A Finite Element Test Bed for Diffraction Tomography

Finite element analysis methods have been successfully applied to the study of ultrasonic wave propagation in elastic solids [1–4]. As a natural part of such numerical solutions. displacements are predicted for every node of the spatial discretization describing the solids geometry and at every instant of time in the temporal discretization used to define the pulse propagation through the material. All of the data constitute a solution to the forward problem and can be used to visualize wavefront propagation and interactions with defects, thus predicting displacement signals at any point in or on the solid

Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Costs & outcomes of hospitalized scrub typhus infection in a tertiary hospital in south India

Background & objectives: Scrub typhus is a rickettsial infection seen along the Asian-Pacific rim and imposes a considerable burden on affected people in low- and middle-income countries. The present study was aimed to determine the direct cost of hospitalization of scrub typhus and its trend over six years. Methods: This was a retrospective, observational, hospital based study of individuals admitted to the hospital, diagnosed with scrub typhus over six years, from January 2013 to December 2018. The potential out of pocket expenditure was evaluated. Results: A total of 198 patients were included in the study. The median cost of admission (adjusted to INR 2020) for the six years (2013 to 2018) was found to be ₹ 37,026 (US $490) [interquartile range (IQR) 22,996-64,992]. The median cost for patients admitted to the intensive care unit (ICU) was ₹ 128,046 (US$ 1695) (IQR 71,575-201,171), while the cost for patients admitted to the ward-alone was ₹ 33,232 (US $ 440) (IQR 19,609-45,373). The multivariable analysis showed that ARDS and SOFA score were the independent predictors of ICU admission. Interpretation & conclusions: Hospitalisation for scrub typhus is associated with a substantial healthcare expense. The predictors of increased cost were the presence of acute respiratory distress syndrome (ARDS), shock, increasing sequential organ failure assessment (SOFA) score and duration of hospital stay

Cost-effectiveness analysis of nivolumab for the treatment of squamous cell carcinoma of the head and neck in the United States.

Aim: To assess the cost-effectiveness of nivolumab monotherapy for recurrent/metastatic (R/M) squamous cell carcinoma of the head and neck (SCCHN) in the US.Methods: We constructed a cohort-based partitioned survival model for three health states (progression-free, progressed disease, and death). Using overall survival and progression-free survival data from the nivolumab and investigator's choice (IC) arms of the CheckMate 141 study, the proportion of patients in each health state was estimated by parametric modeling over a 25-year period. Cost, utility, adverse event, and disease management data inputs were obtained from relevant literature and applied to patients in each health state. A scenario analysis was conducted assuming increased uptake of subsequent immunotherapies. A one-way deterministic sensitivity analysis assessed the impact of variation in multiple parameters. A probabilistic sensitivity analysis in which probabilistic distributions were applied to each input during 1,000 model iterations was also conducted.Results: Total costs incurred were higher with nivolumab ($101,552) than with IC ($38,067). Nivolumab was associated with a higher number of life-years (LY; 1.21) and quality-adjusted life-years (QALYs; 0.89), compared with IC (0.68 and 0.42, respectively). The incremental cost-effectiveness ratio for nivolumab compared with IC was $134,438 per QALY, and this remained qualitatively similar when increased uptake of subsequent immunotherapies was assumed ($129,603 per QALY). Sensitivity analyses supported these findings.Conclusions: These results suggest that, at a willingness-to-pay threshold of $150,000 per QALY, nivolumab is a cost-effective option for therapy of SCCHN in the US

Deletion of parasite immune modulatory sequences combined with immune activating signals enhances vaccine mediated protection against filarial nematodes

<p>Background: Filarial nematodes are tissue-dwelling parasites that can be killed by Th2-driven immune effectors, but that have evolved to withstand immune attack and establish chronic infections by suppressing host immunity. As a consequence, the efficacy of a vaccine against filariasis may depend on its capacity to counter parasite-driven immunomodulation.</p> <p>Methodology and Principal Findings: We immunised mice with DNA plasmids expressing functionally-inactivated forms of two immunomodulatory molecules expressed by the filarial parasite Litomosoides sigmodontis: the abundant larval transcript-1 (LsALT) and cysteine protease inhibitor-2 (LsCPI). The mutant proteins enhanced antibody and cytokine responses to live parasite challenge, and led to more leukocyte recruitment to the site of infection than their native forms. The immune response was further enhanced when the antigens were targeted to dendritic cells using a single chain Fv-αDEC205 antibody and co-administered with plasmids that enhance T helper 2 immunity (IL-4) and antigen-presenting cell recruitment (Flt3L, MIP-1α). Mice immunised simultaneously against the mutated forms of LsALT and LsCPI eliminated adult parasites faster and consistently reduced peripheral microfilaraemia. A multifactorial analysis of the immune response revealed that protection was strongly correlated with the production of parasite-specific IgG1 and with the numbers of leukocytes present at the site of infection.</p> <p>Conclusions: We have developed a successful strategy for DNA vaccination against a nematode infection that specifically targets parasite-driven immunosuppression while simultaneously enhancing Th2 immune responses and parasite antigen presentation by dendritic cells.</p&gt

Determinants for receiving acupuncture for LBP and associated treatments: a prospective cohort study

BACKGROUND: Acupuncture is a frequently used but controversial adjunct to the treatment of chronic low back pain (LBP). Acupuncture is now considered to be effective for chronic LBP and health care systems are pressured to make a decision whether or not acupuncture should be covered. It has been suggested that providing such services might reduce the use of other health care services. Therefore, we explored factors associated with acupuncture treatment for LBP and the relation of acupuncture with other health care services. METHODS: This is a post hoc analysis of a longitudinal prospective cohort study. General practitioners (GPs) recruited consecutive adult patients with LBP. Data on physical function, subjective mood and utilization of health care services was collected at the first consultation and at follow-up telephone interviews for a period of twelve months. RESULTS: A total of 179 (13 %) out of 1,345 patients received acupuncture treatment. The majority of those (59 %) had chronic LBP. Women and elderly patients were more likely to be given acupuncture. Additional determinants of acupuncture therapy were low functional capacity and chronicity of pain. Chronic (vs. acute) back pain OR 1.6 (CL 1.4–2.9) was the only significant disease-related factor associated with the treatment. The strongest predictors for receiving acupuncture were consultation with a GP who offers acupuncture OR 3.5 (CL 2.9–4.1) and consultation with a specialist OR 2.1 (CL 1.9–2.3). After adjustment for patient characteristics, acupuncture remained associated with higher consultation rates and an increased use of other health care services like physiotherapy. CONCLUSION: Receiving acupuncture for LBP depends mostly on the availability of the treatment. It is associated with increased use of other health services even after adjustment for patient characteristics. In our study, we found that receiving acupuncture does not offset the use of other health care resources. A significant proportion of patients who received did not meet the so far only known selection criterion (chonicity). Acupuncture therapy might be a reflection of helplessness in both patients and health care providers

The purpose of United Nations Security Council practice: Contesting competence claims in the normative context created by the Responsibility to Protect.

Practice theory provides important insight into the workings of the Security Council. The contribution is currently limited however by the conjecture that practice theory operates on ‘a different analytical plane’ to norm / normative theory (Adler-Nissen and Pouliot 2014). Building on existing critiques (Duval and Chowdhury 2011; Schindler and Wille 2015) we argue that analyzing practices separately from normative positions risks misappropriating competence and reifying practice that is not fit for purpose. This risk is realized in Adler-Nissen and Pouliot’s (2014) practice based account Libya crisis. By returning the normative context created by the Responsibility to Protect (R2P) to the analytical foreground, and by drawing on a pragmatic conception of 'ethical competence' (Frost 2009), we find that pre-reflexive practices uncritically accepted as markers of competence – e.g. ‘penholding’ – can contribute to the Council’s failure to act collectively in the face of mass atrocity. Drawing on extensive interview material we offer an alternative account of the Libya intervention, finding that the practices of the permanent three (France, UK and US) did not cultivate the kind of collective consciousness that is required to implement R2P. This is further illustrated by an account of the Security Council’s failure in Syria, where the P3’s insistence on regime change instrumentalized the Council at the expense of R2P-appropriate practice. This changed when elected members became ‘penholders’. Practice theory can facilitate learning processes that help the Council meet its responsibilities, but only through an approach that combines its insights with those of norm / normative theory

Cognitive and behavioral predictors of light therapy use

Objective: Although light therapy is effective in the treatment of seasonal affective disorder (SAD) and other mood disorders, only 53-79% of individuals with SAD meet remission criteria after light therapy. Perhaps more importantly, only 12-41% of individuals with SAD continue to use the treatment even after a previous winter of successful treatment. Method: Participants completed surveys regarding (1) social, cognitive, and behavioral variables used to evaluate treatment adherence for other health-related issues, expectations and credibility of light therapy, (2) a depression symptoms scale, and (3) self-reported light therapy use. Results: Individuals age 18 or older responded (n = 40), all reporting having been diagnosed with a mood disorder for which light therapy is indicated. Social support and self-efficacy scores were predictive of light therapy use (p's<.05). Conclusion: The findings suggest that testing social support and self-efficacy in a diagnosed patient population may identify factors related to the decision to use light therapy. Treatments that impact social support and self-efficacy may improve treatment response to light therapy in SAD. © 2012 Roecklein et al

"It's a can of worms": understanding primary care practitioners' behaviours in relation to HPV using the Theoretical Domains Framework

Background: The relationship between infection with high-risk human papillomavirus (HPV) and cervical cancer is transforming cervical cancer prevention. HPV tests and vaccinations have recently become available. In Ireland, as elsewhere, primary care practitioners play a key role in prevention. ATHENS (A Trial of HPV Education and Support) aims to develop a theorybased intervention to support primary care practitioners in their HPV-related practice. This study, the first step in the intervention development process, aimed to: identify HPV-related clinical behaviours that the intervention will target; clarify general practitioners’ (GPs’) and practice nurses’ roles and responsibilities; and determine factors that potentially influence clinical behaviour. A secondary objective was to informally assess the utility of the Theoretical Domains Framework (TDF) in understanding clinical behaviours in an area with an evolving evidence-base. Methods: In-depth semi-structured telephone interviews were conducted with GPs and practice nurses. The topic guide, which contained open questions and HPV-related clinical scenarios, was developed through literature review and clinical experience. Interview transcripts were content-analysed using the TDF as the coding framework. Results: 19 GPs and 14 practice nurses were interviewed. The major HPV-related clinical behaviours were: initiating a discussion about HPV infection with female patients; offering/recommending HPV vaccination to appropriate patients; and answering patients’ questions about HPV testing. While the responsibility for taking smears was considered a female role, both male and female practitioners dealt with HPV-related issues. All 12 theoretical domains arose in relation to HPV infection; the domains judged to be most important were: knowledge, emotion, social influences, beliefs about capabilities and beliefs about consequences. Eleven domains emerged in relation to HPV vaccination, with beliefs about consequences, social influences, knowledge and environmental context and resources judged to be the most important. Nine domains were relevant to HPV testing, with knowledge and beliefs about capabilities judged to be the most important. Conclusions: The findings confirm the need for an intervention to support primary care practitioners around HPV and suggest it should target a range of theoretical domains. The TDF proved valuable in analysing qualitative data collected using a topic guide not specifically designed to capture TDF domains and understanding clinical behaviours in an area with an evolving evidence-base

Eosinophils Are Important for Protection, Immunoregulation and Pathology during Infection with Nematode Microfilariae

Eosinophil responses typify both allergic and parasitic helminth disease. In helminthic disease, the role of eosinophils can be both protective in immune responses and destructive in pathological responses. To investigate whether eosinophils are involved in both protection and pathology during filarial nematode infection, we explored the role of eosinophils and their granule proteins, eosinophil peroxidase (EPO) and major basic protein-1 (MBP-1), during infection with Brugia malayi microfilariae. Using eosinophil-deficient mice (PHIL), we further clarify the role of eosinophils in clearance of microfilariae during primary, but not challenge infection in vivo. Deletion of EPO or MBP-1 alone was insufficient to abrogate parasite clearance suggesting that either these molecules are redundant or eosinophils act indirectly in parasite clearance via augmentation of other protective responses. Absence of eosinophils increased mast cell recruitment, but not other cell types, into the broncho-alveolar lavage fluid during challenge infection. In addition absence of eosinophils or EPO alone, augmented parasite-induced IgE responses, as measured by ELISA, demonstrating that eosinophils are involved in regulation of IgE. Whole body plethysmography indicated that nematode-induced changes in airway physiology were reduced in challenge infection in the absence of eosinophils and also during primary infection in the absence of EPO alone. However lack of eosinophils or MBP-1 actually increased goblet cell mucus production. We did not find any major differences in cytokine responses in the absence of eosinophils, EPO or MBP-1. These results reveal that eosinophils actively participate in regulation of IgE and goblet cell mucus production via granule secretion during nematode-induced pathology and highlight their importance both as effector cells, as damage-inducing cells and as supervisory cells that shape both innate and adaptive immunity