cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12545984.v1
title: Pseudogene identification pipeline

description: This is a manually modified pipeline based on the program suite Psi-Phi (Lerat and Ochman, 2004), which identifies pseudogenes by doing tblastn within a cluster of closely related genomes.<br><b>Input data</b><br>1. Amino acid files of all genomes named *.faa2. Genome fasta files named *.fasta (draft genome) or *.fas (complete genome)3. Genbank files of all genomes named *.gbk<br>Original Psi-Phi scripts are designed for complete genome. For genome assemblies that have not been completely assembled into a single chromosome, all contigs of a genome should be concatenated to an artificially assembled genome first (*.fasta-&gt;*.fas) as the input of Psi-Phi.<br><b>Instructions for pseudogene identification (Psi-Phi)<br></b> 1. Makeblastdb for tblastn<br>In this step, command line will be written as below to make nucleotide database of all artificially assembled genome.<br>makeblastdb -in input.fas -dbtype nucl -parse_seqids -out input.fas<br>2. Run tblastn jobs<br>In this step, command line will be written as below to submit blast jobs for all pairs of the genome sequences. <br>tblastn -query query.faa -db target.fas -outfmt 6 -evalue 1e-15 -out query.vs.target.blast<br>3. Batch run module1 of Psi-Phi using batch.module1.pl<br>This step retrieves particular data from a blast file, output results will be found in 'query.vs.target.sortie.out' files.<br>4. Batch run module2 of Psi-Phi using batch.module2.pl<br>This step determines the list and category of each pseudogene candidate using the output of the first module. Potential pseudogenes will be found in 'pseudo_target_use_query' files.<br><b>Instructions for pseudogene filtering</b><br>The filtering step is further applied to filter out misidentified pseudogenes by Psi-Phi.<br><b>Citation</b><br>If you are interested in using this modified pipeline for pseudogene identification with filtering, please cite:<br>Lerat E, Ochman H. Ψ-Φ: Exploring the outer limits of bacterial pseudogenes. <i>Genome Res</i> 2004; <b>14</b>: 2273–2278.<br><br>Chu X, Li S, Wang S, Luo D, Luo H. Gene Loss through Pseudogenization Contributes to the Ecological Diversification of a Generalist <i>Roseobacter</i> Lineage. (unpublished)
DOI: 10.6084/m9.figshare.17701088.v1
title: EEG Dataset for RSVP and P300 Speller Brain-Computer Interfaces

description: EEG dataset for subject 09
DOI: 10.6084/m9.figshare.28676018.v1
title: Social networks affect redistribution decisions and polarization

description: Data from agent based models and experiments with human participants recruited from Prolific. Individuals observe the wealth of a sample of the population and vote for % tax. The median vote is selected and implemented, where everyone pays that % of their wealth as tax and the collected tax revenue is then evenly split among all.
DOI: 10.6084/m9.figshare.26551309.v1
title: The genome assembly and annotation of the cultivated peanut YZ9102

description: We integrated PacBio HiFi, ultra-long Nanopore, Illumina short reads, and Hi-C data to achieve a T2T-level assembly of the peanut genome. Additionally, leveraging PacBio HiFi transcriptomic data, we constructed a high-quality peanut gene set.
DOI: 10.6084/m9.figshare.6124640.v1
title: Process of dying in a pediatric intensive therapy unit

description: Abstract The recurrent experience of the nursing team in a pediatric intensive care unit is not enough to accept the death of a child, since they bring feelings like guilt, failure and denial of death. The objective of this study is to discuss how nursing professionals deal with the death and dying process, and identify the impacts caused during this process in pediatric intensive care units. The methodology chosen to conduct the research was qualitative and exploratory-descriptive, employing a content analysis proposed by Bardin. We conclude that there are some important gaps in the nursing process in dealing with death and dying in pediatrics. Dealing with this process is extremely painful and requires the pursuit of continuing education in health.
DOI: 10.25402/nnm.21186325.v1
title: Supplementary table - Alpha-fetoprotein mediated targeting of polymeric nanoparticles to treat solid tumors nnm-2022-0097

description: Background: Serious side effects caused by paclitaxel formulation, containing toxic solubilizer
Cremophor R ? EL, and its nonspecific accumulation greatly limit clinical paclitaxel application. Aim: To
design paclitaxel-loaded copolymer of lactic and glycolic acids nanoparticles decorated with alphafetoprotein
third domain (rAFP3d-NP) to increase paclitaxel safety profile. Methods: rAFP3d-NP was
obtained via carbodiimide technique. Results: The particles were characterized with high paclitaxel
loading content of 5% and size of 280 nm. rAFP3d-NP revealed biphasic profile with 67% release
of paclitaxel during 220 h. Increased area under the curveinf and mean residence time values after
rAFP3d-NP administration confirmed prolonged blood circulation compared with paclitaxel. rAFP3d-NP
demonstrated significant tumor growth inhibition at 4T1 and SKOV-3 models. Conclusion: rAFP3d-NP is
a promising delivery system for paclitaxel and can be applied similarly for delivery of other hydrophobic
drugs.
DOI: 10.6084/m9.figshare.21840486.v1
title: Items analizados en el modelo SEM en el cuestionario CAET sobre abandono escolar temprano.

description: Descripción de los ítems que forman el cuestionario CAET sobre abandono escolar temprano.
DOI: 10.6084/m9.figshare.25197059.v1
title: Table_4_2015_Set2_3-2

description: The grapevine is one of most widely perennial crops grown worldwide. As for other species displaying clusters of small fruits, the development of single berries within a bunch is asynchronous and heterogeneous. Because of this, the study of water and solute accumulation kinetics and balance at organ level cannot be directly extrapolated from samples of populations of fruits. In order to have an original and reliable dataset on the accumulation kinetics of the main solutes (primary and secondary metabolites and cations) and water, we analyzed fruits populations sorted according to their density and also individual berries from the onset of sugar importation to the end of phloem unloading. The studies were performed on a panel of varieties representing different metabolic contexts for the relationship between the import of organic and inorganic solutes and fruit growth, including genotypes able to import water at low fruit osmotic potential. These original data sets are suitable to revisit some aspects of the accumulation of main solutes and water in the grapevine fruit development and/or to perform comparative studies with other fleshy fruits.
DOI: 10.6084/m9.figshare.7274312.v4
title: EEG raw data set 1 (subject 1-18): Seeing the intensity of a sound-producing event can modulate the amplitude of the initial auditory evoked

description: The EEG recordings for participants 1-18 (any participants who did not meet our catch trial criterion or who had technical difficulties were excluded)<br>The trigger codes are:The onset of the 65 dB clap sound (weak clap visual) = 129<br>The onset of the 72.5 dB clap sound (weak clap visual) = 130<br>The onset of the 72.5 dB clap sound (strong clap visual) =131 <br>The onset of the 80 dB clap sound (strong clap visual) = 132<br>The onset of the 0 dB clap sound (weak clap visual) = 150 <br>The onset of the 0 dB clap sound (Strong clap visual) 151
DOI: 10.6084/m9.figshare.20052101.v1
title: genome, gff, cds, gene and protein file

description: the genome and annotation file of Z.armatum
DOI: 10.6084/m9.figshare.13378946.v3
title: Warming causes differential seedling mortalities in tropical tree species

description: Amplicon sequencing data of soil fungi for the warming effect on plant-soil feedback in a tropical montane rain forest.
DOI: 10.6084/m9.figshare.28687154.v1
title: <b>Supplementary Data 3</b>. DESeq2 Median Ratio normalization for 165 differentially expressed genes in guts of <i>A. gambiae</i> female mosquito post dietary L-DOPA.

description: DESeq2 Median Ratio normalization for 165 differentially expressed genes in guts of <i>A. gambiae</i> female mosquito post dietary L-DOPA.
DOI: 10.6084/m9.figshare.12765968.v1
title: Franco-Cantabrian dataset

description: 190 Franco-Cantabrian samples genotyped with Affymetrix Axiom® Genome-Wide Human Origins 1 array.
DOI: 10.60893/figshare.jcp.27724563.v1
title: Supplemental Material

description: Calculated Results
DOI: 10.6084/m9.figshare.17031746.v1
title: MAGs

description: The file contains the contigs assembled into MAGs
DOI: 10.6084/m9.figshare.9034145.v2
title: Sequences identical to rfam eukaryotic group II introns

description: Sequences identical to rfam eukaryotic group II introns
DOI: 10.6084/m9.figshare.14872140.v1
title: Alliance Capabilities Measurement items and framework.pdf

description: This document contains the measurement items for alliance capabilities in the context of university-industry R&D.<br><br>
DOI: 10.6084/m9.figshare.14877123.v1
title: Summary of Papers Reviewed for Business Models for Local Authority Smart City.xlsx

description: Summary of papers reviewed for systematic literature review on smart city business models for local authorities, and applicability of frugal innovation
DOI: 10.6084/m9.figshare.21861756.v1
title: final data-tweet.csv

description: mining tweets data from API
DOI: 10.6084/m9.figshare.24412597.v1
title: 无标题项目

description: 使用随机、自控的交叉实验设计。从武汉体育学院招募70名健美运动员，在三种不同的加压模式下进行卧推训练，采用相同的运动干预（运动强度为1%3RM，每组8组3次重复，持续时间为2组，间隔1分钟插行间隔）： T100条件（低压、高阻力模式）： 连续加压模式加压，闭塞压力为2 mmHg;T180（高压，高阻力）：在运动期间进行间歇间隔闭塞压力为&lt;&gt; mmHg;和C（非加压的常规卧推训练 非加压 。使用Delsys Trigno无线表面肌电图记录卧推时目标肌肉（胸大肌、三角肌和三头肌）的表面肌电信号，并在卧推后立即测试主观疲劳。
DOI: 10.6084/m9.figshare.24151317.v1
title: Additional file 3 of Identification and verification of plasma protein biomarkers that accurately identify an ectopic pregnancy

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.13134884.v1
title: Flow phantom simulations (spatial resol 2mm3)

description: VTK temporal phase images in the cycle of the 4D flow MRI phantom's simulation. SMRI velocity field and low-resolution CFD velocity field correspond to 'velocity' and 'U_LR' arrays, respectively. The simulated 4D flow MRI sequence is also included.
DOI: 10.6084/m9.figshare.27193395.v1
title: Leuconeurospora bharatiensis aligned sequences and concatenated tree ITS and LSU tree

description: <i>Leuconeurospora bharatiensis</i> was isolated from accumulated snow sediment from Larsemann Hills, near the Indian research station Bharati, Antarctica.Based on the phylogenetic analyses of the ITS region and D1/D2 domain of the 28S nrRNA gene (LSU), a new species in the genus Leuconeurospora is proposed and positioned in the clade with L. pulcherrima and L. capsici. It represents the fourth species in the genus Leuconeurospora. The LSU sequence of L. polypaeciloides was unavailable for comparison, hence it has been excluded from the phylogenetic analysis.<br>
DOI: 10.6084/m9.figshare.4757989.v5
title: How much money was received in payment of library fines per UK university during academic year 2015/2016?

description: Most university libraries in the UK charge their users fines for overdue and/or recalled library items. To find out how much money each university received in the academic year 2015/16, freedom of information (FOI) requests were sent to 148 UK universities. These FOI requests were made during February/March of 2017 using the website "www.whatdotheyknow.com". <br><br>The results are collated in this spreadsheet,which includes links to the URLs that contain the full FOI correspondence in each case. Some institutions were also able to provide a breakdown of payment by country of origin (e.g. France, Italy) as well as type of user (e.g. undergraduate/postgraduate). Those institutions that were able to provide this information are indicated in the spreadsheet. <br><br>The spreadsheet is organised in descending order, with those institutions receiving the most amount of money at the top of the spreadsheet, with those receiving the least amount of money at the bottom.<br><br>The total amount of money received was £4,808,494.20<br>The text of the FOI request made in each case is as follows:<br><i><br><br>"I am writing to ask about library fines during the academic year 2015/2016. For the time period starting from the first day of term, covering the next 364 days (e.g. one full year), please provide:<br><br>1. The total amount of money the library received from the payment of overdue items. Exclude costs of replacing lost books - this request solely relates to the cost of books that are returned later than their due date.</i><i><br></i><i>2. Information about where this money then goes (is it absorbed into a specific library budget for example? If so what one?)</i><i><br></i><i>3. If possible, from the figure provided in 1, break this down by </i><i><br></i><i>a) category of user paying fine (e.g. undergraduate, postgraduate, staff)</i><i>b) country of origin of user paying fine (e.g. France, Italy, US). If only broader categories are possible e.g. "EU", "non-EU" then please provide this instead. "</i><br>Each response includes a link to the full and original FOI result. Any errors in transcription are accidental; please get in touch if you spot any. <br><br><br><br>
DOI: 10.6084/m9.figshare.11910774.v1
title: Chakraborty Table S1.xlsx

description: Tn5 Salmonella mutants differentially selected after 2h of treatment with 2.5 mM peroxide
DOI: 10.6084/m9.figshare.7927394.v1
title: gVCF_HG02140

description: 1000 Genomes gVCF mapped to hs37d5 for HG02140. Complete collection: https://doi.org/10.6084/m9.figshare.c.4414307
DOI: 10.15468/dl.pzdz3v
title: Occurrence Download

description: A dataset containing 2030 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Observation, Human Observation, Machine Observation, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Eristalis intricaria (Linnaeus, 1758)"
 ]
}

 The dataset includes 2030 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009603-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.20795725.v1
title: data for repository(PONE-D-22-16146).xlsx

description: Data from an online-questionnaire survey on attitudes toward COVID-19 vaccination administered to university students at the Hachioji campus, Teikyo University
DOI: 10.35092/yhjc.11349710.v1
title: Datasets to reproduce Figures 1-3 and associated Extended Data Figures

description: The CHI, HIPC-I (Stanford and Yale), Emory, Yellow fever and SLE data sets used in the study. Unpack this file to your working directory and keep the directory structure. The R codes can be downloaded from github (https://github.com/kotliary/baseline) into the R directory.<br>This item is a part of the collection: https://doi.org/10.35092/yhjc.c.4753772<br><b>If you use our data (including CITE-seq data) or code for your work please cite the following publication</b>:Kotliarov, Y., Sparks, R. et al. Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. DOI: https://doi.org/10.1038/s41591-020-0769-8 (2020)<br><b>Abstract</b><br>Responses to vaccination and to diseases vary widely across individuals, which may be partly due to baseline immune variations. Identifying such baseline predictors and their biological basis are of broad interest given their potential importance for cancer immunotherapy, disease outcomes, vaccination and infection responses. Here we uncover baseline blood transcriptional signatures predictive of antibody responses to both influenza and yellow fever vaccinations in healthy subjects. These same signatures evaluated at clinical quiescence are correlated with disease activity in systemic lupus erythematosus patients with plasmablast-associated flares. CITE-seq profiling of 82 surface proteins and transcriptomes of 53,201 single cells from healthy high and low influenza-vaccination responders revealed that our signatures reflect the extent of activation in a plasmacytoid dendritic cell—Type I IFN—T/B lymphocyte network. Our findings raise the prospect that modulating such immune baseline states may improve vaccine responsiveness and mitigate undesirable autoimmune disease activities.<br><br><b>General contact</b>: John Tsang (john.tsang@nih.gov)<b>Questions about software/code</b>: Yuri Kotliarov (yuri.kotliarov@nih.gov)<br>
DOI: 10.6084/m9.figshare.28891238.v1
title: <b>PS4GR-CN:</b><b> </b><b>A dataset of plant species for green roofs in China based on a large language model</b>

description: As urbanization accelerates, many negative ecological impacts become more prominent. Green roofs offer a sustainable solution to mitigate the urban heat island effect and reduce the carbon footprint. However, the lack of plant species datasets for green roofs in China limits research and practice. Therefore, this study constructs a diversified dataset of plant species for green roofs in China using China National Knowledge Infrastructure (CNKI) and Web of Science (WoS) as data sources. The dataset is generated by integrating the Kimi large language model(Kimi LLM) API with knowledge graph technology, resulting in 2,248 plant records. It includes a statistical CSV file of plant details, a CSV file of species combinations, a CSV file linking plant combinations to cities, and original plant data from papers. The accuracy and efficiency of the dataset in acquiring plant species are validated through technical experiments. This dataset applies to plant selection for green roofs, facilitating in-depth research and broader applications in urban sustainability.<br>
DOI: 10.6084/m9.figshare.5539744.v1
title: Supplementary Material for: Aberrant Expression of Long Non-Coding RNAs in Newly Diagnosed Type 2 Diabetes Indicates Potential Roles in Chronic Inflammation and Insulin Resistance

description: <b><i>Background/Aims:</i></b> Long non-coding RNAs (lncRNAs) have emerged as key players in several biological processes and complex diseases. The risk of type 2 diabetes (T2D) is determined by a combination of environmental factors and genetic susceptibility. The purpose of this study was to identify aberrant lncRNAs involved in T2D pathogenesis. <b><i>Methods:</i></b> Microarray analysis was performed using whole blood samples from patients newly diagnosed with T2D and healthy controls. Pathway and Gene Ontology (GO) analyses were utilized to annotate the target genes. Coding non-coding co-expression (CNC) analysis was performed to construct a co-expression network. <b><i>Results:</i></b> We found 55 lncRNAs and 202 mRNAs were differentially expressed in the T2D group compared to the healthy control group. Pathway and GO analyses demonstrated that dysregulated mRNAs were mainly associated with immune regulation, inflammation, and insulin resistance, whereas CNC analysis identified 10 pairs of co-expressed lncRNA-mRNAs in our patient cohort (R &gt; 0.99). Furthermore, expression of the top three upregulated lncRNAs in the T2D group was correlated with measures of glycometabolism (<i>P</i> &lt; 0.05). <b><i>Conclusion:</i></b> This study identified aberrantly expressed lncRNAs and mRNAs in Han Chinese patients with T2D, and demonstrated that dysregulated lncRNAs may have roles in T2D pathogenesis through regulation of inflammation and insulin resistance.
DOI: 10.6084/m9.figshare.27897243.v1
title: Datos-final.xlsx

description: Data from article: "Vallejos-Torres, G., Gaona-Jimenez, N., Pichis-García, R., Ordoñez, L., García-Gonzales, P., Quinteros, A., Lozano, A., Saavedra-Ramírez, J., Tuesta-Hidalgo, J.C., Reategui, K., Macedo-Córdova, W., Baselly Villanueva, J.R., Marín, C. 2024. Carbon reserves in coffee agroforestry in the Peruvian Amazon. Frontiers in Plant Science."
DOI: 10.17866/rd.salford.22133411.v1
title: DroneNoise Database

description: <strong>DroneNoise Project Founded by EPSRC.</strong> Authors: Carlos Ramos-Romero, Nathan Green, César Asensio and Antonio J Torija Martinez <br> The database was constructed from sUAS noise recorded under field conditions during the measurement campaign in Edzell, Scotland, on 17 August 2022. The first part of the data includes only results from overflight operations. <br>
DOI: 10.26188/24314689.v2
title: Malaysian dengue data

description: Dengue incidence data in release sites for publication
DOI: 10.4121/20485740.v1
title: Dataset underlying the paper: Barriers for implementing large household appliance e-waste reverse logistics in China: a certified disassembler’s perspective

description: Data calculation. Elaborate steps toward a Grey-DEMATAL approach.
DOI: 10.6084/m9.figshare.11816430.v1
title: Data from: Marine cleaning mutualism defies standard logic of supply and demand

description: Market effects in a cleaner fish system<br>
DOI: 10.6084/m9.figshare.25425325.v2
title: Supplementary Material for: Epidemiology, characteristics of disease and unmet needs of patients with generalized pustular psoriasis: a large Italian Delphi consensus

description: Introduction: Generalized pustular psoriasis (GPP) is a rare and chronic, debilitating skin condition characterised, in its acute flare phase, by clinically severe and potentially life-threatening systemic manifestations. Data on GPP are still scanty, particularly in Europe and at a national level. To provide expert indications on several disease-related and patient-related aspects of GPP, with specific focus to the Italian context.

Methods: We conducted an iterative eDelphi study following the recommended criteria for reporting methods and results. After a thorough bibliographic review aimed to identify unknown or controversial issues in GPP, the following areas were investigated through a few specific questions/statements for each area: 1) disease epidemiology; 2) disease characteristics, with specific interest towards GPP flares; 3) diagnosis and diagnostic delay; 4) GPP treatment; 5) GPP patient journey and use of healthcare resources in Italy; 6) unmet needs and quality of life. An Executive Board of 9 principal investigators revised and approved the topics to be examined and overviewed the whole project. A total of 35 experts from different Italian areas, including 34 board-certified Italian dermatologists and one representative of patients’ associations, took part in the study.

Results: A high agreement in responses from Italian experts emerged during two eDelphi iterations on - among several other aspects - GPP prevalence and incidence in Italy, use of European Rare and Severe Psoriasis Expert Network diagnostic criteria, flare frequency and duration, best diagnostic and care pathway, and main unmet needs of Italian patients. On the other hand, a broad spectrum of treatments (of different drug classes) was reported both in the acute and chronic phases of GPP, and no consensus on the issue was thus achieved.

Conclusions: Consensus findings from this Delphi study of GPP experts may be useful to fill gaps of knowledge and improve awareness of this rare disease, as well as to help clinical and public health management of GPP in Italy.