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5,381 results for “deficiencies”
Maize Phosphorus Leaf Deficiency (MPLD) Database | Compact Scientific Camera (original-processed)
<p>This database presents samples of maize leaves placed on a withe background, representing three levels of phosphorus deficiency: complete absence of the nutrient (labeled -P), half dose of the required phosphorus for normal plant development (-P50), and complete supply (C).</p><p>Its composed of two folders:</p><ul><li>Original_dataset: 722 jpg images of 1280 x 1020 pixels size divided into '_C', '-P' and '-P50' folders for class labels.</li><li>Processed_dataset: 2433 png images of 224 x 224 pixels size divided into '-C', '-P' and '-P50' folders for class labels.</li></ul>
Inter-Chemical Correlation results for the study: HHEARx2016-1432 (Micronutrient deficiencies, environmental exposures and severe malaria: Risk factors for adverse neurodevelopmental outcomes in Ugandan children)
Title: Micronutrient deficiencies, environmental exposures and severe malaria: Risk factors for adverse neurodevelopmental outcomes in Ugandan children <br>Species: Homo sapiens <br>Number of samples: 1256 <br>Number of named analytes: 51 <br>Datasource url: https://hheardatacenter.mssm.edu/PublicFile/ViewPublicFile?projectid=5 <br>
Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231) - Variant Calls
<p>Variant Calls from Phase I trial of CX-5461, a first-in-class G-quadruplex stabilizer in patients with advanced solid tumors enriched for DNA-repair deficiencies (CCTG IND.231)</p> <p>See publication for methodology.</p>
TEM Data on Strontium-deficient SrxCoO2–CoO2 nanotubes
<p>Raw data ((scanning) transmission electron microscopy images, diffraction patterns and EDX/EELS spectra) obtained for work on Strontium-deficient SrxCoO2–CoO2 nanotubes as a high ampacity and high conductivity material published in Materials Horizons</p>
Data from: Collaborative Research: Influence of phosphorus deficiency on enigmatic biological methane production in oxic freshwater lakes
<p>Data from: Collaborative Research: Influence of phosphorus deficiency on enigmatic biological methane production in oxic freshwater lakes</p> <p>NSF Projects 1951002 (PI: Matthew J. Church), 1950963 (PI: John E. Dore)</p>
Supplementary files for manuscript "Effects of alpelisib treatment on murine Pten-deficient lipomas"
<p>Supplementary datasets for figures of the manuscript "Effects of alpelisib treatment on murine Pten-deficient lipomas"</p>
Protection from radiation-induced neuroanatomical deficits by CCL2-deficiency is dependent on sex
<p>This project investigated the impact of Ccl2 genotype status (+/+, +/-, -/-) on the brain structure changes induced by cranial radiation. Mn-enhanced MR images were acquired at P14, P23, P42, P63 and P98. Radiation (7-Gy) was delivered on P16 to the whole head, with a lead shield used to limit dose to the rest of the body. Further details are available in the manuscript.</p> <p>For the image processing, the registration was accomplished using the pydpiper toolkit (version 2.0.9), available on GitHub (https://github.com/Mouse-Imaging-Centre/pydpiper/tree/v2.0.9). A two-level registration was used. Key elements of that registration output are provided in this data posting.</p>
Implication of Folate Deficiency in CYP2U1 loss of function
<p>Hereditary spastic paraplegias are heterogeneous neurodegenerative disorders. Understanding of their pathogenic mechanisms remains sparse and therapeutic options are lacking. We characterized a mouse model lacking the Cyp2u1 gene, loss of which is known to be involved in a complex form of these diseases in Humans. We showed that this model partially recapitulated the clinical and biochemical phenotypes of patients. Using electron microscopy, lipidomic, and proteomic studies, we identified vitamin B2 as a substrate of the CYP2U1 enzyme, as well as coenzyme Q, neopterin, and interferon-alpha levels as putative biomarkers in mouse and in fluids obtained from the largest series of CYP2U1- mutated patients reported so far. We also confirmed brain calcifications as a potential biomarker in patients. Our results suggest that CYP2U1 deficiency disrupts mitochondrial function and impacts proper neurodevelopment, which could be prevented by folate supplementation in our mouse model, followed by a neurodegenerative process altering multiple neuronal and extra neuronal tissues.</p>
Open data repository, Boehm-Sturm et al., Phenotyping placental oxygenation in Lgals1 deficient mice using 19F MRI
<p>Open data repository of journal article "Phenotyping placental oxygenation in Lgals1 deficient mice using <sup>19</sup>F MRI"</p>
Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency
<p><strong>Project manager(s)</strong><strong>: </strong>Essam M. Abdelalim</p> <p>Induced pluripotent stem cells (iPSCs) were generated from a patient with a heterozygous deletion of the short arm of chromosome 20 at bands p11.22 to p11.21 (~969 kb deletion), which contains only one gene, <em>FOXA2 </em>(<em>FOXA2<sup>+/-</sup></em>iPSCs) as well as healthy controls (Ctr1 iPSCs and Ctr2 iPSCs). <em>FOXA2<sup>+/-</sup></em>iPSCs were differentiated into different stages of beta cell development to understand the role of FOXA2 during pancreatic beta cell development as described in the article entitled "<strong>Aberrant development of pancreatic beta cells derived from human iPSCs with <em>FOXA2</em> deficiency" by Elsayed et al</strong>. The dataset represents RNA-seq data generated from pancreatic progenitors (PP2) and endocrine progenitors (EPs) derived from Ctr1 iPSCs, Ctr2 iPSCs, and three clones of <em>FOXA2<sup>+/-</sup></em>iPSCs. </p> <p>The file name is: Sample name _overall sample number_read direction_001 where:</p> <p>- PP2-Ctr 1: pancreatic progenitors (PP2) derived from Ctr1 iPSCs (healthy control 1)</p> <p>- PP2-Ctr 2: pancreatic progenitors (PP2) derived from Ctr2 iPSCs (healthy control 2)</p> <p>- PP2-FOX1, PP2-FOX2, and PP2-FOX3: pancreatic progenitors (PP2) derived from three different clones of patient-derived <em>FOXA2<sup>+/-</sup></em>iPSCs.</p> <p>- EP-Ctr1: endocrine progenitors (Eps) derived from Ctr1 iPSCs (healthy control 1)</p> <p>- EP-Ctr2: endocrine progenitors (Eps) derived from Ctr2 iPSCs (healthy control 2)</p> <p>- EP-FOX R1, EP-FOX R2, and EP-FOX R3: endocrine progenitors (EPs) derived from three different clones of patient-derived <em>FOXA2<sup>+/-</sup></em>iPSCs.</p> <p>- The RNA-Seq data were generated from two Ctr-iPSC lines and three FOXA2<sup>+/-</sup>iPSC lines.</p> <p>- Read direction: R1 (Forward), R2 (Reverse).</p>
Maize Phosphorus Leaf Deficiency (MPLD) Database 224x224
<p>Monitoring the nutritional status of crops is crucial to assessing high productivity, optimizing cost, and minimizing environmental impact. Given that nutritional deficiencies primarily manifest through visual characteristics, artificial vision stands out as a competitive choice to assess the nutritional status of individual plants.</p><p>However, in order to train a supervised artificial vision system driven by convolutional neural networks (CNNs), a high amount of data, properly formatted and labeled is necessary. This work presents a curated image database to study single-nutrient deficiencies, specifically, phosphorus deficiency in maize leaves, named Maize Phosphorus Leaf Deficiency (MPLD) Database.</p><p>This database is composed of <strong>20892 </strong>samples of maize leaves placed on a withe background. Images are <strong>224x224</strong> pixels size, representing three levels of phosphorus deficiency: complete absence of the nutrient (labeled -P), half dose of the required phosphorus for normal plant development (-P50), and complete supply (C). </p>
Dataset related to the manuscript entitled "Inhalation with Vitamin D3 Metabolites - A Novel Strategy to Restore Vitamin D3 Deficiencies in Lung Tissue"
<p><strong>The dataset contains the results presented in the manuscript entitled "Inhalation with Vitamin D3 Metabolites - A Novel Strategy to Restore Vitamin D3 Deficiencies in Lung Tissue" Appl. Sci. 2023, 13, 10672. </strong></p><p> </p><p>The presented dataset contains the results of the implementation of the following research project: </p><p><i>Project title</i><strong>:</strong> "Assessment of the possibility of using vitamin D3 in the prevention and treatment of pulmonary fibrosis in the course of hypersensitivity pneumonitis - <i>in vivo</i> studies"</p><p><i>Founder</i><strong>: </strong>National Scientific Center, Poland</p><p><i>Project number</i><strong>:</strong> UMO-2020/38/E/NZ7/00366</p><p><i>Principal Investigator</i>: Marta Kinga Lemieszek</p><p><i>Main investigators:</i><strong> </strong>Michał Chojnacki, Jakub Anisiewicz, Ilona Leśniowska</p><p><i>Place of project implementation</i><strong>:</strong> Department of Medical Biology, Institute of Rural Health, Jaczewskiego 2, 20-090 Lublin, Poland</p>
Dataset related to: Sirt3 deficiency promotes endothelial dysfunction and aggravates renal injury
<p>The .xlsx file contains raw data related to the article "<i><strong>Sirt3</strong></i><strong> deficiency promotes endothelial dysfunction and aggravates renal injury</strong>. <i>PLOS One</i>. 2023 Oct 10;18(10):e0291909<i>", </i>available at the following <a href="https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0291909">link</a>.</p><p> </p><p><strong>Abstract</strong></p><p>Sirtuin 3 (SIRT3), the main deacetylase of mitochondria, modulates the acetylation levels of substrates governing metabolism and oxidative stress. In the kidney, we showed that SIRT3 affects the proper functioning of high energy-demanding cells, such as tubular cells and podocytes. Less is known about the role of SIRT3 in regulating endothelial cell function and its impact on the progression of kidney disease. Here, we found that whole body <i>Sirt3</i>-deficient mice exhibited reduced renal capillary density, reflecting endothelial dysfunction, and VEGFA expression compared to wild-type mice. This was paralleled by activation of hypoxia signaling, upregulation of HIF-1α and Angiopietin-2, and oxidative stress increase. These alterations did not result in kidney disease. However, when <i>Sirt3</i>-deficient mice were exposed to the nephrotoxic stimulus Adriamycin (ADR) they developed aggravated endothelial rarefaction, altered VEGFA signaling, and higher oxidative stress compared to wild-type mice receiving ADR. As a result, ADR-treated <i>Sirt3</i>-deficient mice experienced a more severe injury with exacerbated albuminuria, podocyte loss and fibrotic lesions. These data suggest that SIRT3 is a crucial regulator of renal vascular homeostasis and its dysregulation is a predisposing factor for kidney disease. By extension, our findings indicate SIRT3 as a pharmacologic target in progressive renal disease whose treatments are still imperfect.</p>
Data from: Offspring behavioral outcomes following maternal allergic asthma in the IL-4-deficient mouse
<p>Background: Maternal allergies and asthma during pregnancy have been associated with increased risk of ASD and ADHD to the child. Previous rodent studies have demonstrated that inducing a T helper-2 (Th2)-mediated allergic response during pregnancy leads to an offspring behavioral phenotype characterized by decreased social interaction and increased stereotypies. Interleukin-4 is a key signal in the Th2 immune cascade, but its role in fetal brain development and subsequent impacts of maternal allergic asthma (MAA) on offspring behavioral deficits have yet to be determined.</p> <p>Objective: In this study, we investigated whether the absence of IL-4 signaling would mitigate MAA-induced behavioral changes.</p> <p>Methods: C57BL/6J and Interleukin-4 knockout (IL-4 KO) mice were sensitized to ovalbumin and exposed to repeated allergic asthma aerosol inductions throughout pregnancy. Offspring were assessed on Juvenile Reciprocal Social Interaction, Elevated Plus Maze, Open Field Exploration, Novel Object Recognition, Forced Swim, Marble-burying, and Grooming tasks.</p> <p>Results: MAA during pregnancy resulted in decreased social interactions in male C57 offspring and impaired memory performance in both male and female C57 mice. These deficits were not observed in IL-4 KO mice exposed to MAA. However, we observed genotype effects in IL-4 KO mice including altered motor performance and anxiety-associated responses.</p> <p>Conclusion: MAA-induced social and cognitive behavioral alterations are IL-4 dependent. IL-4KO offspring display genotype-specific differences suggesting IL-4 signaling is important for typical developmental processes.</p>
16S rRNA Sequencing Data of Fecal Microbiota in an Italian Cohort of Patients with CDKL5 Deficiency Disorder
<h3>Summary of the study </h3> <p>CDKL5 deficiency disorder (CDD) is a neurodevelopmental condition characterized by global developmental delay, early-onset seizures, intellectual disability, visual and motor impairments, distinct from Rett Syndrome (RTT) due to the absence of a clear regression period. Gastrointestinal (GI) disturbances and signs of subclinical immune dysregulation are common in CDD patients, yet the underlying causes are unknown. Recent studies hint at a possible link between neurological disorders and gut microbiota, an unexplored area in CDD. In this groundbreaking study, we examined fecal microbiota in CDD patients and their healthy relatives, revealing differences in bacterial diversity and composition. We further investigated microbiota changes based on various factors, including the severity of GI issues, seizure frequency, sleep disorders, food intake type, neuro-behavioral features (assessed through the RTT Behaviour Questionnaire – RSBQ), and ambulation capacity. </p> <p>Our findings suggest a potential connection between CDD, microbiota, and symptom severity. This study represents the first exploration of the gut-microbiota-brain axis in CDD patients, contributing to the growing body of research on the role of gut microbiota in neurodevelopmental disorders. It opens doors to potential interventions targeting intestinal microbes to enhance the well-being of individuals with CDD.</p> <h3>Mehods</h3> <p>The Dataset represent the raw data (.fastq) obtained from the sequencing of the fecal samples from 17 Italian Patients with CDD, and 17 Healthy Relatives (i.e. siblings or mother), collected at a single time-point.</p> <p>Samples from Patients affected by CDD are called CDD, samples from Healthy Relatives are called HC-CDD (i.e. healthy controls of patients affected by CDD). For details about the sample names see the “Explanation Table”.</p> <p>Bacterial DNA was extracted from fecal samples using the QIAmp Powerfexal DNA Kit (Qiagen, Germany) following the manufacturer's protocol. The 16S rRNA sequencing and analysis was performed by a service offered by Zymo Research (Germany).</p> <p><em>Targeted Library Preparation</em>: The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research). The primer sets used were Quick-16S™ Primer Set V3-V4 (Zymo Research). The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™, then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA). </p> <p><em>Sequencing:</em> The final library was sequenced on Illumina® MiSeq™ with a v3 reagent kit (600 cycles). </p>
Dataset from Experimental and Nonlinear Finite Element Modeling Investigating an Innovative Buckling Restrained Bracing System for Rehabilitation of Seismic Deficient Structures
<p>The data presented in this paper were collected experimentally and modeled using the finite element method. A total of six BRBs (i.e., duplicates of three types of BRB core bars) specimens were tested experimentally and verified numerically using the finite element method employing the commercial Software ABAQUS. Specific labeling was used to designate each BRB type. Three core bars were used in the tested BRBs: fully-threaded, threaded-notched, and smooth-shaved. The specimens are labeled according to their core bar type and diameter. i.e., BRB-12-Th stands for a full threaded core bar diameter of 12 mm, the threaded notched type was labeled BRB-12-Th-Nd, and the smooth shave one was labeled BRB-12-Sh.</p> <p>Further details of the tested BRBs are included in the excel file called dimensions and properties of BRBs. The worksheet provides details of the BRB components (i.e., core bar, restraining unit, and innovative end units). The dimensions and strength of the materials were obtained from coupon tests. The experimental data are presented in the second excel file labeled hysteresis with three embedded worksheets, one for each type of BRB. The excel sheets provide the cyclic loading data and plots showing the hysteresis behavior of tested BRBs. A sample of the loading protocol included in the second excel file is presented in Fig.1. The third excel file presents the analytical data extracted from experimental data that has two sheets: stiffness and energy dissipation. The sheet labeled stiffness has the secant stiffness versus deformation plot for the push-pull cycles (compression-tension). The second sheet labeled energy dissipation shows the cumulative energy dissipated.</p>
Vitamin D deficiency and SARS‑CoV‑2 infection: D-COVID study
<p>D-COVID is a proyect to study the association between COVID-19 infection and vitamin D deficiency in patients of a terciary university hospital. To investigate the clinical evolution and prognosis of patients with COVID-19 and vitamin D deficiency, several queries qere launched into a Database containing plain text apparitions of certain terms in medical reports, as well as structured data. These apparitions were detected using NLP technology, and then saved individually in a database. The presented dataset is a bounded version of such database, containing only relevant data to the one extracted for the associated study. As for the strcture of the dataset, each row represents an apparition of a term in plain text, and the columns contain additional information.</p> <p><strong>- reportdate</strong>: date of the report where the term appears up.</p> <p><strong>- admission_days:</strong> strctured data days in hospitalization, if any.</p> <p><strong>- patient_id</strong>: anonymized patient identifier</p> <p><strong>- sex</strong>: patient sex (1=male, 2=female)</p> <p><strong>-birthdate</strong>: patient birthdate</p> <p><strong>- service</strong>: Service where the report was generated</p> <p><strong>- report_type:</strong> Type of report generated (either a discharge report, note, etc)</p> <p><strong>- record</strong>: unique identifier for the report itself</p> <p><strong>- term</strong>: term (that was read (NLP takes synonims and acronyms into account)</p> <p><strong>- exitus</strong>: medical exitus, if available in structured data, it could also be found in plan text in the previous column.</p>
Assessing and Addressing Deficiencies in the HCM Weaving Segment Analyses- Phase II- Project J5
<p>Traffic operation and geometric data from Ramp and Major weaves. These data were used to develop the speed and capacity models under the STRIDE J3 project.</p>
The 48Ca+181Ta reaction: Cross section studies and investigation of neutron-deficient 86≤Z≤93 isotopes
<p>Example for RDM developments:</p> <p>Small result datasets given. Under development metadata schema provided</p> <p>This example dataset describes alpha-decaying chains from an experiment performed at the SHE Physics group at GSI Helmholtzzentrum fuer Schwerionenforschung GmbH. The reaction 48Ca+181Ta was used to produce neutron deficient isotopes of Np, Pa and U. The 48Ca beam was delivered by the UNILAC at a variety of selected energies with 5Hz repitition rate and 5ms pulse width. The evaporation residues were implanted into the focal plane detection system, COMPASS, where their alpha-decay signatures were measured.Further details are given in the linked publication.</p> <p>The data format is in comma-separated values format. Columns are as Energy(keV), Counts per energy bin, decay time (seconds) and counts per decay time bin. The decaying nucleus is given for each chain.</p>
Adenosine deficiency facilitates CA1 synaptic hyperexcitability in the presymptomatic phase of a mouse KI model of Alzheimer disease.
<p><span>All data points, statistical models and raw western blot images from "Adenosine deficiency facilitates CA1 synaptic hyperexcitability in the presymptomatic phase of a mouse KI model of Alzheimer disease" are available. </span></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.