cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11393517.v1
title: MOESM2 of NaCl-responsive ROS scavenging and energy supply in alkaligrass callus revealed from proteomic analysis

description: Additional file 2: Table S1. NaCl-responsive proteins identified in the alkaligrass calli using 2DE gel combined with MALDI-TOF MS/MS.
DOI: 10.6084/m9.figshare.11393535
title: MOESM5 of NaCl-responsive ROS scavenging and energy supply in alkaligrass callus revealed from proteomic analysis

description: Additional file 5: Table S4. Homologs of alkaligrass proteins in Arabidopsis found by sequence BLASTing in TAIR database.
DOI: 10.6084/m9.figshare.24500867.v1
title: Additional file 1 of The anticancer potential of chemical constituents of Moringa oleifera targeting CDK-2 inhibition in estrogen receptor positive breast cancer using in-silico and in vitro approches

description: Additional file 1.
DOI: 10.25545/xwgrbp/zgxjim
title: ATPU_SNPs_rmOutliers_rmRelated_vcf

description: SNP data (with outlier SNPs and related individuals removed) in VCF format.
DOI: 10.25545/xwgrbp/xybrhx
title: ATPU_rmOutliers_rmRelated_bim

description: Plink files used for Admixture analysis. Chromosomes were renamed numerically, individual SampleIDs were renamed, removing the species. Related individuals and outlier SNPs were removed from the dataset.
DOI: 10.25545/xwgrbp/zsdrha
title: ATPU_rmOutliers_rmRelated_log

description: Plink files used for Admixture analysis. Chromosomes were renamed numerically, individual SampleIDs were renamed, removing the species. Related individuals and outlier SNPs were removed from the dataset.
DOI: 10.25545/xwgrbp/sceujk
title: ATPU_rmOutliers_rmRelated_bed

description: Plink files used for Admixture analysis. Chromosomes were renamed numerically, individual SampleIDs were renamed, removing the species. Related individuals and outlier SNPs were removed from the dataset.
DOI: 10.25545/xwgrbp/wwyjyj
title: ATPU_SNPs_rmRelated_vcf

description: SNP data (with related individuals removed) in VCF format. Outliers were not filtered from this dataset.
DOI: 10.25545/xwgrbp/wnmv37
title: ATPU_rmOutliers_rmRelated_map

description: Plink files used for Admixture analysis. Chromosomes were renamed numerically, individual SampleIDs were renamed, removing the species. Related individuals and outlier SNPs were removed from the dataset.
DOI: 10.25545/xwgrbp/fnkbiy
title: ATPU_SNPs_rmOutliers_rmRelated_genepop

description: SNP data (with outlier SNPs and related individuals removed) in genepop format.
DOI: 10.25545/xwgrbp/pdup34
title: QC_heterozygosity_vcf

description: Filtered SNP dataset (in VCF format) with only individuals from the QC breeding colony. Data was used to estimate colony-specific heterozygosity and inbreeding
DOI: 10.6084/m9.figshare.21351224
title: Additional file 4 of Autism-like behaviors regulated by the serotonin receptor 5-HT2B in the dorsal fan-shaped body neurons of Drosophila melanogaster

description: Additional file 4: Table. S1 Information on all primers used in this study.
DOI: 10.6084/m9.figshare.13490804.v2
title: Binary classification method for efficient and accurate system reliability analyses of layered soil slopes

description: To enhance the computational efficiency in slope reliability analyses, a binary classification method (BCM) that takes advantage of a judgement-based strength reduction method (SRM) and an active-learning support vector machine (SVM) was developed to conduct system reliability analyses of layered soil slopes. The SVM was naturally employed to establish a binary classifier via the judgment technique to approximate the true limit state function because the stability state (e.g. stable or unstable) of a slope can be determined without calculating its exact factor of safety according to the SRM. An active-learning technique was developed to iteratively search training samples in the vicinity of the border between safe and failure domains, to update the SVM classifier with the aid of a modified initial sampling rule. Then, Latin hypercube sampling was employed, together with the obtained SVM classifier, to compute the slope system probability of failure. Three representative examples taken from the literature were employed to evaluate the performance of the proposed method. The proposed BCM shows great computational efficiency compared with existing methods. It reduced the computational cost to several minutes for simple slopes and to approximately 30 minutes for a complex real case, while maintaining a good computational accuracy.
DOI: 10.6084/m9.figshare.11393628
title: MOESM4 of Protein expression profiles in Meishan and Duroc sows during mid-gestation reveal differences affecting uterine capacity, endometrial receptivity, and the maternalâ€“fetal Interface

description: Additional file 4: Table S4. List of DEPs and functional enrichment analysis results for DEPs at day 72.
DOI: 10.6084/m9.figshare.11393634
title: MOESM5 of Protein expression profiles in Meishan and Duroc sows during mid-gestation reveal differences affecting uterine capacity, endometrial receptivity, and the maternalâ€“fetal Interface

description: Additional file 5: Table S5. List of DEPs associated to extracellular vesicular exosome.
DOI: 10.6084/m9.figshare.11393610.v1
title: MOESM1 of Protein expression profiles in Meishan and Duroc sows during mid-gestation reveal differences affecting uterine capacity, endometrial receptivity, and the maternalâ€“fetal Interface

description: Additional file 1: Table S1. List of DEPs and functional enrichment analysis results for DEPs in Meishan sows.
DOI: 10.6084/m9.figshare.11393628.v1
title: MOESM4 of Protein expression profiles in Meishan and Duroc sows during mid-gestation reveal differences affecting uterine capacity, endometrial receptivity, and the maternalâ€“fetal Interface

description: Additional file 4: Table S4. List of DEPs and functional enrichment analysis results for DEPs at day 72.
DOI: 10.6084/m9.figshare.13490804.v1
title: Binary classification method for efficient and accurate system reliability analyses of layered soil slopes

description: To enhance the computational efficiency in slope reliability analyses, a binary classification method (BCM) that takes advantage of a judgement-based strength reduction method (SRM) and an active-learning support vector machine (SVM) was developed to conduct system reliability analyses of layered soil slopes. The SVM was naturally employed to establish a binary classifier via the judgment technique to approximate the true limit state function because the stability state (e.g. stable or unstable) of a slope can be determined without calculating its exact factor of safety according to the SRM. An active-learning technique was developed to iteratively search training samples in the vicinity of the border between safe and failure domains, to update the SVM classifier with the aid of a modified initial sampling rule. Then, Latin hypercube sampling was employed, together with the obtained SVM classifier, to compute the slope system probability of failure. Three representative examples taken from the literature were employed to evaluate the performance of the proposed method. The proposed BCM shows great computational efficiency compared with existing methods. It reduced the computational cost to several minutes for simple slopes and to approximately 30 minutes for a complex real case, while maintaining a good computational accuracy.
DOI: 10.6084/m9.figshare.21351284.v1
title: Additional file 2 of Identification of a necroptosis-related prognostic gene signature associated with tumor immune microenvironment in cervical carcinoma and experimental verification

description: Additional file 2: Table S2. 159 NRGs from KEGG in CESC. Abbreviations: CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma.
DOI: 10.6084/m9.figshare.21351287
title: Additional file 3 of Identification of a necroptosis-related prognostic gene signature associated with tumor immune microenvironment in cervical carcinoma and experimental verification

description: Additional file 3: Table S3. 25 NRGs among the DEGs between CESC and normal samples. Abbreviations: CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma.
DOI: 10.6084/m9.figshare.17156960.v1
title: Additional file 10 of Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis)

description: Additional file 10: Table S6. KEGG annotation of differentially expressed metabolites from CK-vs.-A3 d.
DOI: 10.6084/m9.figshare.21351283
title: Additional file 4 of Untargeted metabolomics analysis reveals Mycobacterium tuberculosis strain H37Rv specifically induces tryptophan metabolism in human macrophages

description: Additional file 4.
DOI: 10.6084/m9.figshare.11393661
title: MOESM1 of Prediction and clinical utility of a contralateral breast cancer risk model

description: Additional file 1 Table S1. Data source flowchart. Table S2. Description of the studies included in the analyses. Table S3. Patients and first primary breast cancer characteristics used in the contralateral breast cancer risk prediction model in the complete case and all case analyses. Table S4. Results of multivariable subdistributional hazard model using the complete case dataset. Table S5. List of BCAC studies (including ABCS source) with the corresponding country and geographic area. Table S6. Main patient and disease characteristics. Table S7. Clinical utility of the 5-year contralateral breast cancer risk prediction model. Table S8. Results of multivariable subdistributional hazard model for breast cancer patients without BRCA mutations. Table S9. Clinical utility of the 5-year contralateral breast cancer risk prediction model in non-BRCA tested patients. Table S10. Clinical utility of the 10-year contralateral breast cancer risk prediction model in non-BRCA tested patients.
DOI: 10.6084/m9.figshare.21351290
title: Additional file 4 of Identification of a necroptosis-related prognostic gene signature associated with tumor immune microenvironment in cervical carcinoma and experimental verification

description: Additional file 4: Table S4. Six NRGs associated with prognosis in CESC. Abbreviations: CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma.
DOI: 10.48704/ird_mg2zn11
title: IRD_Mg2Zn11
DOI: 10.6084/m9.figshare.8248061.v1
title: The paternal genetic structure of Jingpo and Dai in southwest China

description: Yunnan province harbours substantial genetic, cultural and linguistic diversity, with the largest number of Aborigines in China, but the relationship among these Aborigines remains enigmatic. This study genotyped 45 Y chromosomal single nucleotide polymorphisms (SNPs) of 500 males from two aboriginal cross-border populations, Jingpo and Dai, from Dehong, Yunnan. It is reported that Haplogroup O2a2b1a1-M117 is the dominant lineage in both Jingpo and Dai. The Jingpo people show affinity with Tibeto-Burman speaking populations with a relatively high frequency of Haplogroup D-M174, and the Dai people are generally genetically similar with Tai-Kadai speaking populations with high frequencies of Haplogroup O1a-M119 and O1b1a1a-M95, which is consistent with their language classification.
DOI: 10.6084/m9.figshare.24183315
title: Simulated models of the various nucleic acid structures from the manuscript.

description: Simulated models of the various nucleic acid structures from the manuscript.<br>A readme is added to add a little bit more context to the various pdb models.
DOI: 10.6084/m9.figshare.17157002.v1
title: Additional file 8 of Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis)

description: Additional file 8: Table S4. DEMs of M. rosivorum in response to R. longicuspis.
DOI: 10.6084/m9.figshare.13491018
title: Long non-coding RNA (LncRNA) MRPL23-AS1 promotes tumor progression and carcinogenesis in osteosarcoma by activating Wnt/β-catenin signaling via inhibiting microRNA miR-30b and upregulating myosin heavy chain 9 (MYH9)

description: Long non-coding RNA (LncRNA) contributes to the occurrence and development of osteosarcoma (OS), although the underlying mechanism is not clear. In the present study, we showed that lncRNA MRPL23-AS1 was remarkably increased in OS tissues and cell lines. Stable knockdown of MRPL23-AS1 evidently attenuated cell viability and invasive ability, meanwhile inhibited <i>in vivo</i> tumor growth and dissemination. In terms of mechanism, luciferase reporter, RNA pull-down and fluorescence in situ hybridization (FISH) assays showed that MRPL23-AS1 competitively interacted with miR-30b, increasing myosin heavy chain 9 (MYH9) expression, a trans- activator of β-catenin, resulting in the activation of Wnt/β-catenin pathway, thereby promoting OS tumorigenesis and metastasis. Importantly, high MRPL23-AS1 was positively correlated with MYH9, while conversely correlated with miR-30b, suggesting that the regulatory axis of MRPL23-AS1/miR-30b/MYH9 does exist in OS. Clinically, OS patients with high MRPL23-AS1 had larger tumor size, higher stage and easier metastasis than those with low MRPL23-AS1, moreover, MRPL23-AS1 was identified as an adverse prognostic factor for OS survival. In conclusion, our results show that MRPL23-AS1 is a key oncogenic lncRNA in OS, targeting of MRPL23-AS1 may be a promising treatment for OS patients.
DOI: 10.6084/m9.figshare.8248166.v1
title: Raw data of confining pressure 7MPa from A new loading–unloading experimental method for simulating the change of mining-induced stress

description: Raw data of confining pressure 7MPa
DOI: 10.6084/m9.figshare.21351203
title: Additional file 3 of Identification of a novel interaction site between the large hepatitis delta antigen and clathrin that regulates the assembly of genotype III hepatitis delta virus

description: Additional file 3. Table S2. Unique HDAg-L C-terminal sequences in the phylogenetic tree and the corresponding NCBI accessions.
DOI: 10.6084/m9.figshare.21351352
title: Additional file 3 of Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

description: Additional file 3: Table S3. Codon-based tests for selection on Pvs230 in China–Myanmar border and Myanmar isolates.
DOI: 10.5281/zenodo.10456554
title: Kennedy et al., 2024 - Microbiota assembly of specific pathogen-free neonatal mice

description: Data, Rmd and Prism files to reproduce figures and statistical analyses presented in Kennedy et al., 2024 "Microbiota assembly of specific pathogen-free neonatal mice"
DOI: 10.5281/zenodo.10456555
title: Kennedy et al., 2024 - Microbiota assembly of specific pathogen-free neonatal mice

description: Data, Rmd and Prism files to reproduce figures and statistical analyses presented in Kennedy et al., 2024 "Microbiota assembly of specific pathogen-free neonatal mice"
DOI: 10.6084/m9.figshare.7205102
title: 192 samples - microbial sequencing data for publishing "Patterned progression of gut microbiota predisposes preterm infants to necrotizing enterocolitis and late-onset sepsis: data from a non-Western population"

description: We selected 24 preterm newborns, among them four subsequently developed NEC, three LOS including bacteremia and pneumonia, and 17 healthy controls. Totally 192 longitudinal fecal samples were prospectively collected, right after admission until discharge day, from each patient. We amplified and sequenced V3~V4 region of bacterial 16s rDNA from each intestinal microbiome sample, using Illumina-MiSeq high-throughput sequencing platform.
DOI: 10.6084/m9.figshare.11393673.v1
title: MOESM2 of Prediction and clinical utility of a contralateral breast cancer risk model

description: Additional file 2 Figure S1. Graphical assessment of non-linear relationship of age with contralateral breast cancer risk. Figure S2. Visual assessment of calibration through calibration plots in the internal-external cross-validation at 5 years for the contralateral breast cancer risk model with BRCA mutation information. Figure S3. Visual assessment of calibration through calibration plots in the internal-external cross-validation at 10 years for the contralateral breast cancer risk model with BRCA mutation information. Figure S4. Decision curve analysis at 5 years for the contralateral breast cancer risk model including BRCA1/2 mutation information. Figure S5. Results of the leave-one-study-out cross-validation for the contralateral breast cancer risk model at 5 and 10 years without BRCA mutation information. Figure S6. Visual assessment of calibration through calibration plots in the internal-external cross-validation at 5 years for the contralateral breast cancer risk model without BRCA mutation information. Figure S7. Visual assessment of calibration through calibration plots in the internal-external cross-validation at 10 years for the contralateral breast cancer risk model without BRCA mutation information. Figure S8. Density distribution of 10-year predicted absolute risk in patients with no family history and patients with a family history. Figure S9. Decision curve analysis at 5 years for the contralateral breast cancer risk model without BRCA mutation information. Figure S10. Decision curve analysis at 10 years for the contralateral breast cancer risk model without BRCA mutation information. Figure S11. Assessment of inclusion of information of contralateral preventive mastectomy (CPM).
DOI: 10.6084/m9.figshare.11393715.v1
title: MOESM2 of OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

description: Additional file 2. Commands for running the TAD calling methods of comparison.
DOI: 10.6084/m9.figshare.24500867
title: Additional file 1 of The anticancer potential of chemical constituents of Moringa oleifera targeting CDK-2 inhibition in estrogen receptor positive breast cancer using in-silico and in vitro approches

description: Additional file 1.
DOI: 10.6084/m9.figshare.11393826
title: MOESM4 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation

description: Additional file 4 : Table S3. Summary of statistical analysis in Figures and Supplementary Figures; .xls, 24â€‰KB.
DOI: 10.6084/m9.figshare.15063739
title: Additional file 2 of Construction of a novel mRNA-signature prediction model for prognosis of bladder cancer based on a statistical analysis

description: Additional file 2. Table S2: Kysoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis of genes correlated with candidate genes.
DOI: 10.6084/m9.figshare.8248061
title: The paternal genetic structure of Jingpo and Dai in southwest China

description: Yunnan province harbours substantial genetic, cultural and linguistic diversity, with the largest number of Aborigines in China, but the relationship among these Aborigines remains enigmatic. This study genotyped 45 Y chromosomal single nucleotide polymorphisms (SNPs) of 500 males from two aboriginal cross-border populations, Jingpo and Dai, from Dehong, Yunnan. It is reported that Haplogroup O2a2b1a1-M117 is the dominant lineage in both Jingpo and Dai. The Jingpo people show affinity with Tibeto-Burman speaking populations with a relatively high frequency of Haplogroup D-M174, and the Dai people are generally genetically similar with Tai-Kadai speaking populations with high frequencies of Haplogroup O1a-M119 and O1b1a1a-M95, which is consistent with their language classification.
DOI: 10.6084/m9.figshare.13491012.v1
title: A genome-wide survey of interaction between rice and <i>Magnaporthe oryzae</i> via microarray analysis

description: The main aim of the work is to study the regulation of gene expression in the interaction between rice and <i>Magnaporthe oryzae</i> by gene chip technology. In this study, we mainly focused on changes of gene expression at 24, 48, and 72 hours post-inoculation (hpi), through which we could conduct a more comprehensive analysis of rice blast-related genes in the process of infection. The results showed that the experimental groups contained 460, 1227, and 3937 significant differentially expressed genes at 24, 48, and 72 hpi, respectively. Furthermore, 115 significantly differentially expressed genes were identified in response to rice blast infection at all three time points. By annotating these 115 genes, they were divided into three categories: metabolic pathways, proteins or enzymes, and organelle components. As expected, many of these genes were known rice blast-related genes; however, we discovered new genes with high fold changes. Most of them encoded conserved hypothetical proteins, and some were hypothetically conserved genes. Our study may contribute to finding new resistance genes and understanding the mechanism of rice blast development.
DOI: 10.6084/m9.figshare.11393817.v1
title: MOESM2 of A KHDC3L mutation resulting in recurrent hydatidiform mole causes genome-wide DNA methylation loss in oocytes and persistent imprinting defects post-fertilisation

description: Additional file 2 : Table S2: Pyrosequencing primer sequences; .xls, 12â€‰KB.
DOI: 10.6084/m9.figshare.13491239
title: Characterization of viruses and viroids in <i>Vitis vinifera</i> ‘Kyoho’ in Hangzhou China by small RNA deep sequencing and molecular detection

description: High throughput sequencing of small RNA and RT-PCR revealed that <i>Vitis vinifera</i> ‘Kyoho’, the main grapevine cultivar in Hangzhou, China, was co-infected with at least three viruses, namely grapevine leafroll-associated virus 3 (GLRaV-3), grapevine geminivirus A (GGVA), and grapevine fleck virus (GFkV), and five viroids, namely hop stunt viroid (HSVd), citrus viroid II (CVd-II), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), and citrus cachexia viroid (CCaVd). Additionally, two new isolates of citrus cachexia viroid, i. e. CCaVd-Kyoho-1 and CCaVd-Kyoho-2, were co-identified. These two isolates consist of 296 and 300 full nucleotides, respectively, with 2.7%–5.0% and 4.6%–6.9% variations individually compared to other CCaVd isolates, and 5.8%–6.1% variations to CVd-II and HSVd in the NCBI database. Point mutations in the form of transitions and transversions, A/T deletions, and A/C insertions were identified. These mutations were mainly distributed in the pathogenic and variation regions. Phylogenetic analysis showed that the two local CCaVd isolates are located in the new evolution clade and could be new members of HSVd in the family <i>Pospiviroidae</i> existing in the grapevine cultivar ‘Kyoho’.