cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/xrwb9m37gd.1
title: RailEnV-PASMVS: a dataset for multi-view stereopsis training and reconstruction applications

description: A Perfectly Accurate, Synthetic dataset featuring a virtual railway EnVironment for Multi-View Stereopsis (RailEnV-PASMVS). The dataset consists of 40 scenes and 79,800 renderings together with ground truth depth maps, camera extrinsic and intrinsic parameters and binary segmentation masks of all the track components and surrounding environment. Every scene is rendered from a set of 3 cameras, each positioned relative to the track for optimal 3D reconstruction of the rail profile. The set of cameras is translated across the 100-meter length of tangent track to yield a total of 1,995 cameras per scene. Photorealistic lighting of each of the 40 scenes is achieved with the implementation of different high-definition, high dynamic range (HDR) environmental textures. Additional variation is introduced in the form of varying camera focal lengths, the addition of random noise for the camera location and rotation parameters and material variation of the rail profile. The power spectral density (PSD) sourced from representative track geometry data is used to generate random and unique vertical alignment data for the rail profile for every scene. File descriptions: + RailEnV-PASMVS.blend (227 Mb) - Blender file (developed using Blender version 2.8.1) used to generate the dataset. The Blender file packs only one of the HDR environmental textures to use as an example, along with all the other asset textures. + RailEnV-PASMVS_sample.png (28 Mb) - A visual collage of 30 scenes, illustrating the variability introduced by using different models, illumination, material properties and camera focal lengths. + geometry.zip (2 Mb) - Geometry CSV files used for all the scenes. The Bezier curve defines the geometry of the rail profile (10 mm interval). + sampleset_19.zip (2.5 Gb) - A single RailEnV-PASMVSD scene sample for easy viewing and evaluations. For the full dataset please use the link provided below. GitHub page to access the full RailEnV-PASMVS dataset (hosted on Google Drive): https://github.com/andrebroekman/RailEnV-PASMVS
DOI: 10.17632/wvpydygkdh.2
title: fISHing with immunohistochemistry for housekeeping gene changes in Alzheimer’s Disease using an automated quantitative analysis workflow dataset

description: This dataset contains the macro/script (ImageJ Macro language) and output for determining the total and neuronal RNAscope expression counts of UBC, PPIB and POLR2A in normal and Alzheimer's Disease middle temporal gyrus tissue microarrays.
DOI: 10.17632/p4cnd87hxh.2
title: QLQ-C30 -QLQ-BR23 Universidad del Valle

description: 80 answers to the QLQ-C30 and QLQ-BR- 23 questionnaire. Some sociodemographic variables were considered, the research team is estimating which variables affect the quality of life by means of Bayesian models and structural equations.
DOI: 10.17632/p727gc8rpf.1
title: Dian

description: Continuous lacustrine records of the Indian Summer Monsoon that span the Pleistocene-Holocene transition to the present are relatively rare, yet crucial to providing context to future changes in hydroclimate. We summarize here a 17,000 year continuous multi-proxy record of hydroclimate and primary productivity from Lake Dian in the central Yunnan Province of China. Analysis of sediment composition, opal, carbon to nitrogen ratios, carbon and nitrogen stable isotope ratios, and magnetic susceptibility (MS) are used to identify four distinct lithologic units in the sediment record. Unit I sediments from 17,000 to 11,500 years BP are characterized by high MS and uniformly low organic and opal content interupted by a decrease in MS during the Bølling-Allerød indicating the influence of the North Atlantic on the Indian Monsoon. We interpret this to reflect cold, dry, and windy conditions during the transition out of the Last Glacial Maximum. Unit II from 11,500 to 5,000 years BP is marked by a pronounced decrease in MS, increase in opal, and decrease in 13Corg of organic carbon driven by peak warmth and wet conditions increasing productivity. Unit III from 5,000 to 1,800 years BP shows further increases in primary productivity, marked by lower carbon to nitrogen ratios and carbonate precipitation, possibly driven by a drop in lake level. A period of aridity is in wide agreement with a number of other records from the region. Unit IV from 1,800 years BP to present is dominated by anthropogenic impacts and hallmark signs of catchment soil erosion and cultural eutrophication. Our interpretations of the Dian sediment record agree well with previous palynological work and add a new dimension to our understanding of lake hydrology and productivity over the past 17,000 years.
DOI: 10.17632/s43brcvg2k.1
title: Dataset_Categorization in COVID-19
DOI: 10.6084/m9.figshare.11981034
title: Single-cell RNA-Seq of human primary lung and bronchial epithelium cells

description: This dataset contains count matrices and per-cells metadata tables for RNA sequencing of 39778 single nuclei from healthy primary lung samples of 12 lung adenocarcinoma patients as well as 17451 single human bronchiole epithelial cells from 4 donors. All samples were processed using the 10X Genomics Chromium platform with v2 chemistry and sequenced with one sample per lane on an Illumina HiSeq4000. Reads were aligned to the hg19 reference genome version 1.2.0 obtained from 10X Genomics. Data processing was performed using Seurat3. The metadata table includes patient ID, sex, age, smoking status, and cell type, as well as QC statistics (number of genes, number of cells, ratio of mitochondrial reads).
DOI: 10.6084/m9.figshare.11981034.v2
title: Single-cell RNA-Seq of human primary lung and bronchial epithelium cells

description: This dataset contains count matrices and per-cells metadata tables for RNA sequencing of 39778 single nuclei from healthy primary lung samples of 12 lung adenocarcinoma patients as well as 17451 single human bronchiole epithelial cells from 4 donors. All samples were processed using the 10X Genomics Chromium platform with v2 chemistry and sequenced with one sample per lane on an Illumina HiSeq4000. Reads were aligned to the hg19 reference genome version 1.2.0 obtained from 10X Genomics. Data processing was performed using Seurat3. The metadata table includes patient ID, sex, age, smoking status, and cell type, as well as QC statistics (number of genes, number of cells, ratio of mitochondrial reads).
DOI: 10.17632/m5npy78mnd.1
title: Raw data for a study of smile aesthetic perception amongst dental professionals, patients and parents towards impacted maxillary canine treatment options

description: Objective To evaluate the smile aesthetics of the different treatment options for impacted maxillary canines as perceived by orthodontists, dentists, patients and parents. Design Four digitally manipulated images were created to imitate different treatment options available for the treatment of ectopic maxillary canines including; alignment of the impacted maxillary canine, substituted premolars, retained deciduous canines or gaps present. The images were embedded into piloted questionnaires. Setting Four rater groups were selected to complete the questionnaire consisting of an Orthodontist group, a GDP group, a Patient group consisting of patients between the ages of 11 and 18 who were considered to be ‘Gillick competent’ and a Parent group consisting of parents/guardians who accompanied the patients to their orthodontic appointments. Method Each participant completing the questionnaire was asked to mark the visual analogue scale underneath each image according to their perception of attractiveness of each image. Quantitative scoring of the perceived attractiveness of the smile was assessed by one calibrated assessor measuring the distance from the start of the scale to the marked cross placed on the VAS scale. A two-way ANOVA (mixed between-within subject’s ANOVA) was used to compare perception of differences in smile aesthetics. Results There were significant differences found in the VAS between the groups (p = 0.002) and between the treatment options (P=&lt;0.001) There was no statistically significant difference found between the aligned canines and substituted premolars images by the patient (p = 0.2) or parent group (p = 0.5). All groups most disliked the treatment option where gaps were present at the end of treatment. Conclusion The patient and parent group showed similar perception in smile aesthetics for aligned canines and substituted premolars and all groups showed a strong dislike to the presence of gaps.
DOI: 10.17632/ygj2yfj9k5.2
title: A study of structural characterization of SARS-CoV-2. Sun et al

description: The supplementary table S1-S7 of our paper entitled "In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs".
DOI: 10.17632/x4yjz735xz.1
title: AMMCR: Ab initio model for mobility and conductivity calculation by using Rode Algorithm

description: We present a module to calculate the mobility and conductivity of semiconducting materials using Rode’s algorithm. This module uses a variety of electronic structure inputs derived from the Density Functional Theory (DFT). We have demonstrated good agreement with experimental results for the case of Cadmium Sulfide (CdS). We also provide a comparison with the widely used method, the so-called relaxation time approximation (RTA) and demonstrated a favorable improvement of the results compared to RTA. The present version of the module is interfaced with the Vienna ab initio simulation package (VASP).
DOI: 10.17632/zgxfx6xk4t.1
title: LBfoam: An open-source software package for the simulation of foaming using the Lattice Boltzmann Method

description: This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated bubbles, bubble dynamics and coalescence, surface tension, the stabilizing disjoining pressure between bubbles, and Newtonian and non-Newtonian rheological models. The software can simulate the growth and interaction of bubbles, and predict final foam structures. The implementation is based on the Palabos library (in C++), which enables large-scale parallel simulations. The software is freely available under the GNU Affero General Public License version 3.
DOI: 10.17632/jw5zd3zbhw.1
title: Microstructures generated by phase field simulated Al-Si solidification

description: Liquid phase fraction resulting from phase field simulations of the microstructure evolution during solidification of an AlSi7Mg0.3 alloy used for premeability simulations. RVE: cube of 150 micrometers edge length, resolution 0.5 micrometer. Format: VTK packed with gzip. Solidification conditions: 240 W/ccm heat extraction rate "equiaxed": No temperature gradient, xyz-periodic "directional": Temperature gradient 5K/mm, xy-periodic
DOI: 10.17632/kzycj3n2mm.1
title: Dataset: Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage

description: This dataset accompanies the manuscript: Ingram & Henthorn et al., Hi-C implementation of genome structure for in silico models of radiation-induced DNA damage. Each directory contains a corresponding About.txt file which details the contents of each data file. The code folder contains a copy of the G-NOME python code at the point of publication. For the best version of the code, we recommend using the version hosted at https://gitlab.com/PRECISE-RT/releases/g-nome . If further guidance is required please contact the corresponding author on the manuscript.
DOI: 10.17632/xvs9sx9t44.1
title: Empirical GPS velocity uncertainty in California

description: Published velocity values compiled in to a composite velocity data set that contains the station name, longitude, latitude, and north/east/up velocity with empirical uncertainty. The interpolated vertical velocity field with uncertainty includes the longitude, latitude, velocity, and error for the grid.
DOI: 10.17632/5dfj2hhnng.1
title: SARS-CoV-2 GISAID UK-US isolates (2020-09-07) genotyping VCF

description: VCF files containing filtered mutated sites in SARS-CoV-2 genomes obtained from GISAID EpiCoV and submitted from the UK and the US, separated by individual mutations. The columns correspond to viral genome accession ID, nucleotide position in the genome, mutation ID (left blank in all rows), reference nucleotide, identified mutation, quality, filter, and information columns (all left blank), format (GT in all rows), column corresponding to reference genome (all 0, referring to reference nucleotide column), and columns corresponding to isolate genomes, with each row identifying the nucleotide in the POS column, and whether it is non-mutant (0), or the mutant indicated in the identified mutation column (1). The files is tab delimited, with the UK file having 12696 rows including the names, and 18135 columns, and the US file having 15588 rows including the names, and 16277 columns. The file was generated to test the hypothesis whether the different SARS-CoV-2 genes or protein coding regions are positively or negatively selected differently between 14408C&gt;T / 23403A&gt;G double mutants and double wildtype isolates, using mutation rate models, and whether regional distributions affect the mutation rates. Our findings have shown that the RdRp coding region and the S gene show the highest amount of selection across viral generations, and that different countries can affect the synonymous and nonsynonymous mutation rates for individual genes.
DOI: 10.17632/gtrdmvszgw.4
title: The inhibition of KDM2B promotes the differentiation of basal-like breast cancer cells via the posttranslational destabilization of SLUG
DOI: 10.17632/8wsddy5y5d.1
title: Design for additive manufacturing of closed cellular structure with thin and thick wall and its effect on energy absorption

description: uniaxial compression tests are performed on a servo-hydraulic MTS 810 material test system equipped with a 100 kN load cell, at a strain rate of 5 mm/min. Compression is imposed on 3 levels, 10, 20, and 30% for open, thin-walled closed-cell, and thick-walled closed-cell lattice structure.
DOI: 10.17632/p2chwmy4sp.1
title: SARS-CoV-2 immune homology with vaccine pathogens

description: Recent epidemiological studies have investigated the potential effects of childhood immunization history on COVID-19 severity. Specifically, prior exposure to Bacillus Calmette–Guérin (BCG) vaccine, oral poliovirus vaccine (OPV), or measles vaccine have been postulated to reduce COVID-19 severity – putative mechanism is via stimulation of the innate immune system to provide broader protection against non-specific pathogens. While these epidemiological results remain inconclusive, we sought to investigate the potential role of adaptive immunity via cross-reactivity between vaccine preventable diseases (VPDs) with SARS-CoV-2. We implemented a comprehensive exploration of immune homology (including sequence homology, immune epitopes, and glycosylation patterns) between SARS-CoV-2 and all pathogens with FDA-approved vaccines. Sequence homology did not reveal significant alignments of protein sequences between SARS-CoV-2 with any VPD pathogens, including BCG-related strains. We also could not identify any shared T or B cell epitopes between SARS-CoV-2 and VPD pathogens among either experimentally validated epitopes or predicted immune epitopes. For N-glycosylation (N-glyc), while sites with the same tripeptides could be found between SARS-CoV-2 and certain VPD pathogens, their glycosylation potentials and positions were different. In summary, lack of immune homology between SARS-CoV-2 and VPD pathogens suggests that childhood immunization history (i.e., BCG vaccination or others) does not provide protection from SARS-CoV-2 through adaptive cross-immunity.
DOI: 10.17632/nbyz8j4j34.1
title: Native mass spectrometry-based screening for optimal sample preparation in single particle cryo-EM Olinares et al

description: We have developed a native MS-based screening platform for optimal single-particle cryo-EM sample preparation. This dataset contains the original, unprocessed native MS RAW files for each of the protein complexes and nucleic acid components that are discussed in the paper. The files are arranged by protein complex and by Figure (where the particular file was used). An Excel worksheet describing sample composition for each file is also included.
DOI: 10.17632/vffwyvbdzy.5
title: The cutting path determination problem: input files and solutions' layouts

description: This contains the input files and solution layouts for the results obtained in the work of Silva et al. (2019) - Exact approaches for the cutting path determination problem. Also in Silva, E. F., 2016. Mathematical models to a cutting path determination problem. Master thesis, University of São Paulo. The input files contain the position of the reference point of each item placed. This positioning was taken from the solutions of Rodrigues and Toledo (2017) - A clique covering MIP model for the irregular strip packing problem. The solutions obtained are the optimal solutions from solving the cutting path determination problem with its characteristics described in detail in the thesis. The files are divided in two folders, one containing the solutions obtained when considering the division of overlapping edges and the other without considering the division.
DOI: 10.17632/5rrxw7y5bj.1
title: Accelerometer Data for Energy Harvesting During Walking Estimation

description: Accelerometer data supporting Inertial Kinetic Energy Harvesters for Wearables: The Benefits of Harvesting at the Foot, this dataset contains accelerometer data from participants walking on a treadmill at a variety of speeds with sensors on the wrist, hip, ankle and foot. If using this data, please cite: C. Beach, A. J. Casson, "Inertial Kinetic Energy Harvesters for Wearables: The Benefits of Harvesting at the Foot," IEEE Access, 2020 (doi: doi.org/10.1109/ACCESS.2020.3037952) Analysis code for this paper is available at https://github.com/CASSON-LAB/kinetic_energy_harvesting This repository includes both the raw data collected by the Axivity AX3 sensors (the raw CWA files and the resampled data in CSV format) and versions of the data that has been trimmed into multiple records corresponding to each speed of the treadmill (in pickled format). Note there is no participant P1. Accessing the raw data: The folders P2 – P13 contain the untrimmed data from the sensors. Sample rate: 100 Hz, units: g Participants were instructed to walk on a treadmill (LifeSpan TR1200i) as close as possible to how they would normally walk, while the speed of the treadmill was controlled by the experimenter. The treadmill was started at 2.4 km/h and the speed increased every 60 s by 0.1 km/h until the treadmill reached 4.3 km/h. Prior to recording each sensor went under a synchronisation procedure where all the sensors were flipped on their z-axis, causing a transition from -1g to +1g. The times of this synchronisation and the time for starting the treadmill is detailed in metadata.xlsx Files ending in .cwa are in Continuous Wave Accelerometer format (a binary format) which can be processed with OmGUI software from Axivity. Files ending in .csv are these files are processed cwa files in a text format, files ending in .resampled.csv have been resampled to 100 Hz using OmGUI. These resampled files account for the fact that the AX3 sensors sample at close to 100 Hz with significant sampling jitter by resampling the data to make the sampling rate exactly 100 Hz. It is recommended to work with the sampled files. 21629: Left wrist 21704: Right wrist 31447: Left hip 32610: Right hip 32784: Left ankle 32798: Right ankle 32816: Left foot 32973: Right foot Accessing the trimmed data: The trimmed data can be accessed by downloading the .pkl files, which are suitable to be imported directly into Python. Each of these can be imported by running the following commands in Python: import pickle import numpy as np pkl_file = open('P2.pkl', 'rb') P2 = pickle.load(pkl_file) The files cached_indexes.h5, cached_data.h5 and cadence_list.csv are required for use with the analysis code used in the paper and available at https://github.com/CASSON-LAB/kinetic_energy_harvesting
DOI: 10.17632/k3mytw52sh.1
title: Data for: Migration rate of the Luzon subduction system during the late Neogene: Sedimentary records from Hengchun accretionary prism turbidites on Taiwan Island

description: This Supporting Information contains two figures (Figs. S1 and S2) and four large datasets (Datasets S1, S2, S3 and S4), which are all uploaded separately. The main article has provided a detailed data compilation and interpretation, supported by this Supporting Information. The sample collection methods are described in the main article. Additionally, please refer to the detailed analytical methods in the paper. All references have been given in the paper.
DOI: 10.6084/m9.figshare.11927025
title: Physician estimated vs. self-reported subjective memory in depressed patients treated with electroconvulsive therapy

description: <b>Background:</b> Subjective memory deficits are common in depression and during series of treatment with electroconvulsive therapy (ECT). There is a need for feasible assessment of memory deficit. In the Swedish National Quality Register for ECT, patients’ subjective memory function is rated by a clinician. Self-ratings would be easier to administer. <b>Objectives:</b> The aim of this study was to analyze the consistency between self-reported and physician estimated subjective memory in depressed patients treated with ECT. <b>Methods:</b> Fifty-two inpatients treated with ECT for major- or bipolar depression were recruited and 41 of them completed the study protocol. Each patient rated their own subjective memory and had it rated in an interview by a physician both before/in the beginning of the ECT series and after the ECT series. The patients’ memory was rated and self-rated with the memory item in the Comprehensive Psychopathological Rating Scale (CPRS). We then analyzed correlations, and differences in distributions, between self-reported assessment and physician estimates of patients’ subjective memory. <b>Results:</b> The correlations between the self-reported and the physician estimated ratings of subjective memory were 0.699 (<i>p</i> p <b>Conclusions:</b> Based on the results in this study, we propose that patients’ self-ratings of subjective memory in association with ECT can be used instead of a physician’s rating of patients’ subjective memory.