cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7370573
title: Supplementary Material for: Integrated Transcriptome Sequencing Analysis Reveals Role of miR-138-5p/ TBL1X in Placenta from Gestational Diabetes Mellitus

description: <b><i>Background/Aims:</i></b> The placenta has been suggested to play a crucial role in the pathology of gestational diabetes mellitus (GDM). Placenta-specific microRNAs (miRNAs) and the corresponding targeting genes involved in the pathology of GDM still remain to be elucidated. We aimed to identify the dysregulated miRNAs and the corresponding mRNA targets through an integrated miRNA and mRNA transcriptomic profiles analysis and investigate the role of differentially expressed miR-138-5p/TBL1X in GDM. <b><i>Methods:</i></b> RNA sequencing (RNA-seq) was performed in 16 placentas from GDM and control group. Differentially expressed mRNAs and miRNAs in GDM were validated by quantitative PCR (qPCR). The wound healing assay and transwell migration assay were used to analyze cell migration ability. The cell proliferation was determined by CCK8 assay. Luciferase assay was used to confirm the direct binding of the targeted <i>TBL1X</i> with miR-138-5p. <b><i>Results:</i></b> Totally, 281 mRNAs and 32 miRNAs were found to be differentially expressed in the GDM placentas. The biological relationships of the miRNA/mRNA pairs were related to cellular development and function and organ morphology. Among the aberrantly expressed molecules, we selected miR-138-5p from the bioinformatics analysis and found that miR-138-5p significantly inhibited the migration and proliferation of trophoblasts (HTR-8/SVneo) by targeting the 3’-UTR of <i>TBL1X</i>. Furthermore, the aberrant expression of miR-138-5p and TBL1X was significantly correlated with the weight of the placenta. <b><i>Conclusion:</i></b> We present the first integrative analysis of miRNA and mRNA expression profiles in GDM placenta and uncover a more detailed role for miR-138-5p, as well as its target <i>TBL1X</i> in the pathology of GDM.
DOI: 10.6084/m9.figshare.7370627.v1
title: Supplementary Material for: Curcumin Protects an SH-SY5Y Cell Model of Parkinson’s Disease Against Toxic Injury by Regulating HSP90

description: <b><i>Background/Aims:</i></b> We aimed to explore the protective role of curcumin (Cur) in a cell model of Parkinson’s disease (PD) and its underlying mechanism. <b><i>Methods:</i></b> In this study, genes concerned with PD-related keywords were screened within DiGSeE database. The association network between Cur and selected genes was downloaded from STITCH, with the interactions analyzed by STRING. We built a mitochondrial toxin 1-methyl-4-phenylpyridinium (MPP<sup>+</sup>)-induced SH-SY5Y cell model of PD. Cell morphology was observed under an electron microscope. MTT assay was applied to detect cell proliferation rate. Western blot assay was conducted to determine the level of apoptotic markers, including cleaved caspase 3, Bcl-2-associated X protein (Bax) and B-cell lymphoma-extra-large (Bcl-xl). Tyrosine hydroxylase (TH), dopamine transporter (DAT) protein levels and dopamine (DA) concentration were identified as dopaminergic neuron markers and measured by western blotting or Enzyme-linked immunosorbent assay (ELISA). <b><i>Results</i></b>: Cur rescued the toxicity effects of MPP<sup>+</sup> on SH-SY5Y cells, by controlling morphological change, promoting cell proliferation and inhibiting apoptosis. Of all PD-related genes, <i>HSP90</i> played an important role in Cur-gene network. HSP90 protein level was elevated by MPP<sup>+</sup>, whereas Cur could reverse this effect. Silencing of <i>HSP90</i> significantly attenuated the curative effect introduced by Cur, while <i>HSP90</i> overexpression enhanced the impact of Cur on PD. <b><i>Conclusion:</i></b> Cur can effectively inhibit the toxic effect of MPP<sup>+</sup> on SH-SY5Y cells and significantly reduce the adverse effects of MPP<sup>+</sup> on dopaminergic neurons via up-regulation of <i>HSP90</i>.
DOI: 10.7284/130067
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1808X 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.7370576.v1
title: Supplementary Material for: The Designer Antimicrobial Peptide A-hBD-2 Facilitates Skin Wound Healing by Stimulating Keratinocyte Migration and Proliferation

description: <b><i>Background/Aims:</i></b> Antimicrobial peptides are effective promoters of wound healing but are susceptible to degradation. In this study, we replaced the GIGDP unit on the N-terminal of the endogenous human antimicrobial peptide hBD-2 with APKAM to produce A-hBD-2 and analyzed the effect on wound healing both <i>in vitro</i> and <i>in vivo</i>. <b><i>Methods:</i></b> The effects of A-hBD-2 and hBD-2 on cytotoxicity and proliferation in keratinocytes were assessed by Cell Counting Kit-8 assay. The structural stability and antimicrobial activity of hBD-2 and A-hBD-2 were evaluated against <i>Staphylococcus aureus</i>. RNA and proteins levels were evaluated by real-time PCR and western blotting, respectively. Cell migration was evaluated using a transwell assay. Cell cycle analysis was performed by flow cytometry. Wound healing was assessed in Sprague-Dawley rats. Epidermal thickness was evaluated by hematoxylin and eosin staining. <b><i>Results:</i></b> We found that hBD-2 exhibited cytotoxicity at high concentrations and decreased the structural stability in the presence of high sodium chloride concentrations. A-hBD-2 exhibited increased structural stability and antimicrobial activity, and had lower cytotoxicity in keratinocytes. A-hBD-2 increased the migration and proliferation of keratinocytes via phosphorylation of EGFR and STAT3 and suppressed terminal differentiation of keratinocytes. We also found that A-hBD-2 elicited mobilization of intracellular Ca<sup>2+</sup> and stimulated keratinocytes to produce pro- and anti-inflammatory cytokines and chemokines via phospholipase C activation. Furthermore, A-hBD-2 promoted wound healing <i>in vivo</i>. <b><i>Conclusion:</i></b> Our data suggest that A-hBD-2 may be a promising candidate therapy for wound healing.
DOI: 10.7284/130070
title: Radiometer data collected during research cruise OC1808X using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.21954/ou.rd.7370444
title: Refining a framework measuring qualification effects

description: The framework is a product of the eSTEeM: Refining a framework for measuring qualification effects project led by Steven Self and Mark Slaymaker investigating a new pedagogical approach applied in Postgraduate teaching.<br><br>The framework supports data extraction and analysis of student forum posts and assignments as part of that project.<br><br>
DOI: 10.7284/130071
title: Water Temperature data collected during research cruise OC1808X using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.21954/ou.rd.7370444.v2
title: Refining a framework measuring qualification effects

description: The framework is a product of the eSTEeM: Refining a framework for measuring qualification effects project led by Steven Self and Mark Slaymaker investigating a new pedagogical approach applied in Postgraduate teaching.<br><br>The framework supports data extraction and analysis of student forum posts and assignments as part of that project.<br><br>
DOI: 10.6084/m9.figshare.7370435
title: bacteria and fungi

description: sequencing data
DOI: 10.7284/130077
title: Water Temperature data collected during research cruise OC1808X using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370423
title: Replication package

description: The folder contains data used in the Systematic literature review. Besides, R scripts are also provided which were used to draw the graphs<br>
DOI: 10.7284/130076
title: Timeserver data collected during research cruise OC1808X 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.7370438
title: DNA Methylome Profiling of Granulosa Cells Reveals Altered Methylation in Genes Vital to Ovarian Functions in PCOS

description: These are the supplemental file-sets for the DNA methylome profiling data of ovarian granulosa cells between controls and women with PCOS. The data was generated using a high throughput methyl-capture sequencing (MC-seq) approach and few of the identified differentially methylated genes (DMGs), which are vital for normal functioning of the ovary were validated using pyrosequencing and real-time PCR. Validation of genes such as <i>AKR1C3</i>, <i>CASR</i>, <i>GHRHR</i>, <i>RETN</i>, <i>MAMLD1</i>, <i>TNF</i> and <i>TF</i> provided novel insights on the involvement of epigenetic modifications in regulation of processes such as folliculogenesis, angiogenesis, steroidogenesis, luteal maintenance, ovulation, oocyte maturation, oocyte developmental competence and many more, which are compromised in women with PCOS. This data also generated valuable information on pathways and biological processes playing crucial roles in the pathophysiology of PCOS.<br>
DOI: 10.7284/130110
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1809B using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130113
title: Anemometer data collected during research cruise OC1809B using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130109
title: Fluorometer data collected during research cruise OC1809B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130114
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1809B using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130120
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1809B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130107
title: Gyrocompass data collected during research cruise OC1809B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130108
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1809B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130111
title: Radiometer data collected during research cruise OC1809B using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130112
title: Water Temperature data collected during research cruise OC1809B using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130118
title: Water Temperature data collected during research cruise OC1809B using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130117
title: Timeserver data collected during research cruise OC1809B using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130097
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1809X using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130100
title: Anemometer data collected during research cruise OC1809X using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130096
title: Fluorometer data collected during research cruise OC1809X 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.7370285
title: Table SI: Geomorphological analysis of gullies on the central peak of Lyot Crater, Mars

description: THEMIS surface temperatures in Lyot Crater and on the central peak
DOI: 10.6084/m9.figshare.7370285.v1
title: Table SI: Geomorphological analysis of gullies on the central peak of Lyot Crater, Mars

description: THEMIS surface temperatures in Lyot Crater and on the central peak
DOI: 10.7284/130101
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1809X using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130106
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1809X 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.7370273
title: Table SII: Geomorphological analysis of gullies on the central peak of Lyot Crater, Mars

description: TES surface temperatures and pressures on Lyot central peak
DOI: 10.6084/m9.figshare.7370273.v1
title: Table SII: Geomorphological analysis of gullies on the central peak of Lyot Crater, Mars

description: TES surface temperatures and pressures on Lyot central peak
DOI: 10.6084/m9.figshare.7370252
title: Studies on the antifungal and serotonin receptor agonist activities of the secondary metabolites from piezotolerant deep-sea fungus <i>Ascotricha</i> sp.

description: The potent antifungal agent sesquiterpenes and serotonin 5-HT<sub>2C</sub> agonist ascotricin were produced by a newly isolated deep-sea fungus <i>Ascotricha</i> sp. This fungus was isolated from deep-sea sediment collected at a depth of 1235 m and characterized. Piezotolerance was successfully tested under high pressure-low temperature (100 bar pressure and 20ºC) microbial cultivation system. Production of secondary metabolites was enhanced at optimized culture conditions. The <i>in-vivo</i> antifungal activity of sesquiterpenes was studied using the <i>Caenorhabditis elegans – Candida albicans</i> model system. The sesquiterpenes affected the virulence of <i>C. albicans</i> and prolonged the life of the host <i>C. elegans</i>. These findings suggest that sesquiterpenes are attractive antifungal drug candidates. The 5-HT<sub>2C</sub> receptor agonist is a potential target for the development of drugs for a range of central nervous system disorders. The interaction of 5-HT<sub>2C</sub> agonist ascotricin with the receptor was studied through bioinformatic analysis. The <i>in silico</i> molecular docking and molecular dynamic simulation studies demonstrated that they fit into the serotonin 5-HT<sub>2C</sub> active site and the crucial amino acid residues involved in the interactions were identified. To our knowledge, this is first report of <i>in vivo</i> antifungal analysis of sesquiterpenes and <i>in silico</i> studies of serotonin 5-HT<sub>2C</sub> receptor-ascotricin complex. MD simulation of interaction of ascotricin with 5-HT2C receptor
DOI: 10.7284/130094
title: Gyrocompass data collected during research cruise OC1809X using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370252.v1
title: Studies on the antifungal and serotonin receptor agonist activities of the secondary metabolites from piezotolerant deep-sea fungus <i>Ascotricha</i> sp.

description: The potent antifungal agent sesquiterpenes and serotonin 5-HT<sub>2C</sub> agonist ascotricin were produced by a newly isolated deep-sea fungus <i>Ascotricha</i> sp. This fungus was isolated from deep-sea sediment collected at a depth of 1235 m and characterized. Piezotolerance was successfully tested under high pressure-low temperature (100 bar pressure and 20ºC) microbial cultivation system. Production of secondary metabolites was enhanced at optimized culture conditions. The <i>in-vivo</i> antifungal activity of sesquiterpenes was studied using the <i>Caenorhabditis elegans – Candida albicans</i> model system. The sesquiterpenes affected the virulence of <i>C. albicans</i> and prolonged the life of the host <i>C. elegans</i>. These findings suggest that sesquiterpenes are attractive antifungal drug candidates. The 5-HT<sub>2C</sub> receptor agonist is a potential target for the development of drugs for a range of central nervous system disorders. The interaction of 5-HT<sub>2C</sub> agonist ascotricin with the receptor was studied through bioinformatic analysis. The <i>in silico</i> molecular docking and molecular dynamic simulation studies demonstrated that they fit into the serotonin 5-HT<sub>2C</sub> active site and the crucial amino acid residues involved in the interactions were identified. To our knowledge, this is first report of <i>in vivo</i> antifungal analysis of sesquiterpenes and <i>in silico</i> studies of serotonin 5-HT<sub>2C</sub> receptor-ascotricin complex. MD simulation of interaction of ascotricin with 5-HT2C receptor
DOI: 10.7284/130095
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1809X using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130098
title: Radiometer data collected during research cruise OC1809X using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130099
title: Water Temperature data collected during research cruise OC1809X using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/130104
title: Water Temperature data collected during research cruise OC1809X using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370210
title: SIS agent-based simulations (fortran code + binary + data)

description: Statistical moments and correlation generated by agent-based numerical simulations<br>*.f90 Fortran source codes*.dat data
DOI: 10.6084/m9.figshare.7370210.v1
title: SIS agent-based simulations (fortran code + binary + data)

description: Statistical moments and correlation generated by agent-based numerical simulations<br>*.f90 Fortran source codes*.dat data
DOI: 10.6084/m9.figshare.7370198
title: Supplementary Material for: Health-Related Quality of Life in Patients with Small Intestine Neuroendocrine Tumors

description: <b><i>Background:</i></b> The prevalence of small intestine neuroendocrine tumors (SI-NETs) is increasing. Disease progression is often slow and treatment options and long-term survival rates have improved, but little is known about health-related quality of life (HRQoL) in these patients. <b><i>Objective:</i></b> To assess HRQoL and its predictors in SI-NET patients receiving contemporary treatments. <b><i>Methods:</i></b> We measured HRQoL with 15D and SF-36 questionnaires in 134 SI-NET patients and compared the 15D results to those of an age- and gender-standardized sample of the general population (<i>n</i> = 1,153). In the patients, we studied the impact of treatments, Ki-67, liver metastases, circulating tumor markers, comorbidities, and/or socioeconomic factors on HRQoL with linear regression analysis. <b><i>Results:</i></b> The mean disease duration of the patients was 81 (4–468) months, 91% had metastatic disease, and 79% received somatostatin analog treatment. Hepatic tumor load was 0% in 44.8%, &lt; 10–25% in 44.0%, and &gt; 25% in 11.2%, respectively. Mean fP-CgA and S-5HIAA concentrations were 15 (1.3–250) and 344 (24–7,470) nmol/L, respectively. Overall, HRQoL was significantly impaired in patients compared to controls (15D score 0.864 ± 0.105 vs. 0.905 ± 0.028, <i>p</i> &lt; 0.001). SI-NET patients scored worse on 9 of 15 dimensions: sleep, excretion (i.e., bladder and bowel function), depression, distress, vitality, sexual activity (<i>p</i> &lt; 0.001), breathing, usual activities, and discomfort and symptoms (<i>p</i> &lt; 0.01–0.05). SF-36 scores were impaired and highly correlated with 15D scores (<i>p</i> &lt; 0.001). HRQoL was impaired in patients with (<i>n</i> = 85) compared to patients without (<i>n</i> = 49) impaired excretion (0.828 vs. 0.933, <i>p</i> &lt; 0.001). In the patient group, number of medications predicted impaired HRQoL. <b><i>Conclusions:</i></b> Despite contemporary treatments, SI-NET patients have severely impaired HRQoL, including diarrhea, sleep, depression, vitality, and sexual activity.
DOI: 10.7284/130103
title: Timeserver data collected during research cruise OC1809X 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.7370183
title: Supplementary Material for: Potassium Iodide for Cutaneous Inflammatory Disorders: A Monocentric, Retrospective Study

description: <b><i>Objectives:</i></b> Potassium iodide (KI) is a medication that has been used for decades in dermatology and it is mentioned as a treatment option in all major dermatology textbooks. Yet, there is little recent information on its efficacy. In our study, we wanted to retrospectively evaluate the therapy response to KI in our patients. <b><i>Methods:</i></b> The hospital information system was searched for patients treated with KI at the Department of Dermatology (University Hospital Zurich) in the last 20 years (January 1, 1998 to December 31, 2017). A total of 52 patients were found and, subsequently, 35 patients were included in our study. <b><i>Results:</i></b> KI was prescribed for the following skin conditions: erythema nodosum, disseminated granuloma anulare, necrobiosis lipoidica, nodular vasculitis, cutaneous sarcoidosis, and granulomatous perioral dermatitis/ rosacea. The median duration of KI intake was 5 ± 7.7 weeks (range 1–26). The global assessment of efficacy by the treating physician showed an improvement of disease in about a third of all patients. No response was seen in 14 patients and 9 even had a progression of disease. An adverse event was documented in 16 cases. <b><i>Conclusions:</i></b> Our findings show that an improvement was reached in only about a third of all cases. High response rates with only mild side effects (in 16 out of 35 patients) were observed.
DOI: 10.7284/130124
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1810A 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.7370150
title: Additional file 10: Figure S6

description: Raw data used for creating Additional file 10: Figure S6 of the paper "A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples". Files are combined in compressed 7-Zip archive(s).