Assessing the impact of autologous neutralizing antibodies on viral rebound in postnatally SHIV-infected ART-treated infant rhesus macaques

While the benefits of early antiretroviral therapy (ART) initiation in perinatally infected infants are well documented, early ART initiation is not always possible in postnatal pediatric HIV infections, which account for the majority of pediatric HIV cases worldwide. The timing of onset of ART initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C.CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.

A simple model for viral decay dynamics and the distribution of infected cell life spans in SHIV-infected infant rhesus macaques

The dynamics of HIV viral load following the initiation of antiretroviral therapy is not well-described by simple, single-phase exponential decay. Several mathematical models have been proposed to describe its more complex behavior, the most popular of which is two-phase exponential decay. The underlying assumption in two-phase exponential decay is that there are two classes of infected cells with different lifespans. However, with the exception of CD4+ T cells, there is not a consensus on all of the cell types that can become productively infected, and the fit of the two-phase exponential decay to observed data from SHIV.C.CH505 infected infant rhesus macaques was relatively poor. Therefore, we propose a new model for viral decay, inspired by the Gompertz model where the decay rate itself is a dynamic variable. We modify the Gompertz model to include a linear term that modulates the decay rate. We show that this simple model performs as well as the two-phase exponential decay model on HIV and SIV data sets, and outperforms it for the infant rhesus macaque SHIV.C.CH505 infection data set. We also show that by using a stochastic differential equation formulation, the modified Gompertz model can be interpreted as being driven by a population of infected cells with a continuous distribution of cell lifespans, and estimate this distribution for the SHIV.C.CH505-infected infant rhesus macaques. Thus, we find that the dynamics of viral decay in this model of infant HIV infection and treatment may be explained by a distribution of cell lifespans, rather than two distinct cell types.

183 DEVELOPING AND FACILITATING ONLINE INTERGENERATIONAL CAFÉS

Background

Many older people throughout their lives will require nursing care, consequentially most nurses will care for older people during their career. It is important that older people and student nurses are provided with shared learning opportunities so that professional caring partnerships can be nurtured and realised for mutual benefit. Intergenerational projects offer opportunities for intergenerational learning. However, few projects explore student nurse-older person dyads and how these can be integrated within undergraduate pre-registration programmes. This paper describes the development and facilitation of online older person-student nurse intergenerational cafés.

Methods

The project was managed by a design team comprising senior administration, lecturers in BSc Nursing programmes and a lecturer in Design for Health and Wellbeing. The ‘world café’ concept along with values of enablement and participation underpinned the design. The initiative was planned to align with a year three community care module. Regular online team meetings were held to agree the aims and outcomes for student nurse-older person cohorts, decide recruitment strategies, agree the process and format of facilitation. Older people were recruited through retirement, church, volunteer, social and sporting organisations, media and also using snowballing methods.

Results

Both student nurse and older person cohorts were offered support on how to access and participate in the café. Participants attended one of three online cafés hosted through Microsoft Teams. Each café followed the same format: 1) Group meeting convened with all participants; 2) Breakout small group ‘table’ discussions with student nurse-older people participants and design team facilitation; 3) The café was reconvened to whole group meeting where feedback was collated to elicit shared learning.

Conclusion

The initiative proved successful and there is merit in embedding intergenerational cafés into professionally accredited health care programmes. Through sharing life experiences and perspectives, intergenerational barriers can be reduced and new insights developed on person-centred gerontological care.

Vancomycin-Resistant Enterococci in Patients Attending for Colonoscopy: An Estimate of Community Prevalence

Aims Ireland has the highest vancomycin-resistant Enterococcus faecium (VRE) bloodstream infection prevalence in Europe. Two patterns of VRE carriage are recognised. European, with widespread community prevalence and North American, where carriage is predominantly nosocomial. It is unclear which pattern is dominant in Ireland. This uncertainty limits infection control measures. This study sought to explore this issue via a cross sectional point prevalence study. Methods Asymptomatic community volunteers, represented by patients undergoing elective outpatient colonoscopy testing, were opportunistically screened for VRE. Demographic and risk factor data were collected via a patient survey. Rectal swabs were collected before colonoscopy and VRE was identified using the VITEK MS system. Results 102 patients were cultured. A single patient tested positive, representing a prevalence rate of 0.98% (95% CI <0.01-5.8%). This patient demonstrated traditional risk factors, suggesting nosocomial rather than community acquisition. 94% (N=94) of patients had no knowledge of VRE, while 83% (N=83) had low levels of concern regarding hospital acquired infections. Conclusion There is a low incidence of VRE in the Irish community setting, in contrast to other European Countries, suggesting asymptomatic community colonization is not responsible for the high rates of VRE seen in Ireland. Wider screening or atypical infection control measures would not be supported by this data.

Re-assessing the importance of linear type traits in predicting genetic merit for survival in an aging Holstein-Friesian dairy cow population

The cumulative improvement achieved in the genetic merit for reproductive performance in dairy populations will likely improve dairy cow longevity; therefore, it is time to reassess whether linear type traits are still suitable predictors of survival in an aging dairy cow population. The objective of the present study was therefore to estimate the genetic correlations between linear type traits and survival from one parity to the next and, in doing so, evaluate if those genetic correlations change with advancing parity. After edits, 152,894 lactation survival records (first to ninth parity) were available from 52,447 Holstein-Friesian cows, along with linear type trait records from 52,121 Holstein-Friesian cows. A series of bivariate random regression models were used to estimate the genetic covariances between survival in different parities and each linear type trait. Heritability estimates for survival per parity ranged from 0.02 (SE = 0.004; first parity) to 0.05 (SE = 0.01; ninth parity). Pairwise genetic correlations between survival among different parities varied from 0.42 (first and ninth parity) to 1.00 (eighth to ninth parity), with the strength of these genetic correlations being inversely related to the interval between the compared parities. The genetic correlations between survival and the individual linear type traits varied across parities for 9 of the 20 linear type traits examined, but the correlations with only 3 of these linear type traits strengthened as the cows aged; these 3 traits were rear udder height, teat length, and udder depth. Given that linear type traits are frequently scored in first parity and are genetically correlated with survival in older parities, they may be suitable early predictors of survival, especially for later parity cows. Additionally, the direction of the genetic correlations between survival and rear udder height, teat length, and udder depth did not change between parities; hence, selection for survival in older parities using these linear type traits should not hinder genetic improvement for survival in younger parities.

Correction to: Who meets national early childhood sleep guidelines in Aotearoa New Zealand? A cross-sectional and longitudinal analysis

[This corrects the article DOI: 10.1093/sleepadvances/zpac002.].

Who meets national early childhood sleep guidelines in Aotearoa New Zealand? A cross-sectional and longitudinal analysis

Study Objectives

To investigate the proportion of children in Aotearoa New Zealand (NZ) who do or do not meet sleep duration and sleep quality guidelines at 24 and 45 months of age and associated sociodemographic factors.

Methods

Participants were children (n = 6490) from the Growing Up in New Zealand longitudinal study of child development with sleep data available at 24 and/or 45 months of age (48.2% girls, 51.8% boys; 22.4% Māori [the Indigenous people of NZ], 12.9% Pacific, 13.4% Asian, 45.2% European/Other). Relationships between sociodemographic factors and maternally reported child sleep duration (across 24 hours) and night wakings were investigated cross-sectionally and longitudinally. Estimates of children in NZ meeting sleep guidelines were calculated using a range of analytical techniques including Bayesian linear regression, negative binomial multiple regression, and growth curve models.

Results

In NZ, 29.8% and 19.5% of children were estimated to have a high probability of not meeting sleep duration guidelines and 15.4% and 8.3% were estimated to have a high probability of not meeting night waking guidelines at 24 and 45 months respectively, after controlling for multiple sociodemographic variables. Factors associated cross-sectionally with children's sleep included ethnicity, socioeconomic deprivation, material standard of living, rurality, and heavy traffic, and longitudinal sleep trajectories differed by gender, ethnicity, and socioeconomic deprivation.

Conclusions

A considerable proportion of young children in NZ have a high probability of not meeting sleep guidelines but this declines across the ages of 24 and 45 months. Sleep health inequities exist as early as 24 months of age in NZ.

An approach to teaching psychiatry to medical students in the time of Covid-19

In this time of Covid-19, life in healthcare has changed immeasurably. It has rapidly been injected with an 'all hands-on deck' approach, to facilitate the necessary adaptations required to reduce the spread of the virus and deliver frontline clinical care. Inevitably aspects of these changes have disrupted the delivery of medical education, notably clinical placements have been cancelled and social distancing guidelines prohibit face-to-face teaching. The training of future doctors is an essential part of this effort. Indeed, the emergence of a global health threat has underlined its continued importance. For medical educators and students alike, we have been presented with a challenge. Concurrently, this presents us with an impetus and opportunity for innovation. For some time now, a transformation in medical education has been called for, with an increasing recognition of the need to prepare students for the changing landscape of healthcare systems. This has included a focus on the use of technology-enhanced and self-directed learning. As a team of educators and clinicians in psychiatry, working in the School of Medicine and Medical Sciences (SMMS) in University College Dublin (UCD), we will share how we have responded. We outline the adaptations made to our 'Psychiatry' module and consider the influence this may have on its future delivery. These changes were informed by direct student input.

Contribution of genetic variability to phenotypic differences in on-farm efficiency metrics of dairy cows based on body weight and milk solids yield

Milk solids per kilogram of body weight (BW) is growing in popularity as a measure of dairy cow lactation efficiency. Little is known on the extent of genetic variability that exist in this trait but also the direction and strength of genetic correlations with other performance traits. Such genetic correlations are important to know if producers are to consider actively selecting cows excelling in milk solids per kilogram of BW. The objective of the present study was to use a large data set of commercial Irish dairy cows to quantify the extent of genetic variability in milk solids per kilogram of BW and related traits but also their genetic and phenotypic inter-relationships. Mid-lactation BW and body condition score (BCS), along with 305-d milk solids yield (i.e., fat plus protein yield) were available on 12,413 lactations from 11,062 cows in 85 different commercial dairy herds. (Co)variance components were estimated using repeatability animal linear mixed models. The genetic correlation between milk solids and body weight was only 0.05, which when coupled with the observed large genetic variability in both traits, indicate massive potential to select for both traits in opposite directions. The genetic correlations between both milk solids and BW with BCS; however, need to be considered in any breeding strategy. The genetic standard deviation, heritability, and repeatability of milk solids per kilogram of BW was 0.08, 0.37, and 0.57, respectively. The genetic correlation between milk solids per kilogram of BW with milk solids, BW, and BCS was 0.62, -0.75, and -0.41, respectively. Therefore, based on genetic regression, each increase of 0.10 units in genetic merit for milk solids per kilogram of BW is expected to result in, on average, an increase in 16.1 kg 305-d milk solids yield, a reduction of 25.6 kg of BW and a reduction of 0.05 BCS units (scale of 1-5 where 1 is emaciated). The genetic standard deviation (heritability) for 305-d milk solids yield adjusted phenotypically to a common BW was 27.3 kg (0.22). The genetic correlation between this adjusted milk solids trait with milk solids, BW, and BCS was 0.91, -0.12, and -0.26, respectively. Once also adjusted phenotypically to a common BCS, the genetic standard deviation (heritability) for milk solids adjusted phenotypically to a common BW was 26.8 kg (0.22) where the genetic correlation with milk solids, BW and BCS was 0.91, -0.21, and -0.07, respectively. The genetic standard deviation (heritability) of BW adjusted phenotypically for differences in milk solids was 35.3 kg (0.61), which reduced to 33.2 kg when also phenotypically adjusted for differences in BCS. Results suggest considerable opportunity exists to change milk solids yield independent of BW, and vice versa. The opportunity is reduced slightly once also corrected for differences in BCS. Inter-animal BCS differences should be considered if selection on such metrics is contemplated.

Close proximity to alcohol outlets is associated with increased crime and hazardous drinking: Pooled nationally representative data from New Zealand

This nationwide study investigated the relationship between proximity to alcohol outlets (off-licence, on-licence, and other-licence) and two adverse outcomes; hazardous drinking and crime (common assault, non-aggravated sexual assault, aggravated sexual assault, and tobacco and liquor offences). After adjustment for important individual- and area-level factors, close proximity to alcohol outlets was associated with increased risk of hazardous drinking, with strong associations for on-licence outlets. Proximity alcohol outlets was also strongly associated with all crime outcomes, often with a dose-response relationship. Nationally representative New Zealand data showed that close proximity to alcohol outlets was associated with increased crime and hazardous drinking.

Blind and Partially Sighted Students’ Access to Mathematics and Computer Technology in Ireland and Belgium

This article presents the results of a survey that investigated two related issues for blind and partially sighted students: (1) mathematical-access difficulties and (2) general experiences using computer technology. The survey was part of the formative evaluation of a workstation for Mathematic Access to Technology and Science (commonly called MATHS). The participants included teachers and blind, partially sighted, and sighted students from a range of special, integrated, and mainstream Irish and Belgian schools.

1031 Exploring the Impact of Cognitive Behavioral Therapy for Insomnia (CBT-I) on Daytime Productivity in Survivors of Breast Cancer

Introduction

Post-treatment insomnia disorder and fatigue symptoms can impair work and daytime productivity in breast cancer survivors. Cognitive Behavioral Therapy for Insomnia (CBT-I) significantly improves insomnia and daytime fatigue. This feasibility study examined whether improving insomnia and fatigue using CBT-I is associated with improved work and activity productivity in breast cancer survivors.

Methods

10 survivors of early stage breast cancer participated in 7 weekly individual CBT-I sessions. The primary outcome was the Work Productivity and Activity Impairment Questionnaire-General Health (WPAIQ-GH) questionnaire. Secondary outcomes were the Insomnia Severity Index (ISI) and the Multidimensional Fatigue Symptom Inventory-Short Form (MFSI-SF). Assessments were conducted at baseline and post-treatment. Paired samples t-tests examined the impact of CBT-I on productivity and fatigue. Linear regression assessed whether change in fatigue was associated with change in productivity.

Results

Participants had a mean age of 50.8 (range 42-63) and the majority were diagnosed with stage II (60%) cancer. There was a significant reduction in fatigue [t(9)= 2.43, p =.04] and activity impairment due to insomnia [t(9)= 3.105, p <.05] following treatment. Insomnia affected 52% of work productivity at baseline with a non-significant decrease to 15% following treatment [t(3)= 2.25 p= .110]. Reductions in fatigue were significantly associated with reductions in activity impairment [F(1,8)= 7.25, p =.03], accounting for 47.5% of the variability.

Conclusion

Treating insomnia with CBT-I significantly improved daytime productivity, activity impairment, and fatigue. Controlled research with larger sample sizes is warranted to confirm these preliminary results.

Support

Nyissa Walsh is a trainee in the Cancer Research Training Program of the Beatrice Hunter Cancer Research Institute (BHCRI). Dr. Sheila Garland is supported by a Scotiabank New Investigator Award from BHCRI.

1030 An Exploration of the Impact of Cognitive Behavioural Therapy of Insomnia (CBT-I) on Perceived Cognitive Impairment in Breast Cancer Survivors

Introduction

Insomnia and cognitive impairment are prevalent and persistent symptoms in cancer survivors. Cognitive Behavior Therapy is effective for improving insomnia and comorbid symptoms in cancer survivors but there are very few empirically supported treatments that can improve cognitive impairment. This feasibility study explored the impact of CBT-I on perceived cognitive impairment in breast cancer survivors.

Methods

We enrolled 10 early stage breast cancer survivors with insomnia disorder and perceived cognitive impairment. Participants received 7 individual sessions of CBT-I over the course of 8 weeks and completed the Insomnia Severity Index (ISI), the Functional Assessment of Cancer Therapy - Cognitive Function (FACT-Cog) questionnaires and The Hospital Anxiety and Depression Scale (HADS) at baseline and post-treatment. Paired samples t-tests were used to assess change over time.

Results

The sample was predominantly diagnosed with stage II breast cancer (60%). Women were an average age of 50.8 (SD 6.84) and 18.2 (SD 3.62) years of education. CBT-I significantly reduced insomnia severity [19.4 to 7.1; t(9)= 6.56, p < .001] and improved perceived cognitive impairment [t(9)= -3.55, p < .01], perceived cognitive ability [t(9)= -2.87, p < .05], quality of life [t(9)= -3.14, p < .05], and overall subjective cognitive function [t(9)= -3.67, p < .01]. Although participants began treatment with low levels of mood disturbance, CBT-I further decreased symptoms of anxiety (baseline: M= 10.10, SD= 4.34; post-treatment M= 8.20, SD= 3.91) and depression (baseline: M= 7.90, SD= 3.45; post-treatment M= 5.30, SD= 2.83), although not statistically significant.

Conclusion

This study suggests CBT-I may improve perceived cognitive impairment in cancer survivors, in addition to insomnia and mood. Future randomized controlled trials with larger samples and objective measurements of cognition are needed.

Support

Nyissa Walsh is a trainee in the Cancer Research Training Program of the Beatrice Hunter Cancer Research Institute (BHCRI). Dr. Sheila Garland is supported by a Scotiabank New Investigator Award from BHCRI.

The Influence of Hydraulic Ankles and Microprocessor-control on the Biomechanics of Trans-tibial Amputees During Quiet Standing on a 5° Slope

BACKGROUND

Lower limb amputees have a high incidence of comorbidities, such as osteoarthritis, which are believed to be caused by kinetic asymmetries. A lack of prosthetic adaptation to different terrains requires kinematic compensations, which may influence these asymmetries.

METHOD

Six SIGAM grade E-F trans-tibial amputees (one bilateral) wore motion capture markers while standing on force plates, facing down a 5° slope. The participants were tested under three prosthetic conditions; a fixed attachment foot (FIX), a hydraulic ankle (HYD) and a microprocessor foot with a 'standing support' mode (MPF). The resultant ground reaction force (GRF) and support moment for prosthetic and sound limbs were chosen as outcome measures. These were compared between prosthetic conditions and to previously captured able-bodied control data.

RESULTS

The distribution of GRF between sound and prosthetic limbs was not significantly affected by foot type. However, the MPF condition required fewer kinematic compensations, leading to a reduction in sound side support moment of 59% (p=0.001) and prosthetic side support moment of 43% (p=0.02) compared to FIX. For the bilateral participant, only the MPF positioned the GRF vector anterior to the knees, reducing the demand on the residual joints to maintain posture.

CONCLUSIONS

For trans-tibial amputees, loading on lower limb joints is affected by prosthetic foot technology, due to the kinematic compensations required for slope adaptation. MPFs with 'standing support' might be considered reasonable and necessary for bilateral amputees, or amputees with stability problems due to the reduced biomechanical compensations evident.

Incorporating external information to improve sparse signal detection in rare-variant gene-set-based analyses

Gene-set analyses are used to assess whether there is any evidence of association with disease among a set of biologically related genes. Such an analysis typically treats all genes within the sets similarly, even though there is substantial, external, information concerning the likely importance of each gene within each set. For example, for traits that are under purifying selection, we would expect genes showing extensive genic constraint to be more likely to be trait associated than unconstrained genes. Here we improve gene-set analyses by incorporating such external information into a higher-criticism-based signal detection analysis. We show that when this external information is predictive of whether a gene is associated with disease, our approach can lead to a significant increase in power. Further, our approach is particularly powerful when the signal is sparse, that is when only a small number of genes within the set are associated with the trait. We illustrate our approach with a gene-set analysis of amyotrophic lateral sclerosis (ALS) and implicate a number of gene-sets containing SOD1 and NEK1 as well as showing enrichment of small p values for gene-sets containing known ALS genes. We implement our approach in the R package wHC.

Association between thyroid nodule size and malignancy rate

INTRODUCTION

The diagnostic performance of ultrasound-fine needle aspiration to identify thyroid nodules harbouring malignancy remains variable. The aim of this study was to determine thyroid nodule size and cytological classification as predictors of malignancy risk.

MATERIALS AND METHODS

We conducted a retrospective cohort analysis at an academic hospital involving 499 consecutive patients who underwent thyroid surgery between 2004 and 2015.

RESULTS

A total of 503 thyroid nodules (499 patients, 84% female; mean age 50.8 years, standard deviation, SD, 15.4 years) were analysed. Of these, 19.5% were malignant. The mean (± SD) nodule size was 3.28 ± 1.63 cm and 3.27 ± 1.54 cm for benign and malignant nodules, respectively. The odds of malignancy for thyroid nodules less than 3.0 cm was similar to those for nodules of 3.0 cm or greater (0.26 compared with 0.29; p=0.77). Overall, the sensitivity and specificity of fine-needle aspiration in this cohort were 71.4% and 100%, respectively. The overall false negative rate was 5.4%. When the cut-off of 3.0 cm was used, the false negative rate in thyroid nodules less than 3.0 cm was 0% compared with 7.0% in nodules of 3.0 cm or greater. Thus, class (p<0.01) but not nodule size (p=0.49), was associated with higher malignancy risk.

CONCLUSIONS

Our results suggest that thyroid nodule size did not accurately predict the risk of thyroid malignancy irrespective of fine-needle aspiration cytology. Routine diagnostic thyroid lobectomy solely owing to thyroid nodule size of 3.0 cm or greater is currently not justified.

Efficient estimation of grouped survival models

Background

Time- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, but rather are inferred from the cycle or dose to which the event is attributed. This exemplifies a prevalent type of imprecise measurement called grouped failure time, where times or doses are restricted to discrete increments. Failure to appropriately account for the grouped nature of the data, when present, may lead to biased analyses.

Results

We present groupedSurv, an R package which implements a statistically rigorous and computationally efficient approach for conducting genome-wide analyses based on grouped failure time phenotypes. Our approach accommodates adjustments for baseline covariates, and analysis at the variant or gene level. We illustrate the statistical properties of the approach and computational performance of the package by simulation. We present the results of a reanalysis of a published genome-wide study to identify common germline variants associated with the risk of taxane-induced peripheral neuropathy in breast cancer patients.

Conclusions

groupedSurv enables fast and rigorous genome-wide analysis on the basis of grouped failure time phenotypes at the variant, gene or pathway level. The package is freely available under a public license through the Comprehensive R Archive Network.

Electronic supplementary material

The online version of this article (10.1186/s12859-019-2899-x) contains supplementary material, which is available to authorized users.

Psychosocial, psychiatric and work-related risk factors associated with suicide in Ireland: optimised methodological approach of a case-control psychological autopsy study

BACKGROUND

Suicide has profound effects on families and communities, but is a statistically rare event. Psychological autopsies using a case-control design allow researchers to examine risk factors for suicide, using a variety of sources to detail the psychological and social characteristics of decedents and to compare them to controls. The Suicide Support and Information System Case Control study (SSIS-ACE) aimed to compare psychosocial, psychiatric and work-related risk factors across three groups of subjects: suicide decedents, patients presenting to hospital with a high-risk self-harm episode, and general practice controls.

METHODS

The study design includes two inter-related studies; one main case-control study: comparing suicide cases to general practice (GP) controls, and one comparative study: comparing suicide cases to patients presenting with high-risk self-harm. Consecutive cases of suicide and probable suicide are identified through coroners' registration of deaths in the defined region (Cork City and County, Ireland) and are frequency-matched for age group and gender with GP patient controls recruited from the same GP practice as the deceased. Data sources for suicide cases include coroners' records, interviews with health care professionals and proxy informants; data sources for GP controls and for high-risk self-harm controls include interviews with control, with proxy informants and with health care professionals. Interviews are semi-structured and consist of quantitative and qualitative parts. The quantitative parts include a range of validated questionnaires addressing psychiatric, psychosocial and occupational factors. The study adopts several methodological innovations, including accessing multiple data sources for suicide cases and controls simultaneously, recruiting proxy informants to examine consistency across sources.

CONCLUSIONS

The study allows for the investigation of consistency across different data sources and contributes to the methodological advancement of psychological autopsy research. The study will also inform clinical and public health practice. The comparison between suicide cases and controls will allow investigation of risk and protective factors for suicide more generally, while the comparison with high-risk self-harm patients will help to identify the factors associated specifically with a fatal outcome to a self-harm episode. A further enhancement is the particular focus on specific work-related risk factors for suicide.

The Influence of Perforated Prosthetic Liners on Residual Limb Wound Healing: a Case Report

CASE DESCRIPTION

Good residual limb skin health is vital to successful prosthetic prescription. Unnatural loading profiles and excessive sweating can lead to skin and soft tissue problems. Perforated liners allow the transport of moisture away from the skin and allow negative pressure (a condition that has been shown to aid wound healing) to act directly on the residuum surface.

AIM

Assess the effects of perforated prosthetic liner use, particularly with respect to wound healing.

METHOD

Three patient histories were retrospectively reviewed following prescription of perforated prosthetic liners due to excessive sweating or prolonged residual limb health concerns. Photographic records from patient files were used to document changes in residual limb condition. Patients also provided subjective feedback regarding their experiences.

FINDINGS

Two cases described active amputees with persistent blistering irritated during exercise. Another case described a patient of low mobility level with a history of residual limb skin infections. All saw their conditions heal and reported a reduction in problematic sweating. Two patients reported cancelling surgical interventions after substantial improvements with the perforated liner.

DISCUSSION

These findings provide evidence that the use of perforated prosthetic liners allow improvements in residual limb health, while still permitting prosthetic use.

A mating advice system in dairy cattle incorporating genomic information

This study investigated the effects of alternative mating programs that incorporate genomic information on expected progeny herd performance and inbreeding, as well as methods to include un-genotyped animals in such mating programs. A total of 54,535 Holstein-Friesian cattle with imputed high-density genotypes (547,650 SNP after edits) were available. First, to quantify the accuracy of imputing un-genotyped animals (often an issue in populations), a sub-population of 729 genotyped animals had their genotypes masked, and their allele dosages were imputed, using linear regression exploiting information on genotyped relatives. The reference population for imputation included all genotyped animals, excluding the 729 selected animals and their sires, dams, and grandsires, and had either (1) their sires' genotypes, (2) their dams' genotypes (3) both their sires' and their dams' genotypes, or (4) both their sires' and maternal grandsires' genotypes introduced into the reference population. The correlations between true genotypes and the imputed allele dosages ranged from 0.58 (sire only) to 0.68 (both sire and dam). A herd of 100 cows was then simulated (1,000 replicates) from the sub-population of 729 imputed animals. The top 10 bulls from the genotyped population, based on their total genetic merit index (TMI) were selected to be used as sires. Three mating allotment methods were investigated: (1) random mating, (2) sequential mating based on maximizing only the expected TMI of the progeny, and (3) linear programming to maximize a generated index constructed to maximize genetic merit and minimize expected progeny inbreeding as well as intra- and inter-progeny variability in genetic merit. Relationships among candidate parents were calculated using either the pedigree relationship matrix or the genomic relationship matrix; the latter was constructed using either the true genotypes of both parents or the true genotypes of the sire plus the imputed allele dosages of the dam. Using the genomic co-ancestry estimates resulted in lower average herd expected genomic inbreeding levels compared with using the pedigree-based co-ancestry estimates. Additionally, if the dams were not genotyped, using their imputed allele dosages also resulted in lower average herd expected inbreeding levels compared with using the pedigree co-ancestry estimates. The inter-progeny coefficient of variation for selected traits, milk and fertility, estimated breeding values were reduced by 12 to 65% using the linear programing method compared with sequential mating.

Risk factors associated with animal mortality in pasture-based, seasonal-calving dairy and beef herds

Animal mortality is indicative of animal health and welfare standards, which are of growing concern to the agricultural industry. The objective of the present study was to ascertain risk factors associated with mortality at multiple life stages in pasture-based, seasonal-calving dairy and beef herds. Males and females were stratified into seven life stages based on age (0 to 2 d, 3 to 7 d, 8 to 30 d, 31 to 182 d, 183 to 365 d, 366 to 730 d, and 731 to 1,095 d) whereas females with ≥1 calving event were further stratified into five life stages based on cow parity number (1, 2, 3, 4, and 5). Mortality was defined as whether an animal died during each life stage; only animals that either survived the entire duration or died during a life stage were considered. The data, following edits, consisted of 4,404,122 records from 1,358,712 animals. Multivariable logistic regression was used to estimate the logit of the probability of mortality in each life stage separately. The odds of a young animal (i.e., aged ≤ 1,095 d) dying was generally greater if veterinary assistance was required at their birth relative to no assistance (odds ratio [OR]: 3.10 to 31.85), if the animal was a twin relative to a singleton (OR: 1.46 to 2.31) or if the animal was male relative to female (OR: 1.14 to 6.15). Moreover, the odds of a cow (i.e., females with ≥1 calving event) dying were greater when she required veterinary assistance at calving (OR: 2.69 to 7.55) compared with a cow that did not require any assistance, if she produced twin relative to singleton progeny (OR: 1.59 to 2.03) or male relative to female progeny (OR: 1.09 to 1.20). Additionally, the odds of a first or second parity cow dying when she herself had received veterinary assistance at birth were only 0.63 to 0.66 times that of a cow that was provided no assistance at birth. For both young animals and cows, the odds of dying generally increased with herd size, whereas animals residing in expanding herds had lower odds of dying. Results from the present study indicate that the risk factors associated with mortality in pasture-based, seasonal-calving herds are similar to those reported in literature in confinement, nonseasonal-calving herds. Moreover, the present study identifies that these risk factors are similar in both dairy and beef herds, yet the magnitude of the association often differs and also changes with life stage.

Advances in the systemic treatment of triple-negative breast cancer

Triple-negative breast cancer constitutes a heterogeneous group of malignancies that are often aggressive and associated with a poor prognosis. Molecular characterization, while not a standard of care, can further subtype triple-negative breast cancer and provide insight into prognostication and behaviour. Optimal chemotherapy regimens have yet to be established; however, there have been advances in the systemic treatment of triple-negative breast cancer in the neoadjuvant, adjuvant, and metastatic settings. In this review, we discuss evidence for the potential benefit of neoadjuvant platinum-based chemotherapy, adjuvant combination chemotherapy with weekly paclitaxel, and BRCA mutation-directed therapy in the metastatic setting. The role for adjuvant capecitabine in patients who do not achieve a pathologic complete response with neoadjuvant chemotherapy is reviewed. Future directions and data concerning novel targeted agents are reviewed, including the most recent data on parp [poly (adp-ribose) polymerase] inhibitors, antiandrogen agents, and immunotherapy.

Transcatheter Mitral Valve-in-Ring Implantation

Failed surgical mitral valve repair using an annuloplasty ring has traditionally been treated with surgical valve replacement or repair1. For patients at high risk for repeat open heart surgery, placement of a trans-catheter aortic valve (i.e., TAVI valve) within the mitral ring (i.e., Mitral-Valve-in-Ring, MViR) has emerged as a novel alternative treatment strategy2-5 . We describe our experience of a failed mitral valve repair that was successfully treated with a TAVI valve delivered via the trans-septal approach, and summarise the data relating to this emerging treatment strategy.

New Challenges in Diagnosis of Haemoglobinopathies: Migration of Populations

The current influx of economic migrants and asylum seekers from countries with a high prevalence of haemoglobinopathies creates new challenges for health care systems and diagnostic laboratories. The migration of carriers introduces new and novel haemoglobinopathy mutations to the diagnostic repertoire of a laboratory, often creating new pressures to improve and update the carrier screening technology and diagnostic scope. For antenatal screening programmes, the marriage of partners from different ethnic groups can lead to the risk of compound heterozygote children being born novel mutation combinations, creating problems in the provision of accurate advice regarding the expected phenotype of the thalassaemia or haemoglobinopathy disorder. In the UK, the impact of immigration required the National Haemoglobinopathy Reference laboratory to change the strategy and techniques used for the molecular diagnosis of thalassaemia and the haemoglobinopathies. In 2005, due to the increasingly large range of β-thalassaemia mutations that needed to be diagnosed, the laboratory switched from a three-step screening procedure using ARMS-PCR to a simpler but more expensive one-step strategy of DNA sequencing of the beta and alpha globin genes for all referrals. After ten years of employing this strategy, a further 57 novel thalassaemia and haemoglobionpopthy alleles were discovered (11 new β-chain variants, 15 α-chain variants, 19 β-thalassaemia mutations and 12 α+-thalassaemia mutations), increasing further the extremely heterogeneous spectrum of globin gene mutations in the UK population.

Characteristics of prisoners with intellectual disabilities

BACKGROUND

Previous studies have found high rates of intellectual disabilities (ID) in prison. However, little is understood about prisoners with ID. This study aimed to identify prisoners with ID and compare their characteristics with prisoners without neurodevelopmental disorders with regard to demographic profile, mental health, suicide risk and offences.

METHOD

This was a descriptive, cross-sectional study carried out using face-to-face interviews with 240 participants in a London Category C prison. Standardised tools were used to assess prisoners for ID and mental disorder.

RESULTS

The study identified 18 prisoners as having ID. Participants with ID were less likely to be from a black or minority ethnic background, be over 35 years of age or have any qualifications. They were more likely to have been single, homeless or unemployed before coming into prison. Prisoners with ID were significantly more likely to have mental health problems and 25% had thought about suicide in the last month and 63% had attempted suicide in the past. Prisoners with ID were also more likely to be housed in the vulnerable prisoners' wing and significantly more likely to have committed robbery than other prisoners.

CONCLUSIONS

The findings confirm the presence of significant numbers of people with ID with high levels of mental illness in a male prison. Services across the CJS are required for this group, specifically, there is a need for raised awareness among those working in prison about ID and improved skills to recognise offenders with ID and address major gaps in current healthcare provision in prison.

Search for massive long-lived particles decaying semileptonically in the LHCb detector

A search is presented for massive long-lived particles decaying into a muon and two quarks. The dataset consists of proton-proton interactions at centre-of-mass energies of 7 and 8 TeV, corresponding to integrated luminosities of 1 and 2[Formula: see text], respectively. The analysis is performed assuming a set of production mechanisms with simple topologies, including the production of a Higgs-like particle decaying into two long-lived particles. The mass range from 20 to 80 [Formula: see text] and lifetimes from 5 to 100[Formula: see text] are explored. Results are also interpreted in terms of neutralino production in different R-Parity violating supersymmetric models, with masses in the 23-198 GeV/[Formula: see text] range. No excess above the background expectation is observed and upper limits are set on the production cross-section for various points in the parameter space of theoretical models.

Rechallenge of clozapine in a low secure setting following pericardial effusion

Introduction

Clozapine is licensed for treatment-resistant schizophrenia and when clozapine is not able to be used, less evidence based practices may be required. Full remission may require combinations or high doses of psychotropic medications having greater potential for interactions and side effects. If this is not successful, symptoms may persist and long-term disability may occur.

Aims

To explore safety and efficacy of a rechallenge of clozapine in a patient with treatment resistant schizoaffective disorder, who previously developed pericardial effusion. Collateral history reported best improvement with clozapine compared to other medications.

Objectives

To improve level of functioning and reduce need for less evidence based choices of medication.

Methods

Initial consultation with clozapine monitoring service over prospects of rechallenge. Full medication history and review. Consultation with a cardiologist regarding validity of local monitoring strategy. Obtain consent from the patient and his family. Titrate clozapine slowly. Once clozapine initiated, measure temperature, blood pressure, pulse rate and monitoring of symptoms of pericarditis including chest pain, cough and dyspnoea daily. ECG and echocardiography at baseline and 2 and 4 weeks after initiation of the rechallenge. ECGs monthly thereafter, with a further echocardiogram at 3 months. Weekly troponin and CRP for three months to monitor developing myocarditis and pericarditis.

Results

Successful rechallenge of clozapine with significant reduction in psychopathology, improvement in functioning and no adverse events reported. Reduction of risk enabled transfer to open ward conditions.

Conclusions

There is increasing evidence of successful rechallenges of clozapine however, further research is necessary to aid such clinical decisions.

Disclosure of interest

The authors have not supplied their declaration of competing interest.

Observation of the Annihilation Decay Mode B^{0}→K^{+}K^{-}

A search for the B^{0}→K^{+}K^{-} decay is performed using pp-collision data collected by LHCb. The data set corresponds to integrated luminosities of 1.0 and 2.0  fb^{-1} at center-of-mass energies of 7 and 8 TeV, respectively. This decay is observed for the first time, with a significance of more than 5 standard deviations. The analysis also results in an improved measurement of the branching fraction for the B_{s}^{0}→π^{+}π^{-} decay. The measured branching fractions are B(B^{0}→K^{+}K^{-})=(7.80±1.27±0.81±0.21)×10^{-8} and B(B_{s}^{0}→π^{+}π^{-})=(6.91±0.54±0.63±0.19±0.40)×10^{-7}. The first uncertainty is statistical, the second is systematic, the third is due to the uncertainty on the B^{0}→K^{+}π^{-} branching fraction used as a normalization. For the B_{s}^{0} mode, the fourth accounts for the uncertainty on the ratio of the probabilities for b quarks to hadronize into B_{s}^{0} and B^{0} mesons.

A regional analysis of epidermal growth factor receptor (EGFR) mutated lung cancer for HSE South

BACKGROUND

EGFR mutated lung cancer represents a subgroup with distinct clinical presentations, prognosis, and management requirements. We investigated the survival, prognostic factors, and real-world treatment of NSCLC patients with EGFR mutation in clinical practice.

METHODS

A retrospective review of all specimens sent for EGFR analysis from December 2009 to September 2015 was performed. Patient demographics, specimen type, EGFR mutation status/type, stage at diagnosis, treatment, response rate, and survival data were recorded.

RESULTS

27/334 (8%) patient specimens sent for EGFR testing tested positive for a sensitising EGFR mutation. The median age was 65 years (40-85 years). Exon 19 deletion represented the most commonly detected alteration, accounting for 39% (n = 11). First-line treatment for those with Exon 18, 19, or 21 alterations (n = 24) was with an EGFR tyrosine kinase inhibitor (TKI) in 79% (n = 19). Objective response rate among these patients was 74% and median duration of response was 13 months (range 7-35 months).

CONCLUSION

The incidence of EGFR mutation in our cohort of NSCLC is 9% which is consistent with mutation incidence reported in other countries. The rate of EGFR mutation in our population is slightly below that reported internationally, but treatment outcomes are consistent with published data. Real-world patient data have important contributions to make with regard to quality measurement, incorporating patient experience into guidelines and identifying safety signals.

Observation of [Formula: see text] and [Formula: see text] decays

The decays [Formula: see text] and [Formula: see text] are observed for the first time using a data sample corresponding to an integrated luminosity of 3.0 fb[Formula: see text], collected by the LHCb experiment in proton-proton collisions at the centre-of-mass energies of 7 and 8[Formula: see text]. The branching fractions relative to that of [Formula: see text] are measured to be [Formula: see text]where the first uncertainties are statistical and the second are systematic.

Measurement of the b-Quark Production Cross Section in 7 and 13 TeV pp Collisions

Measurements of the cross section for producing b quarks in the reaction pp→bb[over ¯]X are reported in 7 and 13 TeV collisions at the LHC as a function of the pseudorapidity η in the range 2<η<5 covered by the acceptance of the LHCb experiment. The measurements are done using semileptonic decays of b-flavored hadrons decaying into a ground-state charmed hadron in association with a muon. The cross sections in the covered η range are 72.0±0.3±6.8 and 154.3±1.5±14.3  μb for 7 and 13 TeV. The ratio is 2.14±0.02±0.13, where the quoted uncertainties are statistical and systematic, respectively. The agreement with theoretical expectation is good at 7 TeV, but differs somewhat at 13 TeV. The measured ratio of cross sections is larger at lower η than the model prediction.

Observation of J/ψϕ Structures Consistent with Exotic States from Amplitude Analysis of B^{+}→J/ψϕK^{+} Decays

The first full amplitude analysis of B^{+}→J/ψϕK^{+} with J/ψ→μ^{+}μ^{-}, ϕ→K^{+}K^{-} decays is performed with a data sample of 3  fb^{-1} of pp collision data collected at sqrt[s]=7 and 8 TeV with the LHCb detector. The data cannot be described by a model that contains only excited kaon states decaying into ϕK^{+}, and four J/ψϕ structures are observed, each with significance over 5 standard deviations. The quantum numbers of these structures are determined with significance of at least 4 standard deviations. The lightest has mass consistent with, but width much larger than, previous measurements of the claimed X(4140) state.

First Experimental Study of Photon Polarization in Radiative B_{s}^{0} Decays

The polarization of photons produced in radiative B_{s}^{0} decays is studied for the first time. The data are recorded by the LHCb experiment in pp collisions corresponding to an integrated luminosity of 3  fb^{-1} at center-of-mass energies of 7 and 8 TeV. A time-dependent analysis of the B_{s}^{0}→ϕγ decay rate is conducted to determine the parameter A^{Δ}, which is related to the ratio of right- over left-handed photon polarization amplitudes in b→sγ transitions. A value of A^{Δ}=-0.98_{-0.52}^{+0.46}_{-0.20}^{+0.23} is measured. This result is consistent with the standard model prediction within 2 standard deviations.

Measurement of CP Violation in B^{0}→D^{+}D^{-} Decays

The CP violation observables S and C in the decay channel B^{0}→D^{+}D^{-} are determined from a sample of proton-proton collisions at center-of-mass energies of 7 and 8 TeV, collected by the LHCb experiment and corresponding to an integrated luminosity of 3  fb^{-1}. The observable S describes CP violation in the interference between mixing and the decay amplitude, and C parametrizes direct CP violation in the decay. The following values are obtained from a flavor-tagged, decay-time-dependent analysis: S=-0.54_{-0.16}^{+0.17}(stat)±0.05(syst), C=0.26_{-0.17}^{+0.18}(stat)±0.02(syst). These values provide evidence for CP violation at a significance level of 4.0 standard deviations. The phase shift due to higher-order standard model corrections is constrained to a small value of Δϕ=-0.16_{-0.21}^{+0.19}  rad.

Search for Higgs-like bosons decaying into long-lived exotic particles

A search is presented for massive long-lived particles, in the 20-60 [Formula: see text] mass range with lifetimes between 5 and 100 [Formula: see text]. The dataset used corresponds to 0.62[Formula: see text] of proton-proton collision data collected by the LHCb detector at [Formula: see text]. The particles are assumed to be pair-produced by the decay of a Higgs-like boson with mass between 80 and 140 [Formula: see text]. No excess above the background expectation is observed and limits are set on the production cross-section as a function of the long-lived particle mass and lifetime and of the Higgs-like boson mass.

Search for Structure in the B_{s}^{0}π^{±} Invariant Mass Spectrum

The B_{s}^{0}π^{±} invariant mass distribution is investigated in order to search for possible exotic meson states. The analysis is based on a data sample recorded with the LHCb detector corresponding to 3  fb^{-1} of pp collision data at sqrt[s]=7 and 8 TeV. No significant excess is found, and upper limits are set on the production rate of the claimed X(5568) state within the LHCb acceptance. Upper limits are also set as a function of the mass and width of a possible exotic meson decaying to the B_{s}^{0}π^{±} final state. The same limits also apply to a possible exotic meson decaying through the chain B_{s}^{*0}π^{±}, B_{s}^{*0}→B_{s}^{0}γ where the photon is excluded from the reconstructed decays.

Comprehensive population screening in the Ashkenazi Jewish population for recurrent disease-causing variants

The Ashkenazi Jewish (AJ) population has an increased risk for a variety of recessive diseases due to historical founder effects and genetic drift. For some, the disease-causing founder mutations have been identified and well-characterized, but for others, further study is necessary. The purpose of this study is to assess the carrier frequencies of 85 pathogenic variants causative of 29 recessive conditions in the AJ population. Up to 3000 AJ individuals were genotyped by Luminex MagPlex^® -TAG^™ bead array or Agena Bioscience^™ MassARRAY assays. We identified seven conditions with carrier frequencies higher than 1 in 100, nine between 1 in 100 and 1 in 200, and four between 1 in 200 and 1 in 500. Variants in nine conditions had a detected carrier rate of less than 1 in 500 or were not identified in approximately 2000 AJ individuals. We assessed the combined AJ carrier frequency for 18 relatively prevalent diseases to be 1 in 6, and the risk of AJ individuals to be a carrier couple for one of these 18 diseases as 1 in 441. We note additional recessive genetic conditions should be considered for AJ carrier screening panels.

Evidence for Exotic Hadron Contributions to Λ_{b}^{0}→J/ψpπ^{-} Decays

A full amplitude analysis of Λ_{b}^{0}→J/ψpπ^{-} decays is performed with a data sample acquired with the LHCb detector from 7 and 8 TeV pp collisions, corresponding to an integrated luminosity of 3  fb^{-1}. A significantly better description of the data is achieved when, in addition to the previously observed nucleon excitations N→pπ^{-}, either the P_{c}(4380)^{+} and P_{c}(4450)^{+}→J/ψp states, previously observed in Λ_{b}^{0}→J/ψpK^{-} decays, or the Z_{c}(4200)^{-}→J/ψπ^{-} state, previously reported in B^{0}→J/ψK^{+}π^{-} decays, or all three, are included in the amplitude models. The data support a model containing all three exotic states, with a significance of more than three standard deviations. Within uncertainties, the data are consistent with the P_{c}(4380)^{+} and P_{c}(4450)^{+} production rates expected from their previous observation taking account of Cabibbo suppression.

Model-Independent Evidence for J/ψp Contributions to Λ_{b}^{0}→J/ψpK^{-} Decays

The data sample of Λ_{b}^{0}→J/ψpK^{-} decays acquired with the LHCb detector from 7 and 8 TeV pp collisions, corresponding to an integrated luminosity of 3  fb^{-1}, is inspected for the presence of J/ψp or J/ψK^{-} contributions with minimal assumptions about K^{-}p contributions. It is demonstrated at more than nine standard deviations that Λ_{b}^{0}→J/ψpK^{-} decays cannot be described with K^{-}p contributions alone, and that J/ψp contributions play a dominant role in this incompatibility. These model-independent results support the previously obtained model-dependent evidence for P_{c}^{+}→J/ψp charmonium-pentaquark states in the same data sample.

Measurement of the CP Asymmetry in B_{s}^{0}-B[over ¯]_{s}^{0} Mixing

The CP asymmetry in the mixing of B_{s}^{0} and B[over ¯]_{s}^{0} mesons is measured in proton-proton collision data corresponding to an integrated luminosity of 3.0  fb^{-1}, recorded by the LHCb experiment at center-of-mass energies of 7 and 8 TeV. Semileptonic B_{s}^{0} and B[over ¯]_{s}^{0} decays are studied in the inclusive mode D_{s}^{∓}μ^{±}ν[over (-)]_{μ}X with the D_{s}^{∓} mesons reconstructed in the K^{+}K^{-}π^{∓} final state. Correcting the observed charge asymmetry for detection and background effects, the CP asymmetry is found to be a_{sl}^{s}=(0.39±0.26±0.20)%, where the first uncertainty is statistical and the second systematic. This is the most precise measurement of a_{sl}^{s} to date. It is consistent with the prediction from the standard model and will constrain new models of particle physics.