cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5920038
title: Dataset used in the assessment of the article "Basic urban services fail to neutralise environmental determinants of 'rattiness', a composite metric of rat abundance"

description: This data was collected in four Brazilian informal settlements located in the city of Salvador - the third largest city of Brazil - in the wet season of the year 2018. The data includes the collection of three rat abundance metrics - namely, rat marks on track plates, rats caught in live traps and removed, and presence of rat signs (faecal droppings, trails and active burrows) - in a total of 529 independent sampling locations. In addition to the single rat metrics, which were also used to compose the rattiness outcome, the data contain the baseline environmental and socioeconomic (surveyed and mapped) variables and the BUS variables considered in Carvalho-Pereira et al., 2023. (the data will be available soon)
description: The study for which this dataset was developed was supported by the Medical Research Council (UK), grant number MR/P024084/1
DOI: 10.5281/zenodo.10372241
title: THE ROLE OF PSYCHOHYGIENE AND PSYCHOPROPHYLAXIS IN FORMING A HEALTHY MENTALITY
DOI: 10.5281/zenodo.10372240
title: THE ROLE OF PSYCHOHYGIENE AND PSYCHOPROPHYLAXIS IN FORMING A HEALTHY MENTALITY
DOI: 10.5281/zenodo.10372205
title: Handling of Personal Data by Smart Home Equipment: an Exploratory Analysis in the Context of LGPD

description: This dataset provides data about an exploratory research that analyzed the Privacy and Security Policies and the Instruction Manuals of 59 home automation equipment for Smart Home in order to verify which personal data was handled and how these documents were providing information about processes performed in personal data. The analysis was conducted with a quantitative approach followed by a qualitative analysis, using content analysis.
DOI: 10.5281/zenodo.10372206
title: Handling of Personal Data by Smart Home Equipment: an Exploratory Analysis in the Context of LGPD

description: This dataset provides data about an exploratory research that analyzed the Privacy and Security Policies and the Instruction Manuals of 59 home automation equipment for Smart Home in order to verify which personal data was handled and how these documents were providing information about processes performed in personal data. The analysis was conducted with a quantitative approach followed by a qualitative analysis, using content analysis.
DOI: 10.5281/zenodo.10372258
title: PROBLEMS IN THE PROCESS OF INFORMATION EXCHANGE IN COMMUNICATION
DOI: 10.5281/zenodo.10372259
title: PROBLEMS IN THE PROCESS OF INFORMATION EXCHANGE IN COMMUNICATION
DOI: 10.5281/zenodo.10372075
title: Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer's disease

description: Connectome, traits and behavior data for APOE234 mice.



1. connectome.zip: mouse brain structural connectivity matrices from diffusion MRI.

2. FAGNN_Phenotype.csv: a sheet of trait information of mice used in the study.


columns: winding numbers, total distance, normalized NE time, normalized NE distance, normalized NW time, normalized NW distance, normalized SE time, normalized SE distance, normlaized SW time, normalized SW distance, island latency to first entry, island entries, normalized thigmataxis time, and normalized thigmotaxis distance

rows: 4 trials for each day from day 1 to day 5 with 1 probing test each at day 5 and day 8



3. mouse_anatomy.csv: brain region information regarding the connectivity matrix.

4. behavior.zip: behavioral data for each mouse from Morris Water Maze experiments.
DOI: 10.5281/zenodo.10372074
title: Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer's disease

description: Connectome, traits and behavior data for APOE234 mice.



1. connectome.zip: mouse brain structural connectivity matrices from diffusion MRI.

2. FAGNN_Phenotype.csv: a sheet of trait information of mice used in the study.


columns: winding numbers, total distance, normalized NE time, normalized NE distance, normalized NW time, normalized NW distance, normalized SE time, normalized SE distance, normlaized SW time, normalized SW distance, island latency to first entry, island entries, normalized thigmataxis time, and normalized thigmotaxis distance

rows: 4 trials for each day from day 1 to day 5 with 1 probing test each at day 5 and day 8



3. mouse_anatomy.csv: brain region information regarding the connectivity matrix.

4. behavior.zip: behavioral data for each mouse from Morris Water Maze experiments.
DOI: 10.5281/zenodo.10372313
title: KLASTERLARDA SABZAVOT YETISHTIRISH, TASHISH, QAYTA ISHLASH, SOTISH JARAYONLARIDA  MENEJMENTI
DOI: 10.5281/zenodo.10372314
title: KLASTERLARDA SABZAVOT YETISHTIRISH, TASHISH, QAYTA ISHLASH, SOTISH JARAYONLARIDA  MENEJMENTI
DOI: 10.25345/c5kp7v27z
title: MassIVE MSV000093658 - G1 Length Dictates Heterochromatin Landscape
title: Overall, this paper demonstrated that the speed of the cell cycle determines the level of H3K27me3 in serum-grown murine embryonic stem cells, with extended G1 phase leading to increased global H3K27me3 levels and accelerated cell cycle leading to decreased H3K27me3 levels. This MassIVE entry contains mass spectrometry files that measured H3K27me3 levels using propionic anhydride derivatization methods.
DOI: 10.5066/p9m2g2p2
title: Water Chemistry data for samples collected at groundwater sites in the Poso Creek Oil Field study area, February 2020-December 2021, Kern County, California

description: The California State Water Resources Control Board (State Water Board) initiated the Oil and Gas Regional Monitoring Program (RMP) to assess effects of oil and gas development on groundwater designated for any beneficial use. The U.S. Geological Survey (USGS) is the technical lead in conducting the RMP through the California Oil, Gas, and Groundwater (COGG) Program, working in cooperation with the State Water Board, and in partnership with other State and local agencies. The USGS collected and analyzed groundwater, surface water, and associated quality control (QC) samples in the Poso Creek Oil Field study area during February 2020-December 2021. Groundwater samples were collected from eleven irrigation, two domestic, two public supply, four monitoring wells, two institutional wells, and two surface water sites located within a five km buffer zone surrounding the Poso Creek Oil Field in Kern County, California. Samples were collected using established groundwater data-collection protocols and procedures. Samples were analyzed for water-quality indicators, major and minor ions, nutrients, trace elements, volatile organic compounds (VOCs), naturally occurring radioactive material, geochemical and age-dating tracers, dissolved organic carbon (DOC), dissolved standard and hydrocarbon gases (methane through hexane), and dissolved noble gasses, atmospheric gases, and surrogates. Approximately two hundred and eight constituents and water-quality indicators were measured. QC samples analyzed as part of the Poso Creek Oil Field study included replicates, source-solution blanks, field and equipment blanks, and laboratory spikes and surrogates.
DOI: 10.5281/zenodo.10372380
title: PREVENTION OF GERIATRIC DISEASES AND SYNDROMES IN THERAPEUTIC PRACTICE USING THE INNOVATIVE PHYTOPREPARATION SARSABIL.
DOI: 10.5281/zenodo.10372347
title: Data supporting "Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly-Polarized Light"

description: This repository contains the set of data to reproduce the computational results shown in "Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly-Polarized Light" published on Journal of the American Chemical Society (DOI: to be assigned).
DOI: 10.5281/zenodo.10372346
title: Data supporting "Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly-Polarized Light"

description: This repository contains the set of data to reproduce the computational results shown in "Stereocontrolled Self-Assembly of a Helicate-Bridged CuI12L4 Cage That Emits Circularly-Polarized Light" published on Journal of the American Chemical Society (DOI: to be assigned).
DOI: 10.5281/zenodo.10372385
title: NAVIGATION METHODS IN SURGICAL TREATMENT OF LIVER CYSTIC FORMATIONS
DOI: 10.5281/zenodo.10372384
title: NAVIGATION METHODS IN SURGICAL TREATMENT OF LIVER CYSTIC FORMATIONS
DOI: 10.5281/zenodo.10372393
title: ХИРУРГИЧЕСКИЙ ЛЕЧЕНИЯ И ДИАГНОСТИКА БОЛЬНЫХ КИСТОЗНЫМИ ОБРАЗОВАНИЯМИ ПЕЧЕНИ
DOI: 10.5281/zenodo.10372392
title: ХИРУРГИЧЕСКИЙ ЛЕЧЕНИЯ И ДИАГНОСТИКА БОЛЬНЫХ КИСТОЗНЫМИ ОБРАЗОВАНИЯМИ ПЕЧЕНИ
DOI: 10.25545/4upj00/bem5p2
title: Main_Outer_Control_Loop.m

description: :unav
DOI: 10.25545/4upj00/z1csxu
title: finite_difference.m

description: :unav
DOI: 10.25545/4upj00/z6jgbi
title: iLQG_function.m

description: :unav
DOI: 10.25545/4upj00/6zcmzd
title: SPKF_function.m

description: :unav
DOI: 10.25545/4upj00/8yfg4a
title: Measurement.m

description: :unav
DOI: 10.25545/4upj00/slpmma
title: ContinuousStateDynamics.m

description: :unav
DOI: 10.25545/4upj00/ubxuhr
title: forward_pass.m

description: :unav
DOI: 10.25545/4upj00/gqapbg
title: simulate_system.m

description: :unav
DOI: 10.25545/4upj00/envi8k
title: l_cost.m

description: :unav
DOI: 10.25545/4upj00/yuwz3s
title: Todorov_estimator.m

description: :unav
DOI: 10.25545/4upj00/1wk8nk
title: boxQP.m

description: :unav
DOI: 10.25545/4upj00/rujpd1
title: sabs.m

description: :unav
DOI: 10.25545/4upj00/i7o3ho
title: makePD.m

description: :unav
DOI: 10.25545/4upj00/cqlsnm
title: pp.m

description: :unav
DOI: 10.25545/4upj00/mlpe4u
title: backward_pass.m

description: :unav
DOI: 10.25545/4upj00/m2cqmd
title: DiscreteStateDynamics.m

description: :unav
DOI: 10.25545/4upj00
title: Dual control of the COVID-19 outbreak

description: This code simulates an outbreak of COVID-19 and uses a dual control algorithm, iterative linear quadratic regulator (iLQG), to minimize an objective function through actively learning the system's uncertain parameters. This is a set of MATLAB scripts that run the dual iLQG algorithm. Data was derived from the following sources: Li and Todorov (2007): Iterative linearization methods for approximately optimal control and estimation of non-linear stochastic system Tassa, Mansard, Todorov (2014): Control-limited differential dynamic programming Kohler et. al (2021): Robust and optimal predictive control of the COVID-19 outbreak These files require MATLAB R2021b or newer and the simulation can be run from the main file Main_Outer_Control_loop.m. Files include: Main_Outer_Control_loop.m iLQG_function.m l_cost.m Measurement.m ContinuousStateDynamics.m DiscreteStateDynamics.m forward_pass.m backward_pass.m Todorov_estimator.m SPKF_function.m simulate_system.m finite_difference.m boxQP.m makePD.m pp.m sabs.m
DOI: 10.5281/zenodo.10372379
title: PREVENTION OF GERIATRIC DISEASES AND SYNDROMES IN THERAPEUTIC PRACTICE USING THE INNOVATIVE PHYTOPREPARATION SARSABIL.
DOI: 10.5281/zenodo.10372435
title: XORIJIY ARMIYALARDA AXLOQIY-RUHIY TAYYORGARLIKKA BO'LGAN YONDASHUVLAR
DOI: 10.5281/zenodo.10372434
title: XORIJIY ARMIYALARDA AXLOQIY-RUHIY TAYYORGARLIKKA BO'LGAN YONDASHUVLAR
DOI: 10.25345/c5fx7484p
title: MassIVE MSV000093659 - Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics
title: Proteomics is making important contributions to drug discovery - from target deconvolution to mechanism of action (MoA) elucidation and the identification of biomarkers of drug response. Here, we introduce decryptE, a proteome-wide approach that measures the full dose-response characteristics of drug-induced protein expression changes which informs cellular drug MoA. Assaying 144 clinical drugs and research compounds against 8,000 proteins resulted in &gt;1 million dose-response curves that can be interactively explored online in ProteomicsDB and a custom-built ShinyApp. Analysis of the collective data provided molecular explanations for known phenotypic drug effects and uncovered novel aspects of the MoAs of human medicines. Most notable, HDAC inhibitors potently and strongly down-regulated the T-cell receptor complex resulting in impaired human T-cell activation in-vitro and ex-vivo. This not only offers a rational explanation for the efficacy of HDAC inhibitors in certain lymphomas and autoimmune diseases but also their poor performance in treating solid tumors.
DOI: 10.5281/zenodo.10372468
title: ТАСАВВУФ МАКТАБЛАРИ ВА ТАРИҚАТ ТУРЛАРИ
DOI: 10.5281/zenodo.10372469
title: ТАСАВВУФ МАКТАБЛАРИ ВА ТАРИҚАТ ТУРЛАРИ
DOI: 10.34740/kaggle/dsv/7187415
title: Axial CT scans with lungs
DOI: 10.6084/m9.figshare.23668770.v1
title: Phylogenetic analysis using plastid genome sequences

description: This research investigated the phylogenetic relationships of the members in the Persicaria amphibia complex.
DOI: 10.5517/ccdc.csd.cc2bpl9y
title: CCDC 2165700: Experimental Crystal Structure Determination

description: Related Article: Zhong-Hua Sun, Xin-Yan Wang, Kun-Lin Huang, Ming-Yang He, Sheng-Chun Chen|2022|Catalysis Communications|169|106472|doi:10.1016/j.catcom.2022.106472
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.34740/kaggle/dsv/7195184
title: Disney's Deadly Incidents
DOI: 10.6084/m9.figshare.24802788
title: PDBbind v.2013 core set prepared

description: PDBbind v.2013 core set manually curated to optimize the hydrogen bond network considering protein and ligand protonation states.The description of this dataset preparation is published in the following reference:Guedes, I. A.; Barreto, A. M. S.; Marinho, D.; Krempser, E.; Kuenemann, M. A.; Sperandio, O.; Dardenne, L. E.; Miteva, M. A. New Machine Learning and Physics-Based Scoring Functions for Drug Discovery. <i>Sci Rep</i> <b>2021</b>, <i>11</i> (1), 3198. https://doi.org/10.1038/s41598-021-82410-1.
DOI: 10.6084/m9.figshare.24802788.v1
title: PDBbind v.2013 core set manually curated

description: PDBbind v.2013 core set manually curated to optimize the hydrogen bond network considering protein and ligand protonation states.The description of this dataset preparation is published in the following reference:Guedes, I. A.; Barreto, A. M. S.; Marinho, D.; Krempser, E.; Kuenemann, M. A.; Sperandio, O.; Dardenne, L. E.; Miteva, M. A. New Machine Learning and Physics-Based Scoring Functions for Drug Discovery. <i>Sci Rep</i> <b>2021</b>, <i>11</i> (1), 3198. https://doi.org/10.1038/s41598-021-82410-1.
DOI: 10.48324/dandi.000469/0.231213.2047
title: Dataset of human-single neuron activity during a Sternberg working memory task.

description: We present a dataset of 1809 single neurons  recorded from the human medial temporal lobe (amygdala and hippocampus) and medial frontal lobe (anterior cingulate cortex, pre-supplementary motor area, ventral medial prefrontal cortex) across 41 sessions from 21 patients that underwent intracranial monitoring for epileptic activity. Subjects first performed a screening task (907 neurons), based on which we identified images for which highly selective cells were present in the medial temporal lobe. Subjects then performed a working memory task (902 neurons), in which they were sequentially presented with 1-3 images, and following a maintenance period, were asked if a probe was identical to one of the currently maintained images. This Neural data without borders (NWB) formatted dataset includes spike times, extracellular spike waveforms, stimuli presented, behavior, electrode locations, and subject demographics. As validation, we replicate previous findings on the existence of concept cells and their persistent activity during working memory maintenance.  This dataset provides a substantial amount of rare human single neuron recordings together with behavior, thereby enabling investigation of the neural mechanisms of working memory at the single-neuron level.

Sample code to access and analyze this dataset has been provided: 
https://github.com/rutishauserlab/workingmem-release-NWB
DOI: 10.6084/m9.figshare.24802932
title: LEADS-PEP dataset

description: LEADS-PEP dataset manually curated to optimize the hydrogen bond network considering protein and ligand protonation states.The description of this dataset preparation and the performance of the DockThor program are published in the following reference:dos Santos, K. B.; Guedes, I. A.; Karl, A. L. M.; Dardenne, L. Highly Flexible Ligand Docking: Benchmarking of the DockThor Program on the LEADS-PEP Protein-Peptide Dataset. <i>J. Chem. Inf. Model.</i> <b>2020</b>, acs.jcim.9b00905. https://doi.org/10.1021/acs.jcim.9b00905.
DOI: 10.6084/m9.figshare.24802944
title: Matlab code for data analysis related to CCA decoding

description: Included are one Matlab script (simpleExample.m) and two functions (bruteDecode.m and opti1DDecode.m). These codes were used to perform the data analysis described in Barreiro et al "<b>Sensory input to cortex encoded on low-dimensional periphery-correlated subspaces</b>" journal TBD
DOI: 10.5066/p9677tsp
title: Microplastics in the Alplaus Kill at Glenridge, NY (01355470), 2018-2019

description: This dataset enumerates the type, size, and color of microplastic particles collected every two weeks from the Alplaus Kill at Glenridge Road in Schenectady, NY (01355470) between November 2018 and December 2019. Ancillary data include stream discharge, sampling net dimensions, and stream velocity. Sampling and analytical methodology are described in the metadata.�
DOI: 10.25345/c5b56dg0v
title: MassIVE MSV000093660 - iPOND analysis of samples from WT and RNF4 knockout B cells
title: iPOND analysis of samples from WT and RNF4 knockout B cells
DOI: 10.26133/nea39
title: Habitable Worlds Observatory Preliminary Input Catalog

description: This is a list of ∼13,000 bright, nearby objects from TESS and Gaia DR3 that are potential targets for space-based direct imaging with the Habitable Worlds Observatory.

This dataset or service is made available by the NASA Exoplanet Science Institute at IPAC, which is operated by the California Institute of Technology under contract with the National Aeronautics and Space Administration.
DOI: 10.6084/m9.figshare.22596871.v1
title: Egg Counter: Parts List

description: Here, we provide parts lists for the various components in the Egg-Counter platform. The Egg Counter is a novel microfluidic research platform for studying egg-laying behavior of <em>Caenorhabditis elegans</em> and related nematodes.
DOI: 10.6084/m9.figshare.22596871
title: Egg Counter: Parts List

description: Here, we provide parts lists for the various components in the Egg-Counter platform. The Egg Counter is a novel microfluidic research platform for studying egg-laying behavior of <em>Caenorhabditis elegans</em> and related nematodes.
DOI: 10.13012/b2idb-2567453_v1
title: Datasets for EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment

description: This upload contains all datasets used in Experiment 2 of the EMMA paper (appeared in WABI 2023): Shen, Chengze, Baqiao Liu, Kelly P. Williams, and Tandy Warnow. "EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment".

The zip file has the following structure (presented as an example):
salma_paper_datasets/
|_README.md
|_10aa/
|_crw/
|_homfam/
 |_aat/
 | |_...
 |_...
|_het/
 |_5000M2-het/
 | |_...
 |_5000M3-het/
 ...
|_rec_res/


Generally, the structure can be viewed as:
[category]/[dataset]/[replicate]/[alignment files]

# Categories:
1. 10aa: There are 10 small biological protein datasets within the `10aa` directory, each with just one replicate.
2. crw: There are 5 selected CRW datasets, namely 5S.3, 5S.E, 5S.T, 16S.3, and 16S.T, each with one replicate. These are the cleaned version from Shen et. al. 2022 (MAGUS+eHMM).
3. homfam: There are the 10 largest Homfam datasets, each with one replicate.
4. het: There are three newly simulated nucleotide datasets from this study, 5000M2-het, 5000M3-het, and 5000M4-het, each with 10 replicates.
5. rec\_res: It contains the Rec and Res datasets. Detailed dataset generation can be found in the supplementary materials of the paper.

# Alignment files
There are at most 6 `.fasta` files in each sub-directory:
1. `all.unaln.fasta`: All unaligned sequences.
2. `all.aln.fasta`: Reference alignments of all sequences. If not all sequences have reference alignments, only the sequences that have will be included.
3. `all-queries.unaln.fasta`: All unaligned query sequences. Query sequences are sequences that do not have lengths within 25% of the median length (i.e., not full-length sequences).
4. `all-queries.aln.fasta`: Reference alignments of query sequences. If not all queries have reference alignments, only the sequences that have will be included.
5. `backbone.unaln.fasta`: All unaligned backbone sequences. Backbone sequences are sequences that have lengths within 25% of the median length (i.e., full-length sequences).
6. `backbone.aln.fasta`: Reference alignments of backbone sequences. If not all backbone sequences have reference alignments, only the sequences that have will be included.

&gt;If all sequences are full-length sequences, then `all-queries.unaln.fasta` will be missing.
&gt;If fewer than two query sequences have reference alignments, then `all-queries.aln.fasta` will be missing.
&gt;If fewer than two backbone sequences have reference alignments, then `backbone.aln.fasta` will be missing.

# Additional file(s)
1. `350378genomes.txt`: the file contains all 350,378 bacterial and archaeal genome names that were used by Prodigal (Hyatt et. al. 2010) to search for protein sequences.
DOI: 10.13012/b2idb-4194451_v1
title: Additional datasets (RNASim10k) for EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment

description: This upload contains one additional set of datasets (RNASim10k, ten replicates) used in Experiment 2 of the EMMA paper (appeared in WABI 2023): Shen, Chengze, Baqiao Liu, Kelly P. Williams, and Tandy Warnow. "EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment".

The zipped file has the following structure:
10k
|__R0
 |__unaln.fas
 |__true.fas
 |__true.tre
|__R1
...

# Alignment files:
1. `unaln.fas`: all unaligned sequences.
2. `true.fas`: the reference alignment of all sequences.
3. `true.tre`: the reference tree on all sequences.

For other datasets that uniquely appeared in EMMA, please refer to the related dataset (which is linked below): Shen, Chengze; Liu, Baqiao; Williams, Kelly P.; Warnow, Tandy (2022): Datasets for EMMA: A New Method for Computing Multiple Sequence Alignments given a Constraint Subset Alignment. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2567453_V1
DOI: 10.5066/p9ka7g04
title: Toxicity data for the evaluation of Ziram to Grass Carp Ctenopharyngodon idella in a laboratory setting

description: Data consists of dose, dose method, solvent, weight, length and survival of test species from bioassays following an Up-and-Down method conducted with Ziram.