Performance of explicit and IMEX MRI multirate methods on complex reactive flow problems within modern parallel adaptive structured grid frameworks

Large-scale multiphysics simulations are computationally challenging due to the coupling of multiple processes with widely disparate time scales. The advent of exascale computing systems exacerbates these challenges, since these enable ever increasing size and complexity. Recently, there has been renewed interest in developing multirate methods as a means to handle the large range of time scales, as these methods may afford greater accuracy and efficiency than more traditional approaches of using IMEX and low-order operator splitting schemes. However, there have been few performance studies that compare different classes of multirate integrators on complex application problems. We study the performance of several newly developed multirate infinitesimal (MRI) methods, implemented in the SUNDIALS solver package, on two reacting flow model problems built on structured mesh frameworks. The first model revisits the work of Emmet et al. (2014) on a compressible reacting flow problem with complex chemistry that is implemented using BoxLib but where we now include comparisons between a new explicit MRI scheme with the multirate spectral deferred correction (SDC) methods in the original paper. The second problem uses the same complex chemistry as the first problem, combined with a simplified flow model, but run at a large spatial scale where explicit methods become infeasible due to stability constraints. Two recently developed implicit-explicit MRI multirate methods are tested. These methods rely on advanced features of the AMReX framework on which the model is built, such as multilevel grids and multilevel preconditioners. The results from these two problems show that MRI multirate methods can offer significant performance benefits on complex multiphysics application problems and that these methods may be combined with advanced spatial discretization to compound the advantages of both

Extramural Venous Invasion as Prognostic Factor of Recurrence in Stage 1 and 2 Colon Cancer

Aim. Extramural venous invasion (EMVI) is a prognostic indicator in patients with colorectal cancer. However, its additional value in patients with stage 1 and 2 colorectal cancer is uncertain. In the present study, the incidence of EMVI and the hazard ratio for recurrence in patients with stage 1 and 2 colon cancer were studied. Methods. 184 patients treated for stage 1 and 2 colon cancer were included with a follow-up of at least 5 years. Chart review was performed and EMVI was assessed by two separate pathologists. EMVI was scored with additional caldesmon staining on the resection specimen. Primary outcomes were recurrence-free survival (RFS) measured through the Cox regression analysis and prevalence of EMVI. Results. There were 10 cases of EMVI and 3 cases of intramural venous invasion (IMVI) all occurring in patients with stage 2 disease corresponding to a prevalence of 9%. Thirty-one percent of the patients with venous invasion experienced recurrence versus 14% in patients without, corresponding with a hazard ratio of 2.39 (p=0.11). Conclusion. The present study demonstrates a trend towards an increased risk of recurrence in patients with stage 2 colon cancer with venous invasion. This warrants consideration of adjuvant chemotherapy despite the lack of lymph node metastases

Analysis of antimicrobial susceptibility and virulence factors in Helicobacter pylori clinical isolates

BACKGROUND: In this study, we evaluated the prevalence of primary resistance of Brazilian H. pylori isolates to metronidazole, clarithromycin, amoxicillin, tetracycline, and furazolidone. In addition, the vacA, iceA, cagA and cagE genotypes of strains isolated from Brazilian patients were determined and associated with clinical data in an effort to correlate these four virulence markers and antibiotic resistance. METHODS: H. pylori was cultured in 155 H. pylori-positive patients and MICs for metronidazole, clarithromycin, amoxicillin, tetracycline, and furazolidone were determined by the agar dilution method. Genomic DNA was extracted, and allelic variants of vacA, iceA, cagA and cagE were identified by the polymerase chain reaction. RESULTS: There was a strong association between the vacA s1/cagA -positive genotype and peptic ulcer disease (OR = 5.42, 95% CI 2.6–11.3, p = 0.0006). Additionally, infection by more virulent strains may protect against GERD, since logistic regression showed a negative association between the more virulent strain, vacA s1/cagA-positive genotype and GERD (OR = 0.26, 95% CI 0.08–0.8, p = 0.03). Resistance to metronidazole was detected in 75 patients (55%), to amoxicillin in 54 individuals (38%), to clarithromycin in 23 patients (16%), to tetracycline in 13 patients (9%), and to furazolidone in 19 individuals (13%). No significant correlation between pathogenicity and resistance or susceptibility was detected when MIC values for each antibiotic were compared with different vacA, iceA, cagA and cagE genotypes. CONCLUSION: The analysis of virulence genes revealed a specific association between H. pylori strains and clinical outcome, furthermore, no significant association was detected among pathogenicity and resistance or susceptibility

A multicenter randomized clinical trial investigating the cost-effectiveness of treatment strategies with or without antibiotics for uncomplicated acute diverticulitis (DIABOLO trial)

Background. Conservative treatment of uncomplicated or mild diverticulitis usually includes antibiotic therapy. It is, however, uncertain whether patients with acute diverticulitis indeed benefit from antibiotics. In most guidelines issued by professional organizations antibiotics are considered mandatory in the treatment of mild diverticulitis. This advice lacks evidence and is merely based on experts' opinion. Adverse effects of the use of antibiotics are well known, including allergic reactions, development of bacterial resistance to antibiotics and other side-effects. Methods. A randomized multicenter pragmatic clinical trial comparin

The state of capacity development evaluation in biodiversity conservation and natural resource management

Capacity development is critical to long-term conservation success, yet we lack a robust and rigorous understanding of how well its effects are being evaluated. A comprehensive summary of who is monitoring and evaluating capacity development interventions, what is being evaluated and how, would help in the development of evidence-based guidance to inform design and implementation decisions for future capacity development interventions and evaluations of their effectiveness. We built an evidence map by reviewing peer-reviewed and grey literature published since 2000, to identify case studies evaluating capacity development interventions in biodiversity conservation and natural resource management. We used inductive and deductive approaches to develop a coding strategy for studies that met our criteria, extracting data on the type of capacity development intervention, evaluation methods, data and analysis types, categories of outputs and outcomes assessed, and whether the study had a clear causal model and/or used a systems approach. We found that almost all studies assessed multiple outcome types: most frequent was change in knowledge, followed by behaviour, then attitude. Few studies evaluated conservation outcomes. Less than half included an explicit causal model linking interventions to expected outcomes. Half of the studies considered external factors that could influence the efficacy of the capacity development intervention, and few used an explicit systems approach. We used framework synthesis to situate our evidence map within the broader literature on capacity development evaluation. Our evidence map (including a visual heat map) highlights areas of low and high representation in investment in research on the evaluation of capacity development

Genetic ancestry is associated with colorectal adenomas and adenocarcinomas in Latino populations

Colorectal cancer rates in Latin American countries are less than half of those observed in the United States. Latin Americans are the resultant of generations of an admixture of Native American, European, and African individuals. The potential role of genetic admixture in colorectal carcinogenesis has not been examined. We evaluate the association of genetic ancestry with colorectal neoplasms in 190 adenocarcinomas, 113 sporadic adenomas and 243 age- and sex-matched controls enrolled in a multicentric case–control study in Colombia. Individual ancestral genetic fractions were estimated using the STRUCTURE software, based on allele frequencies and assuming three distinct population origins. We used the Illumina Cancer Panel to genotype 1,421 sparse single-nucleotide polymorphisms (SNPs), and Northern and Western European ancestry, LWJ and Han Chinese in Beijing, China populations from the HapMap project as references. A total of 678 autosomal SNPs overlapped with the HapMap data set SNPs and were used for ancestry estimations. African mean ancestry fraction was higher in adenomas (0.13, 95% confidence interval (95% CI)=0.11–0.15) and cancer cases (0.14, 95% CI=0.12–0.16) compared with controls (0.11, 95% CI=0.10–0.12). Conditional logistic regression analysis, controlling for known risk factors, showed a positive association of African ancestry per 10% increase with both colorectal adenoma (odds ratio (OR)=1.12, 95% CI=0.97–1.30) and adenocarcinoma (OR=1.19, 95% CI=1.05–1.35). In conclusion, increased African ancestry (or variants linked to it) contributes to the increased susceptibility of colorectal cancer in admixed Latin American population