cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7879382.v1
title: Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective

description: The destruction of mitochondria through macroautophagy (autophagy) has been recognised as a major route of mitochondrial protein degradation since its discovery more than 50 years ago, but fundamental questions remain unanswered. First, how much mitochondrial protein turnover occurs through auto-phagy? Mitochondrial proteins are also degraded by nonautophagic mechanisms, and the proportion of mitochondrial protein turnover that occurs through autophagy is still unknown. Second, does auto-phagy degrade mitochondrial proteins uniformly or selectively? Autophagy was originally thought to degrade all mitochondrial proteins at the same rate, but recent work suggests that mitochondrial autophagy may be protein selective. To investigate these questions, we used a proteomics-based approach in the fruit fly <i>Drosophila melanogaster</i>, comparing mitochondrial protein turnover rates in autophagy-deficient <i>Atg7</i> mutants and controls. We found that ~35% of mitochondrial protein turnover occurred via autophagy. Similar analyses using <i>parkin</i> mutants revealed that parkin-dependent mitophagy accounted for ~25% of mitochondrial protein turnover, suggesting that most mitochondrial autophagy specifically eliminates dysfunctional mitochondria. We also found that our results were incompatible with uniform autophagic turnover of mitochondrial proteins and consistent with protein-selective autophagy. In particular, the autophagic turnover rates of individual mitochondrial proteins varied widely, and only a small amount of the variation could be attributed to tissue differences in mitochondrial composition and autophagy rate. Furthermore, analyses comparing autophagy-deficient and control human fibroblasts revealed diverse autophagy-dependent turnover rates even in homogeneous cells. In summary, our work indicates that autophagy acts selectively on mitochondrial proteins, and that most mitochondrial protein turnover occurs through non-autophagic processes. <b>Abbreviations:</b><i>Atg5: Autophagy-related 5</i> (<i>Drosophila); ATG5: autophagy related 5</i> (human); <i>Atg7: Autophagy-related 7</i> (<i>Drosophila); ATG7: autophagy related 7</i> (human); DNA: deoxyribonucleic acid; ER: endoplasmic reticulum; GFP: green fluorescent protein; MS: mass spectrometry; <i>park: parkin</i> (<i>Drosophila); Pink1: PTEN-induced putative kinase 1</i> (<i>Drosophila); PINK1: PTEN-induced kinase 1</i> (human); <i>PRKN: parkin RBR E3 ubiquitin protein ligase</i> (human); RNA: ribonucleic acid; SD: standard deviation; Ub: ubiquitin/ubiquitinated; WT: wild-type; <i>YME1L: YME1 like ATPase</i> (<i>Drosophila); YME1L1: YME1 like 1 ATPase</i> (human)
DOI: 10.6084/m9.figshare.7879346.v3
title: Computational identification and antifungal bioassay reveals phytosterols as potential inhibitor of <i>Alternaria arborescens</i>

description: <i>Alternaria arborescens</i> is a major pathogen for crops like tomato, tangerine and so on and its control is mostly dependent on the application of chemical agents. Plants as the sources of natural products are very attractive option for developing eco-friendly and natural antifungal agents. In this study, we modeled three-dimensional structure of chorismate synthase (CS) enzyme from <i>A. arborescens</i>. Docking studies of phytosterols, namely, γ-sitosterol and β-sitosterol, with CS showed them to be potential inhibitor of CS. To explore the stability and conformational flexibility of all the <i>AaCS</i> complex systems, molecular dynamics simulations were performed. None of the putative inhibitors as well as β- and γ-sitosterol showed interaction with the FMNH<sub>2</sub> binding pocket of the tomato CS (major host of <i>A. arborescens</i>) indicating their suitability as antifungal compounds inhibiting the shikimate pathway without causing any harm to the host. An <i>in vivo</i> antifungal bioassay showed a significant reduction in fungal growth in the presence of β-sitosterol (500 ppm) which resulted in ∼23% and ∼17% reduction in fungal fresh and dry weight, respectively, at 8 days after inoculation. This study provides experimental evidence establishing natural sterols like β-sitosterol can be useful in curbing <i>A. arborescens</i> damage in an eco-friendly manner. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7879346.v2
title: Computational identification and antifungal bioassay reveals phytosterols as potential inhibitor of <i>Alternaria arborescens</i>

description: <i>Alternaria arborescens</i> is a major pathogen for crops like tomato, tangerine and so on and its control is mostly dependent on the application of chemical agents. Plants as the sources of natural products are very attractive option for developing eco-friendly and natural antifungal agents. In this study, we modeled three-dimensional structure of chorismate synthase (CS) enzyme from <i>A. arborescens</i>. Docking studies of phytosterols, namely, γ-sitosterol and β-sitosterol, with CS showed them to be potential inhibitor of CS. To explore the stability and conformational flexibility of all the <i>AaCS</i> complex systems, molecular dynamics simulations were performed. None of the putative inhibitors as well as β- and γ-sitosterol showed interaction with the FMNH<sub>2</sub> binding pocket of the tomato CS (major host of <i>A. arborescens</i>) indicating their suitability as antifungal compounds inhibiting the shikimate pathway without causing any harm to the host. An <i>in vivo</i> antifungal bioassay showed a significant reduction in fungal growth in the presence of β-sitosterol (500 ppm) which resulted in ∼23% and ∼17% reduction in fungal fresh and dry weight, respectively, at 8 days after inoculation. This study provides experimental evidence establishing natural sterols like β-sitosterol can be useful in curbing <i>A. arborescens</i> damage in an eco-friendly manner. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7879253
title: Additional file 7: of Evolution of Mutator transposable elements across eukaryotic diversity

description: The amino acid alignment used to perform our phylogenetic analysis. (FASTA 6699 kb)
DOI: 10.6084/m9.figshare.7879259
title: Computer Codes for Illustrative Simulations from Multi-resolution dimer models in heat baths with short-range and long-range interactions

description: Computer codes used to compute illustrative results in Figures 3, 4, 5 and 6.
DOI: 10.6084/m9.figshare.7879250
title: Additional file 6: of Evolution of Mutator transposable elements across eukaryotic diversity

description: Output trees from ClusterPicker with each inferred cluster coloured alternately, at the genetic distance thresholds of: 2.6, 3.6, and 4.2%. (ZIP 170 kb)
DOI: 10.6084/m9.figshare.7879253.v1
title: Additional file 7: of Evolution of Mutator transposable elements across eukaryotic diversity

description: The amino acid alignment used to perform our phylogenetic analysis. (FASTA 6699 kb)
DOI: 10.6084/m9.figshare.7879241
title: Additional file 3: of Evolution of Mutator transposable elements across eukaryotic diversity

description: An amino acid alignment of elements that were removed from the phylogenetic analysis as a consequence of their lack of alignment with other MULE DDE domains. (FASTA 94 kb)
DOI: 10.6084/m9.figshare.7879244
title: Additional file 4: of Evolution of Mutator transposable elements across eukaryotic diversity

description: Table S1. Information on the different clusters indicated in Additional file 1. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7879259.v1
title: Computer Codes for Illustrative Simulations from Multi-resolution dimer models in heat baths with short-range and long-range interactions

description: Computer codes used to compute illustrative results in Figures 3, 4, 5 and 6.
DOI: 10.6084/m9.figshare.7879238
title: Additional file 2: of Evolution of Mutator transposable elements across eukaryotic diversity

description: Table S2. Genomic features and characteristics of each Ghost, Spectre and new aphid Phantom elements identified from the aphid genomes analysed. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7879241.v1
title: Additional file 3: of Evolution of Mutator transposable elements across eukaryotic diversity

description: An amino acid alignment of elements that were removed from the phylogenetic analysis as a consequence of their lack of alignment with other MULE DDE domains. (FASTA 94 kb)
DOI: 10.6084/m9.figshare.7879244.v1
title: Additional file 4: of Evolution of Mutator transposable elements across eukaryotic diversity

description: Table S1. Information on the different clusters indicated in Additional file 1. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.7879250.v1
title: Additional file 6: of Evolution of Mutator transposable elements across eukaryotic diversity

description: Output trees from ClusterPicker with each inferred cluster coloured alternately, at the genetic distance thresholds of: 2.6, 3.6, and 4.2%. (ZIP 170 kb)
DOI: 10.6084/m9.figshare.7879238.v1
title: Additional file 2: of Evolution of Mutator transposable elements across eukaryotic diversity

description: Table S2. Genomic features and characteristics of each Ghost, Spectre and new aphid Phantom elements identified from the aphid genomes analysed. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.7879181
title: Additional file 3: of Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium

description: Table S3. Exhaustive and top-20 lists of up- and down-regulated genes in ipsilateral vs. contralateral isthmus in post-partum lactating (L), non-lactating (NL) cows and heifers (H) on Day 3 of the estrous cycle. Lists of associated Gene Ontology (GO) terms are provided for all comparisons. The Biological Process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways/compounds shared between the three groups are also provided. (XLSX 603 kb)
DOI: 10.6084/m9.figshare.7879175
title: Additional file 2: of Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium

description: Table S2. Exhaustive lists of up- and down-regulated genes in ipsilateral vs. contralateral ampulla in post-partum lactating (L), non-lactating (NL) cows and heifers (H) on Day 3 of the estrous cycle. Lists of associated Gene Ontology (GO) terms are provided for ipsilateral vs. contralateral ampullas in NL and H. (XLSX 231 kb)
DOI: 10.6084/m9.figshare.7879181.v1
title: Additional file 3: of Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium

description: Table S3. Exhaustive and top-20 lists of up- and down-regulated genes in ipsilateral vs. contralateral isthmus in post-partum lactating (L), non-lactating (NL) cows and heifers (H) on Day 3 of the estrous cycle. Lists of associated Gene Ontology (GO) terms are provided for all comparisons. The Biological Process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways/compounds shared between the three groups are also provided. (XLSX 603 kb)
DOI: 10.6084/m9.figshare.7879175.v1
title: Additional file 2: of Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium

description: Table S2. Exhaustive lists of up- and down-regulated genes in ipsilateral vs. contralateral ampulla in post-partum lactating (L), non-lactating (NL) cows and heifers (H) on Day 3 of the estrous cycle. Lists of associated Gene Ontology (GO) terms are provided for ipsilateral vs. contralateral ampullas in NL and H. (XLSX 231 kb)
DOI: 10.6084/m9.figshare.7879169
title: Additional file 1: of Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium

description: Table S1. Exhaustive and top-20 lists of up- and down-regulated genes in post-partum lactating (L) vs. non-lactating (NL) cows, heifers (H) vs. L, and H vs. NL comparisons in the ampulla and isthmus ipsilateral to the corpus luteum on Day 3 of the estrous cycle. Lists of associated Gene Ontology (GO) terms are provided for the H vs. NL and H vs. NL comparisons in the isthmus. (XLSX 106 kb)
DOI: 10.5281/zenodo.3999183
title: Unprecedented failure of the Northeastern Indian Monsoon and recent water scarcity

description: Dataset used in the publication on "<strong>Unprecedented failure of the Northeastern Indian Monsoon and recent water scarcity" submitted in GRL.</strong>
DOI: 10.5281/zenodo.3999182
title: Unprecedented failure of the Northeastern Indian Monsoon and recent water scarcity

description: Dataset used in the publication on "<strong>Unprecedented failure of the Northeastern Indian Monsoon and recent water scarcity" submitted in GRL.</strong>
DOI: 10.6084/m9.figshare.7879169.v1
title: Additional file 1: of Relative effects of location relative to the corpus luteum and lactation on the transcriptome of the bovine oviduct epithelium

description: Table S1. Exhaustive and top-20 lists of up- and down-regulated genes in post-partum lactating (L) vs. non-lactating (NL) cows, heifers (H) vs. L, and H vs. NL comparisons in the ampulla and isthmus ipsilateral to the corpus luteum on Day 3 of the estrous cycle. Lists of associated Gene Ontology (GO) terms are provided for the H vs. NL and H vs. NL comparisons in the isthmus. (XLSX 106 kb)
DOI: 10.6084/m9.figshare.7879151
title: Additional file1: of Mortality advantage among migrants according to duration of stay in France, 2004–2014

description: Table S1. Hazard ratios (log) for all-cause mortality among male migrants over duration of stay, ages 20+, baseline and final models. (1) baseline year of entry adjusted for but not shown (2) significant levels at ** p
DOI: 10.6084/m9.figshare.7879145
title: Additional file 2: of Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations

description: 16S rRNA gene sequences produced in the study in text format. (TXT 49 kb)
DOI: 10.6084/m9.figshare.7879148
title: Additional file 3: of Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations

description: 16S rRNA gene sequencesâ BLASTN hits in zipped HTML format. (ZIP 15810 kb)
DOI: 10.6084/m9.figshare.7879151.v1
title: Additional file1: of Mortality advantage among migrants according to duration of stay in France, 2004–2014

description: Table S1. Hazard ratios (log) for all-cause mortality among male migrants over duration of stay, ages 20+, baseline and final models. (1) baseline year of entry adjusted for but not shown (2) significant levels at ** p
DOI: 10.6084/m9.figshare.7879145.v1
title: Additional file 2: of Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations

description: 16S rRNA gene sequences produced in the study in text format. (TXT 49 kb)
DOI: 10.6084/m9.figshare.7879148.v1
title: Additional file 3: of Isothermal microcalorimetry for thermal viable count of microorganisms in pure cultures and stabilized formulations

description: 16S rRNA gene sequencesâ BLASTN hits in zipped HTML format. (ZIP 15810 kb)
DOI: 10.6084/m9.figshare.7879133
title: Additional file 2: of Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization

description: Table S1. The FPKM values of identified EIN3/EIL genes in four major tissues of B. napus and its diploid progenitors (B. rapa and B. oleracea). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7879133.v1
title: Additional file 2: of Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization

description: Table S1. The FPKM values of identified EIN3/EIL genes in four major tissues of B. napus and its diploid progenitors (B. rapa and B. oleracea). (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7879121
title: Additional file 1: of Trabectedin triggers direct and NK-mediated cytotoxicity in multiple myeloma

description: Table S1. List of genes included in DNA repair systems. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7879115
title: Additional file 1: of Impaired chair-to-bed transfer ability leads to longer hospital stays among elderly patients

description: data bank. The file corresponds to the data bank, including every informationâ s related to this article. (XLSX 247 kb)
DOI: 10.6084/m9.figshare.7879109
title: MOESM1 of Estimation of phytochemical constituents and in vitro antioxidant potencies of Brachychiton populneus (Schott & Endl.) R.Br.

description: Additional file 1. Phytochemical and antioxidant assays data. The data include the DPPH, Iron chelation, nitric oxide, hydroxyl, B-carotene, phenolics and flavonoids, phosphomolybdenum and reducing power assays sub files. It include all the data generated and analyzed for this study.
DOI: 10.6084/m9.figshare.7879115.v1
title: Additional file 1: of Impaired chair-to-bed transfer ability leads to longer hospital stays among elderly patients

description: data bank. The file corresponds to the data bank, including every informationâ s related to this article. (XLSX 247 kb)
DOI: 10.6084/m9.figshare.7879121.v1
title: Additional file 1: of Trabectedin triggers direct and NK-mediated cytotoxicity in multiple myeloma

description: Table S1. List of genes included in DNA repair systems. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7879109.v1
title: MOESM1 of Estimation of phytochemical constituents and in vitro antioxidant potencies of Brachychiton populneus (Schott & Endl.) R.Br.

description: Additional file 1. Phytochemical and antioxidant assays data. The data include the DPPH, Iron chelation, nitric oxide, hydroxyl, B-carotene, phenolics and flavonoids, phosphomolybdenum and reducing power assays sub files. It include all the data generated and analyzed for this study.
DOI: 10.6084/m9.figshare.7879097
title: Additional file 1: of Acceptability of a family-centered newborn care model among providers and receivers of care in a Public Health Setting: a qualitative study from India

description: Code list (RTF 52 kb)
DOI: 10.6084/m9.figshare.7879097.v1
title: Additional file 1: of Acceptability of a family-centered newborn care model among providers and receivers of care in a Public Health Setting: a qualitative study from India

description: Code list (RTF 52 kb)
DOI: 10.6084/m9.figshare.7879037
title: MOESM1 of Too many tags spoil the metadata: investigating the knowledge management of scientific research with semantic web technologies

description: Additional file 1. A file describing how to access the focus groups questions and transcripts.
DOI: 10.6084/m9.figshare.7879037.v1
title: MOESM1 of Too many tags spoil the metadata: investigating the knowledge management of scientific research with semantic web technologies

description: Additional file 1. A file describing how to access the focus groups questions and transcripts.
DOI: 10.6084/m9.figshare.7879004
title: Additional file 6: of Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

description: (Movies). Non-targeting siRNA (movie 1) and siPSMA6 (movie 2) were transfected at 25 nM into PANC-1 cells and images were acquired every 4 h with an IncuCyte Live Cell Analysis System. Non-targeting siRNA (movie 3) and siPSMA6 (movie 4) were transfected at 25 nM into HPNE cells and images were acquired every 4 h with an IncuCyte Live Cell Analysis System. (ZIP 34546 kb)
DOI: 10.6084/m9.figshare.7879004.v1
title: Additional file 6: of Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

description: (Movies). Non-targeting siRNA (movie 1) and siPSMA6 (movie 2) were transfected at 25 nM into PANC-1 cells and images were acquired every 4 h with an IncuCyte Live Cell Analysis System. Non-targeting siRNA (movie 3) and siPSMA6 (movie 4) were transfected at 25 nM into HPNE cells and images were acquired every 4 h with an IncuCyte Live Cell Analysis System. (ZIP 34546 kb)
DOI: 10.6084/m9.figshare.7878980
title: Additional file 2: of Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

description: Sequencing primers and barcodes for PCR amplification andÂ Next-Gen Sequencing of amplicons. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7878986
title: Additional file 3: of Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

description: Ranked gene listÂ results from theÂ negative selection CRISPR screen.Â (XLSX 1554 kb)
DOI: 10.6084/m9.figshare.7878977
title: Additional file 5: of An â Axiom Cajanus SNP Arrayâ based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S5. Epistatic QTLs among two yearsâ data for cleistogamous flower and shriveled seed in pigeonpea. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7878986.v1
title: Additional file 3: of Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

description: Ranked gene listÂ results from theÂ negative selection CRISPR screen.Â (XLSX 1554 kb)
DOI: 10.6084/m9.figshare.7878968
title: Additional file 4: of An â Axiom Cajanus SNP Arrayâ based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S4. List of genes and their functions in QTL regions for shriveled seeds trait. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7878977.v1
title: Additional file 5: of An â Axiom Cajanus SNP Arrayâ based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S5. Epistatic QTLs among two yearsâ data for cleistogamous flower and shriveled seed in pigeonpea. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.7878980.v1
title: Additional file 2: of Genome-wide CRISPR screen reveals PSMA6 to be an essential gene in pancreatic cancer cells

description: Sequencing primers and barcodes for PCR amplification andÂ Next-Gen Sequencing of amplicons. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7878953
title: Additional file 2: of An “Axiom Cajanus SNP Array” based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S2. SNP ID, map position, genotyping data and P value for 6 .8K SNPs used to construct genetic map in RILs developed from ICPL 99010 × ICP 5529 (XLSX 1988 kb)
DOI: 10.6084/m9.figshare.7878968.v1
title: Additional file 4: of An â Axiom Cajanus SNP Arrayâ based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S4. List of genes and their functions in QTL regions for shriveled seeds trait. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7878953.v1
title: Additional file 2: of An “Axiom Cajanus SNP Array” based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S2. SNP ID, map position, genotyping data and P value for 6 .8K SNPs used to construct genetic map in RILs developed from ICPL 99010 × ICP 5529 (XLSX 1988 kb)
DOI: 10.6084/m9.figshare.7878962
title: Additional file 3: of An “Axiom Cajanus SNP Array” based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S3. List of genes and their functions in the 42 kb region of the consistent QTL “qCl3.2” for cleistogamous flower. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7878947
title: Additional file 1: of An â Axiom Cajanus SNP Arrayâ based high density genetic map and QTL mapping for high-selfing flower and seed quality traits in pigeonpea

description: Table S1. Chi-square distribution for cleistogamous flower and shriveled seed traits in RILs. (XLSX 10 kb)