cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20331282.v2
title: A high-quality chromosome-scale Japanese flounder (Paralichthys olivaceus) genome assembly

description: Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine flatfish cultured in China, Korea, and Japan. Herein, we produced a high-quality chromosome-scale genome assembly of Japanese flounder using PacBio Circular Consensus Sequencing (CCS) sequencing technologies. pol.gtf is the annotation file of the turbot genome assembly. pol_TPM is the gene expression matrix used for gene co-expression network inference. genes per module.xlsx is genes in every co-expression module. hub genes set.xlsx is the list of hub genes for every co-expression module. DEGs set.xlsx is the list of differential expression genes for each stress. GO enrichment.xlsx and KEGG enrichment.xlsx are the results of function enrichment for genes in co-expression modules that extremely significant correlated with each stress. key hub genes.xlsx is the list of candidate stress-related key hub genes generated by taking the intersection of hub gene set and DEGs set.
DOI: 10.6084/m9.figshare.24155325.v1
title: FUS_data

description: The input structures, topologies and the template mdp files used to initiate the simulations are given in the "inputs" directory.Movies for 500ns trajectories of one of the replicates of all simulated systems in included in the "movies" directory.1 microsecond trajectories (100 frames per ns) for the three replicates of all simulated systems, the tpr file associated with these trajectories and a session to visualize these trajectories in UCSF chimera are given in the "trajectories" directory.
DOI: 10.6084/m9.figshare.6127874.v1
title: Gear Fault Data

description: Time domain gear fault vibration data (DataForClassification_TimeDomain)andGear fault data after angle-frequency domain synchronous analysis (DataForClassification_Stage0)<br>Number of gear fault types=9={'healthy','missing','crack','spall','chip5a','chip4a','chip3a','chip2a','chip1a'}Number of samples per type=104Number of total samples=9x104=903The data are collected in sequence, the first 104 samples are healthy, 105th ~208th samples are missing, and etc.
DOI: 10.6084/m9.figshare.858900.v1
title: MLSMR dual event TB dataset

description: dataset used in PMID:24144044 and elsewhere
DOI: 10.17632/9nsypnxxyy
title: Suspended sediment and estuarine data measured in the magdalena river mouth durant stratified and turbid conditions

description: These data show measurements of suspended sediment concentration, particle size distribution, and estuarine characteristics in the water column of the Magdalena River mouth. Information was collected using a LISST-200X® (Laser In-Situ Scattering and Transmissometry - LISST) device. This optical device estimates the concentration of sediment (µl l-1) and the particle size distribution in 36 different class sizes (1 µm–500 µm) at a sampling rate of 1 Hz. The data collection was carried out approximately 3 km upstream of the Magdalena river mouth. It consisted of a period of 72 hours with the aim of encompassing various tidal cycles and different flow conditions. The depth was standardized using the ratio z/h (relative depth). Each file includes: relative depth and 36 columns with the particle size distribution (Files: Perfil 1 -Perfil 72). The VCT file contains the total concentration volume for the 72 profiles performed. Additionally, the salinity and the temperature were measured with a CastAway-CTD, employing a measurement rate of 4 Hz (Files: Density, Temperature and Salinity). Finally, water samples were also collected with a Niskin horizontal sampler to determine the organic matter content. These samples were collected every four hours at three different depths of the water column (surface, mid-layer, and bottom) and were preserved in amber glass bottles at 4 °C before being brought to the laboratory (File: MO).
DOI: 10.17632/gnpk45vm2m
title: Phosphorylation-dependent Charge Blocks Regulate the Coarsening of Nuclear Speckle Networks

description: All above images data concluded in two files
DOI: 10.25416/edgehill.25061423.v1
title: Creative interventions for the wellbeing of healthcare staff: Quantitative data

description: This dataset is raw data from the RIF-funded project titled: 'An evidence-based creative psychological intervention to support the recovery of NHS clinical staff affected by the COVID-19 pandemic: a feasibility study'. The data is provided in a .sav and .xlsx file. It consists of responses to validated questionnaires completed with participants at Levels 1, 2, and 3 pre- and post-intervention.The data is linked to an article submitted to Arts & Health: 'Supporting the wellbeing of clinical staff in healthcare settings through a multi-levelled creative psychological intervention: a feasibility study’.' A link to the article will be provided when it is published.
DOI: 10.6084/m9.figshare.11627580.v1
title: F_sultana_all_contigs_copy_v2.fsa

description: F. sultana transcriptome containing 85,532 contigs generated by de novo transcriptome assembly of RNA-seq data
DOI: 10.6084/m9.figshare.20398839.v1
title: Goes-Chem simulation results-2017

description: This data includes the results of the GEOS-Chem simulations run in August 2017 to study the ATAL. The files are in .sav format (idl) and include concentration of major aerosols at different altitudes.
DOI: 10.6084/m9.figshare.25587258.v1
title: Archaeal genomes used in the study "<b>Unique minimal and hybrid hydrogenases are active from anaerobic archaea</b>".

description: <br><b>Unique minimal and hybrid hydrogenases are active from anaerobic archaea</b>Chris Greening<sup>1,9</sup> *<b> </b><sup>#</sup><b>, </b>Princess R. Cabotaje<sup>2</sup> <sup>#</sup>, Luis E. Valentin Alvarado<sup>3 #</sup>, Pok Man Leung<sup>1 #</sup>, Henrik Land<sup>2</sup>, Thiago Rodrigues-Oliveira<sup>4</sup>, Rafael I. Ponce-Toledo<sup>4</sup>, Moritz Senger<sup>2</sup>, Max A. Klamke<sup>2</sup>, Michael Milton<sup>1</sup>, Rachael Lappan<sup>1</sup>, Susan Mullen<sup>3</sup>, Jacob West-Roberts<sup>3</sup>, Jie Mao<sup>1,5</sup>, Jiangning Song<sup>5</sup>, Marie Schoelmerich<sup>3</sup>, Courtney W. Stairs<sup>6</sup>, Christa Schleper<sup>4</sup>, Rhys Grinter<sup>1</sup> *,<sup> </sup>Anja Spang<sup>7,8 </sup>*, Jillian F. Banfield<sup>1,3</sup> *, Gustav Berggren<sup>2</sup> *<br><b>Summary</b>Microbial hydrogen (H<sub>2</sub>) cycling underpins the diversity and functionality of diverse anoxic ecosystems. Among the three evolutionarily distinct hydrogenase superfamilies responsible, [FeFe]-hydrogenases were thought to be restricted to bacteria and eukaryotes. Here we show that anaerobic archaea encode diverse, active, and ancient lineages of [FeFe]-hydrogenases through combining analysis of existing and new genomes with extensive biochemical experiments. [FeFe]-hydrogenases are encoded by genomes of nine archaeal phyla and expressed by H<sub>2</sub>-producing Asgard archaeon cultures. We report a novel ultra-minimal hydrogenase in DPANN archaea that binds the catalytic H-cluster and produces H<sub>2</sub>. Moreover, we identified and characterised remarkable hybrid complexes formed through the fusion of [FeFe]- and [NiFe]-hydrogenases in ten other archaeal orders. Phylogenetic analysis and structural modelling suggest a deep evolutionary history of hybrid hydrogenases. These findings reveal new metabolic adaptations of archaea, streamlined H<sub>2</sub> catalysts for biotechnological development, and a surprisingly intertwined evolutionary history between the two major H<sub>2</sub>-metabolizing enzymes.
DOI: 10.6084/m9.figshare.25962184.v2
title: Developing generalized flow-ecology relationships for salmonids

description: This represents supporting data and ancillary material used for the development of flow-ecology relationships for salmonids, as described in Rosenfeld and Enright (2024): <i>Developing generalized flow-ecology relationships for stream salmonids: ecological context resolves variation in response to altered flows.</i>
DOI: 10.6084/m9.figshare.27186126.v1
title: Data for "Recovery of ecosystem productivity in China by the Clean Air Action plan"

description: All data for "Recovery of ecosystem productivity in China by the Clean Air Action plan". The data includes NPP simulations (2013-2020, 8-years) from process-based (PBM) and machine learning (MLM) models, source data for Figs 1-5 and Extended Data Figs 1-5, and all names are explained in the supplementary materials.
DOI: 10.6084/m9.figshare.27938994.v1
title: Breast Cancer Plasma Metabolomics Pilot Study

description: This is a pilot study of breast cancer metabolomics observational case-control. Recruitment of study participants was conducted from July to August 2024. The study protocol was approved by the Health Research Ethics Committee of the Faculty of Medicine, University of Indonesia, under protocol number 24-03-0505. A total of 48 observational case-control design study participants were selected by dividing them into two main groups, namely the healthy control (HC) group (n=24) and the breast cancer (BC) group (n=24). The BC group involved patients diagnosed with invasive breast cancer of all stages recruited from Dr. Cipto Mangunkusumo National General Hospital, Faculty of Medicine, University of Indonesia. The HC group were female participants residing in Jakarta, Indonesia, who had neither been diagnosed nor had a family history of breast cancer. All participants were administered prior written informed consent.Untargeted metabolomic plasma analysis was done by GCMS-QP2020 NX Shimadzu. GC-MS raw data processing was exported using MS-DIAL ver. 4.92, with internal standard normalization.
DOI: 10.6084/m9.figshare.c.3637727_d9.v1
title: Additional file 3: of High-frequency, precise modification of the tomato genome

description: Annotated sequence of the vector pTC144. (GB 53 kb)
DOI: 10.17632/t78mc3s6vv
title: Sanctions news index (SNI) for the period 01/31/2023-01/31/2024

description: The dataset presents the SNI time series for the period 01/31/2023-01/31/2024. SNI is a quantitative index reflecting sanctions pressure on financial markets. In earlier studies, we have proven that SNI causes changes in domestic financial markets. Consequently, the growth of this index shows an increase in sanctions tension and is the reason for the volatility of financial assets.

SNI is justified in the article: Rychkov, V. (2023). Estimate of the Impact of Trade Sanctions on the Russian Financial Markets. In: Isaeva, E., Rocha, Á. (eds) Science and Global Challenges of the 21st Century – Innovations and Technologies in Interdisciplinary Applications. Perm Forum 2022. Lecture Notes in Networks and Systems, vol 622. Springer, Cham. https://doi.org/10.1007/978-3-031-28086-3_70

When using SNI, a link to the Dataset and article is required!
DOI: 10.17632/vswr6v5zb3
title: Digitized building footprints from VHR Worldview3 satellite image

description: This data was generated from randomly selected square patches from the extents of a high-resolution Worldview3 satellite image (2023) for the Ashaiman district, Accra, Ghana. The patches were digitised by an expert in the fields of cartography, surveying, and GIS. This purpose of creating this dataset is to have a representative sample of patches, which was used for subsequent on-screen digitising of 2803 buildings polygons.
DOI: 10.6084/m9.figshare.17087762.v1
title: spatialRNAseq_ileum_processed_suppdata.zip

description: Processed H&E images (JPG), tissue spot position list (CSV), and scale factor (JSON) files for 10x Genomics Visium spatial transcriptomics experiments for reovirus-infected mice ileum tissue. These files are processed files which can directly loaded in Seurat/ scanpy with the count matrices for spatial trasncriptomics analysis. If you want to realign the sequecning data, please download the rawsuppdata (ZIP) instead.
DOI: 10.6084/m9.figshare.17194823.v2
title: Role of English in Agricultural Organisations

description: Raw data of the survey
DOI: 10.6084/m9.figshare.19785364.v1
title: Supplementary Material for: The Identification and Characterization of Immunoreactive Fungal Proteins Recognized by Sera from Zimbabweans Sensitized to Fungi

description: <b><i>Background:</i></b> Exposure to fungal allergens poses a serious threat to human health, especially to mould-allergic individuals. The prevalence of fungal allergic disease is increasing globally but is poorly studied in Africa. Here, we aimed to identify and characterize fungal proteins that were immunoreactive against serum samples from fungal-sensitized Zimbabweans from Shamva district to inform the development of diagnostics and therapeutics. <b><i>Methods:</i></b> Crude protein extracts of the Ascomycota <i>Aspergillus fumigatus, Alternaria alternata, Cladosporium herbarum, Epicoccum nigrum, Penicillium chrysogenum,</i> and <i>Saccharomyces cerevisiae</i> as well as mucoromycota <i>Rhizopus nigricans</i> were individually separated by one-dimensional gel electrophoresis for protein staining and immunoblotting. A pool of eight sera from fungi-sensitive Zimbabwean children aged 3–5 years was used to screen the crude extracts to determine their immunoreactivity. Protein bands recognized by the sera were subjected to mass spectrometry to identify the individual proteins reactive with the sera. <b><i>Results:</i></b> The pooled serum sample reacted with 20 bands, which resolved to 34 distinct proteins, most of which were novel immunogens. The pool was most reactive to <i>A. alternata</i>. The proteins identified included peptidases (8/34), hydrolases (6/34), oxidoreductases (5/34), and glucosidases (4/34), while 11/34 were unknown. Eight of the proteins were predicted to be allergens using the Structural Database of Allergenic Proteins (SDAP). <b><i>Conclusions:</i></b> We identified novel immunogens from fungi expanding the number of known fungal allergens. These form a potential basis for diagnostics specific for the Zimbabwean population. Validation assays will now need to be carried out to further evaluate the cross-reactivity of the identified allergen candidates as well as investigate their potential recognition in a larger cohort of patients. Furthermore, there is now a need to conduct studies relating sensitization to these immunogens and clinical diseases in the population.
DOI: 10.6084/m9.figshare.23180342.v1
title: Hops.zip

description: Source data, supplement with algorithms
DOI: 10.6084/m9.figshare.23969877.v1
title: VNSHypertenManuscript_supp Phys Genomics revision.docx

description: Supplemental data for PG submission
DOI: 10.6084/m9.figshare.24087975.v1
title: data in bried on CSA HDDS and HFIAS.xlsx

description: Data was collected through cross-sectional survey of smallholder farmers in South Africa. A multistage sample technique was use to elicit information from 316 maize farmers in South Africa
DOI: 10.6084/m9.figshare.24825810.v1
title: Supplementary Material for: Glycemic variability and Time in range are associated with the risk of overweight and high LDL-cholesterol in children and youths with Type 1 Diabetes.

description: Introduction: Reducing cardiovascular risk factors (CVRFs) exposure in children and youths with type 1 diabetes (T1D) is critical for cardiovascular diseases (CVD) prevention. Long-term exposure to hyperglycaemia, measured by HbA1c, had been recognized as the main factor affecting CVRFs profile. To date, the possible association between short-term glycaemic control and variability measured by continuous glucose monitoring (CGM) metrics and CVRFs has not been explored. The aim of this study was to test the hypothesis that CGM metrics independently contribute to CVRFs exposure in children and youths with T1D. 
Method: BMI, blood pressure (BP), lipid profile, and CGM data of 895 children and youths with T1D were analysed. Binary multivariable logistic regression analyses were performed to test independent associations between CVRFs (BMI percentile&gt;85th, LDL-c&gt;100 mg/dL, BP&gt;90th percentile) and CGM metrics according to sex and adjusting for confounding factors.
Results: In both sexes, metrics of hypoglycaemia and glycaemic variability (coefficient of variation [%CV]) positively correlated with BMI percentile. LDL-c positively correlated with mean glucose and metrics of hyperglycaemia. A negative correlation was found between LDL-c and time in range (TIR). No significant correlations were found between CGM metrics and BP percentiles. In both sexes, TIR&lt;70% was significantly associated with LDL-c&gt;100 mg/dL (OR 3.2 in males, 2.1 in females). In females, CV&gt;36% was significantly associated with overweight (OR 2.1).
Conclusions: CGM metrics of glycaemic control and variability were significantly associated with the risk of overweight in females and high LDL-c in both sexes.
DOI: 10.6084/m9.figshare.27185985.v1
title: One-year mortality in patients undergoing aortic valve replacement and its relationship with the extent of myocardial damage scale dataset

description: Dataset
DOI: 10.6084/m9.figshare.29095901.v1
title: Source Package

description: Source Package of CASSIA
DOI: 10.6084/m9.figshare.5576392.v2
title: Image dataset (Paper: Paired mini-batch training)

description: This dataset was used in experiments of the paper, “Paired mini-batch training: A new deep network training for image forensics and steganalysis”.<br>All images were generated by Bossbase dataset, “Bas, P., Filler, T., Pevn`y, T., 2011. Break our steganographic system: The ins and outs of organizing boss, in: Information Hiding, Springer. pp. 59–70”.Image size – 256 x 256For forensic – 200,000 normal gray images and codes for generating manipulated images.Manipulation type – Additive white Gaussian noise deviation 1, Median filtering with a 3 x 3 kernel, Gaussian blurring with a 3 x 3 kernel and a standard deviation 0.4.For steganalysis – 160,000 normal gray images and stego images.Stego type – LSB, S-UNIWARD, WOW<br>
DOI: 10.17632/4nxghz7cmr
title: Post shut-in arrest and recession solutions for a deflating hydraulic fracture in a permeable elastic medium

description: This data set provides the numerical solutions generated using an Implicit Moving Mesh Algorithm (IMMA) that has been adapted to include the k-g, r-g multiscale and k and r-vertex asymptotes to model the post-shut-in arrest and recession of a radial hydraulic fracture in a permeable elastic medium.  The theory behind this work is described in the paper "The arrest and recession dynamics of a deflating radial hydraulic fracture in a permeable elastic medium" published in the JMPS (https://doi.org/10.1016/j.jmps.2022.104926).

For the simulations I set the following parameters to unity:
Ep   = 1
mup  = 1 
Cp   = 1
Q0   = 1

Since V0 = Q0*ts, from eq (39)  in the paper you can vary omega = ts/tmm~ = ts (since all the material parameters in t_mm~ are 1) and choose the value of phi^V that you want by setting Kp as follows:
Kp     = (TS'*(phi).^(-65/9)).^(1/26);

Recall: 
tmmt    = (mup^4*Q0^6/Cp^18/Ep^4)^(1/7);
omega  = Ts/tmmt;
phiV     = (Ep^21*mup^5*Cp^10*Q0*Ts/Kp^26)^(9/65);

Issue the command
load(Extract_Radial_MKC1_Ts_1em3_phi_50);
to access the structures Results, which contains the structure Input.
The file names embed the two dimensionless parameters: omega=Ts/tmm~=Ts (since tmm~=1) and phiV.  To avoid decimal points in the file name I have multiplied the phiV value by 100. So the above data file is for the case omega=10^{-3} and phiV=0.5.

Input    = struct('Ep',Ep,...      % Pa plane strain modulus
    'mup',mup,...                      % Pa*s, alternate fluid viscosity
    'Cp',Cp,...                            % m/s^1/2, alternate Carter's leak-off coefficient
    'Kp',Kp,...                            % Pa*m^1/2, alternate fracture toughness    
    'Q0',Q0,...                           % m/s, injection rate
    'Ts',Ts,...                              % shut-in time
    'omega',omega,...              % dimensionless shut-in time
    'phiV',phiV,...                      % arrest regime parameter
    'Nr',Nr,...                            % number of grid points in r direction
    'Nt',itcol);                           % number of time steps till collapse

Results=struct('pt',P(1,1:itcol),...  % wellbore pressure versus t
    'Rt',R(1:itcol),...                       % fracture radius versus t
    'wt',W(1,1:itcol),...                  % wellbore aperture versus t
    'eta',eta(1:itcol),...                   % efficiency versus t    
    'pr',P(:,1:itcol),...                     % fluid pressure versus r at all times Nt
    'wr',W(:,1:itcol),...                   % fracture width versus r at all times Nt (because of the moving mesh to plot in real space use plot(rho*R(it),wr(:,it)))
    'rho',rho,...                              % lateral spatial coordinate
    't',time(1:itcol),...                    % time
    'keyindx',[its ita itd itcol],...    % key indices keyindx(1)=its (shut-in index), keyindx(2)=ita (arrest), keyindx(3)=itr (recession), keyindx(4)=itc (collapse)
    'Input',Input);                         % Input Structure
DOI: 10.17632/h35rwx32mx
title: Table 5 The nexus between quality governance FDI inflow CO2 emissions and Carbon damage in Africa

description: The research examines the causal link between quality governance indicators and carbon emissions through foreign direct investment (FDI) to Africa from 1996 to 2020 using the 2SLS – IV regression
DOI: 10.17632/n2jsf2xfnb
title: BERT and LSTM Research

description: BERT and LSTM Research using Twitter/X user's posts and History of GOTO Stock Market Price
DOI: 10.6084/m9.figshare.24710238.v1
title: Large data files for 3011979 Python demo

description: These are demo data files used to teach machine learning with Python in 3011979 course at Chulalongkorn University in Spring 2021 and Spring 2022
DOI: 10.6084/m9.figshare.3558003.v1
title: Data Paper. Data Paper

description: File List Antarctic_Site_Inventory_census_data_1994_2012.csv (MD5: 00871bd47b6ec30cda68d1506120bfb3) Description This data set represents the accumulation of 19 years of seabird population abundance data collected by the Antarctic Site Inventory, an opportunistic vessel-based monitoring program surveying the Antarctic Peninsula and associated sub-Antarctic Islands. This data paper, which include 1124 records from 113 locations for seven species of seabirds (Adélie Penguin [<i>Pygoscelis adeliae</i>], Gentoo Penguin [<i>P. papua</i>], Chinstrap Penguin [<i>P. antarctica</i>], Macaroni Penguin [<i>Eudyptes chrysolophus</i>], Blue-eyed Shag [<i>Phalacrocorax atriceps</i>], Kelp Gull [<i>Larus dominicanus</i>], and Southern Giant Petrel [<i>Macronectes giganteus</i>]) includes data already published by the Antarctic Site Inventory as well as seven years of recent data not previous published. Census data represent a mix of nest and chick counts; each census record includes the location, date, and precision of the census count, along with any auxiliary notes. Included with the database are maps to clarify the location of specific breeding populations that may be new (and thus not previous reported) or ambiguous. This compilation represents the best single source of raw data on the spatiotemporal dynamics of the <i>Pygoscelis</i> penguins in the Antarctic Peninsula region, and provides population data on several flying bird species less frequently studied. <i>Key words</i>: <i>Adélie penguin; Antarctic Peninsula; Blue-eyed Shag; breeding bird survey; Chinstrap Penguin; Gentoo Penguin; Macaroni Penguin; </i>Pygoscelis;<i> Southern Giant Petrel; vessel-based monitoring.</i>
DOI: 10.60893/figshare.apr.26166994.v1
title: Supplementary Materials

description: Supplementary Materials for

Observation of resilient propagation and free-space skyrmions in toroidal electromagnetic pulses
DOI: 10.17632/w5nd8232nn
title: Number of hospitals in Republic Uzbekistan by region

description: Official Statistical Data: Number of hospitals and outpatient clinics by the Ministry of Health of the Republic of Uzbekistan.