Genomic evolution shapes prostate cancer disease type

The development of cancer is an evolutionary process involving the sequential acquisition of genetic alterations that disrupt normal biological processes, enabling tumor cells to rapidly proliferate and eventually invade and metastasize to other tissues. We investigated the genomic evolution of prostate cancer through the application of three separate classification methods, each designed to investigate a different aspect of tumor evolution. Integrating the results revealed the existence of two distinct types of prostate cancer that arise from divergent evolutionary trajectories, designated as the Canonical and Alternative evolutionary disease types. We therefore propose the evotype model for prostate cancer evolution wherein Alternative-evotype tumors diverge from those of the Canonical-evotype through the stochastic accumulation of genetic alterations associated with disruptions to androgen receptor DNA binding. Our model unifies many previous molecular observations, providing a powerful new framework to investigate prostate cancer disease progression.

Validating hidden Markov models for seabird behavioural inference

Understanding animal movement and behaviour can aid spatial planning and inform conservation management. However, it is difficult to directly observe behaviours in remote and hostile terrain such as the marine environment. Different underlying states can be identified from telemetry data using hidden Markov models (HMMs). The inferred states are subsequently associated with different behaviours, using ecological knowledge of the species. However, the inferred behaviours are not typically validated due to difficulty obtaining 'ground truth' behavioural information. We investigate the accuracy of inferred behaviours by considering a unique data set provided by Joint Nature Conservation Committee. The data consist of simultaneous proxy movement tracks of the boat (defined as visual tracks as birds are followed by eye) and seabird behaviour obtained by observers on the boat. We demonstrate that visual tracking data is suitable for our study. Accuracy of HMMs ranging from 71% to 87% during chick-rearing and 54% to 70% during incubation was generally insensitive to model choice, even when AIC values varied substantially across different models. Finally, we show that for foraging, a state of primary interest for conservation purposes, identified missed foraging bouts lasted for only a few seconds. We conclude that HMMs fitted to tracking data have the potential to accurately identify important conservation-relevant behaviours, demonstrated by a comparison in which visual tracking data provide a 'gold standard' of manually classified behaviours to validate against. Confidence in using HMMs for behavioural inference should increase as a result of these findings, but future work is needed to assess the generalisability of the results, and we recommend that, wherever feasible, validation data be collected alongside GPS tracking data to validate model performance. This work has important implications for animal conservation, where the size and location of protected areas are often informed by behaviours identified using HMMs fitted to movement data.

Valproate-Induced Hyperammonemic Encephalopathy Causing New-Onset Seizures

Valproate-induced hyperammonemic encephalopathy (VHE) is a rare and severe side effect that can occur with valproic acid (VPA) therapy, despite therapeutic doses and normal serum levels of valproate. The typical signs of this condition include a sudden onset of impaired consciousness, focal neurologic symptoms, and an increase in seizure frequency. The exact cause of VHE is unknown, but it is believed to be related to the accumulation of toxic VPA metabolites and increased levels of ammonia that can cause swelling of the astrocytes and cerebral edema. We present a case of a 19-year-old male patient with a history of bipolar disorder on valproic acid 250 mg daily, admitted to the hospital after a new-onset seizure. He was found to have elevated levels of ammonia in his blood, despite having therapeutic levels of valproate and no liver dysfunction. His symptoms improved with discontinuation of the medication and his ammonia levels decreased. We discuss possible mechanisms and risk factors leading to encephalopathy while on valproate therapy. VHE should be considered a possibility when patients treated with valproate show signs of impaired consciousness.

Characteristics of a later life population in a general adult community mental health service setting

OBJECTIVES

Globally, increasing life expectancy has escalated demands on psychiatric services caring for a later life population. It is recognised that those with enduring mental illness may have specific needs with advancing age. In this study, we describe the characteristics of a population aged over 60 years attending a general adult community psychiatric service and compare demographic and clinical features across age and diagnostic categories. The study aims to gather preliminary information which may guide future local mental health service planning.

METHODS

We conducted a cross-sectional observational study using retrospective chart review of all patients aged over 60 years attending four community mental health teams in North Dublin. Cohorts of attenders were stratified by age comparing 60-64 year age group with the population aged 65 years and over. Attenders were also stratified by diagnosis and regression analysis was used to determine predictors of psychotic disorder diagnosis.

RESULTS

The study included 127 patients. There was a higher prevalence of psychotic disorders among those aged 65 years and over (n = 73), while those aged 60-64 years (n = 54) were more likely to have depression and non-affective, non-psychotic disorders. Among the population aged 65 years and over 78% (n = 57) were long-term psychiatric service attenders.

CONCLUSIONS

The majority of the sample aged 65 years and over were long-term service attenders with a diagnosis of severe mental illness. Further research is warranted to determine optimal service delivery for later life psychiatric service attenders.

Pro-arrhythmic effects of gain-of-function potassium channel mutations in the short QT syndrome

The congenital short QT syndrome (SQTS) is a rare condition characterized by abbreviated rate-corrected QT (QTc) intervals on the electrocardiogram and by increased susceptibility to both atrial and ventricular arrhythmias and sudden death. Although mutations to multiple genes have been implicated in the SQTS, evidence of causality is particularly strong for the first three (SQT1-3) variants: these result from gain-of-function mutations in genes that encode K⁺ channel subunits responsible, respectively, for the I_Kr, I_Ks and I_K1 cardiac potassium currents. This article reviews evidence for the impact of SQT1-3 missense potassium channel gene mutations on the electrophysiological properties of I_Kr, I_Ks and I_K1 and of the links between these changes and arrhythmia susceptibility. Data from experimental and simulation studies and future directions for research in this field are considered. This article is part of the theme issue 'The heartbeat: its molecular basis and physiological mechanisms'.

The road to recovery: a synthesis of outcomes from ecosystem restoration in tropical and sub-tropical Asian forests

Current policy is driving renewed impetus to restore forests to return ecological function, protect species, sequester carbon and secure livelihoods. Here we assess the contribution of tree planting to ecosystem restoration in tropical and sub-tropical Asia; we synthesize evidence on mortality and growth of planted trees at 176 sites and assess structural and biodiversity recovery of co-located actively restored and naturally regenerating forest plots. Mean mortality of planted trees was 18% 1 year after planting, increasing to 44% after 5 years. Mortality varied strongly by site and was typically ca 20% higher in open areas than degraded forest, with height at planting positively affecting survival. Size-standardized growth rates were negatively related to species-level wood density in degraded forest and plantations enrichment settings. Based on community-level data from 11 landscapes, active restoration resulted in faster accumulation of tree basal area and structural properties were closer to old-growth reference sites, relative to natural regeneration, but tree species richness did not differ. High variability in outcomes across sites indicates that planting for restoration is potentially rewarding but risky and context-dependent. Restoration projects must prepare for and manage commonly occurring challenges and align with efforts to protect and reconnect remaining forest areas. The abstract of this article is available in Bahasa Indonesia in the electronic supplementary material. This article is part of the theme issue 'Understanding forest landscape restoration: reinforcing scientific foundations for the UN Decade on Ecosystem Restoration'.

Long-term trends of second generation anticoagulant rodenticides (SGARs) show widespread contamination of a bird-eating predator, the Eurasian Sparrowhawk (Accipiter nisus) in Britain

Second generation anticoagulant rodenticides (SGARs) are widely used to control rodents around the world. However, contamination by SGARs is detectable in many non-target species, particularly carnivorous mammals or birds-of-prey that hunt or scavenge on poisoned rodents. The SGAR trophic transfer pathway via rodents and their predators/scavengers appears widespread, but little is known of other pathways of SGAR contamination in non-target wildlife. This is despite the detection of SGARs in predators that do not eat rodents, such as specialist bird-eating hawks. We used a Bayesian modelling framework to examine the extent and spatio-temporal trends of SGAR contamination in the livers of 259 Eurasian Sparrowhawks, a specialist bird-eating raptor, in regions of Britain during 1995-2015. SGARs, predominantly difenacoum, were detected in 81% of birds, with highest concentrations in males and adults. SGAR concentrations in birds were lowest in Scotland and higher or increasing in other regions of Britain, which had a greater arable or urban land cover where SGARs may be widely deployed for rodent control. However, there was no overall trend for Britain, and 97% of SGAR residues in Eurasian Sparrowhawks were below 100 ng/g (wet weight), which is a potential threshold for lethal effects. The results have potential implications for the population decline of Eurasian Sparrowhawks in Britain. Fundamentally, the results indicate an extensive and persistent contamination of the avian trophic transfer pathway on a national scale, where bird-eating raptors and, by extension, their prey appear to be widely exposed to SGARs. Consequently, these findings have implications for wildlife contamination worldwide, wherever these common rodenticides are deployed, as widespread exposure of non-target species can apparently occur via multiple trophic transfer pathways involving birds as well as rodents.

Opposing effects of spatiotemporal variation in resources and temporal variation in climate on density dependent population growth in seabirds

Understanding how ecological processes combine to shape population dynamics is crucial in a rapidly changing world. Evidence has been emerging for how fundamental drivers of density dependence in mobile species are related to two differing types of environmental variation-temporal variation in climate, and spatiotemporal variation in food resources. However, to date, tests of these hypotheses have been largely restricted to mid-trophic species in terrestrial environments and thus their general applicability remains unknown. We tested if these same processes can be identified in marine upper trophic level species. We assembled a multi-decadal data set on population abundance of 10 species of colonial seabirds comprising a large component of the UK breeding seabird biomass, and covering diverse phylogenies, life histories and foraging behaviours. We tested for evidence of density dependence in population growth rates using discrete time state-space population models fit to long time-series of observations of abundance at seabird breeding colonies. We then assessed if the strength of density dependence in population growth rates was exacerbated by temporal variation in climate (sea temperature and swell height), and attenuated by spatiotemporal variation in prey resources (productivity and tidal fronts). The majority of species showed patterns consistent with temporal variation in climate acting to strengthen density dependent feedbacks to population growth. However, fewer species showed evidence for a weakening of density dependence with increasing spatiotemporal variation in prey resources. Our findings extend this emerging theory for how different sources of environmental variation may shape the dynamics and regulation of animal populations, demonstrating its role in upper trophic marine species. We show that environmental variation leaves a signal in long-term population dynamics of seabirds with potentially important consequences for their demography and trophic interactions.

The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates

BACKGROUND

Up to 80% of cases of prostate cancer present with multifocal independent tumour lesions leading to the concept of a field effect present in the normal prostate predisposing to cancer development. In the present study we applied Whole Genome DNA Sequencing (WGS) to a group of morphologically normal tissue (n = 51), including benign prostatic hyperplasia (BPH) and non-BPH samples, from men with and men without prostate cancer. We assess whether the observed genetic changes in morphologically normal tissue are linked to the development of cancer in the prostate.

RESULTS

Single nucleotide variants (P = 7.0 × 10-03, Wilcoxon rank sum test) and small insertions and deletions (indels, P = 8.7 × 10-06) were significantly higher in morphologically normal samples, including BPH, from men with prostate cancer compared to those without. The presence of subclonal expansions under selective pressure, supported by a high level of mutations, were significantly associated with samples from men with prostate cancer (P = 0.035, Fisher exact test). The clonal cell fraction of normal clones was always higher than the proportion of the prostate estimated as epithelial (P = 5.94 × 10-05, paired Wilcoxon signed rank test) which, along with analysis of primary fibroblasts prepared from BPH specimens, suggests a stromal origin. Constructed phylogenies revealed lineages associated with benign tissue that were completely distinct from adjacent tumour clones, but a common lineage between BPH and non-BPH morphologically normal tissues was often observed. Compared to tumours, normal samples have significantly less single nucleotide variants (P = 3.72 × 10-09, paired Wilcoxon signed rank test), have very few rearrangements and a complete lack of copy number alterations.

CONCLUSIONS

Cells within regions of morphologically normal tissue (both BPH and non-BPH) can expand under selective pressure by mechanisms that are distinct from those occurring in adjacent cancer, but that are allied to the presence of cancer. Expansions, which are probably stromal in origin, are characterised by lack of recurrent driver mutations, by almost complete absence of structural variants/copy number alterations, and mutational processes similar to malignant tissue. Our findings have implications for treatment (focal therapy) and early detection approaches.

Unified classification and risk-stratification in Acute Myeloid Leukemia

Clinical recommendations for Acute Myeloid Leukemia (AML) classification and risk-stratification remain heavily reliant on cytogenetic findings at diagnosis, which are present in <50% of patients. Using comprehensive molecular profiling data from 3,653 patients we characterize and validate 16 molecular classes describing 100% of AML patients. Each class represents diverse biological AML subgroups, and is associated with distinct clinical presentation, likelihood of response to induction chemotherapy, risk of relapse and death over time. Secondary AML-2, emerges as the second largest class (24%), associates with high-risk disease, poor prognosis irrespective of flow Minimal Residual Disease (MRD) negativity, and derives significant benefit from transplantation. Guided by class membership we derive a 3-tier risk-stratification score that re-stratifies 26% of patients as compared to standard of care. This results in a unified framework for disease classification and risk-stratification in AML that relies on information from cytogenetics and 32 genes. Last, we develop an open-access patient-tailored clinical decision support tool.

An Investigation of the Cause of Wild Turkey Mortality in Mississippi

Lymphoproliferative disease virus (LPDV) is an exogenous alpharetrovirus that sporadically causes fatal lymphoid neoplasia in affected turkeys. Previous studies of wild turkeys (Meleagridis gallopavo) in the United States have demonstrated geographically widespread LPDV infection and frequent coinfection with avian poxvirus (APV) and reticuloendotheliosis virus (REV). This study was conducted to better understand health risks to Mississippi wild turkeys, including the relative importance of LPDV, APV, and REV in contributing to mortality. Thirteen wild turkeys, which died naturally or were euthanized due to illness, were submitted to Mississippi State University's Poultry Research and Diagnostic Laboratory for postmortem examinations. Birds originated from nine counties across the state over the past 5 yr. Carcasses were submitted as fresh (nonfrozen) or frozen. At autopsy, 9 of 13 turkeys had severe, proliferative cutaneous lesions on the head and neck, with diphtheritic or proliferative oral and esophageal lesions. Samples were collected for molecular diagnostic testing (LPDV and REV PCR), histopathology, and bacterial culture and isolation. External and internal parasites were preserved in formalin for identification. APV (cutaneous and/or diphtheritic forms) was diagnosed in 9 of 13 birds by identification of pathognomonic histologic lesions (including intracytoplasmic inclusion bodies). Interestingly, all birds with APV were also REV PCR positive. Furthermore, eight turkeys were positive for LPDV, and LPDV was commonly associated with coinfections with APV and REV.

Frailty in Secure Forensic Mental Health Settings: A Study from Dundrum Hospital, Ireland

Introduction

Frailty is defined as a clinical syndrome that encompasses a combination of decreased physiological reserve and low resistance to stressors. There is an association between mental illness and frailty among elderly cohorts. Frailty is also associated with obesity and smoking. There are high rates of treatment resistant schizophrenia among patients in secure forensic services. Patients with schizophrenia have high rates of morbidity and early mortality.

Objectives

The primary aim of this study was to examine the rates of frailty present in a complete cohort of forensic in-patients.

Methods

An assessment using Fried Frailty criteria was offered to all in-patients (n=95) in Ireland’s National Forensic Service, which included measures of walking speed, grip strength, low physical activity and exhaustion. Demographic details and details pertaining to diagnoses and medications were also gathered.

Results

Of the 95 in-patients, 92 patients agreed to participate. The majority were male (89%). The most common diagnosis was schizophrenia (71.7%). Mean age was 44.7 years (SD 11.42), and 58.2% met criteria for obesity. Of the total group, 47 patients met criteria for ‘pre-frail’ and 10 met criteria for ‘frail’ using Fried criteria.

Conclusions

This is the first study examining frailty in a cohort of patients in secure forensic settings. We found high rates of patients meeting frailty criteria at very young ages. Rates of frailty in this group were comparable to those found amongst elders in community settings. We consider this demonstrates significant medical vulnerability in this patient group.

Disclosure

No significant relationships.

Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study

BACKGROUND

Germline variants explain more than a third of prostate cancer (PrCa) risk, but very few associations have been identified between heritable factors and clinical progression.

OBJECTIVE

To find rare germline variants that predict time to biochemical recurrence (BCR) after radical treatment in men with PrCa and understand the genetic factors associated with such progression.

DESIGN, SETTING, AND PARTICIPANTS

Whole-genome sequencing data from blood DNA were analysed for 850 PrCa patients with radical treatment from the Pan Prostate Cancer Group (PPCG) consortium from the UK, Canada, Germany, Australia, and France. Findings were validated using 383 patients from The Cancer Genome Atlas (TCGA) dataset.

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS

A total of 15,822 rare (MAF <1%) predicted-deleterious coding germline mutations were identified. Optimal multifactor and univariate Cox regression models were built to predict time to BCR after radical treatment, using germline variants grouped by functionally annotated gene sets. Models were tested for robustness using bootstrap resampling.

RESULTS AND LIMITATIONS

Optimal Cox regression multifactor models showed that rare predicted-deleterious germline variants in "Hallmark" gene sets were consistently associated with altered time to BCR. Three gene sets had a statistically significant association with risk-elevated outcome when modelling all samples: PI3K/AKT/mTOR, Inflammatory response, and KRAS signalling (up). PI3K/AKT/mTOR and KRAS signalling (up) were also associated among patients with higher-grade cancer, as were Pancreas-beta cells, TNFA signalling via NKFB, and Hypoxia, the latter of which was validated in the independent TCGA dataset.

CONCLUSIONS

We demonstrate for the first time that rare deleterious coding germline variants robustly associate with time to BCR after radical treatment, including cohort-independent validation. Our findings suggest that germline testing at diagnosis could aid clinical decisions by stratifying patients for differential clinical management.

PATIENT SUMMARY

Prostate cancer patients with particular genetic mutations have a higher chance of relapsing after initial radical treatment, potentially providing opportunities to identify patients who might need additional treatments earlier.

Phosphodiesterase 5 Inhibitor Use in Patients Undergoing Decompression Surgery for Lumbar Spinal Stenosis

OBJECTIVE

Our objectives were to explore the association between phosphodiesterase 5 inhibitor use and lumbar decompression surgery by evaluating the prevalence of lumbar decompression surgery in a treatment group of patients with lumbar spinal stenosis compared with a control group.

DESIGN

We performed database review and extracted data including lumbar decompression surgery prevalence, phosphodiesterase 5 inhibitor dosage, and fill dates. Treatment group was defined as those with phosphodiesterase 5 inhibitor fill dates of less than 30 days before surgery, and control group was defined as those with phosphodiesterase 5 inhibitor fill dates at any other time. Lumbar decompression surgery prevalence rates for both groups were calculated.

RESULTS

Our study found 599 lumbar spinal stenosis patients who were prescribed phosphodiesterase 5 inhibitor. Three hundred thirty-eight underwent lumbar decompression surgery. Of these, 71 (21%) filled their prescription of less than 30 days before surgery, whereas 267 (79%) filled their prescription during a different period. The majority (94.6%) of surgical patients received decompression at two or more spinal levels.

CONCLUSIONS

Prevalence of lumbar decompression surgery for lumbar spinal stenosis was significantly lower in patients in the treatment group on phosphodiesterase 5 inhibitor therapy compared with the control group. Among many potential explanations, the vasodilatory effect of phosphodiesterase 5 inhibitor may have contributed to a lower surgical rate. This is the first study to explore this novel association. Future prospective studies are necessary to better define the utility of phosphodiesterase 5 inhibitor in lumbar spinal stenosis.

CDKN2A deletion is a frequent event associated with poor outcome in patients with peripheral T-cell lymphoma not otherwise specified (PTCL-NOS)

Nodal peripheral T-cell lymphoma not otherwise specified (PTCL-NOS) remains a diagnosis encompassing a heterogenous group of PTCL cases not fitting criteria for more homogeneous subtypes. They are characterized by a poor clinical outcome when treated with anthracycline-containing regimens. A better understanding of their biology could improve prognostic stratification and foster the development of novel therapeutic approaches. Recent targeted and whole exome sequencing studies have shown recurrent copy number abnormalities (CNAs) with prognostic significance. Here, investigating 5 formalin-fixed, paraffin embedded cases of PTCL-NOS by whole genome sequencing (WGS), we found a high prevalence of structural variants and complex events, such as chromothripsis likely responsible for the observed CNAs. Among them, CDKN2A and PTEN deletions emerged as the most frequent aberration, as confirmed in a final cohort of 143 patients with nodal PTCL. The incidence of CDKN2A and PTEN deletions among PTCL-NOS was 46% and 26%, respectively. Furthermore, we found that co-occurrence of CDKN2A and PTEN deletions is an event associated with PTCL-NOS with absolute specificity. In contrast, these deletions were rare and never co-occurred in angioimmunoblastic and anaplastic lymphomas. CDKN2A deletion was associated with shorter overall survival in multivariate analysis corrected by age, IPI, transplant eligibility and GATA3 expression (adjusted HR =2.53; 95% CI 1.006-6.3; p=0.048). These data suggest that CDKN2A deletions may be relevant for refining the prognosis of PTCL-NOS and their significance should be evaluated in prospective trials.

Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study

BACKGROUND

This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery.

METHODS

This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery.

RESULTS

A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498).

CONCLUSION

There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.

Occupational Health Science in the Time of COVID-19: Now more than Ever

Workers bear a heavy share of the burden of how countries contend with COVID-19; they face numerous serious threats to their occupational health ranging from those associated with direct exposure to the virus to those reflecting the conflicts between work and family demands. Ten experts were invited to comment on occupational health issues unique to their areas of expertise. The topics include work-family issues, occupational health issues faced by emergency medical personnel, the transition to telework, discrimination against Asian-Americans, work stressors, presenteeism, the need for supportive supervision, safety concerns, economic stressors, and reminders of death at work. Their comments describe the nature of the occupational health concerns created by COVID-19 and discuss both unanswered research questions and recommendations to help organizations reduce the impacts of COVID-19 on workers.

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from 38 histological cancer subtypes within the framework of the Pan-Cancer Analysis of Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired retrotransposition events, which affected 35% of samples and spanned a range of event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as the first most frequent type of somatic structural variation in esophageal adenocarcinoma, and the second most frequent in head-and-neck and colorectal cancers. Aberrant L1 integrations can delete megabase-scale regions of a chromosome, which sometimes leads to the removal of tumor-suppressor genes, and can induce complex translocations and large-scale duplications. Somatic retrotranspositions can also initiate breakage-fusion-bridge cycles, leading to high-level amplification of oncogenes. These observations illuminate a relevant role of L1 retrotransposition in remodeling the cancer genome, with potential implications for the development of human tumors.

163 Treatment with gonadotrophin-releasing hormone at the time of AI in beef heifers that fail to express oestrus after an estradiol-based synchronisation protocol improves pregnancies per AI

Oestrus expression between progesterone (P4) withdrawal and fixed-time AI (FTAI) has been shown to improve pregnancies per AI (P/AI) by 27% in beef cattle. As a result, cattle that do not express oestrus after P4 withdrawal present a challenge to the efficiency of FTAI. The present study was designed to test the hypothesis that administration of gonadotrophin-releasing hormone (GnRH) at the time of AI in heifers that do not express oestrus can improve fertility. Two-year-old Angus heifers (n=1032) with a condition score of 2.75 to 3.5 at two locations in Argentina were used. On Day 0, heifers received an intravaginal device containing 0.5g of P4 (Cronipres, Biogenesis) and 2mg of oestradiol benzoate intramuscularly (Bioestrogen, Biogenesis). On Day 8, devices were removed and heifers received 150µg of d-cloprostenol intramuscularly (Enzaprost, Biogenesis), 0.5mg of oestradiol cipionate intramuscularly (Croni-Cip, Biogenesis), and an oestrus detection patch (Estrotect, Rockway Inc.). On Day 10, AI was performed in all heifers 50 to 54h after device removal. Heifers were categorised based on oestrus expression, and those that did not express oestrus were randomised to receive 100µg of gonadorelin acetate intramuscularly (Gonasyn, Syntex; n=158) concurrent with AI or remain as untreated controls (n=151). Pregnancy was determined using ultrasonography at Days 38 and 111 after AI. Differences in fertility were evaluated using generalised linear mixed models, and the results are shown in Table 1. Oestrus expression between device removal and FTAI was 70.1% (723/1032). Pregnancies per AI at Days 38 and 111 were different between groups (P&lt;0.01). Heifers that expressed oestrus had greater P/AI than those that did not regardless of treatment (P&lt;0.01). However, in heifers that did not express oestrus, treatment with GnRH at the time of AI resulted in greater P/AI than in control heifers (P=0.004). Similarly, P/AI at Day 111 were greater in heifers that expressed oestrus than in those that did not regardless of treatment (P&lt;0.01). Heifers that did not express oestrus and were treated with GnRH had greater P/AI than those that did not express oestrus and remained as controls (P=0.02). Pregnancy loss between Days 38 and 111 was not different between groups; however, there was a tendency (P=0.06) for greater pregnancy loss in heifers that did not express oestrus and were treated with GnRH compared with heifers that expressed oestrus. In summary, treatment with GnRH at the time of AI is a suitable strategy to improve P/AI in heifers that fail to exhibit oestrus after an oestradiol-based synchronisation protocol. However, this strategy appears to increase pregnancy loss, and thus further research is needed to confirm this observation and the mechanisms underlying it. Table 1.Pregnancies per AI (P/AI) and pregnancy loss (%; no. in parentheses) in Angus heifers based on oestrus expression and treatment with GnRH Group P/AI Day 38 P/AI Day 111 Pregnancy loss Oestrus 68.9 (498/723)A 65.2 (471/723)A 5.4 (27/498) No oestrus control 29.8 (45/151)B 28.5 (43/151)B 4.4 (2/45) No oestrus + GnRH 45.6 (72/158)C 40.5 (64/158)C 11.1 (8/72) P-value &lt;0.001 &lt;0.001 0.15 A-CValues within a column with different superscripts differ significantly (P&lt;0.05).

Assessment of a large number of empirical plant species niche models by elicitation of knowledge from two national experts

Quantitative models play an increasing role in exploring the impact of global change on biodiversity. To win credibility and trust, they need validating. We show how expert knowledge can be used to assess a large number of empirical species niche models constructed for the British vascular plant and bryophyte flora. Key outcomes were (a) scored assessments of each modeled species and niche axis combination, (b) guidance on models needing further development, (c) exploration of the trade-off between presenting more complex model summaries, which could lead to more thorough validation, versus the longer time these take to evaluate, (d) quantification of the internal consistency of expert opinion based on comparison of assessment scores made on a random subset of models evaluated by both experts. Overall, the experts assessed 39% of species and niche axis combinations to be "poor" and 61% to show a degree of reliability split between "moderate" (30%), "good" (25%), and "excellent" (6%). The two experts agreed in only 43% of cases, reaching greater consensus about poorer models and disagreeing most about models rated as better by either expert. This low agreement rate suggests that a greater number of experts is required to produce reliable assessments and to more fully understand the reasons underlying lack of consensus. While area under curve (AUC) statistics showed generally very good ability of the models to predict random hold-out samples of the data, there was no correspondence between these and the scores given by the experts and no apparent correlation between AUC and species prevalence. Crowd-sourcing further assessments by allowing web-based access to model fits is an obvious next step. To this end, we developed an online application for inspecting and evaluating the fit of each niche surface to its training data.

Making real options analysis more accessible for climate change adaptation. An application to afforestation as a flood management measure in the Scottish Borders

Climate change uncertainty makes decisions for adaptation investments challenging, in particular when long time horizons and large irreversible upfront costs are involved. Often the costs will be immediate and clear, but the benefits may be uncertain and only occur in the distant future. Robust decision-making methods such as real options analysis (ROA) handle uncertainty better and are therefore useful to guide decision-making for climate change adaptation. ROA allows for learning about climate change by developing flexible strategies that can be adjusted over time. Practical examples of ROA to climate change adaptation are still relatively limited and tend to be complex. We propose an application that makes ROA more accessible to policy-makers by using the user-friendly and freely available UK climate data of the UKCP09 weather generator, which provides projections of future rainfall, deriving transition probabilities for the ROA in a straightforward way and demonstrating how the analysis can be implemented in spreadsheet format using backward induction. The application is to afforestation as a natural flood management measure (NFM) in a rural catchment in Scotland. The applicability of ROA to broadleaf afforestation as a NFM has not been previously investigated. Different ROA strategies are presented based on varying the damage cost from flooding, fixed cost and the discount rate. The results illustrate how learning can lower the overall investment cost of climate change adaptation but also that the cost structure of afforestation does not lend itself very well to ROA.

Sublethal effects of natural parasitism act through maternal, but not paternal, reproductive success in a wild population

Parasites are a major component of all animal populations. Males and females often differ in their levels of parasite prevalence, potentially leading to sex differences in the impact of parasitism on fitness, with important implications for the evolution of parasite and host traits including resistance, tolerance, and virulence. However, quantitative measures of the impact of parasitism under free‐living conditions are extremely rare, as they require detailed host demographic data with measures of parasite burden over time. Here, we use endoscopy for direct quantification of natural‐parasite burdens and relate these to reproductive success over 7 yr in a wild population of seabirds. Contrary to predictions, only female burdens were associated with negative impacts of parasitism on breeding success, despite males having significantly higher burdens. Female reproductive success declined by 30% across the range of natural parasite burdens. These effects persisted when accounting for interannual population differences in breeding success. Our results provide quantitative estimates of profound sub‐lethal effects of parasitism on the population. Importantly, they highlight how parasites act unpredictably to shape ecological and evolutionary processes in different components of the same population, with implications for demography and selection on host and parasite traits.

Integration of transcriptional and mutational data simplifies the stratification of peripheral T-cell lymphoma

The histological diagnosis of peripheral T-cell lymphoma (PTCL) can represent a challenge, particularly in the case of closely related entities such as angioimmunoblastic T-lymphoma (AITL), PTCL-not otherwise specified (PTCL-NOS), and ALK-negative anaplastic large-cell lymphoma (ALCL). Although gene expression profiling and next generations sequencing have been proven to define specific features recurrently associated with distinct entities, genomic-based stratifications have not yet led to definitive diagnostic criteria and/or entered into the routine clinical practice. Herein, to improve the current molecular classification between AITL and PTCL-NOS, we analyzed the transcriptional profiles from 503 PTCLs stratified according to their molecular configuration and integrated them with genomic data of recurrently mutated genes (RHOA ^G17V , TET2, IDH2 ^R172 , and DNMT3A) in 53 cases (39 AITLs and 14 PTCL-NOSs) included in the series. Our analysis unraveled that the mutational status of RHOA ^G17V , TET2, and DNMT3A poorly correlated, individually, with peculiar transcriptional fingerprints. Conversely, in IDH2 ^R172 samples a strong transcriptional signature was identified that could act as a surrogate for mutational status. The integrated analysis of clinical, mutational, and molecular data led to a simplified 19-gene signature that retains high accuracy in differentiating the main nodal PTCL entities. The expression levels of those genes were confirmed in an independent cohort profiled by RNA-sequencing.

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR-Cas9 screening

Many gene fusions are reported in tumours and for most their role remains unknown. As fusions are used for diagnostic and prognostic purposes, and are targets for treatment, it is crucial to assess their function in cancer. To systematically investigate the role of fusions in tumour cell fitness, we utilized RNA-sequencing data from 1011 human cancer cell lines to functionally link 8354 fusion events with genomic data, sensitivity to >350 anti-cancer drugs and CRISPR-Cas9 loss-of-fitness effects. Established clinically-relevant fusions were identified. Overall, detection of functional fusions was rare, including those involving cancer driver genes, suggesting that many fusions are dispensable for tumour fitness. Therapeutically actionable fusions involving RAF1, BRD4 and ROS1 were verified in new histologies. In addition, recurrent YAP1-MAML2 fusions were identified as activators of Hippo-pathway signaling in multiple cancer types. Our approach discriminates functional fusions, identifying new drivers of carcinogenesis and fusions that could have clinical implications.

Gene fusions are observed in many cancers but their link to tumour fitness is largely unknown. Here, transcriptomic analysis combined with pharmacological and CRISPR-Cas9 screening of cancer cell lines was used to evaluate the functional linkage between fusions and tumour fitness.

Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation

Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the distribution of PMDs within and between tumor types, and their effects on key functional genomic elements including CGIs are poorly defined. We comprehensively show that loss of methylation in PMDs occurs in a large fraction of the genome and represents the prime source of DNA methylation variation. PMDs are hypervariable in methylation level, size and distribution, and display elevated mutation rates. They impose intermediate DNA methylation levels incognizant of functional genomic elements including CGIs, underpinning a CGI methylator phenotype (CIMP). Repression effects on tumor suppressor genes are negligible as they are generally excluded from PMDs. The genomic distribution of PMDs reports tissue-of-origin and may represent tissue-specific silent regions which tolerate instability at the epigenetic, transcriptomic and genetic level.

The energetic cost of parasitism in a wild population

Parasites have profound fitness effects on their hosts, yet these are often sub-lethal, making them difficult to understand and quantify. A principal sub-lethal mechanism that reduces fitness is parasite-induced increase in energetic costs of specific behaviours, potentially resulting in changes to time and energy budgets. However, quantifying the influence of parasites on these costs has not been undertaken in free-living animals. We used accelerometers to estimate energy expenditure on flying, diving and resting, in relation to a natural gradient of endo-parasite loads in a wild population of European shags Phalacrocorax aristotelis. We found that flight costs were 10% higher in adult females with higher parasite loads and these individuals spent 44% less time flying than females with lower parasite loads. There was no evidence for an effect of parasite load on daily energy expenditure, suggesting the existence of an energy ceiling, with the increase in cost of flight compensated for by a reduction in flight duration. These behaviour specific costs of parasitism will have knock-on effects on reproductive success, if constraints on foraging behaviour detrimentally affect provisioning of young. The findings emphasize the importance of natural parasite loads in shaping the ecology and life-history of their hosts, which can have significant population level consequences.

Meaningful Partnerships: Stages of Development of a Patient and Family Advisory Council at a Family Medicine Residency Clinic

BACKGROUND

Partnering with patients and families is a crucial step in optimizing health. A patient and family advisory council (PFAC) is a group of patients and family members working together collaboratively with providers and staff to improve health care.

OBJECTIVE

This study aimed to describe the creation of a PFAC within a family medicine residency clinic. To understand the successful development of a PFAC, challenges, potential barriers, and positive outcomes of a meaningful partnership will be reported.

METHODS

The stages of PFAC development include leadership team formation and initial training, PFAC member recruitment, and meeting launch. Following a description of each stage, outcomes are outlined and lessons learned are discussed. PFAC members completed an open-ended survey and participated in a focus group interview at the completion of the first year. Interviewees provided feedback regarding (1) favorite aspects or experiences, (2) PFAC impact on a family medicine clinic, and (3) future projects to improve care. Common themes will be presented.

RESULTS

The composition of the PFAC consisted of 18 advisors, including 8 patient and family advisors, 4 staff advisors, 4 resident physician advisors, and 2 faculty physician advisors. The average meeting attendance was 12 members over 11 meetings in the span of the first year. A total of 13 out of 13 (100%) surveyed participants were satisfied with their experience serving on the PFAC.

CONCLUSIONS

PFACs provide a platform for patient engagement and an opportunity to drive home key concepts around collaboration within a residency training program. A framework for the creation of a PFAC, along with lessons learned, can be utilized to advise other residency programs in developing and evaluating meaningful PFACs.

The circular RNome of primary breast cancer

Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.

Imaging of adult intestinal failure

Intestinal failure is the inability to maintain adequate nutrition or hydration through the gut. It is caused by a diverse range of benign and malignant aetiologies. Imaging takes a central role in the multidisciplinary assessment of patients with intestinal failure.

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.

Home haemodialysis in Ireland

BACKGROUND

Home haemodialysis (HHD) has the potential to impact positively on patient outcomes and health resource management. There has been rejuvenated international interest in HHD in recent years.

AIM

We aimed to review the activity and outcomes of the Irish HHD Programme since inception (2009-16).

DESIGN

Retrospective review.

METHODS

Patient data were collected using the national electronic Renal Patient database (eMEDRenal version 3.2.1) and individual centre records. All data were recorded in a coded fashion on a Microsoft Excel Spread-sheet and analysed with Stata SE software.

RESULTS

One hundred and one patients completed training and commenced HHD; a further fourty-five patients were assessed for HHD suitability but did not ultimately dialyse at home. Twenty patients switched to nocturnal HHD when this resource became available. The switch from conventional in-centre dialysis to HHD led to an increase in the mean weekly hours on haemodialysis (HD) and a reduction in medication burden for the majority of patients. The overall rate of arteriovenous fistula (AVF) as primary vascular access was 62%. Most HHD complications were related to access function or access-related infection. Over the 7-years, 29 HHD patients were transplanted and 9 patients died. No deaths resulted directly from a HHD complication or technical issue.

CONCLUSIONS

Patient and technique survival rates compared favourably to published international reports. However, we identified several aspects that require attention. A small number of patients were receiving inadequate dialysis and require targeted education. Ongoing efforts to increase AVF and self-needling rates in HD units must continue. Psychosocial support is critical during the transition between dialysis modalities.

Psychosurgery: description and outcome study of a regional service

The report indicates that a psychosurgery service can be established on a regional basis. The outcome study of the Yorkshire Regional Psychosurgery Service indicates that the treatment should retain a place in the treatment of patients who have failed to respond to other available approaches. For such patients (and their carers) life is a state of persisting torment. Some psychiatrists consider psychosurgery as a procedure not to be countenanced, or outmoded, but patients have a right to know what may be achieved by the treatment and at what cost in terms of possible failure to improve and adverse effects. An audit of the Regional Psychosurgery Service indicates a favourable result of the Intervention. All patients improved to some extent, some very remarkably, and no adverse effects were encountered.

Validating accelerometry estimates of energy expenditure across behaviours using heart rate data in a free-living seabird

Two main techniques have dominated the field of ecological energetics: the heart rate and doubly labelled water methods. Although well established, they are not without their weaknesses, namely expense, intrusiveness and lack of temporal resolution. A new technique has been developed using accelerometers; it uses the overall dynamic body acceleration (ODBA) of an animal as a calibrated proxy for energy expenditure. This method provides high-resolution data without the need for surgery. Significant relationships exist between the rate of oxygen consumption (V̇O2 ) and ODBA in controlled conditions across a number of taxa; however, it is not known whether ODBA represents a robust proxy for energy expenditure consistently in all natural behaviours and there have been specific questions over its validity during diving, in diving endotherms. Here, we simultaneously deployed accelerometers and heart rate loggers in a wild population of European shags (Phalacrocorax aristotelis). Existing calibration relationships were then used to make behaviour-specific estimates of energy expenditure for each of these two techniques. Compared with heart rate-derived estimates, the ODBA method predicts energy expenditure well during flight and diving behaviour, but overestimates the cost of resting behaviour. We then combined these two datasets to generate a new calibration relationship between ODBA and V̇O2  that accounts for this by being informed by heart rate-derived estimates. Across behaviours we found a good relationship between ODBA and V̇O2 Within individual behaviours, we found useable relationships between ODBA and V̇O2  for flight and resting, and a poor relationship during diving. The error associated with these new calibration relationships mostly originates from the previous heart rate calibration rather than the error associated with the ODBA method. The equations provide tools for understanding how energy constrains ecology across the complex behaviour of free-living diving birds.

Assessing uncertainties in land cover projections

Understanding uncertainties in land cover projections is critical to investigating land-based climate mitigation policies, assessing the potential of climate adaptation strategies and quantifying the impacts of land cover change on the climate system. Here, we identify and quantify uncertainties in global and European land cover projections over a diverse range of model types and scenarios, extending the analysis beyond the agro-economic models included in previous comparisons. The results from 75 simulations over 18 models are analysed and show a large range in land cover area projections, with the highest variability occurring in future cropland areas. We demonstrate systematic differences in land cover areas associated with the characteristics of the modelling approach, which is at least as great as the differences attributed to the scenario variations. The results lead us to conclude that a higher degree of uncertainty exists in land use projections than currently included in climate or earth system projections. To account for land use uncertainty, it is recommended to use a diverse set of models and approaches when assessing the potential impacts of land cover change on future climate. Additionally, further work is needed to better understand the assumptions driving land use model results and reveal the causes of uncertainty in more depth, to help reduce model uncertainty and improve the projections of land cover.

Cytomegalovirus Infection and Rates of Antiviral Resistance Following Intestinal and Multivisceral Transplantation

BACKGROUND

Cytomegalovirus (CMV) disease is a common and clinically significant complication following intestinal or multivisceral transplantation. CMV disease is more common in cases of serologic mismatch between donor and recipient. Though in some cases it may be asymptomatic, in the immunosuppressed population it often manifests with evidence of systemic infection or end-organ disease.

METHODS

We conducted a retrospective review of all patients undergoing intestinal or multivisceral transplantation over 8 years at our institution.

RESULTS

Forty-eight transplantations were performed, with 40% of the patients (19/48) having ≥1 episode of CMV viremia, which rose to 90% in the "donor-positive, recipient-negative" (DPRN) serologic mismatch group. The median time to 1st episode following transplantation was 22.3 weeks (range, 1-78) and median duration of each episode was 4.9 weeks (range, 1.6-37.4). Six of the 19 viremic patients (31.6%) developed virologic resistance with 4 of these occurring in the DPRN group. Four of the 6 patients with drug-resistant CMV died with CMV viremia. All patients with drug resistance acquired ganciclovir resistance; these patients were more challenging to manage with second-line toxicity-limited treatments, including foscarnet, cidofovir, and leflunomide. CMV immunoglobulin has been used and we briefly discuss the use of CMV-specific adoptive T-lymphocyte transfer in the management of 1 case.

CONCLUSIONS

Post-transplantation CMV disease continues to be challenging to manage, and there is little consensus on optimal management strategies in this patient group, with a significant requirement for novel therapies; these may be pharmacologic or cell based. Extensive multidisciplinary discussion is important for most cases, but particularly for those patients who acquire virologic resistance.

Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration

A recent comprehensive whole genome analysis of a large breast cancer cohort was used to link known and novel drivers and substitution signatures to the transcriptome of 266 cases. Here, we validate that subtype-specific aberrations show concordant expression changes for, for example, TP53, PIK3CA, PTEN, CCND1 and CDH1. We find that CCND3 expression levels do not correlate with amplification, while increased GATA3 expression in mutant GATA3 cancers suggests GATA3 is an oncogene. In luminal cases the total number of substitutions, irrespective of type, associates with cell cycle gene expression and adverse outcome, whereas the number of mutations of signatures 3 and 13 associates with immune-response specific gene expression, increased numbers of tumour-infiltrating lymphocytes and better outcome. Thus, while earlier reports imply that the sheer number of somatic aberrations could trigger an immune-response, our data suggests that substitutions of a particular type are more effective in doing so than others.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

We analysed whole-genome sequences of 560 breast cancers to advance understanding of the driver mutations conferring clonal advantage and the mutational processes generating somatic mutations. We found that 93 protein-coding cancer genes carried probable driver mutations. Some non-coding regions exhibited high mutation frequencies, but most have distinctive structural features probably causing elevated mutation rates and do not contain driver mutations. Mutational signature analysis was extended to genome rearrangements and revealed twelve base substitution and six rearrangement signatures. Three rearrangement signatures, characterized by tandem duplications or deletions, appear associated with defective homologous-recombination-based DNA repair: one with deficient BRCA1 function, another with deficient BRCA1 or BRCA2 function, the cause of the third is unknown. This analysis of all classes of somatic mutation across exons, introns and intergenic regions highlights the repertoire of cancer genes and mutational processes operating, and progresses towards a comprehensive account of the somatic genetic basis of breast cancer.