cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7246430.v1
title: A new species and molecular phylogeny of Brazilian succulent <i>Euphorbia</i> sect. <i>Brasilienses</i>

description: A new species of <i>Euphorbia</i> sect. <i>Brasilienses</i> V.W. Steinm. & Dorsey is described. <i>Euphorbia tetrangularis</i> Hurbath & Cordeiro is endemic to the Serra de Montevidéu, a part of the Espinhaço Range located in the state of Minas Gerais, Brazil. It differs from other species within the section based on the following characters: 4-ribbed branches, green cyathia, and green cyathial glands with erect appendages. This new species would qualify as critically endangered (CR) according to IUCN criteria. An inferred phylogeny based on a combined dataset of nuclear (ITS1) and plastid regions (<i>psbA-trnH</i>, <i>trnC-ycf6</i>, <i>matK</i>, <i>atpI-atpH</i>, <i>psbJ-petA</i>, <i>trnQ-rps16 × 1</i>) confirms the monophyly of <i>Euphorbia</i> sect. <i>Brasilienses</i> and supports the recognition of <i>E. tetrangularis</i>. The phylogeny also suggests that this group probably underwent a recent radiation.
DOI: 10.6084/m9.figshare.7246355
title: Peripheral arthritis in patients with long-term inflammatory bowel disease. Results from 20 years of follow-up in the IBSEN study

description: <b>Objectives:</b> Peripheral arthritis and related musculoskeletal manifestations, often classified as peripheral spondyloarthritis, are frequently seen in patients with inflammatory bowel disease (IBD). Few long-term studies have reported on the prevalence of these conditions. The aim of this study was to determine the prevalence of IBD-related peripheral arthritis and peripheral spondyloarthritis in IBD patients during 20 years of disease course, and to assess whether these conditions were associated with the intestinal IBD severity and activity. <b>Materials and methods:</b> In an inception cohort (the IBSEN study), IBD patients were followed prospectively for 20 years. At the 5 year follow-up the patients underwent a rheumatological examination and at the 20 year follow-up they completed a questionnaire with identical questions. When peripheral arthritis was characteristic and not explained by other specific diagnoses, it was defined as IBD-related peripheral arthritis. The Assessment of Spondyloarthritis International Society criteria were used to define peripheral spondyloarthritis, including patients with peripheral arthritis, enthesitis and/or dactylitis. <b>Results:</b> After 20 years of follow-up, 441 patients were included (296 ulcerative colitis and 145 Crohn’s disease). The prevalence of IBD-related peripheral arthritis was 17.2% and peripheral spondyloarthritis 27.9% during the disease course. IBD severity and activity were not different between those with a history of IBD-related peripheral arthritis or peripheral spondyloarthritis and those without. A higher proportion of women had IBD-related peripheral arthritis and peripheral spondyloarthritis. <b>Conclusion:</b> During 20 years of disease course, more than every sixth patient had suffered from IBD-related peripheral arthritis and every fourth from peripheral spondyloarthritis.
DOI: 10.6084/m9.figshare.7246358
title: Genetic and transcriptional analysis of inflammatory bowel disease-associated pathways in patients with <i>GUCY2C</i>-linked familial diarrhea

description: <b>Objective:</b> Activating mutations in the <i>GUCY2C</i> gene, which encodes the epithelial receptor guanylate cyclase C, cause diarrhea due to increased loss of sodium chloride to the intestinal lumen. Patients with familial <i>GUCY2C</i> diarrhea syndrome (FGDS) are predisposed to inflammatory bowel disease (IBD). We investigated whether genes in the guanylate cyclase C pathway are enriched for association with IBD and reversely whether genetic or transcriptional changes associated with IBD are found in FGDS patients. <b>Methods: (</b>1) A set of 27 genes from the guanylate cyclase C pathway was tested for enrichment of association with IBD by Gene Set Enrichment Analysis, using genome-wide association summary statistics from 12,882 IBD patients and 21,770 controls. (2) We genotyped 163 known IBD risk loci and sequenced <i>NOD2</i> in 22 patients with FGDS. Eight of them had concomitant Crohn's disease. (3) Global gene expression analysis was performed in ileal tissue from patients with FGDS, Crohn's disease and healthy individuals. <b>Results:</b> The guanylate cyclase C gene set showed a significant enrichment of association in IBD genome-wide association data. Risk variants in <i>NOD2</i> were found in 7/8 FGDS patients with concomitant Crohn's disease and in 2/14 FDGS patients without Crohn's disease. In ileal tissue, downregulation of metallothioneins characterized FGDS patients compared to healthy controls. <b>Conclusions:</b> Our results support a role of guanylate cyclase C signaling and disturbed electrolyte homeostasis in development of IBD. Furthermore, downregulation of metallothioneins in the ileal mucosa of FGDS patients may contribute to IBD development, possibly alongside effects from <i>NOD2</i> risk variants.
DOI: 10.7284/132856
title: Radiometer data collected during research cruise SKQ201818S using a Biospherical QSR-2150 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7246355.v1
title: Peripheral arthritis in patients with long-term inflammatory bowel disease. Results from 20 years of follow-up in the IBSEN study

description: <b>Objectives:</b> Peripheral arthritis and related musculoskeletal manifestations, often classified as peripheral spondyloarthritis, are frequently seen in patients with inflammatory bowel disease (IBD). Few long-term studies have reported on the prevalence of these conditions. The aim of this study was to determine the prevalence of IBD-related peripheral arthritis and peripheral spondyloarthritis in IBD patients during 20 years of disease course, and to assess whether these conditions were associated with the intestinal IBD severity and activity. <b>Materials and methods:</b> In an inception cohort (the IBSEN study), IBD patients were followed prospectively for 20 years. At the 5 year follow-up the patients underwent a rheumatological examination and at the 20 year follow-up they completed a questionnaire with identical questions. When peripheral arthritis was characteristic and not explained by other specific diagnoses, it was defined as IBD-related peripheral arthritis. The Assessment of Spondyloarthritis International Society criteria were used to define peripheral spondyloarthritis, including patients with peripheral arthritis, enthesitis and/or dactylitis. <b>Results:</b> After 20 years of follow-up, 441 patients were included (296 ulcerative colitis and 145 Crohn’s disease). The prevalence of IBD-related peripheral arthritis was 17.2% and peripheral spondyloarthritis 27.9% during the disease course. IBD severity and activity were not different between those with a history of IBD-related peripheral arthritis or peripheral spondyloarthritis and those without. A higher proportion of women had IBD-related peripheral arthritis and peripheral spondyloarthritis. <b>Conclusion:</b> During 20 years of disease course, more than every sixth patient had suffered from IBD-related peripheral arthritis and every fourth from peripheral spondyloarthritis.
DOI: 10.6084/m9.figshare.7246358.v1
title: Genetic and transcriptional analysis of inflammatory bowel disease-associated pathways in patients with <i>GUCY2C</i>-linked familial diarrhea

description: <b>Objective:</b> Activating mutations in the <i>GUCY2C</i> gene, which encodes the epithelial receptor guanylate cyclase C, cause diarrhea due to increased loss of sodium chloride to the intestinal lumen. Patients with familial <i>GUCY2C</i> diarrhea syndrome (FGDS) are predisposed to inflammatory bowel disease (IBD). We investigated whether genes in the guanylate cyclase C pathway are enriched for association with IBD and reversely whether genetic or transcriptional changes associated with IBD are found in FGDS patients. <b>Methods: (</b>1) A set of 27 genes from the guanylate cyclase C pathway was tested for enrichment of association with IBD by Gene Set Enrichment Analysis, using genome-wide association summary statistics from 12,882 IBD patients and 21,770 controls. (2) We genotyped 163 known IBD risk loci and sequenced <i>NOD2</i> in 22 patients with FGDS. Eight of them had concomitant Crohn's disease. (3) Global gene expression analysis was performed in ileal tissue from patients with FGDS, Crohn's disease and healthy individuals. <b>Results:</b> The guanylate cyclase C gene set showed a significant enrichment of association in IBD genome-wide association data. Risk variants in <i>NOD2</i> were found in 7/8 FGDS patients with concomitant Crohn's disease and in 2/14 FDGS patients without Crohn's disease. In ileal tissue, downregulation of metallothioneins characterized FGDS patients compared to healthy controls. <b>Conclusions:</b> Our results support a role of guanylate cyclase C signaling and disturbed electrolyte homeostasis in development of IBD. Furthermore, downregulation of metallothioneins in the ileal mucosa of FGDS patients may contribute to IBD development, possibly alongside effects from <i>NOD2</i> risk variants.
DOI: 10.7284/132857
title: Singlebeam Echosounder data collected during research cruise SKQ201818S using a L-3 ELAC LAZ 5100 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/132858
title: SSV (Sound Speed Velocimeter) data collected during research cruise SKQ201818S using a AML SVXchange instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7246337
title: Table of events from Probing layered arc crust in the Lesser Antilles using receiver functions

description: Details of the events used to create the stacked receiver functions.
DOI: 10.7284/132862
title: Water Temperature data collected during research cruise SKQ201818S using a HEITRONICS CT15.10 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7246337.v1
title: Table of events from Probing layered arc crust in the Lesser Antilles using receiver functions

description: Details of the events used to create the stacked receiver functions.
DOI: 10.6084/m9.figshare.7246316
title: Supplementary Material for: Downregulation of N-Acetylglucosaminyltransferase GCNT3 by miR-302b-3p Decreases Non-Small Cell Lung Cancer (NSCLC) Cell Proliferation, Migration and Invasion

description: <b><i>Background/Aims:</i></b> GCNT3 is a member of N-acetylglucosaminyltransferase family involved with mucin biosynthesis. GCNT3 aberrant expression is known to promote the progression of several human cancers. However, its role in tumorigenesis and the progression of non-small cell lung cancer (NSCLC) has not been well-characterized. Our study investigated the functional mechanisms of GCNT3 regulated by microRNAs (miRNAs) in NSCLC. <b><i>Methods:</i></b> The differential expression of mRNAs in NSCLC tissues and matched adjacent non-cancerous lung tissues from patients in Xuanwei, Yunnan province, China, was screened via mRNA microarray. The expression of GCNT3 and its correlation with NSCLC progression was measured in 92 paired tumor tissues and adjacent normal tissues. The functions of GCNT3 in NSCLC cells and its underlying mechanisms were measured using siRNA and GCNT3-expression vectors. The miRNA immunoprecipitation (miRIP) method was used to identify the miRNAs targeting GCNT3. The protein were measured using western blot assay, and the mRNAs were measured by quantitative real-time PCR (qRT-PCR) assay. Cell proliferation was measured using Cell Counting Kit-8 (CCK-8) and a colony forming assays; cell migration and invasion assays were performed using 24-well Transwell chambers with 8-μm pores filter, and analyses of the cell cycle and apoptosis were performed via flow cytometric analysis. The dual luciferase reporter assay was performed to confirm whether GCNT3 gene was a direct target of miR-302b-3p. <b><i>Results:</i></b> GCNT3 was found to be highly expressed in both NSCLC tissues and cell lines, and higher expression correlated significantly with advanced tumor-node-metastasis (TNM) stage, positive lymph node metastasis, and poor overall survival. Knockdown of GCNT3 inhibited the proliferation, migration and invasion ability of NSCLC cells, while overexpression facilitated these activities. Further mechanistic experiments using miRIP and dual luciferase reporter assays revealed that GCNT3 was a direct target of miR-302b-3p. Low expression of miR-302b-3p was found in NSCLC cells and negatively correlated with GCNT3 levels, while miR-302b-3p overexpression inhibited the proliferation, migration and invasion of NSCLC cells. Co-transfection with miR-302b-3p and the expression vector of GCNT3 abrogated the effects of mir-302b-3p, confirming that miR-302b-3p inhibited NSCLC progression by targeting GCNT3. Western blotting revealed that E-cadherin, N-cadherin, vimentin, p-Erk and cyclin D1 were downstream molecules of miR-302b-3p/GCNT3 pathway. <b><i>Conclusion:</i></b> miR-302b-3p/GCNT3 axis regulated cell proliferation, migration, and invasion by activating the Erk signaling pathway and epithelial-mesenchymal transition (EMT), which was identified as a potential therapeutic target for NSCLC.
DOI: 10.7284/132868
title: Water Temperature data collected during research cruise SKQ201818S using a Sea-Bird SBE-38 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7246295
title: Supplementary Material for: High Glucose-Mediated Cytokine Regulation in Gingival Fibroblasts and THP-1 Macrophage: a Possible Mechanism of Severe Periodontitis with Diabetes

description: <b><i>Background/Aims:</i></b> Diabetic patients are susceptible to severe periodontitis, but the precise mechanism is not fully understood. Aim of this study was to explore the biological pathogenesis of severe periodontitis in diabetic patients focusing on the crosstalk of human gingival fibroblasts (HGFs) and macrophages. <b><i>Methods:</i></b> A total of 70 periodontitis patients with or without diabetes mellitus (DM) were enrolled, and the statistical relationships of diabetic conditions to the periodontal inflammatory parameters were examined by cross-sectional study. In <i>in vitro</i> study, HGFs cell line CRL-2014® (ATCC) and differentiated THP-1 macrophages were cultured with normal glucose (NG: 5.5 mM) or high glucose (HG: 25 mM) condition, and treated with indicated inflammatory factors such as calprotectin (CPT), interleukin (IL)-1β and IL-6. To examine the effects of HG on soluble IL-6 receptor (sIL-6R) production in THP-1 macrophages, the supernatants were collected and the sIL-6R levels were measured by ELISA. To examine the effects of HG on IL-1β or IL-6-induced matrix metalloproteinase (MMPs) production in HGFs, the supernatants were collected. Levels of MMP-1 and tissue inhibitor of MMP-1 (TIMP-1) were measured by ELISA. Finally, after conditioned medium (CM) from THP-1 macrophages cultured with NG or HG conditions was collected, HGFs were treated with the CM. The supernatants were collected 24 hours later and the levels of MMP-1 and TIMP-1 were measured. To examine the specific effects of IL-1β contained in CM on MMP-1 and TIMP-1 production in HGFs, IL-1 receptor antagonist (IL-1ra) was used. <b><i>Results:</i></b> There were statistical correlation between IL-1β and sIL-6R levels in gingival crevicular fluid (GCF) and HbA1c in periodontitis patients with DM (IL-1β: P=0.035, sIL-6R: P=0.040). HG and CPT significantly induced sIL-6R production in THP-1 macrophages. HG significantly enhanced IL-1β or IL-6/sIL-6R-induced MMP-1 production in HGFs. The increase of MMP-1 by both IL-1β and IL-6/sIL-6R was significantly inhibited by specific ERK or IκB inhibitors. Corresponding to the regulation of MMP-1 production, HG condition increased the phosphorylation of p44/42 MAPK and IκBα in HGFs treated with IL-1β or IL-6/sIL-6R. Finally, MMP-1 production in HGFs cultured with HG increased significantly by CM from THP-1 macrophages cultured with HG. The induction of MMP-1 by the CM from THP-1 macrophages cultured with HG was significantly inhibited by dose dependent of IL-1ra in HGFs cultured with HG. <b><i>Conclusion:</i></b> Diabetic conditions such as HG induce IL-1β and sIL-6R production from macrophages in inflammatory periodontal tissues and may exacerbate the periodontitis synergistically via MMP-1 production from HGFs.
DOI: 10.7284/132887
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SKQ201819S using a Hawaii UHDAS instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7246262
title: Supplementary Material for: The Differentially Expressed Circular RNAs in the Substantia Nigra and Corpus Striatum of Nrf2-Knockout Mice

description: <b><i>Background/Aims:</i></b> The nuclear factor erythroid 2-related factor 2 (Nrf2)-antioxidant response element (ARE) pathway plays a protective role in both acute neuronal damage and chronic neurodegeneration-related oxidative stress. Circular RNAs (circRNAs) are involved with various diseases in the central nervous system (CNS). This study aimed to identify the key circRNAs involved in Nrf2-neuroprotection against oxidative stress. <b><i>Methods:</i></b> The differentially expressed circRNAs (DEcircRNAs) in the substantia nigra and corpus striatum between Nrf2 (-/-) and Nrf2 (+/+) mice were identified by microarray analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) was then used to validate the expression of selected DEcircRNAs in the substantia nigra and corpus striatum between Nrf2 (-/-) and Nrf2 (+/+) mice. Based on our previous microarray analysis of the differentially expressed mRNAs (DEmRNAs) in the substantia nigra and corpus striatum between Nrf2 (-/-) and Nrf2 (+/+) mice, the DEcircRNA-miRNA-DEmRNA interaction network was constructed. Functional annotation of DEmRNAs that shared the same binding miRNAs with DEcircRNAs was performed using gene ontology (GO) and pathway analyses. <b><i>Results:</i></b> A total of 65 and 150 significant DEcircRNAs were obtained in the substantia nigra and corpus striatum of Nrf2 (-/-) mice, respectively, and seventeen shared DEcircRNAs were found in both these two tissues. The qRT-PCR results were generally consistent with the microarray results. The DEcircRNA-miRNA-DEmRNA interaction network and pathway analysis indicated that mmu_circRNA_34132, mmu_circRNA_017077 and mmu-circRNA-015216 might be involved with Nrf2-mediated neuroprotection against oxidative stress. Mmu_circRNA_015216 and mmu_circRNA_017077 might play roles in the Nrf2-related transcriptional misregulation and Nrf2-mediated processes of rheumatoid arthritis, respectively. In addition to these two processes, mmu_circRNA_34132 may be a potential regulator of Nrf2-mediated protection for diabetes mellitus and Nrf2-mediated defence against ROS in hearts. <b><i>Conclusion:</i></b> In conclusion, our study identified the key DEcircRNAs in the substantia nigra and corpus striatum of Nrf2 (-/-) mice, which might provide new clues for further exploring the mechanism of Nrf2-mediated neuroprotection against oxidative stress and other Nrf2-mediated processes.
DOI: 10.6084/m9.figshare.7246259
title: Towards Understanding How to Design a Soft Artificial Muscle Actuator?

description: <br>In this manuscript we present a physics based model for sake of understanding<br>the actuation mechanism and the desired blocked force generated with respect<br>to the applied potential field at different geometries.<br>In the experimental work, we have found that the frequency and the am-<br>plitude plays a crucial role in actuation profile of ionic EAP. For estimating<br>the blocked force generated along the spatial domain of ionic EAP, we have<br>implemented Coulomb inverse square law as there is an electrostatic interaction<br>among one mobile ion and N of elementary electric charge which could be re-<br>pulsion or attraction on both surface area of ionic EAP based on the applied<br>potential field phase.<br>The ionic EAP is a tri-layer, assuming that the upper and lower layer which<br>are conductive layer a RC transmission line where we assume that R is constant<br>for sake of simplicity. The potential field at the clamping point is diffused along<br>the muscle, one dimensional diffusion model is implemented for estimating the<br>elementary electric charges diffused in the surface area of the upper layer. As<br>ionic EAP is working as mutual capacitor, we have assumed that the charges<br>of the stored mobile ions in the medium layer has the same initial value of the<br>elementary electric charges in the upper and conductive layer.<br>After estimating the spatial charge of the electrons and ions, the stress-<br>charge coupling is multiplied with the estimated value for having the value of<br>stress, force, strain, and curvature which is important for designing coupled<br>actuators.<br>Following, we have simulated forward and inverse approaches for estimating<br>the force and the desired potential field in each case for a coupled actuators.<br>The stress charge coupling can estimate the steady state final value of the<br>generated force, however, it doesnot capture the stress relaxation behavior or<br>saturation phenomena occurs during the low frequency. We believe that under-<br>standing the physics behind the actuation of ionic EAP artificial muscle could<br>lead us to design a desired artificial muscle for specific application and improving<br>their mechanical properties and response time as well.<br>1
DOI: 10.7284/132884
title: Anemometer data collected during research cruise SKQ201819S using a Gill WindObserver 75 instrument system onboard the platform RV Sikuliaq

description: Original (unprocessed) data collected during a Field_expedition