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8,565 results for “characterization”
Waste Characterization, Quantification, and Composting in Cape Maclear, Malawi
<p>This dataset contains information on waste characterization and quantification, current soil conditions, and agricultural practices of farmers from Cape Maclear, Malawi. </p>
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
Data: Characterizing the sediment dynamics through in-situ measurements in the abyssal Manila Trench, northeast South China Sea
<p>Along the Manila Trench, a total of four moorings were deployed in <a name="OLE_LINK5"></a>September 2019 and recovered in August 2020. The field measurements in velocity and turbidity were resampled to create hourly dataset.</p>
Characterizing the Interaction of the Effects of a Museum Visit on Mobility, Cognition, and Well-being in People with Stroke
<h2><strong>Study description</strong></h2> <p>This exploratory small case study operated by Medical Physics Laboratory & Digital Innovation of School of Medicine of Aristotle University of Thessaloniki (AUTH) is a collaborative study between AUTH and McGill-CRIR-Canada, and for this reason it followed and replicated part of the protocol of the Canadian VITALISE partners described above. The aim of this particular small-case study was to investigate the interaction of the effects of a museum visit (Museum of Casts and Antiquities in Aristotle University of Thessaloniki) on mobility, cognition, well-being and the experience of individuals, as well as to investigate whether cognitively and verbally accessible audio guides of exhibits contribute to a better understanding of the descriptions of these exhibits, through measurements made using advanced technologies. In this context, the data collected aimed also to draw some conclusions regarding the feasibility and user satisfaction of conducting a range of different measurements and interventions in a museum setting.</p> <p>Piloting phase: The piloting phase began in May 2023 and was concluded at the end of the year. Prior to the museum visit, the participants were administered some questionnaires in the Thessaloniki Action for HeAlth & Wellbeing Living Lab - Thess-AHALL, aiming to obtain a holistic view on their cognitive status, as well as dimensions of their physical and mental wellbeing and quality of life. <a href="../api/records/11473970/draft/files/Questionnaires%20during%20the%20museum%20visit.xlsx/content" target="_blank" rel="noopener noreferrer">Questionnaires during the museum visit.xlsx</a></p> <p>Afterwards, the participants, one at a time, entered the museum with the members from the project’s research team, where they were asked to wear some specific equipment. In particular, they initially wore a pair of smart insoles (Digitsole Pro Smart Insoles) (<a href="../api/records/11473970/draft/files/Digitsole-pro-museum-dataset.csv/content" target="_blank" rel="noopener noreferrer">Digitsole-pro-museum-dataset.csv</a>) and a smart watch (Smartwatch-Fitbit Charge 5) <a href="../api/records/11473970/draft/files/Fitbit%20Datasets.zip/content" target="_blank" rel="noopener">Fitbit Datasets.zip</a> and were asked to walk at their own pace following a predetermined guided tour route through the museum spaces and exhibits. Breaks were provided whenever requested by the participants.<br>After completing their guided tour in the museum, they were asked to wear eye-tracking glasses (Pupil Labs) <a href="../api/records/11473970/draft/files/Pupils-dataset.zip/content" target="_blank" rel="noopener noreferrer">Pupils-dataset.zip</a> and headphones to listen to audio descriptions (audio guides) of three selected exhibits, the Tombstone, the Hermes of Praxiteles and the West Pediment from the temple of Zeus at Olympia. Specifically, they were asked to stand in front of three (3) exhibits and listen to the description. For each of the three exhibits, participants first listened to their original description (a description that someone can usually find next to the exhibit or in a relevant educational textbook) and then they listened to the modified, accessible version of the exhibit description (with simpler words, shorter sentences etc.). After each audio description (original and modified), they were asked to answer a number of predetermined questions related to the audio description they had just heard.</p> <p>At the end, after the aforementioned equipment was removed, they were asked to answer a number of questions and questionnaires about their overall museum experience and potential challenges or stress experienced (Satisfaction and feasibility questionnaire, Visual Analog Stress scale, State-Trait Anxiety Inventory) <a href="../api/records/11473970/draft/files/Analysis%20feasibility%20&%20satisfaction%20questionnaire.xlsx/content" target="_blank" rel="noopener noreferrer">Analysis feasibility & satisfaction questionnaire.xlsx</a>.</p>
Figure 3 in Obtainment and characterization of digestive aspartic proteases from the fish Caranx hippos (Linnaeus, 1766)
Figure 3. Effect of NaCl on the EE acidic proteases.
Figure 1 in Obtainment and characterization of digestive aspartic proteases from the fish Caranx hippos (Linnaeus, 1766)
Figure 1. EE Zymogram.
Fig. 1 in Molecular characterization of the re-emerging West Nile virus in avian species and equids in Israel, 2018, and pathological description of the disease
Fig. 1 Meningeal and brain tissue hemorrhages in WNV-infected long eared owl (Asio otus) AV156
Isogeochemical characterization of mountain system recharge processes in the Sierra Nevada, California
<p>Mountain System Recharge processes are significant natural recharge pathways in many arid and semi-arid mountainous regions. However, Mountain System Recharge processes are often poorly understood and characterized in hydrologic models. Mountains are the primary water supply source to valley aquifers via lateral groundwater flow from the mountain block (Mountain Block Recharge) and focused recharge from mountain streams contributing to focused Mountain Front Recharge at the piedmont zone. Here, we present a multi-tool isogeochemical approach to characterize mountain flow paths and Mountain System Recharge in the northern Tulare Basin, California. We used groundwater chemistry data to delineate hydrochemical facies and explain the chemical evolution of groundwater from the Sierra Nevada to the Central Valley aquifer. Stable isotopes and radiogenic groundwater tracers validated Mountain System Recharge processes by differentiating focused from diffuse recharge, and estimating apparent groundwater age, respectively. Novel application of End-Member Mixing Analysis (EMMA) using conservative chemical components revealed three Mountain System Recharge end-members: (1) evaporated Ca-HCO<sub>3</sub> water type associated with focused Mountain Front Recharge, (2) non-evaporated Ca-HCO<sub>3</sub> and Na-HCO<sub>3</sub> water types with short residence times associated with shallow Mountain Block Recharge, and (3) Na-HCO<sub>3</sub> groundwater type with long residence time associated with deep Mountain Block Recharge. We quantified the contribution of each Mountain System Recharge process to the valley aquifer by calculating mixing ratios. Our results show that deep Mountain Block Recharge is a significant recharge component, representing 31 to 53 % of the valley groundwater. Greater hydraulic connectivity between the Sierra Nevada and Central Valley has significant implications for parameterizing groundwater flow models. Our framework is useful for understanding Mountain System Recharge processes in other snow-dominated mountain watersheds.</p>
Immunohistochemical characterization of a gene-targeted UcnCre line of mice
<p><span>Neurons expressing Urocortin-1 (Ucn) in the Edinger Westphal (EW) nucleus have been hypothesized to play an important role in regulating consummatory behaviors and metabolism, affective-like behaviors, and responses to stress. We generated <em>Ucn<sup>Cre</sup></em> mice to allow measurement and manipulation of Ucn neuron activity. The images of immunostaining included here demonstrate Cre-induced protein expression in EW cell bodies and projection fibers following a genetic cross to <em><span>Rosa26<sup>LSL-tdTomato</sup></span></em><sup><span> </span></sup>mice (tdTomato expression) and a viral injection of <span>pAAV1-Ef1a-DIO-Syn:mCherry </span>(eliciting synaptophysin-mCherry expression). The tdTomato expression can also be seen in cell bodies in the anterior insular cortex, likely as a result of those cells transiently expressing Ucn during development.</span></p>
CXCL12-loaded-hydrogel (CLG): a new device for metastatic Circulating Tumor Cells (CTCs) capturing and characterization
<p><strong>Background</strong>: Circulating Tumor Cells (CTCs) represent a small, heterogeneous population that comprise the minority of cells able to develop metastasis. To trap and characterize CTCs with metastatic attitude, a CXCL12-loaded hyaluronic-gel (CLG) was developed. CXCR4+cells with invasive capability would infiltrate CLG.<br><strong>Methods</strong>: Human colon, renal, lung and ovarian cancer cells (HT29, A498, H460 and OVCAR8 respectively) were seeded on 150 µl Empty Gels (EG) or 300 ng/ml CXCL12 loaded gel (CLG) and allowed to infiltrate for 16 hours. Gels were then digested and fixed with 2% FA-HAse for human cancer cell enumeration or digested with HAse and cancer cells recovered. CLG-recovered cells migrated toward CXCL12 and were tested for colonies/spheres formation. Moreover, CXCR4, E-Cadherin and Vimentin expression was assessed through flow cytometry and RT-PCR. The clinical trial “TRAP4MET” recruited 48 metastatic/advanced cancer patients (8 OC, 8 LC, 8 GBM, 8 EC, 8 RCC and 8 EC). 10 cc whole blood were devoted to PBMCs extraction (7cc) and ScreenCell™ filters (3cc) CTCs evaluation. Ficoll-isolated patient’s PBMCs were seeded over CLG and allowed to infiltrate for 16 hours; gels were digested and fixed with 2% FA-HAse, cells stained and DAPI+/CD45-/pan-CK+ cells enumerated as CTCs.<br><strong>Results</strong>: Human cancer cells infiltrate CLG more efficiently than EG (CLG/EG ratio 1.25 for HT29/ 1.58 for A498/ 1.71 for H460 and 2.83 for OVCAR8). CLG- recovered HT29 cells display hybrid-mesenchymal features [low E-cadherin (40%) and high vimentin (235%) as compared to HT29], CXCR4 two-fold higher than HT29, efficiently migrate toward CXCL12 (two-fold higher than HT29) and developed higher number of colonies (171±21 for HT29-CLG vs 131±8 colonies for HT29) /larger spheres (spheroid area: 26561±6142 µm2 for HT29-CLG vs 20297±7238 for HT29). In TRAP4MET clinical trial, CLG-CTCs were isolated in 8/8 patients with OC, 6/8 with LC, 6/8 with CRC, 8/8 with EC, 8/8 with RCC cancer and 5/8 with GBM. Interestingly, in OC, LC and GBM, CLG isolated higher number of CTCs as compared to the conventional ScreenCell™ (CLG/SC ratio=1.88 for OC, 2.47 for LC and 11.89 for GBM). Bland and Altman blot analysis and Passing and Bablok regression analysis showed concordance between the methodological approaches but indicate that SC and CLG are not superimposable suggesting that the two systems select cells with different features.<br><strong>Conclusion</strong>: CLG might represent a new and easy tool to isolate invasive CTCs in multiple cancers such as OC, LC and GBM at today orphan of reliable methods to consistently detect CTCs. </p>
Characterizing multidimensional cellular physiological states with quantitative three-dimensional shape descriptors for cell membranes
<h3>Supplementary dataset and code for the article "<em>Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes</em>"</h3> <p>CShaper Dataset.zip: The 3D cell regions reused from the previously published article <a href="https://doi.org/10.1038/s41467-020-19863-x">https://doi.org/10.1038/s41467-020-19863-x</a>.</p> <p>Cell Shape Descriptors - Code & Data.zip: The code (exemplifed by embryo Sample04) and data (including embryo Sample04-Sample20) of 12 3D shape descriptors for all 3D cell regions in the <em>CShaper</em> dataset.</p> <p>GUI.zip: The user-friendly software <em>Shape Descriptor Tool</em> is a Graphical User Interface based on <em>Matlab</em> for calculating 12 shape descriptors for a 3D cell region (exemplified by embryo Sample20, time point 14, ABpl cell in the <em>CShaper</em> dataset). The instruction guidebook is included in the Supplementary Material of the article.</p>
Figure 1 in First report of morphological and molecular characterization of Moroccan populations of Globodera pallida
Figure 1: Sampled areas and regions infested with GlOBOdeRa pallida in Morocco.
Fig 2 in Morphometrical characterization of the Atlantic mudskipper species (Periophthalmus barbarus) (Linnaeus, 1766) (Perciformes; Gobiiae) from Abonema in Port Harcourt, Rivers State, Nigeria
Fig 2: Principal component plot 1 of the measurements.
Fig 1 in Morphometrical characterization of the Atlantic mudskipper species (Periophthalmus barbarus) (Linnaeus, 1766) (Perciformes; Gobiiae) from Abonema in Port Harcourt, Rivers State, Nigeria
Fig 1: Morphometric and meristic measurements of Mudskipper and their abbreviations.
Fig 3 in Morphometrical characterization of the Atlantic mudskipper species (Periophthalmus barbarus) (Linnaeus, 1766) (Perciformes; Gobiiae) from Abonema in Port Harcourt, Rivers State, Nigeria
Fig 3: Principal component plot 1 of the measurements.
A quantitative approach to easily characterize and predict cell death and escape to β-lactam treatments
<p>This repository contains the raw experimental data corresponding to the paper entitled "A quantitative approach to easily characterize and predict cell death and escape to β-lactam treatments" and authored by Andreani, Gross and colleagues. </p> <p>The analysis of the data and the creation of the figures of the paper can be done using the code available at https://gitlab.inria.fr/InBio/Public/esbl-escape. A README file, briefly describing data organization, is provided.</p>
Seasonal footprints on ecological time series and jumps in dynamic states of protein configurations from a nonlinear forecasting method characterization (DataSet)
<p>Data from the article: <br>"Seasonal footprints on ecological time series and jumps in dynamic states of protein configurations from a nonlinear forecasting method characterization", L. Reyes, K. Campos, G. D. Avendaño, L. González-Paz, A. Vivas, Y. J. Alvarado, and S. Flores.</p> <p>Data to be used with some implementation of the forecasting method of reference:<br>Sugihara G. and May R. M., Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series, <em>Nature</em> <strong>344</strong>, 734–741 (1990).</p>
Figure 1 in Prevalence of Blastocystis sp. in Morocco: Comparative assessment of three diagnostic methods and characterization of parasite forms in Jones' culture medium
Figure 1. Dispersion of intestinal parasitic species among infected individuals.
Dataset for "On Developing an ML-Based Approach for the Automatic Characterization of Behavioral Phenotypes for Dairy Cows Relevant to Thermotolerance"
<p>This dataset consists of 3,421 videos filmed at T & K Dairy in Snyder, TX, over a 24-hour period on March 12-13, 2023. These videos were then used to train, validate, and evaluate a computer vision algorithm that is capable of automatically identifying cows using their coat patterns.</p>
Figure 3 in FlorAl biometrics And phenologicAl chArActeriZAtion of flowering And fruiting of the passion fruit PAssiflorA TrinTAE in southwestern BAhiA, BrAZil
Figure 3. Flowers of Passiflora trintae in the sampling site.
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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.