CcNav: Understanding Compiler Optimizations in Binary Code

Program developers spend significant time on optimizing and tuning programs. During this iterative process, they apply optimizations, analyze the resulting code, and modify the compilation until they are satisfied. Understanding what the compiler did with the code is crucial to this process but is very time-consuming and labor-intensive. Users need to navigate through thousands of lines of binary code and correlate it to source code concepts to understand the results of the compilation and to identify optimizations. We present a design study in collaboration with program developers and performance analysts. Our collaborators work with various artifacts related to the program such as binary code, source code, control flow graphs, and call graphs. Through interviews, feedback, and pair-analytics sessions, we analyzed their tasks and workflow. Based on this task analysis and through a human-centric design process, we designed a visual analytics system Compilation Navigator (CcNav) to aid exploration of the effects of compiler optimizations on the program. CcNav provides a streamlined workflow and a unified context that integrates disparate artifacts. CcNav supports consistent interactions across all the artifacts making it easy to correlate binary code with source code concepts. CcNav enables users to navigate and filter large binary code to identify and summarize optimizations such as inlining, vectorization, loop unrolling, and code hoisting. We evaluate CcNav through guided sessions and semi-structured interviews. We reflect on our design process, particularly the immersive elements, and on the transferability of design studies through our experience with a previous design study on program analysis.Comment: IEEE VIS VAST 202

Investigating rates and risk factors for hepatitis C virus reinfection in people receiving antiviral treatment in England

England has committed to the World Health Organization target to eliminate hepatitis C virus (HCV) as a public threat by the year 2030. Given successful treatments for HCV in recent years, it is unclear whether HCV reinfection will impact England's ability to achieve HCV elimination. We aimed to estimate the HCV reinfection rate among a cohort of patients receiving antiviral treatment using available surveillance data. Linkage between a treatment dataset from 2015-2019 and an HCV RNA testing dataset were used to identify people who experienced reinfection using three criteria. A Cox proportional hazards model was used to determine risk factors associated with HCV reinfection among a cohort who received treatment and had follow-up HCV RNA testing. The reinfection rate among those receiving HCV treatment was 7.91 per 100 person-years (PYs, 95% confidence interval (CI) 7.37-8.49) and highest among current injecting drug users (22.55 per 100 PYs, 95%CI 19.98-25.46) and people who had been in prison (20.42 per 100 PYs, 95%CI 17.21-24.24). In the adjusted model, women had a significantly reduced risk of reinfection. Being of younger age, current injecting drug users, and receipt of first treatment in prison were each significantly associated with increased risk of reinfection. Two-fifths of those with reinfection (43%, n=329/767) were linked to treatment after reinfection, and of those starting treatment, three quarters (75%, n=222/296) achieved a sustained virologic response. Guidance for testing groups at risk of reinfection and harm reduction strategies to minimize transmission should be implemented if England is to achieve HCV elimination targets

Data linkage to monitor hepatitis C-associated end-stage liver disease and hepatocellular carcinoma inpatient stays in England

Persons with chronic hepatitis C (HCV) infection are at increased risk of end-stage liver disease (ESLD) and hepatocellular carcinoma (HCC). The impact of hepatitis treatment scale-up and elimination strategies on ESLD and HCC incidence is a critical measure of progress towards WHO targets. Data from national laboratory surveillance of HCV diagnoses were linked to inpatient care records in Hospital Episode Statistics (HES). For persons first diagnosed with HCV between 1998-2016, we describe the characteristics of those with ESLD and HCC and estimate incidence. Of persons diagnosed with HCV between 1998 and 2016 (104,674), 9.1 % (9,525) had an admission for ESLD and 2.5% (2,610) for HCC. The majority of persons with ESLD and HCC were male (70.7% and 82.7%) and of white ethnicity (89.9% and 82.7%). Crude incidence of ESLD and HCC admission was 10.4 and 3.2 per 1,000 person years respectively. When compared to 2011-2013, incidence of ESLD and HCC admissions in 2014-2017 were lower [ESLD incidence rate ratio (IRR): 0.81; 95% Confidence interval (CI): 0.76-0.86; HCC IRR: 0.90; 95% CI: 0.82-1.00, p=0.045]. Data linkage showed considerable underreporting of HCV in HES coding for ESLD and HCC (16.0% and 11.3% respectively). In conclusion, we found a decline in incidence of ESLD and HCC-related inpatient admissions since 2011-2013. Linked analysis is required for the continued monitoring of ESLD and HCC inpatient incidence. However, HES data quality issues around completeness of identifiers contribute to uncertainty in linkage and may limit our ability to robustly monitor progress towards WHO elimination goals

No Evidence for a Cumulative Impact Effect on Concussion Injury Threshold

Recent studies using a helmet-based accelerometer system (Head Impact Telemetry System [HITS]) have demonstrated that concussions result from a wide range of head impact magnitudes. Variability in concussion thresholds has been proposed to result from the cumulative effect of non-concussive head impacts prior to injury. We used the HITS to collect biomechanical data representing >100,000 head impacts in 95 high school football players over 4 years. The cumulative impact histories prior to 20 concussive impacts in 19 athletes were compared to the cumulative impact histories prior to the three largest magnitude non-concussive head impacts in the same athletes. No differences were present in any impact history variable between the concussive and non-concussive high magnitude impacts. These analyses included the number of head impacts, cumulative HIT severity profile value, cumulative linear acceleration, and cumulative rotational acceleration during the same practice or game session, as well as over the 30-min and 1 week preceding these impacts. Our data do not support the proposal that impact volume or intensity influence concussion threshold in high school football athletes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90490/1/neu-2E2011-2E1910.pd

Core level binding energy for nitrogen doped char: XPS deconvolution analysis from first principles

Amorphous carbon produced from lignocellulosic materials has received much attention in recent years because of its applications in environmental and agricultural management with potential to sequester carbon, serve as a soil amendment, and improve soil aggregation. Modern engineered amorphous carbons with promising properties, such as porous structure, surface functionalities (O, N, P, S) and layers with large number of defects, are used in the field of adsorption and catalysis. There is a growing interest in the production of nitrogen-doped carbonaceous materials because of their excellent properties in a variety of applications such carbon electrodes, heterogenous catalysis adsorption and batteries. However, quantifying the surface nitrogen and oxygen content in amorphous nitrogen doped carbons via deconvolution of C 1s x-ray photoelectron (XPS) spectra remains difficult due to limited information in the literature. No suitable method exists to accurately correlate both the nitrogen and oxygen content to the carbon (C 1s) XPS spectrum in the literature. To improve the interpretation of spectra, the C 1s, N 1s and O 1s core level energy shifts have been calculated for various nitrogenated carbon structures from first principles by performing density functional theory (DFT) based calculations. Furthermore, we propose a new method to improve the self-consistency of the XPS interpretation based on a seven-peak C 1s deconvolution (3 C-C peaks, 3 C-N/-O peaks, and π-π* transition peaks). With the DFT calculations, spectral components arising from surface-defect carbons could be distinguished from aromatic sp2 carbon. The deconvolution method proposed provides C/(N+O) ratios in very good agreement (error less than 5%) with those obtained from total C 1s, N 1s and O 1s peaks. Our deconvolution strategy provides a simple guideline for obtaining high-quality fits to experimental data on the basis of a careful evaluation of experimental conditions and resul

Does high optimism protect against the inter-generational transmission of high BMI? The Cardiovascular Risk in Young Finns Study

Objective: The transmission of overweight from one generation to the next is well established, however little is known about what psychosocial factors may protect against this familial risk. The aim of this study was to examine whether optimism plays a role in the intergenerational transmission of obesity. Methods: Our sample included 1043 participants from the prospective Cardiovascular Risk in Young FINNS Study. Optimism was measured in early adulthood (2001) when the cohort was aged 24-39 years. BMI was measured in 2001 (baseline) and 2012 when they were aged 35-50 years. Parental BMI was measured in 1980. Hierarchical linear regression and logistic regression were used to examine the association between optimism and future BMI/obesity, and whether an interaction existed between optimism and parental BMI when predicting BMI/obesity 11 years later. Results: High optimism in young adulthood demonstrated a negative relationship with high BMI in mid-adulthood, but only in women (beta = - 0.127, p = 0.001). The optimism x maternal BMI interaction term was a significant predictor of future BMI in women (beta = 0.588, p = 0.036). The logistic regression results confirmed that high optimism predicted reduced obesity in women (OR = 0.68, 95% CI, 0.55-0.86), however the optimism x maternal obesity interaction term was not a significant predictor (OR = 0.50, 95% CI, 0.10-2.48). Conclusions: Our findings supported our hypothesis that high optimism mitigated the intergenerational transmission of high BMI, but only in women. These findings also provided evidence that positive psychosocial factors such as optimism are associated with long-term protective effects on BMI in women.Peer reviewe

Skeletal muscle mitochondrial dysfunction in contemporary antiretroviral therapy: a single cell analysis

OBJECTIVE: To quantify mitochondrial function in skeletal muscle of people treated with contemporary antiretroviral therapy. DESIGN: Cross-sectional observational study. METHODS: Quantitative multiplex immunofluorescence was performed to determine mitochondrial mass and respiratory chain complex abundance in individual myofibres from tibialis anterior biopsies. Individual myofibres were captured by laser microdissection and mitochondrial DNA (mtDNA) content and large-scale deletions were measured by real-time PCR. RESULTS: Forty five antiretroviral therapy (ART) treated people with HIV (PWH, mean age 58 years, mean duration of ART 125 months) were compared with 15 HIV negative age-matched controls. Mitochondrial complex I (CI) deficiency was observed at higher proportional levels in PWH than negative controls (P = 0.008). Myofibre mitochondrial mass did not differ by HIV status.No ART class was significantly associated with mitochondrial deficiency, including prior exposure to historical NRTIs (nucleoside analogue reverse transcriptase inhibitors) associated with systemic mitochondrial toxicity.To exclude an effect of untreated HIV, we also studied skeletal muscle from 13 ART-naïve PWH (mean age 37). These showed negligible CI defects, as well as comparable myofibre mitochondrial mass to ART-treated PWH.Most CI-deficient myofibres contained mtDNA deletions. No mtDNA depletion was detected. CONCLUSION: Here, we show that PWH treated with contemporary ART have mitochondrial dysfunction in skeletal muscle, exceeding that expected due to age alone. Surprisingly, this was not mediated by prior exposure to mitochondrially toxic NRTIs, suggesting novel mechanisms of mitochondrial dysfunction in contemporary ART-treated PWH. These findings are relevant for better understanding successful ageing in PWH

Health facility and skilled birth deliveries among poor women with Jamkesmas health insurance in Indonesia: a mixed-methods study

BACKGROUND: The growing momentum for quality and affordable health care for all has given rise to the recent global universal health coverage (UHC) movement. As part of Indonesia’s strategy to achieve the goal of UHC, large investments have been made to increase health access for the poor, resulting in the implementation of various health insurance schemes targeted towards the poor and near-poor, including the Jamkesmas program. In the backdrop of Indonesia’s aspiration to reach UHC is the high rate of maternal mortality that disproportionally affects poor women. The objective of this study was to evaluate the association of health facility and skilled birth deliveries among poor women with and without Jamkesmas and explore perceived barriers to health insurance membership and maternal health service utilization. METHODS: We used a mixed-methods design. Utilizing data from the 2012 Indonesian Demographic and Health Survey (n = 45,607), secondary analysis using propensity score matching was performed on key outcomes of interest: health facility delivery (HFD) and skilled birth delivery (SBD). In-depth interviews (n = 51) were conducted in the provinces of Jakarta and Banten among poor women, midwives, and government representatives. Thematic framework analysis was performed on qualitative data to explore perceived barriers. RESULTS: In 2012, 63.0% of women did not have health insurance; 19.1% had Jamkesmas. Poor women with Jamkesmas were 19% (OR = 1.19 [1.03–1.37]) more likely to have HFD and 17% (OR = 1.17 [1.01–1.35]) more likely to have SBD compared to poor women without insurance. Qualitative interviews highlighted key issues, including: lack of proper documentation for health insurance registration; the preference of pregnant women to deliver in their parents’ village; the use of traditional birth attendants; distance to health facilities; shortage of qualified health providers; overcrowded health facilities; and lack of health facility accreditation. CONCLUSION: Poor women with Jamkesmas membership had a modest increase in HFD and SBD. These findings are consistent with economic theory that health insurance coverage can reduce financial barriers to care and increase service uptake. However, factors such as socio-cultural beliefs, accessibility, and quality of care are important elements that need to be addressed as part of the national UHC agenda to improve maternal health services in Indonesia

The effects of leaflet material properties on the simulated function of regurgitant mitral valves

Advances in three-dimensional imaging provide the ability to construct and analyze finite element (FE) models to evaluate the biomechanical behavior and function of atrioventricular valves. However, while obtaining patient-specific valve geometry is now possible, non-invasive measurement of patient-specific leaflet material properties remains nearly impossible. Both valve geometry and tissue properties play a significant role in governing valve dynamics, leading to the central question of whether clinically relevant insights can be attained from FE analysis of atrioventricular valves without precise knowledge of tissue properties. As such we investigated 1) the influence of tissue extensibility and 2) the effects of constitutive model parameters and leaflet thickness on simulated valve function and mechanics. We compared metrics of valve function (e.g., leaflet coaptation and regurgitant orifice area) and mechanics (e.g., stress and strain) across one normal and three regurgitant mitral valve (MV) models with common mechanisms of regurgitation (annular dilation, leaflet prolapse, leaflet tethering) of both moderate and severe degree. We developed a novel fully-automated approach to accurately quantify regurgitant orifice areas of complex valve geometries. We found that the relative ordering of the mechanical and functional metrics was maintained across a group of valves using material properties up to 15% softer than the representative adult mitral constitutive model. Our findings suggest that FE simulations can be used to qualitatively compare how differences and alterations in valve structure affect relative atrioventricular valve function even in populations where material properties are not precisely known

The Association Between Social Support, Body Mass Index and Increased Risk of Prediabetes : the Cardiovascular Risk in Young Finns Study

The psychosocial determinants of prediabetes are poorly understood. The aims of our study were (1) to analyse the association between perceived social support in young adulthood and fasting glucose levels and prediabetes in mid-adulthood in a cohort of healthy Finns, (2) to explore whether body mass index (BMI), inflammation or depression mediate this relationship, (3) and to examine the association between social support trajectory groups and fasting glucose. A prospective design was used with an analytic sample of 1250 participants aged 3-18 years at baseline (1980) and aged 12-39 years when social support was measured. Fasting glucose and prediabetes were assessed 32 years after baseline. Linear and logistic regression was used to examine the association between social support and the outcome measures. A bootstrapping technique was used to examine mediation effects. Social support was associated with future glucose levels in women after adjusting for childhood socioeconomic status (SES) and youth depression (beta = -0.136, p = 0.001) and also predicted prediabetes in women after adjusting for childhood SES (beta = 1.31, 95 % CI 1.02 to 1.69, p = 0.031). Both associations were attenuated after adjusting for BMI in mid-adulthood. BMI was found to mediate the relationship between social support and prediabetes in women (beta for indirect effect beta = 0.09, SE = 0.03, CI = 0.03 to 0.16). Low perceived social support in young adulthood is associated with high fasting glucose and prediabetes in mid-adulthood in women but not men. The association between social support and prediabetes in women can be partly explained by BMI.Peer reviewe