TriCheck: Memory Model Verification at the Trisection of Software, Hardware, and ISA

Memory consistency models (MCMs) which govern inter-module interactions in a shared memory system, are a significant, yet often under-appreciated, aspect of system design. MCMs are defined at the various layers of the hardware-software stack, requiring thoroughly verified specifications, compilers, and implementations at the interfaces between layers. Current verification techniques evaluate segments of the system stack in isolation, such as proving compiler mappings from a high-level language (HLL) to an ISA or proving validity of a microarchitectural implementation of an ISA. This paper makes a case for full-stack MCM verification and provides a toolflow, TriCheck, capable of verifying that the HLL, compiler, ISA, and implementation collectively uphold MCM requirements. The work showcases TriCheck's ability to evaluate a proposed ISA MCM in order to ensure that each layer and each mapping is correct and complete. Specifically, we apply TriCheck to the open source RISC-V ISA, seeking to verify accurate, efficient, and legal compilations from C11. We uncover under-specifications and potential inefficiencies in the current RISC-V ISA documentation and identify possible solutions for each. As an example, we find that a RISC-V-compliant microarchitecture allows 144 outcomes forbidden by C11 to be observed out of 1,701 litmus tests examined. Overall, this paper demonstrates the necessity of full-stack verification for detecting MCM-related bugs in the hardware-software stack.Comment: Proceedings of the Twenty-Second International Conference on Architectural Support for Programming Languages and Operating System

Rapid Diagnosis of Intestinal Parasitic Protozoa, with a Focus on Entamoeba histolytica

Entamoeba histolytica is an invasive intestinal pathogenic parasitic protozoan that causes amebiasis. It must be distinguished from Entamoeba dispar and E. moshkovskii, nonpathogenic commensal parasites of the human gut lumen that are morphologically identical to E. histolytica. Detection of specific E. histolytica antigens in stools is a fast, sensitive technique that should be considered as the method of choice. Stool real-time PCR is a highly sensitive and specific technique but its high cost make it unsuitable for use in endemic areas where there are economic constraints. Serology is an important component of the diagnosis of intestinal and especially extraintestinal amebiasis as it is a sensitive test that complements the detection of the parasite antigens or DNA. Circulating Gal/GalNac lectin antigens can be detected in the serum of patients with untreated amoebic liver abscess. On the horizon are multiplex real-time PCR assays which permit the identification of multiple enteropathogens with high sensitivity and specificity

A novel alpha kinase EhAK1 phosphorylates actin and regulates phagocytosis in Entamoeba histolytica

Phagocytosis plays a key role in nutrient uptake and virulence of the protist parasite Entamoeba histolytica. Phagosomes have been characterized by proteomics, and their maturation in the cells has been studied. However, there is so far not much understanding about initiation of phagocytosis and formation of phagosomes at the molecular level. Our group has been studying initiation of phagocytosis and formation of phagosomes in E. histolytica, and have described some of the molecules that play key roles in the process. Here we show the involvement of EhAK1, an alpha kinase and a SH3 domain containing protein in the pathway that leads to formation of phagosomes using red blood cell as ligand particle. A number of approaches, such as proteomics, biochemical, confocal imaging using specific antibodies or GFP tagged molecules, expression down regulation by antisense RNA, over expression of wild type and mutant proteins, were used to understand the role of EhAK1 in phagocytosis. EhAK1 was found in the phagocytic cups during the progression of cups, until closure of phagosomes, but not in the phagosomes themselves. It is recruited to the phagosomes through interaction with the calcium binding protein EhCaBP1. A reduction in phagocytosis was observed when EhAK1 was down regulated by antisense RNA, or by over expression of the kinase dead mutant. G-actin was identified as one of the major substrates of EhAK1. Phosphorylated actin preferentially accumulated at the phagocytic cups and over expression of a phosphorylation defective actin led to defects in phagocytosis. In conclusion, we describe an important component of the pathway that is initiated on attachment of red blood cells to E. histolytica cells. The main function of EhAK1 is to couple signalling events initiated after accumulation of EhC2PK to actin dynamics

Clostridioides difficile binary toxin binding component (cdtb) increases virulence in a hamster model

Background Clostridioides difficile is the leading cause of hospital-acquired gastrointestinal infection, in part due to the existence of binary toxin (CDT)-expressing hypervirulent strains. Although the effects of the CDT holotoxin on disease pathogenesis have been previously studied, we sought to investigate the role of the individual components of CDT during in vivo infection. Methods To determine the contribution of the separate components of CDT during infection, we developed strains of C difficile expressing either CDTa or CDTb individually. We then infected both mice and hamsters with these novel mutant strains and monitored them for development of severe illness. Results Although expression of CDTb without CDTa did not induce significant disease in a mouse model of C difficile infection, we found that complementation of a CDT-deficient C difficile strain with CDTb alone restored virulence in a hamster model of C difficile infection. Conclusions Overall, this study demonstrates that the binding component of C difficile binary toxin, CDTb, contributes to virulence in a hamster model of infection

Pathophysiology of environmental enteric dysfunction and its impact on oral vaccine efficacy

Environmental enteric dysfunction (EED) refers to a subclinical disorder of intestinal function common in tropical countries and in settings of poverty and economic disadvantage. The enteropathy that underlies this syndrome is characterized by mucosal inflammation and villus blunting mediated by T cell activation. Epithelial cell disruption and microbial translocation drive systemic inflammation. EED in young children is associated geographically with growth failure, malnutrition, and greatly impaired responses to oral vaccines, notably rotavirus and poliovirus vaccines. In this review, we describe the pathophysiology of EED and examine the evidence linking EED and oral vaccine failure. This evidence is far from conclusive. Although our understanding of EED is still sketchy, there is limited evidence of disturbed innate immunity, B cell disturbances including aggregation into lymphoid follicles, and autoantibody generation. Pathways of T cell activation and the possibility of dendritic cell anergy, which could help explain oral vaccine failure, require further work

Endemic invasive amoebiasis in northern Australia

In October 2000, a 10-year-old Aboriginal boy from the Darwin region of the Northern Territory was referred to hospital with a 24-hour history of abdominal pain, initially generalised, but then localising to the right iliac fossa. The pain was accompanied by occasional vomiting, but no fever or diarrhoea was noted. At laparotomy, a gangrenous, unruptured appendix was removed. Postoperatively, the patient made a good recovery. Neither he nor any family members had travelled outside the Northern Territory.Histological sections of the surgical specimen showed changes typical of acute suppurative appendicitis. Closer examination, however, revealed numerous round-to-oval structures resembling trophozoites (see Box). When the possibility of invasive amoebiasis was raised, staining of the section with Entamoeba histolytica-specific sera confirmed the diagnosis. E. histolytica serology was negative

Entamoeba bangladeshi nov. sp., Bangladesh.

: TO THE EDITOR: Diarrheal diseases have a major effect on global health, particularly the health of malnourished children (1). The enteric parasites Entamoeba histolytica and E. moshkovskii are potential causes of diarrheal disease in children (2). For the past 20 years, we have been studying Entamoeba infections in children from the urban slum of Mirpur in Dhaka, Bangladesh (3)

Regulation of Virulence of Entamoeba histolytica by the URE3-BP Transcription Factor

It is not understood why only some infections with Entamoeba histolytica result in disease. The calcium-regulated transcription factor upstream regulatory element 3-binding protein (URE3-BP) was initially identified by virtue of its role in regulating the expression of two amebic virulence genes, the Gal/GalNac lectin and ferredoxin. Here we tested whether this transcription factor has a broader role in regulating virulence. A comparison of in vivo to in vitro parasite gene expression demonstrated that 39% of in vivo regulated transcripts contained the URE3 motif recognized by URE3-BP, compared to 23% of all promoters (P < 0.0001). Amebae induced to express a dominant positive mutant form of URE3-BP had an increase in an elongated morphology (30% ± 6% versus 14% ± 5%; P = 0.001), a 2-fold competitive advantage at invading the intestinal epithelium (P = 0.017), and a 3-fold increase in liver abscess size (0.1 ± 0.1 g versus 0.036 ± 0.1 g; P = 0.03). These results support a role for URE3-BP in virulence regulation

Impact of maternal respiratory infections on low birth weight - a community based longitudinal study in an urban setting in Pakistan

Background: The health of mothers and their newborns is intricately related. The weight of the infant at birth is a powerful predictor of infant growth and survival, and is considered to be partly dependent on maternal health and nutrition during pregnancy. We conducted a longitudinal study in an urban community within Karachi to determine maternal predictors of newborn birth weight.Methods: Four hundred pregnant women were enrolled in the study during the period 2011-2013. Data related to symptoms of acute respiratory illness (fever, cough, difficulty breathing, runny nose, sore throat, headache, chills, and myalgia/lethargy) in the pregnant women were collected weekly until delivery. Birth weight of the newborn was recorded within 14days of delivery and the weight of \u3c 2.5kg was classified as low birth weight (LBW).Results: A total of 9,853 symptom episodes were recorded of fever, cough, difficulty breathing, runny nose, sore throat, headache, chills, myalgias/lethargy in the enrolled pregnant women during the study. Out of 243 pregnant women whose newborns were weighed within 14days of birth, LBW proportion was 21% (n=53). On multivariate analysis, independent significant risk factors noted for delivering LBW babies were early pregnancy weight of \u3c 57.5kg [odds ratio adjusted (ORadj)=5.1, 95% CI: (1.3, 19.9)] and gestational age [ORadj=0.3, 95% CI (0.2, 0.7) for every one week increase in gestational age]. Among mothers with high socioeconomic status (SES), every 50-unit increase in the number of episodes of respiratory illness/100weeks of pregnancy had a trend of association with an increased risk of delivering LBW infants [ORadj=1.7, 95% CI: (1.0, 3.1)]. However, among mothers belonging to low SES, there was no association of the number of episodes of maternal respiratory illness during pregnancy with infants having LBW [ORadj=0.9, 95% CI: (0.5, 3.5)].CONCLUSIONS: While overall respiratory illnesses during pregnancy did not impact newborn weight in our study, we found this trend in the sub-group of mothers belonging to the higher SES. Whether this is because in mothers belonging to lower SES, the effects of respiratory illnesses were overshadowed by other risk factors associated with poverty need to be further studied

The bradykinin system in stress and anxiety in humans and mice

Pharmacological research in mice and human genetic analyses suggest that the kallikrein-kinin system (KKS) may regulate anxiety. We examined the role of the KKS in anxiety and stress in both species. In human genetic association analysis, variants in genes for the bradykinin precursor (KNG1) and the bradykinin receptors (BDKRB1 and BDKRB2) were associated with anxiety disorders (p <0.05). In mice, however, neither acute nor chronic stress affected B1 receptor gene or protein expression, and B1 receptor antagonists had no effect on anxiety tests measuring approach-avoidance conflict. We thus focused on the B2 receptor and found that mice injected with the B2 antagonist WIN 64338 had lowered levels of a physiological anxiety measure, the stress-induced hyperthermia (SIH), vs controls. In the brown adipose tissue, a major thermoregulator, WIN 64338 increased expression of the mitochondrial regulator Pgc1 alpha and the bradykinin precursor gene Kng2 was upregulated after cold stress. Our data suggests that the bradykinin system modulates a variety of stress responses through B2 receptor-mediated effects, but systemic antagonists of the B2 receptor were not anxiolytic in mice. Genetic variants in the bradykinin receptor genes may predispose to anxiety disorders in humans by affecting their function.Peer reviewe