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39 results for “article selection”
Repositiry for the article: "Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection" by Alain Mbebi & Zoran Nikoloski
<p>This is the repository for the manuscript "Gene regulatory network inference using mixed-norms regularized multivariate model with covariance selection" by Alain J. Mbebi & Zoran Nikoloski.</p> <p><strong>Organisation</strong></p> <ol> <li>The folder Codes contains the following R scripts with the K-folds cross-validation option to learn the hyperparameters:</li> </ol> <ul> <li>Mixed_L1L21_GRN.R which computes L1L21-solution</li> <li>Mixed_L1L21G_GRN.R which computes L1L21G-solution</li> <li>Mixed_L2L21_GRN.R which computes L2L21-solution</li> <li>Mixed_L2L21G_GRN.R which computes L2L21G-solution</li> <li>L1L21_Dream5_Scerevisiae_example_run.R is an example run using the L1L21-solution with S. cerevisiae data (Network 4 in DREAM5 challenge) All files needed to successfully run "L1L21_Dream5_Scerevisiae_example_run" are locaded in the folder Codes.</li> </ul> <p>2. The folder Figures contains all figures in the manuscript.</p> <p>3. The folder Inferred-networks contains all network objects for each dataset and each inference methods in the comparative analysis.</p> <p><strong>Dependencies and required packages</strong></p> <p>The following packages are required for the contending approaches in the comparative analysis: "devtools", "foreach", "plyr", "glmnet" and "randomForest".</p> <p><strong>GENIE3</strong></p> <p>The GENIE3 package can be installed from: <a href="http://bioconductor.org/packages/release/bioc/html/GENIE3.html">http://bioconductor.org/packages/release/bioc/html/GENIE3.html</a></p> <p><strong>TIGRESS</strong></p> <p>The TIGRESS repository can be obtained from: <a href="https://github.com/jpvert/tigress">https://github.com/jpvert/tigress</a></p> <p><strong>ENNET</strong></p> <p>The ENNET repository can be obtained from: <a href="https://github.com/slawekj/ennet">https://github.com/slawekj/ennet</a></p> <p><strong>PLSNET</strong></p> <p>The Matlab source code of PLSNET can be obtained from: <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1398-6#Sec17">https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1398-6#Sec17</a></p> <p><strong>PORTIA</strong></p> <p>The PORTIA repository can be obtained from: <a href="https://github.com/AntoinePassemiers/PORTIA">https://github.com/AntoinePassemiers/PORTIA</a></p> <p><strong>D3GRN</strong></p> <p>The Matlab source code of D3GRN can be obtained from: <a href="https://github.com/chenxofhit/D3GRN">https://github.com/chenxofhit/D3GRN</a></p> <p><strong>Fused-LASSO</strong></p> <p>The fused-LASSO repository can be obtained from: <a href="https://github.com/omranian/inference-of-GRN-using-Fused-LASSO">https://github.com/omranian/inference-of-GRN-using-Fused-LASSO</a></p> <p><strong>ANOVerence</strong></p> <p>Because of some technical issues (e.g code's accessibility: <a href="http://www2.bio.ifi.lmu.de/%CB%9Ckueffner/anova.tar.gz">http://www2.bio.ifi.lmu.de/˜kueffner/anova.tar.gz</a>), we were not able to reproduce ANOVerence results and used the inferred network from DREAM5 challenge instead.</p> <p>4. Although the codes here were tested on Fedora 29 (Workstation Edition) using R (version 4.2.2), they can run under any Linux or Windows OS distributions, as long as all the required packages are compatible with the desired R version.</p>
Dataset related to article "Neutrophils Driving Unconventional T Cells Mediate Resistance against Murine Sarcomas and Selected Human Tumors"
<p>Neutrophils are a component of the tumor microenvironment and have been predominantly associated with cancer progression. Using a genetic approach complemented by adoptive transfer, we found that neutrophils are essential for resistance against primary 3-methylcholantrene-induced carcinogenesis. Neutrophils were essential for the activation of an interferon-γ-dependent pathway of immune resistance, associated with polarization of a subset of CD4<sup>-</sup> CD8<sup>-</sup> unconventional αβ T cells (UTC<sub>αβ</sub>). Bulk and single-cell RNA sequencing (scRNA-seq) analyses unveiled the innate-like features and diversity of UTC<sub>αβ</sub> associated with neutrophil-dependent anti-sarcoma immunity. In selected human tumors, including undifferentiated pleomorphic sarcoma, CSF3R expression, a neutrophil signature and neutrophil infiltration were associated with a type 1 immune response and better clinical outcome. Thus, neutrophils driving UTC<sub>αβ</sub> polarization and type 1 immunity are essential for resistance against murine sarcomas and selected human tumors.</p>
Research data supporting article "Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer"
<p>Gene expression data supporting analyses described in the article "Recurrent horizontal transfer identifies mitochondrial positive selection in a transmissible cancer" (Strakova et al., 2020).</p>
Question-Worthy Sentence Selections for German Wikipedia Articles
<p>This dataset contains our used and optimized wikipedia articles, where teachers selected sentences that are worth asking for. The corresponsing paper can be found in:</p> <p>Rüdian, S., Heuts, A. & Pinkwart, N., (2020). Educational Text Summarizer: Which sentences are worth asking for?. In: Zender, R., Ifenthaler, D., Leonhardt, T. & Schumacher, C. (Hrsg.), DELFI 2020 – Die 18. Fachtagung Bildungstechnologien der Gesellschaft für Informatik e.V.. Bonn: Gesellschaft für Informatik e.V.. (S. 277-288).</p> <p>https://dl.gi.de/handle/20.500.12116/34171</p> <p>Please note that the copyright of the Wikipedia articles remains with the authors.<br> For each text, the original source is given. They are shared under the same, similar or a compatible license as the wikipedia texts.</p>
Envelopes for the article "Realtime Selection of Optimal Source Parameters Using Ground Motion Envelopes" and the python notebook that shows the algorithm usage.
<p>The github repository is available at https://github.com/djozinovi/goodnessOfFitEnv</p>
Supplementary Tables S1-S5 for an article "Square Antiprismatic Chelation Is a Key Determinant for Potassium Ion Selectivity"
<p>This file contain tables S1-S5 for the supporting information from the original paper. These tables describe potassium binding sites indentifieid in potassium channels, other membrane proteins and randomly chosen non-membrane proteins. (See the article text for details)</p> <p> </p>
Raw data for the article "Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy"
<p>Raw NMR, IR and MS data for the article "Homologation of Alkenyl Carbonyls via a Cyclopropanation/Light-Mediated Selective C-C Cleavage Strategy" published in Angewandte Chemie, International Edition, DOI: </p> <div><a href="https://doi.org/10.1002/anie.202417719">https://doi.org/10.1002/anie.202417719</a></div> <p>The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article. For convenience, the word file version of the supporting information can be found on the top of the raw data folder.</p>
Source research data for the article titled "A Nature-Inspired Approach to Energy-Efficient Relay Selection in Low-Power Wide-Area Networks (LPWAN)".
<p>The source research data set developed and utilized while working on the article "A Nature-Inspired Approach to Energy-Efficient Relay Selection in Low-Power Wide-Area Networks (LPWAN)" for Sensors SI. The data set includes simulation results from OMNeT++ and the data to evaluate the parameters of the algorithms.</p>
Data underlying the article: "A patient-centric knowledge graph approach to prioritize mutants for selective anti-cancer targeting"
<p>This repository contains the data and code underlying the article: "A patient-centric knowledge graph approach to prioritize mutants for selective anti-cancer targeting" available on BioRxiv. </p>
Dataset for the article 'Selective electroreduction of acetylene to 1,3-butadiene on iodide-induced Cuδ+-Cu0 sites'
<p>Data sets for the article 'Selective electroreduction of acetylene to 1,3-butadiene on iodide-induced Cuδ+-Cu0 sites', published in Nature catalysis (DOI : 10.1038/s41929-024-01250-0)</p>
Data set for the journal article: The Spatial Distribution of Cobalt Phthalocyanine and Copper Nanocubes Controls the Selectivity towards C2 Products in Tandem Electrocatalytic CO2 Reduction
<p>Data set for the journal article:</p> <p>The coupling of CO-generating molecular catalysts with copper electrodes in tandem schemes is a promising strategy to boost the formation of multi-carbon products in the electrocatalytic reduction of CO<sub>2</sub>. While the spatial distribution of the two components is important, this aspect remains underexplored, especially for molecular-based tandem systems. Herein, we address this knowledge gap by studying tandem catalysts comprising Co-phthalocyanine (CoPc) and Cu nanocubes (Cu<sub>cub</sub>). In particular, we identify the importance of the relative spatial distributions of the two components on the performance of the tandem catalyst by preparing CoPc-Cu<sub>cub</sub>/C, wherein the CoPc and Cu<sub>cub</sub> share an interface, and CoPc-C/Cu<sub>cub</sub>, wherein the CoPc is loaded first on carbon black (C) before mixing with the Cu<sub>cub</sub>. The electrocatalytic measurements of these two catalysts show that the faradaic efficiency towards C<sub>2 </sub>products almost doubles for the CoPc-Cu<sub>cub</sub>/C, whereas it decreases by half for the CoPc-C/Cu<sub>cub</sub>, compared to the Cu<sub>cub</sub>/C. Our results highlight the importance of a direct contact between the CO-generating molecular catalyst and the Cu to promote C-C coupling, which hints at a surface transport mechanism of the CO intermediate between the two components of the tandem catalyst instead of a transfer via CO diffusion in the electrolyte followed by re-adsorption.</p>
Investigate the Exposure to Selected Smoke Constituents in Smokers Switching to Distillation Based Smoking Article
ClinicalTrials.gov study NCT00812279. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Experimental data used in the article entitled "Influences of Energy Density on The Structure and Hardness of Selective Laser Melted AlSi7Mg Alloy"
Open the record for dataset details and reuse information.
DATASET RELATED TO ARTICLE "Resection of primary central nervous system lymphoma: impact of patient selection on overall survival"
<p>Patient characteristics, comorbidities, pre-operatives symptoms, lesion features, post-operatives symptoms, adjuvant therapies, histology, PFS, OS</p> <p> </p>
Dataset related to article "Oligoprogressive castration-resistant prostate cancer treated with metastases-directed stereotactic body radiation therapy: predictive factors for patients' selection"
<p>This record contains raw data related to article "Oligoprogressive castration-resistant prostate cancer treated with metastases-directed stereotactic body radiation therapy: predictive factors for patients' selection"</p> <p> </p> <p>Abstract: Oligoprogression is defined as limited metastatic clone resistant to on-going systemic treatment that grows in a background of stable or responding systemic disease. Aim of the present study was to analyze oligoprogressive prostate cancer (PC) patients treated with stereotactic body radiation therapy (SBRT) during systemic treatment to identify predictive factors and improve patients' selection. We included PC patients treated with SBRT on a maximum of 3 sites of oligoprogression during systemic therapy. Endpoints were freedom from polymetastatic progression (FPP), local control (LC), distant progression free survival (DPFS), overall survival (OS), and next systemic therapy free survival (NEST-FS). Fifty-three patients were treated on 85 oligoprogressive metastases. Lymph nodes were the most common sites (56.47%), followed by bone (39.29%). Median follow-up was 24.9 months. Rates of FPP at 1- and 2-year were 80.1% and 68.9%, respectively. Median time to polymetastatic progression was 33.7 months. Disease free interval (p = 0.004), site of metastases (p = 0.011), and type of systemic therapy (p = 0.003) were significant for FPP. Switch or intensification of systemic therapy after SBRT was observed in 29 (54.72%) patients with a median NEST-FS of 15.2 months. LC at 1- and 2-year was 94.0% and 92.0%, with PSA doubling time resulted to be significantly associated (p = 0.047). Median DPFS was 8.93 months and median OS was 50.6 months. In conclusion, we confirmed the efficacy of SBRT for oligoprogression from PC, with the potential to prolong the on-going systemic therapy and interrupt the metastatic cascade.</p>
Dataset related to article: "Could We Safely Avoid a Second Resection in Selected Patients With T1 Non-Muscle-Invasive Bladder Cancer? Preliminary Results of Cost-Effectiveness Study From HUmanitas New Indications for ReTUR (HuNIRe) Multicenter Prospective Trial"
<p>The paper reports the preliminary results of a study which aims to avoid re-turbt in patients who have pT1</p>
Dataset related to article "Selected memory T cells infused post haploidentical hematopoietic stem cell transplantation persist and hyper-expand"
<p>This record contains raw data related to article “Selected memory T cells infused post haploidentical hematopoietic stem cell transplantation persist and hyper-expand"</p> <p>Abstract</p> <p>Haploidentical hematopoietic stem cell transplantation (haplo-HSCT) with post-transplant cyclophosphamide is a curative treatment for many hematological malignancies, yet a majority of patients still suffers from recurrent infections. Post-transplant infusion of memory T cells could potentially enhance immunological protection without increasing the risk of eliciting acute graft-versus-host disease, which is mainly induced by naïve T cells. Here, we performed longitudinal analysis of the lymphocyte compartment in 19 haplo-HSCT patients previously enrolled in a phase II prospective clinical trial (ClinicalTrials.gov Identifier: <a href="http://clinicaltrials.gov/show/NCT04687982">NCT04687982</a>), in which they received post-transplant CD45RA-depleted donor lymphocyte infusions (DLI). T cell receptor sequencing analysis showed that, surprisingly, CD45RA-depleted DLI do not increase T cell clonal diversity, but lead to prominent expansion of a selected number of infused memory T cell clones, suggestive of recruitment of these cells in the immune response. Pathogen-specific memory T cells, including cytomegalovirus (CMV)-specific cells, engrafted and were able to persist for at least one month. Deep immunophenotyping revealed strong polyfunctional effector CMV-specific T cell responses in the majority of patients, with their expansion correlating with the frequency of CMV-specific cells in the donor. These findings provide a rationale behind the suggested improved protection against viral infections for patients receiving CD45RA-depleted DLI.</p> <p> </p>
Dataset related to article "Selective Cerebrospinal Fluid Hypothermia: Bioengineering Development and In Vivo Study of an Intraventricular Cooling Device (V‑COOL)"
<p><em>The database contains animal models MRI in DICOM and PNG file format.</em></p>
Systematic Literature Review - Selected Articles Data Extraction
<p>The files included are the following:</p> <p>- CSV with the raw data extracted from abstract + full-text review from the selected articles.</p> <p>- CSV with normalized data according to the article.</p> <p> </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.