Find research datasets worth reusing

Sex and Age Impact CD4+ T Cell Susceptibility to HIV In Vitro Through Cell Activation Dynamics

Cellular composition and the responsiveness of the immune system evolve upon aging and are influenced by biological sex. CD4+ T cells from women living with HIV exhibit a decreased viral replication ex vivo compared to men's. We, thus, hypothesized that these findings could be recapitulated in vitro and infected primary CD4+ T cells with HIV-based vectors pseudotyped with VSV-G or HIV envelopes. We used cells isolated from twenty donors to interrogate the effect of sex and age on permissiveness over a six-day activation kinetics. Our data identified an increased permissiveness to HIV between 24 and 72 h post-stimulation. Sex- and age-based analyses at these time points showed an increased susceptibility to HIV of the cells isolated from males and from donors over 50 years of age, respectively. A parallel assessment of surface markers' expression revealed higher frequencies of activation marker CD69 and of immune checkpoint inhibitors (PD-1 and CTLA-4) in the cells from highly permissive donors. Furthermore, positive correlations were identified between the expression kinetics of CD69, PD-1 and CTLA-4 and HIV expression kinetics. The cell population heterogeneity was assessed using a single-cell RNA-Seq analysis and no cell subtype enrichment was identified according to sex. Finally, transcriptomic analyses further highlighted the role of activation in those differences with enriched activation and cell cycle gene sets in male and older female cells. Altogether, this study brought further evidence about the individual features affecting HIV replication at the cellular level and should be considered in latency reactivation studies for an HIV cure.

Raw absorbance data and R codes for analysing enzymatic activities

Raw absorbance data and sample metadata for study by Prokkola et al. (submitted 2023). See README.Statistical analysis of data available in another repository https://doi.org/10.5281/zenodo.8014314.

Dataset for monkeys A and B from AMAG: Additive, Multiplicative and Adaptive Graph Neural Network For Forecasting Neuron Activity

ECoG data from two monkeys, affi (A) and beignet (B) used in AMAG: Additive, Multiplicative and Adaptive Graph Neural Network For Forecasting Neuron Activity. Jingyuan Li, Leo Scholl, Trung Le, Pavithra Rajeswaran, Amy L Orsborn, and Eli Shlizerman. NeurIPS. 2023. https://openreview.net/forum?id=7ntI4kcoqGSee also https://github.com/shlizee/AMAG

Training and test data, plus saved models for the upcoming paper `Top-down perceptual inference shaping the activity of early visual cortex'

Each .pkl file contains a training or test dataset in the form of a Python dictionary (generated with Python 3.8.5) with the following fields:<ul><li>'train_images': 640,000 float32 images used for model training. These are 40px images that contain 1600 pixel intensities each.</li><li>'train_labels': float32 labels for each image in 'train_images'. All natural images are labeled with 0.0. Texture images are labeled with 0.0, 1,0, 2.0, 3.0, or 4.0, according to their texture family.</li><li>'test_images': 64,000 float32 images used for model testing. These are 40px images that contain 1600 pixel intensities each.</li><li>'test_labels': float32 labels for each image in 'test_images'. All natural images are labeled with 0.0. Texture images are labeled with 0.0, 1,0, 2.0, 3.0, or 4.0, according to their texture family.</li></ul>The .zip file contains a saved model snapshot and various intermediate evaluative data. Details on these are coming soon.

opencc-by-4.0Jan 2023View details →

Figure 1 in Effects of commercial oils on the camel tick, Hyalomma dromedarii (Acari: Ixodidae) and their enzyme activities

Figure 1. Mortality percentages of Hyalomma dromedarii semi-engorged females treated with different concentrations of four oils at five successive days after treatment – A. Rosemary; B. Garlic; C. Neem; D. Cyperus. a, b, … etc. indicate significant differences between concentrations (%) of each oil for each day according to Tukey test (P <0.001).

Minute-Level Human Activity and Particulate Matter Exposure Dataset from Ljubljana, Slovenia

This dataset encompasses detailed measurements of human activities and particulate matter exposure at a minute-level resolution, collected in Ljubljana, Slovenia from September 24 to October 31, 2020. Data was gathered from 18 participants using a combination of devices: a personal particulate matter monitor (PPM), a Garmin Vivosmart 3 smart activity tracker (SAT), and the Clockify app. The PPM provided real-time measurements of particulate matter concentrations (PM1, PM2.5, and PM10), as well as environmental parameters like temperature, humidity, and altitude. The SAT tracker offered insights into personal health data, including average heart rate and metabolic equivalent of task (MET). Clockify app was utilized for detailed logging of various activities categorized with minute accuracy. Key variables included in the dataset are: <ol> <li>Participant ID</li> <li>Date of data collection</li> <li>Time of data recording (minute accuracy)</li> <li>Specific task or activity performed</li> <li>Particulate matter - PM1 - concentrations</li> <li>Particulate matter - PM2.5 - concentrations</li> <li>Particulate matter - PM10 - concentrations</li> <li>Environmental temperature</li> <li>Relative humidity</li> <li>Altitude</li> <li>Speed</li> <li>Average heart rate</li> <li>Metabolic equivalent of task</li> </ol> This dataset offers a resource for exploring the interplay between individual behaviors and air pollution exposure, with applications in environmental health research and the development of machine learning models for activity recognition.

opencc-by-4.0Dec 2022View details →

Dataset from the analysis of biological activity of endophytic strain Serratia quinivorans KP32, the expression of biocontrol-related genes and the activity of antioxidant enzymes in bacterial cells treated with pathogenic fungi filtrates

This dataset contains the data from the analyses published in the article entitled "Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens" in the International Journal of Molecular Sciences (https://doi.org/10.3390/ijms232415561). The data consist of results collected for studies on the antifungal activity of KP32 strain towards four fungal phytopathogens, results of primer efficiency determination and studies on the expression of genes potentially involved in biocontrol after treatment of KP32 strain with the fungal phytopathogens filtrates. Additionally, absorbances from activity tests for catalase (CAT) and superoxide dismutase (SOD) in the strain treated with fungal pathogens are included.

Late Quaternary activity of the NW Cardrona Fault, Otago, New Zealand - Supplements S1 and S2

Supplementary material to accompany: van den Berg, E. J., Williams, J. N.*, Stirling, M. W., Barrell, D. J. A., Griffin, J. D., Litchfield, N. J., & Wang, N. (2024). Late Quaternary activity of the NW Cardrona Fault, Otago, New Zealand. New Zealand Journal of Geology and Geophysics, 1–21. https://doi.org/10.1080/00288306.2023.2297962 This dataset includes: <ul> <li>Supplement S1: Supplementary figures S1-S3</li> <li>Supplement S2: Code used to generate the OxCal models for the Macdonalds Creek and Gibbston trenches</li> </ul> *Corresponding author: jack.williams@otago.ac.nz

Supplemental Movie 5: Pattern of slow wave activation in intact stomach as viewed by imaging of Ca2+ transients in ICC-MY.

Supplemental Movie 5:  Pattern of slow wave activation in intact stomach as viewed by imaging of Ca2+ transients in ICC-MY  Ca2+ transients were monitored in canulated whole stomachs taken from mice expressing GCaMP3 exclusively in ICC (upper left panel). The whole stomach from fundus through the pylorus is visualized in the FOV.  Right panel shows differentiated image in which background (unchanged pixels) remains black and active pixels (ICC) are intensity-coded to white.  Activation of Ca2+ waves (which activate currents in ICC-MY and generate slow waves in gastric muscles) develop into a spiral pattern of activation from a dominant pacemaker region near the greater curvature of the corpus.  Ca2+ transients in the whole stomach are plotted as a spatio-temporal map, displaying proximal to distal propagation of Ca2+ waves along the length of the stomach (lower panel). (Provided by Dr. Grant Henning)

opencc-by-4.0Sep 2023View details →

Reporting Database of the INCENTIVE project's monitoring and evaluation activities of the Citizen Science Hubs pilot operation (M16-M31)

The current excel file constitutes the INCENTIVE Reporting Database, meaning a repository of the data that were accumulated in WP4 (described within Deliverable 4.1). The results presented here are the main input for the elaboration of Deliverable 4.2 and Deliverable 4.3.

Manual active layer and and water table depth measurements from the autochamber sites at Stordalen Mire, northern Sweden (2003-2017)

Files: <ul> <li>Active_Layer_Water_Table_03-17.xlsx - Data file, with main data in the "DATA" tab.</li> <li>IsoGenieSite_AL_WTD_MapsVisualNotes_200310.pdf - Visual notes on the measurement locations.</li> </ul> The following site labels (with chamber numbers in parentheses) correspond to the main autochamber sites: <ul> <li>Dry (1,3,5) = Palsa Autochamber Site</li> <li>Mesic (2,4,6) = Sphagnum Autochamber Site</li> <li>Wet (7,8) = Eriophorum Autochamber Site</li> </ul> Water table depth (W D) was measured in wells. Active layer depth (A L) was measured by inserting a metal rod into the surface. The original instruction page is included in page 3 of the pdf. All depths are in centimeters (cm) below peat surface (i.e. peat or Sphagnum spp. vegetation surface = 0), with negative values indicating depth below the surface and positive values (for water table) indicating height of standing water above the surface. Blank data in the Palsa or water table column means no water table observed. Staff gauge was added July 2006 at the edge of a small pond in the fen visible from the shack, with measurements reported in meters. All other measures are in cm.   FUNDING: We thank the Swedish Polar Research Secretariat and SITES for the support of the work done at the Abisko Scientific Research Station. SITES is supported by the Swedish Research Council's grant 4.3-2021-00164. This research is a contribution of the EMERGE Biology Integration Institute, funded by the National Science Foundation, Biology Integration Institutes Program, Award # 2022070. The IsoGenie Project (which funded much of the work at these sites during the measurement period) was funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research, grant #s DE-SC0004632, DE-SC0010580, and DE-SC0016440.

PROCRAFT Final Meeting - Educational activities on WWII aircraft at the Montreal Aviation Museum by Jean Desbiens – Montreal Museum

Open the record for dataset details and reuse information.

opencc-zeroDec 2023View details →

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Livestock activity shifts large herbivore temporal distributions to their crepuscular edges

Wildlife species are transitioning to greater crepuscular and nocturnal activity in response to high human densities. This plasticity in temporal niches may partially mitigate the impacts of human activity but may also result in underestimating human effects on species foraging, predator-prey relationships, and community level interactions. We deployed remote cameras to characterize shifts in herbivore diel activity in protected habitat vs pastoralist landscapes. We then compared species traits including body mass, dietary preferences, and behavioral characteristics as potential predictors of species sensitivity to livestock. Our data capture a significant temporal shift away from core cattle activity for nearly every herbivore species in our study, leading to more crepuscular activity patterns. As livestock were primarily diurnal and predators primarily nocturnal in pastoralist habitat, species that decreased their overlap with livestock were more likely to increase their overlap with potential predators. Other than species' typical daytime activity levels, we found no evidence that any particular trait significantly predicted temporal shifts in response to livestock. Instead, species generally trended toward greater activity levels at dawn, suggesting that cattle have a homogenizing effect on community-wide activity patterns. Our findings highlight how cohabitation with livestock can profoundly alter the temporal niches of wild herbivores. Shifts in diel activity patterns may reduce herbivore foraging time or efficiency and potentially have cascading shifts on predator-prey dynamics. Given that species traits could not predict responses to livestock, our analysis suggests that conservation strategies should consider each species separately when designing interventions for wildlife management.

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Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity

Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared to forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact non-urban areas on both recent and older timescales.

opencc-zeroDec 2023View details →

Code and Data for: Donor activity is associated with US legislators' attention to political issues

Contains data, code, and annotations for: <blockquote> Goel P, Malkin N, Gaynor SW, Jojic N, Miler K, Resnik P (2023) Donor activity is associated with US legislators’ attention to political issues. PLoS ONE 18(9): e0291169. https://doi.org/10.1371/journal.pone.0291169 </blockquote>

On effect of chloroform on electrical activity of proteinoids

Within the scope of this study, titled "On the effect of chloroform on the electrical activity of proteinoids," we present a comprehensive investigation and characterization of various electro-physical parameters. These include impedance, capacitance, resistance, and voltage. These metrics were determined over time to comprehensively understand the system's temporal response, particularly in the presence of chloroform. Furthermore, time-dependent voltage outputs were carefully analyzed to distinguish regular voltage spike trains, which are vital to understanding the system's electrical signal propagation properties.

openJan 2024View details →

Dataset of "A multi-method approach to drafting candidate entrustable professional activities for a general internal medicine residency programme"

The present Dataset is related to a study on "A multi-method approach to drafting candidate entrustable professional activities for a general internal medicine residency programme" and include : <ul> <li>The  "Voting sheet model" used for the 1st round of voting according to the RAND appropriateness method</li> <li>The tables of aggregate results after round 1 and after round 2 of the RAND appropriateness method, with subgroup analysis</li> <li>A document describing which items where chosen to be included in round 2 of voting and why (file name "Summary_Decisions_.....")</li> <li>The list of candidate EPA (Entrustable Professional Activities) selected after 2 round of rating by the expert panel. This list of 225 EPA had not yet undergone the quality check using the EQual-Criteria (DOI: 10.1097/ACM.0000000000001908)</li> </ul> Methods: We set up a multi-step approach including a systematic review of the international literature; four national focus groups; a national consensus process using a RAND appropriateness method and a quality check of the selected candidate EPAs using Equal criteria. Results: These steps generated a final list of 247 candidate EPAs in GIM that were submitted for the national consensus process. After two rounds of rating, experts agreed on the appropriateness for the GIM postgraduate training of 225 of the candidate EPAs. Twenty-two of the proposed EPAs were deemed inappropriate and disagreement persisted only for two EPAs.   General description of the data set  : o   Nature: aggregated, analysed data o   Mode of collection: experimental o   Format: unstructured text, database

opencc-by-4.0Jan 2024View details →

Costless renewable energy distribution model based on cooperative game theory for energy communities considering its members' active contributions

This dataset was used in the case study of the following publication:  - Luis Gomes, Zita Vale, "Costless renewable energy distribution model based on cooperative game theory for energy communities considering its members’ active contributions," Sustainable Cities and Society, Volume 101, 2024, 105060, ISSN 2210-6707, <a href="https://doi.org/10.1016/j.scs.2023.105060">https://doi.org/10.1016/j.scs.2023.105060</a>  (if you used this dataset in your publications, please send us your information so we can add your publication to the list above)   The dataset is composed by energy generation, consumption, and forecast (for generation, and for consumption) expressed in Wh. The data considers an energy community of 10 prosumers in 30 days. The dataset also has energy prices that have been collected from MIBEL (Iberian Electricity Market).   We would be grateful if you could acknowledge the use of this dataset in your publications. Please use the Zenodo publication to cite this work.