Secondary analysis of Staphylococcus aureus whole genomes reveals diverse antimicrobial resistance profiles.

Antimicrobial resistance (AMR) in microorganisms is an ongoing threat to human health across the globe. To better characterize the AMR profiles of six strains of Staphylococcus aureus , we performed a secondary analysis that consisted of the following steps: 1) download fastq files from the Sequence Read Archive, 2) perform a de novo genome assembly from the sequencing reads, 3) annotate the assembled contigs, 4) predict the presence of antimicrobial resistance genes. We predicted the presence of 75 unique genes that conferred resistance against 22 unique antimicrobial compounds.

A large-scale genetic screen identifies genes essential for motility in Agrobacterium fabrum.

The genetic and molecular basis of flagellar motility has been investigated for several decades, with innovative research strategies propelling advances at a steady pace. Furthermore, as the phenomenon is examined in diverse bacteria, new taxon-specific regulatory and structural features are being elucidated. Motility is also a straightforward bacterial phenotype that can allow undergraduate researchers to explore the palette of molecular genetic tools available to microbiologists. This study, driven primarily by undergraduate researchers, evaluated hundreds of flagellar motility mutants in the Gram-negative plant-associated bacterium Agrobacterium fabrum. The nearly saturating screen implicates a total of 37 genes in flagellar biosynthesis, including genes of previously unknown function.

Conceptualizing Trust and Distrust as Alternative Stable States: Lessons from the Flint Water Crisis.

Despite the universally recognized importance of fostering trust and avoiding distrust in governance relationships, there remains considerable debate on core questions like the relation between (dis)trust and the evaluations of the characteristics that make a governance agent appear (un)worthy of trust. In particular, it remains unclear whether levels of (dis)trust simply follow levels of (dis)trustworthiness-such that building trust is primarily a question of increasing evidence of trustworthiness and avoiding evidence of distrustworthiness, or if their dynamics are more complicated. The current paper adds novel theory for thinking about the management of trust and distrust in the governance context through the application of principles borrowed from resilience theory. Specifically, we argue that trust and distrust exist as distinct, self-reinforcing (i.e., stable) states separated by a threshold. We then theorize as to the nature of the self-reinforcing processes and use qualitative data collected from and inductively coded in collaboration with Flint residents as part of a participatory process to look for evidence of our argument in a well-documented governance failure. We conclude by explaining how this novel perspective allows for clearer insight into the experience of this and other communities and speculate as to how it may help to better position governance actors to respond to future crises.

Reference range of liver corrected T1 values in a population at low risk for fatty liver disease-a UK Biobank sub-study, with an appendix of interesting cases.

PURPOSE: Corrected T1 (cT1) value is a novel MRI-based quantitative metric for assessing a composite of liver inflammation and fibrosis. It has been shown to distinguish between non-alcoholic fatty liver disease (NAFL) and non-alcoholic steatohepatitis. However, these studies were conducted in patients at high risk for liver disease. This study establishes the normal reference range of cT1 values for a large UK population, and assesses interactions of age and gender. METHODS: MR data were acquired on a 1.5 T system as part of the UK Biobank Imaging Enhancement study. Measures for Proton Density Fat Fraction and cT1 were calculated from the MRI data using a multiparametric MRI software application. Data that did not meet quality criteria were excluded from further analysis. Inter and intra-reader variability was estimated in a set of data. A cohort at low risk for NAFL was identified by excluding individuals with BMI ≥ 25 kg/m2 and PDFF ≥ 5%. Of the 2816 participants with data of suitable quality, 1037 (37%) were classified as at low risk. RESULTS: The cT1 values in the low-risk population ranged from 573 to 852 ms with a median of 666 ms and interquartile range from 643 to 694 ms. Iron correction of T1 was necessary in 36.5% of this reference population. Age and gender had minimal effect on cT1 values. CONCLUSION: The majority of cT1 values are tightly clustered in a population at low risk for NAFL, suggesting it has the potential to serve as a new quantitative imaging biomarker for studies of liver health and disease.

DNA based diagnostic for the quantification of sugarcane root DNA in the field.

Plant root systems play many key roles including nutrient and water uptake, interface with soil microorganisms and resistance to lodging. As for other crops, large and systematic studies of sugarcane root systems have always been hampered by the opaque and solid nature of the soil. In recent years, methods for efficient extraction of DNA from soil and for species-specific DNA amplification have been developed. Such tools could have potential to greatly improve root phenotyping and health diagnostic capability in sugarcane. In this paper, we present a fast, specific and efficient method for the quantification of sugarcane live root cells in soil samples. Previous studies were typically based on mass and length, so we established a calibration to convert root DNA quantity to live root mass. This diagnostic was validated on field samples and used to investigate the fate of the root system after harvest prior to regrowth of the ratoon crop. Two weeks after harvest, the sugarcane roots from the previous crop were still viable. This raises the question of the role that the root system of the harvested crop plays in the performance of the next crop and demonstrates how this test can be used to answer research questions.

The use of Hall technique preformed metal crowns by specialist paediatric dentists in the UK.

Background Hall technique preformed metal crowns (HTPMCs) have been increasing in use recently, but little is currently known about their use by specialists.Aim To investigate the views and usage of HTPMCs by UK specialist paediatric dentists.Design This was a prospective questionnaire-based study, distributed online to all specialists on the British Society of Paediatric Dentistry email list between July and September 2014.Results Ninety-four questionnaires were completed. The majority of respondents, 65% (61) worked in teaching hospitals, followed by community dental services, 37% (35). Ninety-six percent (89) reported that they used HTPMCs in their practice. Fifty-eight percent (54) used HTPMCs as a treatment option for restoring symptomless carious primary molars, and 15% (14) only when unable to provide conventional restoration. Twenty-three percent (21) used HTPMCs as the treatment of choice. Only 4% (4) of respondents never used them. Sixty percent (53) had been using HTPMCs for over five years. Seventy-six percent (68) would consider placing HTPMCs under inhalation sedation, and 26% (23) under general anaesthesia. Over 90% (85) believed that HTPMCs are suitable for undergraduate teaching, general practice, postgraduate training and specialist practice.Conclusion HTPMCs are widely used among specialist paediatric dentists in the UK.

An evidence-based treatment algorithm for colorectal polyp cancers: results from the Scottish Screen-detected Polyp Cancer Study (SSPoCS).

OBJECTIVES: Colorectal polyp cancers present clinicians with a treatment dilemma. Decisions regarding whether to offer segmental resection or endoscopic surveillance are often taken without reference to good quality evidence. The aim of this study was to develop a treatment algorithm for patients with screen-detected polyp cancers. DESIGN: This national cohort study included all patients with a polyp cancer identified through the Scottish Bowel Screening Programme between 2000 and 2012. Multivariate regression analysis was used to assess the impact of clinical, endoscopic and pathological variables on the rate of adverse events (residual tumour in patients undergoing segmental resection or cancer-related death or disease recurrence in any patient). These data were used to develop a clinically relevant treatment algorithm. RESULTS: 485 patients with polyp cancers were included. 186/485 (38%) underwent segmental resection and residual tumour was identified in 41/186 (22%). The only factor associated with an increased risk of residual tumour in the bowel wall was incomplete excision of the original polyp (OR 5.61, p=0.001), while only lymphovascular invasion was associated with an increased risk of lymph node metastases (OR 5.95, p=0.002). When patients undergoing segmental resection or endoscopic surveillance were considered together, the risk of adverse events was significantly higher in patients with incomplete excision (OR 10.23, p<0.001) or lymphovascular invasion (OR 2.65, p=0.023). CONCLUSION: A policy of surveillance is adequate for the majority of patients with screen-detected colorectal polyp cancers. Consideration of segmental resection should be reserved for those with incomplete excision or evidence of lymphovascular invasion.

Facial Aesthetics in Young Adults after Cleft Lip and Palate Treatment over Five Decades.

Cleft Lip and Palate (CLP) - a common facial malformation in newborns - is typically corrected by surgical intervention to allow for normal speech development, psychosocial adjustment, and facial attractiveness. The long term treatment outcome can be evaluated after a number of years, possibly in adulthood. We investigated the aesthetics of the nasolabial region by subjective ratings. To compare various surgical approaches we recruited 12 raters to evaluate 429 patients. Expert and lay raters judged photographs from patients, who have completed treatment with one of three different surgical strategies performed in our institution over 50 years. Facial photographs were cropped, presented to the raters in a randomized sequence, and judged by the raters on a 5 point Likert scale. The subjective ratings between the raters revealed a fair to substantial inter-rater reliability. The average ratings of the surgical outcome improved continuously over the investigated 5 decades. Despite possible differences between raters and rater groups this overall result was consistently seen in the gender groups (male/female), or expertise related groups (expert/lay). Our analysis revealed that patients with bilateral CLP scored worse than patients with unilateral CLP when treated in the fifties; more recently treated patients of both groups scored similarly.

Response to letter to editor: 'Comment on Arch et al., Trials. 2016;17:517'.

In October 2015 we published the paper 'Measurement of HbA1c in multicentre diabetes trials - should blood samples be tested locally or sent to a central laboratory: an agreement analysis'. Chatterjee and Pradhan have submitted a letter to the editor asking critical questions regarding the methods we used. We offer this letter in response. TRIAL REGISTRATION: Eudract No. 2010-023792-25. Registered on 4 November 2010. ISRCTN No. ISRCTN29255275 . Registered on 12 November 2010.

Endocrinopathies and renal outcomes in lithium therapy: impact of lithium toxicity.

BACKGROUND: Lithium is the mainstay of treatment for bipolar disorder, mania and an augmentation therapy in patients with treatment resistant depression. It has a narrow therapeutic index, with recognized adverse multi-system and endocrine side effects. AIM: To assess the impact of lithium therapy, in particular lithium toxicity, on the development of endocrine and renal disorders in a cohort of patients in a single tertiary referral centre in Ireland. STUDY DESIGN: A retrospective analysis was performed of the prevalence of lithium toxicity and renal, thyroid and parathyroid dysfunction in our study population. METHODS: We collected laboratory data from the Clinical Chemistry department of the Adelaide and Meath Hospital incorporating the National Children's Hospital (AMNCH), Dublin, Ireland. Our study population included all patients who had at least one serum lithium measurement from January 1st 2000 to December 31st 2014 inclusive. RESULTS: A total of 580 patients were included in the study. Among our study group, 70 patients (12.1%) had 1 toxic lithium measurement (lithium level >1.2 mmol/l). 27.8% (n > 161) of patients developed stage 3 Chronic kidney Disease (CKD) or higher, which was commoner in those patients who developed toxic lithium levels (P < 0.0001) and in those who developed hypernatraemia (P > 0.0001). 16.2% of patients (n > 94) had one serum sodium >145 mmol/l during follow up. 60 patients(10.3%) had a TSH >10 mU/l, while complete suppression of TSH (<0.05 mU/l) was observed in 22 patients (3.8%) during follow-up. 4% (n > 37) of the study population had ≥1 serum corrected calcium level > 2.55 mmol/l, and 4 patients had biochemical confirmation of primary hyperparathyroidism but PTH levels were only performed in 2.8% (n > 16) of the studypopulation. CONCLUSION: Stage 3 CKD is common in patients receiving lithium therapy. Lithium toxicity is associated with CKD and hypernatraemia. Thyroid dysfunction and hypercalcaemia are common in patients receiving lithium therapy. Patients receiving lithium therapy require surveillance of renal, thyroid and bone biochemistry.

Efficacy of motivational interviewing and cognitive behavioral therapy for anxiety and depression symptoms following traumatic brain injury.

BACKGROUND: Anxiety and depression are common following traumatic brain injury (TBI), often co-occurring. This study evaluated the efficacy of a 9-week cognitive behavioral therapy (CBT) program in reducing anxiety and depression and whether a three-session motivational interviewing (MI) preparatory intervention increased treatment response. METHOD: A randomized parallel three-group design was employed. Following diagnosis of anxiety and/or depression using the Structured Clinical Interview for DSM-IV, 75 participants with mild-severe TBI (mean age 42.2 years, mean post-traumatic amnesia 22 days) were randomly assigned to an Adapted CBT group: (1) MI + CBT (n = 26), or (2) non-directive counseling (NDC) + CBT (n = 26); or a (3) waitlist control (WC, n = 23) group. Groups did not differ in baseline demographics, injury severity, anxiety or depression. MI and CBT interventions were guided by manuals adapted for individuals with TBI. Three CBT booster sessions were provided at week 21 to intervention groups. RESULTS: Using intention-to-treat analyses, random-effects regressions controlling for baseline scores revealed that Adapted CBT groups (MI + CBT and NDC + CBT) showed significantly greater reduction in anxiety on the Hospital Anxiety and Depression Scale [95% confidence interval (CI) -2.07 to -0.06] and depression on the Depression Anxiety and Stress Scale (95% CI -5.61 to -0.12) (primary outcomes), and greater gains in psychosocial functioning on Sydney Psychosocial Reintegration Scale (95% CI 0.04-3.69) (secondary outcome) over 30 weeks post-baseline relative to WC. The group receiving MI + CBT did not show greater gains than the group receiving NDC + CBT. CONCLUSIONS: Findings suggest that modified CBT with booster sessions over extended periods may alleviate anxiety and depression following TBI.

The Impact of Social Work Intervention in Alcohol-Induced Pancreatitis in Ireland: a Single-Center Experience.

AIM: To evaluate the effect on recurrent admission for alcohol-induced pancreatitis (that can be up to 48%) of a brief social work intervention for alcohol dependence in a single center in Ireland METHODS: Retrospective cohort study of patients admitted with acute alcohol-induced pancreatitis to a tertiary hospital in Ireland from January 2009 to December 2012. RESULTS: The relapse rate in the cohort of 160 patients with alcohol-induced pancreatitis was 28.1%. There was no difference in the relapse rate of those patients who received a social work intervention compared with those who did not (ANOVA, P = 0.229). The employment status was a significant risk factor for relapse (ANOVA, P = 0.027), but did not differ between those who did, and did not, receive the intervention. CONCLUSION: Although the cohort size did not allow great statistical power, it appears that our hospital's current social work intervention for alcohol-induced pancreatitis is ineffective in preventing relapse. Long-term prospective studies are required to formulate and better implement more efficacious interventions for such patients.

Predicting Cereal Root Disease in Western Australia Using Soil DNA and Environmental Parameters.

Root diseases have long been prevalent in Australian grain-growing regions, and most management decisions to reduce the risk of yield loss need to be implemented before the crop is sown. The levels of pathogens that cause the major root diseases can be measured using DNA-based services such as PreDicta B. Although these pathogens are often studied individually, in the field they often occur as mixed populations and their combined effect on crop production is likely to vary across diverse cropping environments. A 3-year survey was conducted covering most cropping regions in Western Australia, utilizing PreDicta B to determine soilborne pathogen levels and visual assessments to score root health and incidence of individual crop root diseases caused by the major root pathogens, including Rhizoctonia solani (anastomosis group [AG]-8), Gaeumannomyces graminis var. tritici (take-all), Fusarium pseudograminearum, and Pratylenchus spp. (root-lesion nematodes) on wheat roots for 115, 50, and 94 fields during 2010, 2011, and 2012, respectively. A predictive model was developed for root health utilizing autumn and summer rainfall and soil temperature parameters. The model showed that pathogen DNA explained 16, 5, and 2% of the variation in root health whereas environmental parameters explained 22, 11, and 1% of the variation in 2010, 2011, and 2012, respectively. Results showed that R. solani AG-8 soil pathogen DNA, environmental soil temperature, and rainfall parameters explained most of the variation in the root health. This research shows that interactions between environment and pathogen levels before seeding can be utilized in predictive models to improve assessment of risk from root diseases to assist growers to plan more profitable cropping programs.

Temporal artery biopsy--how can we improve performance?

INTRODUCTION: Temporal arteritis is a rare systemic disease of undefined aetiology. The British Society for Rheumatology has issued evidence-based guidance in the form of an investigative algorithm, central to which is biopsy of the superficial temporal artery (TA). Currently in Glasgow these patients are being referred to the regional vascular unit. We sought to identify areas where local practice could be improved. METHODS: This was a retrospective review of TA biopsy performed since the amalgamation of vascular services in Glasgow. RESULTS: There were 32 cases with a complete dataset. The majority of patients referred were women (66%), with a mean age of 68 years (range 43-86 years). A variety of different clinical symptoms were reported. The mean ESR was 53 (range 2-122). The median waiting time from referral to surgical biopsy was 6 days (inter-quartile range 2-8 days). Seven patients waited for more than 14 days for the procedure to be performed. There were four positive biopsies in this case series. TA biopsy influenced the duration of glucocorticosteroid therapy. CONCLUSION: From this study we believe that the following changes to local practice would be simple, cost effective and could improve the quality of patient care delivered.

Atypical naevus spilus: detection by in vivo confocal microscopy.

Naevus spilus (NS) is a naevoid disorder characterized by hyperpigmented macules or papules scattered over a café-au-lait macule. Such café-au-lait macules are often present at birth, and the darker pigmented speckles of NS slowly increase in number and size over a period of several years. NS can therefore be difficult to evaluate clinically for the development of melanoma. In vivo confocal microscopy (IVCM) is a novel method that allows examination at cellular resolution of cutaneous lesions in vivo. IVCM has been shown to have twice the specificity of dermoscopy for the diagnosis of melanoma, with comparable sensitivity. It has been shown to be useful in the detection and grading of dysplastic naevi, which are recognized precursors of melanoma in some cases. In this report, we highlight that IVCM can also be used as a tool complementary to dermoscopy to identify areas of dynamic change in clinically and dermoscopically equivocal lesions. IVCM may thereby assist in the early detection of melanocytic atypia and melanoma arising in NS, in turn leading to excision of melanoma at an early stage, which is associated with a favourable outcome. We also outline some of the difficulties encountered in confocal microscopy and histology when differentiating melanoma from dysplastic naevi.

Variation in the prevalence of chronic bronchitis among smokers: a cross-sectional study.

OBJECTIVE: Given the wide variations in prevalence of chronic obstructive pulmonary disease observed between populations with similar levels of exposure to tobacco smoke, we aimed to investigate the possibility of variations in prevalence of chronic bronchitis (CB) between two geographically distinct smoking populations in rural Karnataka, India. DESIGN: The Burden of Obstructive Lung Disease (BOLD) questionnaire was administered to all men aged >30 years in a cross-sectional survey. The χ(2) and Fisher's exact tests were used to compare CB prevalence in the two populations. Logistic regression was used to analyse the impact of multiple variables on the occurrence of CB. RESULTS: Two samples of 2322 and 2182 subjects were included in the study. In non-smokers, CB prevalence did not differ between the populations. However, it was significantly different between smoking populations (44.79% vs. 2.13%, P < 0.0001). Logistic regression indicated that, in addition to smoking, region, age, occupational dust exposure and type of house were associated with higher likelihood of CB. An interaction between smoking and area of residence was found (P < 0.001) and appeared to explain the effect of region (without interaction). CONCLUSION: A significant difference in CB prevalence was observed between male populations from two areas of Karnataka state, including when stratified by smoking status. No significant difference was observed between non-smokers.

Amnioinfusion in very early preterm prelabor rupture of membranes (AMIPROM): pregnancy, neonatal and maternal outcomes in a randomized controlled pilot study.

OBJECTIVE: To assess short- and long-term outcomes of pregnant women with very early rupture of membranes randomized to serial amnioinfusion or expectant management, and to collect data to inform a larger, more definitive clinical trial. METHODS: This was a prospective non-blinded randomized controlled trial with randomization stratified for pregnancies in which the membranes ruptured between 16 + 0 and 19 + 6 weeks' gestation and 20 + 0 and 23 + 6 weeks' gestation to minimize the risk of random imbalance in gestational age distribution between randomized groups. Intention-to-treat analysis was used. The study was conducted in four UK hospital-based fetal medicine units (Liverpool Women's NHS Trust, St Mary's Hospital Manchester, Birmingham Women's NHS Foundation Trust and Wirral University Hospitals Trust). The participants were women with confirmed preterm prelabor rupture of membranes at 16 + 0 to 24 + 0 weeks' gestation. Women with multiple pregnancy, fetal abnormality or obstetric indication for immediate delivery were excluded. Participants were randomly allocated to either serial weekly transabdominal amnioinfusions if the deepest pool of amniotic fluid was < 2 cm or expectant management until 37 weeks' gestation. Short-term maternal, pregnancy and neonatal and long-term outcomes for the child were studied. Long-term respiratory morbidity was assessed using validated respiratory questionnaires at 6, 12 and 18 months of age and infant lung function test at around 12 months of age. Neurodevelopment was assessed using the Bayley Scales of Infant Development, second edition (BSID-II) at corrected age of 2 years. RESULTS: Fifty-eight women were randomized to the study. Two babies were excluded from the analysis because of termination of pregnancy for lethal anomaly, leaving 56 participants (28 assigned to serial amnioinfusion and 28 to expectant management) recruited between 2002 and 2009. There was no significant difference in perinatal mortality (19/28 vs 19/28; relative risk (RR) 1.0 (95% CI, 0.70-1.43)) and maternal or neonatal morbidity. The overall chance of surviving without long-term respiratory or neurodevelopmental disability was 4/56 (7.1%); 4/28 (14.3%) in the amnioinfusion group and 0/28 in the expectant group (RR 9.0 (95% CI, 0.51-159.70)). CONCLUSIONS: This pilot study found no major differences in maternal, perinatal or pregnancy outcomes. The study was not designed to show a difference between the groups and the number of survivors was too small to draw any conclusions about long-term outcomes. It does, however, signal that a larger definitive study to evaluate amnioinfusion for improvement in healthy survival is needed. The pilot suggests that, with appropriate funding, such a study is feasible.

Management of Asthma in School age Children On Therapy (MASCOT): a randomised, double-blind, placebo-controlled, parallel study of efficacy and safety.

BACKGROUND: Asthma affects one in eight children in the UK. National management guidelines have been available for many years but, unlike in adults, studies in children have been few, with their methodologies often based on inappropriate adult models. Sound medical evidence in support of the national guidelines for asthma management in children is lacking. The MASCOT study has been developed to address this need. OBJECTIVES: To determine whether adding salmeterol or montelukast to low-dose inhaled corticosteroids (ICSs) can reduce the number of exacerbations requiring treatment with oral corticosteroids in children with uncontrolled asthma. DESIGN: A randomised, double-blind, placebo-controlled trial with a 4-week run-in period on a fluticasone propionate inhaler (100 µg twice daily) with inhaler technique correction. Patients who met the post run-in period eligibility criteria were randomised in the ratio of 1 : 1 : 1 and were followed for 48 weeks. SETTING: Secondary care hospitals based in England and Scotland with recruitment from primary and secondary care. PARTICIPANTS: Children aged 6-14 years with asthma requiring frequent short-acting beta-2 agonist relief, with symptoms of asthma resulting in nocturnal wakening and/or asthma that has interfered with usual activities. INTERVENTIONS: Three groups were compared: (1) inhaled fluticasone propionate 100 µg twice daily plus placebo tablet once daily; (2) inhaled fluticasone propionate 100 µg and salmeterol 50 µg twice daily (combination inhaler) plus placebo tablet once daily; and (3) inhaled fluticasone propionate 100 µg twice daily plus montelukast 5-mg tablet once daily. MAIN OUTCOME MEASURES: The primary outcome was the number of exacerbations requiring treatment with oral corticosteroids over 48 weeks. Secondary outcome measures included quality of life as measured by the Paediatric Asthma Quality of Life Questionnaire with Standardised Activities [PAQLQ(S)] and the Paediatric Asthma Caregiver's Quality of Life Questionnaire (PACQLQ); time from randomisation to first exacerbation requiring treatment with a short course of oral corticosteroids; school attendance; hospital admissions; amount of rescue beta-2 agonist therapy prescribed; time from randomisation to treatment withdrawal (because of lack of efficacy or side effects); lung function at 48 weeks (as assessed by spirometry); cost-effectiveness; adverse events. RESULTS: The study was closed prematurely because of poor recruitment and the target sample size of 450 was not achieved. In total, 898 children were screened to enter the trial, 166 were registered for the 4-week run-in period and 63 were randomised (group 1: 19, group 2: 23, group 3: 21), with 38 contributing data for the primary outcome analysis. There were no significant differences between groups for any of the outcomes. Adverse events were similar between the groups except for nervous system disorders, which were more frequently reported on fluticasone plus montelukast. CONCLUSIONS: Based on the results of the MASCOT study it is not possible to conclude whether adding salmeterol or montelukast to ICSs can reduce the number of exacerbations requiring treatment with oral corticosteroids in children with uncontrolled asthma. TRIAL REGISTRATION: Current Controlled Trials ISRCTN03556343. FUNDING: This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 17, No. 4. See the HTA programme website for further project information.