cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7387220
title: Supplementary Material for: Early Second-Trimester Peptidomic Identification of Serum Peptides for Potential Prediction of Gestational Diabetes Mellitus

description: <b><i>Background/Aims:</i></b> Early screening and diagnosis is important for minimizing gestational adverse outcomes. Routine screening of gestational diabetes mellitus (GDM) at 24–28 weeks with 75 g oral glucose challenge test (OGCT) leaves limited time for intervention and prevention. This study aims to analyze maternal serum peptides in the early second-trimester for prediction of gestational diabetes mellitus (GDM). <b><i>Methods:</i></b> Serum samples were collected from 16-18-week pregnant women that visited Nanjing Maternity and Child Health Care Hospital from April to August 2015. According to gestational outcome with or without GDM in late pregnancy, 200 of serum samples from GDM mothers and controls were randomly divided into two subgroups. Peptidomic identification of serum peptides was performed by combining ultrafiltration and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to investigate the differentially-expressed peptides between two groups. <b><i>Results:</i></b> A total of 297 identified peptides, originating from 228 proteins, were significantly differentially expressed in the GDM group compared with control. These precursor proteins may play critical roles in cell death of cortical neurons, elongation of cellular protrusions, and stabilization of microtubules. Major networks identified included those involving lipid metabolism, molecular transport and small molecule biochemistry. <b><i>Conclusion:</i></b> We provide for the first time a validated peptidome profile of early second-trimester serum in normal and GDM mothers, and we investigated the potential serum biomarkers for GDM. We concluded that 297 peptides could serve as potential biomarkers for GDM.
DOI: 10.7284/120755
title: Speedlog data collected during research cruise OC1507A using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120756
title: Water Temperature data collected during research cruise OC1507A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7387148
title: A characterization and disproportionality analysis of medication error related adverse events reported to the FAERS database

description: <b>Objectives</b>: To characterize adverse reactions associated with medication errors (ME) reported in US Food and Drug Administration Adverse Event Reporting System (US-FAERS), and to identify the potential signals of disproportionate reporting (SDR) for different drugs. <b>Methods</b>: ME associated Individual Case Study Report (ICSRs) were identified. ICSRs were categorized by patient age groups, affected stages of medication process and Anatomical Therapeutic Chemical classification system. Disproportionality analyses were performed for different age groups. <b>Results</b>: 46,8677 ICSRs were retrieved. An increasing trend in reporting of cases of ME was observed during the studied period. Immunosuppressants and psycholeptic drugs were most frequently involved. Administration errors were reported most frequently, followed by prescribing and dispensing errors. In neonates, SDR following wrong drug administration, wrong dose, and accidental overdose were associated with methylergonovine, zidovudine, and acetaminophen. In elderlies, SDR were found for dose omission and underdose error associated with etanercept and evolocumab. <b>Conclusion</b>: While a detailed root-cause analysis for ME characteristic can rarely be performed on such a dataset, data mining for signals in spontaneous reporting database may assist in identifying potential ME in a more standardized and objective manner. Continued use of spontaneous reporting system for identifying MEs is encouraged to prevent unnecessary patient harm.
DOI: 10.6084/m9.figshare.7387136
title: Supplementary Material for: Pro-Angiogenic Activity of Monocytic-Type Myeloid-Derived Suppressor Cells from Balb/C Mice Infected with Echinococcus Granulosus and the Regulatory Role of miRNAs

description: <b><i>Background/Aims:</i></b> This study aims to predict the pro-angiogenic functions of monocytic-type myeloid-derived suppressor cells (M-MDSCs) derived from mice infected with <i>Echinococcus granulosus</i>. <b><i>Methods:</i></b> M-MDSCs were collected from Balb/c mice infected with <i>E. granulosus</i> and normal mice (control) and cultured <i>in vitro</i>. Human umbilical vein endothelial cells (HUVECs) were stimulated with the cell supernatant, and angiogenesis was investigated and analysed by the Angiogenesis module of the software NIH Image J. RNA was extracted from fresh isolated M-MDSCs and analysed with miRNA microarray; differentially expressed miRNAs and their potential functions were analysed through several bioinformatics tools. Finally, quantitative PCR was used to confirm the results of microarray analysis. <b><i>Results:</i></b> M-MDSCs from mice infected with <i>E. granulosus</i> could promote the formation of tubes from HUVECs <i>in vitro</i>. Moreover, vascular endothelial growth factor (VEGF) showed significantly high expression, whereas soluble fms-like tyrosine kinase-1 (sFlt-1) showed low expression at the transcriptional level in M-MDSCs from mice infected with <i>E. granulosus</i>. Microarray analysis of miRNAs showed that 28 miRNAs were differentially expressed in M-MDSCs from the two experimental mice groups, and 272 target genes were predicted using the microRNA databases TargetScan, PITA and microRNAorg. These target genes were mainly involved in the biological processes of intracellular protein transport, protein targeting to the lysosome and protein transport, and mainly located in the cytoplasm, neuronal cell body and membrane. Moreover, they were mainly involved in the molecular functions of protein binding, metal ion binding and SH3 domain binding. Further, the differentially expressed miRNAs were mainly enriched in the endocytosis, Wnt and axon guidance pathways, as well as the MAPK, focal adhesion, PI3K-Akt, cAMP, mTOR and TGF-β signalling pathways, which are linked to immunoregulation and angiogenesis based on the results of bioinformatics analysis with DIANA-miRPath 3.0. In addition, the expression of eight miRNAs was randomly verified by quantitative PCR independently in three mice infected with <i>E. granulosus</i> and three normal mice. <b><i>Conclusion:</i></b> M-MDSCs have a potential angiogenic role during <i>E. granulosus</i> infection, and miRNAs may play a role in the immune response and angiogenesis functions of M-MDSCs through regulation of the identified signalling pathways.
DOI: 10.6084/m9.figshare.7387148.v1
title: A characterization and disproportionality analysis of medication error related adverse events reported to the FAERS database

description: <b>Objectives</b>: To characterize adverse reactions associated with medication errors (ME) reported in US Food and Drug Administration Adverse Event Reporting System (US-FAERS), and to identify the potential signals of disproportionate reporting (SDR) for different drugs. <b>Methods</b>: ME associated Individual Case Study Report (ICSRs) were identified. ICSRs were categorized by patient age groups, affected stages of medication process and Anatomical Therapeutic Chemical classification system. Disproportionality analyses were performed for different age groups. <b>Results</b>: 46,8677 ICSRs were retrieved. An increasing trend in reporting of cases of ME was observed during the studied period. Immunosuppressants and psycholeptic drugs were most frequently involved. Administration errors were reported most frequently, followed by prescribing and dispensing errors. In neonates, SDR following wrong drug administration, wrong dose, and accidental overdose were associated with methylergonovine, zidovudine, and acetaminophen. In elderlies, SDR were found for dose omission and underdose error associated with etanercept and evolocumab. <b>Conclusion</b>: While a detailed root-cause analysis for ME characteristic can rarely be performed on such a dataset, data mining for signals in spontaneous reporting database may assist in identifying potential ME in a more standardized and objective manner. Continued use of spontaneous reporting system for identifying MEs is encouraged to prevent unnecessary patient harm.
DOI: 10.6084/m9.figshare.7387136.v1
title: Supplementary Material for: Pro-Angiogenic Activity of Monocytic-Type Myeloid-Derived Suppressor Cells from Balb/C Mice Infected with Echinococcus Granulosus and the Regulatory Role of miRNAs

description: <b><i>Background/Aims:</i></b> This study aims to predict the pro-angiogenic functions of monocytic-type myeloid-derived suppressor cells (M-MDSCs) derived from mice infected with <i>Echinococcus granulosus</i>. <b><i>Methods:</i></b> M-MDSCs were collected from Balb/c mice infected with <i>E. granulosus</i> and normal mice (control) and cultured <i>in vitro</i>. Human umbilical vein endothelial cells (HUVECs) were stimulated with the cell supernatant, and angiogenesis was investigated and analysed by the Angiogenesis module of the software NIH Image J. RNA was extracted from fresh isolated M-MDSCs and analysed with miRNA microarray; differentially expressed miRNAs and their potential functions were analysed through several bioinformatics tools. Finally, quantitative PCR was used to confirm the results of microarray analysis. <b><i>Results:</i></b> M-MDSCs from mice infected with <i>E. granulosus</i> could promote the formation of tubes from HUVECs <i>in vitro</i>. Moreover, vascular endothelial growth factor (VEGF) showed significantly high expression, whereas soluble fms-like tyrosine kinase-1 (sFlt-1) showed low expression at the transcriptional level in M-MDSCs from mice infected with <i>E. granulosus</i>. Microarray analysis of miRNAs showed that 28 miRNAs were differentially expressed in M-MDSCs from the two experimental mice groups, and 272 target genes were predicted using the microRNA databases TargetScan, PITA and microRNAorg. These target genes were mainly involved in the biological processes of intracellular protein transport, protein targeting to the lysosome and protein transport, and mainly located in the cytoplasm, neuronal cell body and membrane. Moreover, they were mainly involved in the molecular functions of protein binding, metal ion binding and SH3 domain binding. Further, the differentially expressed miRNAs were mainly enriched in the endocytosis, Wnt and axon guidance pathways, as well as the MAPK, focal adhesion, PI3K-Akt, cAMP, mTOR and TGF-β signalling pathways, which are linked to immunoregulation and angiogenesis based on the results of bioinformatics analysis with DIANA-miRPath 3.0. In addition, the expression of eight miRNAs was randomly verified by quantitative PCR independently in three mice infected with <i>E. granulosus</i> and three normal mice. <b><i>Conclusion:</i></b> M-MDSCs have a potential angiogenic role during <i>E. granulosus</i> infection, and miRNAs may play a role in the immune response and angiogenesis functions of M-MDSCs through regulation of the identified signalling pathways.
DOI: 10.7284/124001
title: Timeserver data collected during research cruise OC1507A using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120757
title: Transmissometer data collected during research cruise OC1507A using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120758
title: TSG (Thermosalinograph) data collected during research cruise OC1507A using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7387127.v1
title: Occurrence of <i>Hylonycteris underwoodi</i> (Chiroptera, Phyllostomidae) and <i>Thyroptera tricolor</i> (Chiroptera, Thyropteridae) in Honduras

description: The geographic distributions of <i>Hylonycteris underwoodi</i> and <i>Thyroptera tricolor</i> in Honduras have been established with specimens collected more than 50 years ago. Here, we describe the occurrence of these bat species captured in the historic city of Ciudad Blanca, Gracias a Dios in northeastern Honduras.
DOI: 10.6084/m9.figshare.7387130.v2
title: Generic Object Decoding

description: fMRI data for Horikawa & Kamitani (2017) "Generic decoding of seen and imagined objects using hierarchical visual features" Nat Common, https://www.nature.com/articles/ncomms15037.<br>
DOI: 10.7284/120772
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1507B using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7387127.v2
title: Occurrence of <i>Hylonycteris underwoodi</i> (Chiroptera, Phyllostomidae) and <i>Thyroptera tricolor</i> (Chiroptera, Thyropteridae) in Honduras

description: The geographic distributions of <i>Hylonycteris underwoodi</i> and <i>Thyroptera tricolor</i> in Honduras have been established with specimens collected more than 50 years ago. Here, we describe the occurrence of these bat species captured in the historic city of Ciudad Blanca, Gracias a Dios in northeastern Honduras.
DOI: 10.7284/120761
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise OC1507B using a Sea-Bird SBE-911+ instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7387094
title: Qualitative evaluation of a guideline supporting shared decision making for extreme preterm birth

description: <b>Background and objectives:</b> The decision to attempt resuscitation or provide palliative care at birth for extremely preterm infants between 22 and 25 weeks remains complex. The purpose of this study was to identify facilitators and barriers to implementation of a clinical practice guideline developed to support shared decision-making for these cases. <b>Methods:</b> A purposeful sample of healthcare providers, involved in the care of one of five cases of anticipated extremely preterm birth, was recruited for interviews. Participants shared their views on the guideline content, implementation process, and facilitators and barriers encountered. Interviews were audio-recorded and transcribed verbatim. Qualitative content analysis was used to code, categorize, and thematically describe the data. The Knowledge-Attitudes-Behaviours framework was used to organize the findings. <b>Results:</b> Twenty-five key informants (16 physicians, nine nurses) were interviewed. Participants described varying levels of knowledge of the guideline. Facilitators to implementation included: (1) an awareness of, familiarity with and belief in the content; (2) hard copy and electronic guideline accessibility; and, (3) institutional expertise to provide necessary care. Barriers included: (1) minimal awareness or familiarity with the content; (2) lack of agreement with the recommendations; (3) inadequate evidence and applicability to support changes in practice; and, (4) lack of resources to care for the most immature infants. <b>Conclusions:</b> Identified facilitators and barriers will inform the development of tailored strategies for improved local and future broader implementation. Other institutions can use the results to facilitate implementation of their guidelines on this ethically charged area.
DOI: 10.7284/120764
title: Fluorometer data collected during research cruise OC1507B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7387094.v1
title: Qualitative evaluation of a guideline supporting shared decision making for extreme preterm birth

description: <b>Background and objectives:</b> The decision to attempt resuscitation or provide palliative care at birth for extremely preterm infants between 22 and 25 weeks remains complex. The purpose of this study was to identify facilitators and barriers to implementation of a clinical practice guideline developed to support shared decision-making for these cases. <b>Methods:</b> A purposeful sample of healthcare providers, involved in the care of one of five cases of anticipated extremely preterm birth, was recruited for interviews. Participants shared their views on the guideline content, implementation process, and facilitators and barriers encountered. Interviews were audio-recorded and transcribed verbatim. Qualitative content analysis was used to code, categorize, and thematically describe the data. The Knowledge-Attitudes-Behaviours framework was used to organize the findings. <b>Results:</b> Twenty-five key informants (16 physicians, nine nurses) were interviewed. Participants described varying levels of knowledge of the guideline. Facilitators to implementation included: (1) an awareness of, familiarity with and belief in the content; (2) hard copy and electronic guideline accessibility; and, (3) institutional expertise to provide necessary care. Barriers included: (1) minimal awareness or familiarity with the content; (2) lack of agreement with the recommendations; (3) inadequate evidence and applicability to support changes in practice; and, (4) lack of resources to care for the most immature infants. <b>Conclusions:</b> Identified facilitators and barriers will inform the development of tailored strategies for improved local and future broader implementation. Other institutions can use the results to facilitate implementation of their guidelines on this ethically charged area.
DOI: 10.7284/120760
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1507B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7387046
title: Dataset and parameter set for STRUCTURE

description: Dataset from MIG-Seq method and parameter set used for STRUCTURE program in phylogeographic study of <i>Suaea malacosperma.</i>
DOI: 10.7284/120765
title: Gyrocompass data collected during research cruise OC1507B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120767
title: Hygrometer data collected during research cruise OC1507B using a Vaisala HMT300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7386683
title: Additional file 8: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S6. Information of fusion transcripts from Iso-Seq. (XLSX 527 kb)
DOI: 10.6084/m9.figshare.7386683.v1
title: Additional file 8: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S6. Information of fusion transcripts from Iso-Seq. (XLSX 527 kb)
DOI: 10.6084/m9.figshare.7386680
title: Additional file 7: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S5. Exon number of mRNAs and lncRNAs from Iso-Seq. (XLSX 1677 kb)
DOI: 10.7284/120766
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1507B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7386680.v1
title: Additional file 7: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S5. Exon number of mRNAs and lncRNAs from Iso-Seq. (XLSX 1677 kb)
DOI: 10.6084/m9.figshare.7386671
title: Additional file 5: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S4. Number of splice isoforms in genes by SMRT. (XLSX 798 kb)
DOI: 10.6084/m9.figshare.7386671.v1
title: Additional file 5: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S4. Number of splice isoforms in genes by SMRT. (XLSX 798 kb)
DOI: 10.7284/120768
title: Speedlog data collected during research cruise OC1507B using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7386662
title: Additional file 3: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S2. Exon number and chromosome location of genes and isoforms detected by SMRT. (XLSX 2109 kb)
DOI: 10.6084/m9.figshare.7386659
title: Additional file 2: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S1. Function annotation of all corrected isoforms by SMRT. (XLSX 6767 kb)
DOI: 10.6084/m9.figshare.7386665
title: Additional file 4: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S3. AS analysis of genes and isoforms by SMRT. (XLSX 382 kb)
DOI: 10.6084/m9.figshare.7386659.v1
title: Additional file 2: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S1. Function annotation of all corrected isoforms by SMRT. (XLSX 6767 kb)
DOI: 10.6084/m9.figshare.7386662.v1
title: Additional file 3: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S2. Exon number and chromosome location of genes and isoforms detected by SMRT. (XLSX 2109 kb)
DOI: 10.6084/m9.figshare.7386665.v1
title: Additional file 4: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S3. AS analysis of genes and isoforms by SMRT. (XLSX 382 kb)
DOI: 10.7284/120769
title: Water Temperature data collected during research cruise OC1507B using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7386650
title: Additional file 12: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S9. Primers used for RT-PCR validation. (XLSX 19 kb)
DOI: 10.7284/124002
title: Timeserver data collected during research cruise OC1507B using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7386650.v1
title: Additional file 12: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S9. Primers used for RT-PCR validation. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7386644
title: Additional file 11: of Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing

description: Table S8. APA sites of genes detected by SMRT. (XLSX 401 kb)