Transactions in Relaxed Memory Architectures

The integration of transactions into hardware relaxed memory architectures is a topic of current research both in industry and academia. In this paper, we provide a general architectural framework for the introduction of transactions into models of relaxed memory in hardware, including the sc, tso, armv8 and ppc models. Our framework incorporates flexible and expressive forms of transaction aborts and execution that have hitherto been in the realm of software transactional memory. In contrast to software transactional memory, we account for the characteristics of relaxed memory as a restricted form of distributed system, without a notion of global time. We prove abstraction theorems to demonstrate that the programmer API matches the intuitions and expectations about transactions

Milling, Nutritional, Physical and Cooking Properties of Four Basmati Rice Varieties

Rice is one of the most popular staple foods produced contributing higher most in agriculture gross domestic production in Nepal. Thus, nutritional, physicochemical, and cooking properties of rice might interplay important roles in their production and farming practice, therefore, it is inevitable to understand these characteristic features. However, there has been only limited information available on such properties, therefore we aimed to examine nutritional, physicochemical and cooking properties of four Basmati varieties of rice namely Red Basmati, White Basmati, Black Basmati and Pokhareli Basmati. These rice varieties were purchased from different places in Nepal in paddy form. In this study various parameters associated with milling, nutritional, physical and cooking properties were evaluated. To measure protein contents in rice, Kjeldal method was implied. Among the varieties, the protein content was maximum in Red Basmati (7.74%) and minimum in Black Basmati (6.51%). The milled rice percentage and head rice recovery were maximum in Pokhareli Basmati represented by 72.02±0.10 and 67.46±0.42, respectively, while and minimum in White Basmati represented by 68.17±0.50 and 65.11±0.28, respectively. The kernel elongation ratio and volume expansion ratio was maximum in Red Basmati represented by 1.62 and 2.85 respectively. Water uptake ratio was maximum 3.11 in Black Basmati and minimum of 2.18 in Red Basmati. Gruel loss was found lowest 1.05% in Red Basmati and highest represented by 2.40% in Black Basmati. The highest starch iodine blue value of 0.21 was observed in Red Basmati and lowest of 0.12 in Black Basmati. The Red Basmati was found to have the better cooking quality among all varieties

Degree of Milling Effect on Cold Water Rice Quality

The aim of this study was to examine the effects of degree of milling on various rice parameters such as proximate composition, and cooking properties using mathematical model. The experiments were performed in the laboratory of Food Research Division, Nepal Agricultural Research Council. The three different medium type rice varieties of Nepal (Lumle-2, Chhomrong and Machhapuchre-3) were exposed to five different degrees of milling (0%, 6%, 8%, 10% and 12%). The degree of milling (DM) level significantly (P≤0.05) affected the milling recovery; head rice yield, nutrient content as well as cooking properties of the rice. Increase in DM resulted in further reduction of protein content, fat content, minerals, milled rice and head rice yield after bran layer was further removed. A positive correlation between DM used in present model, amylose content, kernel elongation and gruel solid loss was observed, however, with an increase in DM; amylose content, kernel elongation and gruel solid loss were found to be increased. Adopting 6 to 8% DM for commercial milling of rice might help to prevent quantitative, qualitative and nutritional loss along with retention of good cooking characteristics

Very long O-antigen chains of Salmonella Paratyphi A inhibit inflammasome activation and pyroptotic cell death.

Salmonella Paratyphi A (SPtA) remains one of the leading causes of enteric (typhoid) fever. Yet, despite the recent increased rate of isolation from patients in Asia, our understanding of its pathogenesis is incomplete. Here we investigated inflammasome activation in human macrophages infected with SPtA. We found that SPtA induces GSDMD-mediated pyroptosis via activation of caspase-1, caspase-4 and caspase-8. Although we observed no cell death in the absence of a functional Salmonella pathogenicity island-1 (SPI-1) injectisome, HilA-mediated overexpression of the SPI-1 regulon enhances pyroptosis. SPtA expresses FepE, an LPS O-antigen length regulator, which induces the production of very long O-antigen chains. Using a ΔfepE mutant we established that the very long O-antigen chains interfere with bacterial interactions with epithelial cells and impair inflammasome-mediated macrophage cell death. Salmonella Typhimurium (STm) serovar has a lower FepE expression than SPtA, and triggers higher pyroptosis, conversely, increasing FepE expression in STm reduced pyroptosis. These results suggest that differential expression of FepE results in serovar-specific inflammasome modulation, which mirrors the pro- and anti-inflammatory strategies employed by STm and SPtA, respectively. Our studies point towards distinct mechanisms of virulence of SPtA, whereby it attenuates inflammasome-mediated detection through the elaboration of very long LPS O-polysaccharides

High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children.

BACKGROUND: Salmonella Typhi (S. Typhi) causes typhoid fever, which remains an important public health issue in many developing countries. Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection. METHODS: We recently defined the population structure of S. Typhi, using new sequencing technologies to identify nearly 2,000 single nucleotide polymorphisms (SNPs) that can be used as unequivocal phylogenetic markers. Here we have used the GoldenGate (Illumina) platform to simultaneously type 1,500 of these SNPs in 62 S. Typhi isolates causing severe typhoid in children admitted to Patan Hospital in Kathmandu. RESULTS: Eight distinct S. Typhi haplotypes were identified during the 20-month study period, with 68% of isolates belonging to a subclone of the previously defined H58 S. Typhi. This subclone was closely associated with resistance to nalidixic acid, with all isolates from this group demonstrating a resistant phenotype and harbouring the same resistance-associated SNP in GyrA (Phe83). A secondary clone, comprising 19% of isolates, was observed only during the second half of the study. CONCLUSIONS: Our data demonstrate the utility of SNP typing for monitoring bacterial populations over a defined period in a single endemic setting. We provide evidence for genotype introduction and define a nalidixic acid resistant subclone of S. Typhi, which appears to be the dominant cause of severe pediatric typhoid in Kathmandu during the study period

A discrete geometric model of concurrent program execution

A trace of the execution of a concurrent object-oriented program can be displayed in two-dimensions as a diagram of a non-metric finite geometry. The actions of a programs are represented by points, its objects and threads by vertical lines, its transactions by horizontal lines, its communications and resource sharing by sloping arrows, and its partial traces by rectangular figures. We prove informally that the geometry satisfies the laws of Concurrent Kleene Algebra (CKA); these describe and justify the interleaved implementation of multithreaded programs on computer systems with a lesser number of concurrent processors. More familiar forms of semantics (e.g., verification-oriented and operational) can be derived from CKA. Programs are represented as sets of all their possible traces of execution, and non-determinism is introduced as union of these sets. The geometry is extended to multiple levels of abstraction and granularity; a method call at a higher level can be modelled by a specification of the method body, which is implemented at a lower level. The final section describes how the axioms and definitions of the geometry have been encoded in the interactive proof tool Isabelle, and reports on progress towards automatic checking of the proofs in the paper

Evaluation of an Electricity-free, Culture-based Approach for Detecting Typhoidal Salmonella Bacteremia during Enteric Fever in a High Burden, Resource-limited Setting

Background: In many rural areas at risk for enteric fever, there are few data on Salmonella enterica serotypes Typhi (S. Typhi) and Paratyphi (S. Paratyphi) incidence, due to limited laboratory capacity for microbiologic culture. Here, we describe an approach that permits recovery of the causative agents of enteric fever in such settings. This approach involves the use of an electricity-free incubator based upon use of phase-change materials. We compared this against conventional blood culture for detection of typhoidal Salmonella. Methodology/Principal Findings: Three hundred and four patients with undifferentiated fever attending the outpatient and emergency departments of a public hospital in the Kathmandu Valley of Nepal were recruited. Conventional blood culture was compared against an electricity-free culture approach. Blood from 66 (21.7%) patients tested positive for a Gram-negative bacterium by at least one of the two methods. Sixty-five (21.4%) patients tested blood culture positive for S. Typhi (30; 9.9%) or S. Paratyphi A (35; 11.5%). From the 65 individuals with culture-confirmed enteric fever, 55 (84.6%) were identified by the conventional blood culture and 60 (92.3%) were identified by the experimental method. Median time-to-positivity was 2 days for both procedures. The experimental approach was falsely positive due to probable skin contaminants in 2 of 239 individuals (0.8%). The percentages of positive and negative agreement for diagnosis of enteric fever were 90.9% (95% CI: 80.0%–97.0%) and 96.0% (92.7%–98.1%), respectively. After initial incubation, Salmonella isolates could be readily recovered from blood culture bottles maintained at room temperature for six months. Conclusions/Significance: A simple culture approach based upon a phase-change incubator can be used to isolate agents of enteric fever. This approach could be used as a surveillance tool to assess incidence and drug resistance of the etiologic agents of enteric fever in settings without reliable local access to electricity or local diagnostic microbiology laboratories.Boston Children's Hospital (Frederick H. Lovejoy Fund)Harvard Global Health InstituteNational Institute of Allergy and Infectious Diseases (U.S.) (Grant AI100023)National Institute of Allergy and Infectious Diseases (U.S.) (Grant AI077883

Direct inference and control of genetic population structure from RNA sequencing data

RNAseq data can be used to infer genetic variants, yet its use for estimating genetic population structure remains underexplored. Here, we construct a freely available computational tool (RGStraP) to estimate RNAseq-based genetic principal components (RG-PCs) and assess whether RG-PCs can be used to control for population structure in gene expression analyses. Using whole blood samples from understudied Nepalese populations and the Geuvadis study, we show that RG-PCs had comparable results to paired array-based genotypes, with high genotype concordance and high correlations of genetic principal components, capturing subpopulations within the dataset. In differential gene expression analysis, we found that inclusion of RG-PCs as covariates reduced test statistic inflation. Our paper demonstrates that genetic population structure can be directly inferred and controlled for using RNAseq data, thus facilitating improved retrospective and future analyses of transcriptomic data

Clinically and microbiologically derived azithromycin susceptibility breakpoints for Salmonella enterica serovars Typhi and Paratyphi A.

Azithromycin is an effective treatment for uncomplicated infections with Salmonella enterica serovar Typhi and serovar Paratyphi A (enteric fever), but there are no clinically validated MIC and disk zone size interpretative guidelines. We studied individual patient data from three randomized controlled trials (RCTs) of antimicrobial treatment in enteric fever in Vietnam, with azithromycin used in one treatment arm, to determine the relationship between azithromycin treatment response and the azithromycin MIC of the infecting isolate. We additionally compared the azithromycin MIC and the disk susceptibility zone sizes of 1,640 S. Typhi and S. Paratyphi A clinical isolates collected from seven Asian countries. In the RCTs, 214 patients who were treated with azithromycin at a dose of 10 to 20 mg/ml for 5 to 7 days were analyzed. Treatment was successful in 195 of 214 (91%) patients, with no significant difference in response (cure rate, fever clearance time) with MICs ranging from 4 to 16 μg/ml. The proportion of Asian enteric fever isolates with an MIC of ≤ 16 μg/ml was 1,452/1,460 (99.5%; 95% confidence interval [CI], 98.9 to 99.7) for S. Typhi and 207/240 (86.3%; 95% CI, 81.2 to 90.3) (P 16 μg/ml and to determine MIC and disk breakpoints for S. Paratyphi A