cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25452/figshare.plus.24160968.v1
title: scPerturb Single-Cell Perturbation Data: ATAC files

description: This repository contains the scATAC-seq datasets from the scperturb database. For each dataset this includes the following feature matrices:ChromVarLSI_embeddinggene_scoresmarkerpeak_targetpeak_bcIn order to facilitate development and benchmarking of computational methods in systems biology, we collected a set of 44 publicly available single-cell perturbation-response datasets with molecular readouts, including transcriptomics, proteomics and epigenomics. We applied uniform quality control pipelines and harmonize feature annotations. The resulting information resource enables efficient development and testing of computational analysis methods, and facilitates direct comparison and integration across datasets. In addition, we describe E-statistics for perturbation effect quantification and significance testing, and demonstrate E-distance as a general distance measure for single-cell data as both a python (scperturb on PyPI) and R (scperturbR on CRAN) package.See the associated publication for info on how the data was handled. We also have an interactive table (Data Explorer) on our website with metadata per dataset.
DOI: 10.6084/m9.figshare.10046558.v1
title: Actinidia chinensis genome data

description: Actinidia chinensis genome fasta and gff3 files
DOI: 10.6084/m9.figshare.19145282.v1
title: Parameterisation.m ‘read me’ file from <i>In silico</i> framework to inform the design of repair constructs for peripheral nerve injury repair

description: File that explains what is required to run the code Parameterisation.m and the architecture of the code.
DOI: 10.17632/5bcrh67xty
title: ARTEMIS: Ab initio restructuring tool enabling the modelling of interface structures

description: A program, ARTEMIS, has been developed for the study of interface structures. This software allows for the generation of interfaces by identifying lattice matches between two parent crystal structures. To allow for further exploration of the energetic space of the interface, multiple surface terminations parallel to the Miller plane, interface alignments and intermixings are used to generate sets of potential interfaces for each lattice match. These interface structures can then be used in atomic simulations to determine the most energetically favourable interface. The software reported here can help to both drastically reduce the work of generating and exploring interfaces, and aid in understanding of how the interface structure influences the subsequent properties. Using several test cases, we demonstrate how ARTEMIS can both identify the location of an interface in existing structures, and also predict an optimum interface separation based upon the parents’ atomic structures, which aims to accelerate and inform the study of interface science.
DOI: 10.17632/b2wvnbnpj9
title: The Impact of Covid-19 Pandemic on the Global Economy: Emphasis on Poverty Alleviation and Economic Growth

description: Data for 170 countries in respect to the impact of covid-19 on the global economy
DOI: 10.17632/vhv3xpp2r8
title: Software and designfiles for an autonomous robot bin picking mixed insect samples using computer vision

description: These software and design files enable the replication of the Insect Handling System (IHS). IHS is an autonomous robotic solution, using various developed manipulators, designed to streamline the processing of insect samples. By integrating advanced robotics, computer vision, and pneumatic systems, the IHS can efficiently manage large volumes of insect samples one sample at a time, significantly reducing the manual workload. This innovation aims to enhance the efficiency of entomological research, enabling large-scale, precise, and automated insect population studies, thereby facilitating a deeper understanding of environmental impacts on biodiversity. The system was created by two project groups at Aarhus University. It consists of a UR5 robot manipulating and changing between multiple tools to separate and move insects in large samples. The system uses computer vision and LabVIEW software, along with Arduino and Polyscope, pertaining to the UR5 robot arm.
DOI: 10.17632/ztc3pmxk7m
title: HOTB: High precision parallel code for calculation of four-particle harmonic oscillator transformation brackets

description: This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract This new version of the HOTB program for calculation of the three and four particle harmonic oscillator transformation brackets provides some enhancements and corrections to the earlier version (Germanas et al., 2010) [1]. In particular, new version allows calculations of harmonic oscillator transformation brackets be performed in parallel using MPI parallel communication standard. Moreover, higher precision of intermediate calculations using GNU Quadruple Precision and arbitrary precision li... Title of program: HOTB_MPI Catalogue Id: AEFQ_v4_0 Nature of problem Calculation of matrices of three-particle harmonic oscillator brackets (3HOB) and four-particle harmonic oscillator brackets (4HOB) in a more effective way, which allows us to calculate a matrix of the brackets up to a few hundred times more rapidly and more accurately than in a previous version. Versions of this program held in the CPC repository in Mendeley Data AEFQ_v1_0; HOTB; 10.1016/j.cpc.2009.10.012 AEFQ_v2_0; HOTB; 10.1016/j.cpc.2011.01.031 AEFQ_v3_0; HOTB_M; 10.1016/j.cpc.2012.09.021 AEFQ_v4_0; HOTB_MPI; 10.1016/j.cpc.2014.06.025
DOI: 10.6084/m9.figshare.1284521.v1
title: phyluce example data

description: Raw fastq example data for phyluce.
DOI: 10.6084/m9.figshare.7374155.v6
title: CRISPR-NHEJ data files

description: These files contain:3 replicates of processed data for CRISPR NHEJ profiling.1 CRPISPR NHEJ profiling with microhomology design1 table for machine learning training
DOI: 10.17632/769zgnsm9w
title: Misperceptions of opposite-sex preferences for thinness and muscularity
DOI: 10.17632/nx2wsksp9k
title: Data for: "PyTorchFire: A GPU-Accelerated Wildfire Simulator with Differentiable Cellular Automata"

description: Data for: "PyTorchFire: A GPU-Accelerated Wildfire Simulator with Differentiable Cellular Automata"
DOI: 10.6084/m9.figshare.25709118.v1
title: <b>Initiation of the Central Tibet Watershed Mountains since Late Jurassic</b> (dataset)

description: <b>This is the detrital zircon U-Pb dataset of 'Initiation of the Central Tibet Watershed Mountains since Late Jurassic'.</b>
DOI: 10.6084/m9.figshare.27175695.v1
title: Chylothorax is closely associated with aggressiveness of lymph node management during pulmonary resection

description: Chylothorax is associated with more aggressive lymph node management during lung cancer resection, particularly with complete and systematic lymph node dissection. It leads to significant postoperative morbidity, including longer hospital stays and higher rates of reoperation and readmission.
DOI: 10.6084/m9.figshare.23713842.v2
title: Materials Project Trajectory (MPtrj) Dataset

description: <br>This data file is the MPtrj dataset.The json file contains 1,580,395 structures, 1,580,395 energies, 7,944,833 magnetic moments, 49,295,660 forces, and 14,223,555 stresses that were used to train the pretrained CHGNetThe structures and labels are parsed from all the GGA/GGA+U static/relaxation trajectories from 2022.9 version Materials Project, with selection method that avoids imcompatible calculations and duplicated structures.The format of the json file looks like this:MPtrj-'mp-id-0'-'frame-id-0'-'structure': dictionary of pymatgen.core.Structure-'uncorrected_total_energy': [eV] raw energy from VASP output-'corrected_total_energy': [eV] VASP total energy after MP2020 compatibility-'energy_per_atom': [eV/atom] corrected energy per atom, this is the energy label used to train CHGNet-'ef_per_atom': [eV/atom] formation energy per atom-'e_per_atom_relaxed': [eV/atom] corrected energy per atom of the relaxed structure, this is the energy you can find for the mp-id on materials project website-'ef_per_atom_relaxed': [eV/atom] formation energy per atom of the relaxed structure-'force': [eV/A] force on the atoms-'stress': [kBar] stress on the cell-'magmom': [muB] magmom on the atoms-'bandgap': [eV] bandgap-'frame-id-1'...-'mp-id-1'...Notes:1. The frame id has syntax: 'task_id-calc_id-ionic_step', where 'calc_id' is 0 (second) or 1 (first) in the double relaxation process for each material project relaxation task.2. Since MPtrj is a diverse dataset that contains both GGA and GGA+U calculation, which has different energy values, MP2020 compatibility is applied to the VASP raw energies to make GGA and GGA+U universally compatible. The 'energy_per_atom' (which is after MP2020 correction) is used for pretrained CHGNet training.see: https://pymatgen.org/pymatgen.entries.html#pymatgen.entries.compatibility.Compatibility3. There're missing MAGMOMs labels in the MPtrj, which we put None as labels. These do not mean the MAGMOM label is 0. CHGNet is trained on absolute value of DFT magmom, which is the absolute value of the labels contained in MPtrj, the unit conversion is automatic if you use the dataset we provide, see: https://github.com/CederGroupHub/chgnet/blob/main/chgnet/data/dataset.py4. The stress values in MPtrj json are raw stress values from VASP. CHGNet output stress is in unit of GPa, which is -0.1 * the VASP raw stress in MPtrj dataset. The unit conversion is also implemented in CHGNet dataset, so you don't have to convert the VASP stress unit when passing them to the dataset object.Reference:If you use CHGNet or MPtrj dataset, please cite:@article{deng_2023_chgnet,title={CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling},DOI={10.1038/s42256-023-00716-3},journal={Nature Machine Intelligence},author={Deng, Bowen and Zhong, Peichen and Jun, KyuJung and Riebesell, Janosh and Han, Kevin and Bartel, Christopher J. and Ceder, Gerbrand},year={2023},pages={1–11}}
DOI: 10.6084/m9.figshare.28180997.v1
title: Supplementary Material for: Tattoo ink products and pigments 2018-19 upfront the new EUREACH regulation: Danish golden benchmark Study of 108 studios and 39687 clients tattooed with inks from 109720 ink bottles

description: ABSTRACT

Background: The new EU regulation on tattoo inks in force January 2022 in a hitherto unregulated market marks a historical change. 

Objective: Mapping of the thousands of tattoo inks de facto used in studios before the new EU regulation and establish a historical reference to tattoo customer exposure, ink toxicology assessment, clinical complications, and the impact on tattooing businesses.

Method: A tattooist-operated electronic system (InkBase) for ink registration required by law is used in Denmark since 2018. A local database in studios refers to a central database. Clients, sessions, ink bottles, brand name, and pigment color index (CI) are registered. Person’s data protection is respected. Tracing harmful inks is possible, with public warning.


Results: Registrations from 108 studios employing about 700 tattooists were collected from March 2018 through 2019. 39687 clients were tattooed in 50604 sessions, using colors from 109720 ink bottles. 10833 were CI-labelled identifying the pigment. 98.1% of inks originated from USA. Detailed statistics on inks and pigments used are provided as a benchmark showing the spontaneous use and preference of “old” tattoo inks before the EU regulation compulsory to member states introduced dramatic restrictions difficult to follow.


Conclusions: Denmark can, having detailed ink registration enforced by law and having a commonly used electronic registration system reporting to a central server, function as an index country in future surveillance of use of tattoo inks in studios, toxicology aspects and the impact of regulatory intervention on the tattooing industry, with a large sample of data collected in 2018-19.

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DOI: 10.17632/6hyrr8typ7
title: CigDet (Cigarette Detection) Dataset

description: Our dataset, named CigDet, is tailored to advance the field of cigarette detection. Leveraging the smoker detection dataset available on the Mendeley Data online repository which was our previous work, we specifically concentrated on images categorized under the Smoking class. In these images, the presence of cigarettes serves as the pivotal attribute for smoker detection. Each image in our dataset is meticulously chosen to depict various scenes containing cigarettes amidst diverse backgrounds and environmental conditions, effectively simulating real-world complexities encountered in cigarette detection tasks.

For precise annotations, we utilized the LabelImg tool, renowned for its efficacy in annotation tasks, adhering strictly to the YOLO format. Employing a streamlined annotation approach, we focused solely on delineating and annotating instances of cigarettes within the images, ensuring accuracy and relevance.

Our dataset comprises 557 images, each representing a valuable sample for the intended task. To facilitate robust model training and thorough evaluation, we divided the dataset into distinct subsets for training and testing, comprising 446 and 111 images, respectively. This partitioning strategy was devised to ensure equitable distribution of instances between training and testing sets, enabling comprehensive evaluation of the model's performance across diverse scenarios.
DOI: 10.17632/7n2h8w3464
title: Data, code, and output files associated with: Polarization-sensitive photoreceptors inform host-seeking in stable flies

description: This dataset is a supplement to the article "Polarization-sensitive photoreceptors inform host-seeking in stable flies". The article included a combination of anatomical, electrophysiological and behavioral investigations of vision in stable flies. The methods describing the generation of this data is fully described in the associated article.

Article Abstract:
"Insects use their polarization-sensitive photoreceptors in a variety of ecological contexts including host-foraging. Here, we investigated the effect of polarized light on host foraging by the blood-feeding stable fly, Stomoxys calcitrans, a pest of livestock. Electroretinogram recordings with chromatic adaptation demonstrated that the spectral sensitivity of stable flies resembles that of other calyptrate flies. Histological studies of the flies’ compound eye revealed differences in microvillar arrangement of pale and yellow ommatidial types, with the pale R7 and R8 photoreceptors having the greatest polarization sensitivity. In behavioural experiments, stable flies preferred to alight on horizontally polarized stimuli with a high degree of linear polarization. This preferential response disappeared when either ultraviolet (UV) or human-visible wavelengths were omitted from light stimuli. Removing specific wavelength bands further revealed that the combination of UV (330–400 nm) and blue (400–525 nm) wavelength bands was sufficient to enable polarized light discrimination by flies. These findings enhance our understanding of polarization vision and foraging behavior among hematophagous insects and should inform future trap designs."


This dataset contains:

---"anatomy"---
Original and modified electron microscopy images of transverse sections of pale and yellow ommatidia taken at multiple points along their length. Along with a 3D slice model used to estimate off axis cutting distortions.

---"behavioral bioassays"---
Data files, R scripts, and output graphs for the behavioral bioassay experiments (Exp 1-11, see table S1)

---"electrophysiology"---
Raw recordings, R scripts, intermediate files, and output files relating to the electroretinogram recordings of female stable fly compound eyes under chromatic adaptation.

---"polarimetry"---
Images and output files associated with photo polarimetry of filter stack stimuli (see Table S1)

---"spectroscopy"---
Emission, transmission, and reflectance measurements, along with the R code used to generate Fig. S1
DOI: 10.6084/m9.figshare.14992410.v1
title: N. fowleri TY protein coding gene sequences

description: N. fowleri TY gene sequences in fasta format
DOI: 10.6084/m9.figshare.5435971.v1
title: dumpDBpedia_LODStats.sql.zip

description: Database index of datatypes from endpoints from LODStats and file dumps from DBpedia.
DOI: 10.17632/5zrjfcky65
title: Les savoirs traditionnels de pêcheurs artisanaux à Huanchaco (La Libertad, Pérou) : la problématique de leur transmission et de leur continuité

description: Au Pérou, la pêche est une activité pratiquée depuis plus de dix mille ans, jusqu’à nos jours, où celle-ci n’a pas perdu de son importance. La communauté de pêcheurs artisanaux du nord de la côte péruvienne, Huanchaco est particulièrement bien connue pour posséder une riche connaissance du milieu marin-côtier et le savoir-faire d’une singulière pratique de pêche millénaire. Celle-ci est caractérisée par l’utilisation d’un bateau en roseaux appelé caballito de totora, construit par les pêcheurs eux-mêmes. Au cours des dernières décennies, ces communautés ont connu des changements importants, comme le déclin des ressources marines, notamment les principales espèces pêchées. Cette situation complexe a eu un impact direct sur la transmission générationnelle des savoirs traditionnels et écologiques liés à la pêche, impact qui affaiblit la réponse adaptative, qui à son tour pourrait avoir un impact direct sur la résilience de ces communautés dans le temps.
DOI: 10.17632/wr9mprpj5k
title: Hybrid Input-Output tables for Saudi Arabia at the year 2013

description: - The IOT_KSA_Val file gives the input-output table in thousands of Riyals for 13 sectors. - The IOT_KSA_Qtities gives the input-output table in quantities for 13 sectors. The energy sectors are in ktoe, the cement and petrochemical sectors in tons, and the others in "pseudo-quantities". - The IOT_KSA_Prices gives the unitary prices that are consistent with IOT in volume and value for intermediate consumption, final consumption, production, and imports. - Income_Distribution gives the secondary income distribution among the represented institutional agents in thousands of Riyals. - The IOT_KSACO2Emis gives the energy-consumption related emissions in KtCO2 for intermediate consumption and final consumption.
DOI: 10.6084/m9.figshare.11620113.v1
title: hgcB-profile

description: HMM profile of hgcB marker to search for. Confirm presence by looking if directly downstream of hgcA or within 4-5 ORFs of hgcA
DOI: 10.6084/m9.figshare.12149091.v1
title: Atrial Fibrillation annotations of electrocardiogram from MIMIC III matched subset

description: We provide some annotations of the Medical Information Mart for Intensive Care (MIMIC) III waveform database matched Subset. The annotations are for the electrocardiogram recordings and denote atrial fibrillation status.<br><br><b>More annotations will be added in future.</b><br>Details about MIMIC III matched subset can be found at Physionet.<br>https://archive.physionet.org/physiobank/database/mimic3wdb/matched/<br><br>If you use the annotations, please cite the following paper:Bashar, S.K., Ding, E., Walkey, A.J., McManus, D.D. and Chon, K.H., 2019. <i>Noise Detection in Electrocardiogram Signals for Intensive Care Unit Patients</i>. IEEE Access, 7, pp.88357-88368
DOI: 10.6084/m9.figshare.25035872.v2
title: Supplementary Data 1

description: tRAM-seq
DOI: 10.6084/m9.figshare.26004370.v2
title: <b>A telomere-to-telomere genome of wild soybean with resistance to multiple soybean cyst nematode races</b>

description: Wild soybean is a promising source of novel genes for efficient soybean improvement due to its substantial genetic diversity. However, the previous version of wild soybean reference genome contains a significant number of missing segments. We reported here a telomere-to-telomere gap-free reference genome of YSD56, a wild soybean accession with resistance to multiple soybean cyst nematode races. <i>YSD56_T2T</i> genome has a size of 1008.52 Mb with scaffold N50 length of 51.97 Mb. Twenty centromeres with 53.43 Mb and forty telomeres with 855.38 Kb were identified. There were 60,951 annotated protein-coding genes and the length of transposable elements accounted for 55.87% of the total genome. Comparative genomics showed that there were 4135 species-specific genes in <i>YSD56_T2T</i>, compared with 1,523 in <i>wild soybean_W05</i> and 340 in <i>Willams82_V4</i>. BUSCO analysis yielded a completeness score of 97.7% using the fabales_odb10 database. We believe that the high-quality genome assembly for wild soybean <i>YSD56</i> would serve as a valuable reference to better understand soybean genetic and breeding, as well as devise effective disease control strategy.
DOI: 10.6084/m9.figshare.26129887.v1
title: Test Data

description: The provided link directs you to a Figshare page where our can download CSV files test datasets for your machine learning project.
DOI: 10.6084/m9.figshare.28607315.v1
title: Sandoval-Serés E, et al. 2025. Spatio-temporal dynamics of African wild dogs in response to larger carnivores in an ecosystem with artificial water provisioning. Biological Conservation.

description: Data and R code used in the publication of:Sandoval-Serés E, Dröge E, Valeix M, van der Meer E, Sousa LL, Seymour-Smith J, Sibanda A, Say-Sallaz E, Campbell L, Naware D, Madhlamoto D, Mandisodza-Chikerema R, and Loveridge AJ. <i>In press 2025</i>.Spatio-temporal dynamics of African wild dogs in response to larger carnivores in an ecosystem with artificial water provisioning. Biological Conservation.
DOI: 10.6084/m9.figshare.28911407.v1
title: Automated S-Wave Arrival Timing in GNSS Instantaneous VelocityData Without Frequency-Domain Pre-Filtering

description: EGU 2025 PosterGSWPicker is scientific software that automatically detects when seismic shear waves arrive and measures how strong and how long ground shaking lasts, using GNSS (Global Navigation Satellite Systems) velocity data.<br>The software reads GNSS position data or difference position data from various processing engines (such as PRIDE PPP and VarioPy). It converts these time series into instantaneous velocities and then runs a three-step process:<br>1. It first reduces noise in the velocity data.<br>2. It then identifies ground shaking signals using three independent methods: two statistical approaches (Median Absolute Deviation and least-squares) and a hypothesis testing method (w-test).<br>3. Finally, it determines the exact time when shear waves arrive and measures the strength and duration of ground shaking.<br>This process allows seismic analysis to be performed on GNSS data automatically, without the need for manual pre-filtering.
DOI: 10.17632/w3cjw46gjw
title: Data for: Apatite fission-track dating by LA-Q-ICP-MS mapping

description: Supplementary data tables associated with the "Apatite fission-track dating by LA-Q-ICP-MS mapping" manuscript