cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17702978.v1
title: New advances in quantitative proteomics research and current applications in asthma

description: Asthma is the most common chronic respiratory disease and has been declared a global public health problem by the World Health Organization. Due to the high heterogeneity and complexity, asthma can be classified into different ‘phenotypes’ and it is still difficult to assess the phenotypes and stages of asthma by traditional methods. In recent years, mass spectrometry-based proteomics studies have made significant progress in sensitivity and accuracy of protein identification and quantitation, and are able to obtain differences in protein expression across samples, which provides new insights into the mechanisms and classification of asthma. In this article, we summarize research strategies in quantitative proteomics, including labeled, label-free and targeted quantification, and highlight the advantages and disadvantages of each. In addition, new applications of quantitative proteomics and the current status of research in asthma have also been discussed. In this study, online resources such as PubMed and Google Scholar were used for literature retrieval. The application of quantitative proteomics in asthma has an important role in identifying asthma subphenotypes, revealing potential pathogenesis and therapeutic targets. But the proteomic studies on asthma are not sufficient, as most of them are in the phase of biomarker discovery.
DOI: 10.6084/m9.figshare.15081552
title: Table S2.xlsx

description: information about the content and structure of 259 metabolites found in ‘BTSC’ and ‘BTZY’ varieties
DOI: 10.6084/m9.figshare.20324439
title: 1-km gridded temperature sensitivity of soil respriation (Q10) accross China

description:   
This is a soil respiration temperature sensitivity (Q10) product (unitless) from 1994 to 2016 (Q10.mask.nc) based on field observations and environmental variables using random forest across China. The Q10 product has a spatial resolution of 1 km and a temporal resolution of one year. 
To save the space, Q10 product is compressed to a zip file. It is easy to unzip the product following https://www.wikihow.com/Unzip-a-File.  
The files with ".R" mean the R code used to produce China Q10 and further analysis, e.g. trend analysis, attribution analysis.
“Q10_dat.csv” is the dataset of field observations of Q10 in China terrestrial ecosystems, which were collected from published literatures.
DOI: 10.5281/zenodo.8359788
title: Supplementary material - Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells

description: Supplementary material containing the data used in the manuscript "Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells"
description: This research was funded by the European Union's Horizon 2020 research and innovation program under grant agreement No. 101016923 and by NIH grant P41EB015871 and UG3CA275687.
DOI: 10.5281/zenodo.8359789
title: Supplementary material - Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells

description: Supplementary material containing the data used in the manuscript "Optical Diffraction Tomography and Raman Confocal Microscopy for the Investigation of Vacuoles Associated with Cancer Senescent Engulfing Cells"
description: This research was funded by the European Union's Horizon 2020 research and innovation program under grant agreement No. 101016923 and by NIH grant P41EB015871 and UG3CA275687.
DOI: 10.6084/m9.figshare.17704792
title: Gene mining to discover pumpkin response genes to gummy stem blight infection caused by <i>Stagonosporopsis cucurbitacearum</i>

description: Pumpkin is one of the region’s main cashcrops in northeast China cultivated for its edible seed and sarcocarp. Gummy stem blight (GSB), caused by the main pathogenic fungus of <i>Stagonosporopsis cucurbitacearum</i> (Sc.) which was identified in our previous study, has hampered pumpkin industry development with the affection of its reduced biological yield and edible quality. To clear the plant immune response mechanisms against Sc. infection, RNA-seq technology was employed to sequence pumpkin leaf transcriptome, the total number of distinct differentially expressed genes (DEGs) between the treatments and control was 2351, 4892, 5285, 4698, and 4213 for 2, 6, 12, 24, and 96 h treatments, respectively. KEGG analysis results revealed 16 distinct significantly up-regulated DEGs associated with MAPK signaling and plant-pathogen interaction pathways that may actively participate in Sc. infection-associated processes, while other five DEGs exhibited significantly altered expression during GSB infection. An apyrase-like gene, Gene3360 (<i>LOC111476496</i>), with significantly different expression levels, was possessing an early-stage primary infection-based function, which was hypothesized an important role in the resistance of pumpkin to Sc. infection. This study further deepens our understanding of the mechanism and mechanism of pumpkin leaf resistance to fungal infection.
DOI: 10.6084/m9.figshare.17704792.v1
title: Gene mining to discover pumpkin response genes to gummy stem blight infection caused by <i>Stagonosporopsis cucurbitacearum</i>

description: Pumpkin is one of the region’s main cashcrops in northeast China cultivated for its edible seed and sarcocarp. Gummy stem blight (GSB), caused by the main pathogenic fungus of <i>Stagonosporopsis cucurbitacearum</i> (Sc.) which was identified in our previous study, has hampered pumpkin industry development with the affection of its reduced biological yield and edible quality. To clear the plant immune response mechanisms against Sc. infection, RNA-seq technology was employed to sequence pumpkin leaf transcriptome, the total number of distinct differentially expressed genes (DEGs) between the treatments and control was 2351, 4892, 5285, 4698, and 4213 for 2, 6, 12, 24, and 96 h treatments, respectively. KEGG analysis results revealed 16 distinct significantly up-regulated DEGs associated with MAPK signaling and plant-pathogen interaction pathways that may actively participate in Sc. infection-associated processes, while other five DEGs exhibited significantly altered expression during GSB infection. An apyrase-like gene, Gene3360 (<i>LOC111476496</i>), with significantly different expression levels, was possessing an early-stage primary infection-based function, which was hypothesized an important role in the resistance of pumpkin to Sc. infection. This study further deepens our understanding of the mechanism and mechanism of pumpkin leaf resistance to fungal infection.
DOI: 10.6084/m9.figshare.14559065
title: Additional file 5 of Tributyltin perturbs femoral cortical architecture and polar moment of inertia in rat

description: Additional file 5.
DOI: 10.6084/m9.figshare.14559065.v1
title: Additional file 5 of Tributyltin perturbs femoral cortical architecture and polar moment of inertia in rat

description: Additional file 5.
DOI: 10.34740/kaggle/dsv/7683963
title: AutoXGB
DOI: 10.6084/m9.figshare.25272523
title: Data for "Tailbeat perturbations improve swimming efficiency by reducing the phase lag between body motion and the resulting fluid response"

description: Data for "Tailbeat perturbations improve swimming efficiency by reducing the phase lag between body motion and the resulting fluid response"
DOI: 10.6084/m9.figshare.25272523.v1
title: Data for "Tailbeat perturbations improve swimming efficiency by reducing the phase lag between body motion and the resulting fluid response"

description: Data for "Tailbeat perturbations improve swimming efficiency by reducing the phase lag between body motion and the resulting fluid response"
DOI: 10.34740/kaggle/dsv/7683964
title: OnlineFree
DOI: 10.6084/m9.figshare.25272547
title: Supplementary Material for: Overlap Syndrome of Diffuse Systemic Sclerosis, Sjögren Syndrome and ANCA-associated Renal-limited Vasculitis: Three Entities in One Patient. Case report.

description: Introduction: The presence of three different entities in a single patient is usually of clinical interest and mostly anecdotal. The overlap of systemic sclerosis (SSc), Sjögren syndrome (SS) and ANCA-associated renal-limited vasculitis has been reported only once previously. Case Report: A 61-year-old female was evaluated at consultation with 2 years of symptomatology, presenting cardboard-like skin, sclerodactyly, limited oral opening and dry skin and eyes. She was admitted for progressive renal failure (serum creatinine, 5.5 mg/dL). Her serology work-up showed positive anti-SCL-70, anti-Ro, anti-La, anti-MPO and antinuclear antibodies. Renal biopsy was performed and confirmed histological findings for SSc, SS, and ANCA-associated vasculitis with active extracapillary glomerulonephritis with fibrous predominance (EUVAS-Berden sclerotic class), active tubulointerstitial nephritis, focal tubular injury and moderate chronic arteriolopathy. Treatment with 6 monthly doses of methylprednisolone and cyclophosphamide was established. At the last follow-up, the patient maintained a stable serum creatinine level of 2.6 mg/dL and had decreased proteinuria, no erythrocyturia, and no requirement for renal replacement therapy. Conclusions: Systemic sclerosis is a rare autoimmune disease; nevertheless, overlap with Sjögren syndrome is relatively common, although its association with ANCA vasculitis is anecdotal. Diagnostic integration presents a challenge for nephrologist to define the prognosis and a specific treatment.
DOI: 10.6084/m9.figshare.6695282
title: Additional file 5: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: The datasets used for the study of sgRNA on-target efficacy prediction. (XLSX 959 kb)
DOI: 10.6084/m9.figshare.6695303
title: Additional file 6: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: The dataset from the human 293-related cell type used for the study of sgRNA off-target profile prediction. (XLSX 49 kb)
DOI: 10.20393/ac6b585d-f3f3-4591-8470-1fd0027474e0
title: INFOMAR Seabed Survey Trackline

description: Survey tracklines delineate the line along which the vessel travelled as it was surveying. The vessel collects multibeam echosounder data (MBES) by emitting a fan of soundwaves and recording the reflected signal. The area of seabed ensonified is known as the footprint and the area surveyed along a transect is commonly called the swath. The size of the footprint depends on the depth: deeper areas will have a larger footprint than shallower areas. The central line of the swath is the trackline and so therefore, tracklines in shallower water will be closer together than those in deeper water.
DOI: 10.6084/m9.figshare.19802509
title: The Effect of Celebrities’ Use of Self-Defeating Humor to Cope with Cyber Spoofing

description: This data used to explore the effect of humor on interpersonal liking.
DOI: 10.6084/m9.figshare.6695315
title: Additional file 7: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: The dataset from the human K562 cell type used for the study of sgRNA off-target profile prediction. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.25045396
title: Additional file 5 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 5: Table S1. All components detected by metabolic analysis. ID, The unique data number of this substance in this qualitative analysis; KEGG_ID, Substance number in KEGG database; EXACT_MASS, Exact molecular weight; NAME_EN, English name of substance; NAME_CH, Chinese name of substance; CLASS_EN, Substance Classification-English; CLASS_CH, Substance Classification-Chinese; ion mode positive and negative ion mode, - is negative, + is positive; rt, sample quantitative value; QC, Quality control samples, After the sample extraction, all samples of equal volume are taken and then mixed
DOI: 10.6084/m9.figshare.25045396.v1
title: Additional file 5 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 5: Table S1. All components detected by metabolic analysis. ID, The unique data number of this substance in this qualitative analysis; KEGG_ID, Substance number in KEGG database; EXACT_MASS, Exact molecular weight; NAME_EN, English name of substance; NAME_CH, Chinese name of substance; CLASS_EN, Substance Classification-English; CLASS_CH, Substance Classification-Chinese; ion mode positive and negative ion mode, - is negative, + is positive; rt, sample quantitative value; QC, Quality control samples, After the sample extraction, all samples of equal volume are taken and then mixed
DOI: 10.20393/3a59d916-a219-45ac-bce2-05b9eb276a52
title: INFOMAR Seabed Survey Coverage

description: This dataset shows the area of seabed mapped by both the INFOMAR and Irish National Seabed Survey projects to date. Each survey leg is represented by a unique polygon whose title is coded using the initials of the vessel that did the survey, the year the survey was completed and the leg number for that year. Attributes contain information on the instruments used and the data acquired during the survey.
DOI: 10.6084/m9.figshare.25045399
title: Additional file 6 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 6: Table S2. Gene lists used for venn plot in Fig 5
DOI: 10.6084/m9.figshare.25045399.v1
title: Additional file 6 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 6: Table S2. Gene lists used for venn plot in Fig 5
DOI: 10.6084/m9.figshare.25045402
title: Additional file 7 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 7: Table S3. Transcription factors identified in defferential expressed genes in EP2 compared to EW2 using plant trancription factor database V4.0 ( http://planttfdb.gao-lab.org/ )
DOI: 10.6084/m9.figshare.25045402.v1
title: Additional file 7 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 7: Table S3. Transcription factors identified in defferential expressed genes in EP2 compared to EW2 using plant trancription factor database V4.0 ( http://planttfdb.gao-lab.org/ )
DOI: 10.6084/m9.figshare.6695324
title: Additional file 8: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: Data augmentation for on-target dataset. (XLSX 2939 kb)
DOI: 10.6084/m9.figshare.6695324.v1
title: Additional file 8: of DeepCRISPR: optimized CRISPR guide RNA design by deep learning

description: Data augmentation for on-target dataset. (XLSX 2939 kb)
DOI: 10.6084/m9.figshare.25045405
title: Additional file 8 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 8: Table S4. Flavonoid biosynthesis DEGs in EP2/EW2 identified by mapman annotation ( https://mapman.gabipd.org/mapman )
DOI: 10.6084/m9.figshare.25045405.v1
title: Additional file 8 of Molecular and metabolic insights into purplish leaf coloration through the investigation of two mulberry (Morus alba) genotypes

description: Supplementary Material 8: Table S4. Flavonoid biosynthesis DEGs in EP2/EW2 identified by mapman annotation ( https://mapman.gabipd.org/mapman )
DOI: 10.6084/m9.figshare.14035377
title: Bioinformatics analysis reveals the competing endogenous RNA (ceRNA) coexpression network in the tumor microenvironment and prognostic biomarkers in soft tissue sarcomas

description: Soft tissue sarcomas (STSs) are rare, heterogeneous mesenchymal neoplasias. Understanding the tumor microenvironment (TME) and identifying potential biomarkers for prognosis associated with the TME of STS might provide effective clues for immune therapy. We evaluated the immune scores and stromal scores of STS patients by using the RNA sequencing dataset from The Cancer Genome Atlas (TCGA) database and the ESTIMATE algorithm. Then, the differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified after comparing the high- and low-score groups. Next, we established a competing endogenous RNA (ceRNA) network and explored the prognostic values of biomarkers involved in the network with the help of bioinformatics analysis. High immune score was significantly associated with favorable overall survival in STS patients. A total of 328 DEGs, 18 DEMs and 67 DELs commonly regulated in the immune and stromal score groups were obtained. A ceRNA network and protein–protein interaction (PPI) network identified some hub nodes with considerable importance in the network. Kaplan–Meier survival analysis demonstrated that nine mRNAs, two miRNAs and three lncRNAs were closely associated with overall survival of STS patients. Gene set enrichment analysis (GSEA) suggested that these three lncRNAs were mainly involved in immune response-associated pathways in STS patients. Finally, the expression levels of five mRNAs (APOL1, EFEMP1, LYZ, RARRES1 and TNFAIP2) were verified, which were consistent with the results of the TCGA cohort. The results of our study confirmed the prognostic value of immune scores for STS patients. We also identified several TME-related biomarkers that might contribute to prognostic prediction and immune therapy.
DOI: 10.6084/m9.figshare.14035377.v1
title: Bioinformatics analysis reveals the competing endogenous RNA (ceRNA) coexpression network in the tumor microenvironment and prognostic biomarkers in soft tissue sarcomas

description: Soft tissue sarcomas (STSs) are rare, heterogeneous mesenchymal neoplasias. Understanding the tumor microenvironment (TME) and identifying potential biomarkers for prognosis associated with the TME of STS might provide effective clues for immune therapy. We evaluated the immune scores and stromal scores of STS patients by using the RNA sequencing dataset from The Cancer Genome Atlas (TCGA) database and the ESTIMATE algorithm. Then, the differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified after comparing the high- and low-score groups. Next, we established a competing endogenous RNA (ceRNA) network and explored the prognostic values of biomarkers involved in the network with the help of bioinformatics analysis. High immune score was significantly associated with favorable overall survival in STS patients. A total of 328 DEGs, 18 DEMs and 67 DELs commonly regulated in the immune and stromal score groups were obtained. A ceRNA network and protein–protein interaction (PPI) network identified some hub nodes with considerable importance in the network. Kaplan–Meier survival analysis demonstrated that nine mRNAs, two miRNAs and three lncRNAs were closely associated with overall survival of STS patients. Gene set enrichment analysis (GSEA) suggested that these three lncRNAs were mainly involved in immune response-associated pathways in STS patients. Finally, the expression levels of five mRNAs (APOL1, EFEMP1, LYZ, RARRES1 and TNFAIP2) were verified, which were consistent with the results of the TCGA cohort. The results of our study confirmed the prognostic value of immune scores for STS patients. We also identified several TME-related biomarkers that might contribute to prognostic prediction and immune therapy.
DOI: 10.6084/m9.figshare.14035379
title: Modelling and monitoring of INAR(1) process with geometrically inflated Poisson innovations

description: To analyse count time series data inflated at the <i>r</i> + 1 values {0,1,…,r}, we propose a new first-order integer-valued autoregressive process with <i>r</i>-geometrically inflated Poisson innovations. Some statistical properties together with conditional maximum likelihood estimate are provided. For the purpose of statistical monitoring, we focus on the cumulative sum chart, exponentially weighted moving average chart and combined jumps chart towards the proposed process. Numerical simulations indicate that the conditional maximum likelihood estimator is unbiased. Moreover, the cumulative sum chart is the best choice to monitor our model in practice. Some applications about telephone complaints data are provided to illustrate the proposed methods.
DOI: 10.6084/m9.figshare.14035379.v1
title: Modelling and monitoring of INAR(1) process with geometrically inflated Poisson innovations

description: To analyse count time series data inflated at the <i>r</i> + 1 values {0,1,…,r}, we propose a new first-order integer-valued autoregressive process with <i>r</i>-geometrically inflated Poisson innovations. Some statistical properties together with conditional maximum likelihood estimate are provided. For the purpose of statistical monitoring, we focus on the cumulative sum chart, exponentially weighted moving average chart and combined jumps chart towards the proposed process. Numerical simulations indicate that the conditional maximum likelihood estimator is unbiased. Moreover, the cumulative sum chart is the best choice to monitor our model in practice. Some applications about telephone complaints data are provided to illustrate the proposed methods.
DOI: 10.15468/dl.p7v37d
title: Occurrence Download

description: A dataset containing 196 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Onoba gelida (E.A.Smith, 1907)"
 ]
}

 The dataset includes 196 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0087631-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c5zcbi
title: Occurrence Download

description: A dataset listing the 23 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus nebrodensis (Guss.) Strobl"
 ]
}

 The dataset's 23 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006964-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2braa8
title: Occurrence Download

description: A dataset containing 284 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pinus merkusii Jungh. & de Vriese"
 ]
}

 The dataset includes 284 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012916-190320150433242/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qpegzs
title: Occurrence Download

description: A dataset containing 70 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Fistularia tabacaria Linnaeus, 1758",
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is less than or equal to 1980",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 70 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006910-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.