SPEDE-sampler: An R Shiny application to assess how methodological choices and taxon sampling can affect Generalized Mixed Yule Coalescent output and interpretation.

Species delimitation tools are vital to taxonomy and the discovery of new species. These tools can make use of genetic data to estimate species boundaries, where one of the most widely used methods is the Generalized Mixed Yule Coalescent (GMYC) model. Despite its popularity, a number of factors are known to influence the performance and resulting inferences of the GMYC. Moreover, the few studies that have assessed model performance to date have been predominantly based on simulated data sets, where model assumptions are not violated. Here, we present a user-friendly R Shiny application, 'SPEDE-sampler' (SPEcies DElimitation sampler), that assesses the effect of computational and methodological choices, in combination with sampling effects, on the GMYC model. Output phylogenies are used to test the effect that (1) sample size, (2) BEAST and GMYC parameters (e.g. prior settings, single vs multiple threshold, clock model), and (3) singletons have on GMYC output. Optional predefined grouping information (e.g. morphospecies/ecotypes) can be uploaded in order to compare it with GMYC species and estimate percentage match scores. Additionally, predefined groups that contribute to inflated species richness estimates are identified by SPEDE-sampler, allowing for the further investigation of potential cryptic species or geographical substructuring in those groups. Merging by the GMYC is also recorded to identify where traditional taxonomy has overestimated species numbers. Four worked examples are provided to illustrate the functionality of the program's workflow, and the variation that can arise when applying the GMYC model to empirical data sets. The R Shiny program is available for download at https://github.com/clarkevansteenderen/spede_sampler_R.

Subacute cutaneous lupus erythematosus and dermatomyositis associated with anti-programmed cell death 1 therapy.

Programmed cell death 1 (PD-1) blockade has rapidly emerged as an effective therapy for a wide variety of metastatic malignancies. It has been associated with multiple immune-related adverse effects, including cutaneous eruptions. We describe two patients with clinical and histological findings that were consistent with subacute cutaneous lupus erythematosus (SCLE) after receiving PD-1 inhibitor therapy for metastatic lung cancer. We successfully treated our first patient with systemic and topical steroids, photoprotection and hydroxychloroquine. However, he subsequently developed dermatomyositis after continuing PD-1 inhibitor therapy. Our second patient presented with a protracted course of a cutaneous eruption in spite of discontinuation of anti-PD-1 therapy and treatment with systemic corticosteroids and infliximab. This patient's SCLE resolved after the addition of topical steroids and photoprotection and discontinuation of anti-tumour necrosis factor therapy. She and her oncology team decided to pursue non-PD-1 inhibitor treatment for lung cancer owing to a lack of tumour response. We add SCLE and dermatomyositis to the growing list of autoimmune complications of PD-1 blockade. Our cases raise a number of questions, particularly in relation to the viability of continuing anti-PD-1 therapy after developing SCLE and the role of immunosuppressive therapy in patients with PD-1 inhibitor-associated connective tissue disease. What's already known about this topic? Programmed cell death 1 (PD-1) blockade, which is rapidly emerging as a therapy for a wide variety of metastatic malignancies, has been associated with multiple immune-related adverse effects. These include systemic autoimmune diseases such as colitis and thyroiditis in addition to numerous cutaneous adverse events. Cutaneous side-effects of PD-1 inhibitors most commonly reported in clinical trials include lichenoid reactions, eczematous dermatitis and vitiligo. What does this study add? We report two cases of PD-1 inhibitor-associated subacute cutaneous lupus erythematosus (SCLE), with one patient progressing to dermatomyositis with continued PD-1 inhibitor treatment. In addition to being a novel cutaneous adverse event, we also demonstrate the possibility of development of multiple autoimmune diseases in one patient, which is different from classic drug-related SCLE. We discuss the treatment challenges for patients with autoimmune skin disease receiving PD-1 inhibitor therapy.

Pilot feasibility study examining a structured self-management diabetes education programme, DESMOND-ID, targeting HbA1c in adults with intellectual disabilities.

AIM: To report on the outcomes of a pilot feasibility study of a structured self-management diabetes education programme targeting HbA1c . METHODS: We conducted a two-arm, individually randomized, pilot superiority trial for adults with intellectual disability and Type 2 diabetes mellitus. A total of 66 adults with disabilities across the UK met the eligibility criteria. Of these, 39 agreed to participate and were randomly assigned to either the DESMOND-ID programme (n = 19) or a control group (n = 20). The programme consisted of seven weekly educational sessions. The primary outcome was HbA1c level, and secondary outcomes included BMI, diabetes illness perceptions, severity of diabetes, quality of life, and attendance rates. RESULTS: This study found that the DESMOND-ID programme was feasible to deliver. With reasonable adjustments, the participants could be recruited successfully, and could provide consent, complete the outcome measures, be randomized to the groups and attend most of the sessions, with minimal loss to follow-up. The fixed-effects model, the interaction between occasion (time) and condition, showed statistically significant results (0.05 level) for HbA1c ; however, the CI was large. CONCLUSION: This is the first published study to adapt and pilot a national structured self-management diabetes education programme for adults with intellectual disability. This study shows it is possible to identify, recruit, consent and randomize adults with intellectual disabilities to an intervention or control group. Internationally, the results of this pilot are promising, demonstrating that a multi-session education programme is acceptable and feasible to deliver. Its effectiveness should be further tested in an adequately powered trial.

Understanding the mechanisms of action of antiangiogenic agents in metastatic colorectal cancer: a clinician's perspective.

Multiple clinical trials using bevacizumab, ziv-aflibercept, and regorafenib have recently demonstrated efficacy for patients with metastatic colorectal cancer. While the net clinical benefit of each of these therapies in the second-line and refractory disease setting appears to be similar, important distinctions exist between the agents at the pharmacodynamic, tumor microenvironment, and clinical levels. The purpose of this review is to survey the preclinical evidence regarding the mechanisms of action of these novel antiangiogenic agents and provide an overview of their respective clinical activity, while highlighting distinctions between therapies. Fundamental understanding of these distinctions may aid in clinical decisions and choice of antiangiogenic therapies.

Genetics of pre-harvest sprouting resistance in a cross of Canadian adapted durum wheat genotypes.

Severe losses attributable to pre-harvest sprouting (PHS) have been reported in Canada in recent years. The genetics of PHS resistance have been more extensively studied in hexaploid wheat and generally not using combinations of elite agronomic parents. The objective of our research was to understand the genetic nature of PHS resistance in an elite durum cross. A doubled haploid (DH) population and checks were phenotyped in replicated trials for grain yield and PHS traits over 3 years in western Canada. The response of intact spikes to sprouting conditions, sampled over two development time points, was measured in a rain simulation chamber. The DH population was genotyped with simple sequence repeat and Diversity Arrays Technology markers. Genotypes were a significant source of variation for grain yield and PHS resistance traits in each tested environment. Transgressive segregant DH genotypes were identified for grain yield and PHS resistance measurements. Low or no correlation was detected between grain yield and PHS, while correlation between PHS resistance measurements was moderate. The heritability of PHS resistance was moderate and higher than grain yield. Significant quantitative trait loci with small effect were detected on chromosomes 1A, 1B, 5B, 7A and 7B. Both parents contributed to the PHS resistance. Promising DH genotypes with high and stable grain yield as well as PHS resistance were identified, suggesting that grain yield and PHS can be improved simultaneously in elite genetic materials, and that these DH genotypes will be useful parental material for durum breeding programs.

Identification and mapping of leaf, stem and stripe rust resistance quantitative trait loci and their interactions in durum wheat.

Leaf rust (Puccinia triticina Eriks.), stripe rust (Puccinia striiformis f. tritici Eriks.) and stem rust (Puccinia graminis f. sp. tritici) cause major production losses in durum wheat (Triticum turgidum L. var. durum). The objective of this research was to identify and map leaf, stripe and stem rust resistance loci from the French cultivar Sachem and Canadian cultivar Strongfield. A doubled haploid population from Sachem/Strongfield and parents were phenotyped for seedling reaction to leaf rust races BBG/BN and BBG/BP and adult plant response was determined in three field rust nurseries near El Batan, Obregon and Toluca, Mexico. Stripe rust response was recorded in 2009 and 2011 nurseries near Toluca and near Njoro, Kenya in 2010. Response to stem rust was recorded in field nurseries near Njoro, Kenya, in 2010 and 2011. Sachem was resistant to leaf, stripe and stem rust. A major leaf rust quantitative trait locus (QTL) was identified on chromosome 7B at Xgwm146 in Sachem. In the same region on 7B, a stripe rust QTL was identified in Strongfield. Leaf and stripe rust QTL around DArT marker wPt3451 were identified on chromosome 1B. On chromosome 2B, a significant leaf rust QTL was detected conferred by Strongfield, and at the same QTL, a Yr gene derived from Sachem conferred resistance. Significant stem rust resistance QTL were detected on chromosome 4B. Consistent interactions among loci for resistance to each rust type across nurseries were detected, especially for leaf rust QTL on 7B. Sachem and Strongfield offer useful sources of rust resistance genes for durum rust breeding.

Novel therapies for the treatment of advanced prostate cancer.

In recent years, great success has been achieved on many fronts in the treatment of men with metastatic castration-resistant prostate cancer (CRPC), including novel chemotherapeutics, immunotherapies, bone microenvironment-targeted agents, and hormonal therapies. Numerous agents are currently in early-phase clinical trial development for the treatment of advanced prostate cancer. These novel therapies target several areas of prostate tumor biology, including the upregulation of androgen signaling and biosynthesis, critical oncogenic intracellular pathways, epigenetic alterations, and cancer immunology. Importantly, the characterization of the prostate cancer genome offers the potential to exploit conserved genetic alterations, which may increase the efficacy of these targeted therapies. Predictive and prognostic biomarkers are urgently needed to maximize therapeutic efficacy and safety of these promising new treatments options in prostate cancer.

Role of ultrasonography in the diagnosis of temporal arteritis.

BACKGROUND: Temporal artery (TA) biopsy is the current standard for diagnosing temporal arteritis, but has limited sensitivity. Colour duplex ultrasonography is a newer, non-invasive method of diagnosing temporal arteritis. METHODS: A systematic review was performed of trials comparing TA biopsy with duplex ultrasonography. Duplex results (halo sign, stenosis or vessel occlusion) were compared with either TA biospy findings or the American College of Rheumatology research criteria for diagnosing temporal arteritis. Trials were identified from MEDLINE, Embase and the Cochrane Library trials register. The performance of duplex ultrasonography was assessed with weighted independent sensitivity and specificity values, and summary receiver operating characteristic curve analysis. RESULTS: There were 17 eligible studies containing 998 patients. When the halo sign on duplex imaging was compared with TA biopsy, the sensitivity was 75 (95 per cent confidence interval 67 to 82) per cent and the specificity was 83 (78 to 88) per cent. There was no heterogeneity across the eligible studies. CONCLUSION: Duplex ultrasonography was relatively accurate for diagnosing temporal arteritis. It should become the first-line investigation, with biopsy reserved for patients with a negative scan.

Targeted mapping of Cdu1, a major locus regulating grain cadmium concentration in durum wheat (Triticum turgidum L. var durum).

Some durum wheat (Triticum turgidum L. var durum) cultivars have the genetic propensity to accumulate cadmium (Cd) in the grain. A major gene controlling grain Cd concentration designated as Cdu1 has been reported on 5B, but the genetic factor(s) conferring the low Cd phenotype are currently unknown. The objectives of this study were to saturate the chromosomal region harboring Cdu1 with newly developed PCR-based markers and to investigate the colinearity of this wheat chromosomal region with rice (Oryza sativa L.) and Brachypodium distachyon genomes. Genetic mapping of markers linked to Cdu1 in a population of recombinant inbred substitution lines revealed that the gene(s) associated with variation in Cd concentration resides in wheat bin 5BL9 between fraction breakpoints 0.76 and 0.79. Genetic mapping and quantitative trait locus (QTL) analysis of grain Cd concentration was performed in 155 doubled haploid lines from the cross W9262-260D3 (low Cd) by Kofa (high Cd) revealed two expressed sequence tag markers (ESMs) and one sequence tagged site (STS) marker that co-segregated with Cdu1 and explained >80% of the phenotypic variation in grain Cd concentration. A second, minor QTL for grain Cd concentration was also identified on 5B, 67 cM proximal to Cdu1. The Cdu1 interval spans 286 kbp of rice chromosome 3 and 282 kbp of Brachypodium chromosome 1. The markers and rice and Brachypodium colinearity described here represent tools that will assist in the positional cloning of Cdu1 and can be used to select for low Cd accumulation in durum wheat breeding programs targeting this trait. The isolation of Cdu1 will further our knowledge of Cd accumulation in cereals as well as metal accumulation in general.

Case series and literature review: popliteal artery injury following total knee replacement.

We present a case series and literature review of injury to the popliteal vessels during total knee replacement (TKR). This is rare but may be limb-threatening with devastating consequences for the patient. An individual surgeon will see few cases. Over a 28-month period 3913 elective TKRs were performed at three hospitals in East Anglia, United Kingdom. We present nine cases (0.23%) of popliteal artery injury following TKR. All required further investigation and intervention. The range of pathology included intra-operative haemorrhage (3 cases), thrombosis (2 cases), pseudo-aneurysm (3 cases) and arteriovenous fistula (1 case). Definitive treatment of the arterial injury was by primary repair (4 cases), interposition graft (2 cases), bypass graft (2 cases), endovascular stenting (1 case) and primary above-knee amputation (AKA; 1 case). There was morbidity in four patients: two AKAs, one case of foot-drop, and one unsightly fasciotomy scar. There was no mortality. Compared to other published studies (totalling 141 cases) complications resulting from direct arterial injury were significantly more common in our series. Incidence remains steady. More careful surgical technique may be the most effective preventative measure. Ongoing awareness is therefore essential for early diagnosis and management of this rare but serious complication.

Anaesthetic specialisation leads to improved early- and medium-term survival following major vascular surgery.

OBJECTIVE: Vascular surgical specialisation is associated with improved outcomes. We aimed to assess the effect of anaesthetic specialisation on outcome following major vascular surgery. DESIGN: Retrospective cohort study. METHODS: Patients undergoing major vascular surgery (lower limb revascularisation, elective and ruptured abdominal aortic aneurysm repair, endovascular aneurysm repair and carotid endarterectomy) over a five-year period were identified from a prospective database. The primary outcomes were death within 30 days and death within two years of surgery. Potential risk factors for mortality were assessed using multivariate logistic regression modelling. RESULTS: The analysis cohort comprised 1155 patients followed up for a median of 583 days. Mortality within two years of surgery was 16%. For the overall cohort, care from vascular anaesthetists was independently associated with reduced 30-day (odds ratio 0.22; 95% CI 0.12-0.62) and medium-term mortality (0.31; 95% CI 0.18-0.55). For elective patients (n=851), vascular anaesthesia reduced two-year mortality (odds ratio 0.29; 95% CI 0.15-0.58; P=0.0004) though not 30-day mortality (odds ratio 0.55; 95% CI 0.15-1.95; P=0.35). For emergency patients, care by a vascular anaesthetist influenced neither 30-day mortality (odds ratio 0.33; 95% CI 0.08-1.41; P=0.13) nor medium-term mortality (odds ratio 0.45; 95% CI 0.17-1.21; P=0.11). CONCLUSIONS: Anaesthetic specialisation reduced early- and medium-term mortality rates following major vascular surgery. If replicated by prospective studies, these results suggest that vascular surgery services would benefit from specialised anaesthetic support.

Chromosomal location of the cadmium uptake gene (Cdu1) in durum wheat.

Levels of the heavy metal cadmium (Cd) in food products are a food safety concern. Grain Cd is higher in durum (Triticum turgidum L. var. durum) than in common wheat, so reduction of Cd in durum grain is a priority of breeding programs. Previous research demonstrated that a single dominant gene, Cdu1, confers the low grain Cd phenotype, but the map location of the gene is not known. A doubled haploid population segregating for Cd concentration, developed from the cross of W9262-260D3 (a Kyle*2/Biodur inbred selection with low Cd uptake) and Kofa (high Cd uptake) and mapped with microsatellite markers, was used to locate Cdu1. Grain Cd concentration was determined by standard laboratory methods on field grain samples in 2000 and 2001. The Cd concentration segregated bimodally, allowing Cdu1 to be mapped qualitatively as well as quantitatively with quantitative trait locus analysis. The Cdu1 gene mapped to the long arm of chromosome 5B.

Identification and validation of quantitative trait loci for grain protein concentration in adapted Canadian durum wheat populations.

Grain protein concentration (GPC) is one of the most important factors influencing pasta-making quality. Durum wheat (Triticum turgidum L. var durum) cultivars with high GPC produce pasta with increased tolerance to overcooking and greater cooked firmness. However, the large environmental effect on expression of GPC and the negative correlation with grain yield have slowed genetic improvement of this important trait. Understanding the genetics and identification of molecular markers associated with high GPC would aid durum wheat breeders in trait selection at earlier generations. The objectives of this study were to identify and validate molecular markers associated with quantitative trait loci (QTL) for elevated GPC in durum wheat. A genetic map was constructed using SSR and DArT markers in an F(1)-derived doubled haploid (DH) population derived from the cross DT695 x Strongfield. The GPC data were collected from replicated trials grown in six Canadian environments from 2002 to 2005. QTL associated with variation for GPC were identified on the group 1, 2, and 7 chromosomes and on 5B and 6B, but only QGpc.usw-B3 on 2B and QGpc.usw-A3 on 7A were expressed consistently in four and six environments, respectively. Positive alleles for GPC at these loci were contributed by the high-GPC parent Strongfield. The QGpc.usw-A3 QTL was validated in a second DH population, and depending on environment, selection for the Strongfield allele at barc108 resulted in +0.4% to +1.0% increase in GPC, with little effect on yield in most environments. Given the consistent expression pattern in multiple populations and environments, barc108 could be useful for marker-assisted selection for high GPC.

Allelic variation at Psy1-A1 and association with yellow pigment in durum wheat grain.

The yellow pigment (YP) of durum wheat (Triticum turgidum L. var durum) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait. Phytoene synthase (Psy) is considered a rate-limiting enzyme in the carotenoid biosynthetic pathway and in this study, three alleles of Psy1-A1 were sequenced from four durum wheat cultivars and a co-dominant marker was developed for genetic mapping. Psy1-A1 mapped to chromosome 7AL near Xwmc809 in three durum mapping populations and was significantly associated with a pigment quantitative trait loci (QTL) identified on that chromosome. A second QTL localized 25 cM proximal to Psy1-A1 in two populations, and the interaction between the two QTL was not significant. Consistent with QTL mapping data, the Psy1-A1o allele was associated with elevated pigment in a validation population comprising 93 diverse cultivars and breeding lines. These results confirm an earlier hypothesis that Psy1, and at least one additional gene in the distal region of 7AL, are associated with grain YP differences in durum wheat. The functional co-dominant marker developed in this study differentiates the Psy1-A1 alleles reported here and could be used as a target to enhance YP selection in durum wheat breeding programs.

Association mapping of yellow pigment in an elite collection of durum wheat cultivars and breeding lines.

Association mapping (AM) is an alternative or complementary strategy to QTL mapping for describing associations between genotype and phenotype based on linkage disequilibrium (LD). Yellow pigment (YP), an important end-use quality trait in durum wheat (Triticum turgidum L. var. durum), was evaluated to determine the ability of AM to identify previously published QTL and to identify genomic regions for further genetic dissection. The YP concentration was determined for 93 durum wheat accessions sampled from a variety of geographic origins. Analysis of population structure using distance- and model-based estimates indicated the presence of five subpopulations. Using subpopulation assignments as covariates, significant (P < 0.05) marker-trait associations for YP were detected on all chromosomes of the durum genome. Using AM, genomic regions housing known YP QTL were confirmed, most notably the group 7 chromosomes. In addition, several markers on the group 1, 2, and 3 chromosomes were identified where QTL have yet to be reported. A phytoene synthase gene, Psy1-B1, a potential candidate gene for YP, was significantly associated with YP and was in strong LD with microsatellite markers on the distal end of 7BL. Our results demonstrated that AM complemented traditional QTL mapping techniques and identified novel QTL that should be the target of further genetic dissection.

Selection and breeding of plant cultivars to minimize cadmium accumulation.

Natural variation occurs in the uptake and distribution of essential and nonessential trace elements among crop species and among cultivars within species. Such variation can be responsible for trace element deficiencies and toxicities, which in turn can affect the quality of food. Plant breeding can be an important tool to both increase the concentration of desirable trace elements and reduce that of potentially harmful trace elements such as cadmium (Cd). Selection programs for a low-Cd content of various crops, including durum wheat, sunflower, rice and soybean have been established and low-Cd durum wheat cultivars and sunflower hybrids have been developed. In durum wheat (Triticum turgidum L. var durum), low-Cd concentration is controlled by a single dominant gene. The trait is highly heritable, and incorporation of the low-Cd allele can help to reduce the average grain Cd to levels below proposed international limits. The allele for low-Cd concentration does not appear to affect major economic traits and should not cause problems when incorporated into durum cultivars. The cost of Cd selection in a breeding program is initially large both in terms of Cd determination and reduced progress towards development of other economic traits, but declines as more breeding lines in the program carry the low-Cd trait and are utilized in new crosses. Production of low-Cd crop cultivars can be used as a tool to reduce the risk of movement of Cd into the human diet.

Identification of QTL and association of a phytoene synthase gene with endosperm colour in durum wheat.

The yellow colour of durum wheat (Triticum turgidum L. var durum) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait. We hypothesized that variation in the genes coding for phytoene synthase (Psy), a critical enzyme in carotenoid biosynthesis, may partially explain the phenotypic variation in endosperm colour observed among durum cultivars. Using rice sequence information, primers were designed to PCR clone and sequence the Psy genes from Kofa (high colour) and W9262-260D3 (medium colour) durum cultivars. Sequencing confirmed the presence of four Psy genes in each parent, corresponding to a two member gene family designated as Psy1-1, Psy1-2 and Psy2-1 and Psy2-2. A genetic map was constructed using 155 F1-derived doubled haploid lines from the cross W9262-260D3/Kofa with 194 simple sequence repeat and DArT markers. Using Psy1-1 and Psy2-1 allele-specific markers and chromosome mapping, the Psy1 and Psy2 genes were located to the group 7 and 5 chromosomes, respectively. Four quantitative trait loci (QTL) underlying phenotypic variation in endosperm colour were identified on chromosomes 2A, 4B, 6B, and 7B. The Psy1-1 locus co-segregated with the 7B QTL, demonstrating an association of this gene with phenotypic variation for endosperm colour. This work is the first report of mapping Psy genes and supports the role of Psy1-1 in elevated levels of endosperm colour in durum wheat. This gene is a target for the further development of a molecular marker to enhance selection for endosperm colour in durum wheat breeding programs.

Effect of season and temperature on mortality in amphibians due to chytridiomycosis.

OBJECTIVE: To investigate the distribution and incidence of chytridiomycosis in eastern Australian frogs and to examine the effects of temperature on this disease. DESIGN: A pathological survey and a transmission experiment were conducted. PROCEDURE: Diagnostic pathology examinations were performed on free-living and captive, ill and dead amphibians collected opportunistically from eastern Australia between October 1993 and December 2000. We conducted a transmission experiment in the laboratory to investigate the effects of temperature: eight great barred frogs (Mixophyes fasciolatus) exposed to zoospores of Batrachochytrium dendrobatidis and six unexposed frogs were housed individually in each of three rooms held at 17 degrees C, 23 degrees C and 27 degrees C. RESULTS: Chytridiomycosis was the cause of death or morbidity for 133 (55.2%) of 241 free-living amphibians and for 66 (58.4%) of 113 captive amphibians. This disease occurred in 34 amphibian species, was widespread around the eastern seaboard of Australia and affected amphibians in a variety of habitats at high and low altitudes on or between the Great Dividing Range and the coast. The incidence of chytridiomycosis was higher in winter, with 53% of wild frogs from Queensland and New South Wales dying in July and August. Other diseases were much less common and were detected mostly in spring and summer. In experimental infections, lower temperatures enhanced the pathogenicity of B. dendrobatidis in M. fasciolatus. All 16 frogs exposed to B. dendrobatidis at 17 degrees C and 23 degrees C died, whereas 4 of 8 frogs exposed at 27 degrees C survived. However, the time until death for the frogs that died at 27 degrees C was shorter than at the lower temperatures. Infections in survivors were eliminated by 98 days. CONCLUSION: Chytridiomycosis is a major cause of mortality in free-living and captive amphibians in Australia and mortality rate increases at lower temperatures.