Vacuolating cytotoxin (vacA) alleles of Helicobacter pylori comprise two geographically widespread types, m1 and m2, and have evolved through limited recombination

Vacuolating cytotoxin (vacA) alleles of Helicobacter pylori vary, particularly in their mid region (which may be type m1 or m2) and their signal peptide coding region (type s1 or s2). We investigated nucleotide diversity among vacA alleles in strains from several locales in Asia, South America, and the USA. Phylogenetic analysis of vacA mid region sequences from 18 strains validated the division into two main groups (m1 and m2) and showed further significant divisions within these groups. Informative site analysis demonstrated one example of recombination between m1 and m2 alleles, and several examples of recombination among alleles within these groups. Recombination was not sufficiently extensive to destroy phylogenetic structure entirely. Synonymous nucleotide substitution rates were markedly different between regions of vacA, suggesting different evolutionary divergence times and implying horizontal transfer of genetic elements within vacA. Non-synonymous/synonymous rate ratios were greater between m1 and m2 sequences than among m1 sequences, consistent with m1 and m2 alleles encoding functions fitting strains for slightly different ecological niches

The "Mathematics Problem": A Plymouth Foundation Year Case Study

Research indicates the transition from school mathematics to university-level STEM courses is often problematic, leading to issues with student satisfaction and retention (the “Mathematics Problem”). An increasing number of HEIs are establishing foundation years in an effort to ameliorate this problem. Undergraduate Mathematics cohorts at Plymouth often contain a sizeable number of exfoundation year students, meaning that efforts to enhance student foundation year experience are vital to student satisfaction, retention and further recruitment. This paper is a report mid-way through a two-year project to examine a partially-flipped learning approach to improve foundation year retention and mathematical knowledge of those progressing to undergraduate study. A preliminary evaluation of this approach is given by using student voice data obtained through focus groups and surveys, and reflections of staff are examined. This paper is an expansion of the work presented at the Foundation Year Network Annual Conference, 2018, the overarching research question being: “Does the Foundation Year provide an enhanced transition to Mathematics degrees compared with the traditional A-level route?”

Psychological interventions for acute psychiatric inpatients with schizophrenia-spectrum disorders: A systematic review and meta-analysis

BACKGROUND: Acute inpatient psychiatric wards are important yet challenging environments in which to implement psychological interventions for people with schizophrenia-spectrum disorders. No meta-analysis to date has evaluated whether psychological interventions are effective in this context. METHODS: We systematically searched Embase, Medline and PsycInfo databases for randomised controlled trials (RCTs) of psychological interventions implemented in acute inpatient psychiatric settings with individuals with schizophrenia-spectrum disorders. We conducted random effects meta-analyses of between-groups outcomes at post-intervention and relapse/re-hospitalisation rates by follow-up. RESULTS: Twenty-nine trials were suitable for meta-analysis. Psychological interventions improved post-intervention positive symptoms, social functioning and treatment compliance and reduced the risk of relapse/ re-hospitalisation, relative to control conditions. Analyses of specific intervention effects found positive effects of psychoeducation on several key outcomes (power > 80%) and preliminary evidence for positive effects of acceptance and commitment therapy (ACT), cognitive behaviour therapy (CBT) and metacognitive training (MCT) on some outcomes (power < 80%). CONCLUSION: Psychological interventions can be helpful for acute inpatients with schizophrenia-spectrum disorders. However, risk of bias was often high or unclear, and some analyses were underpowered. Further research should use more rigorous RCT designs and publish meta-analysable data on positive symptoms, general psychopathology, relapse/ re-hospitalisation, social functioning and treatment compliance

Computational biomechanical modelling of the rabbit cranium during mastication

Although a functional relationship between bone structure and mastication has been shown in some regions of the rabbit skull, the biomechanics of the whole cranium during mastication have yet to be fully explored. In terms of cranial biomechanics, the rabbit is a particularly interesting species due to its uniquely fenestrated rostrum, the mechanical function of which is debated. In addition, the rabbit processes food through incisor and molar biting within a single bite cycle, and the potential influence of these bite modes on skull biomechanics remains unknown. This study combined the in silico methods of multi-body dynamics and finite element analysis to compute musculoskeletal forces associated with a range of incisor and molar biting, and to predict the associated strains. The results show that the majority of the cranium, including the fenestrated rostrum, transmits masticatory strains. The peak strains generated over all bites were found to be attributed to both incisor and molar biting. This could be a consequence of a skull shape adapted to promote an even strain distribution for a combination of infrequent incisor bites and cyclic molar bites. However, some regions, such as the supraorbital process, experienced low peak strain for all masticatory loads considered, suggesting such regions are not designed to resist masticatory forces

Single-stranded genomic architecture constrains optimal codon usage

Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts' genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts' codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes

Infection of a yellow baboon with simian immunodeficiency virus from African green monkeys:evidence for cross-species transmission in the wild

Many African primates are known to be naturally infected with simian immunodeficiency viruses (SIVs), but only a fraction of these viruses has been molecularly characterized. One primate species for which only serological evidence of SIV infection has been reported is the yellow baboon (Papio hamadryas cynocephalus). Two wild-living baboons with strong SIVAGM seroreactivity were previously identified in a Tanzanian national park where baboons and African green monkeys shared the same habitat (T. Kodama, D. P. Silva, M. D. Daniel, J. E. Phillips-Conroy, C. J. Jolly, J. Rogers, and R. C. Desrosiers, AIDS Res. Hum. Retroviruses 5:337-343, 1989). To determine the genetic identity of the viruses infecting these animals, we used PCR to examine SIV sequences directly in uncultured leukocyte DNA. Targeting two different, nonoverlapping genomic regions, we amplified and sequenced a 673-bp gag gene fragment and a 908-bp env gene fragment from one of the two baboons. Phylo-genetic analyses revealed that this baboon was infected with an SIVAGM strain of the vervet subtype. These results provide the first direct evidence for simian-to-simian cross-species transmission of SIV in the wild

Stage, grade and morphology of tumours of the colon and rectum recorded in the Oxford Cancer Registry, 1995–2003

Data on stage, grade and morphology of 12 761 colorectal cancers registered between 1995 and 2003 by Oxford Cancer Registry are reviewed. Dukes stage is recorded for 81% of colon cancers and for 69% of rectal cancers. Incomplete registry data and changing recording practices may affect future evaluation of bowel cancer screening

The effect of blast-furnace slag particle size on the hydration of slag-Portland cement grouts at elevated temperatures

The UK nuclear industry has historically used a unique specification of cement powder that differs from construction industry requirements. However, the slags that complied with this specification have become unavailable. The material now used to meet the requirements of the specification is a blend of standard construction industry ground granulated blast-furnace slag (GGBS), which has high fineness, with Calumite which is a coarser slag powder. Both materials have very similar chemical compositions, and the main reason for blending is to control the particle size distribution (PSD) to replicate the performance of the previous supply. The effect of changing the PSD on the performance properties of the cement paste was investigated. Isothermal conduction calorimetry at elevated temperatures was carried out to monitor the heat of hydration; it was found that the peak heat and total heat evolution increased with an increase in GGBS content. It was also found that Calumite contributes very little to the hydration reaction and thus behaves similarly to an inert filler. As the GGBS content was decreased, the fluidity of the pastes increased up to a certain point, but decreased again for systems dominated by very coarse particles, indicating that there is an optimum balance between the finer and coarser slag particles within this cementing system

Building development and roads: implications for the distribution of stone curlews across the Brecks

Background: Substantial new housing and infrastructure development planned within England has the potential to conflict with the nature conservation interests of protected sites. The Breckland area of eastern England (the Brecks) is designated as a Special Protection Area for a number of bird species, including the stone curlew (for which it holds more than 60% of the UK total population). We explore the effect of buildings and roads on the spatial distribution of stone curlew nests across the Brecks in order to inform strategic development plans to avoid adverse effects on such European protected sites. Methodology: Using data across all years (and subsets of years) over the period 1988 – 2006 but restricted to habitat areas of arable land with suitable soils, we assessed nest density in relation to the distances to nearest settlements and to major roads. Measures of the local density of nearby buildings, roads and traffic levels were assessed using normal kernel distance-weighting functions. Quasi-Poisson generalised linear mixed models allowing for spatial auto-correlation were fitted. Results: Significantly lower densities of stone curlew nests were found at distances up to 1500m from settlements, and distances up to 1000m or more from major (trunk) roads. The best fitting models involved optimally distance-weighted variables for the extent of nearby buildings and the trunk road traffic levels. Significance : The results and predictions from this study of past data suggests there is cause for concern that future housing development and associated road infrastructure within the Breckland area could have negative impacts on the nesting stone curlew population. Given the strict legal protection afforded to the SPA the planning and conservation bodies have subsequently agreed precautionary restrictions on building development within the distances identified and used the modelling predictions to agree mitigation measures for proposed trunk road developments

Transesophageal echocardiography in children: New peephole to the heart

Markers of inflammation, including plasma C-reactive protein (CRP), are associated with an increased risk of cardiovascular disease, and it has been suggested that this association is causal. However, the relationship between inflammation and cardiovascular disease has not been extensively studied in patients with chronic kidney disease. To evaluate this, we used data from the Study of Heart and Renal Protection (SHARP) to assess associations between circulating CRP and LDL cholesterol levels and the risk of vascular and non-vascular outcomes. Major vascular events were defined as nonfatal myocardial infarction, cardiac death, stroke or arterial revascularization, with an expanded outcome of vascular events of any type. Higher baseline CRP was associated with an increased risk of major vascular events (hazard ratio per 3x increase 1.28; 95% confidence interval 1.19-1.38). Higher baseline LDL cholesterol was also associated with an increased risk of major vascular events (hazard ratio per 0.6 mmol/L higher LDL cholesterol; 1.14, 1.06-1.22). Higher baseline CRP was associated with an increased risk of a range of non-vascular events (1.16, 1.12-1.21), but there was a weak inverse association between baseline LDL cholesterol and non-vascular events (0.96, 0.92-0.99). The efficacy of lowering LDL cholesterol with simvastatin/ezetimibe on major vascular events, in the randomized comparison, was similar irrespective of CRP concentration at baseline. Thus, decisions to offer statin-based therapy to patients with chronic kidney disease should continue to be guided by their absolute risk of atherosclerotic events. Estimation of such risk may include plasma biomarkers of inflammation, but there is no evidence that the relative beneficial effects of reducing LDL cholesterol depends on plasma CRP concentration