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36,930 results for “Humanities”
The relevance of signal timing in human-robot collaborative manipulation
<p><em><strong>Dataset version 1.0.1. The data collected here are attached to the following journal article: F. Cini*, T. Banfi*, G. Ciuti, L. Craighero, M. Controzzi, The relevance of signal timing in human-robot collaborative manipulation. Science Robotics Vol. 6 Issue 58, 2021. DOI: 10.1126/scirobotics.abg1308</strong></em></p> <p>To achieve a seamless human-robot collaboration, it is crucial that robots express their intentions without perturbating or interrupting the task that a human partner is performing at that moment. Although it has not received much attention so far, this issue is important when robots assist humans in physical and manipulation tasks. The main question addressed here is whether there is a more appropriate time to inform a human partner that a robot is requesting to pass them an object. This question is posed in a reference scenario where human individuals are involved in a continuous pick-and-place task that cannot be interrupted. Our findings showed that providing a cue at the beginning of a reach-to-grasp movement could severely interfere with the ongoing human action,<br> increasing the number of errors made by humans, slowing down and degrading the smoothness of their arm movement, and deflecting their gaze. These disruptive interferences strongly decreased, until they disappeared, when the robot provided the cue to the human partners shortly after the participants picked up an object, identifying this as the best signaling timing. The results of this work showed how the signaling timing may have a decisive influence on the performances of the human-robot teamwork and contribute to understating the mechanisms underpinning the phenomenon of cognitive-motor interference in humans.</p>
Functional redundancy of non-volant small mammals increases in human-modified habitats
<p>This repository hosts all R codes, data and output supporting the findings of the study "Functional redundancy of non-volant small mammals increases in human-modified habitats", by André L. Luza (UFRGS, BR), Catherine H. Graham (WSL, CH), Sandra M. Hartz (UFRGS, BR), and Dirk, N. Karger (WSL, CH).</p> <p>The only data that are not here are the Ecoregions of WWF. These data can be found in the webpage of WWF.</p>
Data and software supporting the manuscript 'The population frequency of human mitochondrial DNA variants is highly dependent upon mutational bias'
<p>Next-generation sequencing can quickly reveal genetic variation potentially linked to heritable disease. As databases encompassing human variation continue to expand, rare variants have been of high interest, since the frequency of a variant is expected to be low if the genetic change leads to a loss of fitness or fecundity. However, the use of variant frequency when seeking genomic changes linked to disease remains very challenging. Here, we explore the role of selection in controlling human variant frequency using the HelixMT database, which encompasses hundreds of thousands of mitochondrial DNA (mtDNA) samples. We find that a substantial number of synonymous substitutions, which have no effect on protein sequence, were never encountered in this large study, while many other synonymous changes are found at very low frequencies. Further analyses of human and mammalian mtDNA datasets indicate that the population frequency of synonymous variants is predominantly determined by mutational biases rather than by strong selection acting upon nucleotide choice. Our work has important implications that extend to the interpretation of variant frequency for non-synonymous substitutions. </p> <p> </p>
PsPM-FSS7B: Inhibiting human aversive memory by transcranial theta-burst stimulation to primary sensory cortex
<p>This dataset includes skin conductance response (SCR), electromygoram (EMG), and pupil size response (PSR) measurements. Also included are CS and US information, keypress responses, keypress response times and key correctness. The dataset contains data from 68 healthy unmedicated participants (34 females) participating in a classical (Pavlovian) discriminant delay fear conditioning task. Simple and complex CS are deliverd to the intermediate phalanges of the index and middle fingers of the nondominant hand. Simple stimulis are stimulations to either index or middle finger, complex stimulis are stimulations of different temporal structure to both index and middle fingers. CS intensity is set to a perceivable but not unpleasant level. US is a train of electric square pulses delivered with a constant current stimulator (Digitimer DS7A, Digitimer, Welwyn Garden City, UK) on participants' dominant forearm through a pin-cathode/ring-anode configuration. SOA betwen the CS and US is 3.5 s. The ITI is randomly determined on each trial to be 7, 9, or 11 s. The study included fear acquisition (day 1), recall and retest sessions (day 2). Participants are divided into experimental and control groups, where experimental group received continuous theta-burst stimulation on primary somatosensory cortex contralateral to the CS hand immediately prior to fear acquisition, and control group received the same stimulation to the primary somatosensory cortex ipsilateral to the CS hand. For SCR data from the acquisition session, there are 62 datasets (28 experimental, 34 control), and for PSR, 37 datasets (20 experimental, 17 control). For EMG data from the recall session, there are 52 datasets (25 experimental, 27 control). For SCR data from the retest session, there are 56 datasets (27 experimental, 39 control), and for PSR, 42 datasets (22 experimental, 20 control). </p>
Data supplement for "Land use intensification increasingly drives the spatiotemporal patterns of the global human appropriation of net primary production in the last century"
<p>This data supplements the publication "Land use intensification increasingly drives the spatiotemporal patterns of the global human appropriation of net primary production in the last century" by Thomas Kastner, Sarah Matej, Matthew Forrest, Simone Gingrich, Helmut Haberl, Thomas Hickler, Fridolin Krausmann, Gitta Lasslop, Maria Niedertscheider, Christoph Plutzar, Florian Schwarzmüller, Jörg Steinkamp, Karl-Heinz Erb.</p> <p>For details, please refer to the included readme file and to the publication (<a href="https://doi.org/10.1111/gcb.15932">https://doi.org/10.1111/gcb.15932</a>)</p> <p>In this new Version 1.01, we changed the file structure to make the data more accessible, we added data on means across modulations as used in the paper, and we include csv files with national totals for the different HANPP components.</p>
Adipose tissue plasticity in pheochromocytoma patients reveals a key role of the splicing machinery in human adipose browning
<p>RNA-sequencing counts data from omental adipose tissue from control individuals (C1-3) and patients with pheochromocytoma (P1-4) for whole genes (genes-counts.tsv) and individual isoforms (isoform-counts.tsv). Additional details regarding recruited individuals are available in the associated manuscript.</p> <p>Tissue fragments (~150 mg) of adipose biopsies from controls and pheochromocytoma patients were homogenized using a metal bead-based mechanical procedure in a TissueLyser® (QIAGEN, Düsseldorf, Germany). Total RNA was isolated from tissue homogenates using a NucleoSpin® RNA kit (Macherey-Nagel, Dueren, Germany) following the manufacturer’s protocol. mRNA was purified from 2 μg of total RNA using oligo-dT beads; it was then fragmented, retrotranscribed with random primers, and subjected to second-strand synthesis to create double-stranded cDNA fragments. Adaptor ligation, purification of 200-base pair cDNA fragments, amplification of the purified fragments, and library preparation were performed as previously reported by our laboratory. Before sequencing, the RNA integrity number (RIN) of each sample was determined using an Agilent Bioanalyzer 2100; samples with RIN ≥ 7.5 were used for RNA-sequencing. The cDNA library quality and quantity were further analyzed as previously described. Libraries yielding satisfactory results were sequenced on an Illumina HiSeq 2000 sequencer (DNAvision, Charleroi, Belgium). The average reads per sample was 45 million; this level of coverage was previously shown to provide sufficient sequencing depth for gene expression quantification and transcript detection. Quality control of reads was performed using FastQC (version 0.11.8; bioinformatics.babraham.ac.uk/projects/fastqc). Gene expression was quantified using Salmon version 1.1.0 with the additional parameters “– seqBias – gcBias – validateMappings”. GENCODE version 31 (GRCh38.p12) was used as the reference genome and indexed using default parameters; this resulted in 175,775 transcripts corresponding to 35,183 genes.</p>
PALEODEM/ What burned the forest? Wildfires, climate change and human activity during the Mesolithic – Neolithic transition in SE Iberian Peninsula
<p>This repository contains new XRD data from the Villena paleolake, archaeological radiocarbon evidence from the Villena area and the R code used to produce Summed Probability distribution analyses. </p> <p>They correspond to the following reference: </p> <p>Sánchez-García, C., Revelles, J., Burjachs, F., Euba, I., Expósito, I., Ibáñez, J., Schulte, L., Fernández-López de Pablo, J. What burned the forest? Wildfires, climate change and human activity during the Mesolithic – Neolithic transition in SE Iberian Peninsula (submitted to Catena). </p> <p>We specify the content of file further down:</p> <ul> <li>Vinalopo.csv: the list of radiocarbon dates from Villena spanning ca.9500-5500 cal BP from the following sites: Arenal de la Virgen, Cueva del Lagrimal and Casa Corona. </li> <li>ngrip.csv: NGRIP GICC05 paleotemperature record based on oxygen isotope series from Rasmussen SO <em>et al.</em>2006 A new Greenland ice core chronology for the last glacial termination. <em>J. Geophys. Res. Atmos.</em><strong>111</strong>. (doi:10.1029/2005JD006079) and Andersen KK <em>et al.</em>2006 The Greenland Ice Core Chronology 2005, 15–42ka. Part 1: constructing the time scale. <em>Quat. Sci. Rev.</em>25, 3246–3257.</li> <li>Char.csv: Sedimentary charcoal data set from the Villena Paleolake (VL3 core) published by Jones, S.E., Burjachs, F., Fernández-López de Pablo (2018) DOI/10.5281/zenodo.1244003, according to the new Bacon chronological model of the Villena paleolake (Fernández-López de Pablo et al., 2022 . Impacts of Early Holocene environmental dynamics on open-air occupation patterns in the Western Mediterranean: insights from El Arenal de la Virgen (Alicante, Spain). <a href="https://doi.org/10.31235/osf.io/5yqsr">https://doi.org/10.31235/osf.io/5yqsr</a>)</li> <li>SPD_analysis.R: R script with the code to reproduce the SPD analysis presented in the manuscript. </li> <li>SupplMat1xlsl: an excel file This file is composed by 8 spreadsheets:</li> </ul> <ol> <li>‘Selected variables 12.6-5.5’: all the data included in the time frame 12600-5500 cal BP, interpolated to 50 yr time windows. These data have been used for the Spearmans’rs correlation analysis (see spreadsheet ‘Spearmans’rs 12.6-5.5’ to track the results), Detrended Correspondence Analysis (see spreadsheet ‘Figure 5_DCA 12.6-5.5’ to track the results) and have been plotted in Figure 3 and 7. </li> <li>'Selected variables 9.1-5.5’: data included in the analysis focused on the time period 9.1-5.5 cal BP, interpolated to 50 yr time windows. These data have been used for the Spearmans’rs correlation analysis (see spreadsheet ‘Spearmans’rs 9.1-5.5’ to track the results), Detrended Correspondence Analysis (see spreadsheet ‘Figure 6_DCA 9.1-5.5’ to track the results) and have been plotted in Figure 8.</li> <li>‘Spearmans’rs 12.6-5.5’: Spearmans’rs correlation analysis applied to the 12600-5500 cal BP dataset (data from ‘Selected variables 12.6-5.5’).</li> <li>‘Spearmans’rs 9.1-5.5 cal BP’ Spearmans’rs correlation analysis applied to the 9100-5500 cal BP dataset, including here high-resolution XRD data (data from ‘Selected variables 9.1-5.5’).</li> <li>‘Figure 2 charcoal results’: original sedimentary charcoal results provided in this work. Data plotted in Figure 2. </li> <li>‘Figure 4 XRD results’: original XRD results provided in this work. Data plotted in Figure 4.</li> <li>‘Figure 5 DCA 12.6-5.5’: results of Detrended Correspondence analysis focused on the time period from 12600 to 5500 cal BP. Data plotted in Figure 5.</li> <li>‘Figure 6 DCA 9.1-5.5’ results of Detrended Correspondence analysis focused on the time period from 9100 to 5500 cal BP, including here high-resolution XRD data. Data plotted in Figure 6.</li> </ol>
AlphaFold2 models of human DNA polymerase epsilon catalytic subunit A
<p>Models of the structure of human DNA polymerase epsilon catalytic subunit A built with the program AlphaFold2. Files are in mmCIF format. Models include:</p> <p>1) <a href="https://zenodo.org/api/files/c8652c0b-1bc6-44d5-b11e-e8e107dba67e/DPOE1_HUMAN_AF2_NterminalLobe_4m8o.cif">DPOE1_HUMAN_AF2_NterminalLobe_4m8o.cif </a>: AlphaFold2 model built with template PDB:4M8O (yeast DNA polymerase epsilon N-terminal lobe with bound DNA)</p> <p>2) <a href="https://zenodo.org/api/files/c8652c0b-1bc6-44d5-b11e-e8e107dba67e/DPOE1_HUMAN_AF2_FullLength_6wjv.cif">DPOE1_HUMAN_AF2_FullLength_6wjv.cif </a>: AlphaFold2 model built with template PDB:6WJV (yeast DNA polymerase epsilon full-length protein, N and C terminal lobes, without DNA).</p> <p>3) <a href="https://zenodo.org/api/files/c8652c0b-1bc6-44d5-b11e-e8e107dba67e/DPOE1_HUMAN_AF2_NterminalLobe_4m8o_withDNA.cif">DPOE1_HUMAN_AF2_NterminalLobe_4m8o_withDNA.cif</a> : AlphaFold2 model built with template 4M8O (File #1 above) with DNA added from PDB entry 4M8O and subjected to energy minimization with the program AMBER using force field ff14SB.</p> <p>The models were used to estimate the change in free energy of mutations found in patients with ovarian cancer, colon cancer, and endometrial cancer. Paper to be submitted Dec 2022.</p>
Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean
<p>Koptekin et al. (2022) "<strong><em>Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean</em></strong>", Current Biology <a href="https://doi.org/10.1016/j.cub.2022.11.034">https://doi.org/10.1016/j.cub.2022.11.034</a></p>
De Obaldia et al. Differential mosquito attraction to humans is associated with skin-derived carboxylic acid levels
<p>These supplementary files accompany the manuscript by De Obaldia et al. entitled "Differential mosquito attraction to humans is associated with skin-derived carboxylic acid levels." This includes all raw data in the paper, supplementary data, and instructions for the mosquito behavioral assays.</p> <p> </p> <p>On January 2, 2023 we added one new data file and a .readme to explain changes between the original pre-print and the published peer-reviewed version of the paper https://pubmed.ncbi.nlm.nih.gov/36261039/</p>
ΑUTH-AGI OpenDR Humans in Fields Dataset
<p>The OpenDR Humans in Fields dataset is a 2D Object Detection dataset, specifically designed for person detection in agricultural fields. A Robotti robot was deployed by <a href="https://agrointelli.com/">AGI</a> to collect images with a front and back camera, in a realistic scenario to mimic the images that the robot might encounter in the agricultural use case. The cameras are equipped with wide-angle lenses, contributing to the domain shift problem when applying pretrained person detectors to the task. The collected images are saved in JPG format at a resolution of 2048x1536. The dataset is split in train and test sets, and each of these is split in two subsets: a) images depicting humans, and b) images with no humans. The dataset was annotated with bounding boxes by AUTH using the <a href="https://github.com/tzutalin/labelImg">labelImg</a> tool, and the annotations are provided in PASCAL VOC .xml format.</p> <p> </p>
Dataset for presentation Le Digital Humanities nei corsi di studio e di dottorato: questioni formative, disciplinari, istituzionali
<p>This is the dataset upon which the slides of my talk "Le Digital Humanities nei corsi di studio e di dottorato: questioni formative, disciplinari, istituzionali" was based.</p> <ul> <li><strong><em>Singoli insegnamenti di informatica umanistica in Italia (responses).csv </em></strong>is a CSV file including the 'raw' replies of the survey mentioned in the slides. The column "User display name" represents the user filling the survey. It is always "Anonymous user", except when I replyied myself: in this case it is "ilbuonme"</li> <li><strong><em>insegnamenti.ods</em></strong> is an ODS spreadsheet including data and graphs on individual Digital Humanities classes in Italian universities. This spreadsheet derives from the CSV file, but includes additional information deriving from my personal research.</li> <li><em><strong>cds.ods</strong></em> is an ODS spreadsheet including data and graphs on BA and MA programs in the Digital Humanities in Italy. It is not related to the CSV file.</li> </ul>
Data set for publication: Determination of Virulence-Associated Genes and Antimicrobial Resistance Profiles in Brucella Isolates Recovered from Humans and Animals in Iran Using NGS Technology
<p>This dataset includes information on resistance profiling, as well as antimicrobial resistance (AMR) genes and virulence-related factors that were identified in <em>Brucella</em> isolates recovered from humans and animals in different regions of Iran using classical phenotyping and next-generation sequencing (NGS) technology.</p>
Non-invasive modulation of human corticostriatal activity [Dataset]
<p>This dataset contains resting-state functional MRI data used in the study "Non-invasive modulation of human corticostriatal activity" (Caballero-Insaurriaga et al, PNAS, 2023).</p> <p>In this study two datasets were used: one from a transcranial static-magnetic-field stimulation (tSMS) experiment (tSMS20) and another one from the Human Connectome Project (HCP100). The tSMS20 dataset was originally acquired for a previous study tSMS over the Supplementary Motor Area (Pineda-Pardo et al, Commun Biol, 2019). The regions used in the study are also provided.</p> <p>As for the tSMS20 dataset, the stimulation protocol consisted of 30-minute tSMS using a single magnet placed over the supplementary motor area (SMA). Each subject underwent two stimulation sessions (real and sham) in two separate days, whose order was randomized. In each session, structural MRI was acquired before tSMS, and resting-state fMRI before and after. Structural images were T1-weighted (T1w), with 1 mm isotropic voxel. Functional data was acquired in 10 minutes-long sessions, TR/TE 2400/30 ms (250 volumes per session), with 3mm isotropic voxel. The preprocessed resting-state fMRI data are included in this repository (see dataset_description.txt file and Pineda-Pardo et al, Commun Biol, 2019 for more details)</p> <p>As for the HCP100 dataset, only the subject list is included, as data are already publicly available from the HCP initiative.</p> <p>If you use this data in a publication, please cite:</p> <p>Pineda-Pardo, J. A., Obeso, I., Guida, P., Dileone, M., Strange, B. A., Obeso, J. A., Oliviero, A. & Foffani, G. Static magnetic field stimulation of the supplementary motor area modulates resting-state activity and motor behavior. <em>Communications Biology</em> <strong>2,</strong> (2019)</p> <p>Caballero-Insaurriaga, J., Pineda-Pardo, J. A., Obeso, I., Oliviero, A. & Foffani, G. Non-invasive modulation of human corticostriatal activity. <em>Proceedings of the National Academy of Sciences of the United States of America</em> (2023)</p>
Single-molecule DNA methylation patterns of full-length human-specific LINE-1 (L1HS) retrotransposons in a panel of cell lines.
<p>We used bs-ATLAS-seq to comprehensively map the genomic location and assess the DNA methylation status of full-length human-specific LINE-1 elements (L1HS). The approach capture region 1-210 of L1HS elements, which corresponds to the most 5' end of its promoter sequence. This was performed in a panel of 12 human primary or transformed cell lines (BJ, IMR90, MRC5, H1, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep), many being shared with the encode project.</p> <p>These datasets provide a visualization for DNA methylation patterns at the single molecule level for each L1HS loci.</p>
Datasets and codes for the peer review article "Human and natural impacts on the U.S. freshwater salinization and alkalinization: A machine learning approach"
<p>Ongoing salinization and alkalinization in U.S. rivers have been attributed to inputs of road salt and effects of human-accelerated weathering in previous studies. Salinization poses a severe threat to human and ecosystem health, while human derived alkalinization implies increasing uncertainty in the dynamics of terrestrial sequestration of atmospheric carbon dioxide. A mechanistic understanding of whether and how human activities accelerate weathering and contribute to the geochemical changes in U.S. rivers is lacking. To address this uncertainty, we compiled dissolved sodium (salinity proxy) and alkalinity values along with 32 watershed properties ranging from hydrology, climate, geomorphology, geology, soil chemistry, land use, and land cover for 226 river monitoring sites across the coterminous U.S. Using these data, we built two machine-learning models to predict monthly-aggregated sodium and alkalinity fluxes at these sites. The sodium-prediction model detected human activities (represented by population density and impervious surface area) as major contributors to the salinity of U.S. rivers. In contrast, the alkalinity-prediction model identified natural processes as predominantly contributing to variation in riverine alkalinity flux, including runoff, carbonate sediment or siliciclastic sediment, soil pH and soil moisture. Unlike prior studies, our analysis suggests that the alkalinization in U.S. rivers is largely governed by local climatic and hydrogeological conditions.</p>
THÖR-Magni (Demo Subset): a new multi-modal context-rich dataset of human-robot motion
<p>The Magni Human Motion Dataset provides high-quality tracking information from motion capture, eye-gaze trackers, and on-board robot sensors in a semantically rich environment. To induce natural behavior of recorded participants, we utilized loosely scripted task assignment, which induced participants to navigate through a dynamic laboratory environment in a natural and purposeful way. The dataset sets a high-quality standard as realistic and accurate data is enhanced with semantic information, enabling development of new algorithms that rely not only on tracking information but also on contextual cues of moving agents, static and dynamic environments.</p> <p> </p> <p>Link to dashboard that uses the data: https://magni-dash.streamlit.app/</p> <p><br> Here we publish a subset of the final dataset, to accompany the presentation at the 2023 IEEE International Conference on Robotics and Automation (ICRA)</p>
A Curated Gene and Biological System Annotation of Adverse Outcome Pathways Related to Human Health
<p>Adverse Outcome Pathways (AOPs) are multi-scale models of biological mechanisms connecting molecular initiating events to adverse outcomes through measurable key events. AOPs can guide the use and development of new approach methodologies (NAMs) aimed at reducing animal experimentation in chemical safety assessment. Here, we present a comprehensive molecular annotation of AOPs relevant to human health to embed the AOP framework into molecular data interpretation, which supports the development and application of novel AOP-based approaches in biomedical research.</p> <p>Please cite the following publication alongside this Zenodo entry when using the data:</p> <p>Saarimäki, L.A., Fratello, M., Pavel, A. <em>et al.</em> A curated gene and biological system annotation of adverse outcome pathways related to human health. <em>Sci Data</em> <strong>10</strong>, 409 (2023). https://doi.org/10.1038/s41597-023-02321-w</p>
The optimal period for oocyte retrieval after the administration of recombinant human chorionic gonadotropin in in vitro fertilization
<p>This is the dataset of the study called "The optimal period for oocyte retrieval after the administration of recombinant human chorionic gonadotropin in in vitro fertilization".</p> <p><strong>Abstract</strong></p> <p>Background</p> <p>Our objective was to investigate the existence of an optimal period for oocyte retrieval in regards to the clinical pregnancy occurrence after the administration of recombinant human chorionic gonadotropin (rhCG) (Ovitrelle®).</p> <p>Methods</p> <p>We studied the digital records of 3362 middle eastern couples who underwent in vitro fertilization (IVF) treatment between 2019 and 2021.</p> <p>Results</p> <p>Through statistical testing, we found that there is a significant positive correlation between the oocyte retrieval period and the clinical pregnancy occurrence up to the 37th hour, where retrieval at the 37th hour was found to provide the most optimal outcome, especially in the case of gonadotropin-releasing hormone agonist (GnRHa) long protocol.</p> <p>Conclusions</p> <p>This cohort study recommends retrieval at hour 37 after ovulation triggering under the described conditions.</p>
Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies
<p>AIRR Community-compliant information comprising all antibodies described in EMBO Mol Med 15:e17454 [DOI:10.15252/emmm.202317454].</p>
ScienceDex guides
Understand access before you commit
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.