cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7370885.v1
title: Supplementary Material for: Cognitive Status and Functional Dexterity as Outcome Predictors Following Urinary Diversion: A Combined Retrospective and Prospective Observational Study

description: <b><i>Purpose:</i></b> The study aimed to evaluate the impact of the validated functional dexterity test and the Mini-Mental Status test on subjective functional outcomes, medical care situation, and health-related quality of life (HRQoL) after urinary diversion (UD). <b><i>Patients and Methods:</i></b> A total of 106 patients (<i>n</i> = 26 ileal conduits, <i>n</i> = 29 neobladders, and <i>n</i> = 51 ileocecal pouches) were included in this combined retrospective (<i>n</i> = 77) and prospective (<i>n</i> = 29) observational study. All patients performed the 2 tests mentioned above and filled out self-designed questionnaires with diversion and HRQoL items. In the prospective cohort, the tests were performed preoperatively and the questionnaires were filled out preoperatively as well as 3 and 6 months after surgery. <b><i>Results:</i></b> Reduced dexterity and cognitive skills were significantly associated with increased patient age and subjective constraints in stoma care of ileal conduits, self-catheterization in ileocecal pouches, and continence in neobladders. Overall HRQoL, however, was not affected by dexterity or cognitive measures. <b><i>Conclusions:</i></b> Assessing the cognitive status and functional dexterity of patients undergoing UD might provide a useful objective clinical tool to aid in decision-making regarding the type of UD and postoperative medical care situation. Further prospective data are needed to confirm these findings and further simplify the methods used here.
DOI: 10.7284/130072
title: Anemometer data collected during research cruise OC1808X using a Gill WindObserver II instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370840
title: Supplementary Material for: What are the Risk Factors for One-Year Mortality in Older Patients with Chronic Kidney Disease? An Analysis of the Cleveland Clinic CKD Registry

description: <b><i>Background:</i></b> Prognostic factors after dialysis initiation among older chronic kidney disease (CKD) patients are not well studied. In this study, we examined the risk factors associated with 1-year mortality after dialysis initiation among older CKD patients. <b><i>Methods:</i></b> In this retrospective study, we included 621 CKD patients from an electronic medical record based CKD registry that was linked to the United States Renal Data System data. In terms of age, they were all ≥65. We examined the associations of various demographic factors, comorbid conditions, relevant laboratory parameters, the presence of arteriovenous fistula, and inability to take care of oneself with 1-year mortality after dialysis initiation using Cox proportional hazards model. <b><i>Results:</i></b> In our study cohort, 224 older patients died during the first year of dialysis initiation and the estimated survival at 1 year was 65% (95% CI 62–69). After adjusting for covariates, increasing age by each year (Hazard ratio 1.04 [95% CI 1.02–1.06]), congestive heart failure (CHF; 1.57 [1.13–2.18]), an absence of AVF (3.0 [1.7–5.1]) and lack of nephrology care prior to dialysis initiation (1.93 [1.39–2.70]) were associated with increased risk of 1-year mortality. Nearly 60% of deaths were due to non-cardiovascular (CV) causes including cancer. <b><i>Conclusion:</i></b> Risk factors portending high 1-year mortality in older CKD patients are increasing age, CHF, an absence of AVF, and lack of pre-dialysis nephrology care. Clinicians need to be aware of non-CV risks of high mortality in these patients.
DOI: 10.6084/m9.figshare.7370852.v1
title: Supplementary Material for: Genome-Scale Single Nucleotide Resolution Analysis of DNA Methylation in Human Autosomal Dominant Polycystic Kidney Disease

description: <b><i>Background:</i></b> Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the formation of fluid-filled cysts in the kidney and end stage renal disease by the fourth or fifth decade of life. Mutations in the <i>PKD1</i> gene account for 85% of all cases of ADPKD. No curative therapy exists for patients affected by this disease and an underexplored avenue for the treatment of ADPKD is the targeting of epigenetic changes that occur during cystogenesis. Limited data exists on alterations in DNA methylation that are associated with ADPKD. Given the similarities between cyst growth and neoplasia, and the fact that 2 DNA methylation inhibitors are already Food and Drug Administration-approved for the treatment of myelodysplastic syndrome, we hypothesized that global DNA methylation patterns in ADPKD would parallel that observed in neoplasia, and which may provide an opportunity to treat ADPKD with epigenetic inhibitors. To address this hypothesis, we undertook a global DNA methylation analysis of human ADPKD kidney. <b><i>Methods:</i></b> We generated single nucleotide resolution methylomes of cortical kidney tissue from individuals with ADPKD, and from non-ADPKD kidney tissue, using reduced representation bisulfite sequencing. Using quantitative reverse transcription polymerase chain reaction, we investigated expression of the <i>PKD1</i> gene in both ADPKD and non-ADPKD kidney. <b><i>Results:</i></b> We have shown that ADPKD-derived genomic DNA exhibits global hypomethylation when compared with non-ADPKD kidney, a pattern commonly observed in DNA methylation studies of tumor-derived tissue. We have also identified 13 discrete regions that are significantly differentially methylated in ADPKD compared to non-ADPKD, and 8 of these are gene specific. The <i>PKD1</i> gene shows an increase in methylation at the 3′ end of the gene body, but in contrast to previously published data, this is not associated with a decrease in <i>PKD1</i> mRNA expression. <b><i>Conclusion:</i></b> This genome-scale single nucleotide resolution analysis of DNA methylation in human polycystic kidneys suggests that DNA methylation differences at specific loci are associated with ADPKD. Further exploration into the significance of these preliminary results may shed light on the disease process, and potentially reveal new therapeutic possibilities.
DOI: 10.6084/m9.figshare.7370840.v1
title: Supplementary Material for: What are the Risk Factors for One-Year Mortality in Older Patients with Chronic Kidney Disease? An Analysis of the Cleveland Clinic CKD Registry

description: <b><i>Background:</i></b> Prognostic factors after dialysis initiation among older chronic kidney disease (CKD) patients are not well studied. In this study, we examined the risk factors associated with 1-year mortality after dialysis initiation among older CKD patients. <b><i>Methods:</i></b> In this retrospective study, we included 621 CKD patients from an electronic medical record based CKD registry that was linked to the United States Renal Data System data. In terms of age, they were all ≥65. We examined the associations of various demographic factors, comorbid conditions, relevant laboratory parameters, the presence of arteriovenous fistula, and inability to take care of oneself with 1-year mortality after dialysis initiation using Cox proportional hazards model. <b><i>Results:</i></b> In our study cohort, 224 older patients died during the first year of dialysis initiation and the estimated survival at 1 year was 65% (95% CI 62–69). After adjusting for covariates, increasing age by each year (Hazard ratio 1.04 [95% CI 1.02–1.06]), congestive heart failure (CHF; 1.57 [1.13–2.18]), an absence of AVF (3.0 [1.7–5.1]) and lack of nephrology care prior to dialysis initiation (1.93 [1.39–2.70]) were associated with increased risk of 1-year mortality. Nearly 60% of deaths were due to non-cardiovascular (CV) causes including cancer. <b><i>Conclusion:</i></b> Risk factors portending high 1-year mortality in older CKD patients are increasing age, CHF, an absence of AVF, and lack of pre-dialysis nephrology care. Clinicians need to be aware of non-CV risks of high mortality in these patients.
DOI: 10.6084/m9.figshare.7370846
title: Data for "Impacts on cloud radiative effects induced by coexisting aerosols converted from international shipping and maritime DMS emissions"

description: <b>Introduction</b><b><br></b>These data accompany the paper by Qinjian Jin, Benjamin S. Grandey, Daniel Rothenberg, Alexander Avramov, and Chien Wang (2018), <b>Impacts on cloud radiative effects induced by coexisting aerosols converted from international shipping and maritime DMS emissions</b>, https://www.atmos-chem-phys-discuss.net/acp-2018-416/.<br>The files contains the input international shipping emission data and output data from CEMS-MARC simulations.<br>These data are processed using NCL scripts, which are avaliable at: https://doi.org/10.5281/zenodo.1493453.<br>The first two digits of letter/number in the data file names are associated with NCL scripts with the same name prefixes.<br>
DOI: 10.6084/m9.figshare.7370846.v1
title: Data for "Impacts on cloud radiative effects induced by coexisting aerosols converted from international shipping and maritime DMS emissions"

description: <b>Introduction</b><b><br></b>These data accompany the paper by Qinjian Jin, Benjamin S. Grandey, Daniel Rothenberg, Alexander Avramov, and Chien Wang (2018), <b>Impacts on cloud radiative effects induced by coexisting aerosols converted from international shipping and maritime DMS emissions</b>, https://www.atmos-chem-phys-discuss.net/acp-2018-416/.<br>The files contains the input international shipping emission data and output data from CEMS-MARC simulations.<br>These data are processed using NCL scripts, which are avaliable at: https://doi.org/10.5281/zenodo.1493453.<br>The first two digits of letter/number in the data file names are associated with NCL scripts with the same name prefixes.<br>
DOI: 10.6084/m9.figshare.7370783
title: Stability and structure of <i>Penicillium chrysogenum</i> lipase in the presence of organic solvents

description: The present work describes the enzymatic properties of <i>Penicillium chrysogenum</i> lipase and its behavior in the presence of organic solvents. The temperature and pH optima of the purified lipase was found to be 55 °C and pH 8.0 respectively. The lipase displayed remarkable stability in both polar and non-polar solvents upto 50% (v/v) concentrations for 72 h. A structural perspective of the purified lipase in different organic solvents was gained by using circular dichroism and intrinsic fluorescence spectroscopy. The native lipase consisted of a predominant α-helix structure which was maintained in both polar and non-polar solvents with the exception of ethyl butyrate where the activity was decreased and the structure was disrupted. The quenching of fluorescence intensity in the presence of organic solvents indicated the transformation of the lipase microenviroment <i>P. chrysogenum</i> lipase offers an interesting system for understanding the solvent stability mechanisms which could be used for rationale designing of engineered lipase biocatalysts for application in organic synthesis in non-aqueous media.
DOI: 10.6084/m9.figshare.7370801
title: Friends with malefit. The effects of keeping dogs and cats, sustaining animal-related injuries and Toxoplasma infection on health and quality of life

description: Row data for the paper "Friends with malefit. The effects of keeping dogs and cats, sustaining animal-related injuries and <i>Toxoplasma</i> infection on health and quality of life"
DOI: 10.7284/130068
title: Fluorometer data collected during research cruise OC1808X 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.7370783.v1
title: Stability and structure of <i>Penicillium chrysogenum</i> lipase in the presence of organic solvents

description: The present work describes the enzymatic properties of <i>Penicillium chrysogenum</i> lipase and its behavior in the presence of organic solvents. The temperature and pH optima of the purified lipase was found to be 55 °C and pH 8.0 respectively. The lipase displayed remarkable stability in both polar and non-polar solvents upto 50% (v/v) concentrations for 72 h. A structural perspective of the purified lipase in different organic solvents was gained by using circular dichroism and intrinsic fluorescence spectroscopy. The native lipase consisted of a predominant α-helix structure which was maintained in both polar and non-polar solvents with the exception of ethyl butyrate where the activity was decreased and the structure was disrupted. The quenching of fluorescence intensity in the presence of organic solvents indicated the transformation of the lipase microenviroment <i>P. chrysogenum</i> lipase offers an interesting system for understanding the solvent stability mechanisms which could be used for rationale designing of engineered lipase biocatalysts for application in organic synthesis in non-aqueous media.
DOI: 10.7284/130073
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808X using a Furuno GP-90 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7370657
title: Supplementary Material for: Osteogenic Effect of Inducible Nitric Oxide Synthase (iNOS)-Loaded Mineralized Nanoparticles on Embryonic Stem Cells

description: <b><i>Background/Aims:</i></b> This study investigated the effect of inducible nitric oxide synthase-loaded mineralized nanoparticles (iNOS-MNPs) on the osteogenic differentiation of mouse embryonic stem cells (ESCs). <b><i>Methods:</i></b> We prepared iNOS-MNPs using an anionic block copolymer template-mediated calcium carbonate (CaCO<sub>3</sub>) mineralization process in the presence of iNOS. iNOS-MNPs were spherical and had a narrow size distribution. iNOS was stably loaded within MNPs without denaturation. In order to confirm the successful introduction of iNOS-MNPs into the cytosol of ESCs, intracellular levels of nitric oxide (NO) was determined with a fluorometric analysis. A NO effector molecule, cyclic guanosine 3’,5’ monophosphate (cGMP) was also quantified with a competitive enzyme immunoassay. Cell viability in response to iNOS-MNP treatment was determined using the cell counting kit-8 (CCK-8) assay. Alkaline phosphatase (ALP) activity assay, intracellular calcium quantification assay, and Alizarin red S staining for matrix mineralization were performed to investigate osteogenic differentiation of ESCs. The protein levels of Runt-related transcription factor 2 (RUNX2), osteocalcin (OCN), and osterix (OSX) as osteogenic-related factors were also assessed by immunofluorescence staining and Western blot analysis. The complex pathways associated with iNOS-MNP-derived osteogenic differentiation of ESCs were evaluated by network-based analysis. <b><i>Results:</i></b> Cells with iNOS-MNPs displayed a significant increase in NO and cGMP concentration compared with the control group. When cells were exposed to iNOS-MNPs, there were no adverse effects on cell viability. Importantly, iNOS-MNP uptake promoted the osteogenic differentiation of ESCs. Using transcriptome profiling, we obtained 1,836 differentially-induced genes and performed functional enrichment analysis with ClueGO and KEGG. These analyses identified significantly enriched and interconnected molecular pathways such as protein kinase activity, estrogen receptor activity, bone morphogenetic protein (BMP) receptor binding, ligand-gated ion channel activity, and phosphatidylinositol 3-phosphate binding. <b><i>Conclusion:</i></b> These findings suggest that iNOS-MNPs can induce osteogenic differentiation in ESCs by integrating complex signaling pathways.
DOI: 10.7284/130079
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1808X 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.7370642.v1
title: Supplementary Material for: miRNA-1290 Promotes Aggressiveness in Pancreatic Ductal Adenocarcinoma by Targeting IKK1

description: <b><i>Background/Aims:</i></b> MicroRNAs (miRNAs) are a group of non-coding RNAs that play diverse roles in pancreatic carcinogenesis. In pancreatic ductal adenocarcinoma (PDAC), NF-kB is constitutively activated in most patients and is linked to a mutation in KRAS via IkB kinase complex 1 (IKK1, also known as IKKa). We investigated the link between PDAC aggressiveness and miR-1290. <b><i>Methods:</i></b> We used miRCURY<sup>TM</sup> LNA Array and <i>in situ</i> hybridization to investigate candidate miRNAs and validated the findings with PCR. The malignant behavior of cell lines was assessed with Cell Counting Kit-8, colony formation, and Transwell assays. A dual-luciferase reporter assay was used to evaluate the interaction between miR-1290 and IKK1. Protein expression was observed by western blotting. <b><i>Results:</i></b> In this study, 36 miRNAs were dysregulated in high-grade pancreatic intraepithelial neoplasia (PanIN) and PDAC tissues compared with low-grade PanIN tissues. The area under the curve values of miR-1290 and miR-31-5p were 0.829 and 0.848, respectively (95% confidence interval, 0.722–0.936 and 0.749–0.948, both P &lt; 0.001). There was a significant correlation between miR-1290 and histological differentiation (P = 0.029), pT stage (P = 0.006), and lymph node metastasis (P = 0.001). In addition, the <i>in vitro</i> work showed that miR-1290 promoted PDAC cell proliferation, invasion, and migration. Western blotting and the dual-luciferase reporter assay showed that miR-1290 promoted cancer aggressiveness by directly targeting IKK1. The synergist effect of miR-1290 on the proliferation and metastasis of PDAC cells was attenuated and enhanced by IKK1 overexpression and knockdown, respectively. Consistent with the <i>in vitro</i> results, a subcutaneous tumor mouse model showed that miR-1290 functioned as a potent promoter of PDAC <i>in vivo</i>. <b><i>Conclusion:</i></b> MiR-1290 may act as an oncogene by directly targeting the 3’-untranslated region of IKK1, and the miR-1290/IKK1 pathway may prove to be a novel diagnostic and therapeutic target for PDAC.
DOI: 10.6084/m9.figshare.7370627
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: 10.7284/130066
title: Gyrocompass data collected during research cruise OC1808X 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.7370576
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.