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2,100 results for “nodes”
moFluMemB - Dataset : scRNA-seq from Lymph node, Spleen and Lung - 10x_190712_m_moFluMemB
<p><strong>Title</strong></p> <p>Viral infection engenders bona fide and bystander subsets of lung-resident memory B cells through a permissive mechanism<br><br><strong>Authors</strong><br>Claude Gregoire,1 Lionel Spinelli,1 Sergio Villazala-Merino,1 Laurine Gil,1 María Pía Holgado,1 Myriam Moussa,1 Chuang Dong,1 Ana Zarubica,2 Mathieu Fallet,1 Jean-Marc Navarro,1 Bernard Malissen,1,2 Pierre Milpied,1,* and Mauro Gaya1,*<br><br><strong>Affiliations</strong><br>1 Centre d'Immunologie de Marseille-Luminy (CIML), Aix Marseille Université, INSERM, CNRS, Marseille, France<br>2 Centre d'Immunophénomique (CIPHE), Aix Marseille Université, INSERM, CNRS, Marseille, France<br>* Correspondence: milpied@ciml.univ-mrs.fr (P.M.), gaya@ciml.univ-mrs.fr (M.G.)<br><br><strong>Summary</strong><br>Lung-resident memory B cells (MBCs) provide localized protection against reinfection in the respiratory airways. Currently, the biology of these cells remains largely unexplored. Here, we combined influenza and SARS-CoV-2 infection with fluorescent-reporter mice to identify MBCs regardless of antigen specificity. We found that two main transcriptionally distinct subsets of MBCs colonized the lung peribronchial niche after infection. These subsets arose from different progenitors and were both class-switched, somatically mutated and intrinsically biased in their differentiation fate towards plasma cells. Combined analysis of antigen-specificity and B cell receptor repertoire segregated these subsets into “bona fide” virus-specific MBCs and “bystander” MBCs with no apparent specificity for eliciting viruses and generated through an alternative permissive mechanism. Thus, diverse transcriptional programs in MBCs are not linked to specific effector fates but rather to divergent strategies of the immune system to simultaneously provide rapid protection from reinfection while diversifying the initial B cell repertoire.</p> <p><strong>Data: 1</strong>0x_190712_m_moFluMemB_processedData.tar.gz : pre-processed data of 10x 5’ scRNA-Seq on memory B cells sorted from single-cell suspensions of spleen, lymph nodes and lungs with enzymatic digestion of lung tissue at 37°C.</p> <p>See the three other Zenodo deposit for the rest of the data:</p> <p><strong>10.5281/zenodo.5566674</strong></p> <p><strong>10.5281/zenodo.5565863</strong></p> <p><strong>10.5281/zenodo.10559312</strong></p>
Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals
<p><span>The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here we critically examine two such clades: the animals (with focus on the bilaterians); and the mammals (with focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray; and we have every reason to think these problems are general. </span></p>
Node-Pore Coded Coincidence Correcting Microfluidic Channel Framework: Code Design and Sparse Deconvolution
<p>This is the dataset for the work titled and authored by:</p> <p><strong>Node-Pore Coded Coincidence Correcting Microfluidic Channel Framework: Code Design and Sparse Deconvolution</strong></p> <p>Michael Kellman, Francois Rivest, Alina Pechacek, Lydia Sohn, Michael Lustig</p> <p>We present a novel method to perform individual particle (e.g. cells or viruses) coincidence correction through joint channel design and algorithmic methods. Inspired by multiple-user communication theory, we modulate the channel response, with Node-Pore Sensing, to give each particle a binary Barker code signature. When processed with our modified successive interference cancellation method, this signature enables both the separation of coincidence particles and a high sensitivity to small particles. We identify several sources of modeling error and mitigate most effects using a data-driven self-calibration step and robust regression. Additionally, we provide simulation analysis to highlight our robustness, as well as our limitations, to these sources of stochastic system model error. Finally, we conduct experimental validation of our techniques using several encoded devices to screen a heterogeneous sample of several size particles.</p> <p>Software can be found under this DOI:</p> <p>10.5281/zenodo.846448</p>
H&E colorectal lymph node metastasis nuclei dataset
<p>H&E colorectal lymph node metastasis nuclei dataset (neoplastic/non-neoplastic, 224x224 pixels at 40x magnification)</p> <p>This description will be updated soon.</p>
The TCR assigns naive T cells to a preferred lymph node
<p>Naive T cells recirculate between the spleen and lymph nodes where they mount immune responses when meeting dendritic cells presenting foreign antigen. As this may happen anywhere, naive T cells ought to visit all lymph nodes. Here, deep sequencing almost-complete TCR-repertoires led to a comparison of different lymph nodes within and between individual mice. We find strong evidence for a deterministic CD4/CD8 lineage choice and a consistent spatial structure. Specifically, some T cells show a preference for one or multiple lymph nodes, suggesting that their TCR interacts with locally presented (self-)peptides. These findings are mirrored in TCR-transgenic mice showing localized CD69-expression, retention, and cell division. Thus, naïve T cells intermittently sense antigenically dissimilar niches, which is expected to affect their homeostatic competition.</p>
Design and Implementation of a flexible Node for IoT supporting 6loWPAN and a Sensor Shield for Home Automation Application
<p>Simulation data and measurment of the developed flexible IoT board.</p>
Virtual wall 1, 3 metro nets, 3 metro nodes, 2 end nodes
<p>Contains rtts and summaries.</p> <p>See ARCFIRE D4.4 for data analysis.</p>
Virtual wall 1, scaling time, 2 metro nets, 3 metro nodes, 2 end nodes
<p>This contains rtts and summaries thereof.</p> <p>See ARCFIRED D4.4 for data analysis.</p>
Virtual wall 1, 3 metro nets, 5 metro nodes, 2 end nodes
<p>Contains rtts and summaries.</p> <p>See ARCFIRE D4.4 for data analysis.</p>
Scalasca analysis report of the ASCI Sweep3D benchmark on 65,536 processes in virtual-node mode on IBM Blue Gene/P
<p>A Cube3 performance analysis report written by the Scalasca Trace Analyzer of a measurement of the ASCI benchmark Sweep3D, executed in virtual-node mode on 65,536 processes of the IBM Blue Gene/P system JUQUEEN, operated by Forschungszentrum Jülich GmbH.</p>
Scalasca analysis report of the ASCI Sweep3D benchmark on 294,912 processes in virtual-node mode on IBM Blue Gene/P
<p>A Cube3 performance analysis report written by the Scalasca parallel analyzer of a measurement of the ASCI benchmark Sweep3D, executed in virtual-node mode on 294,912 processes of the IBM Blue Gene/P system JUQUEEN, operated by Forschungszentrum Jülich GmbH.</p>
SINS database - Node 1 - Daily activities in a home environment recorded using a Acoustic Sensor Network
<p>The SINS database contains continuous recordings of a single person living in a vacation home over a period of one week. It was collected using a network of 13 microphone arrays distributed over the entire home. The microphone array consists of 4 linearly arranged microphones.Recordings were manually annotated on the level of daily activities performed in the environment.<br> <br> To obtain more information on the database please visit <a href="https://kuleuvenadvise.github.io/SINS_database/">this website</a> and read the published paper.<br> <strong>Please read to license file (available in this repository) before using the database.</strong><br> <br> When using this database you should <strong>cite the following paper</strong>:<br> Gert Dekkers, Steven Lauwereins, Bart Thoen, Mulu Weldegebreal Adhana, Henk Brouckxon, Toon van Waterschoot, Bart Vanrumste, Marian Verhelst, and Peter Karsmakers, The SINS database for detection of daily activities in a home environment using an acoustic sensor network, Proceedings of the Detection and Classification of -Acoustic Scenes and Events 2017 Workshop (DCASE2017), pp 32–36, November 2017.</p>
Attenuation of chronic T cell responses through constitutive COX2-dependent prostanoid synthesis by lymph node fibroblasts
<p>Raw data (in microsoft excel format) which were used to generate the figures in this manuscript. One worksheet per figure.</p>
Benchmark circuits used in the work entitled "Don't-care-based node minimization for threshold logic networks"
<p>Benchmark circuits used in the work entitled "Don't-care-based node minimization for threshold logic networks".<br> There are two sets of threshold logic networks (TLNs), K6 and K15, generated with the method proposed in Effective Logic Synthesis Flow for Threshold Logic Circuit Design (https://ieeexplore.ieee.org/document/8355999) by Augusto Neutzling, et al.<br> In K6, each node has at most 6 fanins.<br> In K15, each node has at most 15 fanins.</p> <p>Contents:<br> ori/blif: Original TLNs in the blif format.<br> ori/th: Original TLNs in the threshold logic format.<br> opt/blif: Optimized TLNs in the blif format.<br> opt/th: Optimized TLNs in the threshold logic format.</p>
Prognostic value of a modified pathological staging system for gastric cancer based on the number of retrieved lymph nodes and metastatic lymph node ratio raw data
<p><span>Clinical data from the US Surveillance, Epidemiology, and End Results (SEER) Program from 2010-2015 (https://seer.cancer.gov/) was extracted and analyzed as training set, data from 2016-2017 was adopted as internal validation set. Data from The Cancer Genome Atlas Program (TCGA) (https://portal.gdc.cancer.gov/) and prognosis data from Gastrointestinal surgery Department, Third Affiliated Hospital of Sun Yat-sen University were applied as external validation sets. </span></p> <p><span>Screening criteria for gastric cancer cases were as follow: exclusion of cases with only autopsy or death certificate, cases where initial tumor location was not stomach, patients with stage 0 and stage IV, cases without radical surgery, non-adenocarcinoma cases, death cases within one month after operation, and cases with unknown lymph node information and AJCC TNM stage.</span></p> <p><span>The study analyzed various factors such as age of diagnosis (<50 years, 50-69 years, >69 years), gender, race (white, black, other), AJCC T stage (T1-T4b), AJCC TNM stage (I-III), primary tumor location (stomach body, antrum/pylorus, cardia/fundus, greater gastric recurve, lesser gastric recurve, overlapping area, NOS), Clinical features such as tumor size (≥5cm,<5cm, unknown), tumor grade (I-IV), chemotherapy, radiotherapy, number of lymph nodes retrieved and number of metastases, and lymph node positive rate. The populations of American Indian/Alaskan and Asian/Pacific Islander were classified as "other" due to small sample sizes. Tumor grade was also analyzed, with grades I-IV representing highly differentiated, moderately differentiated, poorly differentiated, and signed-ring cell carcinoma, respectively. Overall survival (OS) is the time from cancer diagnosis to death from any cause, while disease-specific survival (DSS) is the time from cancer diagnosis to death specifically due to the disease.</span></p> <p><strong><span> </span></strong></p>
Data From: BioSense: An Automated Sensing Node for Organismal and Environmental Biology
<p><strong>Article title</strong></p> <p>BioSense: An Automated Sensing Node for Organismal and Environmental Biology</p> <p> </p> <p><strong>Authors</strong></p> <p>Andrea Contina<sup>a,b</sup>, Eric Abelson<sup>b</sup>, Brendan Allison<sup>b</sup>, Brian Stokes<sup>b</sup>, Kenedy F. Sanchez<sup>c</sup>, Henry M.Hernandez<sup>d</sup>, Anna M. Kepple<sup>b</sup>, Quynhmai Tran<sup>b</sup>, Isabella Kazen<sup>d</sup>, Katherine A. Brown<sup>e,f</sup>, Je'aime H. Powell<sup>g</sup>, Timothy H. Keitt<sup>b</sup></p> <p> </p> <p><strong>Affiliations</strong></p> <p><span>a Permanent address: School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Brownsville, TX 78520, USA. </span></p> <p><span>b Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78703, USA. </span></p> <p><span>c Carnegie Mellon University, Pittsburgh, PA 15213, USA.</span></p> <p><span>d Department of Physics, The University of Texas at Austin, Austin, TX 78712, USA. </span></p> <p><span>e The Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA.</span></p> <p><span>f Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK</span></p> <p><span>g Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX 78758, USA.</span></p> <p> </p> <p><strong>Corresponding author’s email address <br></strong></p> <p><em>Timothy Keitt, </em><a href="mailto:tkeitt@utexas.edu"><em>tkeitt@utexas.edu</em></a><em>. <br></em></p> <p> </p> <p><strong>Abstract </strong></p> <p>Automated remote sensing has revolutionized the fields of wildlife ecology and environmental science. Yet, a cost-effective and flexible approach for large scale monitoring has not been fully developed, resulting in a limited collection of high-resolution data. Here, we describe BioSense, a low-cost and fully programmable automated sensing platform for applications in bioacoustics and environmental studies. Our design offers customization and flexibility to address a broad array of research goals and field conditions. Each BioSense is programmed through an integrated Raspberry Pi computer board and designed to collect and analyze avian vocalizations while simultaneously collecting temperature, humidity, and soil moisture data. We illustrate the different steps involved in manufacturing this sensor including hardware and software design and present the results of our laboratory and field testing in southwestern United States.</p>
Line Theory: Effect, Node, and Line in Space
<p><span>This paper introduces a conceptual framework, denoted as ‘Line Theory,’ which is predicated on the procedural anatomy inherent in ordinary plans. A plan, recognized as a set of instructions for execution, undergoes in-depth scrutiny to analyze its constituent elements. The concise examination delves into the formation of line and effect within real space stemming from procedures. Line theory serves the purpose of elucidating the absolute optimization of plans. It is formulated to inaugurate an exploration into the veracity of procedures and their elemental changes, examining their correlation with space and motion at the most fundamental level. The scientific community has extensively delved into the examination of the behavior and structure of objects at the microscopic level. This paper endeavors to stimulate interest in the analogous analysis of procedures. The fundamental objective within this theoretical framework is to offer a distinct philosophical perspective on changes and effects.</span></p>
Transport chirality generated by a tunable tilt of Weyl nodes in a van der Waals topological magnet
<p>The source ASCII data files for the article entitled "Transport chirality generated by a tunable tilt of Weyl<br>nodes in a van der Waals topological magnet".</p>
Sulfidation of a metal-organic framework via heterolytic splitting of organo sulfides at distorted Zr-nodes
<p>Raw Dataset containing all calculation data of the publication "Sulfidation of a metal-organic framework via heterolytic splitting of organo sulfides at distorted Zr-nodes".</p>
PM_152454_B_Sint_Joost_ten_Node
<u>File Name</u>: PM_152454_B_Sint_Joost_ten_Node.jpg <br><u>Sublocation</u>: Charliermuseum <br><u>Location</u>: Sint-Joost-ten-Node <br><u>Province</u>: Brussels Region <br><u>Country</u>: Belgium <br><u>Header</u>: Schilderij, James Ensor, Bloemen en vlinders; 1889, olieverf op doek, 60x50cm <br><u>Description</u>: Painting James Ensor Flowers and Butterllies 1889 Oilm on canvas 60x50cm <br><u>Keywords</u>: Belgium, Brussels region, Cultural heritage, Europe, Museum/private collection, Painting, Techniques <br><br><u>Author</u>: James Ensor (1860-1949) <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
ScienceDex guides
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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.