A Critical Context-Dependent Role for E Boxes in the Targeting of Somatic Hypermutation

Secondary B cell repertoire diversification occurs by somatic hypermutation (SHM) in germinal centers following Ag stimulation. In SHM, activation-induced cytidine deaminase mutates the V region of the Ig genes to increase the affinity of Abs. Although SHM acts primarily at Ig loci, low levels of off-target mutation can result in oncogenic DNA damage, illustrating the importance of understanding SHM targeting mechanisms. A candidate targeting motif is the E box, a short DNA sequence (CANNTG) found abundantly in the genome and in many SHM target genes. Using a reporter assay in chicken DT40 B cells, we previously identified a 1928-bp portion of the chicken IgL locus capable of supporting robust SHM. In this article, we demonstrate that mutation of all 20 E boxes in this fragment reduces SHM targeting activity by 90%, and that mutation of subsets of E boxes reveals a functional hierarchy in which E boxes within "core" targeting regions are of greatest importance. Strikingly, when the sequence and spacing of the 20 E boxes are preserved but surrounding sequences are altered, SHM targeting activity is eliminated. Hence, although E boxes are vital SHM targeting elements, their function is completely dependent on their surrounding sequence context. These results suggest an intimate cooperation between E boxes and other sequence motifs in SHM targeting to Ig loci and perhaps also in restricting mistargeting to certain non-Ig loci

Data-as-a-Service Platform for Delivering Healthy Lifestyle and Preventive Medicine: Concept and Structure of the DAPHNE Project

Background: Overweight and obesity is related to many health problems and diseases. The current obesity epidemic, which is a major health problem, is closely related to a lack of physical activity, high levels of sedentary behavior, and increased energy intake; with evidence to show increasing incidence of these issues in the younger population. Tackling obesity and its comorbid conditions requires a holistic approach encompassing attention on physical activity, healthy diet, and behavioral activation in order to enable and maintain meaningful and long-term weight loss and weight maintenance. Objective: The objective of the Data-as-a-Service Platform for Healthy Lifestyle and Preventive Medicine (DAPHNE) project is to develop a breakthrough information communications technology (ICT) platform for tracking health, weight, physical activity, diet, lifestyle, and psychological components within health care systems, whereby the platform and clinical support is linked. Methods: The DAPHNE platform aims to deliver personalized guidance services for lifestyle management to the citizen/patient by means of (1) advanced sensors and mobile phone apps to acquire and store continuous/real-time data on lifestyle aspects, behavior, and surrounding environment; (2) individual models to monitor their health and fitness status; (3) intelligent data processing for the recognition of behavioral trends; and (4) specific services for personalized guidance on healthy lifestyle and disease prevention. It is well known that weight loss and maintenance of weight loss are particularly difficult. This tool will address some of the issues found with conventional treatment/advice in that it will collect data in real time, thereby reducing reliability issues known with recalling events once they have passed and will also allow adjustment of behavior through timely support and recommendations sent through the platform without the necessity of formal one-to-one visits between patient and clinician. Patient motivation/compliance is a particular issue with conventional weight loss regimes; DAPHNE aims to increase the individuals’ awareness of their own behavior and fosters their accountability. Results: The project has been funded and the research work has started. Results for the validation of the different components is due imminently. Conclusions: In contrast with previous existing solutions, the DAPHNE project tackles the obesity problem from a clinical point of view, designing the different interfaces for its use by patients (adults and children), physicians, and caregivers. A specific design for children and adolescent patients treated for obesity has been followed, guided by pediatric physicians at hospitals in Europe. The final clinical validation of the DAPHNE platform will be carried out in different European hospitals, testing the platform in both adolescents and adults

Novel Role of Y1 Receptors in the Coordinated Regulation of Bone and Energy Homeostasis

The importance of neuropeptide Y (NPY) and Y2 receptors in the regulation of bone and energy homeostasis has recently been demonstrated. However, the contributions of the other Y recep- tors are less clear. Here we show that Y1 receptors are expressed on osteoblastic cells. Moreover, bone and adipose tissue mass are elevated in Y1/ mice with a generalized increase in bone formation on cortical and cancellous surfaces. Importantly, the inhibitory effects of NPY on bone marrow stromal cells in vitro are absent in cells derived from Y1/ mice, indicating a direct action of NPY on bone cells via this Y receptor. Interestingly, in contrast to Y2 receptor or germ line Y1 receptor deletion, con- ditional deletion of hypothalamic Y1 receptors in adult mice did not alter bone homeostasis, food intake, or adiposity. Further- more, deletion of both Y1 and Y2 receptors did not produce additive effects in bone or adiposity. Thus Y1 receptor pathways act powerfully to inhibit bone production and adiposity by non- hypothalamic pathways, with potentially direct effects on bone tissue through a single pathway with Y2 receptors

A new twist on the geometry of gravitational plane waves

The geometry of twisted null geodesic congruences in gravitational plane wave spacetimes is explored, with special focus on homogeneous plane waves. The role of twist in the relation of the Rosen coordinates adapted to a null congruence with the fundamental Brinkmann coordinates is explained and a generalised form of the Rosen metric describing a gravitational plane wave is derived. The Killing vectors and isometry algebra of homogeneous plane waves (HPWs) are described in both Brinkmann and twisted Rosen form and used to demonstrate the coset space structure of HPWs. The van Vleck-Morette determinant for twisted congruences is evaluated in both Brinkmann and Rosen descriptions. The twisted null congruences of the Ozsvath-Schucking,`anti-Mach' plane wave are investigated in detail. These developments provide the necessary geometric toolkit for future investigations of the role of twist in loop effects in quantum field theory in curved spacetime, where gravitational plane waves arise generically as Penrose limits; in string theory, where they are important as string backgrounds; and potentially in the detection of gravitational waves in astronomy.Comment: 60 pages, 2 figures. Extended version with new material on Rosen geodesics and isometries. Title change

A review of reporting of participant recruitment and retention in RCTs in six major journals

<p>Abstract</p> <p>Background</p> <p>Poor recruitment and retention of participants in randomised controlled trials (RCTs) is problematic but common. Clear and detailed reporting of participant flow is essential to assess the generalisability and comparability of RCTs. Despite improved reporting since the implementation of the CONSORT statement, important problems remain. This paper aims: (i) to update and extend previous reviews evaluating reporting of participant recruitment and retention in RCTs; (ii) to quantify the level of participation throughout RCTs.</p> <p>Methods</p> <p>We reviewed all reports of RCTs of health care interventions and/or processes with individual randomisation, published July–December 2004 in six major journals. Short, secondary or interim reports, and Phase I/II trials were excluded. Data recorded were: general RCT details; inclusion of flow diagram; participant flow throughout trial; reasons for non-participation/withdrawal; target sample sizes.</p> <p>Results</p> <p>133 reports were reviewed. Overall, 79% included a flow diagram, but over a third were incomplete. The majority reported the flow of participants at each stage of the trial after randomisation. However, 40% failed to report the numbers assessed for eligibility. Percentages of participants retained at each stage were high: for example, 90% of eligible individuals were randomised, and 93% of those randomised were outcome assessed. On average, trials met their sample size targets. However, there were some substantial shortfalls: for example 21% of trials reporting a sample size calculation failed to achieve adequate numbers at randomisation, and 48% at outcome assessment. Reporting of losses to follow up was variable and difficult to interpret.</p> <p>Conclusion</p> <p>The majority of RCTs reported the flow of participants well after randomisation, although only two-thirds included a complete flow chart and there was great variability over the definition of "lost to follow up". Reporting of participant eligibility was poor, making assessments of recruitment practice and external validity difficult. Reporting of participant flow throughout RCTs could be improved by small changes to the CONSORT chart.</p

Dynamics of conflicts in Wikipedia

In this work we study the dynamical features of editorial wars in Wikipedia (WP). Based on our previously established algorithm, we build up samples of controversial and peaceful articles and analyze the temporal characteristics of the activity in these samples. On short time scales, we show that there is a clear correspondence between conflict and burstiness of activity patterns, and that memory effects play an important role in controversies. On long time scales, we identify three distinct developmental patterns for the overall behavior of the articles. We are able to distinguish cases eventually leading to consensus from those cases where a compromise is far from achievable. Finally, we analyze discussion networks and conclude that edit wars are mainly fought by few editors only.Comment: Supporting information adde

The challenges faced in the design, conduct and analysis of surgical randomised controlled trials

Randomised evaluations of surgical interventions are rare; some interventions have been widely adopted without rigorous evaluation. Unlike other medical areas, the randomised controlled trial (RCT) design has not become the default study design for the evaluation of surgical interventions. Surgical trials are difficult to successfully undertake and pose particular practical and methodological challenges. However, RCTs have played a role in the assessment of surgical innovations and there is scope and need for greater use. This article will consider the design, conduct and analysis of an RCT of a surgical intervention. The issues will be reviewed under three headings: the timing of the evaluation, defining the research question and trial design issues. Recommendations on the conduct of future surgical RCTs are made. Collaboration between research and surgical communities is needed to address the distinct issues raised by the assessmentof surgical interventions and enable the conduct of appropriate and well-designed trials.The Health Services Research Unit is funded by the Scottish Government Health DirectoratesPeer reviewedPublisher PD

Spike-Timing Precision and Neuronal Synchrony Are Enhanced by an Interaction between Synaptic Inhibition and Membrane Oscillations in the Amygdala

The basolateral complex of the amygdala (BLA) is a critical component of the neural circuit regulating fear learning. During fear learning and recall, the amygdala and other brain regions, including the hippocampus and prefrontal cortex, exhibit phase-locked oscillations in the high delta/low theta frequency band (∼2–6 Hz) that have been shown to contribute to the learning process. Network oscillations are commonly generated by inhibitory synaptic input that coordinates action potentials in groups of neurons. In the rat BLA, principal neurons spontaneously receive synchronized, inhibitory input in the form of compound, rhythmic, inhibitory postsynaptic potentials (IPSPs), likely originating from burst-firing parvalbumin interneurons. Here we investigated the role of compound IPSPs in the rat and rhesus macaque BLA in regulating action potential synchrony and spike-timing precision. Furthermore, because principal neurons exhibit intrinsic oscillatory properties and resonance between 4 and 5 Hz, in the same frequency band observed during fear, we investigated whether compound IPSPs and intrinsic oscillations interact to promote rhythmic activity in the BLA at this frequency. Using whole-cell patch clamp in brain slices, we demonstrate that compound IPSPs, which occur spontaneously and are synchronized across principal neurons in both the rat and primate BLA, significantly improve spike-timing precision in BLA principal neurons for a window of ∼300 ms following each IPSP. We also show that compound IPSPs coordinate the firing of pairs of BLA principal neurons, and significantly improve spike synchrony for a window of ∼130 ms. Compound IPSPs enhance a 5 Hz calcium-dependent membrane potential oscillation (MPO) in these neurons, likely contributing to the improvement in spike-timing precision and synchronization of spiking. Activation of the cAMP-PKA signaling cascade enhanced the MPO, and inhibition of this cascade blocked the MPO. We discuss these results in the context of spike-timing dependent plasticity and modulation by neurotransmitters important for fear learning, such as dopamine