Tracking TCRß sequence clonotype expansions during antiviral therapy using high-throughput sequencing of the hypervariable region

To maintain a persistent infection viruses such as hepatitis C virus (HCV) employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilize either antigen stimulation (e.g., ELISpot, proliferation assays, cytokine production) or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently, high-throughput sequencing (HTS) technologies have been developed for the analysis of T cell repertoires. In the present study, we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR)3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing antiviral therapy, we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study; however, the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high junction region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101-restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of future experiments to accurately address the question of whether T cell responses contribute to SVR upon antiviral therapy. This pipeline represents a novel technique to analyze T cell dynamics in situations where conventional antigen-dependent methods are limited due to suppression of T cell functions and highly diverse antigenic sequences

Improving access to effective care for people with chronic respiratory symptoms in low and middle income countries.

Chronic respiratory symptoms are amongst the most common complaints among low and middle-income country (LMICs) populations and they are expected to remain common over the 10 to 20 year horizon. The underlying diseases (predominantly chronic obstructive pulmonary disease, asthma and tuberculosis) cause, and threaten to increasingly cause, substantial morbidity and mortality. Effective treatment is available for these conditions but LMICs health systems are not well set up to provide accessible clinical diagnostic pathways that lead to sustainable and affordable management plans especially for the chronic non communicable respiratory diseases. There is a need for clinical and academic capacity building together with well-conducted health systems research to underpin health service strengthening, policy and decision-making. There is an opportunity to integrate solutions for improving access to effective care for people with chronic respiratory symptoms with approaches to tackle other major population health issues that depend on well-functioning health services such as chronic communicable (e.g. HIV) and non-communicable (e.g. cardiovascular and metabolic) diseases

Timing of the first vancomycin maintenance dose in an acute hospital setting - room for improvement?

Introduction Intravenous vancomycin therapy typically starts with a loading dose followed by a maintenance dose 12 to 24 hours later. In the acute hospital setting, this often results in doses being administered in the middle of the night, which is impractical for both patients and staff. This audit examined current practice and developed new guidelines to support greater flexibility in the timing of the first maintenance dose. Methods Data recording forms used by pharmacists to support the therapeutic drug monitoring of vancomycin were collected from two hospital sites over six weeks. Forms containing at least two vancomycin concentrations were selected and the time of administration of the first maintenance dose was recorded. Individual vancomycin pharmacokinetic parameter estimates were obtained using MAP Bayesian analysis then used to predict vancomycin concentrations 6, 8, 10, 12 and 14 hours after a banded loading dose and 20 mg/kg (capped at 3000 mg). Predicted concentrations were compared with a target range of 10 – 20 mg/L. Results Data were obtained from 49 patients with a mean (SD) age of 63.1 (16.7) years and weight 80.1 (27.6) kg. In all patients, creatinine clearance estimates were >40 mL/min and, according to current practice guidelines, all patients required 12 hourly maintenance dosing. The time recorded for the administration of the first maintenance dose was between 11 pm and 7 am in 30 (61%) of these patients. In 14 patients (29%), the first maintenance dose was administered >12 hours after loading. The target range was achieved with banded doses (20 mg/kg) in 65% (71%) of concentrations at 6 hours, 74% (84%) at 8 hours, 57% (67%) at 10 hours, 53% (55%) at 12 hours and 39% (43%) at 14 hours. Conclusions This audit has shown that current practice results in a high proportion of vancomycin maintenance doses being administered at impractical times. Allowing a more flexible time window of 6-12 hours after the loading dose for administration of the first vancomycin maintenance dose could help to alleviate this problem and reduce the risk of early subtherapeutic vancomycin trough concentrations

Risk factors of ischemic stroke and subsequent outcome in hemodialysis patients

Background and purpose: End stage renal disease (ESRD) requiring hemodialysis (HD) carries up to a 10-fold greater risk of stroke than normal renal function. Knowledge concerning risk factors and management strategies derived from the general population may not be applicable to those with ESRD. We studied a large ESRD population to identify risk factors and outcomes for stroke. Methods: All adult patients receiving HD for ESRD from 01/01/2007 to 31/12/2012 were extracted from the electronic patient record. Variables associated with stroke were identified by survival analysis; demographic, clinical, imaging and dialysis related variables were assessed and case-fatality determined. Follow-up was until 31/12/2013. Results: 1382 patients were identified (mean age 60.5 years, 58.5% male). The prevalence of AF was 21.2% and 59.4% were incident HD patients. 160 (11.6%) experienced a stroke during 3471 patient-years of follow-up (95% ischemic). Stroke incidence was 41.5/1000 patient-years in prevalent and 50.1/1000 patient-years in incident HD patients. Factors associated with stroke on regression analysis were prior stroke, diabetes and age at starting renal replacement therapy. AF was not significantly associated with stroke and warfarin did not affect stroke risk in warfarin treated patients. Fatality was 18.8% at 7, 26.9% at 28 and 56.3% 365 days after stroke.<p></p> Conclusions: Incidence of stroke is high in patients with ESRD on HD with high case-fatality. Incident HD patients had the highest stroke incidence. Many, but not all, important risk factors commonly associated with stroke in the general population were not associated with stroke in patients receiving HD

Systemic restoration of UBA1 ameliorates disease in spinal muscular atrophy

Acknowledgments Blood biochemistry analysis and serum analysis were performed by the Easter Bush Pathology Department, University of Edinburgh. Animal husbandry was performed by Centre for Integrative Physiology bio-research restructure technical staff, University of Edinburgh. Assistance with intravenous injections was provided by Ian Coldicott (University of Sheffield) and Hannah Shorrock (University of Edinburgh). Human blood cDNA was a gift to GH from Kathy Evans, University of Edinburgh. Imaging was performed at the IMPACT imaging facility, University of Edinburgh, with technical assistance from Anisha Kubasik-Thayil. The authors would also like to thank Lyndsay Murray for technical discussions relating to qRT-PCR analysis. This work was supported by funding from the SMA Trust and the Anatomical Society (via grants to THG); the Euan MacDonald Centre for Motor Neurone Disease Research (via grants to THG and SHP); the Wellcome Trust (via grants to EJNG and THG); Muscular Dystrophy UK (via grants to THG and CGB); a Elphinstone Scholarship from the University of Aberdeen (to SHP); and The French Muscular Dystrophy Association (via grants to CM and JC).Peer reviewedPublisher PD

General practitioner provision of preventive child health care: analysis of routine consultation data

<b>Background</b> GPs contribute to preventive child health care in various ways, including provision of child health surveillance (CHS) reviews, opportunistic preventive care, and more intensive support to vulnerable children. The number of CHS reviews offered in Scotland was reduced from 2005. This study aimed to quantify GPs’ provision of different types of preventive care to pre-school children before and after the changes to the CHS system.<p></p> <b>Methods</b> GP consultation rates with children aged 0–4 years were examined for the 2½ years before and after the changes to the CHS system using routinely available data from 30 practices in Scotland. Consultations for CHS reviews; other aspects of preventive care; and all reasons were considered.<p></p> <b>Results:</b> Prior to the changes to the CHS system, GPs often contributed to CHS reviews at 6–8 weeks and 8–9 and 39–42 months. Following the changes, GP provision of the 6–8 week review continued but other reviews essentially ceased. Few additional consultations with pre-school children are recorded as involving other aspects of preventive care, and the changes to CHS have had no impact on this. In the 2½ years before and after the changes, consultations recorded as involving any form of preventive care accounted for 11% and 7.5% respectively of all consultations with children aged 0–4 years, with the decline due to reductions in CHS reviews.<p></p> <b>Conclusions:</b> Effective preventive care through the early years can help children secure good health and developmental outcomes. GPs are well placed to contribute to the provision of such care. Consultations focused on preventive care form a small minority of GPs’ contacts with pre-school children, however, particularly since the reduction in the number of CHS reviews

Nurturing Equality, Diversity and Inclusion

EPDF and EPUB available Open Access under CC-BY-NC-ND licence. This book provides scientific evidence to support arguments for equality and change in academic institutions both in terms of the business case and the interests of social justice. Familiarising readers with the key equality, diversity and inclusion (EDI) issues in health and biomedicine in relation to research careers and researcher development, it is an essential guide for equality planning team members, researchers, HRM officers and managers across academia

Multiple levels of influence affecting the utilisation of adult asthma services in the private sector in Khartoum

Background Asthma is the third most common cause of hospital visits in Sudan and globally affects more than 300 million people (WHO, 2007) (IUATLD, 2011, 2018). Sudan has a pluralistic health care system with a strong and varied private sector and a three- tiered public health sector (federal, state and district). Most asthma patients in Sudan seek asthma care in hospital emergency rooms or in the private sector. The main constraints of the asthma services in the public sector are lack of resources, lack of medical doctors in certain areas, inconsistent drug supplies and an absence of community involvement in health affairs (Ebrahim et al., 2017). While there has been research examining the low availability of asthma services in the public sector in Sudan (El Sony et al., 2013), very little is known about which asthma services are available in the private sector. Objective The goal of this thesis was to use a mixed method approach to understand the utilisation of adult asthma services in the private sector in Khartoum. Design The research design was constructed using an explanatory sequential mixed method Social Ecological approach (Creswell, 2013). This approach was used to examine the influencing factors of asthma service utilisation in the private sector by considering the five nested, hierarchical levels: individual, familial/interpersonal, community, organisational, and policy/enabling environment. The quantitative research was conducted using a health facility survey of private hospitals, private chest clinics, and pharmacies, in order to describe the asthma services available. This was followed by qualitative research using in-depth interviews with asthma patients who use the private sector, to explore decision-making around facility use and asthma health care seeking behaviour in more detail. Findings The quantitative survey found low rates of spirometers and peak flow meters were available in private hospitals (28% and 33%, respectively). There was very little asthma-specific training for providers and little use of asthma treatment cards and registers. However, the qualitative interviews found that the quality of care in the private sector was viewed as better than in the public sector, with shorter waiting times and better hygiene levels. Patients sought frequent, short-term care at private facilities for acute attacks (predominately in hospital emergency rooms) rather than long-term management of their condition as outpatients. The severity of the disease and the major impact it had, particularly on younger adults’ lives, was striking. Stigma and misconceptions about the disease by the community was expressed strongly particularly by younger women and altered how they sought care and how they interacted with people in their social network and beyond. Conclusion The Social Ecological approach facilitated an in depth understanding of the barriers and enablers of effective care. Effective asthma case management requires input at all levels of service provision: inclusive health policy and government commitment, high quality service delivery, an uninterrupted affordable drug supply, community involvement in care and patient empowerment. Encouraging stakeholders across the different levels of influence to implement this holistic model of asthma case management across both the public and private sector has the potential to lead to a reduction in emergency room admissions, less severe asthma attacks, a reduction in asthma related stigma and less fear of social rejection and concern for the patients