Beyond Travel: Regis’ Service Oriented Field Experience (SOFE) Program

This is a program description of the Service Oriented Field Experience (SOFE), which is a unique blended experiential learning capstone course within the Master of Nonprofit Management (MNM) at Regis University. The SOFE course blends aspects of social justice and nonprofit leadership into an eight-week course that focuses on the mission driven nature of the social sector throughout the world. While appropriating theories of experiential learning, the course builds on Jesuit pedagogical principles of experience, reflection, and action, and it includes deliberate exposure of Nonprofit/Nongovernmental (NP/NGO) leaders into contexts other than their own as a model for leadership development and growth. Leaders learn from this process about the complexity of social and other needs and the innovative approaches for solving them. These global connections support possible long-term engagement with these issues beyond the travel experience

Prevalence and risk factors of previous or active Hepatitis B infection among HIV-1 discordant heterosexual couples

Background: Hepatitis B Virus (HBV) and HIV spread in the same manner, but HBV is more infectious  than HIV-1. Active HBV requires modification of HIV-1 therapy and is associated with increased risk for sexual transmission of HBV.Objective: To determine the prevalence and knowledge of HBV among HIV-1 discordant couples.Design: A cross-sectional study.Setting: Couple Counselling Centres in Nairobi and Thika clinics in Kenya.Subjects: HIV discordant couples attending Couples Counselling Centres in Nairobi and Thika clinics in Kenya.Results: One hundred and sixty one couples with a mean age of 33 years (Standard Deviation 8.4) were enrolled into the study. HBV prevalence was higher among HIV positive women than among HIV negative women (10.2% vs. 5.9%, OR=0.5, 95% CI 0.2-1.0; p=0.05). However, among men, prevalence of HBV was higher among the HIV negative than the HIV positive participants (8.4 vs. 6.2%, OR=3.0, CI  1.3-6.5; p=0.04). There was no association between HBV and HIV (p=0.4) or gender (p=0.5). HIV  positive participants were more likely to have adequate knowledge compared to HIV negative participants (13% vs. 3.7%, OR=2.7, 95% CI 1.95-7.9; p=0.05)Conclusions: Female index participants had the highest HBV prevalence. Knowledge on HBV was lacking, particularly among the HIV negative; a target group for health education regarding risk factors and prevention of HBV infection

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the need for a standardized approach to accurately determine what constitutes an active, viable virus infection after detection by molecular based methods

Prevalence of substance use among college students in Eldoret, western Kenya

<p>Abstract</p> <p>Background</p> <p>Substance use among college and university students predicts substance related problems in later life. Few studies on this phenomenon have been carried out in low income countries, and most focus on primary and secondary school students. This study therefore aimed to establish the prevalence and factors associated with drug use among university and college students in a low income country.</p> <p>Methods</p> <p><it>Design: </it>A descriptive cross-sectional survey using the Self-Administered WHO Model Core Questionnaire to collect information on use of various drugs among students in colleges and university campuses within Eldoret Municipality in Western Kenya. <it>Setting: </it>Four tertiary learning institutions in Eldoret Municipality were randomly selected for inclusion in the study- three tertiary level non-university institutions and one university campus. <it>Subjects: </it>Five hundred students who gave consent to participate in the study, 125 from each of the four participating institutions. The mean age was 22.9 years (18-32, s.d. 2.5), and males made up 52.2% of the sample.</p> <p>Results</p> <p>Lifetime prevalence rate of any substance use was 69.8%, and none of the socio-demographic factors was significantly associated with this. Lifetime prevalence rate of alcohol use was 51.9%, and 97.6% of alcohol users had consumed alcohol in the week prior to the study. The prevalence rate of cigarette use was 42.8%, with males having statistically significantly higher rates than females (p < 0.05). Other substances used were cannabis (2%) and cocaine (0.6%). Among those who admitted to using substances, 75.1% were introduced by a friend while 23.5% were introduced by a relative other than a member of the nuclear family. Majority of those using substances wanted to relax (62.2%) or relieve stress (60.8%). Problems associated with alcohol use included quarrelling and fights, loss and damage to property, problems with parents, medical problems and unplanned unprotected sex.</p> <p>Conclusion</p> <p>The prevalence of substance use among college and university students in Eldoret is high and causes significant physical and psychosocial problems in this population. A large proportion of those using alcohol reported serious adverse effects, raising the necessity of targeted interventions to reduce the risk of subsequent substance dependence and other deleterious consequences.</p

Investigation of the sequential validity of quality improvement team self-assessments in a health facility HIV improvement collaborative in Tanzania

Background: Self-assessment is widely used in the health care improvement collaboratives quality improvement (QI) teams’ to assess their own performance. There is mixed evidence on the validity of this approach. This study investigated sequential validity of self-assessments in a QI HIV collaborative in Tanzania.Objectives: Define the separate self-assessment steps in QI process; determine if the validity of self-assessments improved over time; determine if validity improvement is the same for the different self-assessment activities and determine if validity is the same for the different facilities and type of care.Design: Prospective semi-quantitative study.Setting: The study was undertaken over 10 months in nine facilities in Mtwara region of Tanzania following appropriate approvals. Study did not interfere with routine services and processes of continuous quality improvement at the facilities.Subjects:Trained investigators retrieved information from records and the computers using data capture forms. Patients of service providers were not questioned or participate in the study.Conclusion:The validity of self-assessments in the HIV/ART/PMTCT Improvement Collaborative in Mtwara region of Tanzania improved as the collaborative matured. Data from computerised data bases unreliable, calling for more training in the use of computers. The weakness in communication should be addressed by collaborative designers and coaches

‘Candidatus Phytoplasma stylosanthis’, a novel taxon with a diverse host range in Australia, characterised using multilocus sequence analysis of 16S rRNA, secA, tuf, and rp genes

In Australia, Stylosanthes little leaf (StLL) phytoplasma has been detected in Stylosanthes scabra Vogel, Arachis pintoi Krapov, Saccharum officinarum L., Carica papaya L., Medicago sativa L., and Solanum tuberosum L. The 16S rRNA gene sequence of StLL phytoplasma strains from S. scabra, C. papaya, S. officinarum and S. tuberosum were compared and share 99.93–100 % nucleotide sequence identity. Phylogenetic comparisons between the 16S rRNA genes of StLL phytoplasma and other ‘Candidatus Phytoplasma’ species indicate that StLL represents a distinct phytoplasma lineage. It shares its most recent known ancestry with ‘Ca. Phytoplasma luffae’ (16SrVIII-A), with which it has 97.17–97.25 % nucleotide identity. In silico RFLP analysis of the 16S rRNA amplicon using iPhyClassifier indicate that StLL phytoplasmas have a unique pattern (similarity coefficient below 0.85) that is most similar to that of ‘Ca. Phytoplasma luffae’. The unique in silico RFLP patterns were confirmed in vitro. Nucleotide sequences of genes that are more variable than the 16S rRNA gene, namely tuf (tu-elongation factor), secA (partial translocation gene), and the partial ribosomal protein (rp) gene operon (rps19-rpl22-rps3), produced phylogenetic trees with similar branching patterns to the 16S rRNA gene tree. Sequence comparisons between the StLL 16S rRNA spacer region confirmed previous reports of rrn interoperon sequence heterogeneity for StLL, where the spacer region of rrnB encodes a complete tRNA-Isoleucine gene and the rrnA spacer region does not. Together these results suggest that the Australian phytoplasma, StLL, is unique according to the International Organization for Mycoplasmology (IRPCM) recommendations. The novel taxon ‘Ca. Phytoplasma stylosanthis’ is proposed, with the most recent strain from a potato crop in Victoria, Australia, serving as the reference strain (deposited in the Victorian Plant Pathology Herbarium as VPRI 43683)

Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing

Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant viruses, but this can be overcome by enrichment of target nucleic acid. A targeted whole genome sequencing (TWG-Seq) approach for the detection of cucumber green mottle mosaic virus (CGMMV) has been developed where overlapping amplicons generated using two multiplex RT-PCR assays are then sequenced using the Oxford Nanopore MinION. Near complete coding region sequences were assembled with ≥100× coverage for infected leaf tissue dilution samples with RT-qPCR cycle quantification (Cq) values from 11.8 to 38 and in seed dilution samples with Cq values 13.8 to 27. Consensus sequences assembled using this approach showed greater than 99% nucleotide similarity when compared to genomes produced using metagenomic sequencing. CGMMV could be confidently detected in historical seed isolates with degraded RNA. Whilst limited access to, and costs associated with second-generation sequencing platforms can influence diagnostic outputs, the portable Nanopore technology offers an affordable high throughput sequencing alternative when combined with TWG-Seq for low copy or degraded samples