cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12955801
title: Additional file 2 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 2: Table S2. Identification of lncRNA transcripts of 16 libraries by RNA-sequencing.
DOI: 10.6084/m9.figshare.12955822.v1
title: Additional file 9 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 9: Table S9. GO and KEGG pathway analysis of the targets for differentially expressed miRNAs.
DOI: 10.6084/m9.figshare.12955807.v1
title: Additional file 4 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 4: Table S4. Summary of draft reads of 16 libraries by small RNA-sequencing.
DOI: 10.6084/m9.figshare.12955795
title: Additional file 11 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 11: Table S11. Quantitative real-time PCR primer sequences used in this study.
DOI: 10.6084/m9.figshare.12955807
title: Additional file 4 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 4: Table S4. Summary of draft reads of 16 libraries by small RNA-sequencing.
DOI: 10.6084/m9.figshare.12955813
title: Additional file 6 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 6: Table S6. Differential expression analysis of lncRNAs, mRNAs and miRNAs.
DOI: 10.6084/m9.figshare.12955951.v1
title: Additional file 4 of Identification of miPEP133 as a novel tumor-suppressor microprotein encoded by miR-34a pri-miRNA

description: Additional file 4. This Excel file contains 3 sheets. They are the lists of proteins identified in control cells, proteins identified in miPEP133-overexpressing cells, and miPEP133-binding proteins confidently identified by excluding the backgrounds in the control cells.
DOI: 10.6084/m9.figshare.12955804.v1
title: Additional file 3 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 3: Table S3. Summary of mRNA transcripts of 16 libraries by RNA-sequencing.
DOI: 10.6084/m9.figshare.17157790
title: Tea extracts inhibit the attachment of streptococci to oral/dental substrata by reducing hydrogen bonding energies

description: Previous work in the authors’ lab demonstrated that tea extracts significantly suppressed streptococcal colonization of abiotic substrata by coating the bacterial cell surfaces with tea components. In this study, the physico-chemical mechanisms by which the tea coating inhibits cellular attachment are demonstrated. The changes in the cell surface physico-chemical properties of streptococci, induced by tea extracts, were measured. Using these results, surface interaction energies were calculated between streptococcal cells and hard surfaces (glass, stainless steel, hydroxyapatite and titanium) within the cellular attachment system exploiting the extended Derjaguin-Landau-Verwey-Overbeek theory. The net energy outcomes were compared with experiment results of attachment assays to validate the predictability of the model. The results showed that the tea extracts inhibited the attachment of the bacteria by 11.1%–91.5%, and reduced the interaction energy by 15.4%–94.9%. It was also demonstrated that the abilities of the bacteria to attach to hard surfaces correlated well with their net interaction energies. The predominant interaction in the systems was found to be hydrogen bonding. In conclusion, tea extracts suppress streptococcal attachment to hard substrata by limiting the formation of hydrogen bonds.
DOI: 10.6084/m9.figshare.12955937.v1
title: Additional file 1 of Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

description: Additional file 1: Table S1. Predicted target genes by CAMTA.
DOI: 10.6084/m9.figshare.12955940
title: Additional file 2 of Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

description: Additional file 2: Table S2. Primer sequences of TaCAMTA and TaActin genes used for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.12955940.v1
title: Additional file 2 of Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

description: Additional file 2: Table S2. Primer sequences of TaCAMTA and TaActin genes used for qRT-PCR analysis.
DOI: 10.15468/qv45w4
title: 2017 Scottish Environment Protection Agency (SEPA) Montrose Basin Intertidal Seagrass Survey

description: Trial Intertidal seagrass survey in conjunction with a Macroalgal Blooming (MAB) survey in the Montrose Basin, Scotland. This was for the EU Water Framework Directive Monitoring using the WFD (Angiosperm) Intertidal Seagrass tool. The tool looks at the species composition of the seagrass bed, the density (as percent cover) and the extent of the seagrass bed.
DOI: 10.6084/m9.figshare.12955819.v1
title: Additional file 8 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 8: Table S8. Identification of miRNA–mRNA pairs.
DOI: 10.6084/m9.figshare.7713113.v1
title: Partial Identification of Economic Mobility: With an Application to the United States

description: The economic mobility of individuals and households is of fundamental interest. While many measures of economic mobility exist, reliance on transition matrices remains pervasive due to simplicity and ease of interpretation. However, estimation of transition matrices is complicated by the well-acknowledged problem of measurement error in self-reported and even administrative data. Existing methods of addressing measurement error are complex, rely on numerous strong assumptions, and often require data from more than two periods. In this article, we investigate what can be learned about economic mobility as measured via transition matrices while formally accounting for measurement error in a reasonably transparent manner. To do so, we develop a nonparametric partial identification approach to bound transition probabilities under various assumptions on the measurement error and mobility processes. This approach is applied to panel data from the United States to explore short-run mobility before and after the Great Recession.
DOI: 10.6084/m9.figshare.25226873
title: 2024-AEM-Bedore and Waters-plasmid stability

description: This folder includes the raw data for the 2024 Applied and Environmental Microbiology paper by Bedore and Waters titled "Plasmid-free cheater cells commonly evolve during laboratory growth" that describes how laboratory plasmids can be lost even in the presence of selection.
DOI: 10.6084/m9.figshare.25226873.v1
title: 2024-AEM-Bedore and Waters-plasmid stability

description: This folder includes the raw data for the 2024 Applied and Environmental Microbiology paper by Bedore and Waters titled "Plasmid-free cheater cells commonly evolve during laboratory growth" that describes how laboratory plasmids can be lost even in the presence of selection.
DOI: 10.6084/m9.figshare.8245019.v1
title: Additional file 13: of Population structure, demographic history and local adaptation of the grass carp

description: Table S6. Enriched KEGG pathways and the gene counts under putative selection identified by outlier tests and Bayenv association tests. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.12955798
title: Additional file 1 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 1: Table S1. Summary of the sequencing reads alignment to the reference genome.
DOI: 10.6084/m9.figshare.12955951
title: Additional file 4 of Identification of miPEP133 as a novel tumor-suppressor microprotein encoded by miR-34a pri-miRNA

description: Additional file 4. This Excel file contains 3 sheets. They are the lists of proteins identified in control cells, proteins identified in miPEP133-overexpressing cells, and miPEP133-binding proteins confidently identified by excluding the backgrounds in the control cells.
DOI: 10.6084/m9.figshare.20295766.v1
title: Additional file 6 of DUB1 suppresses Hippo signaling by modulating TAZ protein expression in gastric cancer

description: Additional file 6.
DOI: 10.6084/m9.figshare.20295757.v1
title: Additional file 5 of DUB1 suppresses Hippo signaling by modulating TAZ protein expression in gastric cancer

description: Additional file 5.
DOI: 10.6084/m9.figshare.12955937
title: Additional file 1 of Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

description: Additional file 1: Table S1. Predicted target genes by CAMTA.
DOI: 10.6084/m9.figshare.20295766
title: Additional file 6 of DUB1 suppresses Hippo signaling by modulating TAZ protein expression in gastric cancer

description: Additional file 6.
DOI: 10.6084/m9.figshare.12955798.v1
title: Additional file 1 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 1: Table S1. Summary of the sequencing reads alignment to the reference genome.
DOI: 10.6084/m9.figshare.12955801.v1
title: Additional file 2 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 2: Table S2. Identification of lncRNA transcripts of 16 libraries by RNA-sequencing.
DOI: 10.6084/m9.figshare.12955810
title: Additional file 5 of Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

description: Additional file 5: Table S5. Information of miRNAs.
DOI: 10.6084/m9.figshare.20295757
title: Additional file 5 of DUB1 suppresses Hippo signaling by modulating TAZ protein expression in gastric cancer

description: Additional file 5.
DOI: 10.6084/m9.figshare.12956164
title: Additional file 3 of Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum

description: Additional file 3. The protein sequences of SPS genes in S. spontaneum genome.
DOI: 10.6084/m9.figshare.12956164.v1
title: Additional file 3 of Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum

description: Additional file 3. The protein sequences of SPS genes in S. spontaneum genome.
DOI: 10.6084/m9.figshare.20296198.v1
title: Additional file 1 of Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging

description: Additional file 1: Table S1. Deletions strains analyzed in this study.
DOI: 10.6084/m9.figshare.19767796.v1
title: Additional file 1 of Development pattern of ocular biometric parameters and refractive error in young Chinese adults: a longitudinal study of first-year university students

description: Additional file 1. Ocular biometry measurements results.
DOI: 10.6084/m9.figshare.8245190
title: Additional file 6: of Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella

description: Table S3. Mis-annotated genes list identified by Iso-Seq. (TXT 199 kb)
DOI: 10.6084/m9.figshare.20296198
title: Additional file 1 of Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging

description: Additional file 1: Table S1. Deletions strains analyzed in this study.
DOI: 10.6084/m9.figshare.20296204.v1
title: Additional file 3 of Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging

description: Additional file 3:  Table S3. Gene Ontology enrichment analysis.
DOI: 10.6084/m9.figshare.14767233.v1
title: Additional file 2 of Identification of a tumor microenvironment-related seven-gene signature for predicting prognosis in bladder cancer

description: Additional file 2: Table S2. Protein-Protein interaction network information.
DOI: 10.6084/m9.figshare.14767233
title: Additional file 2 of Identification of a tumor microenvironment-related seven-gene signature for predicting prognosis in bladder cancer

description: Additional file 2: Table S2. Protein-Protein interaction network information.
DOI: 10.6084/m9.figshare.12956236
title: Additional file 4 of The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

description: Additional file 4: Table S3. Gene numbers of 124 kinase families.
DOI: 10.6084/m9.figshare.5099830
title: Association of knowledge and belief with self-efficacy in osteoporosis prevention among middle-aged and older community residents in urban Shanghai

description: This study aimed to determine the factors associated with self-efficacy in osteoporosis prevention, and support further intervention.
DOI: 10.6084/m9.figshare.23974317
title: Dataset S1.xlsx

description: Paddy fields, as the largest anthropogenic wetlands on Earth, face a high risk of micronutrient loss through surface runoff and leaching due to their frequent irrigation-drainage cycles, as well as removal with crop harvest. While micronutrient’s losses largely impede biological nitrogen fixation (BNF) in soils, agricultural practices that retain micronutrients and thus increase BNF in paddy soils remain underexplored. Using a long-term (40 years) field experiment, we showed that manure and straw inputs substantially increased the content and bioavailability of micronutrients, including molybdenum (Mo) and vanadium (V), compared to the soil without fertilization or with mineral fertilization only. The total content and bioavailability of Mo and V had a strong correlation with microbial necromass and short-range ordered minerals. Metagenomic sequencing analysis further indicated that the content and bioavailability of micronutrients were strongly correlated with the abundance of the key N-fixing genera (i.e., Azospirillum and Bradyrhizobium). Unexpectedly, structural equation modeling (SEM) identified that microbial necromass exerted the strongest control on N-fixing genera, highlighting an underappreciated role of microbial necromass as a reservoir of micronutrients. Based on micronutrient’s bioavailability and metagenomic sequencing, we conclude that micronutrients are the key factor for BNF in paddy soils, offering significant implications for managing BNF in paddy soils.
DOI: 10.6084/m9.figshare.23974359
title: Downregulation of cancer-associated fibroblast exosome-derived miR-29b-1-5p restrains vasculogenic mimicry and apoptosis while accelerating migration and invasion of gastric cancer cells via immunoglobulin domain-containing 1/zonula occluden-1 axis

description: <b>Background:</b> Cancer-associated fibroblast (CAF) exosomal miRNAs have gradually a hot spot in cancer therapy. This study mainly explores the effect of CAF-derived exosomal miR-29b-1-5p on gastric cancer (GC) cells. <b>Methods:</b> CAFs and exosomes were identified by Western blot and transmission electron microscopy. CAF-derived exosomes-GC cells co-culture systems were constructed. Effects of CAF-derived exosomal miR-29b-1-5p on GC cells were determined by cell counting kit-8, flow cytometry, wound healing, Transwell assays and Western blot. The relationship between miR-29b-1-5p and immunoglobulin domain-containing 1 (VSIG1) was assessed by TargetScan, dual-luciferase reporter and RNA immunoprecipitation (RIP) experiments. The interaction between VSIG1 and zonula occluden-1 (ZO-1) was detected by co-immunoprecipitation. Expressions of miR-29b-1-5p, VSIG1 and ZO-1 were determined by quantitative real-time PCR. Vascular mimicry (VM) was detected using immunohistochemistry and tube formation assays. Rescue experiments and xenograft tumor assays were used to further determine the effect of CAF-derived exosomal miR-29b-1-5p/VSIG1 on GC. <b>Results:</b> VM structure, upregulation of miR-29b-1-5p, and downregulation of VSIG1 and ZO-1 were shown in GC tissues. MiR-29b-1-5p targeted VSIG1, which interacted with ZO-1. CAF-derived exosomal miR-29b-1-5p inhibitor suppressed the viability, migration, invasion and VM formation, but promoted the apoptosis of GC cells. MiR-29b-1-5p inhibitor increased levels of VSIG1, ZO-1 and E-cadherin, whilst decreasing levels of VE-cadherin, N-cadherin and Vimentin in vitro and in vivo, which however was partially reversed by shVSIG1. Downregulation of CAF-derived exosomal miR-29b-1-5p impeded GC tumorigenesis and VM structure in vivo by upregulating VSIG1/ZO-1 expression. <b>Conclusion:</b> Downregulation of CAF-derived exosomal miR-29b-1-5p inhibits GC progression via VSIG1/ZO-1 axis.
DOI: 10.6084/m9.figshare.23974359.v1
title: Downregulation of cancer-associated fibroblast exosome-derived miR-29b-1-5p restrains vasculogenic mimicry and apoptosis while accelerating migration and invasion of gastric cancer cells via immunoglobulin domain-containing 1/zonula occluden-1 axis

description: <b>Background:</b> Cancer-associated fibroblast (CAF) exosomal miRNAs have gradually a hot spot in cancer therapy. This study mainly explores the effect of CAF-derived exosomal miR-29b-1-5p on gastric cancer (GC) cells. <b>Methods:</b> CAFs and exosomes were identified by Western blot and transmission electron microscopy. CAF-derived exosomes-GC cells co-culture systems were constructed. Effects of CAF-derived exosomal miR-29b-1-5p on GC cells were determined by cell counting kit-8, flow cytometry, wound healing, Transwell assays and Western blot. The relationship between miR-29b-1-5p and immunoglobulin domain-containing 1 (VSIG1) was assessed by TargetScan, dual-luciferase reporter and RNA immunoprecipitation (RIP) experiments. The interaction between VSIG1 and zonula occluden-1 (ZO-1) was detected by co-immunoprecipitation. Expressions of miR-29b-1-5p, VSIG1 and ZO-1 were determined by quantitative real-time PCR. Vascular mimicry (VM) was detected using immunohistochemistry and tube formation assays. Rescue experiments and xenograft tumor assays were used to further determine the effect of CAF-derived exosomal miR-29b-1-5p/VSIG1 on GC. <b>Results:</b> VM structure, upregulation of miR-29b-1-5p, and downregulation of VSIG1 and ZO-1 were shown in GC tissues. MiR-29b-1-5p targeted VSIG1, which interacted with ZO-1. CAF-derived exosomal miR-29b-1-5p inhibitor suppressed the viability, migration, invasion and VM formation, but promoted the apoptosis of GC cells. MiR-29b-1-5p inhibitor increased levels of VSIG1, ZO-1 and E-cadherin, whilst decreasing levels of VE-cadherin, N-cadherin and Vimentin in vitro and in vivo, which however was partially reversed by shVSIG1. Downregulation of CAF-derived exosomal miR-29b-1-5p impeded GC tumorigenesis and VM structure in vivo by upregulating VSIG1/ZO-1 expression. <b>Conclusion:</b> Downregulation of CAF-derived exosomal miR-29b-1-5p inhibits GC progression via VSIG1/ZO-1 axis.
DOI: 10.6084/m9.figshare.17158637
title: Mouse Left Atria Optical Mapping Data

description: All data are provided in .mat format, and organised so that each folder contains an individual experiment (i.e. whole heart or isolated atrium). All PCLs are within single experimental files. .txt are also provided that contain suggested setting for use in ElectroMap, and regions of interest. Filenames include animal ID and intervention.
DOI: 10.6084/m9.figshare.17158637.v1
title: Mouse Left Atria Optical Mapping Data

description: All data are provided in .mat format, and organised so that each folder contains an individual experiment (i.e. whole heart or isolated atrium). All PCLs are within single experimental files. .txt are also provided that contain suggested setting for use in ElectroMap, and regions of interest. Filenames include animal ID and intervention.
DOI: 10.6084/m9.figshare.21352976
title: Analysis of oil vapor diffusion after oil spill from tank group based on wind tunnel experiment and numerical simulation

description: The diffusion of oil vapor after oil spill from tank caused serious consequences. It is studied by combining wind tunnel experiment and numerical simulation. Results show that the higher the fire dike, the more oil vapor accumulates at the inner corner of fire dike; the explosion limit area is the largest when the oil spills in front of single tank on the windward side; concentration of multi-spills will superimpose to induce the presenting of multi-explosion limit areas. It can provide a reference for the research and development of the oil vapor traceability system and prevent explosion accidents in oil depots.
DOI: 10.6084/m9.figshare.21352976.v1
title: Analysis of oil vapor diffusion after oil spill from tank group based on wind tunnel experiment and numerical simulation

description: The diffusion of oil vapor after oil spill from tank caused serious consequences. It is studied by combining wind tunnel experiment and numerical simulation. Results show that the higher the fire dike, the more oil vapor accumulates at the inner corner of fire dike; the explosion limit area is the largest when the oil spills in front of single tank on the windward side; concentration of multi-spills will superimpose to induce the presenting of multi-explosion limit areas. It can provide a reference for the research and development of the oil vapor traceability system and prevent explosion accidents in oil depots.
DOI: 10.6084/m9.figshare.12956245
title: Additional file 7 of The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

description: Additional file 7: Table S6. List of all the duplicated strawberry protein kinases.
DOI: 10.6084/m9.figshare.20296201
title: Additional file 2 of Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging

description: Additional file 2: Table S2. Short and long-lived mutants identified in this study.
DOI: 10.6084/m9.figshare.12956245.v1
title: Additional file 7 of The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

description: Additional file 7: Table S6. List of all the duplicated strawberry protein kinases.
DOI: 10.6084/m9.figshare.12956056.v1
title: Additional file 8 of Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance

description: Additional file 8: Table S4 . List of the maternal-effect gene variants associated with MLID in the offspring identified so far and corresponding clinical phenotype.
DOI: 10.6084/m9.figshare.12956233
title: Additional file 3 of The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection

description: Additional file 3: Table S2. Sub-family classification of woodland protein kinases and their related information.
DOI: 10.6084/m9.figshare.12956050
title: Additional file 6 of Loss-of-function maternal-effect mutations of PADI6 are associated with familial and sporadic Beckwith-Wiedemann syndrome with multi-locus imprinting disturbance

description: Additional file 6: Table S3. Maternal genetic variants in homozigosity or compound heterozigosity identified by WES.