cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19540389.v1
title: Integrative analysis of TRPV family to prognosis and immune infiltration in renal clear cell carcinoma

description: The transient receptor potential vanilloid (TRPV) family has been preliminarily discovered to play an important role in various cancers, including clear cell renal cell carcinoma (ccRCC), which is closely associated with immune infiltration. However, the expression and prognosis of TRPV family and tumor-infiltrating immune cells in ccRCC are obscure. This study aimed to explore the prognostic and therapeutic value of the TRPV family expression in ccRCC from the perspective of bioinformatics. We analyzed the transcriptome and clinical data of kidney renal clear cell carcinoma (KIRC) from The Cancer Genome Atlas (TCGA) database. A clustering analysis and immune infiltration analysis were conducted to investigate the influence of the TRPV family genes on ccRCC. Our study found that the TRPV family is an excellent prognostic stratification for ccRCC. Among them, TRPV3 is the most significant prognostic marker of ccRCC. In addition, we performed a drug sensitivity analysis to identify the drugs with the strongest association with TRPV3. As a result, the TRPV family, particularly TRPV3, can act as a prognostic biomarker in ccRCC to determine prognosis and levels of immune infiltration.
DOI: 10.6084/m9.figshare.20064346.v1
title: Additional file 3 of GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

description: Additional file 3. GenErode pipeline report for analyses of the test dataset based on the Sumatran rhinoceros reference.
DOI: 10.17632/5ytp5mwdvb.1
title: CLINICAL AND HISTOLOGICAL ANALYSIS OF THE EFFECT OF OZONE OIL AND LASER PHOTOBIOMODULATION ON THE TISSUE REPAIR OF TRAUMATIC ULCER ON THE RAT ORAL MUCOSA

description: Tissue repair is a complex event that begins at the time of injury, resulting in an attempt to restore fisiological balance. In an attempt to find alternatives that accelerate healing and consider these promising therapies for modulating this process, as well as to address the identified gap in the current literature regarding the combined use of LPBM with ozonized oil during tissue repair, no studies have addressed the combination of these agents. Thus, the aim of this study was to evaluate the effect of ozonized oil, with or without LPBM, on the healing of traumatic ulcers on the dorsal surface of the rat tongue. A total of 60 male Wistar rats underwent tongue ulceration on the dorsal surface using a six-mm diameter punch. Animals were divided into four experimental groups: control, LPBM, Ozonized oil, and LPBM + Ozonized oil. Euthanasia was performed on days three, seven, and 14 after surgery. Clinical analysis of the wound size and histomorphological evaluation using hematoxylin and eosin and Sirius red staining were conducted to identify edema, inflammatory infiltrates, fibroblastic cellularity, reepithelialization, and collagen characterization. Descriptive and exploratory analyses were performed and inferential statistics were calculated using Fisher's exact tests. Analyses were performed using R, with a significance level of 5%. LPBM and Ozonized oil positively modulated the repair phases clinically (p&lt;0.05) and histologically, showing reepithelialization, fibroblastic population, and thick collagen fiber deposition from the 3rd day of the experiment. LPBM + Ozonized oil exhibited a significant difference from control in the clinical parameters (p&lt;0.05), but did not demonstrate superiority in histomorphological terms of tissue repair. Isolated use of LPBM and Ozonized oil improved tissue repair in rat tongues.
DOI: 10.6084/m9.figshare.6963395.v1
title: Additional file 4: of Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data

description: Table S4. DS kinase genes detected by both DSGseq and DEXseq. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.25163312
title: <b>Lateef_my-repo</b>

description: The suitability of laterite for engineering constructions depends largely on the extensive examination of its compaction and strength characteristics but this is lacking these days due to their cumbersome, costly and time-consuming laboratory tests unlike index properties with cheap and simple tests. To overcome this limitation, artificial neural network (ANN), Gaussian process regression (GPR), and multilinear regression (MLR)models have been developed in this study to predict laterite compaction and strength characteristics from the index properties. To achieve this, laboratory tests were conducted on three hundred samples taken from thirty different laterite deposits within southwest, Nigeria and the experimental dataset obtained was randomly divided into modeling dataset comprising two hundred and forty data points which were used to develop the models and trialing dataset with sixty data points which were used to compare and validate the developed models. Specific gravity (SG), linear shrinkage (LS), liquid limit (LL), plasticity index (PI), and fines content (FC) were selected as the models’ predictors while maximum dry density (MDD), optimum moisture content (OMC) and unconfined compressive strength (UCS) are the targeted output. The developed models’ performances were appraised using various prediction performance metrics.
DOI: 10.6084/m9.figshare.25163312.v5
title: <b>Lateef my-repo</b>

description: The suitability of laterite for engineering constructions depends largely on the extensive examination of its compaction and strength characteristics but this is lacking these days due to their cumbersome, costly and time-consuming laboratory tests unlike index properties with cheap and simple tests. To overcome this limitation, artificial neural network (ANN), Gaussian process regression (GPR), and multilinear regression (MLR)models have been developed in this study to predict laterite compaction and strength characteristics from the index properties. To achieve this, laboratory tests were conducted on three hundred samples taken from thirty different laterite deposits within southwest, Nigeria and the experimental dataset obtained was randomly divided into modeling dataset comprising two hundred and forty data points which were used to develop the models and trialing dataset with sixty data points which were used to compare and validate the developed models. Specific gravity (SG), linear shrinkage (LS), liquid limit (LL), plasticity index (PI), and fines content (FC) were selected as the models’ predictors while maximum dry density (MDD), optimum moisture content (OMC) and unconfined compressive strength (UCS) are the targeted output. The developed models’ performances were appraised using various prediction performance metrics.
DOI: 10.6084/m9.figshare.20064160
title: Additional file 10 of The transcription factor LaMYC4 from lavender regulates volatile Terpenoid biosynthesis

description: Additional file 10: Table S1. Volatile compounds from control or treated with methyl jasmonate (MeJA) of lavender.
DOI: 10.6084/m9.figshare.20064169.v1
title: Additional file 13 of The transcription factor LaMYC4 from lavender regulates volatile Terpenoid biosynthesis

description: Additional file 13: Table S4. Sequences of HMGR, FPPS, DXS, DXR, GPPS and TPS21.
DOI: 10.6084/m9.figshare.20064166
title: Additional file 12 of The transcription factor LaMYC4 from lavender regulates volatile Terpenoid biosynthesis

description: Additional file 12: Table S3. Promoter sequence of LaMYC4 and Prediction element.
DOI: 10.6084/m9.figshare.6957452.v1
title: Plant Stature Related receptor-like Kinanse2 (PSRK2) acts as a factor that determines stem elongation toward gibberellins response in rice

description: Gibberellins (GAs) are a family of plant hormones that are important to multiple aspects of plant growth and development, especially stem elongation. A <i>PSRK2</i> was obtained through screening and identifying RLK dominant negative mutants. Phenotype of the loss-of-function mutants, <i>psrk2-DN</i> and <i>psrk2-RNAi</i>, showed that <i>PSRK2</i> could influence the length of the uppermost and fourth internodes, indicating that PSRK2 might regulate cell division in the intercalary meristems and/or cell elongation in the internodes. Moreover, the expression pattern showed that <i>PSRK2</i> was strongly expressed in the joined-nodes after the start-up of reproductive growth, but undetectable in leaves. <i>PSRK2</i> expression was also found to be induced by GA<sub>3</sub>, and PSRK2 was involved in GA signaling in cereal aleurone cells, and PSRK2 influence the relative length of the second leaf sheaths in seedling stage. These results indicate PSRK2 is a component of GA signaling pathway that controls stem elongation by negatively regulating GA responses. <b>Abbreviations</b>: <i>Os: Oryza sativa; At: Arabidopsis thaliana</i>; RNAi: RNA interfere; DN: Dominate Negative; SMART: Simple Modular Architecture Research Tool; Uni : Uniconazol; PSRK2: Plant Stature Related receptor-like Kinase 2; RLK: Receptor-like Kinase; GA: Gibberellin; IAA: indole-3-acetic acid; BL: Brassinosteroid PSRK2 could influence the length of internodes in rice, indicating that PSRK2 might regulate cell division and/or cell elongation in GA signaling pathway
DOI: 10.21227/8edj-fk63
title: Dataset used in toward ground-truth optical coherence tomography

description: 3D datasets used in Toward-ground-truth optical coherence tomography. Guangming Ni et al., "Toward ground-truth optical coherence tomography via three-dimensional unsupervised deep learning processing and data", 2023 There are two dataset: OCT-R1 and OCT-R2. OCT-R1 contains three-dimensional (3D) data collected from 41 human eyes using a BM-400K BMizar (Topi Ltd.) OCT scanner at Sichuan Provincial People's Hospital. To enhance the diversity of the data, we performed scans over two different ranges. OCT-R2 contains five 3D images of the human retina acquired using Spectralis OCT scanner (Heidelberg Engineering Inc.). Copyright @ UESTC (University of Electronic Science and Technology of China). For more information, please contact Dr. Guangming Ni (email: guangmingni@uestc.edu.cn).
DOI: 10.6084/m9.figshare.6963665
title: MOESM3 of Comparative 1D Blue-Native electrophoresis analysis of Plasmodium falciparum and human proteins associated with cytoadherence

description: Additional file 3. List of human proteins identified in each band for the 3D7-HUVEC and ItG-HUVEC samples. Dark and light blue shaded IDs in the ItG column show common bands also seen in relevant 3D7 bands removed by manual curation. Yellow highlighted sequence identifiers represent bands identified by the computer pipeline as being unique to the ItG-HUVEC sample when compared with the corresponding band and one band either side. Numbers of peptides identified for each protein are indicated.
DOI: 10.6084/m9.figshare.20064361.v1
title: Additional file 3 of Postoperative hyperprogression disease of pancreatic ductal adenocarcinoma after curative resection: a retrospective cohort study

description: Additional file 3: Supplementary Fig. 1. Dot-box plots of TMB (A), MATH(B) and CNI(C) in PO-HPD and ER + LR groups. TMB: tumor mutational burden; MATH: mutant allele tumor heterogeneity; CNI: copy number instability; SR-HPD: surgery-related hyper-progression disease; ER: early recurrence; LR: late recurrence.
DOI: 10.5281/zenodo.10649511
title: АҲОЛИНИ ИШ БИЛАН БАНДЛИГИ НАЗАРИЯЛАРИ ВА УЛАРНИ АМАЛДА ҚЎЛЛАНИЛИШИ
DOI: 10.5281/zenodo.10649512
title: АҲОЛИНИ ИШ БИЛАН БАНДЛИГИ НАЗАРИЯЛАРИ ВА УЛАРНИ АМАЛДА ҚЎЛЛАНИЛИШИ
DOI: 10.6084/m9.figshare.20064361
title: Additional file 3 of Postoperative hyperprogression disease of pancreatic ductal adenocarcinoma after curative resection: a retrospective cohort study

description: Additional file 3: Supplementary Fig. 1. Dot-box plots of TMB (A), MATH(B) and CNI(C) in PO-HPD and ER + LR groups. TMB: tumor mutational burden; MATH: mutant allele tumor heterogeneity; CNI: copy number instability; SR-HPD: surgery-related hyper-progression disease; ER: early recurrence; LR: late recurrence.
DOI: 10.6084/m9.figshare.6957452
title: Plant Stature Related receptor-like Kinanse2 (PSRK2) acts as a factor that determines stem elongation toward gibberellins response in rice

description: Gibberellins (GAs) are a family of plant hormones that are important to multiple aspects of plant growth and development, especially stem elongation. A <i>PSRK2</i> was obtained through screening and identifying RLK dominant negative mutants. Phenotype of the loss-of-function mutants, <i>psrk2-DN</i> and <i>psrk2-RNAi</i>, showed that <i>PSRK2</i> could influence the length of the uppermost and fourth internodes, indicating that PSRK2 might regulate cell division in the intercalary meristems and/or cell elongation in the internodes. Moreover, the expression pattern showed that <i>PSRK2</i> was strongly expressed in the joined-nodes after the start-up of reproductive growth, but undetectable in leaves. <i>PSRK2</i> expression was also found to be induced by GA<sub>3</sub>, and PSRK2 was involved in GA signaling in cereal aleurone cells, and PSRK2 influence the relative length of the second leaf sheaths in seedling stage. These results indicate PSRK2 is a component of GA signaling pathway that controls stem elongation by negatively regulating GA responses. <b>Abbreviations</b>: <i>Os: Oryza sativa; At: Arabidopsis thaliana</i>; RNAi: RNA interfere; DN: Dominate Negative; SMART: Simple Modular Architecture Research Tool; Uni : Uniconazol; PSRK2: Plant Stature Related receptor-like Kinase 2; RLK: Receptor-like Kinase; GA: Gibberellin; IAA: indole-3-acetic acid; BL: Brassinosteroid PSRK2 could influence the length of internodes in rice, indicating that PSRK2 might regulate cell division and/or cell elongation in GA signaling pathway
DOI: 10.5281/zenodo.10649469
title: HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology - Singularity Container

description: This repository contains an appropriate singularity container for training and inference of HoVer-NeXt from the publication:

HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology

(Under review at MIDL2024)

more info at https://github.com/digitalpathologybern/hover_next_inference
DOI: 10.5281/zenodo.10649470
title: HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology - Singularity Container

description: This repository contains an appropriate singularity container for training and inference of HoVer-NeXt from the publication:

HoVer-NeXt: A Fast Nuclei Segmentation and Classification Pipeline for Next Generation Histopathology

(Under review at MIDL2024)

more info at https://github.com/digitalpathologybern/hover_next_inference
DOI: 10.6084/m9.figshare.6963929.v1
title: Additional file 6: of Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period

description: The expression file of novel DELs in the dry and lactation periods. (XLSX 230 kb)
DOI: 10.6084/m9.figshare.6963950
title: Additional file 8: of Transcriptome sequencing to detect the potential role of long non-coding RNAs in bovine mammary gland during the dry and lactation period

description: Stage specific expressed lncRNAs in the dry or lactation periods. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.6963998
title: Additional file 2: of Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development

description: Table S2. Statistics of circRNAs in plant leaves. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6964022
title: Additional file 5: of Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development

description: Table S5. CeRNA clusters in global ceRNA network. (XLSX 33 kb)
DOI: 10.6084/m9.figshare.14828346
title: Supporting Information for "Petrogenesis of Himalayan leucogranites: perspective from a combined elemental and Fe-Sr-Nd isotope study"

description: Supplementary files incluing two figures and seven tables.
DOI: 10.5281/zenodo.10221411
title: Replication package for the paper "A configurational approach to job quality analysis: forms of inequalities at work in Europe"

description: The following replication package is appended to the article Étienne Penissat, Cécile Rodrigues & Alexis Spire (2024) "A configurational approach to job quality analysis: forms of inequalities at work in Europe", European Societies, DOI: 10.1080/14616696.2024.2312950

The scripts to be run in the following order are:

- 1_Penissat_EuropeanSocieties_2023_DataPreparation.R : Recoding, formatting and scope of data used

- 2_Penissat_EuropeanSocieties_2023_DataAnalysis.Rmd : Analysis and statistical results

The data used in the article comes from the EWCS (2015) - European Working Condition Survey - provided by the European foundation for the improvement of living and working conditions. The data is not available on free access but can be obtained on request. Information on the survey wave used can be found here : https://www.eurofound.europa.eu/surveys/european-working-conditions-surveys/sixth-european-working-conditions-survey-2015

- In the first "1_Penissat_EuropeanSocieties_DataPreparation.R" script, the file containing data named "ewcs_1991-2015.dta" is used. The file called "eseg2_trad.csv" contains english labels for the nomenclature of professional positions ESeG. As "ewcs_1991-2015.dta" is not freely available, it is not included in the package and "eseg2_trad.csv" is located in the "data" folder.

- The first script creates the data file "Penissat_EuropeanSocieties_2023_EWCS15_cleanData.rds" in the "results" folder.

- The second script called "2_Penissat_EuropeanSocieties_DataAnalysis.Rmd" uses the "Penissat_EuropeanSocieties_2023_EWCS15_cleanData.rds" data file and produces the "2_Penissat_EuropeanSocieties_DataAnalysis.html" file containing all code and results presented in the article.
DOI: 10.5281/zenodo.10221412
title: Replication package for the paper "A configurational approach to job quality analysis: forms of inequalities at work in Europe"

description: The following replication package is appended to the article Étienne Penissat, Cécile Rodrigues & Alexis Spire (2024) "A configurational approach to job quality analysis: forms of inequalities at work in Europe", European Societies, DOI: 10.1080/14616696.2024.2312950

The scripts to be run in the following order are:

- 1_Penissat_EuropeanSocieties_2023_DataPreparation.R : Recoding, formatting and scope of data used

- 2_Penissat_EuropeanSocieties_2023_DataAnalysis.Rmd : Analysis and statistical results

The data used in the article comes from the EWCS (2015) - European Working Condition Survey - provided by the European foundation for the improvement of living and working conditions. The data is not available on free access but can be obtained on request. Information on the survey wave used can be found here : https://www.eurofound.europa.eu/surveys/european-working-conditions-surveys/sixth-european-working-conditions-survey-2015

- In the first "1_Penissat_EuropeanSocieties_DataPreparation.R" script, the file containing data named "ewcs_1991-2015.dta" is used. The file called "eseg2_trad.csv" contains english labels for the nomenclature of professional positions ESeG. As "ewcs_1991-2015.dta" is not freely available, it is not included in the package and "eseg2_trad.csv" is located in the "data" folder.

- The first script creates the data file "Penissat_EuropeanSocieties_2023_EWCS15_cleanData.rds" in the "results" folder.

- The second script called "2_Penissat_EuropeanSocieties_DataAnalysis.Rmd" uses the "Penissat_EuropeanSocieties_2023_EWCS15_cleanData.rds" data file and produces the "2_Penissat_EuropeanSocieties_DataAnalysis.html" file containing all code and results presented in the article.
DOI: 10.6084/m9.figshare.20064659
title: Additional file 1 of Suppression of NF-κB signaling by ECN in an arthritic model of inflammation

description: Additional file 1.
DOI: 10.15129/03c8db41-7031-4ca9-99bc-2a0f5ed982fa
title: Data for "Theoretical and Numerical Studies of Magnetic Field-Induced Wakefield Radiation and Proton Beam Synchrotron Radiation in the AWAKE Experiment"

description: Simulation input scripts
DOI: 10.24403/jp.1329171
title: Weymar, H.: Buch der Kreuzblütler. - Leipzig ; Radebeul : Neumann Verlag, 1988 / [rezensiert von] H. Manitz
DOI: 10.6084/m9.figshare.16909626.v1
title: Additional file 1 of Norovirus GII.2[P16] strain in Shenzhen, China: a retrospective study

description: Additional file 1: Table S1. Primes used in this study. Table S2. Amino acid mutations of full-length VP1 sequences of the NoV GII.2. Reference sequences: Reference sequences used in this study.
DOI: 10.24403/jp.1329174
title: Haussknecht’s malakologische Aufsammlungen / Dietrich von Knorre
DOI: 10.5517/ccdc.csd.cc2fhds4
title: CCDC 2249136: Experimental Crystal Structure Determination

description: Related Article: sahaya infant lasalle B, Muthu Senthil pandian, K. Anitha, P. Ramasamy|2023|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.8006303.v1
title: The patent antimicrobial peptides of DRAMP database

description: 'DRAMP_patent_amps.xlsx' is the patent dataset of the DRAMP database, containing as much as possible of patent antimicrobial peptides. Patent dataset were annotated with sequence, length, name, source, activity, Patent ID, patent type, publication date, also publication as, title, abstract.
DOI: 10.6084/m9.figshare.8006309.v1
title: The general antimicrobial peptides of DRAMP database

description: 'DRAMP_general_amps.xlsx' contains all natural and synthetic antimicrobial peptides in the DRAMP database. Each entry of General dataset contains following major fields: general field including peptide sequence, length, name, Swiss-prot ID, family, gene, source; activity field containing biological activity, target organisms with MIC values, binding target; structure field including structure type, description, PDB ID; physicochemical field such as Boman index, mass and half-life; literature field including Pubmed ID, journal, author, title; comment field describing detailed biological function of peptides.
DOI: 10.34740/kaggle/dsv/7611061
title: Global Genomic Neurofibromatosis Neoplasia
DOI: 10.34740/kaggle/dsv/7611070
title: UNET Lung Segmentation Weights for Chest X Rays
DOI: 10.6084/m9.figshare.11158637
title: MOESM1 of Risk of stroke-associated pneumonia during hospitalization: predictive ability of combined A2DS2 score and hyperglycemia

description: Additional file 1. Supplementary material
DOI: 10.6084/m9.figshare.11158637.v1
title: MOESM1 of Risk of stroke-associated pneumonia during hospitalization: predictive ability of combined A2DS2 score and hyperglycemia

description: Additional file 1. Supplementary material
DOI: 10.6084/m9.figshare.8006303
title: The patent antimicrobial peptides of DRAMP database

description: 'DRAMP_patent_amps.xlsx' is the patent dataset of the DRAMP database, containing as much as possible of patent antimicrobial peptides. Patent dataset were annotated with sequence, length, name, source, activity, Patent ID, patent type, publication date, also publication as, title, abstract.
DOI: 10.6084/m9.figshare.8006306
title: The clinical antimicrobial peptides of DRAMP database

description: 'DRAMP_clinical_amps.xlsx. is the antimicrobial peptide dataset involved in clinical research. Data in this dataset were organized as sequence, name, description, activity, medical use, stage of development, comments, company and reference. It is worthy to note that some clinical peptides whose amino acid sequences are absent were also included in this dataset as we don’t want to lose any clinical information.