Open Science via HUBzero: Exploring Five Science Gateways Supporting and Growing their Open Science Communities

The research landscape applying computational methods has become increasingly interdisciplinary and complex regarding the research computing ecosystem with novel hardware, software, data, and lab instruments. Reproducibility of research results, the usability of tools, and sharing of methods are all crucial for timely collaboration for research and teaching. HUBzero is a widely used science gateway framework designed to support online communities with efficient sharing and publication processes. The paper discusses the growth of communities for the five science gateways nanoHUB, MyGeoHub, QUBEShub & SCORE, CUE4CHNG, and HubICL using the HUBzero Platform to foster open science and tackling education with a diverse set of approaches and target communities. The presented methods and magnitude of the communities elucidate successful means for science gateways for fostering open science and open education

Assessing the optimized precision of the aircraft mass balance method for measurement of urban greenhouse gas emission rates through averaging

To effectively address climate change, aggressive mitigation policies need to be implemented to reduce greenhouse gas emissions. Anthropogenic carbon emissions are mostly generated from urban environments, where human activities are spatially concentrated. Improvements in uncertainty determinations and precision of measurement techniques are critical to permit accurate and precise tracking of emissions changes relative to the reduction targets. As part of the INFLUX project, we quantified carbon dioxide (CO2), carbon monoxide (CO) and methane (CH4) emission rates for the city of Indianapolis by averaging results from nine aircraft-based mass balance experiments performed in November-December 2014. Our goal was to assess the achievable precision of the aircraft-based mass balance method through averaging, assuming constant CO2, CH4 and CO emissions during a three-week field campaign in late fall. The averaging method leads to an emission rate of 14,600 mol/s for CO2, assumed to be largely fossil-derived for this period of the year, and 108 mol/s for CO. The relative standard error of the mean is 17% and 16%, for CO2 and CO, respectively, at the 95% confidence level (CL), i.e. a more than 2-fold improvement from the previous estimate of ~40% for single-flight measurements for Indianapolis. For CH4, the averaged emission rate is 67 mol/s, while the standard error of the mean at 95% CL is large, i.e. ±60%. Given the results for CO2 and CO for the same flight data, we conclude that this much larger scatter in the observed CH4 emission rate is most likely due to variability of CH4 emissions, suggesting that the assumption of constant daily emissions is not correct for CH4 sources. This work shows that repeated measurements using aircraft-based mass balance methods can yield sufficient precision of the mean to inform emissions reduction efforts by detecting changes over time in urban emissions

NASH limits anti-tumour surveillance in immunotherapy-treated HCC.

Hepatocellular carcinoma (HCC) can have viral or non-viral causes1-5. Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need6,7. Here we report the progressive accumulation of exhausted, unconventionally activated CD8+PD1+ T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8+PD1+ T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH-HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8+PD1+CXCR6+, TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8+ T cells or TNF neutralization, suggesting that CD8+ T cells help to induce NASH-HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8+PD1+ T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH-HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment

SGX3: Novel Concepts to Enhance Knowledge and Extend the Community Around Science Gateways

<p>SGX3 is an NSF-funded Center of Excellence for Science Gateways complementing the mission of the Science Gateways Community Institute (SGCI) to serve the community of users, developers and providers of science gateways. The experiences and lessons learned via the over six years of SGCI has informed, which novel areas SGX3 offers, which areas are enhanced, which areas are continued in SGCI via community-funded opportunities and which areas are taken out. While SGCI has been successful in growing the community, there is still a lower uptake in different research domains such as social sciences. Computational sciences and engineering present the domains that are mostly covered by members. SGX3 focuses especially on growing the community for different sciences and research domains and growing a diverse workforce. This paper compares the SGX3 and SGCI offerings and goes into detail for the novel services of SGX3 and the expected impact. <br> </p&gt

Common Usability Problems and Solutions for Science Gateways

Science gateways require a wide range of considerations to make them successful and sustainable. One important consideration is usability. Gateway creators typically lack usability expertise and do not know how to avoid common usability problems. The Science Gateways Community Institute (SGCI) has provided numerous workshops, webinars, and consulting services to the community to improve gateway usability. Based on more than 30 in-depth usability evaluations conducted over the past three years, we identify a small set of common usability problems that gateways have. We characterize these problems and present some possible solutions. Additionally, we show examples of problems and solutions from gateways we have worked with. This paper can help gateways creators identify common usability problems along with solutions that are easy for non-experts to implement

Phenotypic features of genetically modified DMD-XKOXWT pigs

Introduction: Duchenne muscular dystrophy (DMD) is a hereditary neuromuscular disorder caused by mutation in the dystrophin gene (DMD) on the X chromosome. Female DMD carriers occasionally exhibit symptoms such as muscle weakness and heart failure. Here, we investigated the characteristics and representativeness of female DMD carrier (DMD-XKOXWT) pigs as a suitable disease model. Methods: In vitro fertilization using sperm from a DMD-XKOY↔XWTXWT chimeric boar yielded DMD-XKOXWT females, which were used to generate F2 and F3 progeny, including DMD-XKOXWT females. F1–F3 piglets were genotyped and subjected to biochemical analysis for blood creatine kinase (CK), aspartate aminotransferase, and lactate dehydrogenase. Skeletal muscle and myocardial tissue were analyzed for the expression of dystrophin and utrophin, as well as for lymphocyte and macrophage infiltration. Results: DMD-XKOXWT pigs exhibited various characteristics common to human DMD carrier patients, namely, asymptomatic hyperCKemia, dystrophin expression patterns in the skeletal and cardiac muscles, histopathological features of skeletal muscle degeneration, myocardial lesions in adulthood, and sporadic death. Pathological abnormalities observed in the skeletal muscles in DMD-XKOXWT pigs point to a frequent incidence of pathological abnormalities in the musculoskeletal tissues of latent DMD carriers. Our findings suggest a higher risk of myocardial abnormalities in DMD carrier women than previously believed. Conclusions: We demonstrated that DMD-XKOXWT pigs could serve as a suitable large animal model for understanding the pathogenic mechanism in DMD carriers and developing therapies for female DMD carriers

A scalable, clinically severe pig model for Duchenne muscular dystrophy

Large animal models for Duchenne muscular dystrophy (DMD) are crucial for evaluation of diagnostic procedures and treatment strategies. Pigs cloned from male cells lacking DMD exon 52 (DMDΔ52) resemble molecular, clinical and pathological hallmarks of DMD, but die before sexual maturity and cannot be propagated by breeding. Therefore, we generated female DMD+/- carriers. A single founder animal had 11 litters with 29 DMDY/-, 34 DMD+/- as well as 36 male and 29 female wild-type offspring. Breeding with F1 and F2 DMD+/- carriers resulted in additional 114 DMDY/- piglets. With intensive neonatal management, the majority survived for 3-4 months, providing statistically relevant cohorts for experimental studies. Pathological investigations and proteome studies of skeletal muscles and myocardium confirmed the resemblance of human disease mechanisms. Importantly, DMDY/- pigs reveal progressive myocardial fibrosis and increased expression of connexin-43, associated with significantly reduced left ventricular ejection fraction already at age 3 months. Furthermore, behavioral tests provided evidence for impaired cognitive ability. Our breeding cohort of DMDΔ52 pigs and standardized tissue repositories provide important resources for studying DMD disease mechanisms and for testing novel treatment strategies