Exome sequencing in single cells from the cerebrospinal fluid in multiple sclerosis

Background:

Genome-wide association studies (GWAS) have identified over 100 germline variants that influence susceptibility to multiple sclerosis, most of which map within or near to genes with immunological function. However, the role of somatic mutations in multiple sclerosis has not been investigated.

Objective:

The objective of this paper is to explore the role that somatic mutations might play in the development of multiple sclerosis.

Methods:

We exome-sequenced in total 21 individual CD4+ lymphocytes isolated from cerebrospinal fluid of two patients. In addition we sequenced DNA from the patients’ peripheral blood to serve as germline reference.

Results:

In comparison with the respective germline sequence, each cell differed at an average of 1784 positions, but as anticipated subsequent analysis confirms that most, if not all, of these potential mutations are likely to represent artefacts generated during the amplification of a single genome and/or by sequencing. Fifty-six of the potential mutations were predicted to have likely functional effects on genes that have previously been implicated by GWAS, including three in the CD6 gene.

Conclusion:

More robust methods applied to larger numbers of cells will be needed to define the role of somatic mutations.

Survey of stereotactic ablative body radiotherapy in the UK by the QA group on behalf of the UK SABR Consortium

OBJECTIVE

To ascertain the progress being made towards the implementation of stereotactic ablative body radiotherapy (SABR) treatment in the UK, to obtain details of current practice in centres with an active treatment programme and to assess the projected future provision.

METHODS

In August 2012, an online questionnaire was sent to all 65 UK radiotherapy institutions. The included questions covered the current number of patients being treated and the intended number of patients for each clinical site; immobilization and motion management methods; CT scanning protocols; target and organ-at-risk delineation; treatment planning; image-guidance and treatment protocols; and quality assurance methods.

RESULTS

48/65 (74%) institutions responded by the end of November 2012, with 15 indicating an active SABR programme. A further four centres indicated that a SABR protocol had been established but was not yet in clinical use. 14 of the 29 remaining responses stated an intention to develop a SABR programme in the next 2 years.

CONCLUSION

The survey responses confirm that SABR provision in the UK is increasing and that this should be expected to continue in the next 2 years. A projection of the future uptake would suggest that by the end of 2014, UK SABR provision will be broadly in line with international practice.

Inferring the spatiotemporal DNA replication program from noisy data

We generalize a stochastic model of DNA replication to the case where replication-origin-initiation rates vary locally along the genome and with time. Using this generalized model, we address the inverse problem of inferring initiation rates from experimental data concerning replication in cell populations. Previous work based on curve fitting depended on arbitrarily chosen functional forms for the initiation rate, with free parameters that were constrained by the data. We introduce a nonparametric method of inference that is based on Gaussian process regression. The method replaces specific assumptions about the functional form of the initiation rate with more general prior expectations about the smoothness of variation of this rate, along the genome and in time. Using this inference method, we recover, with high precision, simulated replication schemes from noisy data that are typical of current experiments.

Mortality, survival and residual injury burden of Royal Navy and Royal Marine combat casualties sustained in 11-years of operations in Iraq and Afghanistan

We present eleven years of prospectively-gathered data defining the full spectrum of the United Kingdom's (UK) Naval Service (Royal Navy and Royal Marines) casualties, and characterise the injury patterns, recovery and residual functional burden from the conflicts of the last decade. The UK Military Trauma Registry was searched for all Naval Service personnel injured between March 2003 and April 2013. These records were then cross-referenced with the records of the Naval Service Medical Board of Survey (NSMBOS), which evaluates injured Naval Service personnel for medical discharge, continued service in a reduced capacity or Return to Full Duty (RTD). Population at risk data was calculated from service records. There were 277 casualties in the study period: 63 (23%) of these were fatalities. Of the 214 survivors, 63 or 29% (23% of total) were medically discharged; 24 or 11% (9% of total) were placed in a reduced fitness category with medical restrictions placed on their continued military service. A total of 127 individuals (46% of the total and 59% of survivors) RTD without any restriction. The greatest number of casualties was sustained in 2007. There was a 3% casualty risk per year of operational service for Naval Service personnel. The most common reason cited by Naval Service Medical Board of Survey (NSMBOS) for medical downgrading or discharge was injury to the lower limb, with upper limb trauma the next most frequent. This study characterises the spectrum of injuries sustained by the Naval Service during recent conflicts with a very high rate of follow-up. Extremity injuries pose the biggest challenge to reconstructive and rehabilitative services striving to maximise the functional outcomes of injured service personnel.

A qualitative study exploring female patients' experiences of self-harm in a medium secure unit

This study utilized a social constructivist model and reports upon interviews conducted with five female patients in a medium secure service. Their perception of self-harm is considered. Six themes emerged from the data, 'the traumatized individual', 'interrupted maturation process', 'the hidden experience', 'crossing the line', 'individual and systemic repercussions', 'nascent potential protection'. In addition to the six themes that emerged, we concluded that, although individual perceptions of self-harm varied, commonalities existed across accounts and that individual formulation may assist both patients and staff to gain a personalized understanding, thus, enabling less harmful ways of coping to be established.

A glimmer of hope? Evaluation of time for non-genitourinary medicine physicians to diagnose HIV infection in patients presenting with HIV-related illness

A study conducted in 2002-2003 at three UK south coast hospitals measuring the length of time for non-genitourinary medicine physicians to diagnose HIV when patients presented with an HIV-related illness, found a median time to diagnosis of four days with 70% of diagnoses being made within seven days. This retrospective cohort study of all patients newly diagnosed with HIV between 1 January 2010 and 31 December 2011 was conducted at the same three hospitals. Thirty-seven patients were newly diagnosed with HIV in non-genitourinary (GU) medicine inpatient and outpatient settings (24 men, 13 women), with a mean age of 43 years. The median time to diagnosis was one day (interquartile range of 0-4 days), with 81% of diagnoses made within seven days of first presentation. Late diagnosis of HIV remains a significant challenge, but delayed diagnosis in a patient admitted with an HIV-related illness is reducing in this setting.

Stereotactic ablative radiotherapy in the UK: current status and developments

Stereotactic ablative radiotherapy (SABR) has developed from the principles and techniques used in the stereotactic radiosurgery treatment of brain metastases. Advances in computer technology, imaging, planning and treatment delivery and evidence from retrospective analysis of single- and multi-institutional early-phase studies have established SABR in the treatment of medically inoperable early lung cancer. Effective multidisciplinary team working is crucial to safe delivery of SABR. The variation in patient selection, radiotherapy planning and delivery techniques has led to a collective approach to SABR implementation across the UK. Centres developing the technique are represented in the UK SABR Consortium, which is supported by the relevant UK professional bodies and represents a platform to develop extracranial SABR across the UK. The uptake of SABR in the UK has been slowed by workforce issues, but at least 15 centres are currently delivering treatment with over 500 patients treated using UK SABR Consortium guidance. A mentoring program is being piloted helping new centres to develop their programs, and over 30 UK centres are expected to be offering SABR treatment by the end of 2014. The use of consistent guidance for patient selection, treatment planning and delivery in the UK gives the opportunity to collect and audit toxicity and outcome across the centres, contributing to the internationally reported SABR experience. Having established this service in the UK, the development of SABR through clinical research is a priority, and with input from the Radiotherapy Trials Quality Assurance Group, the UK is developing a national study program that includes participation in international trials.

Increasing screening frequency in men who have sex with men: impact of guidance on risk profiling on workload and earlier diagnosis of sexually transmitted infection and HIV

Increasing screening frequency in men who have sex with men (MSM) engaging in high-risk behaviours can reduce prevalence of sexually transmitted infections (STIs). This evaluation investigated the impact of applying stricter screening guidelines for MSM on service workload and earlier STI diagnoses. A validated risk assessment tool (RAT) was distributed to MSM attending a level 3 sexual health service over three months. Australian screening guidelines were applied to the data to identify MSM requiring more frequent screening and data projected to the larger MSM population. The RAT identified a 2-5-fold increase in the number of STI and HIV screenings required based on six- and three-monthly screening intervals, respectively, in the MSM cohort. When screening intervals are reduced from three-monthly to six-monthly there is a potential loss of 66.7% of earlier HIV diagnoses. The use of RATs will increase workload in sexual health services, but potentially diagnose a large proportion of disease earlier.

The effect of a Bacillus-based direct-fed microbial supplemented to sows on the gastrointestinal microbiota of their neonatal piglets

Direct-fed microbials (DFM) supplemented in sow diets may confer health benefits to the host and their piglets by reducing pathogens in the sow and environment. In this study we evaluated the effect of a Bacillus-based DFM on the gastrointestinal microbiota of neonatal piglets. A total of 208 sows were divided into 2 treatments: a control diet and the control diet supplemented with a Bacillus subtilis-based DFM (3.75 × 10(5) cfu/g feed). Twenty-one piglets sampled from each sow treatment group were euthanized on d 3 of lactation followed by an additional 15 piglets per treatment on d 10 of lactation. Litters from DFM-supplemented sows had greater (P = 0.02) weaning weights and a tendency (P = 0.09) for improvement in litter ADG. Sows supplemented with the DFM weaned more pigs (P = 0.06) than control sows which was reflected in numerically lower but not statistically different (P = 0.12) decrease in piglet mortality in DFM litters. Terminal RFLP was used to characterize gastrointestinal (GI) microbial populations in the ileum and colon of the piglets. Terminal restriction fragments (T-RF) were compared between control and DFM treatments. There was a greater incidence and quantity of T-RF B423 and H330 (binary P = 0.01, 0.08; quantitative P = 0.01, 0.05, respectively), putatively identified as Lactobacillus gasseri/johnsonii, in the ileum of pigs nursing sows supplemented with DFM at d 3. Terminal restriction fragment peaks B423 and H330 were also greater (binary P = 0.01, 0.08; quantitative P = 0.01, 0.01, respectively) in the colon of pigs nursing sows supplemented with DFM at d 3. Peaks M495 and B394, putatively identified as E. coli, were greater (binary P = 0.01, 0.04; quantitative P = 0.01, 0.01, respectively) in the colon of the control pigs at d 3. At d 10, both the presence and quantity of Lactobacillus species were greater (P < 0.05) in the colon of pigs with the DFM treatment. Additionally, there was a tendency for T-RF B227 and H257 (binary P = 0.07, 0.07, respectively), putatively identified as Clostridium perfringens, to be present in the ileum of the control pigs at d 10 compared with treated pigs. Results of this study reveal that the developing gastrointestinal microbiota of a neonatal piglet can be affected by DFM supplementation to the sow.

Aggression in a high secure hospital: staff and patient attitudes

Responding to aggressive behaviour is a key activity for nurses and other care staff in high secure hospitals. The attitudes and beliefs of staff regarding patient aggression will influence the management strategies they adopt. Patients will also hold attitudes regarding the causes of and best ways to respond to aggressive behaviour. This study measured the attitudes towards aggression of staff (n= 109) and patients (n= 27) in a high secure hospital in the UK using the Management of Aggression and Violence Attitude Scale (MAVAS). There was considerable concordance of views, staff and patients disagreeing on only two items on the MAVAS. Aggression was felt to have a range of causes, embracing factors internal to the person, factors in the external environment and situational or interactional factors. Interpersonal means of managing aggression were supported, but both staff and patients also advocated the use of controlling management strategies such as medication, seclusion and restraint. The implications of these findings for aggression management in high secure settings are discussed in the light of best practice guidelines that promote interpersonal approaches over controlling strategies.