cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1412637.v1
title: ChemDraw Markush

description: Using ChemDraw to draw out Markush structure and R fragments
DOI: 10.6084/m9.figshare.21505428.v1
title: PaiNN dataset and model for LGPS

description: Can be used to run MD with the NeuralForceField repository. Units for the dataset are: kcal/mol for energy, kcal/mol-Å for forces, Å for units of length.
DOI: 10.6084/m9.figshare.22020452.v1
title: Data for "Mapping global nitrogen deposition impacts on soil respiration"

description: This is the data file for the meta-analysis " Mapping global N deposition impacts on soil respiration". Please contact the authors if you have any questions about the dataset.
DOI: 10.17632/cbd8bnhg3n
title: Effects of Virtual Reality-based Motor Control Training on Inflammation, Oxidative Stress and Neuroplasticity in Patients with Chronic Stroke: A randomized controlled trial

description: Background: Virtual reality (VR)-based rehabilitation is the innovative approach in motor control training in individuals with stroke. Currently, most outcome assessments of motor performance in stroke were based on subjective functional scales and instruments. Detecting serum biomarkers related to inflammation, oxidative stress, and neuroplasticity, might provide precise and subtle changes after motor control training in patients with stroke. Objectives: This study aims to identify the effects of immersive VR-based intervention of motor control training on motor function improvement, inflammation, oxidative stress, and neuroplasticity in patients with stroke. Methods: This is an assessor-blinded, randomized controlled study. Patients with stroke will be randomly assigned to the VR training (VRT) group or the conventional occupational therapy (COT) group. Clinical assessments will include motor performance and active range of motion (AROM) of the upper limb. Serum concentrations of inflammation, oxidative stress, and neuroplasticity will be assessed, including interleukin 6 (IL-6), intracellular adhesion molecule 1 (ICAM-1), heme oxygenase 1 (HO-1), 8-hydroxy-2-deoxyguanosine (8-OHdG), and brain-derived neurotrophic factor (BDNF). Expected outcomes: After the intervention, both groups will show improvements in motor performance and the changes of inflammation, oxidative stress, and neuroplasticity. As compared to the COT group, the VRT group will show greater improvements in motor performance and AROM of the upper limb, greater induction of HO-1 and BDNF levels, and greater reductions in 8-OHdG.
DOI: 10.6084/m9.figshare.1190767.v3
title: photodissociation cross sections for the hydrogen molecular ion

description: photodissociation cross sections for the hydrogen molecular ion. v=0, ..., 18,N=0. Photodissociation cross sections for the hydrogen molecular were calculated using quantum-mechanical methods. The Born-Oppenheimer approximation is used (adiabatic, relativisitic, and non-adiabatic corrections are ignored) for (v,N) with v=0...18, and N=0. There are published tables with some of these values [1,2] with log plots for (v=0,N=1) and (v=9,N=1). The present values are in good agreement with those listed in [1]. Refs.[3] and [4] give log plots for (0,0), (0,5), (0,8) and Ref. [3] gives a log plot for (7,0) and (7,8). Ref.[5] gives a linear plot for (10,0), (10,10), (10,15), and (10,20). References: [1] Gordon H. Dunn, JILA Report #92, Jan. 30, 1968 (University of Colorado). https://jila.colorado.edu/publications/photodissociation-h2-and-d2-theory-and-tables [2] Gordon H. Dunn, Phys. Rev. A <strong>172, </strong>1 (1968). doi:10.1103/PhysRev.172.1 [3] J. D. Argyros, J. Phys. B <strong>7</strong>, 2025 (1974). doi:10.1088/0022-3700/7/15/011 [4] P. C. Stancil, Ap. J. <strong>430</strong>, 360 (1994). doi:10.1086/174411 [5] V. S. Lebedev and L. P. Presnyakov, J. Phys. B <strong>35</strong>, 2347 (2002). doi:10.1088/0953-4075/35/21/303
DOI: 10.6084/m9.figshare.21591351.v1
title: RNA-Seq raw counts and meta data for INVADE cohort

description: RNA-Seq raw counts and meta data for INVADE cohort
DOI: 10.6084/m9.figshare.26941993.v3
title: USPTO-multistep.csv

description: A multi-step reaction dataset comprising 95,670 reactions was developed by extracting reactions involving more than five reagents from the Lowe dataset. In contrast to the conventional USPTO data, this dataset is systematically organized on a step-by-step basis, with each reaction step delineated by the '&gt;' delimiter.
DOI: 10.6084/m9.figshare.29098154.v1
title: <b>Impact of multiphasic pore-scale interactions on gas hydrate formation and dissociation characteristics and kinetics: a microfluidic study</b>

description: Understanding the multiphasic interactions governing gas hydrate formation and dissociation is critical for optimizing natural gas storage and extraction. This study investigates the characteristics and kinetics of methane hydrate formation and dissociation within porous media using a microfluidic chip platform designed to simulate natural conditions. By introducing methylene blue for enhanced phase differentiation, five distinct hydrate morphologies—block, vein, point, membrane, and shell—were identified.The relevant quantitative original data are shown as in this dataset.
DOI: 10.6084/m9.figshare.5125624.v1
title: Supplementary Material for: Vasopressin-Induced Constriction of the Isolated Rat Occipital Artery is Segment Dependent

description: <b><i>Background:</i></b> Circulating factors delivered to the nodose ganglion (NG) by the occipital artery (OA) have been shown to affect vagal afferent activity, and thus the contractile state of the OA may influence blood flow to the NG. <b><i>Methods:</i></b> OA were isolated and bisected into proximal and distal segments relative to the external carotid artery. <b><i>Results:</i></b> Bisection highlighted stark differences between maximal contractile responses and OA sensitivity. Specifically, maximum responses to vasopressin and the V<sub>1</sub> receptor agonist were significantly higher in distal than proximal segments. Distal segments were significantly more sensitive to 5-hydroxytryptamine (5-HT) and the 5-HT<sub>2</sub> receptor agonist than proximal segments. Angiotensin II (AT)<sub>2</sub>, V<sub>2</sub> and 5-HT<sub>1B/1D</sub> receptor agonists did not elicit vascular responses. Additionally, AT<sub>1</sub> receptor agonists elicited mild, yet not significantly different maximal responses between segments. <b><i>Conclusion:</i></b> The results of this study are consistent with contractile properties of rat OA being mediated via AT<sub>1</sub>, V<sub>1</sub> and 5-HT<sub>2</sub> receptors and dependent upon the OA segment. Furthermore, vasopressin-induced constriction of the OA, regardless of a bolus dose or a first and second concentration-response curve, retained this unique segmental difference. We hypothesize that these segmental differences may be important in the regulation of blood flow through the OA in health and disease.
DOI: 10.17632/drx9wzhn75
title: CellMatch: Combining two unit cells into a common supercell with minimal strain

description: Abstract Recent emergence of 2D materials (the so-called van der Waals materials), of which graphene is the most famous one, opens new routes in creation of novel materials by mere layer-by-layer combinations. Moreover, a growth of such materials is typically done on a substrate. In both cases structures appear that are periodical in the plane but the periodicity is very different from simple 1 × 1 commensurate unit cells combinations which appears for materials with very similar values of lattice con... Title of program: CellMatch Catalogue Id: AEYD_v1_0 Nature of problem Contracting a common supercell that fits the atoms of two unit cells with minimal strain. This is used as input for any total energy or electronic structure code. Versions of this program held in the CPC repository in Mendeley Data AEYD_v1_0; CellMatch; 10.1016/j.cpc.2015.08.038 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)
DOI: 10.17632/j87c9jshxy
title: Diagnostic performance of artificial intelligence for histologic melanoma recognition compared to 18 international expert pathologists: Supplementary Material

description: The study was designed to compare the performance of classifiers based on image analyses by convolutionnal neural networks (CNNs) with that of 18 expert dermatopathologists in a binary classification task for pigmented skin lesions. Mendeley Supplementary Figure 1 shows a schematic representation of the testing approach. The CNNs were trained by cross-testing. Each iteration consists of five folds. Orange rectangles represent the folds used for testing and blue rectangles represent folds for training. For each iteration a CNN is trained and tested on the respective folds. Each trained CNN has a performance that is determined on the fold. To calculate the overall performance, the sum of all 5 performances is taken. This procedure was repeated 3 times and the results were combined to generate an ensemble. Mendeley Supplementary Figure 2 depicts the whole slide image (WSI) analysis. Tissue sections on whole slide images (top) were divided into tiles (middle). The CNN (a pre-trained ResNeXt50) assigned a malignancy score to every individual tile (bottom). Red tiles were classified as melanoma, blue tiles as nevus. Scores for all tiles on one image were averaged to a final malignancy score for the complete slide. Supplementary Table 1 shows the characteristics of the pigmented skin lesions included in the test set. Supplementary Table 2 provides an analysis of statistical differences between the performance of pathologists and CNN classifiers.
DOI: 10.17632/37v53gwhyg
title: raw STR data

description: Cell Line Authentication Service STR Profile Report
DOI: 10.17632/rn8677dv33
title: Fault tree analysis_ The proposal of simple simulation

description: The aim of the research paper is to calculate the probability of the top event - the failure of the process using the FTA and the proposal of a simulation performed to reduce the probability of failure of the top event based on the requirements of the manufacturers. We have constructed a qualitative fault tree for the production of office components packed and sealed in blister packs, which takes place on KOCH KBS - PL machinery. We defined the top event G. Then we defined events leading to top events down to individual failure factors. Based on the links between the fault tree and the probability of failure, we performed a quantitative analysis to determine the probability of failure of individual events. We found out that the probability of failure of G is 5.04%. Subsequently, by the stimulation, we have found out which factors are the most significant contributors to the reduction of the resulting probability of failure of the factor G. These are the factors: E, F, AL and D. It has been proved that by controlling these 4 factors we can reduce the probability of failure of top event G to 2.36%. The condition is the application of effective measures. The final proposal was to meet the requirements of several manufacturers for a fast, efficient and undemanding solution. The proposed simulation met the requirements of manu-facturers. It was time and maintenance saving, not demanding on software and hardware re-quirements and has proven its effectiveness and efficiency by reducing the number of top event failure modes.

The file itself contains all the data that led to the creation of the final proposal. 

Proposal for reducing the probability of failure based on quantitative analysis of FT. The chosen proposal will respect the requirements of production organizations. Based on this, we defined 5 simulation requirements: 1) time-saving; 2) minimum software requirements; 3) minimum hardware requirements; 4) easy to use; 5) efficient and ef-fective. 
The proposal will be a simulation based on the calculations of quantitative analysis using MS Excel software. The aim is to find out which gateways of the fault tree need to be addressed as a matter of priority and what effect this effect will ultimately have in reducing the probability of failure of the TOP event. Then, based on the links and gateways of FT, we will create such a comprehensive system, where by reducing the probability of every single factor, we will also see a change in the probability of the top event G.

The proposal of the simulation itself is the work of the authors of the paper. Its simplicity takes into account the requirements of manufacturers. However, the result must be a clear demonstration of increased production efficiency and effectiveness (by reducing the number of top event failure modes), as evidenced by the diagram in Excel.
DOI: 10.6084/m9.figshare.13344758.v1
title: Mussismilia hispida enriched metatranscriptomic gene models

description: The coral-metaorganism transcriptomes response from T3 was explored in order to understand the mechanisms associated with the different phenotypes observed at the end of the experiment. RNA samples were extracted from both the BMC and placebo treatment from the high-temperature (30 °C) and ambient (26 °C) experiment for sequence analysis. Transcriptomic sequencing was performed using Illumina HiSeq 6000 platform (Illumina Inc., San Diego, CA, USA). Transcriptomic reads were quality-controlled using KneadData v0.7.4 with the GRCh38.p13 human genome as a reference for potential decontamination yielding between 14,372,271 and 74,483,759 paired-end (PE) reads at 2×150 bp per sample after quality trimming and filtering. De-novo transcriptomes were co-assembled using rnaSPAdes v3.13.1 (71), producing 520,555 representative transcripts from 496,603 putative genes; genes were estimated by rnaSPAdes. We used TransDecoder v5.5.0 (72) for gene modeling in a multistep process to minimize false positives. In particular, we used the following procedure: i) TransDecoder.LongOrfs, with transcript-to-gene mappings assigned by rnaSPAdes, to generate putative open reading frames (ORFs); ii) hmmscan (hmmer v3.3.1 suite) (73) to identify protein domains using the PFAM v33.1 and TIGRFAM v15.0 databases; iii) Diamond v0.9.30.131 (74) blastp against all Scleractinia (stony corals) proteomes available in NCBI (GCA_002571385.1, GCF_002042975.1, GCA_003704095.1, GCF_004143615.1, GCF_002571385.1, GCF_003704095.1, and GCF_000222465.1); and iv) TransDecoder.Predict with the putative ORFs from (i), the protein domains from (ii), and the alignments from (iii) using the --single_best_only argument. This procedure generated a single ORF per transcript to yield 130,183 ORFs from 114,118 genes. High-quality genes were annotated by using Diamond’s blastp against NCBI’s nr database (v2020.04.01), and taxonomic lineages were extrapolated from NCBItaxid using the get_taxonomy_lineage_from_identifier function from soothsayer v2020.08.24 (https://github.com/jolespin/soothsayer) with ete3 backend (75). PhyloDB v1.076 was used for additional annotations such as KEGG ortholog assignments. <br>
DOI: 10.6084/m9.figshare.24648150.v1
title: PlantSR Dataset

description: PlantSR dataset. 830 images of plant for training, 200 images of plant for testing.
DOI: 10.6084/m9.figshare.28202600.v1
title: Force_Characterization

description: The force characterization data of BarBot individuals, corresponding to the contents in SI Appendix, Table S1.
DOI: 10.17035/d.2017.0032930333
title: Gear tooth root fatigue test monitoring with continuous acoustic emission

description: A test rig is used to load an individual gear tooth in static bending fatigue. The two gears are meshed together, with the lower (fully restrained, rotation prevented) gear attached to a fixed shaft whilst the upper (free) gear is mounted on a shaft held in bearings.  A torque is applied to this shaft using a compression testing machine via a loading arm.  Acoustic Emission signals were collected by a Pancom P15 sensor (50 – 500 kHz) coupled to the free gear adjacent to the tooth under test using cyanoacrylate adhesive.  The data was recorded by a MISTRAS group PCI 2 data acquisition system. Complete wavestreams were captured over one loading cycle. These wavestreams capture the sensor output without any interpretation by the data acquisition system, and are independent of threshold.  Each wavestream was collected every 10 cycles, sampled at 2MHz, 16-bit resolution and a duration of 1s, which covers one complete tooth loading cycle.
DOI: 10.17632/bwpb4jjf3j
title: Clinical information of patients with atherosclerotic plaque: exome sequenced

description: The data contains Patient ID, age, sex, height, weight, body mass index (BMI), waist circumference (WC), ischemic heart disease (IHD) symptoms, comorbidities, plaque description, and echocardiogram symptoms. All patients had coronary artery disease, abdominal obesity, arterial hypertension, and hypercholesterolemia, New York Heart Association (NYHA) II Class.
DOI: 10.17632/wzx7k93zg9
title: Table of legal window tinting limits and medical exemption information for all 50 states and Washington, D.C.

description: There are significant variations in legal window tinting limits and medical exemption laws across the United States, with potential implications for patients with photosensitive dermatoses and their healthcare providers. In this study, we collected data from government websites and online legal codes for all 50 states and Washington, D.C., focusing exclusively on passenger vehicle window tinting laws. Legal tinting limits were measured as a percentage of transmission of visible light (Tvis), with lower Tvis indicating darker tint and greater photoprotection. Data was stratified by window location (e.g., front side, rear side, rear).Information regarding medical exemptions, including qualifying conditions and provider requirements, was extracted. The data highlighted whether states specify medical qualifications, acceptable levels of Tvis for exemptions, or provider roles (e.g., dermatologist, general physician, optometrist).

This supplement material is a table describing the legal window tinting limits for passenger vehicles, stratified by window type, as well as specific information on medical exemptions across all 50 states and Washington, D.C.

The findings demonstrate variability and vagueness in tinting regulations and medical exemption policies across the U.S., highlighting a lack of standardization and potential impacts on patient care and provider responsibility.
DOI: 10.17632/zss7v6j9kz
title: Data for: Psychological responses to natural patterns in architecture

description: These data files correspond to the manuscript "psychological responses to natural patterns in architecture."
DOI: 10.23645/epacomptox.28934363.v1
title: Non-targeted analysis of field collected sediment and water from California vernal pools

description: Non-targeted analysis datasets for identification of chemicals in field collected sediment and water from California vernal pools.Search for CCTE records in EPA’s Science Inventory by typing in the title at this link:https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25
DOI: 10.6084/m9.figshare.21308391.v2
title: GazeBaseVR Data Repository

description: GazeBaseVR is a large-scale, longitudinal, binocular eye-tracking (ET) dataset collected at 250 Hz with an ET-enabled virtual-reality (VR) headset. GazeBaseVR comprises 5,020 binocular recordings from a diverse population of 407 college-aged participants. Participants were recorded up to six times each over a 26-month period, each time performing a series of five different ET tasks: (1) a vergence task, (2) a horizontal smooth pursuit task, (3) a video-viewing task, (4) a self-paced reading task, and (5) a random oblique saccade task. Many of these participants have also been recorded for two previously published datasets with different ET devices, and 11 participants were recorded before and after COVID-19 infection and recovery. GazeBaseVR is suitable for a wide range of research on ET data in VR devices, especially eye movement biometrics due to its large population and longitudinal nature. In addition to ET data, additional participant details are provided to enable further research on topics such as fairness. For more details regarding the experimental methodology, please refer to the corresponding manuscript.
DOI: 10.6084/m9.figshare.11688516.v1
title: Growth curves Gardnerella and Lactobacillus crispatus.pdf

description: Update from the lab on the Master internship results of Ritesh Panchoe. Growth curves of Gardnerella vaginalis and Lactobacillus crispatus on glucose and glycogen.
DOI: 10.6084/m9.figshare.13551176.v1
title: Interactions BridgeDb ID Mapping Database (20210109)

description: BridgeDb ID mapping database for interactions, using Rhea (version 116, 2020-12-02) as data source.<br>Quality control was performed with BridgeDb (2.3.3) against version 2020-10-07 [https://doi.org/10.6084/m9.figshare.13187585.v1], including 2 changes to the regex patterns for Reactome and EcoCyc, see https://github.com/bridgedb/BridgeDb/pull/162 .<br><br><br>
DOI: 10.15468/dl.x5yab8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Argentina silus (Ascanius, 1775)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.9648 19.8496,8.9648 19.8496,8.9648 10.8496,17.9648 10.8496,17.9648 19.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013372-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.3502733.v1
title: Patent Citations

description: This is a list of patent citations found in the OECD or Dataverse databases. Non-patent citations (e.g. to journals) are not included. Patent citations can be added by the applicant or the examiner in the office (the latter suggesting it is relevant but the inventor may not have been aware of it). A typical USPTO patent has significantly more outgoing citations than a typical EPO/PCT patent, and depending on the research topic under study, one may need to carefully consider the impact of this difference between US and European offices when looking at citation statistics. 4 columns, 42.5M lines, "|" delimited; the columns are:--citing: the patent on which the citation is found--cited: the patent that is cited.--cite\_origin: whether the citation was supplied by the applicant (labeled "a") or examiner (labeled "e"). --data\_source: whether the citation information originated in the USPTO database ("u"), in the EPO's database ("e"), or in the PCT database ("w").
DOI: 10.6084/m9.figshare.7240457.v1
title: Dynamic and non-contact 3D sample rotation for microscopy

description: CAD files for the setups published in 'Dynamic and non-contact 3D sample rotation for microscopy' saved as SolidWorks Part and Assembly and as STEP file.<br>
DOI: 10.17632/8sjny373pz
title: Alphonso Mangoes Image Dataset

description: The dataset folder contains images of Alphonso mangoes. There are total of 71 samples each with images of two orientations. Thus , the total mango  images is 142. Each image is of resolution 2048 X 1536. The folder size for the dataset is 44.7 MB and is provided for convenient downloading. Each sample is separated in a folder labeled with a number that corresponds to the sampleID. 

Dataset  contains the following information:
• sampleID – one for the entire fruit and other two for the 2 orientations  (pertaining to the labeled folders in the ‘Alphonso mangoes image dataset folder)
• Physical parameters - the extracted physical features of the whole fruits such as fruit diameter (mm), width across shoulder (mm) and actual weight(gms) stored in .xls file.