The Java Memory Model

After many years, support for multithreading has been integrated into mainstream programming languages. Inclusion of this feature brings with it a need for a clear and direct explanation of how threads interact through memory. Programmers need to be told, simply and clearly, what might happen when their programs execute. Compiler writers need to be able to work their magic without interfering with the promises that are made to programmers. Java's original threading specification, its memory model, was fundamentally flawed. Some language features, like volatile fields, were under-specified: their treatment was so weak as to render them useless. Other features, including fields without access modifiers, were over-specified: the memory model prevents almost all optimizations of code containing these "normal" fields. Finally, some features, like final fields, had no specification at all beyond that of normal fields; no additional guarantees were provided about what will happen when they are used. This work has attempted to remedy these limitations. We provide a clear and concise definition of thread interaction. It is sufficiently simple for programmers to work with, and flexible enough to take advantage of compiler and processor-level optimizations. We also provide formal and informal techniques for verifying that the model provides this balance. These issues had never been addressed for any programming language: in addressing them for Java, this dissertation provides a framework for all multithreaded languages. The work described in this dissertation has been incorporated into the version 5.0 of the Java programming language

SmartTrack: Efficient Predictive Race Detection

Widely used data race detectors, including the state-of-the-art FastTrack algorithm, incur performance costs that are acceptable for regular in-house testing, but miss races detectable from the analyzed execution. Predictive analyses detect more data races in an analyzed execution than FastTrack detects, but at significantly higher performance cost. This paper presents SmartTrack, an algorithm that optimizes predictive race detection analyses, including two analyses from prior work and a new analysis introduced in this paper. SmartTrack's algorithm incorporates two main optimizations: (1) epoch and ownership optimizations from prior work, applied to predictive analysis for the first time; and (2) novel conflicting critical section optimizations introduced by this paper. Our evaluation shows that SmartTrack achieves performance competitive with FastTrack-a qualitative improvement in the state of the art for data race detection.Comment: Extended arXiv version of PLDI 2020 paper (adds Appendices A-E) #228 SmartTrack: Efficient Predictive Race Detectio

Viscoelastic phase diagram of fluorinated and grafted polymer films and proton-exchange membranes for fuel cell applications

The influence of temperature and moisture activity on the viscoelastic behavior of fluorinated membranes for fuel cell applications was investigated. Uncrosslinked and crosslinked ethylene tetrafluoroethylene (ETFE)-based proton-conducting membranes were prepared by radiation grafting and subsequent sulfonation and their behavior was compared with ETFE base film and commercial Nafion (R) NR212 membrane. Uniaxial tensile tests and stress relaxation tests at controlled temperature and relative humidity (RH) were carried out at 30 and 50 degrees C for 10%60%, with an almost single relaxation time exponential. An exponential decrease of relaxation time with RH from 60 s to 10 s was obtained at RH70% and 30 degrees C. The general behavior of grafted films observed at 30 degrees C was also obtained at 50 degrees C. However, an anomalous result was noticed for the membranes, with a higher modulus at 50 degrees C when compared with 30 degrees C. This behavior was explained by solvation of the sulfonic acid groups by water absorption creating hydrogen bonding within the clusters. A viscoelastic phase diagram was elaborated to map critical conditions (temperature and RH) for transitions in time-dependent behavior, from power-law scaling to exponential scaling. (c) 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2013, 51, 1139-114

Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

<p>Abstract</p> <p>Background</p> <p>The sequence of the pathogen <it>Mycobacterium tuberculosis </it>(<it>Mtb</it>) strain <it>H37Rv </it>has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other <it>Mtb </it>strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of <it>Mtb </it>pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of <it>Mtb </it>and <it>M. bovis</it>, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, <it>Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes</it>, and <it>Bifidobacterium longum</it>.</p> <p>Results</p> <p>Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four.</p> <p>Conclusions</p> <p>Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of <it>Mtb </it>in a comparative context, and are available online and through TBDB.org.</p

Misinformation as Immigration Control

It is wrong to force refugees to return to the countries they fled from. It is similarly wrong, many argue, to force migrants back to countries with life-threatening conditions. I argue that it is additionally wrong to help such refugees and migrants voluntarily return whilst failing to inform them of the risks. Drawing on existing data, and original data from East Africa, I describe distinct types of cases where such a wrong arises. In ‘Misinformation Cases’ officials tell refugees that it is safe to return, when it is not, and refugees return who would have otherwise stayed. In ‘Omission Cases’ officials do not provide any information on countries of origin, and this omission causes refugees to repatriate. In ‘Relevancy Cases’ refugees are misinformed or uninformed, but would have returned even if better informed. In all of these cases, at least some state officials are blameworthy for their failure to inform refugees, and are engaging in a form of wrongful immigration control

Progression of coronary calcification in healthy postmenopausal women

BACKGROUND: Coronary artery calcium score incrementally improves coronary risk prediction beyond that provided by conventional risk factors. Limited information is available regarding rates of progression of coronary calcification in women, particularly those with baseline scores above zero. Further, determinants of progression of coronary artery calcification in women are not well understood. This study prospectively evaluated rates and determinants of progression of coronary artery calcium score in a group of healthy postmenopausal women. METHODS: We determined coronary calcium score by computed tomography and recorded demographic, lifestyle and health characteristics of 914 postmenopausal women, a subset of those enrolled in the Women's Health Initiative Observational Study. The 305 women with calcium score ≥10 Agatston units at baseline were invited for repeat scan. This analysis includes the 94 women who underwent second scans. RESULTS: Mean age of study participants was 65 ± 9 years (mean ± SD), body mass index was 26.1 ± 6.1 kg/m(2), and baseline calcium score was 162 ± 220 Agatston units. Mean interval between scans was 3.3 ± 0.7 years. A wide range of changes in coronary calcium score was observed, from -53 to +452 Agatston units/year. Women with lower scores at baseline had smaller annual increases in absolute calcium score. Coronary calcium scores increased 11, 31 and 79 Agatston units/year among women with baseline calcium score in the lowest, middle and highest tertiles. In multivariate analysis, age was not an independent predictor of absolute change in coronary calcium score. Hydroxymethylglutaryl coenzyme A reductase inhibitor (statin) use at baseline was a negative predictor (p = 0.015), whereas baseline calcium score was a strong, positive predictor (p < 0.0001) of progression of coronary calcification. CONCLUSION: Among postmenopausal women with coronary calcium score ≥ 10 Agatston units, rates of change of coronary calcium score varied widely. In multivariate analysis, statin use was a negative independent determinant, whereas baseline calcium score was a strong positive predictor of annual change in coronary calcium score

Risk communication and informed consent in the medical tourism industry: A thematic content analysis of canadian broker websites

<p>Abstract</p> <p>Background</p> <p>Medical tourism, thought of as patients seeking non-emergency medical care outside of their home countries, is a growing industry worldwide. Canadians are amongst those engaging in medical tourism, and many are helped in the process of accessing care abroad by medical tourism brokers - agents who specialize in making international medical care arrangements for patients. As a key source of information for these patients, brokers are likely to play an important role in communicating the risks and benefits of undergoing surgery or other procedures abroad to their clientele. This raises important ethical concerns regarding processes such as informed consent and the liability of brokers in the event that complications arise from procedures. The purpose of this article is to examine the language, information, and online marketing of Canadian medical tourism brokers' websites in light of such ethical concerns.</p> <p>Methods</p> <p>An exhaustive online search using multiple search engines and keywords was performed to compile a comprehensive directory of English-language Canadian medical tourism brokerage websites. These websites were examined using thematic content analysis, which included identifying informational themes, generating frequency counts of these themes, and comparing trends in these counts to the established literature.</p> <p>Results</p> <p>Seventeen websites were identified for inclusion in this study. It was found that Canadian medical tourism broker websites varied widely in scope, content, professionalism and depth of information. Three themes emerged from the thematic content analysis: training and accreditation, risk communication, and business dimensions. Third party accreditation bodies of debatable regulatory value were regularly mentioned on the reviewed websites, and discussion of surgical risk was absent on 47% of the websites reviewed, with limited discussion of risk on the remaining ones. Terminology describing brokers' roles was somewhat inconsistent across the websites. Finally, brokers' roles in follow up care, their prices, and the speed of surgery were the most commonly included business dimensions on the reviewed websites.</p> <p>Conclusion</p> <p>Canadian medical tourism brokers currently lack a common standard of care and accreditation, and are widely lacking in providing adequate risk communication for potential medical tourists. This has implications for the informed consent and consequent safety of Canadian medical tourists.</p

Helpful Female Subordinate Cichlids Are More Likely to Reproduce

BACKGROUND: In many cooperatively breeding vertebrates, subordinates assist a dominant pair to raise the dominants' offspring. Previously, it has been suggested that subordinates may help in payment for continued residency on the territory (the 'pay-to-stay hypothesis'), but payment might also be reciprocated or might allow subordinates access to reproductive opportunities. METHODOLOGY/PRINCIPAL FINDINGS: We measured dominant and subordinate female alloparental brood care and reproductive success in four separate experiments and show that unrelated female dominant and subordinate cichlid fish care for each other's broods (alloparental brood care), but that there is no evidence for reciprocal 'altruism' (no correlation between alloparental care received and given). Instead, subordinate females appear to pay with alloparental care for own direct reproduction. CONCLUSIONS/SIGNIFICANCE: Our results suggest subordinate females pay with alloparental care to ensure access to the breeding substrate and thereby increase their opportunities to lay their own clutches. Subordinates' eggs are laid, on average, five days after the dominant female has produced her first brood. We suggest that immediate reproductive benefits need to be considered in tests of the pay-to-stay hypothesis