Direct and indirect effects of hepatitis B vaccination in four low- and middle-income countries.

Population-level vaccination effects of the hepatitis B vaccine were investigated in four low- and middle-income countries with different levels of vertical and horizontal transmission. Indirect vaccination effects constitute a large proportion of overall vaccination effects of the vaccination programmes in all four countries (over 70% by 2030 in all four countries). However, countries with higher levels of vertical transmission benefit less from indirect vaccination effects from the infant hepatitis B vaccine series during the first decades of the vaccination programme, making the birth dose vaccine more important in these countries.

Designing and delivering bioinformatics project-based learning in East Africa.

Background: The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings.

Structural expression of bovine milk and meat factors in tissues of colorectal, lung and pancreatic cancer patients.

Chronic inflammation, linked to the presence of bovine milk and meat factors (BMMFs) and specific subsets of macrophages, results in oxygen radical synthesis and induction of mutations in DNA of actively replicating cells and replicating single stranded DNA. Cancers arising from this process have been characterized as indirect carcinogenesis by infectious agents (without persistence of genes of the agent in premalignant or cancers cells). Here, we investigate structural properties of pleomorphic vesicles, regularly identified by staining peritumor tissues of colorectal, lung and pancreatic cancer for expression of BMMF Rep.

Case Report: Diffuse Lumbar Hyperostosis Causing Vertebral Canal Stenosis in a Dog With Concurrent Multicentric T-Cell Lymphoma.

A 4-year-old female spayed Bullmastiff-cross presented with a 24-h history of progressive paraparesis. Neurological examination was consistent with L4-S3 myelopathy. On magnetic resonance imaging (MRI), all vertebrae showed homogenously increased short tau inversion recovery (STIR) signal with strong contrast enhancement.

In vitro susceptibility of canine corneal bacterial pathogens to three cross-linking protocols.

Objective: To assess in vitro antibacterial efficacy of three cross-linking (XL) protocols on bacteria associated with canine ulcerative keratitis.

Methods: Three XL protocols: UVA 3 mW/cm for 60 min, UVA 3 mW/cm for 30 min, and UVA 30 mW/cm for 3 min with and without application of riboflavin and a riboflavin-only protocol were performed in vitro on the four most common bacterial genera isolated from cases of canine ulcerative keratitis treated at Dick White Referrals, UK. Zones of bacterial growth inhibition (GIZ) associated with treatment were measured and compared.

Comparison of corneal culture results obtained using the ESwab™ and Amies charcoal swab in canine and feline patients.

Objective: The objective of the study was to compare corneal culture results using the ESwab™ and Amies charcoal swab.

Animals Studied: One hundred fourteen canine and fifteen feline eyes.

Procedures: Retrospective analysis of Dick White Referrals bacterial and fungal corneal culture data was conducted.

Bovine Meat and Milk Factors (BMMFs): Their Proposed Role in Common Human Cancers and Type 2 Diabetes Mellitus.

Exemplified by infections with bovine meat and milk factors (BMMFs), this manuscript emphasizes the different mechanistic aspects of infectious agents contributing to human cancers by "direct" or "indirect" interactions. The epidemiology of cancers linked to direct carcinogens (e.g.

Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean.

Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO).

Virtual Environment Rehabilitation for Patients with Motor Neglect Trial (VERMONT): A Single-Center Randomized Controlled Feasibility Trial.

Background: Motor neglect occurs in patients with chronic pain conditions. Virtual environments (VE) help rehabilitation through biofeedback and improving motivation.

Aim: To assess the feasibility of a VE for patients with motor neglect with chronic pain.

Analysis of chronic inflammatory lesions of the colon for BMMF Rep antigen expression and CD68 macrophage interactions.

Consumption of Eurasian bovine meat and milk has been associated with cancer development, in particular with colorectal cancer (CRC). In addition, zoonotic infectious agents from bovine products were proposed to cause colon cancer (zur Hausen et al., 2009).

The utility of Escherichia coli as a contamination indicator for rural drinking water: Evidence from whole genome sequencing.

Across the water sector, Escherichia coli is the preferred microbial water quality indicator and current guidance upholds that it indicates recent faecal contamination. This has been challenged, however, by research demonstrating growth of E. coli in the environment.

Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes.

Background: The crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes.

Methods: This was a laboratory based cross sectional study.

Comparative analysis of the vaginal microbiome of pregnant women with either Trichomonas vaginalis or Chlamydia trachomatis.

Background: Although the significance of the human vaginal microbiome for health and disease is increasingly acknowledged, there is paucity of data on the differences in the composition of the vaginal microbiome upon infection with different sexually transmitted pathogens.

Method: The composition of the vaginal bacterial community of women with Trichomonas vaginalis (TV, N = 18) was compared to that of women with Chlamydia trachomatis (CT, N = 14), and to that of controls (N = 21) (women negative for TV, CT and bacterial vaginosis). The vaginal bacterial composition was determined using high throughput sequencing with the Ion 16S metagenomics kit of the variable regions 2, 4 and 8 of the bacterial 16S ribosomal RNA gene from the vaginal swab DNA extract of the women.

Peripheral blood mononuclear cell transcriptomes reveal an over-representation of down-regulated genes associated with immunity in HIV-exposed uninfected infants.

HIV-exposed uninfected (HEU) infants are disproportionately at a higher risk of morbidity and mortality, as compared to HIV-unexposed uninfected (HUU) infants. Here, we used transcriptional profiling of peripheral blood mononuclear cells to determine immunological signatures of in utero HIV exposure. We identified 262 differentially expressed genes (DEGs) in HEU compared to HUU infants.

Infestation mechanisms of two woodborer species in the mangrove Sonneratia alba J. Smith in Kenya and co-occurring endophytic fungi.

Insect damage on trees can severely affect the quality of timber, reduce the fecundity of the host and render it susceptible to fungal infestation and disease. Such pathology weakens or eventually kills the host. Infestation by two insect woodborer species (a moth and a beetle) is causing mortality of Sonneratia alba, a wide-ranging pioneer mangrove species of the Indo-Pacific.

A randomised controlled comparison of aspiration and non-aspiration fine-needle techniques for obtaining ultrasound-guided cytological samples from canine livers.

Ultrasound-guided fine-needle sampling to obtain cytological samples is a well-established technique. However, the application of suction during sampling is controversial. Evidence from the human literature and one previous veterinary study suggest that non-aspiration may be superior for a number of organs.

A specific class of infectious agents isolated from bovine serum and dairy products and peritumoral colon cancer tissue.

The analyses of 109 replication-competent genomic DNA sequences isolated from cow milk and its products (97 in the bovine meat and milk factors 2 group - BMMF2, and additional 4 in BMMF1) seems to place these in a specific class of infectious agents spanning between bacterial plasmid and circular ssDNA viruses. Satellite-type small plasmids with partial homology to larger genomes, were also isolated in both groups. A member of the BMMF1 group H1MBS.

Repeated clinical malaria episodes are associated with modification of the immune system in children.

Background: There are over 200 million reported cases of malaria each year, and most children living in endemic areas will experience multiple episodes of clinical disease before puberty. We set out to understand how frequent clinical malaria, which elicits a strong inflammatory response, affects the immune system and whether these modifications are observable in the absence of detectable parasitaemia.

Methods: We used a multi-dimensional approach comprising whole blood transcriptomic, cellular and plasma cytokine analyses on a cohort of children living with endemic malaria, but uninfected at sampling, who had been under active surveillance for malaria for 8 years.

Validation of a spectrophotometric method for GGT measurement in canine urine and determination of the urine GGT-to-creatinine ratio reference interval and biological variation in 41 healthy dogs.

The urine gamma-glutamyl transferase (GGT)-to-creatinine ratio has been used to monitor patients at risk of acute renal injury. We validated the spectrophotometric quantification of GGT in urine in a commercial biochemistry analyzer. The assay was precise, accurate, and linear.

Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells.

The true importance of cell-free DNA in human biology, together with the potential scale of its clinical utility, is tarnished by a lack of understanding of its composition and origin. In investigating the cell-free DNA present in the growth medium of cultured 143B cells, we previously demonstrated that the majority of cell-free DNA is neither a product of apoptosis nor necrosis. In the present study, we investigated the composition and origin of this cell-free DNA population using next-generation sequencing.

Indolent, T-cell, large granular lymphocytic leukaemia in a dog presenting with severe neutropenia and an absence of lymphocytosis.

In humans, large granular lymphocytic leukaemia (LGLL) is a low-grade, indolent lymphoproliferative disorder of large granular lymphocytes (LGL) associated with autoimmune disorders; including rheumatoid arthritis and single or multiple cytopenias; particularly neutropenia. Therapy largely centres around immunosuppression which aims to resolve the immune-mediated secondary pathology, often without eradicating the neoplastic clone. The most effective agents appear to be cyclophosphamide, cyclosporine and methotrexate.

Assessment of Lymphoid Molecular Clonality in Canine Thymoma.

The aim of this study was to document the molecular clonality of lymphoid cells in canine thymoma using polymerase chain reaction for antigen receptor rearrangement (PARR). Fifteen formalin-fixed and paraffin wax-embedded samples of canine thymoma were analyzed for T- and B-cell receptor clonality. Two of these 15 cases were excluded from the study due to insufficient DNA concentration.

Geographic-genetic analysis of parasite populations from surveys of primary school children in Western Kenya.

Malaria control, and finally malaria elimination, requires the identification and targeting of residual foci or hotspots of transmission. However, the level of parasite mixing within and between geographical locations is likely to impact the effectiveness and durability of control interventions and thus should be taken into consideration when developing control programs. In order to determine the geographic-genetic patterns of parasite populations at a sub-national level in Kenya, we used the Sequenom platform to genotype 111 genome-wide distributed single nucleotide polymorphic (SNP) positions in 2486 isolates collected from children in 95 primary schools in western Kenya.

The eBioKit, a stand-alone educational platform for bioinformatics.

Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment.