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10,735 results for “dependability”
Influence of CPM-dependent sorting on the multi-omics profile of hepatocyte-like cells matured in microscale biochips.
GEO Series GSE179713. Homo sapiens. 13 samples. Type: Expression profiling by high throughput sequencing.
Enhancement of ubiquitination-dependent mitophagy by unconventionally-acting PROTACs
GEO Series GSE255354. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Effects on transcriptional regulation and lipid droplet characteristics in the liver of female juvenile pigs after early postnatal feed restriction and refeeding are dependent on birth weight
GEO Series GSE43826. Sus scrofa. 30 samples. Type: Expression profiling by array.
Dihydrocoumarin, an extract of Melilotus officinalis, inhibits IgE-dependent mast cell activation in vitro and in vivo
GEO Series GSE189876. Rattus norvegicus. 6 samples. Type: Expression profiling by high throughput sequencing.
Dataset related to article "mTOR-Dependent Stimulation of IL20RA Orchestrates Immune Cell Trafficking through Lymphatic Endothelium in Patients with Crohn's Disease."
<p>Crohn's disease (CD) is a chronic inflammatory condition that can affect different portions of the gastrointestinal tract. Lymphatic drainage was demonstrated to be dysfunctional in CD pathogenesis, ultimately causing the failure of the resolution of intestinal inflammation. To investigate the molecular mechanisms underlying these dysfunctions, we isolated human intestinal lymphatic endothelial cells (HILECs) from surgical specimens of patients undergoing resection for complicated CD (CD HILEC) and from a disease-free margin of surgical specimens of patients undergoing resection for cancer (healthy HILEC). Both cell types underwent transcriptomic profiling, and their barrier functionality was tested using a transwell-based co-culture system between HILEC and lamina propria mononuclear cells (LPMCs). Results showed CD HILEC displayed a peculiar transcriptomic signature that highlighted mTOR signaling as an orchestrator of leukocyte trafficking through the lymphatic barrier of CD patients. Moreover, we demonstrated that LPMC transmigration through the lymphatic endothelium of patients with CD depends on the capability of mTOR to trigger interleukin 20 receptor subunit α (IL20RA)-mediated intracellular signaling. Conclusively, our study suggests that leukocyte trafficking through the intestinal lymphatic microvasculature can be controlled by modulating IL20RA, thus leading to the resolution of chronic inflammation in patients with CD.</p>
Scale-dependent effects of urbanization on avian diversity in a Neotropical region
<p>RDA_birds script: This is the script that contains the Redundancy Analysis (RDA), whose database is named: "Rda_birds.txt". RDA is a multivariate statistical technique that combines elements of Principal Component Analysis (PCA) and Multiple Regression to explore the relationships between sets of variables. This technique is often used to analyze data where there are multiple responses (dependent variables) and multiple predictors (independent variables). In this case, we used this statistical technique to explore multivariate relationships between sets of variables, where we explored how local environmental and landscape characteristics (independent variables) can explain patterns in bird species communities (dependent variables).</p> <p>MOBr_birds script: This is the script that contains the Biodiversity Measurement Analysis (Mob), whose database is named: "Mobr_birds". Mob is a multi-scale approach to dissecting the roles of species abundance distribution (SAD), total community abundance and spatial aggregation within species along continuous environmental gradients.</p>
Nufix: Escape From NuGet Dependency Maze
<p>With the rapid evolution of the .NET ecosystem, managing dependencies in .NET projects becomes a critical challenge. Due to the fragmentation of .NET ecosystem, developers often suffer from dependency maze (DM) issues, i.e., package dependency constraints are violated (e.g, constraints on package versions and target platforms) when updating a project’s platform or dependency versions. DM issues are serious, since they can block the package installations, causing build errors. Fixing a DM issue can be challenging. Multiple DM issues often occur in a project at the same time. For those projects with large dependency graphs, fixing such issues is a time-consuming and error-prone process that exercises a series of changes in dependency constraints in response to newly induced DM issues. More importantly, when deciding a fixing solution, developers often consider their desired properties of configuration (e.g., installing fewer packages, inducing fewer risky build warnings). However, it is difficult for developers to imagine all possible dependency graphs affected by dependency changes, to figure out an optimal solution that satisfies their preferences. To help .NET developers tackle DM issues, we developed a tool, <strong>NuFix</strong> (VS plugin)(Homepage: <a href="http://www.nufix-dependency-maze.com/">http://www.nufix-dependency-maze.com/</a>), to automatically generate fixes. It is built on top of our comprehensive study of developers’ preferences in fixing DM issues. By encoding the empirical findings into a linear optimization model, NuFix seeks for the global optimal fixing solution. One interesting feature of NuFix is that, it allows developers to customize and iteratively refine the search scope of package versions based on their requirements. A video demo is available at: <a href="https://youtu.be/8NECIM0wjhw">https://youtu.be/8NECIM0wjhw</a></p> <p>Our evaluation shows that NuFix can generate fixes for a given .NET project within 12 seconds and achieves a 100% fixing ratio for 262 real DM issues. We invited ten experienced .NET experts working in MSRA to evaluate the quality our generated fixes. Their feedback indicates that the generated fixes meet the developers' desired properties for the build management. Encouragingly, 20 projects (including affected projects such as Dropbox) have approved and merged our generated fixes, and shown great interests in our technique (the merged PRs are available on NuFix's website).</p>
Dataset related to article "Multifaceted and age-dependent phenotypes associated with biallelic PNPLA6 gene variants: eight novel cases and review of the literature."
<p>Genetic data in VCF format and Sanger electropherograms of an Italian patient with spastic ataxia phenotype</p>
Nufix: Escape From NuGet Dependency Maze
<p>Developers usually suffer from dependency maze (DM) issues, i.e., package dependency constraints are violated when a project’s platform or dependencies are changed. This problem is especially serious in .NET ecosystem due to its fragmented platforms (e.g., .NET Framework, .NET Core, and .NET Standard). Fixing DM issues is challenging due to the complexity of dependency constraints: multiple DM issues often occur in one project; solving one DM issue usually causes another DM issue cropping up; the exponential search space of possible dependency combinations is also a barrier. On the other hand, as observed in our empirical study, fixing DM issues for a .NET project is, however, a challenging task, which multiple DM issues often occur in a project at the same time. For those projects with large dependency graphs, fixing such issues is a time-consuming and error prone process that exercises a series of changes in dependency constraints in response to newly induced DM issues and it is difficult for developers to imagine all possible dependency graphs affected by dependency changes, to figure out an optimal solution that satisfies their preferences.</p> <p>To help .NET developers combat DM issues, we propose <strong>NuFix</strong>, an automated technique to repair DM issues. NuFix is implemented as a Visual Studio plugin, whose main features include: 1) building on top of a comprehensive study of developers’ preferences in fixing DC issues (e.g., installing fewer packages, inducing fewer risky build warnings); 2) seeking for the global optimal fixing solution based on a linear optimization model; 3) allowing developers to customize and iteratively refine the search scope of package versions based on their requirements; 4) visualizing dependency graph after adopting the derived fixes.</p> <p>Our evaluation shows that <strong>NuFix</strong> can generate fixes for a given .NET project within 12 seconds and achieves a 100% fixing ratio for 262 real DC issues. We invited ten experienced .NET experts working in a leading IT enterprise to evaluate the quality our generated fixes. Their feedback indicates that the generated fixes meet the developers’ desired properties for the build management. Encouragingly, 20 projects (including affected projects such as Dropbox) have approved and merged our generated fixes, and shown great interests in our technique.</p>
Dataset related to article "Tumor treating fields affect mesothelioma cell proliferation by exerting histotype-dependent cell cycle checkpoint activations and transcriptional modulations"
<p>This record contains data related to article "Tumor treating fields affect mesothelioma cell proliferation by exerting histotype-dependent cell cycle checkpoint activations and transcriptional modulations"</p> <p>Although clinical antitumor activity of Tumor Treating Fields (TTFields) has been reported in malignant pleural mesothelioma (MPM) patients, the mechanisms behind the different selectivity displayed by the various MPM histotypes to this physical therapy has not been elucidated yet.</p> <p>Taking advantage of the development of well characterized human MPM cell lines derived from pleural effusion and/or lavages of patients’ thoracic cavity, we investigated the biological effects of TTFields against these cells, representative of epithelioid, biphasic and sarcomatoid histotypes. Growth inhibition and cell cycle perturbations caused by TTFields were investigated side by side with RNA-Seq analyses at different exposure times to identify pathways involved in cell response to treatment.</p> <p>We observed significant differences of response to TTFields among the cell lines. Cell cycle analysis revealed that the most sensitive cells (epithelioid CD473) were blocked in G<sub>2</sub>M phase followed by formation of polyploid cells. The least sensitive cells (sarcomatoid CD60) were only slightly affected by TTFields with a general delay in all cell cycle phases. Apoptosis was present in all samples, but while epithelioid cell death was already observed during the first 24h of treatment, sarcomatoid cells needed longer times before they engaged apoptotic pathways.</p> <p>RNA-Seq experiments demonstrated that TTFields induced a transcriptional response already detectable at early time points (8h). The number of differentially expressed genes was higher in CD473 than in CD60 cells, involving several pathways, such as those pertinent to cell cycle checkpoints, DNA repair and histone modifications.</p> <p>Our data provide further support to the notion that the antitumor effects of TTFields are not simply related to a non-specific reaction to a physical stimulus, but are dependent on the biological background of the cells and the particular sensitivity to TTFields observed in epithelioid MPM cells is associated with a higher transcriptional activity than that observed in sarcomatoid models.</p>
Insect herbivores and soil fertility drive variation in density-dependent seedling dynamics across a fragmented landscape
Open the record for dataset details and reuse information.
Dataset related to article "Dose-Dependent Impairment of the Immune Response to the Moderna-1273 mRNA Vaccine by Mycophenolate Mofetil in Patients with Rheumatic and Autoimmune Liver Diseases"
<p>This record contains data related to article "Dose-Dependent Impairment of the Immune Response to the Moderna-1273 mRNA Vaccine by Mycophenolate Mofetil in Patients with Rheumatic and Autoimmune Liver Diseases"</p> <p>The purpose of this study was to evaluate the efficacy and safety of the Moderna-1273 mRNA vaccine for SARS-CoV-2 in patients with immune-mediated diseases under different treatments. Anti-trimeric spike protein antibodies were tested in 287 patients with rheumatic or autoimmune diseases (10% receiving mycophenolate mofetil, 15% low-dose glucocorticoids, 21% methotrexate, and 58% biologic/targeted synthetic drugs) at baseline and in 219 (76%) 4 weeks after the second Moderna-1273 mRNA vaccine dose. Family members or caretakers were enrolled as the controls. The neutralizing serum activity against SARS-CoV-2-G614, alpha, and beta variants in vitro and the cytotoxic T cell response to SARS-CoV-2 peptides were determined in a subgroup of patients and controls. Anti-SARS-CoV-2 antibody development, i.e., seroconversion, was observed in 69% of the mycophenolate-treated patients compared to 100% of both the patients taking other treatments and the controls (p &amp;lt; 0.0001). A dose-dependent impairment of the humoral response was observed in the mycophenolate-treated patients. A daily dose of &amp;gt;1 g at vaccination was a significant risk factor for non-seroconversion (ROC AUC 0.89, 95% CI 0.80-98, p &amp;lt; 0.0001). Moreover, in the seroconverted patients, a daily dose of &amp;gt;1 g of mycophenolate was associated with significantly lower anti-SARS-CoV-2 antibody titers, showing slightly reduced neutralizing serum activity but a comparable cytotoxic response compared to other immunosuppressants. In non-seroconverted patients treated with mycophenolate at a daily dose of &amp;gt;1 g, the cytotoxic activity elicited by viral peptides was also impaired. Mycophenolate treatment affects the Moderna-1273 mRNA vaccine immunogenicity in a dose-dependent manner, independent of rheumatological disease.</p>
Phenotypes controlled by the Brucella abortus two component system BvrR/BvrS differ in their dependence on the phosphorylation of the response regulator BvrR
<p><em>Brucella abortus</em> is a zoonotic pathogen whose ability to survive intracellularly at the endoplasmic reticulum is essential for its virulence. The two-component system BvrR/BvrS is essential for intracellular survival due to the transcriptional control of the type IV secretion system VirB and its transcriptional regulator VjbR. In addition, this system is a master regulator of several traits including membrane conformation by controlling proteins such as Omp25. To understand the regulatory strategies used by BvrR we generated dominant positive and negative versions of this response regulator which, in addition to the wild type version, were introduced in a BvrR- background. We then characterized BvrRS-controlled phenotypes and the expression of proteins controlled by the system. We found two regulatory patterns exerted by BvrR. The first pattern was represented by resistance to polymyxin and expression of Omp25 (membrane conformation) which were restored to normal levels by the dominant positive and the wild type version, but not the dominant negative version, of BvrR. The second pattern was represented by intracellular survival and expression of VjbR and VirB (virulence) which were, again, fully complemented by wild type and the dominant versions of BvrR but, significantly restored by complementation with the dominant negative version of the response regulator. These results suggested a differential binding of unphosphorylated BvrR with promoters of the genes it controls. We confirmed this hypothesis by showing that the dominant negative version of BvrR was not able to interact with the promoter of <em>omp25</em> but was able to interact with the promoter of <em>vjbR</em>. Furthermore, a global transcriptional analysis indicated that some genes respond to the presence of the dominant negative version of BvrR. Thus, BvrR possesses diverse strategies to exert transcriptional control on the genes it regulates and as consequence on the phenotypes controlled by this response regulator.</p> <p>Here, we include the raw count data (rawcounts.txt) for all analyzed samples, as well as the experimental designed used to perform the statistical results (target.txt).</p>
DATASET RELATED TO ARTICLE: "Multifaceted and Age-Dependent Phenotypes Associated With Biallelic PNPLA6 Gene Variants: Eight Novel Cases and Review of the Literature"
<p>Description of clinical and genetic data of eight PNPLA6 patients diagnosed at Besta Institute and summary of the literature previuos data for patients with the same disease.</p>
Dataset related to the article "Reduction of Cardiac Fibrosis by Interference With YAP-Dependent Transactivation"
<p>This record contains raw data related to the article "Reduction of Cardiac Fibrosis by Interference With YAP-Dependent Transactivation".</p> <p>Abstract</p> <p><strong>Background: </strong>Conversion of cardiac stromal cells into myofibroblasts is typically associated with hypoxia conditions, metabolic insults, and/or inflammation, all of which are predisposing factors to cardiac fibrosis and heart failure. We hypothesized that this conversion could be also mediated by response of these cells to mechanical cues through activation of the Hippo transcriptional pathway. The objective of the present study was to assess the role of cellular/nuclear straining forces acting in myofibroblast differentiation of cardiac stromal cells under the control of YAP (yes-associated protein) transcription factor and to validate this finding using a pharmacological agent that interferes with the interactions of the YAP/TAZ (transcriptional coactivator with PDZ-binding motif) complex with their cognate transcription factors TEADs (TEA domain transcription factors), under high-strain and profibrotic stimulation.</p> <p><strong>Methods: </strong>We employed high content imaging, 2-dimensional/3-dimensional culture, atomic force microscopy mapping, and molecular methods to prove the role of cell/nuclear straining in YAP-dependent fibrotic programming in a mouse model of ischemia-dependent cardiac fibrosis and in human-derived primitive cardiac stromal cells. We also tested treatment of cells with Verteporfin, a drug known to prevent the association of the YAP/TAZ complex with their cognate transcription factors TEADs.</p> <p><strong>Results: </strong>Our experiments suggested that pharmacologically targeting the YAP-dependent pathway overrides the profibrotic activation of cardiac stromal cells by mechanical cues in vitro, and that this occurs even in the presence of profibrotic signaling mediated by TGF-β1 (transforming growth factor beta-1). In vivo administration of Verteporfin in mice with permanent cardiac ischemia reduced significantly fibrosis and morphometric remodeling but did not improve cardiac performance.</p> <p><strong>Conclusions: </strong>Our study indicates that preventing molecular translation of mechanical cues in cardiac stromal cells reduces the impact of cardiac maladaptive remodeling with a positive effect on fibrosis.</p>
Dataset of the paper "Software Supply Chain Meets Large Language Models: Can Dependency-related Problems Be Solved?"
<p>This is the dataset of the paper "Software Supply Chain Meets Large Language Models: Can Dependency-related Problems Be Solved?"</p>
Insulin Dependent Gestational Diabetes Mellitus: Randomized Trial of Induction of Labour at 38 and 40 Weeks of Gestation
ClinicalTrials.gov study NCT01256892. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Exploring Origin-dependent Susceptibility of Smooth Muscle Cells to Aortic Diseases via Intersectional Genetics
GEO Series GSE278774. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Hypothalamic and dorsal vagal glucose-dependent insulinotropic polypeptide receptor (GIPR) neurons employ distinct mechanisms to affect feeding
GEO Series GSE228192. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
A new AdpA-dependent gene, required for morphological differentiation, in Streptomyces griseus.
GEO Series GSE36949. Streptomyces griseus. 2 samples. Type: Expression profiling by array.
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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.