cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21382985.v1
title: Additional file 9 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 9: Table S6. Differentially expressed miRNAs in atm mutated flies.
DOI: 10.58032/agh/kw3dmk
title: Data collected via Scopus API showing scientific cooperation between authors based on their country of affiliation

description: To build a set of 13 810 394 scientific papers, we collect and analyse bibliographic descriptions of papers available through the Scopus API [accessed on July 2022].
DOI: 10.6084/m9.figshare.11945811
title: Additional file 8 of Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo

description: Additional file 8. The known DGAT amino acid sequences in different organisms obtained from UniProt (https://www.uniprot.org/).
DOI: 10.6084/m9.figshare.11945811.v1
title: Additional file 8 of Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo

description: Additional file 8. The known DGAT amino acid sequences in different organisms obtained from UniProt (https://www.uniprot.org/).
DOI: 10.6084/m9.figshare.11945817
title: Additional file 9 of Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo

description: Additional file 9. The identified SNP within 0.5â€‰Mb genomic window around each DGAT in buffalo.
DOI: 10.6084/m9.figshare.11945817.v1
title: Additional file 9 of Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo

description: Additional file 9. The identified SNP within 0.5â€‰Mb genomic window around each DGAT in buffalo.
DOI: 10.6084/m9.figshare.16664426
title: Additional file 10 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 10: Supplementary Table 4. REDI input. 107,053 distinct RNA-editing sites provided as input to SCReadCounts.
DOI: 10.6084/m9.figshare.16664426.v1
title: Additional file 10 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 10: Supplementary Table 4. REDI input. 107,053 distinct RNA-editing sites provided as input to SCReadCounts.
DOI: 10.6084/m9.figshare.16664438
title: Additional file 14 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 14: Supplementary Table 8. KRAS output in Discovery mode. 30 distinct SNVs that do not coincide with known germline variants in the coding sequence of KRAS.
DOI: 10.6084/m9.figshare.21382954.v1
title: Additional file 1 of Comparison of femoral mechanics before and after internal fixation removal and the effect of sclerosis on femoral stress: a finite element analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.21382957.v1
title: Additional file 2 of Comparison of femoral mechanics before and after internal fixation removal and the effect of sclerosis on femoral stress: a finite element analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.16664438.v1
title: Additional file 14 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 14: Supplementary Table 8. KRAS output in Discovery mode. 30 distinct SNVs that do not coincide with known germline variants in the coding sequence of KRAS.
DOI: 10.6084/m9.figshare.16664353
title: Additional file 1 of Perceived social support and diet quality among ethnic minority groups in Yunnan Province, Southwestern China: a cross-sectional study

description: Additional file 1: Table S1. Components of DBI-16.
DOI: 10.6084/m9.figshare.16664429.v1
title: Additional file 11 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 11: Supplementary Table 5. REDI output. 72 positions found by SCReadCounts to be edited in at least 2 cells in one or more of the 7 neuroblastoma samples.
DOI: 10.6084/m9.figshare.16664353.v1
title: Additional file 1 of Perceived social support and diet quality among ethnic minority groups in Yunnan Province, Southwestern China: a cross-sectional study

description: Additional file 1: Table S1. Components of DBI-16.
DOI: 10.6084/m9.figshare.16664429
title: Additional file 11 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 11: Supplementary Table 5. REDI output. 72 positions found by SCReadCounts to be edited in at least 2 cells in one or more of the 7 neuroblastoma samples.
DOI: 10.6084/m9.figshare.21382954
title: Additional file 1 of Comparison of femoral mechanics before and after internal fixation removal and the effect of sclerosis on femoral stress: a finite element analysis

description: Additional file 1.
DOI: 10.6084/m9.figshare.21382957
title: Additional file 2 of Comparison of femoral mechanics before and after internal fixation removal and the effect of sclerosis on femoral stress: a finite element analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.25273348
title: RNA sequencing data TBP ARPE

description: Data related to Frank van Gemert et al. 2024Files to contain the the fastsq files and normalized gene expression values of TBP ARPE cells. These data were used to generate to Figure 6A, Supplemental Figure 2J and 4.
DOI: 10.6084/m9.figshare.25273348.v1
title: RNA sequencing data TBP ARPE

description: Data related to Frank van Gemert et al. 2024Files to contain the the fastsq files and normalized gene expression values of TBP ARPE cells. These data were used to generate to Figure 6A, Supplemental Figure 2J and 4.
DOI: 10.6084/m9.figshare.25273600
title: Supplementary Material for: Clinical Utility of Whole-Genome Analysis as One-for-All Test for Breast Cancer: A Case Series

description: <b><i>Introduction:</i></b> Breast cancer exhibits vast genomic diversity, leading to varied clinical manifestations. Integrating molecular subtyping with in-depth genomic profiling is pivotal for informed treatment choices and prognostic insights. Whole-genome clinical analysis provides a holistic view of genome-wide variations, capturing structural changes and affirming tumor suppressor gene loss of heterozygosity. <b><i>Case Presentation:</i></b> Here we detail four unique breast cancer cases from Seoul St. Mary’s Hospital, highlighting the actionable benefits and clinical value of whole-genome sequencing (WGS). As an all-in-one test, WGS demonstrates significant clinical utility in these cases, including: (1) detecting homologous recombination deficiency with underlying somatic causal variants (case 1), (2) distinguishing double primary cancer from metastasis (case 2), (3) uncovering microsatellite instability (case 3), and (4) identifying rare germline pathogenic variants in TP53 gene (case 4). Our observations underscore the enhanced clinical relevance of WGS-based testing beyond pinpointing a few driver mutations in conventional targeted panel sequencing platforms. <b><i>Conclusion:</i></b> With genomic advancements and decreasing sequencing costs, WGS stands out as a transformative tool in oncology, paving the way for personalized treatment plans rooted in individual genetic blueprints.
DOI: 10.6084/m9.figshare.25273240
title: original data.rar

description: ATG5-mediated keratinocyte ferroptosis promotes M1 polarizationof macrophages to aggravate UVB-induced skin inflammation
DOI: 10.6084/m9.figshare.25273240.v1
title: original data.rar

description: ATG5-mediated keratinocyte ferroptosis promotes M1 polarizationof macrophages to aggravate UVB-induced skin inflammation
DOI: 10.6084/m9.figshare.25273600.v1
title: Supplementary Material for: Clinical Utility of Whole-Genome Analysis as One-for-All Test for Breast Cancer: A Case Series

description: <b><i>Introduction:</i></b> Breast cancer exhibits vast genomic diversity, leading to varied clinical manifestations. Integrating molecular subtyping with in-depth genomic profiling is pivotal for informed treatment choices and prognostic insights. Whole-genome clinical analysis provides a holistic view of genome-wide variations, capturing structural changes and affirming tumor suppressor gene loss of heterozygosity. <b><i>Case Presentation:</i></b> Here we detail four unique breast cancer cases from Seoul St. Mary’s Hospital, highlighting the actionable benefits and clinical value of whole-genome sequencing (WGS). As an all-in-one test, WGS demonstrates significant clinical utility in these cases, including: (1) detecting homologous recombination deficiency with underlying somatic causal variants (case 1), (2) distinguishing double primary cancer from metastasis (case 2), (3) uncovering microsatellite instability (case 3), and (4) identifying rare germline pathogenic variants in TP53 gene (case 4). Our observations underscore the enhanced clinical relevance of WGS-based testing beyond pinpointing a few driver mutations in conventional targeted panel sequencing platforms. <b><i>Conclusion:</i></b> With genomic advancements and decreasing sequencing costs, WGS stands out as a transformative tool in oncology, paving the way for personalized treatment plans rooted in individual genetic blueprints.
DOI: 10.6084/m9.figshare.11945877.v1
title: Additional file 2 of Different adiposity indices and their associations with hypertension among Chinese population from Jiangxi province

description: Additional file 2 Table S1. Minimal data set. This is the S1_S1 Table. Minimal data set Title. This is the S1 Table. Minimal data set legend.
DOI: 10.6084/m9.figshare.11945925
title: Additional file 8 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 8: Data Set S1. lncRNA TPM result.
DOI: 10.6084/m9.figshare.11945877
title: Additional file 2 of Different adiposity indices and their associations with hypertension among Chinese population from Jiangxi province

description: Additional file 2 Table S1. Minimal data set. This is the S1_S1 Table. Minimal data set Title. This is the S1 Table. Minimal data set legend.
DOI: 10.6084/m9.figshare.11945925.v1
title: Additional file 8 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 8: Data Set S1. lncRNA TPM result.
DOI: 10.6084/m9.figshare.11945928
title: Additional file 9 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 9: Data Set S2. lncRNA sequence.
DOI: 10.6084/m9.figshare.11945928.v1
title: Additional file 9 of Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

description: Additional file 9: Data Set S2. lncRNA sequence.
DOI: 10.6084/m9.figshare.16664465
title: Additional file 9 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 9: Supplementary Table 3. COSMIC output. 450 distinct COSMIC mutations found by SCReadCounts to be expressed in at least 4 individual cells in one or more of the 7 neuroblastoma samples.
DOI: 10.6084/m9.figshare.16664465.v1
title: Additional file 9 of SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data

description: Additional file 9: Supplementary Table 3. COSMIC output. 450 distinct COSMIC mutations found by SCReadCounts to be expressed in at least 4 individual cells in one or more of the 7 neuroblastoma samples.
DOI: 10.6084/m9.figshare.7227326
title: A non-canonical autophagy-dependent role of the ATG16L1<sup>T300A</sup> variant in urothelial vesicular trafficking and uropathogenic <i>Escherichia coli</i> persistence

description: 50% of Caucasians carry a Thr300Ala variant (T300A) in the protein encoded by the macroautophagy/autophagy gene <i>ATG16L1</i>. Here, we show that the T300A variant confers protection against urinary tract infections (UTIs), the most common infectious disease in women. Using knockin mice carrying the human T300A variant, we show that the variant limits the UTI-causing bacteria, uropathogenic <i>Escherichia coli</i> (UPEC), from establishing persistent intracellular reservoirs, which can seed UTI recurrence. This phenotype is recapitulated in mice lacking <i>Atg16l1</i> or <i>Atg7</i> exclusively in the urothelium. We further show that mice with the T300A variant exhibit urothelial cellular abnormalities, including vesicular congestion and aberrant accumulation of UPK (uroplakin) proteins. Importantly, presence of the T300A variant in humans is associated with similar urothelial architectural abnormalities, indicating an evolutionarily conserved impact. Mechanistically, we show that the reduced bacterial persistence is independent of basal autophagic flux or proinflammatory cytokine responses and does not involve <i>Atg14</i> or <i>Epg5</i>. However, the T300A variant is associated with increased expression of the small GTPase <i>Rab33b</i>; RAB33B interacts with ATG16L1, as well as other secretory RABs, RAB27B and RAB11A, important for UPEC exocytosis from the urothelium. Finally, inhibition of secretory RABs in bladder epithelial cells increases intracellular UPEC load. Together, our results reveal that UPEC selectively utilize genes important for autophagosome formation to persist in the urothelium, and that the presence of the T300A variant in ATG16L1 is associated with changes in urothelial vesicle trafficking, which disrupts the ability of UPEC to persist, thereby limiting the risk of recurrent UTIs. <b>Abbreviations</b>: 3-PEHPC: 3-pyridinyl ethylidene hydroxyl phosphonocarboxylate; ATG: autophagy; ATG16L1: autophagy related 16 like 1; BECs: bladder epithelial cells; dpi: days post infection; hpi: hours post infection; IF: immunofluorescence; IL1B: interleukin 1 beta; IL6: interleukin 6; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MVB: multivesicular bodies; T300A: Thr300Ala; TNF: tumor necrosis factor; QIR(s): quiescent intracellular reservoir(s); siRNA: short interfering RNA; UPEC: uropathogenic <i>Escherichia coli</i>; UTI(s): urinary tract infection(s); TEM: transmission electron microscopy; WT: wild type
DOI: 10.6084/m9.figshare.11945931
title: Additional file 10 of Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant

description: Additional file 10 Table S7. Primers for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.7227326.v1
title: A non-canonical autophagy-dependent role of the ATG16L1<sup>T300A</sup> variant in urothelial vesicular trafficking and uropathogenic <i>Escherichia coli</i> persistence

description: 50% of Caucasians carry a Thr300Ala variant (T300A) in the protein encoded by the macroautophagy/autophagy gene <i>ATG16L1</i>. Here, we show that the T300A variant confers protection against urinary tract infections (UTIs), the most common infectious disease in women. Using knockin mice carrying the human T300A variant, we show that the variant limits the UTI-causing bacteria, uropathogenic <i>Escherichia coli</i> (UPEC), from establishing persistent intracellular reservoirs, which can seed UTI recurrence. This phenotype is recapitulated in mice lacking <i>Atg16l1</i> or <i>Atg7</i> exclusively in the urothelium. We further show that mice with the T300A variant exhibit urothelial cellular abnormalities, including vesicular congestion and aberrant accumulation of UPK (uroplakin) proteins. Importantly, presence of the T300A variant in humans is associated with similar urothelial architectural abnormalities, indicating an evolutionarily conserved impact. Mechanistically, we show that the reduced bacterial persistence is independent of basal autophagic flux or proinflammatory cytokine responses and does not involve <i>Atg14</i> or <i>Epg5</i>. However, the T300A variant is associated with increased expression of the small GTPase <i>Rab33b</i>; RAB33B interacts with ATG16L1, as well as other secretory RABs, RAB27B and RAB11A, important for UPEC exocytosis from the urothelium. Finally, inhibition of secretory RABs in bladder epithelial cells increases intracellular UPEC load. Together, our results reveal that UPEC selectively utilize genes important for autophagosome formation to persist in the urothelium, and that the presence of the T300A variant in ATG16L1 is associated with changes in urothelial vesicle trafficking, which disrupts the ability of UPEC to persist, thereby limiting the risk of recurrent UTIs. <b>Abbreviations</b>: 3-PEHPC: 3-pyridinyl ethylidene hydroxyl phosphonocarboxylate; ATG: autophagy; ATG16L1: autophagy related 16 like 1; BECs: bladder epithelial cells; dpi: days post infection; hpi: hours post infection; IF: immunofluorescence; IL1B: interleukin 1 beta; IL6: interleukin 6; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MVB: multivesicular bodies; T300A: Thr300Ala; TNF: tumor necrosis factor; QIR(s): quiescent intracellular reservoir(s); siRNA: short interfering RNA; UPEC: uropathogenic <i>Escherichia coli</i>; UTI(s): urinary tract infection(s); TEM: transmission electron microscopy; WT: wild type
DOI: 10.6084/m9.figshare.11945931.v1
title: Additional file 10 of Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant

description: Additional file 10 Table S7. Primers for qRT-PCR analysis.
DOI: 10.6084/m9.figshare.25102763
title: EARSAP

description: we manually listened to all the sounds and classified them into four categories: [Type-0] Sounds that are completely irrelevant to the corresponding labels; [Type-1] Earcon (The identification of Earcon is based on the guideline of Earcons design reported by Blattner, Sumikawa and Greenberg); [Type-2] Auditory icon (which is made by capturing the sounds in everyday life); [Type-3] Music/vocal/other sounds that are relevant to the label description. To study the relationship between semantic descriptors and sound features of Earcon, we first obtained 270 earcons with short, structured musical messages from a mixed database containing 1053 sound samples with different types.
DOI: 10.6084/m9.figshare.25102763.v5
title: EARSAP

description: we manually listened to all the sounds and classified them into four categories: [Type-0] Sounds that are completely irrelevant to the corresponding labels; [Type-1] Earcon (The identification of Earcon is based on the guideline of Earcons design reported by Blattner, Sumikawa and Greenberg); [Type-2] Auditory icon (which is made by capturing the sounds in everyday life); [Type-3] Music/vocal/other sounds that are relevant to the label description. To study the relationship between semantic descriptors and sound features of Earcon, we first obtained 270 earcons with short, structured musical messages from a mixed database containing 1053 sound samples with different types.
DOI: 10.6084/m9.figshare.25102763.v4
title: sounddatabase

description: we manually listened to all the sounds and classified them into four categories: [Type-0] Sounds that are completely irrelevant to the corresponding labels; [Type-1] Earcon (The identification of Earcon is based on the guideline of Earcons design reported by Blattner, Sumikawa and Greenberg); [Type-2] Auditory icon (which is made by capturing the sounds in everyday life); [Type-3] Music/vocal/other sounds that are relevant to the label description. To study the relationship between semantic descriptors and sound features of Earcon, we first obtained 270 earcons with short, structured musical messages from a mixed database containing 1053 sound samples with different types.
DOI: 10.6084/m9.figshare.25273627
title: Supplementary Material for: Acquired Angioedema Associated with Lymphoproliferative Disorders

description: <b><i>Introduction:</i></b> Acquired angioedema due to C1 esterase inhibitor deficiency (C1INH-AAE) is most associated with lymphoproliferative disorders (LPDs), particularly low-grade B-cell subtypes. The condition remains under-recognized with long diagnostic delays due to various challenges including a lack of awareness of the condition. <b><i>Case Presentation:</i></b> We discuss 4 cases of C1INH-AAE associated with low-grade B-cell LPDs, including various diagnostic and management challenges. As our cases illustrate, constitutional symptoms or overt manifestations of LPD at diagnosis are often absent. Hence, a comprehensive multimodal approach to screening for an underlying B-LPD is important when a diagnosis of acquired angioedema is made. Levels of complement C4, C1q, and C1INH are useful for diagnosing C1INH-AAE and for monitoring disease activity. Changes in these parameters may also indicate relapse of the underlying hematological malignancy. Treating the underlying disorder is important as this commonly leads to clinical improvement with decreased episodes of angioedema and normalization of complement studies. <b><i>Conclusion:</i></b> Awareness of C1INH-AAE can lead to an early diagnosis of hematological malignancies. The absence of constitutional symptoms emphasizes the need for a comprehensive multimodal approach to screening for LPD in C1INH-AAE. C4, C1INH level, and function are useful for monitoring disease activity.
DOI: 10.6084/m9.figshare.25273627.v1
title: Supplementary Material for: Acquired Angioedema Associated with Lymphoproliferative Disorders

description: <b><i>Introduction:</i></b> Acquired angioedema due to C1 esterase inhibitor deficiency (C1INH-AAE) is most associated with lymphoproliferative disorders (LPDs), particularly low-grade B-cell subtypes. The condition remains under-recognized with long diagnostic delays due to various challenges including a lack of awareness of the condition. <b><i>Case Presentation:</i></b> We discuss 4 cases of C1INH-AAE associated with low-grade B-cell LPDs, including various diagnostic and management challenges. As our cases illustrate, constitutional symptoms or overt manifestations of LPD at diagnosis are often absent. Hence, a comprehensive multimodal approach to screening for an underlying B-LPD is important when a diagnosis of acquired angioedema is made. Levels of complement C4, C1q, and C1INH are useful for diagnosing C1INH-AAE and for monitoring disease activity. Changes in these parameters may also indicate relapse of the underlying hematological malignancy. Treating the underlying disorder is important as this commonly leads to clinical improvement with decreased episodes of angioedema and normalization of complement studies. <b><i>Conclusion:</i></b> Awareness of C1INH-AAE can lead to an early diagnosis of hematological malignancies. The absence of constitutional symptoms emphasizes the need for a comprehensive multimodal approach to screening for LPD in C1INH-AAE. C4, C1INH level, and function are useful for monitoring disease activity.
DOI: 10.5281/zenodo.4630453
title: Data for Effects of different scratch mat designs... paper (Animals, MDPI) https://doi.org/10.3390/ ani11061544

description: Data set use for paper on Effects of different scratch mat designs on hen behaviour and eggs laid in enriched cages, submitted to journal 'Animals' (MDPI publishers)

https://doi.org/10.3390/ani11061544

Published 25 May 2021
DOI: 10.5281/zenodo.4630454
title: Data for Effects of different scratch mat designs... paper (Animals, MDPI) https://doi.org/10.3390/ ani11061544

description: Data set use for paper on Effects of different scratch mat designs on hen behaviour and eggs laid in enriched cages, submitted to journal 'Animals' (MDPI publishers)

https://doi.org/10.3390/ani11061544

Published 25 May 2021
DOI: 10.6084/m9.figshare.11945952
title: Additional file 3 of Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant

description: Additional file 3 Table S1. Differentially expressed genes of stem between sdm2 and FH1.
DOI: 10.6084/m9.figshare.11945952.v1
title: Additional file 3 of Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant

description: Additional file 3 Table S1. Differentially expressed genes of stem between sdm2 and FH1.