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5,145 results for “CO₂”
Cestode infection facilitates co-infection by other parasites in a metapopulation of threespine stickleback
<p><span><span><span><span><span><span><span><span><span><span><span>Parasitic infections are a global occurrence and impact the health of many species. Co-infections, where two or more species of parasite are present in a host, are a common phenomenon across species. Co-infecting parasites can interact directly or indirectly via their manipulation of (and susceptibility to) the immune system of their shared host. Helminths, such as the cestode <i>Schistocephalus solidus</i>, are well known to suppress immunity of their host (threespine stickleback), potentially facilitating other parasite species. Yet, hosts can evolve a more robust immune response (as seen in some stickleback populations), potentially turning facilitation into inhibition. Using wild-caught stickleback from 21 populations with non-zero <i>S. solidus</i> prevalence, we show there is an overall tendency towards facilitation: individuals with <i>S. solidus</i> infections have 28% higher diversity of other parasites, compared to <i>S. solidus</i>-uninfected individuals from the corresponding lakes. This facilitation effect, however, is stronger in lakes where <i>S. solidus</i> is particularly successful but tends towards inhibition in lakes with sparse and smaller cestodes (indicative of stronger host immune response). These results illustrate how even a single parasite species can vary geographically in their capacity for facilitation or inhibition of co-infections.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from Schaffter, S.W. and Strychalski, E.A. "Co-transcriptionally encoded RNA strand displacement circuits" Science Advances (2022)
<p>The <strong>ctRSD_data_upload.xlsx</strong> file contains both the raw and normalized fluorescence data from this manuscript.</p> <p>In the Excel file, rows highlighted in green indicate the times when T7 RNAP was added to the samples. Plots of data in the manuscript designate this time as time = 0 min.</p> <p>The <strong>figure2D_fluorescence_data_plotting.py</strong> file is an example showing how the data was imported from the Excel file and plotted in the manuscript.</p> <p>In the script, the save_loc variable will need to be changed to the path pointing to where the ctRSD_data_upload.xlsx file (Data S1) is saved on a user’s local computer.</p>
KMC Models and CFD Simulations for Catalytic CO Oxidation over RuO2
<p>The large tar.gz file (~15GB) has the CFD Data Set for CFD Simulations for Catalytic CO Oxidation over RuO2 associated with the publication: doi: 10.1021/acscatal.8b00713 , https://pubs.acs.org/doi/abs/10.1021/acscatal.8b00713</p> <p>The smaller zip file(s) have the KMC model creation files, which are actually from this publication: https://doi.org/10.1088/1361-648X/aacb6d https://iopscience.iop.org/article/10.1088/1361-648X/aacb6d</p> <p>For the 110 KMC file, it must be compiled using the lat_int backend of kmos. The xml file generated takes less than an hour, though the exporting (compiling) may take 5 to 10 hours. With lateral interactions, the 110 xml file is >25MB. Without lateral interactions, the xml file is very small ( << 1 MB). Setting the "upToDistance" to 0 for each reaction in the python file called CO_O_RuO2_110.py will create a 110 model without lateral interactions (currently the "upToDistance" is set at 1 for each reaction, and thus includes nearest neighbor interactions). How to compile the model requires reading the documentation for the KMC software. The final syntax is " kmos export -b lat_int CO_O_RuO2_110.xml "</p> <p>For the 111 KMC file, it should be compiled with the default ( local_smart ) backend of kmos. The lateral interactions are already included and cannot be easily turned off. The resulting files are small. How to compile the model requires reading the documentation for the KMC software. The final syntax is " kmos export -b local_smart CO_O_RuO2_111.xml "</p> <p>Primitive example KMC runfiles are included, which would need to be run in the compiled KMC model's directories, though current conventions of kmos simulations use more advanced runfiles.</p> <p> </p>
Novel Pixelwise Co-Registered Hematoxylin-Eosin and Multiphoton Microscopy Image Dataset for Human Colon Lesion Diagnosis
<p><strong>General Description:</strong></p> <p>The dataset consists of a set of 50 samples of lesions obtained by colonoscopies and colectomies carried out between the years 2012 and 2017 at at Digestive Service at OSI Bilbao Basurto. These are 24 malignant neoplasms (adenocarcinoma), 19 preneoplastic lesions (adenoma) and 2 hyperplasia and 5 healthy tissues, obtained from 24 men and 19 women. The samples were diagnosed by the Pathological Anatomy Department at OSI Bilbao Basurto and the FFPE (Formalin-Fixed Paraffin-Embedded) blocks were stored in the Basque Biobank. All the samples were processed after signing Informed Consent and following standard operation procedures. The samples were scanned using a multiphoton microscope (Lens, Florence, Italy) both for multi-photon fluorescence (MPM) and second harmonic generation (SHG) and later stained with H&E (Hematoxylin & Eosin).</p> <p>The different image modalities were reconstructed and corregistered by performing non-rigid deformation (Tecnalia, Bilbao, Spain) allowing pixel correspondence among the different modalities. Pathologists from Basurto Hospital manually labeled the regions where the lession is present. Scale of current dataset is 0.5um/px.</p> <p><strong>Technical Details:</strong></p> <p>On the data_info.csv information for each sample is included:<br> - SAMPLE_ID: Includes the tag "PICCOLO_XX_YY", where XX stands for the patient ID number and YY to the lesion suffix ID.<br> - LESION_ID: The lesion is classified as healthy, hyperplasia, benign neoplasia, and malign neoplasia.<br> - HISTOLOGICAL ANALYSIS: It includes informative test about the lesion.<br> - GRADE: In the case for malign neoplasia universal grading system grade is included.</p>
Co-Optimization of Reservoir and Power Systems (COREGS) for Seasonal Planning and Operation
<p>Input and output data associated with the paper Co-Optimization of Reservoir and Power Systems (COREGS) for Seasonal Planning and Operation. Can be used with the COREGS model at https://github.com/lcford2/coregs.</p>
Human-robot co-manipulation of soft materials: enable a robot manual guidance using a depth map feedback [Video]
<p>Video of the paper submitted at RO-MAN 2022 </p> <p>Human-robot co-manipulation of soft materials: enable a robot manual guidance using a depth map feedback<br> Giorgio Nicola, Enrico Villagrossi, Nicola Pedrocchi</p> <p>Code for trainings and test available at:</p> <p>https://github.com/giorgionicola/SMAHRCO</p>
Data from: Trait hierarchies are stronger than trait dissimilarities in structuring spatial co-occurrence patterns of common tree species in a subtropical forest
<p>1. The dissimilarity and hierarchy of trait values that characterize niche and fitness differences, respectively, have been increasingly applied to infer mechanisms driving community assembly and to explain species co-occurrence patterns. Here, we predict that limiting similarity should result in the spatial segregation of functionally similar species, while functionally similar species will be more likely to co-occur either due to environmental filtering or competitive exclusion of inferior competitors (hereafter hierarchical competition).</p> <p>2. We used a fully mapped 50-ha subtropical forest plot in southern China to explore how pairwise spatial associations between saplings and between adult trees were influenced by trait dissimilarity and hierarchy in order to gain insight into assembly mechanisms. We assessed pairwise spatial associations using two summary statistics of spatial point patterns at different spatial scales and compared the effects of trait dissimilarity and trait hierarchy of different functional traits on the interspecific spatial associations. These comparisons allow us to disentangle the effects of limiting similarity, environmental filtering and hierarchical competition on species co-occurrence.</p> <p>3. We found that trait dissimilarity was generally negatively related with interspecific spatial associations for both saplings and adult trees across spatial scales, meaning that species with similar trait values were more likely to co-occur and thus supporting environmental filtering or hierarchical competition. We further found that trait hierarchy outweighed trait dissimilarity in structuring pairwise spatial associations, suggesting that hierarchical competition played a more important role in structuring our forest community than environmental filtering across life stages.</p> <p>4. This study employed a novel method, by offering the integration of pairwise spatial association and trait dissimilarity as well as trait hierarchy, to disentangle the relative importance of multiple assembly mechanisms in structuring co-occurrence patterns, especially the mechanisms of environmental filtering and hierarchical competition, which lead to indistinguishable co-occurrence patterns. This study also reinforced the importance of trait hierarchy rather than trait dissimilarity in driving neighborhood competition.</p>
Multicolor flow cytometry of monocultures and co-cultures of Bacteroides species
<p>Dataset of FCS (Flow Cytometry Standard) files, along with meta-data, related to a flow cytometry analysis of monocultures and co-cultures of <em>Bacteroides </em>species under several different conditions. </p> <p><strong>Data Collection. </strong>This<strong> </strong>dataset accompanies a journal artcle which was published in <em>Frontiers in Microbiology</em> (<a href="https://doi.org/10.3389/fmicb.2022.910390">https://doi.org/10.3389/fmicb.2022.910390</a>). The "Methods and Materials" section in this article fully describes the biological nature of these samples and how the samples were processed for flow analysis and analyzed with flow cytometry. </p> <p><strong>Data Organization. </strong>Dataset includes 1832 samples. See mapping.xlsx and mapping_key.xlsx for list of samples and their meta-data. Folders are formatted as {run_data}_{time_point} and contains only samples belonging to either a run performed on 2018/07/17 or 2018/07/21 for time points of either 0, 24, 48, 72, or 102 hours. </p> <p><strong>Data Analysis. </strong>Code used for manipulating and analyzing these samples is publicly available (<a href="https://github.com/firasmidani/BacteroidesFlowCytometry">https://github.com/firasmidani/BacteroidesFlowCytometry</a>).</p> <p><strong>Data Integrity</strong>. "hardac-hashes.txt" stores the MD5 hashes of the original folders created by the authors prior to uploading data to Zenodo.</p>
Co-LivEn : COllective LIVing ENergy Dataset
<p>The dataset contains detailed electricity measurements of appliances in a collective living (co-living) student apartment at KTH Live-in-Lab. The measurements included are RMS voltage, RMS current, real power, and power factor. The data was collected over a period of 277 days between 28th August 2020 and 31st May 2021 with 1 second time resolution. The compressed file "<a href="../api/files/a7c4dc9b-99f1-4497-ae6c-7a1c2cb1b669/appliance_csv.zip">appliance_csv.zip</a>" contains data in plain CSV file format, whereas "<a href="../api/files/a7c4dc9b-99f1-4497-ae6c-7a1c2cb1b669/appliance_mat.zip">appliance_mat.zip</a>" contains data in MATLAB file format. </p> <p>For more detailed information and insights into the dataset and the data collection process, refer to the following article. Kindly cite this when using the dataset.</p> <ul> <li>R. R. Avula, T. J. Oechtering and D. Månsson, "Adversarial Inference Control in Cyber-Physical Systems: A Bayesian Approach With Application to Smart Meters," in IEEE Access, vol. 12, pp. 24933-24948, 2024, doi: 10.1109/ACCESS.2024.3365270. </li> </ul>
UAV-based DEM along the Beng Co fault, central Tibet
<p>These data are the unmanned aerial vehicle (UAV) topography surveying data (.tif) of several offset lake shorelines and fluvial terraces/fans along the Beng Co fault. </p> <p>The UAV data were acquired by ~80 m high aerial photographs using a DJI (Dajiang Innovations Science and Technology Co., Ltd.) Phantom 4 quadrotor copter mounted with a 12.4-megapixel digital camera and measured 12 ground control points (GCPs) using a Trimble R8 RTK-GPS with an accuracy of several centimeters. High-resolution digital elevation models (DEM) were produced by PhotoScan software.</p>
Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall
<p>Reproducibility in organ size and shape is a fundamental trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. In the manuscript <a href="https://www.biorxiv.org/content/10.1101/2022.04.26.489498v1"><strong>"Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall", </strong>doi: https://doi.org/10.1101/2022.04.26.489498</a>, we took the sepal of Arabidopsis as a model, and we investigated whether variability of gene expression plays a role in variation of organ morphology.</p> <p>To address this question, we produced a dataset composed of both transcriptomic and morphological information obtained from 27 individual sepals from wild-type plants.</p> <p>This repository contains the raw confocal image of 30 sepals used as starting point for the analysis, as well as their extracted contours as binary images. These images were used to recover the 3D shape of the sepals.</p> <p>The 30 abaxial sepals were collected at early stage 11, from three different Col-0 wild-type plants, labeled D, E and F, grown simultaneously in experimentally controlled standard conditions. Each sepal was imaged under a confocal microscope using autofluorescence. Immediately following imaging, the sepal was frozen in liquid nitrogen for RNA extraction, on which an RNA-seq analysis was performed.</p> <p><strong>Related informations :</strong></p> <ul> <li>The repository of the numerical tools used for 3D shape extraction as well as the results of geometrical measurements is <a href="http://forge.cbp.ens-lyon.fr/redmine/projects/florivar">here</a>.</li> <li>The repository of RNA-Seq analysis results of these same sepals is here.</li> <li>And the analysis tools used to relate geometrical measurements to RNA-seq data are here.</li> </ul>
A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation
<p>B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.</p>
3D co-culture of pleura
<p>Pleural mesothelial cells are the predominant cell type in the pleural cavity, but their role in the pathogenesis of pleural diseases needs to be further elucidated. 3D organotypic models are a encouraging approach for an <em>in vivo</em> understanding of molecular disease development. The aim of the present study was to develop a 3D organotypic model of the pleural mesothelium. Specimens of human <em>pleura parietalis</em> were obtained from patients undergoing surgery at the University Hospital Leipzig, Germany. 3D co-culture model of pleura was established from human pleural mesothelial cells and fibroblasts. The model was compared to human pleura tissue by phase-contrast and light microscopy, immunochemistry and -fluorescence as well as solute permeation test. Histological assessment of the 3D co-culture model displayed the presence of both cell types mimicking the morphology of the human pleura. Vimentin and Cytokeratin, PHD1 showed a similar expression pattern in pleural biopsies and 3D model. Expression of Ki-67 indicates the presence of proliferating cells. Tight junctional marker ZO-1 was found localized at contact zones between mesothelial cells. Each of these markers were expressed in both the 3D co-culture model and human biopsies. Permeability of 3D organotypic co-culture model of pleura was found to be higher for 70 kDa-Dextran and no significant difference was seen in the permeability for small dextran (4kDa). In summary, the presented 3D organoid of pleura functions as a robust assay for pleural research serving as a precise reproduction of the <em>in vivo</em> morphology and microenvironment.</p>
Documenting And Assessing Open Innovation: Co-creation Of An Open Data Model For Surgical Training (Additional materials, tables 2 & 3)
<p>Challenge competitions have recently resurged for promoting open innovation in areas where markets fail to provide incentives, such as the Sustainable Development Goals (SDGs). Challenges call for the general public to contribute novel solutions to a well-defined problem, in exchange for prizes, credentials and the promise of further development of selected solutions. The aim of this paper is to report on the development of an open and collaborative data model to document and evaluate innovations in the context of a challenge competition, while also being compatible with the work of other open source communities to validate and improve them. By reusing open documentation standards and embedding them into a semantic collaborative platform, the model aimed to be flexible enough to respond to the evaluation needs of the project organisers and self-assessment for participants. We expect our experience provides insights on the potential of semantic, collaborative platforms and standards for increasing the impact of innovations towards the SDGs.</p> <p>The developer team defined the goal and scope of the ontology in collaboration with the GSTC organisers. This was done by agreeing on scenarios where the ontology will be used and establishing competency questions that the ontology has to be able to respond to. Table 2 describes the four motivating scenarios, including actors involved, requirements, sequence of actions and main problems identified. Table 3 details the competency questions for each scenario.</p>
Earthworms increase the potential for enzymatic bio-activation of biochars made from co-pyrolyzing animal manures and plastic wastes
<p>We assessed the enzymatic activation of four different biochars produced from pyrolyzing swine manure and poultry litter, and by co-pyrolyzing these livestock residues with agricultural spent mulch plastic film wastes (plastichars). Enzymatic activation consisted of incubating biochars in soil inoculated with earthworms (<em>Lumbricus terrestris</em>), which acted as biological vectors to facilitate retention of extracellular enzymes onto biochar surface. The activity of carboxylesterase ‒a pesticide-detoxifying enzyme‒ was measured in non-bioturbed soils (reference), linings of the burrows created by earthworms, casts (feces) and biochar particles recovered from the soil.</p>
Data from: Timbres of tolerance: Co-feeding tolerance in chimpanzees and bonobos is better explained by group-specific variation than species differences
<p><span>The human species exhibits a remarkable level of social tolerance which has propelled a plethora of behavioural expressions pivotal to our biological success. To date, the evolutionary origins of humans' "ultra-sociality" remain unclear, despite a substantial research focus on our closest living evolutionary relatives, the great apes. Bonobos are typically portrayed as more socially tolerant than chimpanzees and consequentially (sometimes) presented as a better model to study the evolutionary roots of human sociality. Yet, the current evidence supporting such a species-level categorization is equivocal. Here, we used validated group-level co-feeding tasks to test 16 independent <em>Pan </em>groups living in zoo (n=9) and sanctuary (n=7) settings, representing 225 individuals. We found that the expressions of social tolerance substantially overlapped between species, thus precluding categorical inference at the species level. Instead, marked differences were observed among groups, with some bonobo groups exhibiting higher social tolerance than chimpanzee groups, and vice versa. Interestingly, substantial intergroup variation was found within species living in the same environment, which attests to Pan's behavioural flexibility. We conclude that the pervasive dichotomy between the tolerant bonobo and the belligerent chimpanzee requires quantitative nuance, and that accurate phylogenetic tracing of (human) social behaviour necessitates estimations of intraspecific intergroup variation.</span></p>
Data for Vibrational Couplings between Protein and Co-factor in Bacterial Phytochrome Agp1revealed by 2D-IR Spectroscopy
<p>2D-IR data for the bacteriophytochrome Agp1 in the Pr and Pfr states </p>
Co-added optical spectra of globular clusters around M87 in the Virgo Cluster
<p>This dataset provides the co-added optical spectra of globular clusters in the Virgo core region. The spectra were used in the stellar population analysis of the paper "The Next Generation Virgo Cluster Survey. XXXIII. Stellar Population Gradients in the Virgo Cluster Core Globular Cluster System" by Ko et al. (2022). The detailed description can be found in the README file.</p>
Flower color and flowering phenology mediate plant-pollinator interaction assembly in a diverse co-flowering community
<p>Uncovering the role of competition and facilitation in community assembly is central for developing a predictive understanding of the forces that organize biodiversity. Standard trait-based approaches however rely on detection of only one assembly mechanism (competition or facilitation) along a single trait even though pollinator-mediated plant-plant interactions can be structured along multiple phenotypic, phenological and ecological traits. We evaluated plant species distribution along multiple phenotypic and ecological traits (flower color, flowering time, pollinator sharing) and described an entire co-flowering community as a set of modules with unique patterns of assembly, to test predictions regarding the relative contribution of competition and facilitation to the assembly of a diverse co-flowering community. We show a modular pattern of flower color assembly. Flower color modules differ in their spectral reflectance patterns including color hue and saturation. Within modules, however, species are differentially assembled along phenological and ecological traits (pollinator sharing) depending on the main pollinator group visiting plant species within each module. Results suggest different trait assembly patterns within individual trait-modules in the same co-flowering community and that different trait-patterns can result from the same type of ecological interaction. This study reveals empirical evidence of community assembly along multiple axes of trait differentiation and raises caution when interpreting assembly patterns based on a single trait.</p>
Experimental data linked to publication "Process optimization and study of the co-sintering behaviour of Cu-Ni multi-material 3D structures fabricated by spark plasma sintering (SPS)"
<p>Those are all the experimental data used to produce the plots in the article</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.
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
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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.
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