cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5126686.v1
title: Supplementary Material for: A New System Identification Approach to Identify Genetic Variants in Sequencing Studies for a Binary Phenotype

description: We propose in this paper a set-valued (SV) system model, which is a generalized form of logistic (LG) and Probit (Probit) regression, to be considered as a method for discovering genetic variants, especially rare genetic variants in next-generation sequencing studies, for a binary phenotype. We propose a new SV system identification method to estimate all underlying key system parameters for the Probit model and compare it with the LG model in the setting of genetic association studies. Across an extensive series of simulation studies, the Probit method maintained type I error control and had similar or greater power than the LG method, which is robust to different distributions of noise: logistic, normal, or t distributions. Additionally, the Probit association parameter estimate was 2.7-46.8-fold less variable than the LG log-odds ratio association parameter estimate. Less variability in the association parameter estimate translates to greater power and robustness across the spectrum of minor allele frequencies (MAFs), and these advantages are the most pronounced for rare variants. For instance, in a simulation that generated data from an additive logistic model with an odds ratio of 7.4 for a rare single nucleotide polymorphism with a MAF of 0.005 and a sample size of 2,300, the Probit method had 60% power whereas the LG method had 25% power at the α = 10<sup>-6</sup> level. Consistent with these simulation results, the set of variants identified by the LG method was a subset of those identified by the Probit method in two example analyses. Thus, we suggest the Probit method may be a competitive alternative to the LG method in genetic association studies such as candidate gene, genome-wide, or next-generation sequencing studies for a binary phenotype.
DOI: 10.6084/m9.figshare.5656018.v1
title: DataRepository_ImpactSecondaryBasins

description: Historical bathymetry Western Scheldt Estuary, Delft3D model output data <br>
DOI: 10.6084/m9.figshare.7309163.v2
title: Wellcome Review of PhD Training in Biomedical Research

description: In 2017, Wellcome undertook a review of biomedical research PhD training to develop an evidence base on which to frame future funding decisions. The review included analysis of the literature, UK-wide and in-house datasets, and a community consultation involving both interviews and an online survey.<br>Version 2: 08/11/2018 Correction of author names
DOI: 10.6084/m9.figshare.8139359.v2
title: IPA scaffold files after selecting for mitochondrial proteins by the Scaffold software

description: IPA Proteomic Scaffold files of cFCMs 40 and 115 days vs 12 days, dFCMs 39 and 105 days Vs 12 days and Adult (90 days) vs neonate (1 day) selected for mitochondrial proteins by the Scaffold software.
DOI: 10.17632/ttb63krg6d
title: Ultrasonic guided waves data for structural health monitoring of pipelines

description: Structural Health Monitoring (SHM) techniques are intended to assess the integrity of structures, such as pipelines. They aim at detecting the initiation of damage (i.e. at early stages) to perform thereafter the maintenance of the damaged area of the structure, without any delay. Ultrasonic guided waves (UGW) technique is one among them. It relies on the use of permanently installed sensors on the structure being monitored. These sensors emit and receive signals which propagate through the medium and interact with defects. The comparison between the signal from the healthy state and the actual signal helps to determine whether the structure is damaged or not. However, the variation of the environmental and operational conditions (EOCs) where the structure operates could have a strong impact on the  acquired data. Consequently, it will be very difficult to ascertain whether the changes in the received signal are due to the presence of structural defect or just caused by the variation of the EOCs. Therefore, the aim of constructing this database was to develop a damage detection method which is sensitive to damage but robust to the variation of EOCs. 

The specimen used to build the database consists of a steel tube with 6.4 m length. It was placed in laboratory conditions where temperature fluctuates between 19°C and 26°C during the monitoring period. This variation is due to the weather changes. A 1 m portion of the tube was wrapped by a composite reparation, deposited by Prokem company with multiple number of layers. The data were collected using Wavemaker G4 system, which is commercialized by Guided Ultrasonic Ltd company and is intended for pipeline testing. This acquisition system is linked to a probe, which acts as an emitter and a receiver at the same time. This probe consists of two lines of circumferentially equidistant ultrasonic transducers, in order to master the direction of propagation of the UGW. In tubular structures, three types of propagation modes of UGW can coexist: Longitudinal, Torsional and Flexural. Each mode propagates with a specific phase and group velocities. These velocities are generally dependant of the frequency, which confer to the UGW the nature of being dispersive. The used probe allows operating with two separate guided waves modes, which are Torsional (non-dispersive mode) and Flexural (dispersive mode). A corrosion-like defect was machined by removing material from the inside of the pipe-wall in the half-axial length of the composite reparation. The distance between the probe and the created damage is 2.6 m.
DOI: 10.6084/m9.figshare.17126303.v1
title: Trypoxylus dichotomus genome assembly TdicSn1.0

description: NiimiG_kabutomushi_180830_maxread265M_supernova210_min500_pseudohap.fasta -- Genome assembly of Japanese rhinoceros beetle Trypoxylus dichotomus. Version: TdicSn1.0.<br>
DOI: 10.6084/m9.figshare.21806457.v1
title: Global long-term daily 1km surface soil moisture dataset with physics-informed machine learning (GSSM1km)

description: Although soil moisture is a key factor of hydrologic and climate applications, global continuous high resolution soil moisture datasets are still limited. Here we use physics-informed machine learning to generate a global, long-term, spatially continuous high resolution dataset of surface soil moisture, using International Soil Moisture Network (ISMN), remote sensing and meteorological data, guided with the knowledge of physical processes impacting soil moisture dynamics. Global Surface Soil Moisture (GSSM1km) provides surface soil moisture (0-5 cm) at 1 km spatial and daily temporal resolution over the period 2000-2020. The performance of the GSSM1km dataset is evaluated with testing and validation datasets, and via inter-comparisons with existing soil moisture products. The root mean square error of GSSM1km in testing set is 0.05 cm3/cm3, and correlation coefficient is 0.9. In terms of the feature importance, Antecedent Precipitation Evaporation Index (APEI) is the most important significant predictor among 18 predictors, followed by evaporation and longitude. GSSM1km product can support the investigation of large-scale climate extremes and long-term trend analyses. Due to the whole dataset for the global scale is too big (779GB) to deposit at once, we uploaded the data in the Netherlands to figshare. For other areas, the data is stored in Google Earth Engine (https://code.earthengine.google.com/?asset=users/qianrswaterr/GlobalSSM1km0509), and we provide codes to download our data (https://code.earthengine.google.com/4b577bb83981e1ac43fd77127cfbdb4a). Due to the dataset is exported from Google Earth Engine, the bandNames can’t display in ArcGIS, the band is displayed as band1, band2,…. Just in case other softwares also can't display, I put the bandNames in the csv file “bandNames2000-2020”.
DOI: 10.6084/m9.figshare.29206592
title: 青藏高原多年冻土地温和活动层厚度数据（2001–2020）

description: 该数据集包长期多年冻土监测数据
DOI: 10.17632/rdzkmzh4gw
title: VOIGTL — a fast subroutine for Voigt function evaluation on vector processors

description: Abstract Voigt function evaluations account for a significant proportion of computer time used in calculating synthetic stellar spectra, particularly if local thermodynamic equilibrium is assumed. A vectorised Voigt function evaluation routine is presented which, in typical applications, achieves a speed of 180 Mflops on a CRAY-XMP and is accurate to 13 decimal digits. A derived formula gives an order of magnitude estimate of the Voigt function absolute accuracy required for synthetic spectrum calcula... Title of program: VOIGTL Catalogue Id: ACLT_v1_0 Nature of problem Stellar line absorption coefficients are, in most cases, Voigt profiles which are convolutions of Doppler and Lorentz profiles. Voigt function evaluation is required repeatedly in synthetic stellar spectrum calculations and, in the case of local thermodynamic equilibrium being assumed, is dominant in determining computer time required. Versions of this program held in the CPC repository in Mendeley Data ACLT_v1_0; VOIGTL; 10.1016/0010-4655(93)90171-8 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)
DOI: 10.6084/m9.figshare.1211896.v1
title: Kinetoplast and nuclear DNA staining in Leishmania mexicana

description: Kinetoplast and nuclear DNA in kinetoplastids bind different DNA stains with different affinities. Staining of <em>Leishmania mexicana</em> promastigotes was optimised for five DNA stains (DAPI, propidium iodide, SYTO16, DRAQ5 and hoechst 33342). Maximum brightness (maximum pixel intensity) and total signal (sum pixel intensity) of the kinetoplast and nucleus were quantified from widefield epifluorescence micrographs for each stain. Two stains were analysed from methanol fixed cells mounted in glycerol DABCO: DAPI and propidium iodide. The others were analysed from live cells in PBS. Propidium iodide staining included an RNase A digestion. This resource lets the relative contribution of kinetoplast and nuclear DNA be determined from signal intensity data from fluorescence micrographs and flow cytometry. This is a useful resource if working with the methods in one of my previous papers; see links.
DOI: 10.6084/m9.figshare.22776413.v2
title: all cytochrome bd sequences

description: animal rumina and engineered digesters are golden models for concept of nanaerobic digestion
DOI: 10.6084/m9.figshare.23600460.v1
title: ESD Efficiency HPLC Data.zip

description: Raw HPLC data corresponding to the manuscript titled "Efficient Electrospray Deposition of Surfaces Smaller than the Spray Plume" by Park et al.
DOI: 10.6084/m9.figshare.28794542.v1
title: Metadata - Exploring the Essential Role of Blockchain in Supply Chain Integration, Resilience,and Performance

description: This study aims to explore how blockchain operational capabilities affect supply chain management – especially in the context of integration, resilience, and performance. Using a systematic literature review approach, the study analyzed recent academic publications from 2018 to 2024, focusing on key constructs such as blockchain, supply chain integration, and resilience. The results indicate that blockchain significantly enhances transparency, traceability, and trust within supply chains, improving performance and resilience, especially in industries with higher operational complexity. Blockchain’s ability to automate processes and provide real-time information supports better supply chain coordination. Additionally, supply chain integration, when combined with blockchain, improves responsiveness and operational efficiency. One of the key outcomes of this study is the proposed conceptual framework, designed to guide further empirical research on the relationships between blockchain operational capabilities, supply chain integration, resilience, and performance. The study recommends future exploration of blockchain’s long-term effects on sustainability and performance in various sectors, while addressing challenges related to trust and technological readiness to fully leverage its potential.
DOI: 10.6084/m9.figshare.29206592.v2
title: 青藏高原多年冻土地温和活动层厚度数据（2001–2020）

description: 该数据集包含了 2001 年至 2020 年青藏高原 （QTP） 的长期多年冻土监测数据。它包括来自不同高山植被区和海拔的多个地点的地面温度和活性层厚度 （ALT） 的年度记录。Excel 文件提供了不同深度（TTOP、10 m 和 15 m）的地面温度的年平均值，以及从温度曲线得出的 ALT 值。这些数据可用于研究高海拔永久冻土区的永久冻土动态、气候变化影响和模型验证。
DOI: 10.6084/m9.figshare.29206592.v3
title: 青藏高原多年冻土地温和活动层厚度数据（2001–2020）

description: 该数据集包长期多年冻土监测数据
DOI: 10.6084/m9.figshare.9776111.v1
title: Datasets.xlsx

description: Quantitative data of T cell activation and function<br>
DOI: 10.17632/3sd4x9zcfk
title: Printing Away the Mortgages:Fiscal Inflation and the Post-Covid Boom

description: This contains a readme file (Readme_replicationpackage) and all relevant code to replicate results in the main text of the paper "Printing Away the Mortgages: Fiscal Inflation and the Post-Covid Boom" in the Journal of Financial Economics.
DOI: 10.17632/bnfzdtbmzf
title: Open dataset for: "Delta-beta cross-frequency coupling as an index of stress regulation during social-evaluative threat"

description: Open data and R analysis scripts for the paper as submitted for publication: "Poppelaars, E. S., Klackl, J., Pletzer, B., & Jonas, E. (2021). Delta-beta cross-frequency coupling as an index of stress regulation during social-evaluative threat." Hypotheses and analyses were preregistered: Poppelaars, E. S., Klackl, J., Pletzer, B., & Jonas, E. (2018). Delta-beta cross-frequency coupling as an index of stress regulation during social-evaluative threat. Open Science Framework. https://osf.io/8gchf/register/565fb3678c5e4a66b5582f67. Description of the dataset: A dataset of 37 men and 30 women (tested in the luteal phase of their menstrual cycle) participated in a public speaking task to induce social-evaluative threat. Responses of multiple stress systems were measured (sympathetic and parasympathetic nervous system activity, self-reported affect, and hypothalamic–pituitary–adrenal axis activity), as well as personality traits (e.g. trait social anxiety), and EEG delta-beta cross-frequency coupling (e.g., frontal and parietal amplitude-amplitude correlation and phase-amplitude coupling).
DOI: 10.6084/m9.figshare.7992866.v1
title: Reliability of estimating blood loss in epistaxis

description: Reliability of estimating blood loss in epistaxisRaw data
DOI: 10.17632/7x5t7jggzj
title: Protein O-GlcNAcylation and hexokinase mitochondrial dissociation drive heart failure with preserved ejection fraction_Proteomics data

description: For proteomics with pulled down biotinylated samples, MS-grade trypsin (Promega, Madison WI) was added each sample at an enzyme-to-substrate ratio of 1:50 for overnight digestion at 37 ⁰C. Digestion was halted with the addition of 10% formic acid to a final concentration of 0.5%. The peptides were de-salted with C18 spin columns and completely dried prior to running on the mass-spectrometer. LC-MS analysis was performed on Vanquish Neo UHPLC (Thermo Fisher, VN-S10-A-01) coupled to Orbitrap Exploris 240 mass spectrometer (Thermo Fisher, BRE725535). Analytical separation was conducted using a UHPLC C18 column (Ion Opticks, AUR3-15075C18-CSI). For each run, 1ug equivalent of sample was injected. The flow rate was set at 0.2 µl/min. Elution of peptides from analytical separation column was performed using a 120 min gradient between buffer A (0.1% Formic acid and 99.9% Optima LC/MS grade water) and buffer B (80% Acetonitrile, 19.9% Optima LC/MS grade water, and 0.1% formic acid): 0 % B at the beginning, 8 % B at 1 min, 28 % B at 86 min, 50 % B at 106 min, 100 % B from 107 to 110 min, 0 % B from 111 to 120 min.

Electrospray ionization was performed using a Nanospray Flex Ion Source (Thermo Fisher, ES071) and positive static spray voltage was set at 2200 V. For full Scan range was set to 350-1600 m/z with RF lens: 60%, Orbitrap resolution: 120,000, Normalized AGC Target (%): 300, Maximum injection time (ms): 25, microscans: 1, and Intensity threshold: 5.0e3.

Data-dependent acquisition (DDA) by TopN was performed through fragmentation isolated precursor ions with charges between +2 to +5. The following parameters were used for DDA: Dynamic exclusion mode: exclusion duration (s) = 30, mass tolerance: 5 ppm (low) and 5 ppm (high). Data dependent mode: cycle time (s): 2, ddMS2 parameters isolation window (m/z) = 1.5, Normalized collisional energy = 30%, Orbitrap resolution 15,000, scan range mode: define first mass, first mass (m/z) 200, Normalized AGC target (%): 100, Maximum injection time (ms) = 50.

Proteins were identified from the MS raw files using the Mascot search engine (Matrix Science, London, UK. version 2.5.1). MS/MS spectra were searched against the SwissProt Human database. All searches included oxidized Methionine, deamidated asparagine and aspartic Acid, and acetylated

N-term as variable modifications. Two missed tryptic cleavages were allowed. 1% false discovery rate cutoff was applied at the peptide level. Only proteins with a minimum of two peptides above the cutoff were considered for further study. Identified peptides/protein were visualized by Scaffold software (version 5.0, Proteome Software Inc., Portland, OR)."
DOI: 10.17632/9sy7zhtxr7
title: Data for: Excessive outlier removal may result in cut points that are not suitable for immunogenicity assessments

description: Raw data data generated during validation of immunogenicity assays for seven monoclonal antibody drug candidates presented in Table 3.
DOI: 10.17632/ybxsttf2by
title: Seven years simulating hybrid energy systems with Homer Legacy

description: Homer Legacy software is a well-known software for simulation of small hybrid energy systems that can be used for both design and research. This dataset is a set of files generated by Homer Legacy bringing the simulation results of hybrid energy systems over the last seven years, as a consequence of the research work led by Dr. Alexandre Beluco, Federal University of Rio Grande do Sul, in southern Brazil. This dataset is being published in conjunction with a paper in Data Science Journal, which presents further explanations about the hybrid energy systems that were simulated and the papers that publish and discuss the results. The readme.pdf file included in this dataset and the associated article provide more details. These files are made available both for their educational nature, as case studies, and for the possibilities of research that can always be opened from the dissemination of research data. The next steps of this research point to the study of the influence of energetic complementarity on the performance of hybrid systems and to the study of hybrid systems equipped with hybrid storage,
DOI: 10.6084/m9.figshare.25551474.v3
title: <b>Ser/Thr protein kinase Stk1 phosphorylates the key transcriptional regulator AlgR to modulate virulence and resistance in </b><b><i>Pseudomonas aeruginosa</i></b>

description: We identified AlgR, an important transcriptional regulator, as a substrate for Stk1, with its phosphorylation at the Ser143 site catalyzed by Stk1. Intriguingly, both the deletion of <i>stk1</i> and the mutation of Ser143 of AlgR to Ala result in similar changes in some physiological functions. Furthermore, assays of <i>algR</i> expression in these strains suggest that changes in the phosphorylation state of AlgR, rather than its expression level, underlie changes in these physiological functions. These findings uncover Stk1-mediated phosphorylation of AlgR as an important mechanism for regulating virulence and resistance in <i>Pseudomonas aeruginosa</i>.
DOI: 10.6084/m9.figshare.28929923.v1
title: rrl_data.zip

description: <b>RRL Dataset</b>: Visible and Infrared Image Fusion and Object Detection dataset for Railway applications
DOI: 10.1184/r1/12152088.v1
title: Fig. 4f_varying holding potentials.xlsx

description: Data set supporting the publication
DOI: 10.6084/m9.figshare.12847814.v1
title: ECRdatabase.xlsx

description: A free and comprehensive ECR based resource list for all to use. This database comprises of links to tools and websites for students as well as graduates and professionals to use.
DOI: 10.6084/m9.figshare.25361383.v1
title: Maucieri_etal_2024_GlobChangBiol_Data

description: Data accompanying:<b>Enduring a major heatwave: the role of kelp forests and cold refugia in promoting marine invertebrate community resilience</b>
DOI: 10.6084/m9.figshare.28379096.v3
title: Clay data of Site U1490 during 5.1-2.6 Ma

description: Site U1490 (05°48.9507ʹN, 142°39.2698ʹE) is located at the northern end of the Eauripik Rise within the core area of the WPWP, at a water depth of 2341 m (Figure S1). Using the three holes (U1490A, U1490B, and U1490C) retrieved from Site U1490, a continuous Pliocene deposition was reconstructed at interval between 37.7 m and 96.6 m CCSF (Rosenthal et al., 2018). A high-resolution chronological framework for Site U1490 during 5.1-2.6 Ma has been established by comparing the Cibicidoides wuellerstorfi δ18O profile (VPDB, Vienna Peedee Belemnite) and the standard LR04 stack (Lisiecki & Raymo, 2005; Shi et al. 2022)The clay mineral compositions, illite chemical index and crystallinity at Site U1490 sediments in this dataset.
DOI: 10.17632/6n3hr2s8js
title: Factors intention to use e-wallet among university students in Central Java, Indonesia

description: The dataset contains information on factors influencing the usage of e-wallets (OVO, DANA, Gopay, Shopeepay, LinkAja, i-saku, Tapcash) among university students in Central Java, Indonesia. The dataset includes both raw (filtered) data and the results of the analysis conducted using SmartPLS 3.
DOI: 10.6084/m9.figshare.16727317.v1
title: Metadata record for: Dataset of human intracranial recordings during famous landmark identification

description: This dataset contains key characteristics about the data described in the Data Descriptor Dataset of human intracranial recordings during famous landmark identification. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.27873024.v2
title: Encoding and Decoding Illegal Wildlife Trade Networks

description: The illegal wildlife trade (IWT) is a key driver of biodiversity loss and a barrier to desired transformations in socio-environmental systems. IWT is known to exploit licit networks, such as the global airline flight network, yet the ability of science to support societal efforts to reduce IWT remains underdeveloped. Research on IWT relies on aggregate, context-specific, and biased counts of observed incidents leading to potential policy misguidance. Our study utilizing this data uses computational methods, centrality analysis and predictive modeling, to help encode and decode IWT-related airline flight networks to improve sensemaking with implications for sustainable futures. Methods advance existing analyses by revealing factors traffickers consider when selecting routes, identifying different airports' roles within the IWT network, and uncovering trafficking hotspots not observed in data. Computational science methods using these data sources can help overcome existing limitations and transform knowledge into action to reduce IWT and biodiversity loss. The files included herein include our cleaned dataset on an airport level, documenting incident counts from TRAFFIC’s Wildlife Trade Portal and ROUTES. Other covariates considered as potential features in our predictive model are included and broken down per airport. Additionally, the network files of the full flight and trafficking networks are available. A supplementary data file including definitions of all these features has been included as well.