Comparison of T-cell receptor diversity of people with myalgic encephalomyelitis versus controls.

OBJECTIVE: Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from other fatiguing illnesses by the experience of post-exertional malaise, the worsening of symptoms even after minor physical or mental exertion. Its frequent onset after infection suggests autoimmune involvement or that it arises from abnormal T-cell activation. RESULTS: To test this hypothesis, we sequenced the genomic loci of α/δ, ß and γ T-cell receptors (TCR) from 40 human blood samples from each of four groups: severely affected people with ME; mildly or moderately affected people with ME; people diagnosed with Multiple Sclerosis, as disease controls; and, healthy controls. Seeking to automatically classify these individuals' samples by their TCR repertoires, we applied P-SVM, a machine learning method. However, despite working well on a simulated data set, this approach did not allow statistically significant partitioning of samples into the four subgroups. Our findings do not support the hypothesis that blood samples from people with ME frequently contain altered T-cell receptor diversity.

Prehospital Ultrasound Diagnosis of Massive Pulmonary Embolism by Non-Physicians: A Case Series.

Massive pulmonary embolism (hemodynamically unstable, defined as systolic BP <90 mmHg) has significant morbidity and mortality. Point of care ultrasound (POCUS) has allowed clinicians to detect evidence of massive pulmonary embolism much earlier in the patient's clinical course, especially when patient instability precludes computerized tomography confirmation. POCUS detection of massive pulmonary embolism has traditionally been performed by physicians. This case series demonstrates four cases of massive pulmonary embolism diagnosed with POCUS performed by non-physician prehospital personnel.

A global call for action to include gender in research impact assessment.

Global investment in biomedical research has grown significantly over the last decades, reaching approximately a quarter of a trillion US dollars in 2010. However, not all of this investment is distributed evenly by gender. It follows, arguably, that scarce research resources may not be optimally invested (by either not supporting the best science or by failing to investigate topics that benefit women and men equitably). Women across the world tend to be significantly underrepresented in research both as researchers and research participants, receive less research funding, and appear less frequently than men as authors on research publications. There is also some evidence that women are relatively disadvantaged as the beneficiaries of research, in terms of its health, societal and economic impacts. Historical gender biases may have created a path dependency that means that the research system and the impacts of research are biased towards male researchers and male beneficiaries, making it inherently difficult (though not impossible) to eliminate gender bias. In this commentary, we - a group of scholars and practitioners from Africa, America, Asia and Europe - argue that gender-sensitive research impact assessment could become a force for good in moving science policy and practice towards gender equity. Research impact assessment is the multidisciplinary field of scientific inquiry that examines the research process to maximise scientific, societal and economic returns on investment in research. It encompasses many theoretical and methodological approaches that can be used to investigate gender bias and recommend actions for change to maximise research impact. We offer a set of recommendations to research funders, research institutions and research evaluators who conduct impact assessment on how to include and strengthen analysis of gender equity in research impact assessment and issue a global call for action.

Violation of the 12/23 rule of genomic V(D)J recombination is common in lymphocytes.

V(D)J genomic recombination joins single gene segments to encode an extensive repertoire of antigen receptor specificities in T and B lymphocytes. This process initiates with double-stranded breaks adjacent to conserved recombination signal sequences that contain either 12- or 23-nucleotide spacer regions. Only recombination between signal sequences with unequal spacers results in productive coding genes, a phenomenon known as the "12/23 rule." Here we present two novel genomic tools that allow the capture and analysis of immune locus rearrangements from whole thymic and splenic tissues using second-generation sequencing. Further, we provide strong evidence that the 12/23 rule of genomic recombination is frequently violated under physiological conditions, resulting in unanticipated hybrid recombinations in ∼10% of Tcra excision circles. Hence, we demonstrate that strict adherence to the 12/23 rule is intrinsic neither to recombination signal sequences nor to the catalytic process of recombination and propose that nonclassical excision circles are liberated during the formation of antigen receptor diversity.

Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA.

New sequencing technologies can address diverse biomedical questions but are limited by a minimum required DNA input of typically 1 µg. We describe how sequencing libraries can be reproducibly created from 20 pg of input DNA using a modified transpososome-mediated fragmentation technique. Resulting libraries incorporate in-line bar-coding, which facilitates sample multiplexes that can be sequenced using Illumina platforms with the manufacturer's sequencing primer. We demonstrate this technique by providing deep coverage sequence of the Escherichia coli K-12 genome that shows equivalent target coverage to a 1-µg input library prepared using standard Illumina methods. Reducing template quantity does, however, increase the proportion of duplicate reads and enriches coverage in low-GC regions. This finding was confirmed with exhaustive resequencing of a mouse library constructed from 20 pg of gDNA input (about seven haploid genomes) resulting in ∼0.4-fold statistical coverage of uniquely mapped fragments. This implies that a near-complete coverage of the mouse genome is obtainable with this approach using 20 genomes as input. Application of this new method now allows genomic studies from low mass samples and routine preparation of sequencing libraries from enrichment procedures.

Reactivity and reactions to regulatory transparency in medicine, psychotherapy and counselling.

We explore how doctors, psychotherapists and counsellors in the U.K. react to regulatory transparency, drawing on qualitative research involving 51 semi-structured interviews conducted during 2008-10. We use the concept of 'reactivity mechanisms' (Espeland & Sauder, 2007) to explain how regulatory transparency disrupts practices through simplifying and decontextualizing them, altering practitioners' reflexivity, leading to defensive forms of practice. We make an empirical contribution by exploring the impact of transparency on doctors compared with psychotherapists and counsellors, who represent an extreme case due to their uniquely complex practice, which is particularly affected by this form of regulation. We make a contribution to knowledge by developing a model of reactivity mechanisms, which explains how clinical professionals make sense of media and professional narratives about regulation in ways that produce emotional reactions and, in turn, defensive reactivity to transparency.