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540 results for “Data Normalization”
Data from: Oncogene inference optimization using constraint-based modelling incorporated with protein expression in normal and tumour tissues
Cancer cells are known to exhibit unusual metabolic activity and yet, few metabolic cancer driver genes are known. Genetic alterations and epigenetic modi cations of cancer cells result in the abnormal regulation of cellular metabolic pathways that are different when compared to normal cells. Such a metabolic reprogramming can be simulated using constraint-based modelling approaches towards predicting oncogenes. We introduced the tri-level optimization problem to use the metabolic reprogramming towards inferring oncogenes. The algorithm incorporated Recon 2.2 network with the Human Protein Atlas to reconstruct genome-scale metabolic network models of the tissue-speci fic cells at normal and cancer states, respectively. Such reconstructed models were applied to build the templates of the metabolic reprogramming between normal and cancer cell metabolism. The inference optimization problem was formulated to use the templates as a measure towards predicting oncogenes. The nested hybrid differential evolution algorithm was applied to solve the problem to overcome solving difficulty for transferring the inner optimization problem into the single one. Head and neck squamous cells were applied as a case study to evaluate the algorithm. We detected 13 of the top ranked one-hit dysregulations and 17 of the top ranked two-hit oncogenes with high similarity ratios to the templates. According literature survey, most inferred oncogenes are consistent with the observation in various tissues. Furthermore, the inferred oncogenes were highly connected with the TP53/AKT/IGF/MTOR signalling pathway through PTEN, which is one of the most frequently detected tumour suppressor genes in human cancer.
Data from: The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment in order to refine our understanding of adaptive divergence between dwarf and normal lake whitefish species (Coregonus clupeaformis spp.). The objectives were to: (1) investigate transcriptomic divergence as measured by liver RNA-Seq; (2) test the correlation between divergence in expression and sequence polymorphism and (3) investigate the extent of allelic imbalance. We also compared the results of RNA-seq with those of a previous microarray study performed on the same fish. Following de novo assembly, results showed that normal whitefish over-expressed more contigs associated with protein synthesis while dwarf fish over-expressed more contigs related to energy metabolism, immunity and DNA replication and repair. Moreover, 63 SNPs showed significant allelic imbalance, and this phenomenon prevailed in the recently diverged dwarf whitefish. Results also showed an absence of correlation between gene expression divergence as measured by RNA-Seq and either polymorphism rate or sequence divergence between normal and dwarf whitefish. This study reiterates an important role for gene expression divergence, and provides evidence for allele-specific expression divergence as well as evolutionary decoupling of regulatory and coding sequences in the adaptive divergence of normal and dwarf whitefish. It also demonstrates how next-generation sequencing can lead to a more comprehensive understanding of transcriptomic divergence in a young species pair.
Data from: Sex-dependent differences in central artery hemodynamics in normal and fibulin-5 deficient mice: implications for ageing
Mouse models provide unique opportunities to study vascular disease, but they demand increased experimental and computational resolution. We describe a workflow for combining in vivo and in vitro biomechanical data to build mouse-specific computational models of the central vasculature including regional variations in biaxial wall stiffness, thickness and perivascular support. These fluid–solid interaction models are informed by micro-computed tomography imaging and in vivo ultrasound and pressure measurements, and include mouse-specific inflow and outflow boundary conditions. Hence, the model can capture three-dimensional unsteady flows and pulse wave characteristics. The utility of this experimental–computational approach is illustrated by comparing central artery biomechanics in adult wild-type and fibulin-5 deficient mice, a model of early vascular ageing. Findings are also examined as a function of sex. Computational results compare well with measurements and data available in the literature and suggest that pulse wave velocity, a spatially integrated measure of arterial stiffness, does not reflect well the presence of regional differences in stiffening, particularly those manifested in male versus female mice. Modelling results are also useful for comparing quantities that are difficult to measure or infer experimentally, including local pulse pressures at the renal arteries and characteristics of the peripheral vascular bed that may differ with disease.
Data from: The utility of normalized difference vegetation index for predicting African buffalo forage quality
Many studies of mammalian herbivores have employed remotely sensed vegetation greenness, in the form of Normalized Difference Vegetation Index (NDVI) as a proxy for forage quality. The assumption that reflected greenness represents forage quality often goes untested, and limited data exist on the relationships between remotely sensed and traditional forage nutrient indicators. We provide the first study connecting NDVI and forage nutrient indicators within a free-ranging African herbivore ecosystem. We examined the relationships between fecal nutrient levels (nitrogen and phosphorus), forage nutrient levels, body condition, and NDVI for African buffalo (Syncerus caffer) in a South African savanna ecosystem over a 2-year period (2001 and 2002). We used an information-theoretic approach to rank models of fecal nitrogen (Nf) and phosphorus (Pf) as functions of geology, season, and NDVI in each year separately. For each year, the highest ranked models for Nf accounted for 61% and 65% of the observed variance, and these models included geology, season, and NDVI. The top-ranked model for Pf in 2001, although capturing 54% of the variability, did not include NDVI. In 2002, we could not identify a top ranking model for phosphorus (i.e., all models were within 2 AICc of each other). Body condition was most highly correlated (equation image; P ≤ 0.001) with NDVI at a 1 month time lag and with Nf at a 3 months time lag (equation image; P ≤ 0.001), but was not significantly correlated with Pf. Our findings suggest that NDVI can be used to index nitrogen content of forage and is correlated with improved body condition in African buffalo. Thus, NDVI provides a useful means to assess forage quality where crude protein is a limiting resource. We found that NDVI accounted for more than a seasonal effect, and in a system where standing biomass may be high but of low quality, understanding available nutrients is useful for management.
Data related to "Modeling the Diverse Effects of Divisive Normalization on Noise Correlations"
<p>Data files for the paper, Modeling the Diverse Effects of Divisive Normalization on Noise Correlations, available on <a href="https://www.biorxiv.org/content/10.1101/2022.06.08.495145v3.abstract">bioRxiv</a></p><p> </p><p>For the corresponding code toolbox, please see the <a href="https://github.com/oren-weiss/pairwiseRatioGaussians">Github repository</a></p><p> </p><p>Please cite as:</p><blockquote><p>Modeling the Diverse Effects of Divisive Normalization on Noise Correlations</p><p>Oren Weiss, Hayley A. Bounds, Hillel Adesnik, Ruben Coen-Cagli</p><p>bioRxiv 2022.06.08.495145; doi: https://doi.org/10.1101/2022.06.08.495145</p></blockquote><p> </p><p> </p>
Dataset for Active shortening simultaneous to normal faulting based on GNSS, geophysical and geological data: The seismogenic Ventas de Zafarraya Fault (Betic Cordillera). Tectonics
<p>Dataset for "Active shortening simultaneous to normal faulting based on GNSS, geophysical and geological data: The seismogenic Ventas de Zafarraya Fault (Betic Cordillera)" Tectonics<br><br>File "hypoDD_10_300.reloc.txt" compile all the relocated seismicity in the study area.<br>Files "810_.NEU, 811_.NEU, 812_.NEU, 813_.NEU, 814_.NEU, 815_.NEU, and 816_.NEU" presents the time series data of GNSS sites of the Zafarraya network.</p>
Data for Kinetic isotope effects during reduction of Fe(III) to Fe(II): Large normal and inverse isotope effects for abiotic reduction and smaller fractionations by phytoplankton in culture
<p>Supplemental data for the manuscript "Kinetic isotope effects during reduction of Fe(III) to Fe(II): Large normal and inverse isotope effects for abiotic reduction and smaller fractionations by phytoplankton in culture."</p>
Raw data for: Coherent supercontinuum generation in all-normal dispersion Si3N4 waveguides
<p>This document includes the raw data and Matlab/Python scripts to post-process data and plot the figures included in the paper "Coherent supercontinuum generation in all-normal dispersion Si3N4 waveguides".</p>
Remaining bands of Back scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America
<p><strong>Title: Remaining bands of Back scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America</strong></p> <p>Ricardo Dalagnol (ricds@hotmail.com)</p> <p> </p> <p><strong>This dataset is associated with the dataset found in the Zenodo repository below and a paper under review. Feel free to use this dataset, but please cite the repository below (while the paper is under review).</strong></p> <p>Dalagnol, Ricardo; Galvão, Lênio Soares; Wagner, Fabien Hubert; Moura, Yhasmin Mendes; Gonçalves, Nathan; Wang, Yujie; Lyapustin, Alexei; Yang, Yan; Saatchi, Sassan; Aragão, Luiz Eduardo Oliveira e Cruz. (2022). "AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America". (Version v1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3878879</p>
Back scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America
<p><strong>Title: Back scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America</strong></p> <p>Ricardo Dalagnol (ricds@hotmail.com)</p> <p> </p> <p><strong>This dataset is associated with the dataset found in the Zenodo repository below and a paper under review. Feel free to use this dataset, but please cite the repository below (while the paper is under review).</strong></p> <p>Dalagnol, Ricardo; Galvão, Lênio Soares; Wagner, Fabien Hubert; Moura, Yhasmin Mendes; Gonçalves, Nathan; Wang, Yujie; Lyapustin, Alexei; Yang, Yan; Saatchi, Sassan; Aragão, Luiz Eduardo Oliveira e Cruz. (2022). "AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America". (Version v1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3878879</p>
Remaining bands of Forward scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America
<p><strong>Title: Remaining bands of Forward scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America</strong></p> <p>Ricardo Dalagnol (ricds@hotmail.com)</p> <p> </p> <p><strong>This dataset is associated with the dataset found in the Zenodo repository below and a paper under review. Feel free to use this dataset, but please cite the repository below (while the paper is under review).</strong></p> <p>Dalagnol, Ricardo; Galvão, Lênio Soares; Wagner, Fabien Hubert; Moura, Yhasmin Mendes; Gonçalves, Nathan; Wang, Yujie; Lyapustin, Alexei; Yang, Yan; Saatchi, Sassan; Aragão, Luiz Eduardo Oliveira e Cruz. (2022). "AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America". (Version v1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3878879</p>
Forward scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America
<p><strong>Title: Forward scattering data of AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America</strong></p> <p>Ricardo Dalagnol (ricds@hotmail.com)</p> <p> </p> <p><strong>This dataset is associated with the dataset found in the Zenodo repository below and a paper under review. Feel free to use this dataset, but please cite the repository below (while the paper is under review).</strong></p> <p>Dalagnol, Ricardo; Galvão, Lênio Soares; Wagner, Fabien Hubert; Moura, Yhasmin Mendes; Gonçalves, Nathan; Wang, Yujie; Lyapustin, Alexei; Yang, Yan; Saatchi, Sassan; Aragão, Luiz Eduardo Oliveira e Cruz. (2022). "AnisoVeg: Anisotropy and Nadir-normalized MODIS MAIAC datasets for satellite vegetation studies in South America". (Version v1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3878879</p>
Figures data for "Investigation of Kinetic Ballooning Instability in 2D Harris Sheet Equilibrium with Finite Normal $B_z$ Field"
<p>To make it simpler for readers to understand and reproduce the work, the data for all the figures in the article titled "Investigation of Kinetic Ballooning Instability in 2D Harris Sheet Equilibrium with Finite Normal $B z$ Field" are being uploaded.</p>
Data and analysis for: Differential effects of ankle constraints on foot placement control between normal and split belt treadmills
<p>Here we compared the effect of ankle moment constraints (LesSchuh; a shoe with a narrow ridge along the length of the shoe's sole), on a single and a split-belt treadmill. To this end we considered the foot placement model as proposed by Wang and Srinivasan (2014), and used the R^2 of this model as an outcome measure. In addition, step width, stride frequency and toe-out angles have been computed. The results have been written up in our publication in the journal of biomechanics.<br> <br> Wang, Y., & Srinivasan, M. (2014). Stepping in the direction of the fall: the next foot placement can be predicted from current upper body state in steady-state walking. <em>Biology letters</em>, <em>10</em>(9), 20140405.</p>
Processed data - DegNorm: Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
<p>Processed data from DegNorm:</p> <ul> <li>"_raw.txt": raw read counts matrix;</li> <li>"_DI.txt": Degradation index score matrix;</li> <li>"_DegNorm.txt": normalized read counts matrix from DegNorm output;</li> <li>"_coverage.Rdata": list of coverage matrix for the sample;</li> <li>"_countsTIN.txt": TIN normalized counts.</li> </ul> <p> </p>
Data for "Earthquake nucleation and slip behavior altered by stochastic normal stress heterogeneity"
Open the record for dataset details and reuse information.
Research data supporting: "Extended sampling of macromolecular conformations from uniformly distributed points on multidimensional normal mode hyperspheres"
<p>This repository contains protein structures generated by the approach "distributed points Molecular Dynamics using Normal Modes" (dpMDNM). dpMDNM is an enhanced-sampling approach that allows large protein conformational sampling based on normal mode (NM) vector combinations.</p> <p>Input parameter and equilibrated files for Lysozyme and CYP3A4 are provided, including their respective ensemble of structures after conformational exploration combining from 2 to 8 NMs.</p> <p>For more information, please visit the <a href="https://github.com/antonielgomes/dpMDNM">dpMDNM GitHub repository</a>.</p>
Data used for the Master Thesis "Multi Modal Generative Learning utilizing Normalizing Flows"
<p>Dataset needed to reproduce the Master Thesis "Multi Modal Generative Learning utilizing Normalizing Flows".</p> <p>It contains trained models and their evaluation results.</p> <p>For more details see the <a href="https://github.com/Jimmy2027/MMNF_RepSeP">github repository</a>.</p>
Raw data of visual search parameters of individuals with normal trichromacy and colour vision deficiency
<p><strong><span>Background</span></strong><span>: Colour-related search tasks are common in many professional fields. The study investigated whether increasing chromatic saturation can enhance the visual performance of individuals with colour vision deficiency (CVD) in colour-related search tasks.</span></p> <p><strong><span>Methods</span></strong><span>: 10 normal trichromats (5M, 5F; Mean (SD) age: 23.1 (3.3) years) and 15 individuals with CVD [8 deutans and 7 protans identified by HRR plates] (14M, 1F; aged 28.6 (8.7) years) participated in this study. Four naturalistic sceneries of everyday tasks/ birds, animals, and flowers of 15 different colour combinations (1 pair of colours in each combination. e.g., 'brown/black' or 'red/green') were presented in 'low' saturation, 'original' (unaltered images) and 'high' saturation condition using the Psychopy program on a colour-calibrated monitor. On each trial, the subject was asked to identify a specific-coloured target. </span></p> <p><span><strong>Results</strong>: </span><span>Overall, the visual search performance index (expressed as product of accuracy and a reciprocal of reaction time (%correct*s<sup>-1</sup>) of the normal trichromats [Mean (SD):77.76% correct*s<sup>-1</sup> (16.32)] was significantly higher than CVD [45.71 % correct*s<sup>-1</sup> (18.95)] in the "original" test images (p = 0.001), but in individuals with CVD, there was no significant difference between 'original' [45.71 % correct*s<sup>-1</sup> (18.95)] and 'high' saturation condition ([47.43 % correct*s<sup>-1</sup> (20.07)]; p > 0.05). However, colour-wise, increased saturation showed improvements (≥ 10 %) in protans mainly for 'red' combinations with other colours such as white (i.e., 'red/white'), purple, orange, grey, green, brown, and black.</span></p> <p><strong><span>Conclusion</span></strong><span>:</span><span> The study suggests that increasing the saturation of certain colour combinations can potentially aid in the visual search performance of individuals with CVD. This knowledge will help in better counselling and management of the patients.</span></p>
Data Collection for the Assessment of Acute and Late Normal Tissue in Patients Treated With Proton Therapy
ClinicalTrials.gov study NCT00991094. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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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.