cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11730951.v1
title: Autophagy-Mediated Compartmental Cytoplasmic Deletion is Essential for Tobacco Pollen Germination and Male Fertility

description: In plants, macroautophagy/autophagy has mainly been associated with stress-related processes but how it impacts normal physiological and developmental processes remains largely unexplored. Pollen germination is the critical first step towards fertilization in flowering plants. It is metabolically demanding and relies on high levels of cytoplasmic reorganization activities to support a dramatic morphological transformation that underlies the development of a pollen tube as the conduit to deliver sperm for fertilization. The role of autophagy in this process remains unclear. Here we provide evidence that pollen germination is accompanied by elevated autophagic activity and successful pollen tube emergence depends on autophagy-mediated cytoplasmic deletion. Genetic and cytological experiments demonstrate that inhibition of autophagy prevents pollen germination while induces the persistence of a layer of undegraded cytoplasm at the germination aperture. Together, these results unveil a novel compartmentalized autophagy. Furthermore, high-throughput comparative lipidomic analyses show that suppressed autophagy-induced inhibition of pollen germination is accompanied by altered profiles of stored and signaling lipids. Proteomic analyses reveal that autophagy likely exert its role in pollen germination via downstream mitochondria-related pathways. These findings reveal a critical role for autophagy in initiating pollen germination and provide evidences for compartmental cytoplasmic deletion being crucial for male fertility.
DOI: 10.6084/m9.figshare.11731002.v1
title: Transcription of lncRNA <i>ACoS-AS1</i> is essential to <i>trans</i>-splicing between <i>SlPsy1</i> and <i>ACoS-AS1</i> that causes yellow fruit in tomato

description: Phytoene synthase (PSY) has been considered as an important regulatory enzyme in carotenoids biosynthesis pathway. Previous study finds that the yellow fruit in <i>Solanum lycopersicum</i> var. <i>cerasiforme</i> accession PI 114490 is caused by loss-of-function of SlPSY1 due to <i>trans</i>-splicing between <i>SlPsy1</i> and an unknown gene transcribed from neighbor opposite strand DNA of <i>SlPsy1</i>. The genomic DNA sequences of <i>SlPsy1</i> between red and yellow-fruited tomato lines have one single nucleotide polymorphism (SNP) in the fourth intron and one SSR in the intergenic region. In the current study, the cause of <i>trans</i>-splicing event was further investigated. The data showed that the previously defined unknown gene was a putative long non-coding RNA <i>ACoS-AS1</i> with three variants in many yellow-fruited tomato lines. The intronic SNP and intergenic SSR were tightly associated with <i>trans</i>-splicing event <i>SlPsy1-ACoS-AS1</i>. However, transgenic tomato lines carrying the genomic DNA of <i>SlPsy1</i> from PI 114490 did not generate transcripts of <i>ACoS-AS1</i>and <i>SlPsy1-ACoS-AS1</i> suggesting that only the intronic SNP could not cause the <i>trans</i>-splicing event. Over-expression of <i>SlPsy1-ACoS-AS1</i> in red-fruited tomato line M82 did not have any phenotype change while over-expression of wild type <i>SlPsy1</i> resulted in altered leaf color. Sub-cellular localization analysis showed that SlPSY1-ACoS-AS1 could not enter plastids where SlPSY1 has its enzyme activity. Mutation of <i>ACoS-AS1</i> in PI 114490 generated by CRISPR/Cas9 techniques resulted in red fruits implying that <i>ACoS-AS1</i> was essential to <i>trans</i>-splicing event <i>SlPsy1-ACoS-AS1</i>. The results obtained here will extend knowledge to understand the mechanism of <i>trans</i>-splicing event <i>SlPsy1-ACoS-AS1</i> and provide additional information for regulation of carotenoids biosynthesis.
DOI: 10.6084/m9.figshare.24314023
title: <b>Hydrophobic bulk conservation</b><b> and genetic code determine </b><b>the pattern of </b><b>prokaryotic</b><b> genome</b><b> </b><b>organization</b><b>.</b>

description: Prokaryotic genomes in general exhibit marked organizational asymmetry, and differ substantially in GC-skew, AT-skew, and GS-bias (gene strand bias). Despite enigmatic origins, these organizational features and genomic GC-content have been described to be widely associated with each other recently, providing an opportunity to probe the evolutionary mechanisms. By analyzing sequence data of 4,012 leading strands from all available representative genomes, we found that the unusual nucleotide usage of coding genes under low GC-content contributed to a shift between two organizational patterns in the context of mutational biases. Analysis of artificially established neutral and natural models further suggests that in genes both GC-skew and AT-skew increase with decreasing GC-content, mostly contributed by synonymous substitutions because of genetic code, and by nonsynonymous substitutions because of hydrophobic bulk conservation in amino acid usage, respectively. This novel mechanistic framework in our study highlights the importance of evolutionary processes “operating at lower levels of organization” in the microbial world.
DOI: 10.6084/m9.figshare.24314026
title: Northeast Indian Ocean metagenome dataset

description: Data for contigs, MAGs and other files generated using the Northeastern Indian Ocean microbial dataset.Dataset includes:EIO-MAG.tar.gz 675 non-redundant prokaryotic genomes with ≥ 50% completeness and ≤ 5% contamination.EIO-Contigs.tar.gz: the contigs generated from 25 metagenome.EIO_prokka_annotation.tar.gz: MAG prokka annotation.vOTU.fa.tar.gz : The sequences of the vOTUs .Nonredundant_gene.tar.gz: The Nonredundant gene with KEGG annotation.Compare the MAGs with Ocean DNA and Tara Ocean.zip: The MAGs ecovered here with Ocean DNA and Tara Oceans comparison analysis table.<br><br>
DOI: 10.6084/m9.figshare.7012643
title: Time Series Seasonal Adjustment Using Regularized Singular Value Decomposition

description: We propose a new seasonal adjustment method based on the Regularized Singular Value Decomposition (RSVD) of the matrix obtained by reshaping the seasonal time series data. The method is flexible enough to capture two kinds of seasonality: the fixed seasonality that does not change over time and the time-varying seasonality that varies from one season to another. RSVD represents the time-varying seasonality by a linear combination of several seasonal patterns. The right singular vectors capture multiple seasonal patterns, and the corresponding left singular vectors capture the magnitudes of those seasonal patterns and how they change over time. By assuming the time-varying seasonal patterns change smoothly over time, the RSVD uses penalized least squares with a roughness penalty to effectively extract the left singular vectors. The proposed method applies to seasonal time-series data with a stationary or nonstationary nonseasonal component. The method also has a variant that can handle the case that an abrupt change (i.e., break) may occur in the magnitudes of seasonal patterns. Our proposed method compares favorably with the state-of-art X-13ARIMA-SEATS program on both simulated and real data examples.
DOI: 10.6084/m9.figshare.24314197
title: Table S4. Distribution of FAHFAs

description: This file summarizes the distribution of FAHFAs (family and regioisomer) detected in 12 food samples (kelp, Spirulina, Nostoc commune Vauch, Lentinus edodes, tomato, apple, peanut, black sesame, wheat grains, and rice grains, egg, and fish) and 4 medicinal food samples (lotus plumule, Chinese yam, Lycium chinense, and Coptis chinensis).
DOI: 10.6084/m9.figshare.24314197.v1
title: Table S4. Distribution of FAHFAs

description: This file summarizes the distribution of FAHFAs (family and regioisomer) detected in 12 food samples (kelp, Spirulina, Nostoc commune Vauch, Lentinus edodes, tomato, apple, peanut, black sesame, wheat grains, and rice grains, egg, and fish) and 4 medicinal food samples (lotus plumule, Chinese yam, Lycium chinense, and Coptis chinensis).
DOI: 10.6084/m9.figshare.24314200
title: Table S5. Detected FAHFA lists

description: This file gives the detected FAHFA lists in 12 food samples and 4 medicinal food samples in detail. This table included 16 sheets, and each sheet offers comprehensive information about the detected FAHFA families from one specific food sample, including normal name, FAHFA ID, m/z of the DMED labeling and d4-DMED labeling, and the retention index for each regioisomer.
DOI: 10.6084/m9.figshare.24314200.v1
title: Table S5. Detected FAHFA lists

description: This file gives the detected FAHFA lists in 12 food samples and 4 medicinal food samples in detail. This table included 16 sheets, and each sheet offers comprehensive information about the detected FAHFA families from one specific food sample, including normal name, FAHFA ID, m/z of the DMED labeling and d4-DMED labeling, and the retention index for each regioisomer.
DOI: 10.6084/m9.figshare.24314203
title: Table S6. MS intensity of FAHFA familes

description: This file summarizes the MS intensity of FAHFA families detected in 12 food samples (kelp, Spirulina, Nostoc commune Vauch, Lentinus edodes, tomato, apple, peanut, black sesame, wheat grains, and rice grains, egg, and fish) and 4 medicinal food samples (lotus plumule, Chinese yam, Lycium chinense, and Coptis chinensis).
DOI: 10.6084/m9.figshare.24314203.v1
title: Table S6. MS intensity of FAHFA familes

description: This file summarizes the MS intensity of FAHFA families detected in 12 food samples (kelp, Spirulina, Nostoc commune Vauch, Lentinus edodes, tomato, apple, peanut, black sesame, wheat grains, and rice grains, egg, and fish) and 4 medicinal food samples (lotus plumule, Chinese yam, Lycium chinense, and Coptis chinensis).
DOI: 10.6084/m9.figshare.24314206
title: Table S7. MS intensity of FAHFA regioisomers

description: This file provides the abundance of the detected FAHFA regioisomers in 12 food samples and 4 medicinal food samples in detail. This table included 16 sheets, and each sheet offers comprehensive information about the detected FAHFA families from one specific food sample, including normal name, FAHFA ID, m/z of the DMED labeling and d4-DMED labeling, and the MS intensity for each regioisomer.
DOI: 10.6084/m9.figshare.24314206.v1
title: Table S7. MS intensity of FAHFA regioisomers

description: This file provides the abundance of the detected FAHFA regioisomers in 12 food samples and 4 medicinal food samples in detail. This table included 16 sheets, and each sheet offers comprehensive information about the detected FAHFA families from one specific food sample, including normal name, FAHFA ID, m/z of the DMED labeling and d4-DMED labeling, and the MS intensity for each regioisomer.
DOI: 10.6084/m9.figshare.24314209
title: Table S8. Identified FAHFA regioisomers list

description: This file presents the FAHFA name, MRM transition for both DMED labeling and d4-DMED labeling, retention index, monoisotopic mass (unlabeled), molecular formula, SMILES number and InChIKey number for each identified FAHFA regioisomer.
DOI: 10.6084/m9.figshare.24314209.v1
title: Table S8. Identified FAHFA regioisomers list

description: This file presents the FAHFA name, MRM transition for both DMED labeling and d4-DMED labeling, retention index, monoisotopic mass (unlabeled), molecular formula, SMILES number and InChIKey number for each identified FAHFA regioisomer.
DOI: 10.6084/m9.figshare.12246554
title: Additional file 1 of Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid

description: Additional file 1: Table S1. The demographic and clinical characteristics of PD patients and control individuals.
DOI: 10.6084/m9.figshare.12246581.v1
title: Additional file 4 of Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid

description: Additional file 4. Skyline files of the quantification results for pY39 αβ-syn peptide in the CSF of PD patients and control individuals.
DOI: 10.6084/m9.figshare.12246575
title: Additional file 3 of Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid

description: Additional file 3: Table S2. Quantification results for Y39 αβ-syn and pY39 αβ-syn peptides in the CSF of PD patients and control individuals.
DOI: 10.6084/m9.figshare.14877141
title: Triglyceride–glucose index predicts the risk of gestational diabetes mellitus: a systematic review and meta-analysis

description: We aimed to investigate the potential predictive efficacy of triglyceride–glucose (T/Gly) index for gestational diabetes mellitus (GDM) in a systematic review and meta-analysis. Cohort studies demonstrating the association between T/Gly index measured at the first trimester or before pregnancy and the subsequent incidence of GDM were identified by search of PubMed, Embase, China National Knowledge Infrastructure, and WanFang databases. A random-effect model incorporating the heterogeneity was applied to pool the results. Five cohort studies including 382,213 women were included in this meta-analysis. Compared to those with the lowest category of T/Gly index, women with the highest category of T/Gly index were independently associated with higher risk of subsequent GDM (odds ratio [OR]: 2.52, 95% confidence interval [CI]: 1.33 ∼ 4.67, <i>I</i><sup>2</sup>=65%, <i>p</i>=.004) after adjustment of potential confounding factors including age, body mass index, and family history of diabetes. The association was stronger in prospective cohort studies than retrospective cohort studies (<i>p</i> for subgroup difference=.007), and a significant association was detected in Asian women (OR: 3.30, 95% CI: 1.50–7.28, <i>p</i> =.003), but not in non-Asian women (OR: 0.96, 95% CI: 0.35–2.63, <i>p</i>=.94). Higher T/Gly index may independently predict the risk of GDM in Asian women.
DOI: 10.6084/m9.figshare.7527896
title: Additional file 2: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: PED file of SNP data. (PARTIAL 776 kb)
DOI: 10.6084/m9.figshare.7528037
title: Additional file 2: of RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer

description: DataÂ 1. Fifteen new circRNAs identified by RNA-seq in 4 pairs of CRC and adjacent normal mucosa tissues. (XLS 34 kb)
DOI: 10.6084/m9.figshare.7528037.v1
title: Additional file 2: of RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer

description: DataÂ 1. Fifteen new circRNAs identified by RNA-seq in 4 pairs of CRC and adjacent normal mucosa tissues. (XLS 34 kb)
DOI: 10.6084/m9.figshare.7528049
title: Additional file 4: of RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer

description: DataÂ 3. Analyses of circRNA-miRNA interaction in CRC. Analyses were performed by using miRanda v3.3a software, DIANA-miRPath v.3 platform (Reverse Search module) and KEGG pathways of COLORECTAL CANCER and MicroRNAs in cancer. (XLS 498 kb)
DOI: 10.6084/m9.figshare.7528049.v1
title: Additional file 4: of RNA sequencing reveals the expression profiles of circRNA and indicates that circDDX17 acts as a tumor suppressor in colorectal cancer

description: DataÂ 3. Analyses of circRNA-miRNA interaction in CRC. Analyses were performed by using miRanda v3.3a software, DIANA-miRPath v.3 platform (Reverse Search module) and KEGG pathways of COLORECTAL CANCER and MicroRNAs in cancer. (XLS 498 kb)
DOI: 10.6084/m9.figshare.7527890
title: Additional file 1: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: MAP file of SNP data. (MAP 3577 kb)
DOI: 10.6084/m9.figshare.12246461.v1
title: Additional file 7 of Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth

description: Additional file 7: Table S7. Tissue specificity regulatory elements found in the GaCASP27 promoter region.
DOI: 10.6084/m9.figshare.19586561.v1
title: H22954, a long non-coding RNA, inhibits glucose uptake in leukemia cells in a GLUT10-dependent manner

description: To investigate the performance of H22954, a novel long non-coding RNA (lncRNA), in inhibiting glucose uptake in leukemia cells. <sup>18</sup>F-FDG uptake, RNA half-life quantitative real-time polymerase chain reaction (qRT-PCR) and luciferase assays were performed to detect the glucose uptake in the condition of leukemia. Microarrays and qRT-PCR analyses were used to identify the related genes or proteins and elucidate the underlying these processes. H22954, a novel lncRNA, inhibited glucose uptake in leukemia cells. Using bioinformatics and microarray analyses, GLUT10 was identified as a possible target molecule of H22954. H22954 targeted the 3′untranslated region of GLUT10. In the luciferase assay, the luciferase activity of pGL3-GLUT10 was inhibited by H22954. Consistently, H22954 expression levels were inversely correlated with GLUT10 expression in cell lines and acute myeloid leukemia (AML) samples. Conversely, the degradation rate of <i>GLUT10</i> mRNA was increased after H22954 overexpression. Moreover, glucose uptake was recovered when the GLUT10-interaction sites in H22954 were mutated. The lncRNA H22954 regulated GLUT10 expression to inhibit glucose uptake in leukemia cells. Our findings provide potentially valuable data for designing new targeted strategies based on H22954.
DOI: 10.6084/m9.figshare.7527926
title: Additional file 7: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S2. The features of genes based on RODATRIPS. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7527926.v1
title: Additional file 7: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S2. The features of genes based on RODATRIPS. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7527929
title: Additional file 8: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S3. The features of genes based on GRAMMAR-GC and RODATRIPS. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7527953.v1
title: Additional file 2 of Evaluation of top-down mass spectral identification with homologous protein sequences

description: Identifications from the EC data set. (XLSX 583 kb)
DOI: 10.6084/m9.figshare.12246554.v1
title: Additional file 1 of Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid

description: Additional file 1: Table S1. The demographic and clinical characteristics of PD patients and control individuals.
DOI: 10.6084/m9.figshare.7527917
title: Additional file 6: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S1. The features of genes based on GRAMMAR-GC. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.7527929.v1
title: Additional file 8: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S3. The features of genes based on GRAMMAR-GC and RODATRIPS. (XLSX 26 kb)
DOI: 10.6084/m9.figshare.7527935
title: Additional file 9: of Genome-wide association study of Mycobacterium avium subspecies Paratuberculosis infection in Chinese Holstein

description: Table S4. Functional enrichment of GO and Pathway analysis of 343 genes. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.7013156
title: <i>P–T–time</i> (phengite Ar closure) history of spatially close-outcropping HP and UHP oceanic eclogites (southwestern Tianshan): implication for a potential deep juxtaposing process during exhumation?

description: The Chinese southwestern Tianshan HP–UHP/LT metamorphic complex possesses well-preserved mafic layers, tectonic slices/blocks, boudins/lens of different sizes, and lithology embedded within dominant metavolcanoclastics. A recent study on the ultra-high pressure (UHP) eclogite revealed a short timescale of exhumation (≤10 Ma, ~315 ± 5 Ma). However, controversies still exist on some key questions: (1) the reasonable interpretation of spatially close-outcropped high pressure (HP) and UHP slices with respect to regional geodynamics, and (2) if the previous regional scatter Ar–Ar ages proved the existence of internally coherent sub-belts or troubled by dating on samples with notable <sup>40</sup>Ar retention. This study focusses on detailed <i>P</i>–<i>T</i>–time (phengite Ar closure) recovery of samples from a HP eclogite lens and its host rock, the UHP thick-layered eclogite. Based on data from bulk–rock, microprobe analysis, and muscovite Ar–Ar chronological dating, we link phengite growth to potential garnet growth stages via thermodynamic modelling. Facilitated by the <i>P</i>–<i>T</i>–Ar retention% graph, we collect all the regional muscovite Ar–Ar data together with results in this study for evaluating the significance of regional muscovite Ar–Ar ages and set back to geodynamics. According to modelling results, the HP lens eclogite reached peak metamorphism at ~550°C, 2.50 GPa with an Ar–Ar muscovite plateau age of 316.9 ± 1.0 Ma that could date the mass phengite growth event during prograde metamorphism. In contrast, the UHP layered eclogite experienced UHP peak burial at ~510°C, 2.95 GPa, and then to HP peak metamorphism at ~560°C, 2.60 GPa with ~311.6 ± 0.7 Ma plateau age that may constrain the cooling age during early exhumation. Noteworthy, both of them share a quite similar early exhumation path despite bearing contrasting prograde metamorphic experiences. With considering updated regional exhumation pattern, this might imply the existence of a potential deep juxtaposing (capture) process between HP slices and exhumating UHP complex, at about 45–60 km depth along subduction plate interface.
DOI: 10.6084/m9.figshare.7527959.v1
title: Additional file 3 of Evaluation of top-down mass spectral identification with homologous protein sequences

description: Identifications from the MCF-7 data set. (XLSX 351 kb)