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4,725 results for “Normalization”
Histological image tiles for TCGA-CRC-DX, color-normalized, sorted by MSI status, train/test split
<p>These are histological images of colorectal cancer, derived from the TCGA database at https://portal.cdc.cancer.gov. Tumor tissue was outlined manually and the tumor region was cut into tiles of 256 µm edge length, saved as 512 px images (effective magnification 0.5 µm/px). All image tiles were color-normalized with the Macenko method. Patients were split into training and test set in a 2:1 ratio. For all patients, MSI status was acquired (patients with MSI-H = MSIH; patients with MSI-L and MSS = NonMSIH) and all tiles inherited the label of the parent patient. Then, tiles in the training set were randomly undersampled to equalize classes. The test set was not undersampled. Further info: www.kather.ai</p>
Pancreas Normalized and HVG selected dataset
<p>Normalized 5 pancreatic datasets</p>
The limits of normal approximation for adult height - old version
<p>Supplementary tables from the article "The limits of normal approximation for adult height".</p>
Sequencing data and normalized counts for tripartite RNAseq of Drosophila, Wolbachia, and SINV virus
<p><span><i>Wolbachia</i> is a maternally transmitted bacterium that manipulates arthropod and nematode biology in myriad ways. The <i>Wolbachia</i> strain colonizing <i>Drosophila melanogaster</i> creates sperm-egg incompatibilities and protects its host against RNA viruses, making it a promising tool for vector control. Despite successful trials using <i>Wolbachia</i>-transfected mosquitoes for Dengue control, knowledge of how <i>Wolbachia</i> and viruses jointly affect insect biology remains limited. Using the <i>Drosophila melanogaster </i>model, transcriptomics and gene expression network analyses revealed pathways with altered expression and splicing due to <i>Wolbachia</i> colonization and virus infection. Included are metabolic pathways previously unknown to be important for <i>Wolbachia</i>-host interactions. Additionally, <i>Wolbachia</i>-colonized flies exhibit a dampened transcriptomic response to virus infection, consistent with early blocking of virus replication. Finally, using <i>Drosophila</i> genetics, we show <i>Wolbachia</i> and expression of nucleotide metabolism genes have interactive effects on virus replication. Understanding the mechanisms of pathogen blocking will contribute to the effective development of <i>Wolbachia</i>-mediated vector control programs.</span></p>
New Cladosporium species from normal and galled flowers of Lamiaceae
<p>Alignments and philogenetic trees underlying the figures presented in : "<strong>New <em>Cladosporium</em> species from normal and galled flowers of Lamiaceae"</strong></p>
The Altotiberina Low-angle normal fault and Gubbio fault in seismic cluster of 2014-2015 period.
<p>Seismology data fron INGV and ISC catalogue.</p>
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.
Western Normal - Mobile GameReady
all in 1 atlas , give a like if it's usefull to you ;) Source: Objaverse 1.0 / Sketchfab
#001 - Daytime - Normal
<p>Zoom - H4 - Stereo - 96 kHz - 24-bit - Low Gain - Hive Top</p>
#001 - Daytime - Normal
<p>Zoom H4 - Stereo - 96 kHz - 24-bit - High Gain - Top of Hive</p>
#001 - Daytime - Normal
<p>Normal daytime hive activity.</p> <p>96 kHz</p> <p>24-bit</p> <p>Low Gain</p> <p>Hive Top</p>
Base de datos: lesiones y variaciones de la anatomía normal de la mucosa oral en niños y adolescentes. Revisión sistemática de la literatura
<p>Base de datos pública que contiene información a partir de una revisión sistemática de la literatura. El objetivo de esta revisión es determinar la frecuencia o prevalencia de las principales lesiones de la mucosa oral en niños y adolescentes alrededor del mundo. Adicionalmente se agregaron los principales diagnósticos obtenidos entre el año 2001-2014 en la Universidad de Talca (UTALCA), Región del Maule, Chile.</p>
FIGURE 9. A mated pair showing the normal H in A review of the Caribbean hamlets (Serranidae, Hypoplectrus) with description of two new species
FIGURE 9. A mated pair showing the normal H. unicolor spot pattern on the caudal peduncle (lower right) and an individual with the double spot (upper). This was a mating pair, Discovery Bay, Jamaica.
and metatarsal trichobothria as well as the bristles and the tibial and metatarsal bristleshaped hairs are drawn but no normal hairs; 6) retrolateral aspect of the left retroclaw IV; 7) genital area in front of the epigastral furrow in which no epiandrous gland spigots are recognizable. Not all of the hairs anteriorly of the pit are drawn; 8) outline of the anterior spinnerets, ventral aspect; 9) retrolateral aspect of the right pedipalpus; 10) prolateral aspect of the right pedipalpus. Only two of the long retrolateral bristle-shaped cymbial hairs are drawn; 11) ventral aspect of the right pedipalpus; 12) slightly different retroventral aspects of the distal part of the right pedipalpus. C = conductor, E = embolus, M = median apophysis, O = proventral-distal outgrowth of the pedipalpal tibia. Scale bars 0.5 mm in figs. 1-2 and 5, 0.05 in fig. 4 and 6, 0.1 in fig. 7, 0.2 in the remaining figs; in On European Spiders Of The Nominal Families Liocranidae, Miturgidae And Zoridae (Araneae), With Descriptions Of New Taxa
and metatarsal trichobothria as well as the bristles and the tibial and metatarsal bristleshaped hairs are drawn but no normal hairs; 6) retrolateral aspect of the left retroclaw IV; 7) genital area in front of the epigastral furrow in which no epiandrous gland spigots are recognizable. Not all of the hairs anteriorly of the pit are drawn; 8) outline of the anterior spinnerets, ventral aspect; 9) retrolateral aspect of the right pedipalpus; 10) prolateral aspect of the right pedipalpus. Only two of the long retrolateral bristle-shaped cymbial hairs are drawn; 11) ventral aspect of the right pedipalpus; 12) slightly different retroventral aspects of the distal part of the right pedipalpus. C = conductor, E = embolus, M = median apophysis, O = proventral-distal outgrowth of the pedipalpal tibia. Scale bars 0.5 mm in figs. 1-2 and 5, 0.05 in fig. 4 and 6, 0.1 in fig. 7, 0.2 in the remaining figs;
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>
Phasor Dataset generated at NEST (Scuola Normale Superiore)
<p>The folder contains sub-folders used in the work "Phasor Identifier: A Cloud-based Analysis of Phasor-FLIM Data on Python Notebooks" by M.Bernardi and F.Cardarelli. The data served for specific examples on Phasor-FLIM customary analysis within the framework of the Python Notebook ran in Google Colab, extensively documented and available at: <a href="https://github.com/Mariochem92/PhasorIdentifier">https://github.com/Mariochem92/PhasorIdentifier</a></p><p> </p><p> </p><p><strong>Irinotecan and its metabolite SN-38 in solution at different pH</strong></p><p><strong>File format: </strong>.R64</p><p><strong>FLIM Acquisition:</strong> DFD-FLIM </p><p><strong>Laser repetition frequency:</strong> 80 MHz</p><p><strong>Instrumentation: </strong>Olympus FVMPE-RS with FLIM box system (ISS, Urbana Champaign)</p><p>Can be used to test any functionality in the analysis of evolutions within the phasor plot. Specially designed for pH analysis within the pH range of 2 to 12.<br><strong>Reference: </strong>Bernardi et al., A Cloud-based Analysis of Phasor-FLIM Data on Python Notebooks, 2023</p><p> </p><p><strong>Encapsulated irinotecan in commercial liposomal nanoformulation Onivyde </strong></p><p><strong>File format: </strong>.R64</p><p><strong>FLIM Acquisition:</strong> DFD-FLIM </p><p><strong>Laser repetition frequency:</strong> 80 MHz</p><p><strong>Instrumentation: </strong>Olympus FVMPE-RS with FLIM box system (ISS, Urbana Champaign)</p><p>Can be used to test any functionality in the analysis of the supramolecular organization. </p><p><strong>Reference: </strong>Bernardi et al., Fluorescence Lifetime Nanoscopy of Liposomal Irinotecan Onivyde: From Manufacturing to Intracellular Processing, ACS Appl. Bio Mater., 2023</p><p> </p><p><strong>INS1-E cells upon cytokine treatment</strong></p><p><strong>File format: </strong>.R64</p><p><strong>FLIM Acquisition:</strong> DFD-FLIM </p><p><strong>Laser repetition frequency:</strong> 80 MHz</p><p><strong>Instrumentation: </strong>Olympus FVMPE-RS with FLIM box system (ISS, Urbana Champaign)</p><p>INS1E control and INS1E cytokines, can be used to test any functionality in the analysis of the supramolecular organization. <br><strong>Reference: </strong>Pugliese et al, Unveiling nanoscale optical signatures of cytokine-induced β-cell dysfunction, Sci Rep, 2023</p><p> </p><p><strong>Encapsulated doxorubicin </strong></p><p><strong>File format: </strong>.ref</p><p><strong>FLIM Acquisition:</strong> TD-FLIM </p><p><strong>Laser repetition frequency:</strong> 40 MHz</p><p><strong>Instrumentation: </strong>Leica TCS SP5 confocal microscope</p><p>Can be used to test any functionality in the analysis of the supramolecular organization and signal evolution. Specially designed for storage analysis at temperature 4°C, 25°C and 37°C.<br><strong>Reference: </strong>Carretta et al, Monitoring drug stability by label-free fluorescence lifetime imaging: a case study on liposomal doxorubicin. ,J. Phys. : Conf Ser, 2023</p><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>
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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.
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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.