Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon which their works are built. To highlight some of these issues and share experiences, the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) was held in November 2013 in conjunction with the SC13 Conference. The workshop featured keynote presentations and a large number (54) of solicited extended abstracts that were grouped into three themes and presented via panels. A set of collaborative notes of the presentations and discussion was taken during the workshop. Unique perspectives were captured about issues such as comprehensive documentation, development and deployment practices, software licenses and career paths for developers. Attribution systems that account for evidence of software contribution and impact were also discussed. These include mechanisms such as Digital Object Identifiers, publication of “software papers”, and the use of online systems, for example source code repositories like GitHub. This paper summarizes the issues and shared experiences that were discussed, including cross-cutting issues and use cases. It joins a nascent literature seeking to understand what drives software work in science, and how it is impacted by the reward systems of science. These incentives can determine the extent to which developers are motivated to build software for the long-term, for the use of others, and whether to work collaboratively or separately. It also explores community building, leadership, and dynamics in relation to successful scientific software

Randomized trial of complete versus lesion-only revascularization in patients undergoing primary percutaneous coronary intervention for STEMI and Multivessel Disease

BACKGROUND: The optimal management of patients found to have multivessel disease while undergoing primary percutaneous coronary intervention (P-PCI) for ST-segment elevation myocardial infarction is uncertain.   OBJECTIVES: CvLPRIT (Complete versus Lesion-only Primary PCI trial) is a U.K. open-label randomized study comparing complete revascularization at index admission with treatment of the infarct-related artery (IRA) only.   METHODS: After they provided verbal assent and underwent coronary angiography, 296 patients in 7 U.K. centers were randomized through an interactive voice-response program to either in-hospital complete revascularization (n = 150) or IRA-only revascularization (n = 146). Complete revascularization was performed either at the time of P-PCI or before hospital discharge. Randomization was stratified by infarct location (anterior/nonanterior) and symptom onset (≤3 h or >3 h). The primary endpoint was a composite of all-cause death, recurrent myocardial infarction (MI), heart failure, and ischemia-driven revascularization within 12 months.   RESULTS: Patient groups were well matched for baseline clinical characteristics. The primary endpoint occurred in 10.0% of the complete revascularization group versus 21.2% in the IRA-only revascularization group (hazard ratio: 0.45; 95% confidence interval: 0.24 to 0.84; p = 0.009). A trend toward benefit was seen early after complete revascularization (p = 0.055 at 30 days). Although there was no significant reduction in death or MI, a nonsignificant reduction in all primary endpoint components was seen. There was no reduction in ischemic burden on myocardial perfusion scintigraphy or in the safety endpoints of major bleeding, contrast-induced nephropathy, or stroke between the groups.   CONCLUSIONS: In patients presenting for P-PCI with multivessel disease, index admission complete revascularization significantly lowered the rate of the composite primary endpoint at 12 months compared with treating only the IRA. In such patients, inpatient total revascularization may be considered, but larger clinical trials are required to confirm this result and specifically address whether this strategy is associated with improved survival. (Complete Versus Lesion-only Primary PCI Pilot Study [CvLPRIT]; ISRCTN70913605)

Immunogenicity of unprocessed and photooxidized bovine and human osteochondral grafts in collagen-sensitive mice

BACKGROUND: Autologous and allogeneic osteochondral grafts have been used to repair damaged or diseased cartilage. There are drawbacks to both of these methods, however. Another possible source for osteochondral grafting is photooxidized xenograft scaffolds. The purpose of this study was to evaluate the adaptive immune response to unprocessed and photooxidized xenogeneic osteochondral grafts in a collagen-sensitive mouse model. METHODS: Unprocessed and photooxidized bovine and human osteochondral grafts were used. The grafts were implanted subcutaneously in collagen-sensitive DBA/1LacJ mice for four or twelve weeks. ELISPOT assays were conducted with spleen cells to evaluate the number of collagen-specific T cells that produce IL-2, IL-4, IL-5 or IFN-γ. Serum was collected and ELISA assays were performed to determine the titers of collagen-specific and total IgG, IgG1, IgG2a, or IgM antibodies. Histology was conducted on the retrieved osteochondral grafts. RESULTS: Results indicated that, with respect to adaptive T cell immunity, the photooxidized bovine grafts, unprocessed human grafts and photooxidized human grafts did not induce a significant response to collagen. The unprocessed bovine grafts, however, were slightly more immunogenic, inducing a weak immune response. With respect to antibody production, the bovine grafts were less immunogenic than the human grafts. Bovine collagen-specific IgG antibodies were not induced by these grafts, but production of IgM after twelve weeks was observed with both the unprocessed and photooxidized bovine grafts. In contrast, photooxidized human osteochondral grafts induced IgG1 and IgG2a antibodies, while the unprocessed human grafts did not. Pre-existing human collagen-specific IgM antibodies were present in all mice, including sham-operated negative controls that did not receive an implant. Histological analysis revealed some degree of fibrous encapsulation and inflammatory infiltrations in both bovine and human implants, whether unprocessed or photooxidized. CONCLUSION: Both bovine and human cartilage grafts showed weak, but clear immunogenicity in the DBA/1LacJ mice, indicating that immunogenic collagen was still contained in the grafts, even after cleaning and photooxidation. The process of photooxidation is still important in osteochondral grafting, since it stabilizes the surface of the cartilage by cross-linking the collagen fibers, and allows for immediate load bearing and joint resurfacing

Concepts of adversity, risk, vulnerability and resilience: A discussion in the context of the 'Child Protection System'

This paper explores the concepts of adversity, risk, vulnerability and resilience in the context of child protection systems with the aim of contributing to the debate about the ways in which risk of ‘harm’ and ‘abuse’ are conceptualised at different stages of the lifespan and in relation to different groups of people. The recent developments in the policy and legislative framework for state intervention on behalf of children in the UK are described and linked with an exploration of the underlying assumptions about abuse and neglect. Concepts of adversity, risk, vulnerability and resilience and the ways in which the complexity of the routes and pathways to ‘harm’ pose a challenge to the current UK state protective system are discussed

Health Outcomes for Clients of Needle and Syringe Programs in Prisons

High levels of drug dependence have been observed in the prison population globally, and the sharing of injecting drug equipment in prisons has contributed to higher prevalence of bloodborne diseases in prisoners than in the general population. Few prison needle and syringe programs (PNSPs) exist. We conducted a systematic review to assess evidence regarding health outcomes of PNSPs. We searched peer-reviewed databases for data relating to needle and syringe programs in prisons. The search methodology was conducted in accordance with accepted guidelines. Five studies met review inclusion criteria, and all presented evidence associating PNSPs with one or more health benefits, but the strength of the evidence was low. The outcomes for which the studies collectively demonstrated the strongest evidence were prevention of human immunodeficiency virus and viral hepatitis. Few negative consequences from PNSPs were observed, consistent with previous evidence assessments. More research is needed on PNSP effectiveness, and innovative study designs are needed to overcome methodological limitations of previous research. Until stronger evidence becomes available, policymakers are urged to recognize that not implementing PNSPs has the potential to cause considerable harm, in light of what is currently known about the risks and benefits of needle and syringe programs and PNSPs and about the high prevalence of human immunodeficiency virus and viral hepatitis in prisons

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group's future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happen

Report on the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group’s future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happe

Report on the 3rd Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3)

This report records and discusses the Third Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE3). The report includes a description of the keynote presentation of the workshop, which served as an overview of sustainable scientific software. It also summarizes a set of lightning talks in which speakers highlighted to-the-point lessons and challenges pertaining to sustaining scientific software. The final and main contribution of the report is a summary of the discussions, future steps, and future organization for a set of self-organized working groups on topics including developing pathways to funding scientific software; constructing useful common metrics for crediting software stakeholders; identifying principles for sustainable software engineering design; reaching out to research software organizations around the world; and building communities for software sustainability. For each group, we include a point of contact and a landing page that can be used by those who want to join that group's future activities. The main challenge left by the workshop is to see if the groups will execute these activities that they have scheduled, and how the WSSSPE community can encourage this to happen

Enhanced simulations on the Athena/Wide Field Imager instrumental background

The Wide Field Imager (WFI) is one of two focal plane instruments of the Advanced Telescope for High-Energy Astrophysics (Athena), ESA’s next large x-ray observatory, planned for launch in the early 2030s. The current baseline halo orbit is around L2, and the second Lagrangian point of the Sun-Earth system L1 is under consideration. For both potential halo orbits, the radiation environment, solar and cosmic protons, electrons, and He-ions will affect the performance of the instruments. A further critical contribution to the instrument background arises from the unfocused cosmic hard x-ray background. It is important to understand and estimate the expected instrumental background and to investigate measures, such as design modifications or analysis methods, which could improve the expected background level to achieve the challenging scientific requirement (−3 counts  /  cm2  /  keV  /  s at 2 to 7 keV). Previous WFI background simulations done in Geant4 have been improved by taking into account new information about the proton flux at L2. In addition, the simulation model of the WFI instrument and its surroundings employed in Geant4 simulations has been refined to follow the technological development of the WFI camera