Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA.

The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment.Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome.These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies

Blast mines: physics, injury mechanisms and vehicle protection.

Since World War II, more vehicles have been lost to land mines than all other threats combined. Anti-vehicular (AV) mines are capable of disabling a heavy vehicle, or completely destroying a lighter vehicle. The most common form of AV mine is the blast mine, which uses a large amount of explosive to directly damage the target. In a conventional military setting, landmines are used as a defensive force-multiplier and to restrict the movements of the opposing force. They are relatively cheap to purchase and easy to acquire, hence landmines are also potent weapons in the insurgents armamentarium. The stand-offnature of its design has allowed insurgents to cause significant injuries to security forces in current conflicts with little personal risk. As a result, AV mines and improvised explosive devices (IEDs) have become the most common cause of death and injury to Coalition and local security forces operating in Iraq and Afghanistan. Detonation of an AV mine causes an explosive, exothermic reaction which results in the formation of a shockwave followed by a rapid expansion of gases. The shockwave is mainly reflected by the soillair interface and fractures the soil cap overthe mine. The detonation products then vent through the voids in the soil, resulting in a hollow inverse cone which consists of the detonation gases surrounded by the soil ejecta. It is the combination of the detonation products and soil ejecta that interact with the target vehicle and cause injury to the vehicle occupants. A number of different strategies are required to mitigate the blast effects of an explosion. Primary blast effects can be reduced by increasing the standoff distance between the seat of the explosion and the crew compartment. Enhancement of armour on the base of the vehicle, as well as improvements in personal protection can prevent penetration of fragments. Mitigating tertiary effects can be achieved by altering the vehicle geometry and structure, increasing vehicle mass, as well as developing new strategies to reduce the transfer of the impulse through the vehicle to the occupants. Protection from thermal injury can be provided by incorporating fire resistant materials into the vehicle and in personal clothing. The challenge for the vehicle designer is the incorporation of these protective measures within an operationally effective platform.Published versio

Characterization of the fecal microbiota of pigs before and after inoculation with "Brachyspira hampsonii".

Brachyspira hampsonii causes disease indistinguishable from swine dysentery, and the structure of the intestinal microbiome likely plays a role in determining susceptibility of individual pigs to infection and development of clinical disease. The objectives of the current study were to determine if the pre-inoculation fecal microbiota differed between inoculated pigs that did (INOC MH) or did not (INOC non-MH) develop mucohaemorrhagic diarrhea following challenge with B. hampsonii , and to quantify changes in the structure of the microbiome following development of clinical disease. Fecal microbiota profiles were generated based on amplification and sequencing of the cpn60 universal target sequence from 89 samples from 18 pigs collected at -8, -5, -3 and 0 days post-inoculation, and at termination. No significant differences in richness, diversity or taxonomic composition distinguished the pre-inoculation microbiomes of INOC MH and INOC non-MH pigs. However, the development of bloody diarrhea in inoculated pigs was associated with perturbation of the microbiota relative to INOC non-MH or sham-inoculated control pigs. Specifically, the fecal microbiota of INOC MH pigs was less dense (fewer total 16S rRNA copies per gram of feces), and had a lower Bacteroidetes:Firmicutes ratio. Further investigation of the potential long-term effects of Brachyspira disease on intestinal health and performance is warranted

Selection on testis size as an indicator of maturity in growing animals. II Correlated responses in reproductive rate

International audienc

Selection on testis size as an indicator of maturity in growing animals. I Direct and correlated responses in growth

International audienc

Feasibility of the STarT back screening tool in chiropractic clinics: a cross-sectional study of patients with low back pain

The STarT back screening tool (SBT) allocates low back pain (LBP) patients into three risk groups and is intended to assist clinicians in their decisions about choice of treatment. The tool consists of domains from larger questionnaires that previously have been shown to be predictive of non-recovery from LBP. This study was performed to describe the distribution of depression, fear avoidance and catastrophising in relation to the SBT risk groups. A total of 475 primary care patients were included from 19 chiropractic clinics. They completed the SBT, the Major Depression Inventory (MDI), the Fear Avoidance Beliefs Questionnaire (FABQ), and the Coping Strategies Questionnaire. Associations between the continuous scores of the psychological questionnaires and the SBT were tested by means of linear regression, and the diagnostic performance of the SBT in relation to the other questionnaires was described in terms of sensitivity, specificity and likelihood ratios

General Practitioners' and patients' perceptions towards stratified care: a theory informed investigation

Background Stratified primary care involves changing General Practitioners’ (GPs) clinical behaviour in treating patients, away from the current stepped care approach to instead identifying early treatment options that are matched to patients’ risk of persistent disabling pain. This article explores the perspectives of UK-based GPs and patients about a prognostic stratified care model being developed for patients with the five most common primary care musculoskeletal pain presentations. The focus was on views about acceptability, and anticipated barriers and facilitators to the use of stratified care in routine practice. Methods Four focus groups and six semi-structured telephone interviews were conducted with GPs (n = 23), and three focus groups with patients (n = 20). Data were analysed thematically; and identified themes examined in relation to the Theoretical Domains Framework (TDF), which facilitates comprehensive identification of behaviour change determinants. A critical approach was taken in using the TDF, examining the nuanced interrelationships between theoretical domains. Results Four key themes were identified: Acceptability of clinical decision-making guided by stratified care; impact on the therapeutic relationship; embedding a prognostic approach within a biomedical model; and practical issues in using stratified care. Whilst within each theme specific findings are reported, common across themes was the identified relationships between the theoretical domains of knowledge, skills, professional role and identity, environmental context and resources, and goals. Through analysis of these identified relationships it was found that, for GPs and patients to perceive stratified care as being acceptable, it must be seen to enhance GPs’ knowledge and skills, not undermine GPs’ and patients’ respective identities and be integrated within the environmental context of the consultation with minimal disruption. Conclusions Findings highlight the importance of taking into account the context of general practice when intervening to support GPs to make changes to their clinical behaviour. Findings will inform further stages of the research programme; specifically, the intervention format and content of support packages for GPs participating in a future randomised controlled trial (RCT). This study also contributes to the theoretical debate on how best to encourage clinical behaviour change in general practice, and the possible role of the TDF in that process

Health professionals’ and coroners’ views on less invasive perinatal and paediatric autopsy: a qualitative study

OBJECTIVE: To assess health professionals’ and coroners’ attitudes towards non-minimally and minimally invasive autopsy in the perinatal and paediatric setting. METHODS: A qualitative study using semistructured interviews. Data were analysed thematically. RESULTS: Twenty-five health professionals (including perinatal/paediatric pathologists and anatomical pathology technologists, obstetricians, fetal medicine consultants and bereavement midwives, intensive care consultants and family liaison nurses, a consultant neonatologist and a paediatric radiologist) and four coroners participated. Participants viewed less invasive methods of autopsy as a positive development in prenatal and paediatric care that could increase autopsy rates. Several procedural and psychological benefits were highlighted including improved diagnostic accuracy in some circumstances, potential for faster turnaround times, parental familiarity with imaging and laparoscopic approaches, and benefits to parents and faith groups who object to invasive approaches. Concerns around the limitations of the technology such not reaching the same levels of certainty as full autopsy, unsuitability of imaging in certain circumstances, the potential for missing a diagnosis (or misdiagnosis) and de-skilling the workforce were identified. Finally, a number of implementation issues were raised including skills and training requirements for pathologists and radiologists, access to scanning equipment, required computational infrastructure, need for a multidisciplinary approach to interpret results, cost implications, equity of access and acceptance from health professionals and hospital managers. CONCLUSION: Health professionals and coroners viewed less invasive autopsy as a positive development in perinatal and paediatric care. However, to inform implementation a detailed health economic analysis and further exploration of parental views, particularly in different religious groups, are required

Comparison of the Swedish STarT Back Screening Tool and the Short Form of the Örebro Musculoskeletal Pain Screening Questionnaire in patients with acute or subacute back and neck pain

BACKGROUND: Patients with back and neck pain are often seen in primary care and it is important to provide them with tailored interventions based on risk stratification/triage. The STarT Back Screening Tool (SBT) is a widely used screening questionnaire which has not yet been validated for a population with back and/or neck pain with short duration. Our aim was to compare the concurrent validity of the SBT and the short form of the ÖMPSQ including psychometric properties and clinical utility in a primary care setting. METHODS: Patients who applied for physiotherapy by direct access (January 2013 to January 2014) at 35 primary care centers in south Sweden, with acute or subacute back and/or neck pain, aged 18–67 years, who were not currently on sick leave or had been on sick leave less than 60 days were asked to complete the SBT and ÖMPSQ-short questionnaire (n = 329). We used the Spearman’s rank correlations to study correlations, cross tabulation and Cohen’s kappa to analyze agreement of patient classification. Clinical utility was described as clinician scoring miscalculations and misclassifications of total and/or subscale scores. RESULTS: Completed SBT (9-items) and ÖMPSQ-short (10-items) data were available for 315/329 patients respectively. The statistical correlation for SBT and ÖMPSQ-short total scores was moderately strong (0.62, p < 0.01). In subgroup analyses, the correlations were 0.69 (p < 0.01) for males and 0.57 (p < 0.01) for females. The correlations were lower among older age groups, especially females over 50 years (0.21, p = 0.11). Classification to high or low risk for long-term pain and disability had moderate agreement (κ = 0.42). Observed classification agreement was 70.2%. The SBT had fewer miscalculations (13/315) than the ÖMPSQ-short (54/315). CONCLUSIONS: The correlation between the SBT and the ÖMPSQ-short scores were moderately strong for individuals with acute or subacute back and/or neck pain. SBT seemed to be clinically feasible to use in clinical practice. We therefore suggest that SBT can be used for individuals with both BP and/or NP in primary care settings but it is important to be aware of that SBT’s agreement with the ÖMPSQ-short was poor among females aged over 50 years. TRIAL REGISTRATION: ClinicalTrials.gov ID: NCT02609750 Registered: November 18, 2015