cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8335265.v2
title: Pangenome gene alignments of 41 Pseudorhizobium and Neorhizobium strains

description: All predicted protein sequence were extracted from the 571Rhizob genome dataset and clustered into homologous gene families (with possibly multiple copies per genome) using MMSeqs2 release 2 (commit e5d64b2) (Steinegger & Söding 2017). Protein sequences from each gene family were aligned using ClustalOmega (Sievers et al. 2011) and reverse-translated into coding sequence (CDS) alignments using PAL2NAL (Suyama et al. 2006).This resulted in the extensive Dataset presented in https://doi.org/10.6084/m9.figshare.8343473. Alignment file set and sequence content were then restricted to sequences occurring in the the 41NeoPseudo sub-dataset, resulting into 6,714 gene family alignments.
DOI: 10.17632/jfjbvnr6fw
title: (U-Th)/He & 26Al/10Be geochronology data and MATLAB code for 26Al/10Be min-max age calculations

description: The .xlsx file in this dataset provides raw data used for (U-Th)/He and 26Al/10Be age calculations in Odom et al. (2020). The accompanying .zip file includes MATLAB code for calculating minimum-maximum burial age likelihood functions using 26Al/10Be data, as well as a guide for use.
DOI: 10.6084/m9.figshare.21602697.v2
title: Data files for the study "Plastid translocon recycling in dinoflagellates demonstrates the portability of complex plastids between hosts"

description: The following datasets for phylogenetic analysis of proteins Cdc48, Uba1, Der1, Ubc4, Ubi, Hsp70, Tic110, Tic20 and Tic22 are provided: Unaligned sequences (fasta format), aligned sequences (fasta format), trimmed alignments (fasta format) and IQ-TREE 2 output files.<br><br>Transcipts, predicted gene sequences and predicted protein sequences for the Karlodinium veneficum PLY720 transcriptome are provided. Corresponding raw sequencing reads are available from the NCBI Sequence Read Archive under the BioProject accession PRJNA1117636 (BioSample accession SAMN41577327).
DOI: 10.6084/m9.figshare.25029554.v1
title: Ecomorphotype R code and input files

description: Code and input files for the paper: A quantitative test of the “Ecomorphotype Hypothesis” for fossil true seals (Family Phocidae)Acronyms in files (from Churchill & Uhen, 2019):DDDC: diameter of diaphysis at deltopectoral crest<br>HHH: height of head of humerus<br>HTL: height of capitulum<br>HTS: height of trochlea<br>LDC: length of deltopectoral crest<br>TLH: total length of humerus<br>WDC: width of deltopectoral crest<br>WDEH: maximum width of distal epiphysis<br>WDH: minimum width of diaphysis<br>WHH: width of humeral head<br>WPDH: width of proximal epiphysis head to deltopectoral crest<br>WPEH: width of proximal epiphysis head to lesser tubercle<br>WTA: width of trochlea in anterior view<br>WTD: width of trochlea and capitulum in posterior view<br>GAP: distance between head of humerus and deltopectoral crest<br>PIT: depth of coronoid fossa<br>DCF: distance between condyles<br>DN: diameter of the neck of the femur<br>HHF: height of the head of the femur<br>HPS: height of the patellar surface<br>ITW: intertrochlear width of the femur<br>LGTF: length of the greater trochanter<br>LLF: length of the lateral side of the femur<br>MLF: length of the femur on the medial side<br>LMCF: length of the medial condyle<br>LLCF: length of the lateral condyle<br>WCF: width across condyles<br>WDEF: maximum width of distal diaphysis<br>WDF: minimum width of diaphysis<br>WPEF: maximum width of proximal diaphysis<br>WLCF: width of lateral condyle<br>WMCF: width of medial condyle<br>_S: scaled measurementChurchill M, Uhen MD. 2019. Taxonomic implications of morphometric analysis of earless seal limb bones. Acta Palaeontologica Polonica 64(2).
DOI: 10.6084/m9.figshare.27325284.v1
title: <i>Batrachochytrium dendrobatidis</i> JEL423 genome assembly and annotation (ONT and Hi-C) V3

description: <i>B. dendrobatidis </i>is a fungus that has been implicated in the extinctions and declines of dozens of amphibians globally. Here we describe a new genome assembly for the commonly used <i>B. dendrobatidis</i> isolate JEL423, which is a substantial improvement from the previously used assembly.
DOI: 10.6084/m9.figshare.26364112.v1
title: KP-IPHS-2017

description: This is the data set of the Khyber Pakhtunkhwa Integrated Population and Health Survey (KP-IPHS), which aims to fill these gaps by providing comprehensive data on various health indicators, including the leading CDs, NCDs, and disabilities in the province. Utilizing a multi-stage stratified cluster sampling method, the survey was conducted in 24 districts, covering urban areas divided into income-based enumeration blocks and rural areas divided into mohallas/villages. Ethical approval was secured from Khyber Medical University. The survey’s findings aim to inform and reform health and population welfare policies in the region.
DOI: 10.6084/m9.figshare.16618255.v1
title: Pearl River estuary microbiome and virome

description: <b>Project description:</b> Deep metagenomic sequencing on microbial and viral communities in surface waters of the Pearl River estuary (PRE), a typical subtropical. <b>Data description: </b>Data for assembly, MAGs, viral like contigs and populations generated using the PRE microbial metagenomic data sets - data includes:PRET1608S??F00_idba-ud_final.fna.gz: the contigs generated from virome(&lt;0.2 μm) (5 files)PRET1608S??F0{2/7}_megahit_final.fna.gz: the contigs generated from cellular metagenome(0.2-0.7 μm and 0.7-2.7μm) (10 files)PRE_viral_contigs.fasta: Putative viral contigs identified from contigs of all the three size fractions in PRE (1 file\)PRE_viral_contigs_95-80.fna: Viral populations based on 95% nucleotide identity and 80% of the genome coverage criterion ((1 file)
DOI: 10.6084/m9.figshare.12344486.v1
title: Analysis of endogenous competitive RNA in platelets of patients with Hepatocellular carcinoma based on high-throughput sequencing.zip

description: 通过 使用生物信息学分析探索了 ceRNA在血小板中的可能性，为进一步阐明血小板参与HCC的机制提供了线索。
DOI: 10.6084/m9.figshare.19085150.v1
title: Supplementary Material for: A Novel Homozygous <b><i>KLHL3</i></b> Mutation as a Cause of Autosomal Recessive Pseudohypoaldosteronism Type II Diagnosed Late in Life

description: <b><i>Introduction:</i></b> Pseudohypoaldosteronism type II (PHA II) is a Mendelian disorder, featuring hyperkalemic acidosis and low plasma renin levels, typically associated with hypertension. Mutations in <i>WNK1</i>, <i>WNK4</i>, <i>CUL3</i>, and <i>KLHL3</i> cause PHA II, with dominant mutations in <i>WNK1</i>, <i>WNK4</i>, and <i>CUL3</i> and either dominant or recessive mutations in <i>KLHL3</i>. Fourteen families with recessive <i>KLHL3</i> mutations have been reported, with diagnosis at the age of 3 months to 56 years, typically in individuals with normal kidney function. <b><i>Methods:</i></b> We performed clinical and genetic investigations in a patient with hyperkalemic hypertension and used molecular dynamics simulations, heterologous expression in COS7 cells, and Western blotting to investigate the effect of a <i>KLHL3</i> candidate disease mutation on WNK4 protein expression. <b><i>Results:</i></b> The patient, a 58-year-old woman from a consanguineous family, showed hypertension, persistent hyperkalemic acidosis associated with severe muscle pain, nephrolithiasis, chronic kidney disease (CKD), and coronary heart disease. Therapy with hydrochlorothiazide corrected hyperkalemia, hypertension, and muscle pain. Genetic analysis revealed a homozygous p.Arg431Trp mutation at a highly conserved KLHL3 position. Simulations suggested reduced stability of the mutant protein, which was confirmed by Western blot. Compared with wild-type KLHL3, cotransfection of p.Arg431Trp KLHL3 led to increased WNK4 protein levels, inferred to cause increased NaCl reabsorption via the thiazide-sensitive carrier and PHA II. <b><i>Conclusions:</i></b> Even in patients presenting late in life and in the presence of CKD, PHA II should be suspected if renin levels are low and hyperkalemic acidosis and hypertension are inadequate for CKD stage, particularly in the presence of a suspicious family history.
DOI: 10.6084/m9.figshare.20290782.v3
title: Dataset to accompany paper: Measured inherent optical properties of Jerlov water types

description: Dataset to accompany paper: Measured inherent optical properties of Jerlov water types
DOI: 10.6084/m9.figshare.23503896.v1
title: HMAP Dataset 10: Catalonian Coast

description: This dataset was generated following the HMAP Mediterranean workshop, held in Barcelona in September 2004. All the participants recognised the necessity of obtaining reliable and relevant historical data about the different Mediterranean ecosystems, in order to generate hypothesises about change over time.Statistical data about Spanish fisheries has been compiled in conjunction with the Institute of Marine Science - Mediterranean Marine and Environmental Centre (ICM- CMIMA) biologists. The resulting dataset comprises information about the historical Catalan sea fisheries. Online delivery to the scientific research community and beyond aims to contribute and improve upon current knowledge. Catalan biologists are now working on future applications in the reconstruction of marine ecosystems using ecological models and developing temporal simulations and model comparisons. The reconstruction of past ecosystems - and subsequent comparison with the present status - will facilitate the evaluation of its changes through the last century.
DOI: 10.6084/m9.figshare.29077709.v1
title: Supplementary materials: Global spatiotemporal multi-criteria analysis of coastal risk current and future hot spots and clusters

description: Clustering results include final raster maps obtained from clustering procedure.Risk index and uncertainty supplementary includes raster maps for risk index and uncertainty under all different scenarios descibed in the paper.Main codes include pre-processing , risk index (WOWA) and PCA/clustering scripts.Raw data supplementary includes initial datasets in csv format and auxiliary data.Countries_statistics contains a summary of risk index, uncertainty and clustering results for the different countries.<br>
DOI: 10.6084/m9.figshare.12824861.v1
title: The effects of sample size and sample prevalence on cellular automata based urban growth simulation

description: This dataset is used in the research of "The effects of sample size and sample prevalence on cellular automata based urban growth simulation".<br><b>Abstract: </b>In this paper, we take cellular automata (CA) models based on an artificial neural network (ANN), logistic regression (LR), and support vector machine (SVM) as examples. The effects of the sample size and sample prevalence on the CA simulation are investigated by simulating the urban growth of the city of Wuhan in China and the Wuhan Metropolitan Area under different sampling schemes. The results of the CA models based on the ANN, LR, and SVM methods are generally consistent, and show that sampling schemes with a small sample size and low sample prevalence should be discarded because of the high uncertainty. The sample size determines the robustness of a CA model, whereas the sample prevalence affects the performance of a CA model when there are sufficient samples. In particular, the closer the sample prevalence is to the population prevalence, the higher the simulation accuracy and the lower the shape complexity and fragmentation of the simulated urban landscape. We show that the optimal sampling scheme has a sample rate of 1% and a sample prevalence that is the same as the population prevalence, and is independent of the population sizes represented by different study areas.<br>
DOI: 10.6084/m9.figshare.21191515.v1
title: Commodity Price Shocks and Battle Deaths in Civil Wars

description: Replication data and code for Commodity Price Shocks and Battle Deaths in Civil Wars
DOI: 10.6084/m9.figshare.26124853.v1
title: data and code.zip

description: data and code used in paper '<b>A novel crossed hysteresis response pattern of sap flux to solar radiation</b>'
DOI: 10.6084/m9.figshare.5598556.v1
title: UI Snapshots - Design Iteration II

description: UI Snapshots through the iterative cycles of design, development and evaluation - assorted visualisation modules exploring skills analysis in the EDSA project.
DOI: 10.17632/r8tc2hrk3w
title: Supplementary data - cSCC nodal metastasis risk models

description: PRISMA checklist, PRISMA flow diagram, search strategy table, risk bias assessment and references.
DOI: 10.6084/m9.figshare.27153441.v4
title: On the Impact of Requirements Smells in Prompts: The Case of Automated Traceability

description: <pre>This is the dataset for the paper <i>On the Impact of Requirements Smells in Prompts: The Case of Automated Traceability</i>. See the <i>README.md</i> for more information.</pre><br>
DOI: 10.17632/7d4285x2rp
title: Unbiased profiling reveals concomitant ER stress and oxidative dysregulation
DOI: 10.25442/hku.26861653.v1
title: Supporting data for "Second language processing of derived words in English: an ERP investigation"

description: Dataset and all files necessary to replicate the research done for thesis "Second language processing of derived words in English: an ERP investigation"<br>The dataset consists of three csv files that consist of ERP data that can be used for ERP analysis, along with the respective R scripts to analyze and perform ANOVAS on that data. A behavioral data file that consists of reaction time data to each stimuli as well as the script to analyze the behavioral data is also included. For plotting of ERPs, four files have been included named "Acquisition_XX" that are grouped by participant group. Using the matlab scripts this data can be plotted to reproduce all of the figures from the project.<br>In sum, ERP data analysis can be reproduced using the three ERP csv files and R scripts for ERP analysis, behavioral analysis can be reproduced with the excel file beginning with "4_groupanalysis_" and the R script for behavioral analysis, and figures can be reproduced using the "Acquisition_XX" files along with the matlab scripts
DOI: 10.6084/m9.figshare.9159824.v1
title: Risk of bias assessments for Cochrane Review 'Altering the availability or proximity of food, alcohol, and tobacco products to change their selection and consumption' (2019)

description: Risk of bias assessments for Cochrane Review 'Altering the availability or proximity of food, alcohol, and tobacco products to change their selection and consumption' (2019)
DOI: 10.6084/m9.figshare.11880579.v2
title: Social organisation and breeding biology of the western grasswren

description: Data of the social organisation and reproductive output of western grasswren fom 2019 - 2021 in Western Australia.
DOI: 10.6084/m9.figshare.28589138.v1
title: Data associated with "Growth and assemblage dynamics of temperate forest tree species match physiological resilience to changes in atmospheric chemistry"

description: The <b>DATABASE_environment.txt</b> dataset captures environmental factors associated with tree growth and isotopic composition, featuring data for air temperatures, precipitation indices, d18O in precipitation, nitrogen deposition, and precipitation pH. The <b>DATABASE_raw_isotope.txt</b> dataset offers detailed isotopic and growth data on individual trees, including raw isotopic ratios, tree-ring metrics, and growth measurements such as tree ring width and basal area increments. A detailed description of both datasets is provided in a PDF titled "Database description."
DOI: 10.6084/m9.figshare.14215307.v1
title: Dataset for 3D motional induction

description: This dataset is for the paper "Electromagnetic field generated by an earthquake source due to motional induction effect in 3D stratified media and application to 2008 Mw 6.1 Qingchuan earthquake".
DOI: 10.6084/m9.figshare.11877789.v1
title: Thinking style, conspiracy and schizotypy

description: Data examining links between conspiracy and thinking
DOI: 10.6084/m9.figshare.12792554.v1
title: raw-image-data

description: raw data
DOI: 10.6084/m9.figshare.26063611.v1
title: The flow cytometry .wsp file showing our gating strategy in this manuscript

description: This is the FlowJo .wsp file used for gating our flow cytometry data.
DOI: 10.6084/m9.figshare.3528077.v1
title: Appendix A. A table of species names and habitats of plants, as well as a list of seed suppliers for the species and references.

description: A table of species names and habitats of plants, as well as a list of seed suppliers for the species and references.
DOI: 10.6084/m9.figshare.24564373.v1
title: Data from: Responses of the collared flycatcher to the changing climate: a more comprehensive view

description: Global climate change involves various aspects of climate, including precipitation changes and declining surface wind speeds, but studies investigating biological responses have mainly focused on the impacts of rising temperatures. Additionally, related studies on bird reproduction often focus on breeding onset, even though the sensitivity of a species can vary among different breeding components influenced by diverse weather aspects. We used an almost four-decade-long data set to investigate how the different aspects of breeding parameters of a collared flycatcher (<i>Ficedula albicollis</i>) population in the Carpathian Basin were associated with various local weather parameters. We also investigated the temporal trends of weather and breeding parameters. Higher temperatures and lower wind speeds were accompanied by earlier breeding onset. Breeding season length correlated positively with rains and negatively with the magnitude of within-season temperature rise. Hatching delay increased with cooler temperatures and rainier weather. Clutch size increased with the number of cool days. There were significant temporal trends in all breeding variables and, in parallel, the related weather parameters. For example, an advance in breeding onset and a decrease in wind speed were observed. The phenological mismatch between prey availability and breeding has notably increased in the last decade. Our results highlight the intricate interplay between climate change and the reproductive patterns of migratory birds, emphasizing the need for a holistic approach. It also underscores the potential threats posed by climate change to bird populations and the importance of adaptive responses to changing environmental conditions.
DOI: 10.6084/m9.figshare.14888121.v1
title: Test Data of Ultralow Temperature Refrigeration for COVID 19 Vaccine Distribution Solution

description: test dataset to assist the development of a quick, effective, secure, and safe solution to mitigate the challenges faced by vaccine distribution logistics
DOI: 10.6084/m9.figshare.26983963.v1
title: VL VM - grids

description: Mat files with EMG signals recorded from the vastus medialis and vastus lateralis with one grid of 64 surface electrodes per muscle and edited motor unit pulse trains.
DOI: 10.6084/m9.figshare.5127475.v1
title: Supplementary Material for: Factors Influencing Lymph Node Metastasis in Patients with Ampullary Adenocarcinoma

description: <b><i>Aim:</i></b> In cases of ampullary carcinoma, lymph node involvement affects the selection of treatment strategies. This study aimed to identify clinicopathologic features of ampullary carcinoma with lymph node metastases. <b><i>Methods:</i></b> The records of 74 consecutive patients with ampullary adenocarcinoma who underwent pancreaticoduodenectomy (PD) with regional lymph node dissection were retrospectively analyzed. <b><i>Results:</i></b> Twenty-two patients (30%) with lymph node metastasis had significantly worse survival after resection than those without lymph node metastasis (p = 0.017). Univariate analyses revealed that preoperative biliary drainage; elevated serum carbohydrate antigen 19-9 (≥36 U/ml); moderate-to-poor pathologic grade (G2/3); perineural, vascular, lymphatic, pancreas, and duodenal invasion; and T category were significantly associated with lymph node metastasis. In multivariate analysis, only pathologic grade (G2/3) remained significantly associated with lymph node metastasis (hazard ratio, 6.51; p = 0.035). In sub-classified analysis for T category, lymph node metastasis was found in 5 of 22 cases (22.7%) of T1 tumors. Four of five cases with lymph node metastases had a dominant G2/3 component, whereas only 2 of 17 cases without lymph node metastases had a G2/3 component in T1 tumors (p = 0.0036). <b><i>Conclusions:</i></b> Pathologic grade (G2/3) was significantly and independently associated with lymph node metastasis and was also a significant predictor in T1 tumor cases.
DOI: 10.6084/m9.figshare.21473238.v1
title: Shifting settling regimes of clean and biofouled aquatic microplastics in fluvial to marine waters dataset

description: Dataset of results for paper "Shifting settling regimes of clean and biofouled aquatic microplastics in fluvial to marine waters". <br> Includes: Settling_exp_results_all - the results from the settling experiments of PET, PVC fragments and NP&A fibres at various salinity and clay concentrations. Time_trials - the settling results for PET over 0-8 weeks as biofouling occurs Expected_calculations - the results from using Ferguson & Church (2004) to predict microplastic settling for PET and PVC fragments
DOI: 10.6084/m9.figshare.24101748.v1
title: Medicare Part D Spending by Drug DYT2016-2019.zip

description: Historical Medicare Part D drug spend data provided by the Centers for Medicare and Medicaid Services by year from 2016-2019
DOI: 10.6084/m9.figshare.17920322.v1
title: Supplementary Material for 'Red deer Cervus elaphus blink more in larger groups'

description: Text files: Dataset and annotated R code.
DOI: 10.6084/m9.figshare.12762923.v1
title: Dataset S15 - MCC.tre

description: Maximum Clade Credibility tree.
DOI: 10.6084/m9.figshare.13099949.v1
title: Supplementary Table 2: Reasons for exclusion

description: Some data were not collected or were lost due to factors including scheduling constraints/study overlap, ECG artifact, or acute mountain sickness (AMS) symptoms on day of testing.<br>a = AMS b = ECG artifact c = Scheduling constraints d= Did not participate <br>
DOI: 10.6084/m9.figshare.27619767.v1
title: DLPFC_donor3.h5ad

description: Raw human DLPFC dataset from Maynard et al. (<i>Nat Neurosci.</i>, 2021), containing 4 slices (Slice 151673, 151674, 151675, and 151676) from the same donor with the layer labels. The scVI (<i>Nat Methods.,</i> 2018) embedding as well as the Cell2location (<i>Nat Biotechnol.</i>, 2022) deconvolution results are also provided.<br><br><br><br>