Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology

Evidence suggests that innate and adaptive cellular responses mediate resistance to the influenza virus and confer protection after vaccination. However, few studies have resolved the contribution of cellular responses within the context of preexisting antibody titers. Here, we measured the peripheral immune profiles of 206 vaccinated or unvaccinated adults to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza. Protection correlated with diverse and polyfunctional CD4+ and CD8+ T, circulating T follicular helper, T helper type 17, myeloid dendritic and CD16+ natural killer (NK) cell subsets. Conversely, increased susceptibility was predominantly attributed to nonspecific inflammatory populations, including γδ T cells and activated CD16- NK cells, as well as TNFα+ single-cytokine-producing CD8+ T cells. Multivariate and predictive modeling indicated that cellular subsets (1) work synergistically with humoral immunity to confer protection, (2) improve model performance over demographic and serologic factors alone and (3) comprise the most important predictive covariates. Together, these results demonstrate that preinfection peripheral cell composition improves the prediction of symptomatic influenza susceptibility over vaccination, demographics or serology alone.

Circulation of influenza and other respiratory viruses during the COVID-19 pandemic in Australia and New Zealand, 2020-2021

Objective

Circulation patterns of influenza and other respiratory viruses have been globally disrupted since the emergence of coronavirus disease (COVID-19) and the introduction of public health and social measures (PHSMs) aimed at reducing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission.

Methods

We reviewed respiratory virus laboratory data, Google mobility data and PHSMs in five geographically diverse regions in Australia and New Zealand. We also described respiratory virus activity from January 2017 to August 2021.

Results

We observed a change in the prevalence of circulating respiratory viruses following the emergence of SARS-CoV-2 in early 2020. Influenza activity levels were very low in all regions, lower than those recorded in 2017-2019, with less than 1% of laboratory samples testing positive for influenza virus. In contrast, rates of human rhinovirus infection were increased. Respiratory syncytial virus (RSV) activity was delayed; however, once it returned, most regions experienced activity levels well above those seen in 2017-2019. The timing of the resurgence in the circulation of both rhinovirus and RSV differed within and between the two countries.

Discussion

The findings of this study suggest that as domestic and international borders are opened up and other COVID-19 PHSMs are lifted, clinicians and public health professionals should be prepared for resurgences in influenza and other respiratory viruses. Recent patterns in RSV activity suggest that these resurgences in non-COVID-19 viruses have the potential to occur out of season and with increased impact.

Posterior Shoulder Instability in Tennis Players: Aetiology, Classification, Assessment and Management

Background

Micro-traumatic posterior shoulder instability (PSI) is an often missed and misdiagnosed pathology presenting in tennis players. The aetiology of micro-traumatic PSI in tennis players is multifactorial, including congenital factors, loss of strength and motor control, and sport-specific repetitive microtrauma. Repetitive forces placed on the dominant shoulder, particularly combinations of flexion, horizontal adduction, and internal rotation contribute to the microtrauma. These positions are characteristic for kick serves, backhand volleys, and the follow-through phase of forehands and serves. The aim of this clinical commentary is to present an overview of the aetiology, classification, clinical presentation, and treatment of micro-traumatic PSI, with a particular focus on tennis players.

Level of Evidence

5.

Safe Prescribing Practices: Clinicians' Views on Prescribing Opioids to Patients With Early-Stage Cancer

PURPOSE

Opioids are often necessary for patients experiencing high-intensity pain. However, side effects exist and some patients may misuse opioids. To better understand how opioids are prescribed to patients with early-stage cancer and how to enhance opioid safety, clinicians' views of opioid prescribing were explored.

METHODS

This was a qualitative inquiry including any Alberta clinician prescribing opioids to patients with early-stage cancer. Semistructured interviews were conducted with nurse practitioners (NP), medical oncologists (MO), radiation oncologists (RO), surgeons (S), primary care physicians (PCP), and palliative care physicians (PC) between June 2021 and March 2022. Interpretive description was used to analyze the data using two coders (C.C. and T.W.). Debriefing sessions were used to resolve and discrepancies.

RESULTS

Twenty-four clinicians were interviewed (NP [n = 5], MO [n = 4], RO [n = 4], S [n = 5], PCP [n = 3], and PC [n = 3]). The majority had been in practice at least 10 years. Prescribing practices were related to disciplinary perspective, goals of care, patient condition, and resource availability. Most clinicians did not see opioid misuse as a problem but were aware that specific patient risk factors are present and that long-term use can be problematic. Most clinicians undertake safe prescribing approaches tacitly (eg, screening for past opioid misuse and reviewing number of prescribers) and not all agreed they should be universally applied. Barriers (eg, procedural and time) and facilitators (eg, education) to safe prescribing approaches were identified.

CONCLUSION

To enhance uptake and cross-disciplinary consistency of safe prescribing approaches, clinician education regarding opioid misuse and benefits of safe prescribing practices, and addressing procedural barriers are necessary.

Characterization of a novel exonic deletion in the GALNS gene causing Morquio A syndrome

Mucopolysaccharidosis IVA or Morquio A syndrome is a rare lysosomal storage disorder caused by N-acetylgalactosamine-6-sulfatase deficiency. A diagnosis can be provided by the identification of reduced N-acetylgalactosamine-6-sulfatase activity as well as detection of compound heterozygous or homozygous pathogenic variants in GALNS. We present a case of two sisters of healthy non-consanguineous parents with a severe classical phenotype of Morquio A syndrome. Both patients were found to carry a novel homozygous deletion of exon 9, which was initially suspected by next generation sequencing (NGS) due to lack of coverage, but could not be confirmed by this methodology. Therefore, an allele specific polymerase chain reaction assay was designed to confirm the exon 9 deletion and determine the precise deletion breakpoints (c.899-397_1003-1862del) for our patients. Recognizing limitations of molecular testing is important to ensure proper diagnosis and subsequent treatment for individuals with Morquio A syndrome.

Examining the adaptability and validity of interRAI acute care quality indicators in a surgical context

Background:

Currently, the use of quality indicators in the surgical setting may be challenged by diverse patient needs, clinical complexity, and health trajectories. Therefore, the objective of this study was to examine the adaptability of existing quality indicators to a surgical context and propose new time points.

Methods:

A multi-method approach included an environmental scan of the literature, consultation with multinational experts, and analysis of surgical patient data. Quality indicators from the nurse-administered interRAI Acute Care instrument were examined within a surgical context using secondary data from a hospital in Brisbane, Australia (N = 1006 surgical cases).

Results:

A lack of relevancy of existing time points can preclude meaningful quality indicator measurement. Definitions of some quality indicators were adapted to ensure relevancy for the surgical population. As well, a surgical baseline (measured preoperative and post-injury) and a 48-h postoperative time point were added to the existing measurement timeline.

Conclusion:

Distinct measurement timelines were created for elective and non-elective surgical patients. The use of surgery-specific time points that can be embedded into an existing Acute Care measurement framework supports consistent quality indicator reporting. This study represents the first steps towards standardized quality reporting for health information systems across different care settings.

Increasing experience with the LIFT procedure in Crohn's disease patients with complex anal fistula

BACKGROUND

Surgical management of anal fistulas in Crohn's disease (CD) is associated with high failure rates, and treatment options are limited due to ongoing proctitis, multiple tracts, and concern for incontinence and non-healing wounds. The aim of this study was to investigate the healing rate of ligation of the inters-sphincteric fistula tract (LIFT) for anal fistulas in Crohn's disease and identify prognostic factors for healing.

METHODS

This prospective analysis compared long-term healing rates of CD patients undergoing LIFT for anal fistulas. Consecutive patients with CD who underwent LIFT procedure at our institution, in the period from March 2012 to September 2019 were included. The main outcome was anal fistula healing rate.

RESULTS

The study cohort of 46 patients (mean age of 34.2 ± 13.0 years, 18 (40%) males). After a mean follow-up time of 33 ± 28 months, fistula healing was seen in 30 (65%) patients. A total of 8 patients were noted to have inter-sphincteric recurrence and 8 patients had trans-sphincteric recurrence. Smoking at the time of surgery was significantly associated with LIFT failure (HR 3.18, 95% CI 1.18-8.61, p = 0.02). Other factors, such as age, sex, race, disease duration and location, type of fistula history of proctitis, preoperatively use of biologics or a seton, and previous repair attempts, did not appear to influence LIFT healing. Although not statistically significant, there was a trend toward increase in failure among patients with active proctitis at the time of surgery (HR 1.97, 95% CI 0.71-5.42, p = 0.19).

CONCLUSION

Our increasing experience with LIFT for anal fistula in CD demonstrates a higher rate of healing (65%) than previously reported (48%). Smoking appears to negatively influence healing of LIFT in CD.

Cardiac rehabilitation program: An exploration of patient experiences and perspectives on program dropout

Background

Cardiac rehabilitation programs (CRP) are effective evidence‐based secondary prevention programs that reduce morbidity and mortality in patients with cardiovascular disease (CVD). However, participation remains suboptimal, resulting in under‐treatment and greater risk for recurrent cardiac events. Understanding the reasons behind CRP dropout is urgently needed to inform the development of programs that best meet patient needs and support sustained engagement.

Aims

The aim of this study was to identify and understand factors impacting CRP dropout from the patient perspective.

Methods

A qualitative study using semi‐structured interviews was undertaken to examine the experience of 23 patients who dropped out of a CRP within a large urban hospital in British Columbia, Canada. Data were coded, analyzed using the constant comparison technique, and organized thematically.

Results

Participants described multiple challenges when attempting to complete CRP. Analysis of the data led to the identification of three main categories: (1) challenges living with CVD, (2) perceived advantages and disadvantages of CRP, and (3) unmet needs during CRP.

Linking evidence to action

In the practice setting, assessment of readiness to engage in CRP, alongside patient preferences and engagement needs, should be undertaken for maximum CRP uptake and completion. Providing diverse modes of CRP delivery, along with exploring the impact of virtual options as compared to traditional in‐person programs, will further advance the CRP evidence and may help address pervasive access barriers.

Technologies and the Effects On Social Engagement In Long-Term Care Facilities During COVID-19: A Scoping Review

During the COVID-19 pandemic, the sense of loneliness and social isolation felt by older adults in long-term care facilities has been exacerbated. Although there has been an increase in the number of digital solutions to mitigate social isolation during COVID-19, facilities in northern British Columbia do not have sufficient information regarding the technologies to support social connectedness. To support evidence-based policy decisions, a scoping review was conducted to identify existing virtual technology solutions, apps, and platforms that promote social connectedness among older adults residing in long-term care. A combination of keywords and subject headings were used to identify relevant literature within PubMed, CINAHL EBSCO, PsychINFO EBSCO, Embase OVIDSP, and Web of Science ISI databases. DistillerSR was used to screen and summarize the article selection process. Twenty-three articles were identified for full-text analysis. A variety of technologies are described which can be used to mitigate the impacts of social isolation felt by long-term care residents. However, many of these digital solutions require stable highspeed internet. This remains a challenge for facilities in northern areas as many have limited access to reliable internet. Metrics used to evaluate social engagement in the context of long-term care are also outlined. This research provides the preliminary groundwork necessary to better inform policy decisions about which technologies are available and, of these, which are effective at enhancing social connectedness for older adults in long-term care.

ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing

Clonal hematopoiesis results from somatic mutations in cancer driver genes in hematopoietic stem cells. We sought to identify novel drivers of clonal expansion using an unbiased analysis of sequencing data from 84,683 persons and identified common mutations in the 5-methylcytosine reader, ZBTB33, as well as in YLPM1, SRCAP, and ZNF318. We also identified these mutations at low frequency in myelodysplastic syndrome patients. Zbtb33 edited mouse hematopoietic stem and progenitor cells exhibited a competitive advantage in vivo and increased genome-wide intron retention. ZBTB33 mutations potentially link DNA methylation and RNA splicing, the two most commonly mutated pathways in clonal hematopoiesis and MDS.

Lineage-specific protection and immune imprinting shape the age distributions of influenza B cases

How a history of influenza virus infections contributes to protection is not fully understood, but such protection might explain the contrasting age distributions of cases of the two lineages of influenza B, B/Victoria and B/Yamagata. Fitting a statistical model to those distributions using surveillance data from New Zealand, we found they could be explained by historical changes in lineage frequencies combined with cross-protection between strains of the same lineage. We found additional protection against B/Yamagata in people for whom it was their first influenza B infection, similar to the immune imprinting observed in influenza A. While the data were not informative about B/Victoria imprinting, B/Yamagata imprinting could explain the fewer B/Yamagata than B/Victoria cases in cohorts born in the 1990s and the bimodal age distribution of B/Yamagata cases. Longitudinal studies can test if these forms of protection inferred from historical data extend to more recent strains and other populations.

Genomic Surveillance of a Globally Circulating Distinct Group W Clonal Complex 11 Meningococcal Variant, New Zealand, 2013-2018

Genomic surveillance is an essential part of effective disease control, enabling identification of emerging and expanding strains and monitoring of subsequent interventions. Whole-genome sequencing was used to analyze the genomic diversity of all Neisseria meningitidis isolates submitted to the New Zealand Meningococcal Reference Laboratory during 2013–2018. Of the 347 isolates submitted for whole-genome sequencing, we identified 68 sequence types belonging to 18 clonal complexes (CC). The predominant CC was CC41/44; next in predominance was CC11. Comparison of the 45 New Zealand group W CC11 isolates with worldwide representatives of group W CC11 isolates revealed that the original UK strain, the 2013 UK strain, and a distinctive variant (the 2015 strain) were causing invasive group W meningococcal disease in New Zealand. The 2015 strain also demonstrated increased resistance to penicillin and has been circulating in Canada and several countries in Europe, highlighting that close monitoring is needed to prevent future outbreaks around the world.

Exploring user perspectives of factors associated with use of teletrauma in rural areas

BACKGROUND

Despite the existence of universal health care for Canadians, health inequalities persist and those residing in rural regions experience disparities when accessing appropriate services. To enhance access, a teletrauma program was implemented in a rural northern region in western Canada, connecting rural clinicians to urban emergency physicians and trauma specialists during emergency cases.

OBJECTIVE

To explore reasons why teletrauma is used in rural contexts from the perspectives of service users and stakeholders.

METHODS

14 semi-structured interviews were conducted with stakeholders, clinicians (physicians, specialists), management, and researchers. Interpretive description methodology guided the study and analysis, and findings were organized thematically.

RESULTS

Teletrauma was used to connect clinicians, manage complex cases when weather or distance delayed transfer, and to enable appropriate and timely treatment locally. Teletrauma was more likely to be activated when clinicians were uncomfortable with clinical management, when relationships were established, and when technology was familiar and easy to use.

CONCLUSIONS

Teletrauma is more than just the technology that is deployed. The establishment of relationships between teletrauma users was vital to the success of teletrauma. To design effective, integrated, and sustainable services, rural clinicians must remain at the center of teletrauma models.

Defining cellular correlates of protection and vaccine failure to influenza across two human cohorts

Influenza viruses are endemic viral pathogens causing mild to severe respiratory illness in humans. Immunologic protection against influenza is determined by immune correlates of protection– factors associated with reduced infection or severe disease. While antibodies specific to viral surface proteins are known correlates, waning seasonal vaccine efficacy and reported infection of patients despite elevated antibody titers suggest that humoral responses alone do not provide complete protective immunity. Indeed, evidence points to a larger role for cell-mediated immunity (CMI; innate cells and antigen-specific T cells) in conferring protection. CMI correlates, which act independently from humoral responses, have yet to be identified. Here, we analyzed samples from adult human subjects across two influenza infection and vaccination cohorts to identify distinct CMI correlates of protection to influenza. We profiled CMI responses using high-dimension flow cytometry from PBMCs collected pre- and post-exposure to influenza infection or vaccination. Statistical comparison of cell frequency and infection status identified candidate CMI correlates, which were validated using logistic regression accounting for vaccination, demographic (age, sex, BMI), and serologic (antibody) covariates. We identified 9 individual and 6 cell clusters across myeloid and lymphoid compartments associated with protection. The strongest correlations were observed in Th17, cTfh, and subsets of NK and dendritic cells. Further, AUROC models identified 3 baseline CMI infection classifiers. Lastly, our study identified correlates of vaccine failure– pre-exposure CMI profiles correlated with positive infection status despite vaccination.

Activated CD4+ T cells and CD14hiCD16+ monocytes correlate with antibody response following influenza virus infection in humans

The failure to mount an antibody response following viral infection or seroconversion failure is a largely underappreciated and poorly understood phenomenon. Here, we identified immunologic markers associated with robust antibody responses after influenza virus infection in two independent human cohorts, SHIVERS and FLU09, based in Auckland, New Zealand and Memphis, Tennessee, USA, respectively. In the SHIVERS cohort, seroconversion significantly associates with (1) hospitalization, (2) greater numbers of proliferating, activated CD4⁺ T cells, but not CD8⁺ T cells, in the periphery during the acute phase of illness, and (3) fewer inflammatory monocytes (CD14^hiCD16⁺) by convalescence. In the FLU09 cohort, fewer CD14^hiCD16⁺ monocytes during early illness in the nasal mucosa were also associated with the generation of influenza-specific mucosal immunoglobulin A (IgA) and IgG antibodies. Our study demonstrates that seroconversion failure after infection is a definable immunological phenomenon, associated with quantifiable cellular markers that can be used to improve diagnostics, vaccine efficacy, and epidemiologic efforts.

Post-infection seroconversion is associated with severity of influenza virus infection

Seroconverters have early proliferation and activation of CD4⁺ T cells

CD8⁺ T cells are unaffected

CD14^hiCD16⁺ monocytes in the blood and nasal mucosa is associated with antibody response

Placental pathology in an unsuspected case of mucolipidosis type II with secondary hyperparathyroidism in a premature infant

Mucolipidosis type II (MLII, MIM 252500) is a lysosomal storage disorders caused by defects in GNPTAB gene which encodes alpha and beta subunits of N-acetylglucosamine (GlcNAc)-1-phosphotransferase. Neonatal presentation includes coarse facial features, restricted postnatal growth, generalized hypotonia, gingival hypertrophy and multiple skeletal anomalies. Here we present a case of a 26-week gestational age preterm infant with MLII who did not exhibit the typical facial features at birth; however, the diagnosis was suggested from abnormal placental pathology showing trophoblastic lipidosis and initial skeletal abnormalities from chest radiograph revealing generalized diffuse severe bone demineralizing disease and multiple fractures. Biochemical testing revealed elevation of plasma lysosomal enzymes. Homozygous pathogenic variant, designated c.3505_3504del, was discovered from GNPTAB sequencing. Her course was complicated by respiratory distress, secondary hyperparathyroidism, abdominal distention and feeding difficulties. Urine mucopolysaccharides analysis revealed mild elevation of total and individual glycosaminoglycan species in a non-specific pattern. To our knowledge, our case is the most premature example of mucolipidosis type II that has ever been reported to date. This report highlights the importance of placental pathological studies in the diagnosis of lysosomal storage disorders.

Common and Less Well-known Upper-limb Injuries in Elite Tennis Players

A recent increase in epidemiology studies on injuries in elite tennis players has helped to shed light on the types of injuries these athletes sustain. This article reviews the common upper-limb injuries in elite players and includes less well known, but important, injuries. A search was conducted to identify current relevant studies involving elite tennis players. Injury frequency rates, injuries by regions, and types of injuries together with a list of commonly reported injuries in the upper limb were established. This list was then reviewed and refined by a sports medicine physician who cares for elite tennis players to include both those injuries of the upper limb that are common and those that are less well known but still important and frequently encountered. Common injuries include internal shoulder impingement, rotator cuff pathology, labral tears, elbow tendinopathies, as well as extensor carpi ulnaris tendinopathies and subluxation. Posterior shoulder instability, distal humeral bone stress, elbow medial collateral ligament, and nondominant wrist ulnar collateral ligament injuries are not commonly reported injuries, but they are of significant clinical importance.

Factors associated with teletrauma utilization in rural areas: a review of the literature

INTRODUCTION

Trauma patients residing in rural areas face increased challenges to accessing timely and appropriate health services as a result of large geographic distances and limited resource availability. Virtual trauma supports, coined 'teletrauma', are one solution offered to address gaps in rural trauma care. Teletrauma represents a new and innovative solution to addressing health system gaps and optimizing patient care within rural settings. Here, the authors synthesize the empirical evidence on teletrauma research.

METHODS

A review of literature, with no date limiters, was guided by Arksey and O'Malley's (2005) scoping review methodology. The aim of the review was to provide an overview of the current landscape of teletrauma research while identifying factors associated with utilization.

RESULTS

Following a systematic search of key health databases, 1484 articles were initially identified, of which 28 met the inclusion criteria and were included for final analysis. From the review of the literature, the benefits of teletrauma for rural and remote areas were well-recognized. Several factors were found to be significantly associated with teletrauma utilization, including younger patient age, penetrating injury, and higher injury or illness severity. Lack of access to resources and clinician characteristics were also identified as reasons that sites adopted teletrauma services.

CONCLUSION

By identifying factors associated with teletrauma utilization, teletrauma programs may be used more judiciously and effectively in rural areas as a means of enhancing access to definitive trauma care in rural areas. Gaps in current knowledge were also identified, along with recommendations for future research.

Use of tracheobronchial tree 3-dimensional printed model: does it improve trainees' understanding of segmentation anatomy? A prospective study

Background

This prospective study investigated whether the use of 3D-printed model facilitates novice learning of radiology anatomy on multiplanar computed tomography (CT) when compared to traditional 2D-based learning tools. Specifically, whether the use of a 3D printed model improved interpretation of multiplanar CT tracheobronchial anatomy.

Methods

Thirty-one medical students (10F, 21 M) from years one to three were recruited, matched for gender and level of training and randomized to 2D or 3D group. Students underwent 20-min self-study session using 2D-printed image or 3D-printed model of the tracheobronchial tree. Immediately after, students answered 10 multiple-choice questions (Test 1) to identify tracheobronchial tree branches on multiplanar CT images. Two weeks later, identical test (Test 2) was used to assess retention of information. Mean scores of 2D and 3D groups were calculated. Student’s t test was used to compare mean differences in tests scores and analysis of variance (ANOVA) was used to assess the interaction of gender, CT imaging plane and time on test scores between the two groups.

Results

For test 1, 2D group had higher mean score than 3D group although not statistically significant (7.69 and 7.43, p = 0.39). Mean scores for Test 2 were significantly lower than for Test 1 (7 and 7.57, p = 0.03) with mean score decline for 2D group (Test 1 = 7.69, Test 2 = 6.63, p = 0.03), and similar score for 3D group (Test 1 and 2 = 7.43). There was no statistically significant interaction of gender and test score over time. Significant interaction between group and time of test was found for axial CT images but not for coronal images.

Conclusions

Use of a 3D-printed model of the tracheobronchial anatomy had no immediate advantage over traditional 2D-printed images for learning CT anatomy. However, use of a 3D model improved students’ ability to retain learned information, irrespective of gender.

Heterogeneity in influenza seasonality and vaccine effectiveness in Australia, Chile, New Zealand and South Africa: early estimates of the 2019 influenza season

We compared 2019 influenza seasonality and vaccine effectiveness (VE) in four southern hemisphere countries: Australia, Chile, New Zealand and South Africa. Influenza seasons differed in timing, duration, intensity and predominant circulating viruses. VE estimates were also heterogeneous, with all-ages point estimates ranging from 7-70% (I2: 33%) for A(H1N1)pdm09, 4-57% (I2: 49%) for A(H3N2) and 29-66% (I2: 0%) for B. Caution should be applied when attempting to use southern hemisphere data to predict the northern hemisphere influenza season.

ISIS Penning source extraction studies reveal the 3-dimensional Child-Langmuir effect

The standard 1X ISIS negative Penning surface plasma source has reliably produced an H^- beam for ISIS operations for 35 years. In order to meet the 60 mA, 2 ms, and 50 Hz beam current and duty cycle required for the front end test stand (Letchford et al., in Proceedings of IPAC2015, Richmond, VA, USA, 2015), a 2X scaled source has been developed [Faircloth et al., AIP Conf. Proc. 2052, 050004 (2018)]. The 2X source has a plasma chamber twice the linear dimensions of the 1X source. This paper investigates the comparison between different emission areas (plasma electrode aperture dimensions) for both the 1X and 2X sources. Slit and circular extraction schemes are studied. A 3D Child-Langmuir relationship is observed where the space charge limited current density depends on the aspect ratio of the extraction aperture.

MRI does not effectively diagnose ulnar-sided wrist pain in elite tennis players

OBJECTIVES

Ulnar-sided injuries of the non-dominant wrist are common in elite tennis players using a double-handed backhand technique. This study investigated the radiological changes of the non-dominant wrist in elite symptomatic and asymptomatic players using this technique as well as healthy controls. We compared clinical findings to radiological abnormalities.

DESIGN

Cross-sectional design with blinded radiological assessment, and contemporaneous clinical assessment of symptomatic players.

METHODS

Magnetic resonance images (MRI) of wrists related to non-dominant ulnar-sided pain, were taken in 14 symptomatic tennis players, 14 asymptomatic tennis players, and 12 healthy controls which were then independently reviewed for abnormalities by blinded radiologists. Total abnormalities and global between-group differences in the triangular fibrocartilage complex (TFC), ulnar collateral ligament (UCL), extensor carpi ulnaris (ECU) and supporting structures, osseous-articular lesions and ganglia were assessed. These were then compared to clinical examinations of the symptomatic players to assess agreement.

RESULTS

Symptomatic players reported a mean 3.64 abnormalities, being exactly 1 abnormality greater than asymptomatic players (2.64) and controls (2.50), suggesting similar asymptomatic lesions in all three groups. Players with pain reported significantly more osseous-articular lesions, ECU tendon and dorsal radio-ulnar ligament abnormalities, while changes to the UCL may reflect an isolated problem in specific wrists. There were no between-group differences in the presence of ganglia, most TFC structures nor ECU subsheath tear and subluxation.

CONCLUSIONS

Clinicians should carefully consider radiological changes alongside their clinical diagnosis of non-dominant wrist pain in tennis players due to possible tennis-related changes and/or asymptomatic findings.

Efficacy of Climate Forcings in PDRMIP Models

Quantifying the efficacy of different climate forcings is important for understanding the real-world climate sensitivity. This study presents a systematic multimodel analysis of different climate driver efficacies using simulations from the Precipitation Driver and Response Model Intercomparison Project (PDRMIP). Efficacies calculated from instantaneous radiative forcing deviate considerably from unity across forcing agents and models. Effective radiative forcing (ERF) is a better predictor of global mean near-surface air temperature (GSAT) change. Efficacies are closest to one when ERF is computed using fixed sea surface temperature experiments and adjusted for land surface temperature changes using radiative kernels. Multimodel mean efficacies based on ERF are close to one for global perturbations of methane, sulfate, black carbon, and insolation, but there is notable intermodel spread. We do not find robust evidence that the geographic location of sulfate aerosol affects its efficacy. GSAT is found to respond more slowly to aerosol forcing than CO2 in the early stages of simulations. Despite these differences, we find that there is no evidence for an efficacy effect on historical GSAT trend estimates based on simulations with an impulse response model, nor on the resulting estimates of climate sensitivity derived from the historical period. However, the considerable intermodel spread in the computed efficacies means that we cannot rule out an efficacy-induced bias of ±0.4 K in equilibrium climate sensitivity to CO2 doubling when estimated using the historical GSAT trend.

A Modular Cytokine Analysis Method Reveals Novel Associations With Clinical Phenotypes and Identifies Sets of Co-signaling Cytokines Across Influenza Natural Infection Cohorts and Healthy Controls

Cytokines and chemokines are key signaling molecules of the immune system. Recent technological advances enable measurement of multiplexed cytokine profiles in biological samples. These profiles can then be used to identify potential biomarkers of a variety of clinical phenotypes. However, testing for such associations for each cytokine separately ignores the highly context-dependent covariation in cytokine secretion and decreases statistical power to detect associations due to multiple hypothesis testing. Here we present CytoMod—a novel data-driven approach for analysis of cytokine profiles that uses unsupervised clustering and regression to identify putative functional modules of co-signaling cytokines. Each module represents a biosignature of co-signaling cytokines. We applied this approach to three independent clinical cohorts of subjects naturally infected with influenza in which cytokine profiles and clinical phenotypes were collected. We found that in two out of three cohorts, cytokine modules were significantly associated with clinical phenotypes, and in many cases these associations were stronger than the associations of the individual cytokines within them. By comparing cytokine modules across datasets, we identified cytokine “cores”—specific subsets of co-expressed cytokines that clustered together across the three cohorts. Cytokine cores were also associated with clinical phenotypes. Interestingly, most of these cores were also co-expressed in a cohort of healthy controls, suggesting that in part, patterns of cytokine co-signaling may be generalizable. CytoMod can be readily applied to any cytokine profile dataset regardless of measurement technology, increases the statistical power to detect associations with clinical phenotypes and may help shed light on the complex co-signaling networks of cytokines in both health and infection.

Does Cardiac Physical Exam Teaching Using a Cardiac Simulator Improve Medical Students' Diagnostic Skills?

Background

Challenges in bedside teaching may be overcome by the use of high-fidelity simulators for teaching the cardiac physical exam. The purpose of this study is to compare the ability of first-year medical students (MS1) to perform a cardiac physical exam and make the correct diagnosis after instruction using standardized patients (SPs) as compared to a cardiac simulator (Harvey, Laerdal Medical Corporation, NY, US).

Methods

Thirty-two MS1 were randomized to a teaching module on either SPs or Harvey. Their performance and ability to make the correct diagnosis were evaluated during a posttest objective structured clinical examination (OSCE) on real patients.

Results

No difference in the mean OSCE score was observed (SP: M=62.2% vs. Harvey: M=57.2%, p=0.32). The SP group obtained a higher frequency of correct diagnoses (M=61.5% SP vs. M=21.0% Harvey, p=0.03). Student feedback revealed that Harvey offered superior clinical findings; however, 34.4% of students requested a combination of teaching modalities as opposed to either method alone.

Conclusions

Performance in examination skills did not differ between the SP and Harvey groups but the SP group demonstrated an improved ability to arrive at a unifying diagnosis. A combined teaching program may be ideal for transferability to patients.

Severe Influenza Is Characterized by Prolonged Immune Activation: Results From the SHIVERS Cohort Study

Background

The immunologic factors underlying severe influenza are poorly understood. To address this, we compared the immune responses of influenza-confirmed hospitalized individuals with severe acute respiratory illness (SARI) to those of nonhospitalized individuals with influenza-like illness (ILI).

Methods

Peripheral blood lymphocytes were collected from 27 patients with ILI and 27 with SARI, at time of enrollment and then 2 weeks later. Innate and adaptive cellular immune responses were assessed by flow cytometry, and serum cytokine levels were assessed by a bead-based assay.

Results

During the acute phase, SARI was associated with significantly reduced numbers of circulating myeloid dendritic cells, CD192+ monocytes, and influenza virus-specific CD8+ and CD4+ T cells as compared to ILI. By the convalescent phase, however, most SARI cases displayed continued immune activation characterized by increased numbers of CD16+ monocytes and proliferating, and influenza virus-specific, CD8+ T cells as compared to ILI cases. SARI was also associated with reduced amounts of cytokines that regulate T-cell responses (ie, interleukin 4, interleukin 13, interleukin 12, interleukin 10, and tumor necrosis factor β) and hematopoiesis (interleukin 3 and granulocyte-macrophage colony-stimulating factor) but increased amounts of a proinflammatory cytokine (tumor necrosis factor α), chemotactic cytokines (MDC, MCP-1, GRO, and fractalkine), and growth-promoting cytokines (PDGFBB/AA, VEGF, and EGF) as compared to ILI.

Conclusions

Severe influenza cases showed a delay in the peripheral immune activation that likely led prolonged inflammation, compared with mild influenza cases.

Avoid reinventing the wheel: implementation of the Ottawa Clinic Assessment Tool (OCAT) in Internal Medicine

BACKGROUND

Workplace based assessment (WBA) is crucial to competency-based education. The majority of healthcare is delivered in the ambulatory setting making the ability to run an entire clinic a crucial core competency for Internal Medicine (IM) trainees. Current WBA tools used in IM do not allow a thorough assessment of this skill. Further, most tools are not aligned with the way clinical assessors conceptualize performances. To address this, many tools aligned with entrustment decisions have recently been published. The Ottawa Clinic Assessment Tool (OCAT) is an entrustment-aligned tool that allows for such an assessment but was developed in the surgical setting and it is not known if it can perform well in an entirely different context. The aim of this study was to implement the OCAT in an IM program and collect psychometric data in this different setting. Using one tool across multiple contexts may reduce the need for tool development and ensure that tools used have proper psychometric data to support them.

METHODS

Psychometrics characteristics were determined. Descriptive statistics and effect sizes were calculated. Scores were compared between levels of training (juniors (PGY1), seniors (PGY2s and PGY3s) & fellows (PGY4s and PGY5s)) using a one-way ANOVA. Safety for independent practice was analyzed with a dichotomous score. Variance components were generated and used to estimate the reliability of the OCAT.

RESULTS

Three hundred ninety OCATs were completed over 52 weeks by 86 physicians assessing 44 residents. The range of ratings varied from 2 (I had to talk them through) to 5 (I did not need to be there) for most items. Mean scores differed significantly by training level (p < .001) with juniors having lower ratings (M = 3.80 (out of 5), SD = 0.49) than seniors (M = 4.22, SD = - 0.47) who had lower ratings than fellows (4.70, SD = 0.36). Trainees deemed safe to run the clinic independently had significantly higher mean scores than those deemed not safe (p < .001). The generalizability coefficient that corresponds to internal consistency is 0.92.

CONCLUSIONS

This study's psychometric data demonstrates that we can reliably use the OCAT in IM. We support assessing existing tools within different contexts rather than continuous developing discipline-specific instruments.

Freshwater bryozoans of Lithuania (Bryozoa)

Nine species of freshwater bryozoans were recorded in Lithuania in a survey of 18 various types of freshwater bodies. Eight species were assigned to the Class Phylactolaemata and families Plumatellidae and Cristatellidae (Plumatellarepens, Plumatellafungosa, Plumatellafruticosa, Plumatellacasmiana, Plumatellaemarginata, Plumatellageimermassardi, Hyalinellapunctata and Cristatellamucedo). The ninth species, Paludicellaarticulata, represented the Class Gymnolaemata.

Plumatellageimermassardi and P.casmiana were recorded for the first time in Lithuania. For the plumatellids, species identification was achieved partly by analysing statoblasts’ morphological ultrastructures by scanning electron microscopy.

Recent H- diagnostics, plasma simulations, and 2X scaled Penning ion source developments at the Rutherford Appleton Laboratory

A vessel for extraction and source plasma analyses is being used for Penning H^- ion source development at the Rutherford Appleton Laboratory. A new set of optical elements including an einzel lens has been installed, which transports over 80 mA of H^- beam successfully. Simultaneously, a 2X scaled Penning source has been developed to reduce cathode power density. The 2X source is now delivering a 65 mA H^- ion beam at 10% duty factor, meeting its design criteria. The long-term viability of the einzel lens and 2X source is now being evaluated, so new diagnostic devices have been installed. A pair of electrostatic deflector plates is used to correct beam misalignment and perform fast chopping, with a voltage rise time of 24 ns. A suite of four quartz crystal microbalances has shown that the cesium flux in the vacuum vessel is only increased by a factor of two, despite the absence of a dedicated cold trap. Finally, an infrared camera has demonstrated good agreement with thermal simulations but has indicated unexpected heating due to beam loss on the downstream electrode. These types of diagnostics are suitable for monitoring all operational ion sources. In addition to experimental campaigns and new diagnostic tools, the high-performance VSim and COMSOL software packages are being used for plasma simulations of two novel ion thrusters for space propulsion applications. In parallel, a VSim framework has been established to include arbitrary temperature and cesium fields to allow the modeling of surface physics in H^- ion sources.

Direct Observation of Clinical Skills Feedback Scale: Development and Validity Evidence

Construct: This article describes the development and validity evidence behind a new rating scale to assess feedback quality in the clinical workplace.

BACKGROUND

Competency-based medical education has mandated a shift to learner-centeredness, authentic observation, and frequent formative assessments with a focus on the delivery of effective feedback. Because feedback has been shown to be of variable quality and effectiveness, an assessment of feedback quality in the workplace is important to ensure we are providing trainees with optimal learning opportunities. The purposes of this project were to develop a rating scale for the quality of verbal feedback in the workplace (the Direct Observation of Clinical Skills Feedback Scale [DOCS-FBS]) and to gather validity evidence for its use.

APPROACH

Two panels of experts (local and national) took part in a nominal group technique to identify features of high-quality feedback. Through multiple iterations and review, 9 features were developed into the DOCS-FBS. Four rater types (residents n = 21, medical students n = 8, faculty n = 12, and educators n = 12) used the DOCS-FBS to rate videotaped feedback encounters of variable quality. The psychometric properties of the scale were determined using a generalizability analysis. Participants also completed a survey to gather data on a 5-point Likert scale to inform the ease of use, clarity, knowledge acquisition, and acceptability of the scale.

RESULTS

Mean video ratings ranged from 1.38 to 2.96 out of 3 and followed the intended pattern suggesting that the tool allowed raters to distinguish between examples of higher and lower quality feedback. There were no significant differences between rater type (range = 2.36-2.49), suggesting that all groups of raters used the tool in the same way. The generalizability coefficients for the scale ranged from 0.97 to 0.99. Item-total correlations were all above 0.80, suggesting some redundancy in items. Participants found the scale easy to use (M = 4.31/5) and clear (M = 4.23/5), and most would recommend its use (M = 4.15/5). Use of DOCS-FBS was acceptable to both trainees (M = 4.34/5) and supervisors (M = 4.22/5).

CONCLUSIONS

The DOCS-FBS can reliably differentiate between feedback encounters of higher and lower quality. The scale has been shown to have excellent internal consistency. We foresee the DOCS-FBS being used as a means to provide objective evidence that faculty development efforts aimed at improving feedback skills can yield results through formal assessment of feedback quality.

A New Instrument for Assessing Resident Competence in Surgical Clinic: The Ottawa Clinic Assessment Tool

BACKGROUND

The shift toward competency-based medical education has created a demand for feasible workplace-based assessment tools. Perhaps, more important than competence to assess an individual patient is the ability to successfully manage a surgical clinic. Trainee performance in clinic is a critical component of learning to manage a surgical practice, yet no assessment tool currently exists to assess daily performance in outpatient clinics for surgery residents. The development of a competency-based assessment tool, the Ottawa Clinic Assessment Tool (OCAT), is described here to address this gap.

STUDY DESIGN

A consensus group of experts was gathered to generate dimensions of performance reflective of a competent "generalist" surgeon in clinic. A 6-month pilot study of the OCAT was conducted in orthopedics, general surgery, and obstetrics and gynecology with quantitative and qualitative evidence of validity collected. In all, 2 subsequent feedback sessions and a survey for staff and residents evaluated the OCAT for clarity and utility.

RESULTS

The OCAT is a 9-item tool, with a global assessment item and 2 short-answer questions. Among the 2 divisions, 44 staff surgeons completed 132 OCAT assessments of 79 residents. Psychometric data was collected as evidence of validity. Analysis of feedback indicated that the entrustability rating scale was useful for surgeons and residents and that the items could be correlated with individual competencies.

CONCLUSIONS

Multiple sources of validity evidence collected in this study demonstrate that the OCAT can measure resident clinic competency in a valid and feasible manner.

Learning environment: assessing resident experience

BACKGROUND

Given their essential role in developing professional identity, academic institutions now require formal assessment of the learning environment (LE). We describe the experience of introducing a novel and practical tool in postgraduate programmes. The Learning Environment for Professionalism (LEP) survey, validated in the undergraduate setting, is relatively short, with 11 questions balanced for positive and negative professionalism behaviours. LEP is anonymous and focused on rotation setting, not an individual, and can be used on an iterative basis. We describe how we implemented the LEP, preliminary results, challenges encountered and suggestions for future application. Academic institutions now require formal assessment of the learning environment METHODS: The study was designed to test the feasibility of introducing the LEP in the postgraduate setting, and to establish the validity and the reliability of the survey. Residents in four programmes completed 187 ratings using LEP at the end of one of 11 rotations.

RESULTS

The resident response rate was 87 per cent. Programme and rotation ratings were similar but not identical. All items rated positively (favourably), but displays of altruism tended to have lower ratings (meaning less desirable behaviour was witnessed), as were ratings for derogatory comments (again meaning that less desirable behaviour was witnessed).

DISCUSSION

We have shown that the LEP is a feasible and valid tool that can be implemented on an iterative basis to examine the LE. Two LEP questions in particular, regarding derogatory remarks and demonstrating altruism, recorded the lowest scores, and these areas deserve attention at our institution. Implementation in diverse programmes is planned at our teaching hospitals to further assess reliability. This work may influence other postgraduate programmes to introduce this assessment tool.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. 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Effectiveness of a care bundle to reduce surgical site infections in patients having open colorectal surgery

Introduction In 2010 a care bundle was introduced by the Department of Health (DH) to reduce surgical site infections (SSIs) in England. To date, use of the care bundle has not been evaluated despite incorporating interventions with resource implications. The aim of this study was to evaluate the DH SSI care bundle in open colorectal surgery. Methods A prospective cohort design was used at two teaching hospitals in England. The baseline group consisted of 127 consecutive patients having colorectal surgery during a 6-month period while the intervention group comprised 166 patients in the subsequent 6 months. SSI and care bundle compliance data were collected using dedicated surveillance staff. Results Just under a quarter (24%) of the patients in the baseline group developed a SSI compared with just over a quarter (28%) in the care bundle group (p>0.05). However, compliance rates with individual interventions, both before and after the implementation of the bundle, were similar. Interestingly, in only 19% of cases was there compliance with the total care bundle. The single intervention that showed an associated reduction in SSI was preoperative warming (p=0.032). Conclusions The DH care bundle did not reduce SSIs after open colorectal surgery. Despite this, it is not possible to state that the bundle is ineffective as compliance rates before and after bundle implementation were similar. All studies evaluating the effectiveness of care bundles must include data for compliance with interventions both before and after implementation of the care bundle; poor compliance may be one of the reasons for the lower than expected reduction of SSIs.

Detailed beam and plasma measurements on the vessel for extraction and source plasma analyses (VESPA) Penning H⁻ ion source

A vessel for extraction and source plasma analyses (VESPA) is operational at the Rutherford Appleton Laboratory (RAL). This project supports and guides the overall ion source R&D effort for the ISIS spallation neutron and muon facility at RAL. The VESPA produces 100 mA of pulsed H(-) beam, but perveance scans indicate that the source is production-limited at extraction voltages above 12 kV unless the arc current is increased. A high resolution optical monochromator is used to measure plasma properties using argon as a diagnostic gas. The atomic hydrogen temperature increases linearly with arc current, up to 2.8 eV for 50 A; whereas the electron temperature has a slight linear decrease toward 2.2 eV. The gas density is 10(21) m(-3), whilst the electron density is two orders of magnitude lower. Densities follow square root relationships with arc current, with gas density decreasing whilst electron (and hence ion) density increases. Stopping and range of ions in matter calculations prove that operating a high current arc with an argon admixture is extremely difficult because cathode-coated cesium is heavily sputtered by argon.

The ISIS pre-injector reconfiguration

With the introduction of a new "low energy beams" group at ISIS, the decision was taken to expand the ion source area. This paper will explain what actions were taken, how this has improved the present working environment and how the space will be used to accommodate a medium energy beam transport (MEBT) section after the existing radio-frequency quadrupole. The MEBT will incorporate three 202.5 MHz re-bunching cavities and will achieve a transmission of 96% with minimal emittance growth.

Resonance modulated amplified emission from CdSSe nanoribbons

We present evidence of amplified emission mediated by surface plasmon polaritons (SPPs) from a CdS0.2Se0.8 nanoribbon (NR) supported on a gold-coated silicon substrate. Room temperature amplified emission is observed from the nanoribbon above excitation irradiances ~ 25 W/cm(2) when it is supported on the gold coated silicon substrate. The nanoribbon is shown to act as a resonator cavity, leading to amplification of discrete wavelengths in the emission spectrum. Evidence for the formation of SPP waves between the gold-coated substrate and the nanoribbon is shown, and the resulting wavenumber increase allows for the matching of theoretical resonance wavelengths with those observed experimentally.

Variations in Neisseria meningitidis carriage by socioeconomic status: a cross-sectional study

BACKGROUND

Deprivation is associated with an increased risk of invasive Neisseria meningitidis disease, but little is known about the relationship between deprivation and asymptomatic carriage of N. meningitidis. This analysis was conducted to examine the relationship between meningococcal carriage and deprivation.

METHODS

As part of a rapid meningococcal carriage prevalence study conducted in West Cumbria to investigate an apparent cluster of invasive meningococcal disease, data were collected on lifestyle and social factors, including area-level indicators of socioeconomic status, to identify factors associated with meningococcal carriage.

RESULTS

In a multivariable log binomial regression model adjusted for age, lower socioeconomic status was significantly associated with higher prevalence of meningococcal carriage. A 1-unit increase in Index of Multiple Deprivation (2010) score was associated with a 1.7% increase in meningococcal carriage prevalence (95% confidence interval 0.3-3.0%). Age was the only significant predictor of carriage of Neisseria lactamica.

CONCLUSIONS

Living in a deprived area is associated with increased carriage of Group B meningococcus. Deprivation is an important factor to consider in the evaluation of the effectiveness and cost-effectiveness of the introduction of new meningococcal B vaccines and the development and implementation of immunization policies. Further work is required to understand whether deprivation has an effect on meningococcal carriage through other factors such as smoking.