UPC++ v1.0 Programmer’s Guide, Revision 2020.3.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

A cost analysis of operative repair of major laparoscopic bile duct injuries

Background. Major bile duct injuries occur infrequently after laparoscopic cholecystectomy, but may result in life-threatening complications. Few data exist on the financial implications of duct repair. This study calculated the costs of operative repair in a cohort of patients who underwent reconstruction of the bile duct after major ductal injury.Objective. To calculate the total in-hospital cost of surgical repair of patients referred with major bile duct injuries.Methods. A prospective database was reviewed to identify all patients referred to the University of Cape Town Private Academic Hospital, South Africa, between 2002 and 2013 for assessment and repair of major laparoscopic bile duct injuries. The detailed clinical records and billing information were evaluated to determine all costs from admission to discharge. Total costs for each patient were adjusted for inflation between the year of repair and 2013.Results. Forty-four patients (33 women, 11 men; median age 48 years, range 30 - 78) underwent reconstruction of a major bile duct injury. First-time repairs were performed at a median of 24.5 days (range 1 - 3 662) after initial surgery. Median hospital stay was 15 days (range 6 - 86). Mean cost of repair was ZAR215 711 (range ZAR68 764 - 980 830). Major contributors to cost were theatre expenses (22%), admission to intensive care (21%), radiology (17%) and specialist fees (12%). Admission to a general ward (10%), consumables (7%), pharmacy (5%), endoscopy (3%) and laboratory costs (3%) made up the balance.Conclusions. The cost of repair of a major laparoscopic bile duct injury is substantial owing to prolonged hospitalisation, complex surgical intervention and intensive imaging requirements

Post-laparotomy haemoptysis due to broncho-abdominal fistula caused by retained abdominal surgical swab

The case presented describes the migration of a surgical swab across the left hemidiaphragm over four years. The patient had at least two episodes of haemoptysis in that period and was misdiagnosed and treated for Pulmonary Tuberculosis. When the proper diagnosis was made and a lobectomy was planned for removal of the swab, the act of anaesthesia revealed a major bronchoabdominal fistula that was resolved by simply isolating that lung with an endobronchial tube. According to our search, such a left-sided broncho-abdominal fistula has, to date, not been described in the literature.Keywords: broncho-abdominal fistula, gossypibom

Comparison of System Call Representations for Intrusion Detection

Over the years, artificial neural networks have been applied successfully in many areas including IT security. Yet, neural networks can only process continuous input data. This is particularly challenging for security-related non-continuous data like system calls. This work focuses on four different options to preprocess sequences of system calls so that they can be processed by neural networks. These input options are based on one-hot encoding and learning word2vec or GloVe representations of system calls. As an additional option, we analyze if the mapping of system calls to their respective kernel modules is an adequate generalization step for (a) replacing system calls or (b) enhancing system call data with additional information regarding their context. However, when performing such preprocessing steps it is important to ensure that no relevant information is lost during the process. The overall objective of system call based intrusion detection is to categorize sequences of system calls as benign or malicious behavior. Therefore, this scenario is used to evaluate the different input options as a classification task. The results show, that each of the four different methods is a valid option when preprocessing input data, but the use of kernel modules only is not recommended because too much information is being lost during the mapping process.Comment: 12 pages, 1 figure, submitted to CISIS 201

Guest Editorial: Growing wilderness and expedition medicine education in southern Africa

No Abstrac

Mathematics and biology

CITATION: Hofmeyr, J. H. S. 2017. Mathematics and biology. South African Journal of Science, 113(3/4), Art. #a0203, doi:10.17159/sajs.2017/a0203.The original publication is available at http://sajs.co.zaNo abstract availablehttps://www.sajs.co.za/article/view/3628Publisher's versio

Calcium supplementation commencing before or early in pregnancy, or food fortification with calcium, for preventing hypertensive disorders of pregnancy

Background Pre-eclampsia is considerably more prevalent in low- than high-income countries. One possible explanation for this discrepancy is dietary diKerences, particularly calcium deficiency. Calcium supplementation in the second half of pregnancy reduces the serious consequences of pre-eclampsia and is recommended by the WorldHealthOrganization (WHO) for women with low dietary calcium intake, but has limited eKect on the overallrisk of pre-eclampsia. It is important to establish whether calcium supplementation before and in early pregnancy has added benefit. Such evidence would be justification for population-level fortification of staple foods with calcium. Objectives To determine the eKect of calcium supplementation or food fortification with calcium, commenced before or early in pregnancy and continued at least until mid-pregnancy, on pre-eclampsia and other hypertensive disorders, maternal morbidity and mortality, as well as fetal and neonatal outcomes. Search methods We searched the Cochrane Pregnancy and Childbirth Trials Register (10 August 2017), PubMed (29 June 2017), ClinicalTrials.gov, the WHO International Clinical Trials Registry Platform (ICTRP) (10 August 2017) and reference lists of retrieved studies. Selection criteria Randomised controlled trials of calcium supplementation orfood fortification which include women of child bearing age not yet pregnant, or in early pregnancy. Cluster-RCTs, quasi-RCTs and trials published in abstract form only would have been eligible for inclusion in this review but none were identified. Cross-over designs are not appropriate for this intervention. The scope of this review is to consider interventions including calcium supplementation with or without additional supplements or treatments, compared with placebo or no intervention. Data collection and analysis Two review authors independently assessed trials for inclusion and risk of bias, extracted data and checked them for accuracy. Main results This review is based on one RCT (involving 60 women) which looked at calcium plus additional supplements versus control. The women (who had lowantioxidant status)were in the early stages of pregnancy.We did notidentify any studieswhere supplementation commenced pre-pregnancy. Another RCT comparing calcium versus placebo is ongoing but not yet complete. We did not identify any studies looking at any of our other planned comparisons. Calcium plus antioxidants and other supplements versus placebo We included one small study (involving 60 women with low antioxidantlevels) which was conducted in an academic hospital in Indondesia. The study was at low risk of bias for all domains with the exception of selective reporting, for which it was unclear. Women in the intervention group received calcium (800 mg) plus N-acetylcysteine (200 mg), Cu (2 mg), Zn (15 mg), Mn (0.5 mg) and selenium (100 mcg) and vitamins A (1000 IU), B6 (2.2 mg), B12 (2.2 mcg), C (200 mg), and E (400 IU) versus the placebo control group of women who received similar looking tablets containing iron and folic acid. Both groups received iron (30 mg) and folic acid (400 mcg). Tablets were taken twice daily from eight to 12 weeks of gestation and then throughout pregnancy. The included study found that calcium supplementation plus antioxidants and other supplements may slightly reduce pre-eclampsia (gestational hypertension and proteinuria) (risk ratio (RR) 0.24, 95% confidence interval (CI) 0.06 to 1.01; low-quality evidence), but this is uncertain due to wide confidence intervals just crossing the line of no eKect, and small sample size. It appears that earlypregnancy loss before 20 weeks' gestation (RR 0.06, 95% CI 0.00 to 1.04; moderate-quality evidence) may be slightly reduced by calcium plus antioxidants and other supplements, but this outcome also has wide confidence intervals, which just cross the line of no eKect. Very few events were reported under the composite outcome, severe maternal morbidity and mortality index and no clear diKerence was seen between groups (RR 0.36, 95% CI 0.04 to 3.23; low-quality evidence). However, the included study observed a reduction in the composite outcome pre-eclampsia and/or pregnancy loss at any gestational age (RR 0.13, 95% CI 0.03 to 0.50; moderate-quality evidence), and pregnancy loss/stillbirth at any gestational age (RR 0.06, 95% CI 0.00 to 0.92;moderate-quality evidence)in the calcium plus antioxidant/supplement group. Other outcomes reported (placental abruption, severe pre-eclampsia and preterm birth (less than 37 weeks' gestation)) were too infrequent for meaningful analysis. No data were reported for the outcomes caesarean section, birthweight less 2500 g, Apgar score less than seven at five minutes, death or admission to neonatal intensive care unit (ICU), or pregnancy loss, stillbirth or neonatal death before discharge from hospital. Authors' conclusions The results of this review are based on one small study in which the calcium intervention group also received antioxidants and other supplements. Therefore, we are uncertain whether any of the eKects observed in the study were due to calcium supplementation or not. The evidence in this review was graded low to moderate due to imprecision. There is insuKicient evidence on the eKectiveness or otherwise of pre- or early-pregnancy calcium supplementation, or food fortification for preventing hypertensive disorders of pregnancy. Furtherresearch is needed to determine whether pre- or early-pregnancy supplementation, orfood fortification with calcium is associated with a reduction in adverse pregnancy outcomes such as pre-eclampsia and pregnancy loss. Such studies should be adequately powered, limited to calcium supplementation, placebo-controlled, and include relevant outcomes such as those chosen for this review. There is one ongoing study of calcium supplementation alone versus placebo and this may provide additional evidence in future update

UPC++ v1.0 Specification, Revision 2019.9.0

UPC++ is a C++11 library providing classes and functions that support Partitioned Global Address Space (PGAS) programming. We are revising the library under the auspices of the DOE’s Exascale Computing Project, to meet the needs of applications requiring PGAS support. UPC++ is intended for implementing elaborate distributed data structures where communication is irregular or fine-grained. The UPC++ interfaces for moving non-contiguous data and handling memories with different optimal access methods are composable and similar to those used in conventional C++. The UPC++ programmer can expect communication to run at close to hardware speeds. The key facilities in UPC++ are global pointers, that enable the programmer to express ownership information for improving locality, one-sided communication, both put/get and RPC, futures and continuations. Futures capture data readiness state, which is useful in making scheduling decisions, and continuations provide for completion handling via callbacks. Together, these enable the programmer to chain together a DAG of operations to execute asynchronously as high-latency dependencies become satisfied

UPC++ v1.0 Programmer’s Guide, Revision 2019.9.0

UPC++ is a C++11 library that provides Partitioned Global Address Space (PGAS) programming. It is designed for writing parallel programs that run efficiently and scale well on distributed-memory parallel computers. The PGAS model is single program, multiple-data (SPMD), with each separate constituent process having access to local memory as it would in C++. However, PGAS also provides access to a global address space, which is allocated in shared segments that are distributed over the processes. UPC++ provides numerous methods for accessing and using global memory. In UPC++, all operations that access remote memory are explicit, which encourages programmers to be aware of the cost of communication and data movement. Moreover, all remote-memory access operations are by default asynchronous, to enable programmers to write code that scales well even on hundreds of thousands of cores

UPC++: A high-performance communication framework for asynchronous computation

UPC++ is a C++ library that supports high-performance computation via an asynchronous communication framework. This paper describes a new incarnation that differs substantially from its predecessor, and we discuss the reasons for our design decisions. We present new design features, including future-based asynchrony management, distributed objects, and generalized Remote Procedure Call (RPC). We show microbenchmark performance results demonstrating that one-sided Remote Memory Access (RMA) in UPC++ is competitive with MPI-3 RMA; on a Cray XC40 UPC++ delivers up to a 25% improvement in the latency of blocking RMA put, and up to a 33% bandwidth improvement in an RMA throughput test. We showcase the benefits of UPC++ with irregular applications through a pair of application motifs, a distributed hash table and a sparse solver component. Our distributed hash table in UPC++ delivers near-linear weak scaling up to 34816 cores of a Cray XC40. Our UPC++ implementation of the sparse solver component shows robust strong scaling up to 2048 cores, where it outperforms variants communicating using MPI by up to 3.1x. UPC++ encourages the use of aggressive asynchrony in low-overhead RMA and RPC, improving programmer productivity and delivering high performance in irregular applications