Chemical_Universe">Exploring the Chemical Universe</a></p> <p>Editors: Piero Ugliengo, Luca Bizzocchi, Ankan Das</p>
Supporting material of "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints"
<p>Supporting material of the paper "A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints".</p> <p>The directory is fully documented with README files.</p> <p>Differences of V2.0 with V1.0:</p> <ul> <li>Due to a software bug we had to re-parametrize the ligands whose torsions were parametized with ANI-2.X (ligand 6 and 7).</li> <li>During the peer reviewing process we also parametrized with ANI-2.X and docked ligand 8.</li> </ul>
Validation run C3S SM COMBINED v202212 vs v202012 vs ISMN FRMs (absolute) 5-10 cm
QA4SM validation: C3S SM combined v202212 vs C3S SM combined v202012 vs ISMN 20230110 global. URL: https://qa4sm.eu/ui/validation-result/6a33bb0a-7744-4950-8478-d55b234d4b29. Produced on QA4SM (https://qa4sm.eu)
Validation run C3S SM COMBINED v202212 vs v202012 vs ISMN FRMs (absolute) 0-5 cm
QA4SM validation: C3S SM combined v202212 vs C3S SM combined v202012 vs ISMN 20230110 global. URL: https://qa4sm.eu/ui/validation-result/44c5ab62-c46e-4ebb-b99d-0bbf33e8b17f. Produced on QA4SM (https://qa4sm.eu)
"The sound comes from a meadow in the Sierra Nevada Mountains in California. The meadow is at an elevation of 2400 meters near a mountain named Olancha Peak, which is 3700 meters in altitude. Ihave a group of friends with which Ibackpack (trek) into the mountains. Our goal was to spend some time in the mountains and hike to the top of Olancha Peak (…) By the time we reached the meadow, we were in a forest and there was still snow on the ground in some places. We took the trip in June of 2006. The Sierra Nevada Mountains are a large mountain range. Much of the range is protected by national parks or preserved areas we call 'wilderness areas' (…) Ihave been backpacking for nearly 40 years and Iwill hopefully continue with this challenging activity for 40 years more! Many of my friends are much younger than Iam and it gives me much satisfaction to be able to have as much or more stamina for this activity than they have! When we are on these trips, we hike up peaks, catch fish, drink some whiskey around campfires and enjoy our time in the beautiful solitude. My memories of this trip were of the steep, hot hike from the desert to the cool meadow; the overall beauty of the nature, the absolute solitude of our campsite near the meadow; the strenuous hike to the top of Olancha Peak; the camaraderie of my friends; and, of course the sound of the frogs in the meadow. The frog sounds were astounding to me and Iwould listen in awe of the creature's instinctual desire to reproduce and continue the existence of their kind. Surely there were different species in the meadow for some of the frog sounds were different than others. The sounds only occurred after the Sun went down for the evening. Istood next to the creek in the meadow and recorded the sounds using my digital camera." [Peter/plentz1960]16 in Collecting Sounds. Online Sharing of Field Recordings as Cultural Practice
"The sound comes from a meadow in the Sierra Nevada Mountains in California. The meadow is at an elevation of 2400 meters near a mountain named Olancha Peak, which is 3700 meters in altitude. Ihave a group of friends with which Ibackpack (trek) into the mountains. Our goal was to spend some time in the mountains and hike to the top of Olancha Peak (…) By the time we reached the meadow, we were in a forest and there was still snow on the ground in some places. We took the trip in June of 2006. The Sierra Nevada Mountains are a large mountain range. Much of the range is protected by national parks or preserved areas we call 'wilderness areas' (…) Ihave been backpacking for nearly 40 years and Iwill hopefully continue with this challenging activity for 40 years more! Many of my friends are much younger than Iam and it gives me much satisfaction to be able to have as much or more stamina for this activity than they have! When we are on these trips, we hike up peaks, catch fish, drink some whiskey around campfires and enjoy our time in the beautiful solitude. My memories of this trip were of the steep, hot hike from the desert to the cool meadow; the overall beauty of the nature, the absolute solitude of our campsite near the meadow; the strenuous hike to the top of Olancha Peak; the camaraderie of my friends; and, of course the sound of the frogs in the meadow. The frog sounds were astounding to me and Iwould listen in awe of the creature's instinctual desire to reproduce and continue the existence of their kind. Surely there were different species in the meadow for some of the frog sounds were different than others. The sounds only occurred after the Sun went down for the evening. Istood next to the creek in the meadow and recorded the sounds using my digital camera." [Peter/plentz1960]16
Absolute and arbitrary orientation of single molecule shapes
<p>All software for the kinetic, thermodynamic, and EM simulations associated with the journal paper are presented here. Additionally the AFM images and codes for analyzing the orientation of right triangles as well as e-beam and DNA origami design files associated with the paper is included.</p>
Absolutely Whacked Dog
My first dog! and it's a hillarious disaster so of course I'm publishing it. Source: Objaverse 1.0 / Sketchfab
Wild bumblebees use both absolute and relative evaluation when foraging
<p>Foraging theory assumes that animals assess value based on objective payoffs, however, animals often evaluate rewards comparatively, forming expectations based on recent experience. This form of evaluation may be particularly relevant for nectar foragers such as bumblebees, where individuals can visit thousands of flowers daily that vary in nectar quality. While many animals, including bees, demonstrate reference-based evaluation in experimental contexts, it is unclear whether this occurs in the wild. Here we asked how daily experience with wildflower nectar influenced wild bumblebees' reward evaluation.<strong> </strong>We measured the daily nectar concentration of bee-visited wildflowers (<em>Penstemon </em>spp<em>.</em>), before presenting foragers with conspecific flowers filled with a range of artificial nectar concentrations. We recorded bees' acceptance of artificial nectar, probability of subsequent visits to flowers on the same plant, and residence time. While bees had a minimum threshold of nectar acceptability that was unaffected by experience, when there was higher-concentration environmental nectar, they were less likely to accept lower-quality rewards on manipulated plants. Bees also visited more flowers and stayed longer on plants with higher-concentration nectar. This study shows evidence for both absolute and reference-based evaluation in wild bees and points towards differences between bees' behavior in lab- and wild-foraging contexts.</p>
The Absolute Age of NGC3021
<p>Differential reddening corrected HST ACS photometry, MC Parameters and MC isochrones used to estimate the absolute age of NGC3201.</p> <p>The columns in the NGC3201_fitstars_DRCR.dat file are:<br>x = star x position on the master frame<br>y = star y position on the master frame<br>v = F606W VEGA mag<br>i = F814W VEGA mag<br>vi = V-I VEGAmag</p> <p>Detailed instruction to read MC parameters and MC isochrones can be found in the notebook: Instruction on reading NGC3201 isochrones.ipynb</p>
ScienceDex guides
Understand access before you commit
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.