Find research datasets worth reusing

Data and Scripts associated with "Fisher activity patterns show potential for behavioural adaptations to human modified landscapes"

Script and data for running both models from manuscript. Data contains daily and nightly mean activity levels (ODBA) for fisher captured from 2021-2023 in Rhode Island, USA.

DNA sequences for: Synthetic control of actin polymerization and symmetry breaking in active protocells

Non-linear biomolecular interactions on membranes drive membrane remodeling crucial for biological processes including chemotaxis, cytokinesis, and endocytosis. The complexity of biomolecular interactions, their redundancy, and the importance of spatiotemporal context in membrane organization impede understanding of the physical principles governing membrane mechanics. Developing a minimal in vitro system that mimics molecular signaling and mem- brane remodeling while maintaining physiological fidelity poses a significant challenge. Inspired by chemotaxis, we reconstructed chemically regulated actin polymerization inside vesicles, guiding membrane self-organization. An external, undirected chemical input induced directed actin polymerization and membrane deformation uncorrelated with upstream biochemical cues, suggesting symmetry breaking. A biophysical model incorporating actin dynamics and membrane mechanics proposes that uneven actin distributions cause non-linear membrane deformations, consistent with experimental findings. This protocellular system illuminates the interplay between actin dynamics and membrane shape during symmetry breaking, offering insights into chemotaxis and other cell biological processes.

Experimental Measurements of Active Vibration Reduction via Current Injection in an Electric Motor

For each considered condition (650 and 800 rpm), two recordings of the motor under test in normal operation without current injection can be found, as well as the 25 current injection tests obtained by combining different values of amplitude and phase. For each case, an excel file with data analysis can also be found. The recordings are provided in the form of .wav files. Each .wav file has 7 channels, arranged as follows: CH1     -> Accelerometer X (Dytran, type 3233A) CH2     -> Accelerometer Y (Dytran, type 3233A) CH3     -> Accelerometer Z (Dytran, type 3233A) CH4     -> Microphone (Bruel&Kjaer, type 4189) CH5    -> Current U CH6    -> Current V CH7    -> Current W

Data from: Steatotic liver disease induced by TCPOBOP-activated hepatic constitutive androstane receptor: Primary and secondary gene responses with links to disease progression

Constitutive Androstane Receptor (CAR, Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid and lipid metabolizing enzymes, stimulates liver hypertrophy and hyperplasia, and ultimately, hepatocellular carcinogenesis. The mechanisms linking early CAR responses to later disease development are poorly understood. Here we show that exposure of CD-1 mice to TCPOBOP, a halogenated xenochemical and selective CAR agonist ligand, induces pericentral steatosis marked by hepatic accumulation of cholesterol and neutral lipid, and elevated circulating alanine aminotransferase, indicating hepatocyte damage. TCPOBOP-induced steatosis was weaker in the pericentral region but stronger in the periportal region in females compared to males. Early (1-day) TCPOBOP transcriptional responses were enriched for CAR-bound primary response genes, and for lipogenesis and xenobiotic metabolism and oxidative stress protection pathways; late (2-wk) TCPOBOP responses included many CAR binding-independent secondary response genes, with enrichment for macrophage activation, immune response and cytokine and reactive oxygen species production. Late upstream regulators specific to TCPOBOP-exposed male liver were linked to pro-inflammatory responses and hepatocellular carcinoma progression. TCPOBOP administered weekly to male mice using a high corn oil vehicle activated carbohydrate-responsive transcription factor (MLXIPL)-regulated target genes, dysregulated mitochondrial respiratory and translation regulatory pathways, and induced more advanced liver pathology. Overall, TCPOBOP exposure recapitulates histological and gene expression changes characteristic of emerging steatotic liver disease, including secondary gene responses in liver non-parenchymal cells indicative of transition to a more advanced disease state. Upstream regulators of both the early and late TCPOBOP response genes include novel biomarkers for foreign chemical-induced metabolic dysfunction-associated steatotic liver disease.

Mobile Sensor Readings of Activities

This collection contains mobile sensor readings used to train an activity recognition classifier. The sensor data was accessed via the Generic Sensor API. Mobile sensor readings from the following sensors: <ul> <li>accelerometer</li> <li>gyroscope</li> <li>magnetometer</li> <li>gravity sensor</li> <li>relative orientation sensor</li> <li>absolute orientation sensor</li> <li>linear acceleration sensor</li> </ul> Recording were measured while the following activities were measured: <ul> <li>Lying</li> <li>Sitting</li> <li>Standing</li> <li>Walking</li> <li>Stairs up</li> <li>Stairs down</li> <li>Running</li> <li>Taking the car</li> <li>Taking the bus</li> <li>Taking the tram</li> <li>Taking the train</li> <li>Taking the metro</li> </ul> <h3>Structure of the dataset</h3> The collected data in each recording includes the start time timestamp readingID, the activity label activity, the duration of the recording in elapsedTime, and an object sensorData, which contains the lengthy sensor measurements. The measurements for each sensor is stored in the form of an array containing on each index a series of four values. The time of when the measurement was taken t, and the value in the three axes x,y and z. A minimalistic example of the format of the collected data: { "readingID": 1710151914418, "activity": ""walk"", "elapsedTime": 17312 "sensorData": { "acce": [ ... { "t": 1624, "x": 0.05, "y": -0.61, "z": 0.21, }, ... ] "gyro": Array (844) "magnet": Array (136) } }   A big thanks to all the volunteers who helped collect this dataset.

Categorisation of monogenic disorders: Underlying a deficit of type I IFN activity / observed type I IFN signalling upregulation

<div>The last 20 years have seen the definition of human monogenic disorders and their autoimmune phenocopies underlying either defective or enhanced type I interferon (IFN) activity. These disorders delineate the impact of type I IFNs in natural conditions. Remarkably, only a narrow window of type I IFN activity is beneficial. Insufficient type I IFN predisposes humans to life-threatening viral diseases, albeit surprisingly few, with a central role in immunity to respiratory and cerebral viral infection. Excessive type I IFN, perhaps unexpectedly, appears to underlie a greater number of autoinflammatory and/or autoimmune conditions known as type I interferonopathies, whose study has revealed multiple molecular programs involved in the induction of type I IFN signaling. These observations suggest the manipulation of type I IFN activity to within a physiological range may be clinically relevant for the prevention and treatment of viral and inflammatory disease.</div>

Data for: Post-translational regulation of photosynthetic activity via the TOR kinase in plants

Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photo-oxidative damage. We have identified a post-translational mechanism linking the eukaryotic Target of Rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origins that regulates chloroplast activity, and photosynthesis in particular. We find that RelA SpoT Homologue 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific N-terminal region which is phosphorylated in a TOR-dependent manner. Downregulating TOR activity causes a rapid increase in ppGpp synthesis in RSH3 overexpressors and reduces photosynthetic capacity in an RSH-dependent manner in wild-type plants. The TOR-RSH3 signaling axis therefore regulates the equilibrium between chloroplast activity and plant growth, setting a precedent for the regulation of organellar function by TOR.

UI Logs for Screenshot and for Activity Identification

These data correspond to the set of Problems used for the evaluation of the proposal From Screenshots to Process Models: Improving Activity Identification through Screen Text. Each problem includes a User-Interaction (UI) Log that contains comprehensive process information. Accompanying the UI Log are directories with 58 screenshots from different instances of processes recorded on Odoo or Gmail interfaces and directories containing all on-screen text extracted from each screenshot using OCR. The UI Log references the screenshots and their corresponding OCR files for each row. Additionally, results for every execution run per Problem are available. The results directories include subdirectories, differentiated by the image/text weight in the execution, containing the expanded base UI Log with columns resulting from feature extraction and clustering. Each Problem has its summary file, providing an overview of all executions and the relevant clustering and evaluation metrics. A precise breakdown and description of each of the directories and files present in this assessment is provided below: input/Problem_X-Y/ (where X represents the number of the Problem given in the article and Y its full name). <ul> <li>screenshots/: contains the screenshots from Odoo and Gmail interfaces. The naming pattern is X_img.png where X is the corresponding identifier. Each record contains up to 58 screenshots representing different activities within the instantiation of a business process.</li> <li>ocr_results/: stores the results of applying OCR techniques to all screenshots for extracting all on-screen text. This directory includes a .txt file for each image, containing the extracted text. The naming pattern is similar to the previous one: X_ocr.txt where X is the identifier. These files are used for executions that use all on-screen text as a source along with the images.</li> <li>log.csv: .csv file representing the UI Log of the process. It contains the following columns: <ul> <li>id: identifier corresponding to a screenshot within the UI log.</li> <li>screenshot: path to the image corresponding to the row in the UI log within screenshots/.</li> <li>timestamp: time marker for defining the sequential order of actions in the UI log</li> <li>header: text string extracted from the browser’s tab.</li> <li>header_txt: path to each corresponding text file within ocr_results/.</li> <li>ground_truth: label assigned to identify and group images by activity. Compared with the activity_label column after algorithm application to determine execution’s evaluation metrics.</li> </ul> </li> </ul> output/X_Y/ (where X represents an abbreviation of the Problem chosen for execution and Y specifies whether all on-screen text, browser’s tab text or image hash was used). <ul> <li>X_Y_a_b/ (where a,b refers to image/text weight for each execution). Each directory represents one specific execution from a Problem. <ul> <li>df.csv: .csv file representing the expanded UI Log with the experimentation results after the algorithm has been applied. The new columns are described below: <ul> <li>combined_features: contains the features extracted per image, either individually using hash or CLIP, or, in the latter case, combining them with those from the text source used.</li> <li>activity_label: represents the group assigned by the algorithm through clustering based on feature comparison.</li> <li>mapped_prediction: mapping of the cluster assigned by the algorithm to the group distribution established manually by ground_truth.</li> </ul> </li> <li>summary.csv: file which contains a summary of all executions from a Problem. It contains the following information: <ul> <li>exec: number indicating the row identifier.</li> <li>image_weight: parameter that determines the importance of image features in the model.</li> <li>text_weight: parameter that determines the importance of text features in the model.</li> <li>Evaluation metrics: <ul> <li>Precision: the ratio of true positives to the sum of true positives and false positives. It measures the accuracy of not labeling different activities as the same.</li> <li>Recall: the ratio of true positives to the sum of true positives and false negatives. It measures the ability to identify all the activities properly grouped.</li> <li>F1-Score: a harmonic mean of precision and recall. It balances the relative contribution of precision and recall equally.</li> </ul> </li> <li>Clustering related metrics. (Calculated for testing purposes; in the article, our approach focuses solely on evaluation metrics). <ul> <li>Silhoutte Coefficient: measures how similar is an object to its cluster compared to other clusters. Values range from -1 to 1, with higher values indicating better-defined clusters.</li> <li>Davies-Bouldin Index: assesses cluster quality by comparing the distance between clusters to the size of the clusters themselves. Lower values indicate better-defined clusters.</li> <li>Calinski-Harabasz Index: evaluate cluster quality by comparing the spread within clusters to the spread between clusters. Higher values mean better-defined clusters.</li> </ul> </li> </ul> </li> </ul> </li> </ul>

openmit-licenseMay 2024View details →

Data underlying the article: "Excuse me, there is a mutant in my bioactivity soup! A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling"

This repository contains the data underlying the article: “Excuse me, there is a mutant in my bioactivity soup! A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling” available as a preprint on ChemRxiv. Main authors: Marina Gorostiola González & Olivier J.M. Béquignon (Leiden University) Senior author: Gerard J.P. van Westen (Leiden University) This analysis was performed using the code available at <a href="https://github.com/CDDLeiden/chembl_variants" target="_blank" rel="noopener">https://github.com/CDDLeiden/chembl_variants</a>

openmit-licenseMay 2024View details →

CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues

Cis-regulatory elements (CREs) play a pivotal role in gene expression regulation, allowing cells to serve diverse functions and respond to external stimuli. To address this gap, we have created CREdb, a comprehensive database of over 10 million human regulatory elements across 1,058 cell types and 315 tissues. Data from 11 sources were curated and mapped to standard ontological terms. 11,223,434 combined elements are present in the final database, and these were merged into 5,666,240 consensus elements representing the combined ranges of the individual elements informed by their overlap. Each consensus element contains metadata including the number of elements supporting it and a hash linking to the source databases. The inferred activity of each consensus element in various cell-type and tissue context is also provided.

opencc-zeroJun 2024View details →

Assessing the potential of camera traps for estimating activity pattern compared to collar-mounted activity sensors: A case study on Eurasian lynx (Lynx lynx) in South-Eastern Norway

<div> <div> <div> <div> The diel activity patterns of animals convey information about physiology, ecological niches and animal behaviour relevant for both applied conservation and more theoretical research. However, these patterns are challenging to study in the field. The current gold-standard approach to quantify the movements and activity patterns of medium to large wildlife species is to use Global Positioning Systems (GPS) collars equipped with activity sensors (e.g., accelerometers). A more recent approach consists of inferring activity patterns from the time-stamped pictures of wildlife obtained from the camera traps now routinely used in wildlife monitoring projects. However, few studies have attempted to validate estimates of activity patterns obtained from camera traps against those obtained from activity sensors. In this study, we compared the diel activity pattern of the Eurasian lynx Lynx lynx inferred from detections by a network of over 300 camera traps active between 2010 and 2020, to activity patterns obtained from 18 GPS-collared lynx (8 females, 10 males) equipped with 2-axis accelerometer sensors, in the same area of southern Norway. Our results suggest that camera traps can be used to estimate diel activity curves that are comparable to those obtained from accelerometers. In our study 75 detections were sufficient to approximate the diel activity pattern obtained from accelerometer. Subsampling indicated that a low number of detections results in a coarser approximation of the diel activity pattern. </div> </div> </div> </div>

opencc-by-nc-sa-4.0Jun 2024View details →

VHAKG: Multi-modal Knowledge Graphs with Multi-view Videos of Daily Activities

<h2>Outline</h2> <ul> <li>This dataset is a multimodal knowledge graph (MMKG) of daily activity videos.</li> <li>This dataset integrates a KG with embedded multi-view videos created by <a href="https://github.com/aistairc/virtualhome_aist">VirtualHome-AIST</a>, an extended version of the VirtualHome simulator, and an event-centric KG generated by <a href="https://github.com/aistairc/virtualhome2kg">VirtualHome2KG</a>.</li> <li>We named this dataset VHAKG (VirtualHome-AIST-KG).</li> </ul> <h2>Details</h2> <ul> <li>VHAKG describes 2D bounding boxes of objects every five frames, compositional activities, primitive actions, target objects, object states, 3D bounding boxes, and their time-series changes.</li> <li>The videos are encoded in base64 and embedded as a literal value.</li> <li>VHAKG consists of 706 daily activity scenarios (e.g., clean desk, cook fried bread, and relax on sofa) and 3,530 videos captured by five synchronized cameras per scenario.</li> <li>The file format is <a href="https://www.w3.org/RDF/">RDF</a> (<a href="https://en.wikipedia.org/wiki/Turtle_(syntax)">Turtle</a>), which can be loaded into various <a href="https://en.wikipedia.org/wiki/Triplestore">Triplestores</a>.</li> <li>VHAKG's vocabularies are defined as an ontology and can be found in vh2kg_schema_v2.0.0.ttl.</li> </ul> <h2>Contents</h2> <ul> <li>vh2kg_video_base64.tar.gz <ul> <li>{activity name}{scene}_{camera}_2dbbox.ttl: KG with video embedded in base64 format, including 2D bounding box data every 5 frames. <ul> <li>To learn more about {scene}, check <a href="https://github.com/xavierpuigf/virtualhome/tree/v2.2.0/simulation#environment">here</a>.</li> <li>To learn more about {camera}, check <a href="https://github.com/aistairc/virtualhome_unity_aist?tab=readme-ov-file#addition-of-new-four-cameras">here</a>.</li> </ul> </li> </ul> </li> <li>vh2kg_event.tar.gz <ul> <li>{activity name}_{scene}.ttl: Event-centric KGs representing video content as sequences of events.</li> <li>vh2kg_schema_v2.0.0.ttl: The ontology file of this dataset.</li> <li>affordance.ttl: The affordance data of objects that were created by crowdsourcing. <ul> <li>Please see Section III.B of <a href="https://doi.org/10.1109/ACCESS.2023.3253807" target="_blank" rel="noopener">this paper</a> for more information.</li> </ul> </li> <li>add_places.ttl: Events in which agents moved from one room to another.</li> </ul> </li> </ul> <h2>Tools</h2> <ul> <li><a href="https://github.com/aistairc/vhakg-tools">A set of tools</a> for searching and extracting videos from VHAKG is available.</li> </ul>

opencc-by-4.0Jun 2024View details →

Data and Script used in "Effects of canopy gaps on microclimate, soil biological activity and their relationship in a European mixed floodplain forest"

The R code and data provided in this repository allow to reproduce the data carpentry, analysis and visualization of “Effects of canopy gaps on microclimate, soil biological activity and their relationship in a European mixed floodplain forest” (https://doi.org/10.1016/j.scitotenv.2024.173572).   Folder structure   Data abstracts: Data_abstract_climate.pdf Data_abstract_soil_biotics.pdf Data_abstract_soil_abiotics_openness.pdf   Data: Climate_data.xlsx Soil_biotics.xlsx Soil_abiotics_openness.xlsx   R Scripts: 00-preamble.R loads all required packages 01-data-carpentry.R loads all datasets and prepares the analysis of all experimental periods. 02-data-analyses-microclimate.R compares understorey air and soil microclimate between forest types and treatments, presents diurnal and seasonal variations and tests the relationship of under- and overstorey openness on microclimate. 03-data-analyses-decomposition.R compares decomposition rates and feeding activity between forest types and treatments and models the dependencies of soil biological activity on microclimate and soil abiotic factors.   Information of related software and package versions used in the script: R version 4.3.2 (2023-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default   Contact Please contact me at annalena.lenk@uni-leipzig.de if you have further questions.

opencc-by-4.0Jun 2024View details →

PRB Exciton-activated effective phonon magnetic moment in monolayer MoS2

Optical excitation of chiral phonons plays a vital role in studying the phonon-driven magnetic phenomena in solids. Transition metal dichalcogenides host chiral phonons at high symmetry points of the Brillouin zone, providing an ideal platform to explore the interplay between chiral phonons and valley degree of freedom. Here, we investigate the helicity-resolved magneto-Raman response of monolayer MoS2 and identify a doubly degenerate Brillouin-zone-center chiral phonon mode at &sim;270cm−1. Our wavelength- and temperature-dependent measurements show that this chiral phonon is activated through the resonant excitation of 𝐴 exciton. Under an out-of-plane magnetic field, the chiral phonon exhibits giant Zeeman splitting, which corresponds to an effective magnetic moment of &sim;2.5⁢𝜇𝐵. Moreover, we carry out theoretical calculations based on the morphic effects in nonmagnetic crystals, which reproduce the linear Zeeman splitting and Raman cross section of the chiral phonon. Our study provides important insights into lifting the chiral phonon degeneracy in an achiral covalent material, paving a route to excite and control chiral phonons.

Data and analysis for "Association of self-reported musculoskeletal pain with school furniture suitability and daily activities among primary school and university students"

Datasets and R analysis code and report for the article "Association of self-reported musculoskeletal pain with school furniture suitability and daily activities among primary school and university students".

opencc-by-4.0Jun 2024View details →

Data Release Scrutinising evidence for the triggering of Active Galactic Nuclei in the outskirts of massive galaxy clusters at z~1

Dataset of the paper "Scrutinising evidence for the triggering of Active Galactic Nuclei in the outskirts of massive galaxy clusters at z~1".   All the necessary code to deal with these data can be found at: https://github.com/IvanMuro/agn_frac_data_release

opencc-by-4.0Aug 2023View details →

Fig. 1 in Antimicrobial activity of the crude peptide extracts from Blackfin sea catfish Arius jella Day, 1877

Fig. 1 — Photograph of experimental species Arius jella

opencc-by-4.0Sep 2022View details →

Fig. 8 in The cytotoxic activity of Sponges and Tunicates from Turkish Aegean Sea

Fig. 8 — Microscopic images of PC-3 cells treated with extracts for 24 h (Scale bar: 100 µm)

opencc-by-4.0Sep 2022View details →

Fig. 7 in The cytotoxic activity of Sponges and Tunicates from Turkish Aegean Sea

Fig. 7 — Cell viability of PC-3 cell line with various extract concentrations treatment for 24 h