cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7127120.v1
title: Mitochondrial and glycolysis-regulatory gene expression profiles are associated with intrauterine growth restriction

description: <b>Introduction:</b> Intrauterine growth restriction (IUGR) is a major pregnancy complication with significant postnatal implications. IUGR is characterized by high placental oxidative stress (OS) and increased mitochondrial DNA (mtDNA) abundance that altogether alter the placental metabolism. Such alterations may be captured by changes in the expression of mitochondrial-encoded oxidative phosphorylation genes and glycolysis-regulatory genes. <b>Study design:</b> We aimed here to determine the association between the placental expression of all 13 protein-coding mitochondrial-encoded genes and seven key nuclear glycolysis-regulatory genes, <i>PDK1</i>, <i>PDK2</i>, <i>PDK3</i>, <i>PDK4</i>, <i>PKLR</i>, <i>PKM</i>, <i>OGT</i>, with IUGR, within a case-control study including 50 IUGR and 100 control pregnancies. We additionally assessed placental mtDNA abundance and OS. <b>Results:</b> Three mitochondrial genes, <i>MT-ND5</i>, <i>MT-ND6</i>, and <i>MT-ATP6</i> were found negatively associated with IUGR, while one glycolysis-regulatory gene, <i>PDK1</i> was positively associated with IUGR. mtDNA abundance and OS were positively associated with IUGR. Our study confirmed the existing data on IUGR inducing increased placental OS and mtDNA abundance. Further, our data highlighted the significant involvement of mitochondria and glucose metabolism in the OS-challenged IUGR placentas, which might modulate the placental expression of genes affecting the OXPHOS and promoting glycolysis. <b>Brief rationale:</b> By using banked placenta samples available at Icahn School of Medicine at Mount Sinai, this study aims at laying the foundation for the characterization of the role of mitochondria epi/genetics in IUGR. IUGR is a highly prevalent pregnancy outcome with long-term effects on the progeny that, at present, has limited tools that can be used for its diagnosis and characterization, thus limiting the efficacy of both clinical and public health interventions. The alterations of mitochondrial copy number, OS and mitochondrial and glycolysis-regulatory gene expression that we detected, together, provide the first evidence that these phenomena are playing an important role in the pathophysiology of IUGR. These findings suggest possible new research paths for the full characterization of mitochondrial biomarkers of IUGR.
DOI: 10.6084/m9.figshare.7127096
title: Supplementary Material for: Expression of Duplex shRNAs through a Lentiviral Vector against Cellular and Viral Genes Inflicts Sustained Inhibition of Hepatitis C Virus Replication

description: <b><i>Background:</i></b> The RNAi-based transient therapeutic approach has been well explored for its potential against the hepatitis V virus (HCV). However, to achieve a sustained virological response, a consistent presence of siRNA is needed and it can be achieved by constitutively expressing shRNAs. In this context, the lentiviral vector has emerged as an attractive tool for shRNA delivery against HCV. <b><i>Methods:</i></b> We monitored HCV inhibition after single and multiple rounds of siRNA treatments against La autoantigen and HCV-NS5B in Huh-7.5 cells infected with the FL-J6/JFH chimeric HCV strain. A bicistronic self-inactivating third-generation lentiviral vector expressing shRNA under U6 and H1 promoters was constructed. To ascertain the long-term HCV inhibition, cells were transduced with lentiviral vectors and HCV inhibition was monitored by RT-PCR and Western blotting at regular intervals. <b><i>Results:</i></b> We observed transient antiviral activity after a single round of siRNA treatment, and consecutive rounds of treatments with siRNA demonstrated a sustained HCV inhibition. Delivery of duplex shRNA expressing lentiviral vectors provided constant expression of shRNA leading to synergistic and sustained HCV inhibition. <b><i>Conclusion:</i></b> A lentiviral vector-based delivery system is a “single-shot” therapeutic strategy. It can express duplex shRNA for long-term synergistic inhibition of HCV and qualify as a promising therapeutic approach for sustained inhibition of HCV replication.
DOI: 10.6084/m9.figshare.7127096.v1
title: Supplementary Material for: Expression of Duplex shRNAs through a Lentiviral Vector against Cellular and Viral Genes Inflicts Sustained Inhibition of Hepatitis C Virus Replication

description: <b><i>Background:</i></b> The RNAi-based transient therapeutic approach has been well explored for its potential against the hepatitis V virus (HCV). However, to achieve a sustained virological response, a consistent presence of siRNA is needed and it can be achieved by constitutively expressing shRNAs. In this context, the lentiviral vector has emerged as an attractive tool for shRNA delivery against HCV. <b><i>Methods:</i></b> We monitored HCV inhibition after single and multiple rounds of siRNA treatments against La autoantigen and HCV-NS5B in Huh-7.5 cells infected with the FL-J6/JFH chimeric HCV strain. A bicistronic self-inactivating third-generation lentiviral vector expressing shRNA under U6 and H1 promoters was constructed. To ascertain the long-term HCV inhibition, cells were transduced with lentiviral vectors and HCV inhibition was monitored by RT-PCR and Western blotting at regular intervals. <b><i>Results:</i></b> We observed transient antiviral activity after a single round of siRNA treatment, and consecutive rounds of treatments with siRNA demonstrated a sustained HCV inhibition. Delivery of duplex shRNA expressing lentiviral vectors provided constant expression of shRNA leading to synergistic and sustained HCV inhibition. <b><i>Conclusion:</i></b> A lentiviral vector-based delivery system is a “single-shot” therapeutic strategy. It can express duplex shRNA for long-term synergistic inhibition of HCV and qualify as a promising therapeutic approach for sustained inhibition of HCV replication.
DOI: 10.6084/m9.figshare.7127072
title: Supplementary Material for: Does the Addition of Non-Approved Inclusion and Exclusion Criteria for rtPA Impact Treatment Rates? Findings in Australia, the UK, and the USA

description: <b><i>Background:</i></b> Strict criteria for recombinant tissue plasminogen activator (rtPA) eligibility are stipulated on licences for use in ischaemic stroke; however, practitioners may also add non-standard rtPA criteria. We examined eligibility criteria variation in 3 English-speaking countries including use of non-standard criteria, in relation to rtPA treatment rates. <b><i>Methods:</i></b> Surveys were mailed to 566 eligible hospitals in Australia (AUS), the UK, and the USA. Criteria were pre-classified as standard (approved indication and contraindications) or non-standard (approved warning or researcher “decoy”). Percentage for criterion selection was calculated/compared; linear regression was used to assess the association between use of non-standard criteria and rtPA treatment rates, and to identify factors associated with addition of non-standard criteria. <b><i>Results:</i></b> Response rates were 74% AUS, 65% UK, and 68% USA; mean rtPA treatment rates were 8.7% AUS, 12.7% UK, and 8.7% USA. Median percentage of non-standard inclusions was 33% (all 3 countries) and included National Institutes of Health Stroke Scale (NIHSS) scores &gt; 4, computed tomography (CT) angiography documented occlusion, and favourable CT perfusion. Median percentage of non-standard exclusions was 25% AUS, 28% UK, and 60% USA, and included depressed consciousness, NIHSS &gt; 25, and use of antihypertensive infusions. No AUS or UK sites selected 100% of standard exclusions. <b><i>Conclusions:</i></b> Non-standard criteria for rtPA eligibility were evident in all three countries and could, in part, explain comparably low use of rtPA. Differences in the use of standard criteria may signify practitioner intolerance for those derived from original efficacy studies that are no longer relevant.
DOI: 10.6084/m9.figshare.7127057
title: Supplementary Material for: The Incidence Prognosis and Risk Factors of Cognitive Impairment in Maintenance Haemodialysis Patients

description: <b><i>Objective:</i></b> To investigate the incidence and the prognosis of cognitive impairment (CI) and to find out the risk factors associated with the outcome in maintenance haemodialysis (MHD) patients. <b><i>Methods:</i></b> Enrolled the patients who met the criteria as below: MHD (≥3 months) patients before July 2014, ≥18 years old and could carry on the cognitive function test (Montreal Cognitive Assessment [MoCA]). All enrolled patients were divided into 2 groups: CI group (MoCA &lt; 26) and non-CI group (MoCA ≥26). All patients were followed up for 36 months. The incidence, demography data, medical history, haemodialysis data, laboratory examination and prognosis of CI in haemodialysis patients were prospectively compared and analyzed. Multivariate logistic regression analysis was used to investigate the risk factors of CI. Kaplan-Meier survival curve was used for survival analysis. <b><i>Results:</i></b> In the present study, 219 patients were enrolled. The ratio of male to female was 1.46: 1. Age was 60.07 ± 12.44 and dialysis vintage was 100.79 ± 70.23 months. One hundred thirteen patients’ MoCA scores were lower than 26 were divided into CI group. Education status (OR 3.428), post-dialysis diastolic pressure (OR 2.234) and spKt/V (OR 1.982) were independent risk factors for CI in MHD patients. During the follow-up period, 15 patients died (13.2%) in the CI group and 5 died (4.72%) in the non-CI group (<i>p</i> &lt; 0.05). The Kaplan-Meier survival curve analysis showed that the survival rate of patients with CI was lower than that of non-CI group in MHD patients during 3 years follow-up (<i>p</i> = 0.046). <b><i>Conclusion:</i></b> CI is one of the most common complications in MHD patients. The mortality is high in patients who had CI. Education status, post-dialysis diastolic pressure and spKt/V are independent risk factors for CI in MHD patients.
DOI: 10.6084/m9.figshare.7127069
title: PLS Analysis of Cooperative Thinking

description: Raw data & calculations of our PLS-SEM analysis to explore Cooperative Thinking.
DOI: 10.6084/m9.figshare.7127042
title: Supplementary Material for: Dysregulated Network of Immune, Endocrine and Metabolic Markers is Associated to More Severe Human Chronic Chagas Cardiomyopathy

description: Individuals who are infected with <i>Trypanosoma cruzi</i> develop chronic Chagas cardiomyopathy (CCC), which is a complication involving a series of immune pathogenetic mechanisms, although an association between immune and metabolic alterations was more recently proposed. Accordingly, we investigated the immuno-metabolic response in chagasic patients and their possible influence on CCC pathogenesis. To this end, <i>T. cruzi</i>-seropositive (asymptomatic or with CCC) and sero-negative individuals were studied. Serum tumour necrosis factor (TNF)-α, interleukin (IL)-6, adipocytokines and the expression of their receptors in peripheral blood mononuclear cell (PBMC) were evaluated, together with other factors influencing the immune response. CCC patients showed major metabolic and hormonal abnormalities, in parallel with increased IL-6 and leptin serum levels. TNF-α receptor s, leptin and adiponectin receptors (ObR and Adipo-Rs respectively), as well as PPAR-γ expression in PBMCs from CCC patients were compatible with a counteracting response leading to an unfavourable immune-metabolic profile. These results suggest that persistently increased levels of immune-metabolic pro-inflammatory mediators along with the adverse endocrine anti-inflammatory response of CCC individuals, may contribute to the underlying mechanisms dealing with myocardial tissue damage.
DOI: 10.6084/m9.figshare.7126976
title: Supplementary Material for: Development of a Simple Risk Score Model to Predict Renal Artery Stenosis

description: <b><i>Background/Aims:</i></b> Renal artery stenosis (RAS) is a known cause of secondary hypertension and renal failure. Although renal artery angiography is the gold standard for diagnosing RAS, a simple method to estimate if patients will develop RAS is required. The aim of this retrospective study was to develop a simple risk score to predict significant RAS. <b><i>Methods:</i></b> Four thousand one hundred seventy-seven patients who underwent renal angiography between 2002 and 2016 at Tehran Heart Center were included. Significant RAS was defined as narrowing of the renal artery by at least 70%. Multiple predictors of the RAS were determined using multivariable logistic regression with a backward elimination method. The scoring system obtained from the final model was presented as nomogram. The possible nonlinear effect of continuous variables was evaluated using restricted cubic splines. Overfitting of the final model was assessed applying the tenfold cross-validation method. Model performance was checked using calibration plot as well as Hosmer-Lemeshow goodness of fit test, and area under the receiver operating characteristics (ROC) curve. <b><i>Results:</i></b> The prevalence of RAS was 14.1%. Female sex (OR [95% CI]: 1.53 [1.26–1.85]), hypertension (OR [95% CI]: 1.38 [1.08–1.77]), estimated glomerular filtration rate (OR [95% CI]: 0.98 [0.97–0.98]), body mass index (OR [95% CI]: 0.97 [0.95–0.99]), and age (OR [95% CI]: 1.01 [1.00–1.02]) were determined as the multiple predictors of RAS. The area under the ROC curve of the final predictive model was 0.702 (95% CI: 0.679–0.725). <b><i>Conclusion:</i></b> This model assesses the risk of RAS using available information. This model can be used for both clinical and research purposes.
DOI: 10.6084/m9.figshare.7126979
title: Supplementary Material for: Serum Glutaredoxin Activity as a Marker of Oxidative Stress in Chronic Kidney Disease: A Pilot Study

description: <b><i>Background:</i></b> Inflammation and oxidative stress play important roles in the pathogenesis and progression of chronic kidney disease (CKD) and in its complications, in particular cardiovascular disease, a major cause of death among patients undergoing dialysis treatment. We recently described that Glutaredoxin1 (Grx), an intracellular antioxidant, catalyzes oxidoreductase reactions also extracellularly, and that serum Grx levels correlate to disease severity in type 2 diabetes. <b><i>Aim:</i></b> In the current study we assess Grx as a potential clinical marker of oxidative stress in CKD. <b><i>Methods:</i></b> We examined Grx activity in 25 patients with different stages of chronic kidney failure, 19 control subjects, and 36 patients at initiation of dialysis and after 2 years of dialysis. <b><i>Results:</i></b> We found that Grx activity was significantly higher in CKD patients compared to control subjects, indicating an oxidized extracellular environment in CKD. Grx levels correlated to interleukin-6 and pentosidine, but not to age or GFR. In dialysis patients with Grx sampling before dialysis start and after 2 years of dialysis, Grx levels increased more in hemodialysis (HD) patients than in peritoneal dialysis patients, indicating an increased oxidative stress imbalance in HD patients. Patients who experienced a stroke or myocardial infarction at any time had a significantly higher increase in Grx during the 2 years of dialysis, compared to patients without stroke or myocardial infarction, indicating a possible association between high Grx levels and a cardiovascular event. <b><i>Conclusion:</i></b> Our pilot study indicates that Grx may be a useful marker for assessing the degree of oxidative stress in CKD, however this needs further investigation in a larger prospective patient cohort.
DOI: 10.6084/m9.figshare.7126976.v1
title: Supplementary Material for: Development of a Simple Risk Score Model to Predict Renal Artery Stenosis

description: <b><i>Background/Aims:</i></b> Renal artery stenosis (RAS) is a known cause of secondary hypertension and renal failure. Although renal artery angiography is the gold standard for diagnosing RAS, a simple method to estimate if patients will develop RAS is required. The aim of this retrospective study was to develop a simple risk score to predict significant RAS. <b><i>Methods:</i></b> Four thousand one hundred seventy-seven patients who underwent renal angiography between 2002 and 2016 at Tehran Heart Center were included. Significant RAS was defined as narrowing of the renal artery by at least 70%. Multiple predictors of the RAS were determined using multivariable logistic regression with a backward elimination method. The scoring system obtained from the final model was presented as nomogram. The possible nonlinear effect of continuous variables was evaluated using restricted cubic splines. Overfitting of the final model was assessed applying the tenfold cross-validation method. Model performance was checked using calibration plot as well as Hosmer-Lemeshow goodness of fit test, and area under the receiver operating characteristics (ROC) curve. <b><i>Results:</i></b> The prevalence of RAS was 14.1%. Female sex (OR [95% CI]: 1.53 [1.26–1.85]), hypertension (OR [95% CI]: 1.38 [1.08–1.77]), estimated glomerular filtration rate (OR [95% CI]: 0.98 [0.97–0.98]), body mass index (OR [95% CI]: 0.97 [0.95–0.99]), and age (OR [95% CI]: 1.01 [1.00–1.02]) were determined as the multiple predictors of RAS. The area under the ROC curve of the final predictive model was 0.702 (95% CI: 0.679–0.725). <b><i>Conclusion:</i></b> This model assesses the risk of RAS using available information. This model can be used for both clinical and research purposes.
DOI: 10.6084/m9.figshare.7126979.v1
title: Supplementary Material for: Serum Glutaredoxin Activity as a Marker of Oxidative Stress in Chronic Kidney Disease: A Pilot Study

description: <b><i>Background:</i></b> Inflammation and oxidative stress play important roles in the pathogenesis and progression of chronic kidney disease (CKD) and in its complications, in particular cardiovascular disease, a major cause of death among patients undergoing dialysis treatment. We recently described that Glutaredoxin1 (Grx), an intracellular antioxidant, catalyzes oxidoreductase reactions also extracellularly, and that serum Grx levels correlate to disease severity in type 2 diabetes. <b><i>Aim:</i></b> In the current study we assess Grx as a potential clinical marker of oxidative stress in CKD. <b><i>Methods:</i></b> We examined Grx activity in 25 patients with different stages of chronic kidney failure, 19 control subjects, and 36 patients at initiation of dialysis and after 2 years of dialysis. <b><i>Results:</i></b> We found that Grx activity was significantly higher in CKD patients compared to control subjects, indicating an oxidized extracellular environment in CKD. Grx levels correlated to interleukin-6 and pentosidine, but not to age or GFR. In dialysis patients with Grx sampling before dialysis start and after 2 years of dialysis, Grx levels increased more in hemodialysis (HD) patients than in peritoneal dialysis patients, indicating an increased oxidative stress imbalance in HD patients. Patients who experienced a stroke or myocardial infarction at any time had a significantly higher increase in Grx during the 2 years of dialysis, compared to patients without stroke or myocardial infarction, indicating a possible association between high Grx levels and a cardiovascular event. <b><i>Conclusion:</i></b> Our pilot study indicates that Grx may be a useful marker for assessing the degree of oxidative stress in CKD, however this needs further investigation in a larger prospective patient cohort.
DOI: 10.6084/m9.figshare.7126964
title: results.zip

description: Simulation results for "Efficient implementation of penalized regression for genetic risk prediction" (Privé et al.)<br>
DOI: 10.6084/m9.figshare.7126964.v1
title: results.zip

description: Simulation results for "Efficient implementation of penalized regression for genetic risk prediction" (Privé et al.)<br>
DOI: 10.6084/m9.figshare.7126925
title: Maryna_Kochina_Info.tech.for_estim.the_func.state_of_HVS.zip

description: Research data required by Research Data Policy from Medical & Biological Engineering & Computing journal
DOI: 10.6084/m9.figshare.7126922
title: Multiplex cytokine assay in age-related macular degeneration

description: Dataset for calculate the relationship between cytokine concentrations and prognosis.
DOI: 10.6084/m9.figshare.7126925.v1
title: Maryna_Kochina_Info.tech.for_estim.the_func.state_of_HVS.zip

description: Research data required by Research Data Policy from Medical & Biological Engineering & Computing journal
DOI: 10.6084/m9.figshare.7126922.v1
title: Multiplex cytokine assay in age-related macular degeneration

description: Dataset for calculate the relationship between cytokine concentrations and prognosis.
DOI: 10.6084/m9.figshare.7126505
title: OmicsSIMLA simulation files

description: These are the simulated files for the three scenarios as described in the OmicsSIMLA paper.
DOI: 10.6084/m9.figshare.7126376
title: From Linux Desktop Tools to Jupyter Notebooks to web-based widgets: Deploying your application on the Hubzero Platform

description: Anyone can deploy their unique application on the Hubzero platform - ranging from a novice programmer to a research scientist, to a seasoned software engineer, and everyone in-between. On a Hub, a single instance of the Hubzero science gateway framework, users have access to previously created simulation tools via a modern web browser. Many users throughout the world are developing tools for plant phenotyping, geospatial simulation, nanotechnology, cancer research, among other research focused fields. Like the broad range of potential application developers, Hubzero, i.e. Hubs, have the ability to provide a range of methods to publish an application as well, and it is the goal of this tutorial is to provide the knowledge to “get-started” creating an application on the platform.
DOI: 10.6084/m9.figshare.7126505.v1
title: OmicsSIMLA simulation files

description: These are the simulated files for the three scenarios as described in the OmicsSIMLA paper.
DOI: 10.6084/m9.figshare.7126376.v1
title: HubzeroTutorialGateways2018v5.pdf

description: Anyone can deploy their unique application on the Hubzero platform - ranging from a novice programmer to a research scientist, to a seasoned software engineer, and everyone in-between. On a Hub, a single instance of the Hubzero science gateway framework, users have access to previously created simulation tools via a modern web browser. Many users throughout the world are developing tools for plant phenotyping, geospatial simulation, nanotechnology, cancer research, among other research focused fields. Like the broad range of potential application developers, Hubzero, i.e. Hubs, have the ability to provide a range of methods to publish an application as well, and it is the goal of this tutorial is to provide the knowledge to “get-started” creating an application on the platform.
DOI: 10.6084/m9.figshare.7126505.v2
title: OmicsSIMLA simulation files

description: These are the simulated files for the three scenarios as described in the OmicsSIMLA paper.
DOI: 10.6084/m9.figshare.7126376.v3
title: From Linux Desktop Tools to Jupyter Notebooks to web-based widgets: Deploying your application on the Hubzero Platform

description: Anyone can deploy their unique application on the Hubzero platform - ranging from a novice programmer to a research scientist, to a seasoned software engineer, and everyone in-between. On a Hub, a single instance of the Hubzero science gateway framework, users have access to previously created simulation tools via a modern web browser. Many users throughout the world are developing tools for plant phenotyping, geospatial simulation, nanotechnology, cancer research, among other research focused fields. Like the broad range of potential application developers, Hubzero, i.e. Hubs, have the ability to provide a range of methods to publish an application as well, and it is the goal of this tutorial is to provide the knowledge to “get-started” creating an application on the platform.