Parallel Computation of the Jacobian Matrix for Nonlinear Equation Solvers Using MATLAB

Demonstrating speedup for parallel code on a multicore shared memory PC can be challenging in MATLAB due to underlying parallel operations that are often opaque to the user. This can limit potential for improvement of serial code even for the so-called embarrassingly parallel applications. One such application is the computation of the Jacobian matrix inherent to most nonlinear equation solvers. Computation of this matrix represents the primary bottleneck in nonlinear solver speed such that commercial finite element (FE) and multi-body-dynamic (MBD) codes attempt to minimize computations. A timing study using MATLAB's Parallel Computing Toolbox was performed for numerical computation of the Jacobian. Several approaches for implementing parallel code were investigated while only the single program multiple data (spmd) method using composite objects provided positive results. Parallel code speedup is demonstrated but the goal of linear speedup through the addition of processors was not achieved due to PC architecture

First-Line Anti-Tuberculosis Drug Susceptibility Patterns of Mycobacterium tuberculosis Complex Strains Responsible for New Cases of Human Pulmonary Tuberculosis in Kisumu County, Western Kenya

Background: Tuberculosis (TB) remains a major cause of morbidity and mortality worldwide, drug-resistant tuberculosis being a major public health problem. The emergence and spread of multidrug resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains poses significant challenges to disease control. Continued surveillance of drug susceptibility helps determining proper treatment regimen. The effectiveness of a standard anti-tuberculosis (TB) treatment regimen correlates with in vitro drug susceptibility pattern of the infecting tubercle bacilli. The results of the drug susceptibility tests help select a proper treatment regimen or modify treatment regimen for a better management of patients and surveillance and timely control of the spread of the drug resistant TB in the community. Treatment of drug resistant TB is costly, and the outcomes, including survivorship, can be poor. As the result, the drug susceptibility test has become more important than ever. Objective: This study aimed to investigate the patterns of first line anti-tuberculosis drug-susceptibility against Mycobacterium tuberculosis complex isolates from new cases of pulmonary TB patients in Kisumu County, Western Kenya. Method: This was a cross sectional study which included a total of 290 isolates from pulmonary TB patients in JOOTRH and Kisumu County Hospital between February and August 2016. The MTBC isolates identified were M. tuberculosis, M. africanum, and M. bovis. Drug susceptibility test was performed on the 283 M. tuberculosis, 5 M. africanum and 2 M. bovis isolates by BD BACTEC MGIT 960 SIRE and PZA DST system using five first-line anti-TB drugs: Isoniazid, Rifampicin, Streptomycin, Ethambutol and Pyrazinamide. Results: M. tuberculosis was highly sensitive to all the anti-TB drugs; Streptomycin(S) 96.8%, Isoniazid (H) 89.8%, Rifampin(R) 98.2%, Ethambutol (E) 94.4%, Pyrazinamide (PZA) 89.8%. M. bovis TB species was 100% sensitive to all drug except Pyrazinamide where there was 100% resistance. M. africanum varied in its sensitivity to anti-TB drugs; Streptomycin 80%, Isoniazid 60%), Pyrazinamide 4 (80%). Resistance was Streptomycin 20%, Isoniazid 40%, and Pyrazinamide 20%. M. africanum was neither resistant to Rifampin(R) nor Ethambutol (E). A total of 20.8% of M. tuberculosis strains showed resistance to at least one drug tested, while 79.2% were sensitive. 16.3% were resistant to one drug (mono resistance), 2.1% to two drugs (double resistance), 0.7% to three drugs (triple resistance), 0.4% to four drugs (quadruples) and 1.4% to five drugs (pentagon-resistance). Two isolates of M. bovis were resistant to one drug. Two isolates of M. africanum were resistance, one case to one drug and another one case to three drugs. Conclusion: This study showed high level of resistance in M. tuberculosis isolates warranting proper use of anti-TB drugs in Kisumu County. Keywords: Tuberculosis, M. tuberculosis complex, Multi Drug Resistanc

Molecular Identity of Mycobacteria Isolates in New Cases of Pulmonary Tuberculosis Patients in Kisumu County, Western Kenya

Background: Pulmonary tuberculosis (TB) remains one of the most challenging diseases to control in the world today and it has become a major global health problem especially in immunocompromised people such as HIV/AIDS. The problem is compounded by the emergence of non-tuberculous mycobacteria (NTM) of which its treatment is not directly analogous to that of MTB. Objective: This study determined the identity of Mycobacteria isolates in new cases of human pulmonary TB patients. Methods: It was a cross-sectional study that involved 316 confirmed new cases of pulmonary TB attending JOOTRH and Kisumu County Hospital. Sputa specimen was cultured in MGIT liquid culture medium. The isolates were identified to species level using GenoType® Mycobacterium CM/AS and MTBC Assay from Hain Lifescience Germany. Results. Of the 316 culture positive isolates, 91.8% were identified as MTBC and 8.2% were NTM species. Of the 290 MTBC, three different species were identified, 97.6% were M. tuberculosis, 1.7% were M. africanum and 0.7% were M. bovis. The Fisher’s exact test was used to assess the associations between patient characteristics and MTBC species identified showed that age category of patients less than 35 years and above 35 years were statistically significant with MTBC species (p=0.020). While sex was not statistically significant with MTBC species (p=0.696). Four different NTM species were identified as 61.5% M. intracellulare, 19.2% M. abscessus, 11.5% M. kansasii and 7.7% M. fortuitum. The Fisher’s exact test done to assess the associations between patient characteristics and NTM species was identified. Age category (p=0.608) and sex (p=0.182) of patients was not statistically significant to NTM species. Conclusion: There is a need for routine speciation among members of the MTBC and NTM as it is an important prerequisite for the proper management of patients with mycobacterial infections. Keywords: Mycobacterium tuberculosis complex, Non tuberculous mycobacteria, Tuberculosi

Trials and tribulations of recruiting 2,000 older women onto a clinical trial investigating falls and fractures : vital D study

Background Randomised, placebo-controlled trials are needed to provide evidence demonstrating safe, effective interventions that reduce falls and fractures in the elderly. The quality of a clinical trial is dependent on successful recruitment of the target participant group. This paper documents the successes and failures of recruiting over 2,000 women aged at least 70 years and at higher risk of falls or fractures onto a placebo-controlled trial of six years duration. The characteristics of study participants at baseline are also described for this study.Methods The Vital D Study recruited older women identified at high risk of fracture through the use of an eligibility algorithm, adapted from identified risk factors for hip fracture. Participants were randomised to orally receive either 500,000 IU vitamin D3 (cholecalciferol) or placebo every autumn for five consecutive years. A variety of recruitment strategies were employed to attract potential participants.Results Of the 2,317 participants randomised onto the study, 74% (n = 1716/2317) were consented onto the study in the last five months of recruiting. This was largely due to the success of a targeted mail-out. Prior to this only 541 women were consented in the 18 months of recruiting. A total of 70% of all participants were recruited as a result of targeted mail-out. The response rate from the letters increased from 2 to 7% following revision of the material by a public relations company. Participant demographic or risk factor profile did not differ between those recruited by targeted mail-outs compared with other methods.Conclusion The most successful recruitment strategy was the targeted mail-out and the response rate was no higher in the local region where the study had extensive exposure through other recruiting strategies. The strategies that were labour-intensive and did not result in successful recruitment include the activities directed towards the GP medical centres. Comprehensive recruitment programs employ overlapping strategies simultaneously with ongoing assessment of recruitment rates. In our experience, and others direct mail-outs work best although rights to privacy must be respected. <br /

Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis)

Erysipelothrix spp., including E. rhusiopathiae, are zoonotic bacterial pathogens that can cause morbidity and mortality in mammals, fish, reptiles, birds, and humans. The southern sea otter (SSO; Enhydra lutris nereis) is a federally-listed threatened species for which infectious disease is a major cause of mortality. We estimated the frequency of detection of these opportunistic pathogens in dead SSOs, described pathology associated with Erysipelothrix infections in SSOs, characterized the genetic diversity and antimicrobial susceptibility of SSO isolates, and evaluated the virulence of two novel Erysipelothrix isolates from SSOs using an in vivo fish model. From 1998 to 2021 Erysipelothrix spp. were isolated from six of &gt;500 necropsied SSOs. Erysipelothrix spp. were isolated in pure culture from three cases, while the other three were mixed cultures. Bacterial septicemia was a primary or contributing cause of death in five of the six cases. Other pathology observed included suppurative lymphadenopathy, fibrinosuppurative arteritis with thrombosis and infarction, bilateral uveitis and endophthalmitis, hypopyon, petechia and ecchymoses, mucosal infarction, and suppurative meningoencephalitis and ventriculitis. Short to long slender Gram-positive or Gram-variable bacterial rods were identified within lesions, alone or with other opportunistic bacteria. All six SSO isolates had the spaA genotype–four isolates clustered with spaA E. rhusiopathiae strains from various terrestrial and marine animal hosts. Two isolates did not cluster with any known Erysipelothrix spp.; whole genome sequencing revealed a novel Erysipelothrix species and a novel E. rhusiopathiae subspecies. We propose the names Erysipelothrix enhydrae sp. nov. and Erysipelothrix rhusiopathiae ohloneorum ssp. nov. respectively. The type strains are E. enhydrae UCD-4322-04 and E. rhusiopathiae ohloneorum UCD-4724-06, respectively. Experimental injection of tiger barbs (Puntigrus tetrazona) resulted in infection and mortality from the two novel Erysipelothrix spp. Antimicrobial susceptibility testing of Erysipelothrix isolates from SSOs shows similar susceptibility profiles to isolates from other terrestrial and aquatic animals. This is the first description of the pathology, microbial characteristics, and genetic diversity of Erysipelothrix isolates recovered from diseased SSOs. Methods presented here can facilitate case recognition, aid characterization of Erysipelothrix isolates, and illustrate assessment of virulence using fish models

Genome sequence of the tsetse fly (Glossina morsitans):Vector of African trypanosomiasis

Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.IS

Comparative Genomic Analysis of six Glossina Genomes, Vectors of African Trypanosomes

Background: Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout subSaharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. Results: Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Visionassociated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. Conclusions: Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies