cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.15063736.v1
title: Additional file 1 of Construction of a novel mRNA-signature prediction model for prognosis of bladder cancer based on a statistical analysis

description: Additional file 1. Table S1: Gene ontology (GO) enrichment analysis of genes correlated with candidate genes.
DOI: 10.6084/m9.figshare.23452839.v1
title: The complete chloroplast genome and phylogenetic analysis of <i>Lemmaphyllum carnosum</i> var. <i>drymoglossoides</i> (baker) X. P. Wei, 2013

description: <i>Lemmaphyllum carnosum</i> var. <i>drymoglossoides (Baker)</i> X. P. Wei, 2013 is a valuable medicinal fern in China. Its complete chloroplast genome was determined using Illumina paired-end sequencing. The genome was 157,571 bp in length with 130 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 35 tRNA genes. It displayed a quadripartite structure consisting of a small single-copy (SSC) of 21,691 bp, a large single-copy (LSC) of 81,106 bp, and two inverted repeats (IRs) of 27,387 bp, respectively. The phylogenetic results indicated that <i>L. carnosum</i> var. <i>drymoglossoides</i> exhibited the closest relationship with <i>L. intermedium</i>, and this study provided new information for the phylogenetic relationship of the Polypodiaceae family.
DOI: 10.6084/m9.figshare.11393817
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.13491090.v1
title: Upregulation of polycistronic microRNA-143 and microRNA-145 in colonocytes suppresses colitis and inflammation-associated colon cancer

description: Because ADAM17 promotes colonic tumorigenesis, we investigated potential miRNAs regulating ADAM17; and examined effects of diet and tumorigenesis on these miRNAs. We also examined pre-miRNA processing and tumour suppressor roles of several of these miRNAs in experimental colon cancer. Using TargetScan, miR-145, miR-148a, and miR-152 were predicted to regulate ADAM17. miR-143 was also investigated as miR-143 and miR-145 are co-transcribed and associated with decreased tumour growth. HCT116 colon cancer cells (CCC) were co-transfected with predicted ADAM17-regulating miRNAs and luciferase reporters controlled by ADAM17-3’UTR. Separately, pre-miR-143 processing by colonic cells was measured. miRNAs were quantified by RT-PCR. Tumours were induced with AOM/DSS in WT and transgenic mice (Tg) expressing pre-miR-143/miR-145 under villin promoter. HCT116 transfection with miR-145, −148a or −152, but not scrambled miRNA inhibited ADAM17 expression and luciferase activity. The latter was suppressed by mutations in ADAM17-3’UTR. Lysates from colonocytes, but not CCC, processed pre-miR-143 and mixing experiments suggested CCC lacked a competency factor. Colonic miR-143, miR-145, miR-148a, and miR-152 were downregulated in tumours and more moderately by feeding mice a Western diet. Tg mice were resistant to DSS colitis and had significantly lower cancer incidence and tumour multiplicity. Tg expression blocked up-regulation of putative targets of miR-143 and miR-145, including ADAM17, K-Ras, XPO5, and SET. miR-145, miR-148a, and miR-152 directly suppress colonocyte ADAM17 and are down-regulated in colon cancer. This is the first direct demonstration of tumour suppressor roles for miR-143 and miR-145 in an <i>in vivo</i> model of colonic tumorigenesis.
DOI: 10.6084/m9.figshare.7729940
title: Additional file 19: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between wheat and Arabidopsis thaliana. (XLSX 14 kb)
DOI: 10.25407/jacbts.8254235.v1
title: Figure 4: Prolonged PF-1355 Treatment Improves Cardiac Function and Remodeling

description: Infarcted mice were divided into 3 groups: untreated (MI-no Tx, n = 6), treated for 21 days (MI-21 days Tx, n = 5), and treated for first 7 days only and then treatment stopped until day 21 for imaging (MI-7 days Tx, n = 8). <b>(A to C)</b> Representative midventricular magnetic resonance images obtained at day 21 after MI. Videos obtained from the same mice at day 2 and day 21 are shown in the Supplemental Video 1. <b>(D)</b> There is significant improvement in ejection fraction (EF) in the 21-day treatment group as compared with untreated infarcts; however, the 7-day treatment group did not show significant improvement. <b>(E) Bar graphs</b> representing end-diastolic volume (EDV). <b>(F)</b> Left ventricular mass is less in the 21-day treatment group representing decreased remote myocardial hypertrophy and improved remodeling. Data plotted as mean ± SEM. *p &lt; 0.05; ***p &lt; 0.001. MI = myocardial infarction; Tx = treatment.
DOI: 10.6084/m9.figshare.21351284
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.7724228.v1
title: Additional file 2: of Helicobacter pylori infection as a risk factor for serum bilirubin change and less favourable lipid profiles: a hospital-based health examination survey

description: Database. Primary database of this study. (SAV 181 kb)
DOI: 10.6084/m9.figshare.17156996
title: Additional file 6 of Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis)

description: Additional file 6: Table S2. qPCR primer.
DOI: 10.6084/m9.figshare.23452895
title: The complete mitochondrial genome of <i>Stibochiona nicea</i> (Gray, 1846) (Lepidoptera: Nymphalidae) and phylogenetic analysis

description: In this study, the complete mitochondrial genome (mitogenome) of <i>Stibochiona nicea</i> (Gray, 1846) (Lepidoptera: Nymphalidae) was first reported with 15,298 bp in size, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes (<i>rrnL</i> and <i>rrnS</i>), and one control region. The nucleotide composition of the entire mitogenome is highly A + T biased (81.5%). The gene content and arrangement of the newly sequenced mitogenome are identical to those of the other available mitogenomes of Nymphalidae. All PCGs start with the conventional ATN codons, except for <i>cox1</i> initiating with atypical CGA(R). Nine PCGs (<i>atp8</i>, <i>atp6</i>, <i>cox3</i>, <i>nad1</i>, <i>nad2</i>, <i>nad3</i>, <i>nad4l</i>, <i>nad6</i>, and <i>cob</i>) utilize a typical stop codon TAA, whereas the remaining PCGs (<i>cox1</i>, <i>cox2</i>, <i>nad4</i>, and <i>nad5</i>) end with an incomplete stop codon T–. Phylogenetic analysis revealed that <i>S. nicea</i> is closely related to <i>Dichorragia nesimachus</i> within Pseudergolinae, which further forms the sister group to the grouping of (Nymphalinae + (Cyrestinae + (Biblidinae + Apaturinae))). The complete mitogenome of <i>S. nicea</i> will provide useful genetic information for improving the taxonomic system and phylogenetics of Nymphalidae.
DOI: 10.6084/m9.figshare.17157002
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.11393835.v1
title: MOESM6 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 6 : Table S5. DNA methylation sequencing summary; .xls, 10â€‰KB.
DOI: 10.6084/m9.figshare.7729994
title: Additional file 24: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between B. distachyon and Arabidopsis thaliana. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7729994.v1
title: Additional file 24: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: Orthologous Trihelix gene pairs between B. distachyon and Arabidopsis thaliana. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.15063985
title: Additional file 1 of Counting colonies of clonogenic assays by using densitometric software

description: Additional File 1: Clono-Counter. Contains a manual for the program, the program itself and an example. (ZIP 331 KB)
DOI: 10.6084/m9.figshare.7730072
title: Additional file 8: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The 31 Oryza sativa Trihelix genes, 50 Zea mays Trihelix genes, 25 Hordeum vulgare Trihelix genes and 30 Sorghum bicolor Trihelix genes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7730072.v1
title: Additional file 8: of Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

description: The 31 Oryza sativa Trihelix genes, 50 Zea mays Trihelix genes, 25 Hordeum vulgare Trihelix genes and 30 Sorghum bicolor Trihelix genes. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.15063955
title: Additional file 11 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 11: Table S7.The GO and KEGG analyses of down-regulated DEmiRNAs in child vs. adult group.
DOI: 10.6084/m9.figshare.15063976
title: Additional file 14 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 14: Table S10. The primers of reference gene and miRNAs.
DOI: 10.6084/m9.figshare.15064009.v1
title: Additional file 7 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 7: Table S3:All identified DEmiRNAs. Sheet 1 ("TPM"): All DEmiRNAs and their expression levels. Sheet 2 ("Average"): The average expression and total expression of all DEmiRNAs. Sheet 3-5: DEmiRNAs identified in different groups.
DOI: 10.6084/m9.figshare.15064012.v1
title: Additional file 8 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 8: Table S4.The GO and KEGG analyses of up-regulated DEmiRNAs in fetus vs. child group.
DOI: 10.6084/m9.figshare.15063967
title: Additional file 13 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 13: Table S9. miRNA-mRNA network for localization (sheet 1) and regulation of actin cytoskeleton (sheet 2).
DOI: 10.6084/m9.figshare.8248163
title: Raw data of confining pressure 6MPa from A new loading–unloading experimental method for simulating the change of mining-induced stress

description: Raw data of confining pressure 6MPa
DOI: 10.6084/m9.figshare.15064000
title: Additional file 5 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 5: Table S1.The overview of RNA-seq data.
DOI: 10.6084/m9.figshare.15063949
title: Additional file 10 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 10: Table S6:The GO and KEGG analyses of up-regulated DEmiRNAs in child vs. adult group.
DOI: 10.6084/m9.figshare.15064009
title: Additional file 7 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 7: Table S3:All identified DEmiRNAs. Sheet 1 ("TPM"): All DEmiRNAs and their expression levels. Sheet 2 ("Average"): The average expression and total expression of all DEmiRNAs. Sheet 3-5: DEmiRNAs identified in different groups.
DOI: 10.6084/m9.figshare.6151127
title: Full dataset for high-throughput phenotyping-enabled genetic dissection of crop lodging in wheat.

description: The primary objective of this research was to evaluate the potential of 
unmanned aerial systems-based imaging for quantification of crop lodging in wheat. This dataset contains images and associated files collected from large wheat breeding trials over the course of two seasons in 2016 and 2017. Using the validated digital lodging scores, we performed Genome-Wide Assocation Analysis on 1035 wheat genotypes and found a consistent peak at chromosome 2A. To follow up, we tested the hypothesis of complex genetic architecture of lodging in wheat by applying genomic prediction cross-validations within and across environments. Our findings provide a strong proof-of-concept in support of the application of unmanned aerial systems in breeding and genetic studies. This work was published in Frontiers in Plant Science (2019). This dataset provides a comprehensive collection of files to replicate the proposed methods and analysis. <br>
DOI: 10.6084/m9.figshare.8248166
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.15063961.v1
title: Additional file 12 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 12: Table S8. The primers of reference gene and miRNAs.
DOI: 10.6084/m9.figshare.15063949.v1
title: Additional file 10 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 10: Table S6:The GO and KEGG analyses of up-regulated DEmiRNAs in child vs. adult group.
DOI: 10.6084/m9.figshare.15063967.v1
title: Additional file 13 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 13: Table S9. miRNA-mRNA network for localization (sheet 1) and regulation of actin cytoskeleton (sheet 2).
DOI: 10.6084/m9.figshare.7200005.v1
title: MOESM1 of No association of TP53 codon 72 and intron 3 16-bp duplication polymorphisms with breast cancer risk in Chinese Han women: new evidence from a population-based caseâ control investigation

description: Additional file 1: Table S1. Distributions of the genotype frequencies of codon 72 and intron 3 16-bp duplication polymorphisms in breast cancer patients with different clinicopathological features.
DOI: 10.6084/m9.figshare.7724162
title: Additional file 4: of Taxonomy, virulence genes and antimicrobial resistance of Aeromonas isolated from extra-intestinal and intestinal infections

description: Clinical data, genes of toxins and drug resistant patterns for 17 patients related to Aeromonas spp. in extra-intestinal infections. (XLS 49 kb)
DOI: 10.6084/m9.figshare.17157006
title: Additional file 1 of Lifestyle correlates of eight breast cancer-related metabolites: a cross-sectional study within the EPIC cohort

description: Additional file 1: Associations between metabolites and all variables tested as correlates, in discovery set and, for significant associations, in validation set (Supplementary Table 1); Stratified analyses by BMI, menopausal status, and fasting status at blood collection, for metabolites and variables showing a P-int &lt; 0.20 after correction for multiple testing, in discovery set (Supplementary Table 2). Abbreviations: AICR American Institute for Cancer Research; Asn asparagine; BMI body mass index; C2 acetylcarnitine; HLI Healthy lifestyle index; PC aa phosphatidylcholine diacyl; PC ae phosphatidylcholine acyl-alkyl; SD Standard deviation; SE: Standard error of estimate; WCRF World Cancer Research Fund. (XLS 177 kb)
DOI: 10.6084/m9.figshare.15063961
title: Additional file 12 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 12: Table S8. The primers of reference gene and miRNAs.
DOI: 10.6084/m9.figshare.7724141
title: Additional file 1: of Rare disease knowledge enrichment through a data-driven approach

description: Top Associations. This file includes 13,742 top phenotype-disease associations selected by support and confidence. (XLSX 218 kb)
DOI: 10.6084/m9.figshare.13491222
title: Antarctic-wide annual ice flow maps from Landsat 8 imagery between 2013 and 2019

description: Ice velocity constitutes a key parameter for quantifying ice-sheet discharge rates and is thus crucial for improving the coupled models of the Antarctic ice sheet towards accurately predict its contribution to future global sea-level rise. However, in Antarctica, high-resolution and continuous ice velocity estimates remain elusive, which is key to unravel Antarctica’s present-day ice mass balance processes. Here, we present a suite of newly estimated Antarctic-wide, annually-sampled ice velocity products at 105-m grid-spacing observed by Landsat 8 optical images data. We first describe a procedure that can automatically calibrate and integrate ice displacement maps to generate Antarctic-wide seamless ice velocity products. The annual ice velocity mosaics are assembled using a total of 250,000 displacement maps inferred from more than 80,000 Landsat 8 images acquired between December 2013 and April 2019. The new annual Antarctic ice velocity data product exhibits an improved quantification of near-decadal Antarctic-wide ice flow, and an opportunity to investigate ice dynamics at a higher spatial resolution and annual sampling, as compared to existing data products. Validation studies confirmed improved accuracy and consistency of this new data product, when compared with independently estimated optical and radar ice velocity data products, as well as <i>in situ</i> data.
DOI: 10.6084/m9.figshare.15063976.v1
title: Additional file 14 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 14: Table S10. The primers of reference gene and miRNAs.
DOI: 10.6084/m9.figshare.17157005.v1
title: Additional file 9 of Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis)

description: Additional file 9: Table S5. KEGG annotation of metabolites.
DOI: 10.6084/m9.figshare.15063985.v1
title: Additional file 1 of Counting colonies of clonogenic assays by using densitometric software

description: Additional File 1: Clono-Counter. Contains a manual for the program, the program itself and an example. (ZIP 331 KB)
DOI: 10.6084/m9.figshare.15063955.v1
title: Additional file 11 of Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

description: Additional file 11: Table S7.The GO and KEGG analyses of down-regulated DEmiRNAs in child vs. adult group.
DOI: 10.6084/m9.figshare.21351346
title: Additional file 1 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 1: Table S1. Primers used in Pvs230 amplification and sequencing.
DOI: 10.6084/m9.figshare.14540108.v1
title: Isolation, characterization, and application of <i>Salmonella paratyphi</i> phage KM16 against <i>Salmonella paratyphi</i> biofilm

description: <i>Salmonella</i> biofilm prevention and control is of great importance. This study, investigated the use of the isolated phage KM16 belonging to the family Myoviridae in the order Caudovirales. The phage genome size was 170,126<b> </b>bp. Almost all phages were adsorbed to the host within 20<b> </b>min. KM16 had a latent period of 70<b> </b>min followed by a rise period of 40<b> </b>min. Phage KM16 had the ability to lytically infect 10 out of the 12 clinical strains of <i>S. paratyphi</i> tested. Phylogenetic analysis indicated that the <i>S. paratyphi</i> 16S rRNA<i>, crispr 1</i> and <i>fimA</i> genes correlated with the lytic spectrum of phage KM16. The lytic spectrum of phage KM16 correlated with <i>Salmonella</i> pili (<i>fimA</i>), and <i>Salmonella</i> pili were the recognition site for phage adsorption to the host. Phage KM16 (MOI<b> </b>=<b> </b>0.1) had a better anti-biofilm effect than kanamycin sulfate (10 ug ml<sup>−1</sup>) in high-concentration <i>Salmonella</i> cultures.
DOI: 10.6084/m9.figshare.14540108
title: Isolation, characterization, and application of <i>Salmonella paratyphi</i> phage KM16 against <i>Salmonella paratyphi</i> biofilm

description: <i>Salmonella</i> biofilm prevention and control is of great importance. This study, investigated the use of the isolated phage KM16 belonging to the family Myoviridae in the order Caudovirales. The phage genome size was 170,126<b> </b>bp. Almost all phages were adsorbed to the host within 20<b> </b>min. KM16 had a latent period of 70<b> </b>min followed by a rise period of 40<b> </b>min. Phage KM16 had the ability to lytically infect 10 out of the 12 clinical strains of <i>S. paratyphi</i> tested. Phylogenetic analysis indicated that the <i>S. paratyphi</i> 16S rRNA<i>, crispr 1</i> and <i>fimA</i> genes correlated with the lytic spectrum of phage KM16. The lytic spectrum of phage KM16 correlated with <i>Salmonella</i> pili (<i>fimA</i>), and <i>Salmonella</i> pili were the recognition site for phage adsorption to the host. Phage KM16 (MOI<b> </b>=<b> </b>0.1) had a better anti-biofilm effect than kanamycin sulfate (10 ug ml<sup>−1</sup>) in high-concentration <i>Salmonella</i> cultures.
DOI: 10.6084/m9.figshare.21351349
title: Additional file 2 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 2: Table S2. The diversity pattern of the N-terminal repeat region in IVP of Pvs230 from global isolates. Related to Fig. 2.
DOI: 10.6084/m9.figshare.7724225.v1
title: Additional file 5: of Co-expression of SpSOS1 and SpAHA1 in transgenic Arabidopsis plants improves salinity tolerance

description: Table S1. Sequences of primers used in this study. Small letters indicate restriction enzyme sites. (XLS 18 kb)
DOI: 10.6084/m9.figshare.17161573
title: Additional file 3 of Multi-omics analysis of an immune-based prognostic predictor in non-small cell lung cancer

description: Additional file 3.
DOI: 10.6084/m9.figshare.17161570
title: Additional file 2 of Multi-omics analysis of an immune-based prognostic predictor in non-small cell lung cancer

description: Additional file 2.
DOI: 10.6084/m9.figshare.17161573.v1
title: Additional file 3 of Multi-omics analysis of an immune-based prognostic predictor in non-small cell lung cancer

description: Additional file 3.