Expressing the human proteome for affinity proteomics: optimising expression of soluble protein domains and in vivo biotinylation

The generation of affinity reagents to large numbers of human proteins depends on the ability to express the target proteins as high-quality antigens. The Structural Genomics Consortium (SGC) focuses on the production and structure determination of human proteins. In a 7-year period, the SGC has deposited crystal structures of >800 human protein domains, and has additionally expressed and purified a similar number of protein domains that have not yet been crystallised. The targets include a diversity of protein domains, with an attempt to provide high coverage of protein families. The family approach provides an excellent basis for characterising the selectivity of affinity reagents. We present a summary of the approaches used to generate purified human proteins or protein domains, a test case demonstrating the ability to rapidly generate new proteins, and an optimisation study on the modification of >70 proteins by biotinylation in vivo. These results provide a unique synergy between large-scale structural projects and the recent efforts to produce a wide coverage of affinity reagents to the human proteome

Beyond Undetectable: Modeling the Clinical Benefit of Improved Antiretroviral Adherence in Persons With Human Immunodeficiency Virus With Virologic Suppression

BACKGROUND: Incomplete antiretroviral therapy (ART) adherence has been linked to deleterious immunologic, inflammatory, and clinical consequences, even among virally suppressed (<50 copies/mL) persons with human immunodeficiency virus (PWH). The impact of improving adherence in the risk of severe non-AIDS events (SNAEs) and death in this population is unknown. METHODS: We estimated the reduction in the risk of SNAEs or death resulting from an increase in ART adherence by (1) applying existing data on the association between adherence with high residual inflammation/coagulopathy in virally suppressed PWH, and (2) using a Cox proportional hazards model derived from changes in plasma interleukin 6 (IL-6) and D-dimer from 3 randomized clinical trials. Comparatively, assuming 100% ART adherence in a PWH who achieves viral suppression, we estimated the number of persons in whom a decrease in adherence to <100% would need to be observed for an additional SNAE or death event to occur during 3- and 5-year follow-up. RESULTS: Increasing ART adherence to 100% in PWH who are suppressed on ART despite imperfect adherence translated into a 6%-37% reduction in the risk of SNAEs or death. Comparatively, based on an anticipated 12% increase in IL-6, 254 and 165 PWH would need to decrease their adherence from 100% to <100% for an additional event to occur over 3- and 5-year follow-up, respectively. CONCLUSIONS: Modest gains in ART adherence could have clinical benefits beyond virologic suppression. Increasing ART adherence (eg, via an intervention or switch to long-acting ART) in PWH who remain virally suppressed despite incomplete adherence should be evaluated

Immunochip analysis identifies multiple susceptibility loci for systemic sclerosis

In this study, 1,833 systemic sclerosis (SSc) cases and 3,466 controls were genotyped with the Immunochip array. Classical alleles, amino acid residues, and SNPs across the human leukocyte antigen (HLA) region were imputed and tested. These analyses resulted in a model composed of six polymorphic amino acid positions and seven SNPs that explained the observed significant associations in the region. In addition, a replication step comprising 4,017 SSc cases and 5,935 controls was carried out for several selected non-HLA variants, reaching a total of 5,850 cases and 9,401 controls of European ancestry. Following this strategy, we identified and validated three SSc risk loci, including DNASE1L3 at 3p14, the SCHIP1-IL12A locus at 3q25, and ATG5 at 6q21, as well as a suggested association of the TREH-DDX6 locus at 11q23. The associations of several previously reported SSc risk loci were validated and further refined, and the observed peak of association in PXK was related to DNASE1L3. Our study has increased the number of known genetic associations with SSc, provided further insight into the pleiotropic effects of shared autoimmune risk factors, and highlighted the power of dense mapping for detecting previously overlooked susceptibility loci

EBM in primary care: a qualitative multicenter study in Spain

<p>Abstract</p> <p>Background</p> <p>Evidence based medicine (EBM) has made a substantial impact on primary care in Spain over the last few years. However, little research has been done into family physicians (FPs)' attitudes related to EBM. The present study investigates FPs' perceptions of EBM in the primary care context.</p> <p>Methods</p> <p>This study used qualitative methodology. Information was obtained from 8 focus groups composed of 67 FPs from 47 health centers in 4 autonomous regions in Spain. Intentional sampling considered participants' previous education in EBM, and their experience as tutors in family medicine or working groups' members of the Spanish Society of Family Practice. Sociological discourse analysis was used with the support of the MAXqda software. Results were validated by means of triangulation among researchers and contrast with participants.</p> <p>Results</p> <p>Findings were grouped into three main areas: 1) The tug-of-war between the "science" of EBM and "experience" in the search for good clinical practice in primary care; 2) The development of EBM sensemaking as a reaction to contextual factors and interests; 3) The paradox of doubt and trust in the new EBM experts.</p> <p>The meaning of EBM was dynamically constructed within the primary care context. FPs did not consider good clinical practice was limited to the vision of science that EBM represents. Its use appeared to be conditioned by several factors that transcended the common concept of barriers. Along with concerns about its objectivity, participants showed a tendency to see EBM as the use of simplified guidelines developed by EBM experts.</p> <p>Conclusions</p> <p>The identification of science with EBM and its recognition as a useful but insufficient tool for the good clinical practice requires rethinking new meanings of evidence within the primary care reality. Beyond the barriers related to accessing and putting into practice the EBM, its reactive use can determine FPs' questions and EBM development in a direction not always centred on patients' needs. The questioning of experts' authority as a pillar of EBM could be challenged by the emergence of new kinds of EBM texts and experts to believe in.</p

Perceptions, attitudes and knowledge of evidence-based medicine in primary care in Spain: a study protocol

<p>Abstract</p> <p>Background</p> <p>The philosophy of evidence-based medicine (EBM) was introduced in the early 90s as a new approach to the practice of medicine, using the best available evidence to make decisions about health care. Despite ongoing controversy, EBM has developed enormously and physicians' attitude towards it is generally positive. Nevertheless, in Spain little is known about this topic. We will therefore undertake a study to explore perceptions, attitudes and knowledge about EBM among primary care physicians.</p> <p>Methods and design</p> <p>A mixed-method study combining qualitative and quantitative designs will target family practitioners in Spain with the objective of evaluating current attitudes and perceptions about evidence-based medicine. The project will consist of two phases: a first phase running focus groups to identify perceptions and attitudes of participants, and a second phase assessing their attitudes and knowledge about EBM by means of a survey. Both phases will explore these issues in three different subgroups: family practitioners, with or without previous formal education in EBM; members of working groups that formulate healthcare recommendations; and physicians in charge of training family practice residents. Additionally, we will undertake a systematic review to identify and synthesize the available evidence on this topic.</p> <p>Discussion</p> <p>The study will identify and gain insight into the perceived problems and barriers to the practice of evidence-based medicine among general practitioners in Spain. The project will also evaluate the main knowledge gaps and training needs, and explore how evidence-based medicine is being taught to family medicine residents, the medical practitioners of the future. Our results will aid researchers and health care planners in developing strategies to improve the practice of evidence-based medicine in our country.</p

The clinical effectiveness of individual behaviour change interventions to reduce risky sexual behaviour after a negative human immunodeficiency virus test in men who have sex with men: systematic and realist reviews and intervention development

Background: Men who have sex with men (MSM) experience significant inequalities in health and well-being. They are the group in the UK at the highest risk of acquiring a human immunodeficiency virus (HIV) infection. Guidance relating to both HIV infection prevention, in general, and individual-level behaviour change interventions, in particular, is very limited. Objectives: To conduct an evidence synthesis of the clinical effectiveness of behaviour change interventions to reduce risky sexual behaviour among MSM after a negative HIV infection test. To identify effective components within interventions in reducing HIV risk-related behaviours and develop a candidate intervention. To host expert events addressing the implementation and optimisation of a candidate intervention. Data sources: All major electronic databases (British Education Index, BioMed Central, Cumulative Index to Nursing and Allied Health Literature, EMBASE, Educational Resource Index and Abstracts, Health and Medical Complete, MEDLINE, PsycARTICLES, PsycINFO, PubMed and Social Science Citation Index) were searched between January 2000 and December 2014. Review methods: A systematic review of the clinical effectiveness of individual behaviour change interventions was conducted. Interventions were examined using the behaviour change technique (BCT) taxonomy, theory coding assessment, mode of delivery and proximity to HIV infection testing. Data were summarised in narrative review and, when appropriate, meta-analysis was carried out. Supplemental analyses for the development of the candidate intervention focused on post hoc realist review method, the assessment of the sequential delivery and content of intervention components, and the social and historical context of primary studies. Expert panels reviewed the candidate intervention for issues of implementation and optimisation. Results: Overall, trials included in this review (n = 10) demonstrated that individual-level behaviour change interventions are effective in reducing key HIV infection risk-related behaviours. However, there was considerable clinical and methodological heterogeneity among the trials. Exploratory meta-analysis showed a statistically significant reduction in behaviours associated with high risk of HIV transmission (risk ratio 0.75, 95% confidence interval 0.62 to 0.91). Additional stratified analyses suggested that effectiveness may be enhanced through face-to-face contact immediately after testing, and that theory-based content and BCTs drawn from ‘goals and planning’ and ‘identity’ groups are important. All evidence collated in the review was synthesised to develop a candidate intervention. Experts highlighted overall acceptability of the intervention and outlined key ways that the candidate intervention could be optimised to enhance UK implementation. Limitations: There was a limited number of primary studies. All were from outside the UK and were subject to considerable clinical, methodological and statistical heterogeneity. The findings of the meta-analysis must therefore be treated with caution. The lack of detailed intervention manuals limited the assessment of intervention content, delivery and fidelity. Conclusions: Evidence regarding the effectiveness of behaviour change interventions suggests that they are effective in changing behaviour associated with HIV transmission. Exploratory stratified meta-analyses suggested that interventions should be delivered face to face and immediately after testing. There are uncertainties around the generalisability of these findings to the UK setting. However, UK experts found the intervention acceptable and provided ways of optimising the candidate intervention. Future work: There is a need for well-designed, UK-based trials of individual behaviour change interventions that clearly articulate intervention content and demonstrate intervention fidelity

GABAA receptor subtype involvement in addictive behaviour

GABAA receptors form the major class of inhibitory neurotransmitter receptors in the mammalian brain. This review sets out to summarise the evidence that variations in genes encoding GABAA receptor isoforms are associated with aspects of addictive behaviour in humans, while animal models of addictive behaviour also implicate certain subtypes of GABAA receptor. In addition to outlining the evidence for the involvement of specific subtypes in addiction, we summarise the particular contributions of these isoforms in control over the functioning of brain circuits, especially the mesolimbic system, and make a first attempt to bring together evidence from several fields to understanding potential involvement of GABAA Receptor Subtypes in addictive behaviour. While the weight of the published literature is on alcohol dependency, the underlying principles outlined are relevant across a number of different aspects of addictive behaviour

Homologous recombination DNA repair defects in PALB2- associated breast cancers

Abstract: Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD

Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation

Objectives: No randomized controlled trials have yet reported an individual patient benefit of initiating combination antiretroviral therapy (cART) at CD4 counts > 350 cells/μL. It is hypothesized that earlier initiation of cART in asymptomatic and otherwise healthy individuals may lead to poorer adherence and subsequently higher rates of resistance development. Methods: In a large cohort of HIV-positive individuals, we investigated the emergence of new resistance mutations upon virological treatment failure according to the CD4 count at the initiation of cART. Results: Of 7918 included individuals, 6514 (82.3%), 996 (12.6%) and 408 (5.2%) started cART with a CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Virological rebound occurred while on cART in 488 (7.5%), 46 (4.6%) and 30 (7.4%) with a baseline CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Only four (13.0%) individuals with a baseline CD4 count > 350 cells/μL in receipt of a resistance test at viral load rebound were found to have developed new resistance mutations. This compared to 107 (41.2%) of those with virological failure who had initiated cART with a CD4 count < 350 cells/μL. Conclusions: We found no evidence of increased rates of resistance development when cART was initiated at CD4 counts above 350 cells/μL. HIV Medicin

Identity Work and Organizational Identification

In this paper, I analyse five approaches to identity work - discursive, dramaturgical, symbolic, socio-cognitive, and psychodynamic - and show how these are helpful in exploring the ways people draw on their membership of organizations in their constructions of self, processes generally referred to as organizational identification. Collectively, these approaches constitute a distinctive perspective on identities and identifications which suggests that they are ‘worked on’ by embedded social actors who are both constrained and enabled by context. In so doing, I draw attention to issues of agency and process, the always dynamic and complex, often fractured, and sometimes contradictory nature of identities and identifications, and raise a series of issues and questions for further research