cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/64sy6w5vkz
title: Experimental dataset on water levels in the study of flash flood wave without sediment (clear water) over bumpy downstream

description: Experimental dataset of free surface water level: In this file, all water level data associated with 3 different dam break scenarios were extracted from high-quality experimental video images. The dataset are collected, classified and presented a total of 3 tables in 3 categories based on the radiuses of downstream semi-circular obstacles; 0, 4.5 and 7.5 cm. Initial upstream sediment depth was 0 cm and the upstream reservoir was filled-up with clear water. Table 1, presents the free surface water level data at 20 different locations along the flume and 15 snap times after the dam break, while the radius of downstream semi-circular obstacle was 4.5 cm. Table 2, provides the free surface water level data at all abovementioned sections and snap times while the radius of downstream semi-circular obstacle was 7.5 cm. Table 3, presents the free surface water level data at all abovementioned sections and snap times while there were no obstacles in the dam downstream. The unit that has been used to measure data is centimeter and the abbreviation of O_r is the radiuses of downstream semi-circular obstacles. Time also refer to the time snaps after sudden removal of the gate using second as a unit of measurement. It should be noted that the vertical column on the left of the tables indicates the distances of different locations in centimeter from the beginning point of the laboratory flume. So, L column indicates all 20 distinct locations along the flume and their distances from the reservoir beginning in centimeter as a unit of measurement.
DOI: 10.17632/jnwgsn98tt
title: Geochemistry of Arapaima well sediments Roddaz et al in Revision to Marine Geology

description: Here we present total organic carbon (TOC) content, δ13CTOC, major and trace element concentrations, and Sr-Nd isotopic data of nineteen clay-size fraction samples from one industrial well (Arapaima-1) located in the Guyana-Suriname basin. These data are used to infer the provenance of the Cretaceous-Paleocene sedimentary succession deposited in the Guyana-Suriname basin. The related paper is submitted to Marine Geology  (Roddaz et al.  Provenance constraints on the Cretaceous-Paleocene erosional history of the Guiana Shield as determined from the geochemistry of clay-size fraction of sediments from the Arapaima-1 well (Guyana-Suriname basin))
DOI: 10.6084/m9.figshare.28184309.v1
title: <i>Inkjet-Printed Monodisperse Microsphere Biolasers</i>

description: This is the data for the paper submitted to <i>Journal of Physics D: Applied Physics</i>
DOI: 10.6084/m9.figshare.7117928.v2
title: Phylogenetic Trees & Data

description: Phylogenetic trees in nexus format of parasitic weevils within the genera <i>Gymnetron</i> and <i>Rhinusa</i>.Lists of taxa with coded traits of host plant use in csv format.<br>Codes for plant families:0 = Scrophulariaceae1 = PlantaginaceaeCodes for parasitic behavior on different plant organs:1 = Roots<br>2 = Stems3 = Fruits & seed capsulesCodes for galling behavior:0 = Non-galler1 = Gall inducer<br>
DOI: 10.17632/7h3n5rxtf4
title: SHape Analyser for Particle Engineering (SHAPE): Seamless characterisation and simplification of particle morphology from imaging data

description: The mechanical and rheological behaviour of particulate and granular assemblies is significantly influenced by the shape of their individual particles. We present a code that implements shape characterisation of three-dimensional particles in an automated and rigorous manner, allowing for the processing of samples composed of thousands of irregular particles within affordable time runs. The input particle geometries can be provided in one of the following forms: segmented labelled images, three-dimensional surface meshes, tetrahedral meshes or point-clouds. These can be complemented with surface texture profiles. Shape characterisation is implemented for three key aspects of shape, namely surface roughness, roundness and form. Also, simplified particle shapes are generated by the code which can be used in numerical simulations to characterise the mechanical behaviour of particulate assemblies, using numerical approaches such as the Discrete Element method and Molecular Dynamics. Combining these two features in one automated framework, the code allows not only to characterise the original granular material but also to monitor how its morphological characteristics change as the shape of the particles is simplified according to the chosen fidelity level for the application of interest.
DOI: 10.17632/jwy9z6z6n2
title: serum metabolites and Crohn's disease

description: This metabolite dataset consists of untargeted metabolites collected at enrollment from 389 healthy first-degree relatives of Crohn's disease patients in the GEM project.
DOI: 10.17632/79ccm6kfc2
title: Data for: Effects of MFHAS1 on Cognitive Impairment and Dendritic Pathology in the Hippocampus of Septic Rats

description: Aims: To investigate the effects of malignant fibrous histiocytoma amplified sequence 1 (MFHAS1) on cognitive dysfunction, the expression of tumor necrosis factor-α (TNF-α), interleukin (IL)-1β and amyloid β peptide (Aβ) in the hippocampus, as well as dendritic pathology in the hippocampal CA1 region in sepsis-associated encephalopathy (SAE) rats. Main methods: The rats were randomly divided into four groups, 1) control group (subjected to sham surgery), 2) control plus Mfhas1 siRNA group (rats received intracerebroventricular injection of Mfhas1 siRNA after sham surgery), 3) CLP plus control siRNA group (rats received intracerebroventricular injection of control siRNA after cecal ligation and puncture (CLP)), 4) CLP plus Mfhas1 siRNA group (rats received intracerebroventricular injection of Mfhas1 siRNA after CLP). The learning and memory capabilities of the rats were examined by means of fear conditioning and Barnes maze test. The concentration of TNF-α and IL-1β was determined by enzyme-linked immunosorbent assay. The efficiency of siRNA transfection, MFHAS1 and Aβ expression were detected by Western blotting. Total branch lengths of the pyramidal dendrites of the CA1 basilar tree and spine density were determined by Golgi staining. Key findings: We observed that MFHAS1 knock-down by Mfhas1 siRNA intracerebroventricular injection could improve cognitive impairment, reduce the expression of TNF-α, IL-1β and Aβ in the hippocampus induced by CLP, and alleviate the dendritic spinal loss of the pyramidal neurons, as well as increase the dendritic branching of the CA1 basilar tree of septic rats. Significance: MFHAS1 knock-down can alleviate cognitive impairment, neuroinflammation and dendritic spinal loss in SAE rats. Key Words: MFHAS1, sepsis-associated encephalopathy, IL-1β, dendritic spine density
DOI: 10.17632/ctmn5f5bzk
title: A massively parallel spatially resolved stochastic cluster dynamics method for simulations of irradiated materials

description: The spatially resolved stochastic cluster dynamics (SRSCD) method is one of the most important methods for simulating the time-evolution of spatially correlated microstructures in irradiated materials. It is a kinetic Monte Carlo-based method for stochastically evolving integer-valued populations of defects within multi finite volume elements according to reaction rates. However, the increasing spatial scale and complexity of the simulated systems have exceeded the capabilities of serial SRSCD. To extend SRSCD to simulate large-scale complex systems, we propose a massively parallel SRSCD method in this paper and implement the program named MISA-SLSCD. It contains four contributions: (1) a dynamic Defect-Reaction Tree data structure to efficiently store and update millions of defect species and reactions; (2) a double-grouping search strategy to speed up the search for defects and reactions; (3) an adaptive synchronous algorithm to balance the accuracy and efficiency of simulations; and (4) an on-demand communication strategy to eliminate communication redundancy. A series of numerical simulation results show that our method has high accuracy in simulating damage accumulation in irradiated materials and obtains a good performance of over 90% parallel efficiency on 32, 000 CPU cores with a 32 million-volume-element system.
DOI: 10.17632/pgkf3mtb4m
title: DATASET S2: MS/MS raw data from Pollicipes pollicipes Cement Gland

description: Data for the article: Domínguez-Pérez, D.; Almeida, D.; Wissing, J.; Machado, A.M.; Jänsch, L.; Castro, L.F.; Antunes, A.; Vasconcelos, V.; Campos, A.; Cunha, I. The Quantitative Proteome of the Cement and Adhesive Gland of the Pedunculate Barnacle, Pollicipes pollicipes. Int. J. Mol. Sci. 2020, 21, 2524. https://doi.org/10.3390/ijms21072524 PPCIM: MS/MS raw data files comprising three biological replicates of P. pollicipes cement multicomplex obtained using label-free LC-MS high throughput proteomic analysis. LC-MS/MS system was composed by a Dionex UltiMate 3000 n-RSLC connected to an Orbitrap FusionTM TribridTM mass spectrometer (Thermo Scientific, Waltham, MA, USA).
DOI: 10.17632/y6njk5znjs
title: Journal of Islamic Education; No. 23

description: The journal is set to publish original articles on a wide range of issues including;

 Philosophy of Islamic education;
 Schools and approaches to Islamic education;
 Educational jurisprudence (Fiqh);
 Foundations, principles and methodology of Islamic education;
 History of Islamic education;
 Educational thoughts, views and ideas of Muslim scholars;
 Educational sciences such as educational management, curriculum planning and educational psychology with an Islamic approach;
 Comparative studies;
 The areas and dimensions of education in Islam include religious education, devotional education, moral education, sexual education, political education, and so on;
 Methodology of research in Islamic education;
 Examining different aspects of formal education with Islamic perspective;
 Religious education in the thought of international scholars, a comparative approach to Islamic education.

JIE is an international, professional refereed journal in the interdisciplinary fields that relevant to Islamic education. JIE serves as a platform for presenting and discussing the emerging issues on Islamic education. The journal is committed in publishing high quality articles in persian and welcomes articles in English, ranging from original research papers in the area of Islamic education. This journal welcomes original and qualified researches on all aspects of Islamic education and religious education. The topics may include, but are not limited to: 
Philosophy of Islamic education, schools and approaches in Islamic education, educational Islamic jurisprudence, foundations, principles and methods of Islamic education, history of Islamic education, educational approaches and ideas of Muslim scholars, educational management, curriculum and educational planning, educational psychology with an Islamic perspective, comparative issues, areas and dimensions of education in Islam, religious education, devotional education, moral education, sexual education, political education, research methodology in Islamic education and examination of various aspects of formal education with an Islamic outlook.
DOI: 10.6084/m9.figshare.3458921.v2
title: Documentation of Information (Forms)

description: The establishment and maintenance of relevant documentation and reports are necessary to facilitate an effective and efficient operation.
DOI: 10.17632/m3mkm5snmf
title: exercise and trp

description: Data analysis was performed with GraphPad Prism 6.0 (GraphPad Software, Inc., La Jolla, CA, USA). All experimental data were expressed as mean ± SEM. Differences between groups were determined by Student’s t-test (two groups) or one-way analysis of variance (ANOVA) followed by Dunnett’s test or Tukey’s test (Multiple groups). P-values less than 0.05 were considered statistically significant. All experiments were repeated three times at least.
DOI: 10.6084/m9.figshare.24081390.v1
title: Spherical dataset

description: A spherical camera was used for generating this dataset (the Spherical Camera Dataset). A spherical camera is a camera that has its field of view enclosed in a sphere. The sphere is modelled as a surface, and the camera’s field of view can be defined as the region between the centre of the sphere and the surface.The spherical sensor includes six active vision sensors that investigate the six directions of space in the following order: front, top, back, bottom, left, and right. The resulting images provide an overview of the scene surrounding the robot. The robot can thus sense much more of the scene around it than when using a forward-facing camera.Our aim in this approach was to permit the robot to define the situation in an autonomous way without needing to concatenate images from other robots.We ran the simulator for five minutes to ensure the behaviour was stable before recording the sequences. A total of 2,519 sequences were generated as training data for the detection algorithm. Each video or image sequence had 75 frames at a resolution of 256 × 256.<br>
DOI: 10.6084/m9.figshare.8317085.v1
title: AIBECS-OCIM0.1

description: This file contains the circulation output and grid information from the Ocean Circulation Inverse Model (OCIM) version 0.1 [DeVries and Primeau, 2011; Primeau et al., 2013].<br>The data was converted for use by the Algebraic Implicit Biogeochemical Element Cycling System (AIBECS).<br>References: <br>- Primeau, F. W., Holzer, M., and DeVries, T. ( 2013), Southern Ocean nutrient trapping and the efficiency of the biological pump, <i>J. Geophys. Res. Oceans</i>, 118, 2547– 2564, doi:10.1002/jgrc.20181. - DeVries, T. and F. Primeau, 2011: Dynamically and Observationally Constrained Estimates of Water-Mass Distributions and Ages in the Global Ocean. <i>J. Phys. Oceanogr.,</i> <b>41</b>, 2381–2401, https://doi.org/10.1175/JPO-D-10-05011.1<br>- Benoit Pasquier. (2019, May 23). AIBECS.jl: The ideal tool for exploring global marine biogeochemical cycles (v0.2.0). Zenodo. http://doi.org/10.5281/zenodo.3192180
DOI: 10.17632/nbz7hs4ckn
title: Data from Block-on-Ring Wear Tests of Victrex FG340 in Dry Sliding versus AISI 52000 steel

description: The data has been collected during Block-on-Ring Wear Tests on "Victrex PEEK FG340". The tests were done in dry sliding against AISI 52000 steel rings, ground twist-free to 𝑅a = 0.14–0.19 μm, 𝑅z = 1.5–1.9 μm and with a hardness of 60–62 HRc in standard laboratory atmosphere (21–25 °C, 40–60% rH). The research objective was to determine the coefficient of friction of this material pair for use in the calculation of transient temperatures and dimensions during the process of designing a journal bearing. Test conditons were conducted on an ASTM G137-compliant Block-on-Ring tribometer from Tribologic GmbH, Germany. The tests were conducted at 1 MPa in uniform, unidirectional sliding at 1.0 m/s and lasted 6 hours each, resulting in a total sliding distance of 21,600 m for each test. Block cross section was 16 mm² and fiber orientation (if applicable) was nominally parallel (with respect to an ISO 527-1A speciment). Individual test results for the coefficient of friction, the linear, time-dependent wear rate and the counter body temperature were calculated from time-resolved sensor data. For this, data from the running-in phase of each experiment was ignored. For statistical reasons eight individual tests were conducted and - after elimination of outliers using Nalimov's variant of the Grubbs test - arithmetic mean and (frequentist) confidence intervals (95 %) were determined for the aforementioned quantities. This resulted in a COF of 0.28-0.32, a linear, time-dependent wear rate of 0.6 - 1.0 µm/h and a counter body temperature of 31.2 - 32.4 °C.

For each of the 8 conducted tests, a plain-text columnar data file is provided ("*.proc"). Instead of including one or more header lines for denoting the meaning, name and unit of each column, a yaml-formatted, human-readable header file is provided ("*.yaml"). Column-indexing starts at 0, i.e. the first column of the data file is represented by index 0. Data and header files are matched by their test ids, which range from 555689 to 555696 in this data set.
DOI: 10.5281/zenodo.15176058
title: Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to ⍺-synuclein - Cytotoxic CD4 T cell staining experiment 2 FCS files

description: FCS files for Cytotoxic CD4 T cell staining, and an excel key indicating disease status for each donor. See README file for more instructions.
DOI: 10.5281/zenodo.15238626
title: Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to ⍺-synuclein - Cytotoxic CD4 T cell staining experiment 2 FCS files

description: FCS files for Cytotoxic CD4 T cell staining, and an excel key indicating disease status for each donor. See README file for more instructions.
DOI: 10.6084/m9.figshare.157261.v5
title: Raw data: average amino acid identiy

description: Percentage of average amino acid identity (AAI) between Streptococcus strains.
DOI: 10.17632/2swswwjn76
title: Using thermal imagery and changes to stem radius to assess water stress in two coniferous tree species 

description: With a warming climate and greater evaporative demand, many forest ecosystems are increasingly affected by water limitation as prolonged water deficits reduce tree-level growth and survival. Monitoring water deficit traditionally requires daily measurements of sap flow or radial flux from automated sensors mounted on individual trees. As an alternative approach, we evaluated the use of airborne thermal imagery from unmanned aerial vehicles as a rapid, scalable tool for assessing tree-level water stress. Plant water stress leads to higher leaf temperatures when soil moisture is low and evaporative demand is high. To detect this response, we modelled the difference between leaf and air temperature (∆T) as a function of local soil moisture vapour pressure deficit, and wind speed for two tree species, lodgepole pine (Pinus contorta var. latifolia) and white spruce (Picea glauca). We used those same weather and soil conditions to model dendrometer-based measurements of daily changes in internal tree water deficit (∆TWD). While canopy leaf temperature and daily change in tree water deficit showed little direct correlation with one another, both variables responded to soil moisture, vapour pressure deficit, and wind speed in a manner that reflects a common response to water stress as soil became progressively drier over the summer months. The two species showed similar responses to environmental conditions, with some differences related to species-specific strategies for drought avoidance. The application of thermal imagery to detect water stress in natural ecosystems can improve understanding how trees experience water stress across species and environmental conditions.
DOI: 10.17632/cgptcyhvd5
title: Alignment of a Ribo-seq dataset against Leishmania donovani (HU3) genome

description: The origin of the samples and the ribosome-footprint methodology are described in the article by Bifeld et al., 2018 (PMID: 30505948). Raw sequencing reads (Illumina single-end reads in FASTQ format) were downloaded at the NCBI Sequence Read Archive (SRA), under project number PRJNA495919. In particular, the 24,741,340 (1×76 nucleotides) Ribo-Seq reads from sample ID sample SRR8040414 (derived from L. donovani promastigotes, control sample) were used to prepare this dataset. 
Trimmomatic tool (Bolger et al., 2014; PMID: 24695404) was used to clip adapters. Additionally, rRNA-containing reads were filtered after aligning them against the rRNA sequences existing in the L. donovani genome by using the BWA-MEM aligner (Li, 2013; ArXiv ID: 1303.3997v2) according the sqtk3 pipeline (https://github.com/lh3/seqtk). The L. donovani genome used as reference (Camacho et al., 2019; PMID: 30992521) is available thought the following Mendeley dataset: https://data.mendeley.com/datasets/b82fm2w2h9/2. Thereafter, the BWA-MEM aligner was used to map remaining reads to the genome and the resulting alignment files were sorted and indexed using SAMtools (Li et al., 2009; PMID: 19505943). This final file (and its accompanying bam.bai) is linked to this dataset.
DOI: 10.17632/ydx4d365rw
title: MRI and Computational Modelling of Current Flow for taVNS Dataset

description: We performed a high-resolution T1 and T2 weighted magnetization prepared gradient echo (MPRAGE) MRI scans at the Advanced Science Research Center (ASRC), The Graduate Center, City University of New York (CUNY), using a 3-T Siemens Prisma scanner (Siemens Healthineers, Germany). Ear scan was acquired using ZOOMit technology for high-resolution zoomed FOV imaging allowing high contrast and less artifact for region of interest with 0.47 voxel size. Based on optimized high-resolution (0.47 mm) T1 and T2 weighted images from a single healthy adult female (age: 30) subject, we developed an anatomical model of the left ear and the surrounding head tissues including brain/grey-matter, CSF/meninges skull, muscle, blood vessels, fat, cartilage, and skin, included here as RAW files, we developed an anatomical model of the left ear and the surrounding head tissues including brain, CSF/meninges, skull, muscle, blood vessels, fat, cartilage, and skin. 

Six regions of interest (ROIs): cavum concha, cymba concha, crus of helix, tragus, antitragus, and earlobe were also segmented and are all within the folder 'Segmentation Masks Raw Files'. A range of taVNS electrode montages were reproduced spanning varied electrodes sizes and placements over the tragus, cymba concha, earlobe, cavum concha, and crus of helix. Electric field across the ear (for both skin and cartilage) for each montage at 1 mA or 2 mA taVNS, assuming an activation threshold of 6.15 V/m, 12.3 V/m or 24.6 V/m, was predicted using a Finite element method (FEM). These are also included here in 'STL and MPHTXT Files of Montage FE Models'. 

Relative targeting was robust across assumptions of activation threshold and tissue properties. 

Computational models provide additional insight on how details in electrode shape and placement impact sensitivity, current density distribution, selectivity, and location, thereby supporting analysis of existing approaches and optimization of new devices. Our result suggest taVNS current patterns and relative target are robust across individuals, through (variance in) axon morphology were not represented.

Also included here is the full Simpleware ScanIP (Synopsys, CA, USA) file containing all of the FE models and tissue masks. RAW files of the tissue masks and STL and MPHTXT files are included within their respective folders. All files are labeled for their MRI sequence description, what tissue is contained within the mask, and what montage is within the STL or MPHTXT respectively in their folders.