Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici

Zymoseptoria tritici is a host-specific, necrotrophic pathogen of wheat. Infection by Z. tritici is characterized by its extended latent period, which typically lasts two weeks, and is followed by extensive host cell death and rapid proliferation of fungal biomass. This work characterizes the level of genomic variation in 13 isolates for which we have measured virulence on 11 wheat cultivars with differential resistance genes. Between the reference isolate, IPO323, and the 13 Australian isolates we identified over 800,000 single nucleotide polymorphisms, of which ~10% had an effect on the coding regions of the genome. Furthermore we identified over 1700 probable presence/absence polymorphisms in genes across the Australian isolates using de novo assembly. Finally, we developed a gene tree sorting method that quickly identifies groups of isolates within a single gene alignment whose sequence haplotypes correspond with virulence scores on a single wheat cultivar. Using this method we have identified <100 candidate effector genes whose gene sequence correlates with virulence towards a wheat cultivar carrying a major resistance gene

The significance and lag-time of deep through flow: an example from a small, ephemeral catchment with contrasting soil types in the Adelaide Hills, South Australia

The importance of deep throughflow in a small (3.4 km2) ephemeral catchment in the Adelaide Hills of South Australia was investigated by detailed hydrochemical analysis of soil water and stream flow during autumn and early winter rains. In this Mediterranean climate with strong summer moisture deficits, several significant rainfalls are required to generate soil throughflow and stream flow (in ephemeral streams). During Autumn 2007, a large (127 mm) drought-breaking rain occurred in April followed by significant May rains; most of this precipitation occurred prior to the initiation of stream flow in late May. These early events, especially the 127 mm event, had low (depleted) stable water isotope values compared with both later rains and average winter precipitation. Thus, this large depleted early rain event provided an excellent natural tracer. During the June and July rainfall events, daily stream and soil water samples were collected and analysed. Results from major and trace elements, water isotopes (δ18O, δD), and dissolved organic carbon analysis clearly demonstrate that a large component of this early April and May rain was stored and later pushed out of deep soil or regolith zones. This pre-event water was identified in the stream as well as identified in deeper soil horizons due to its different isotopic signature which contrasted sharply with the June–July event water. Based on this data, the regolith and throughflow system for this catchment has been re-thought. The catchment area consists of about half sandy and half clayey soils. Regolith flow is now thought to be dominated by the sandy soil system not the clayey soil system. The clayey duplex soils had rapid response to rain events and saturation excess overland flow. The sandy soils had delayed soil throughflow and infiltration excess overland flow. A pulse of macropore throughflow was observed in the sandy soils three days after the rainfall event largely ended. The macropore water was a mixture of pre-event and event water, demonstrating the lag-time and mixing of the water masses in the sandy soil system. By contrast, the clayey soil horizons were dominated by pre-event water to a much lesser degree, demonstrating the quicker response and shallow flow through of the clayey soil system. Thus, the sandy terrain has a greater vadose zone storage and greater lag time of through-flow than the clayey terrain.E. Bestland, S. Milgate, D. Chittleborough, J. VanLeeuwen, M. Pichler and L. Solonink

Hospital Performance, the Local Economy, and the Local Workforce: Findings from a US National Longitudinal Study

Blustein and colleagues examine the associations between changes in hospital performance and their local economic resources. Locationally disadvantaged hospitals perform poorly on key indicators, raising concerns that pay-for-performance models may not reduce inequality

The European Union in disequilibrium: new intergovernmentalism, postfunctionalism and integration theory in the post-Maastricht period

The crises that weigh heavily on the European Union (EU) in the 2010s have underlined the continued importance of integration theory, albeit in ways that go beyond classic debates. Postfunctionalism, in particular, has shown how European integration and its problems stand on shifting political cleavages. And yet, postfunctionalist claims that such changes would create a constraining dissensus in the EU rests uneasily with the intensification of European integration since the Maastricht Treaty was signed. This article offers a new intergovernmentalist explanation of this puzzle, which shows how mainstream governing parties have circumvented rather than being constrained by Eurosceptic challenger parties and challenger governments. The result, it contends, is not a constraining but a destructive dissensus that adds to the EU’s political disequilibrium. Understanding the persistence of this disequilibrium and its potential to unwind disruptively is a key challenge for contemporary integration theory

Schools out : Adam Smith and pre-disciplinary international political economy

In this article, I argue that invocations of Adam Smith in international political economy (IPE) often reveal the influence therein of a disciplinary ontological disaggregation of economic and non-economic rationality, which I claim is obscured by the tendency to map its complex intellectual contours in terms of competing schools. I trace the origins of the disciplinary characterisation of Smith as the founder of IPE's liberal tradition to invocations of his thought by centrally important figures in the perceived Austrian, Chicago and German historical schools of economics, and reflect upon the significance to IPE of the reiteration of this portrayal by apparent members of its so-called American and British schools. I additionally contrast these interpretations to those put forward by scholars who seek to interpret IPE and Smith's contribution to it in pre-disciplinary terms, which I claim reflects a distinct ontology to that attributed to the British school of IPE with which their work is often associated. I therefore contend that reflection upon invocations of Smith's thought in IPE problematises the longstanding tendency to map its intellectual terrain in terms of competing schools, reveals that the disciplinary ontological consensus that informs this tendency impacts upon articulations of its core concerns and suggests that a pre-disciplinary approach offers an alternative lens through which such concerns might be more effectively framed

Impact of renal impairment on atrial fibrillation: ESC-EHRA EORP-AF Long-Term General Registry

Background: Atrial fibrillation (AF) and renal impairment share a bidirectional relationship with important pathophysiological interactions. We evaluated the impact of renal impairment in a contemporary cohort of patients with AF. Methods: We utilised the ESC-EHRA EORP-AF Long-Term General Registry. Outcomes were analysed according to renal function by CKD-EPI equation. The primary endpoint was a composite of thromboembolism, major bleeding, acute coronary syndrome and all-cause death. Secondary endpoints were each of these separately including ischaemic stroke, haemorrhagic event, intracranial haemorrhage, cardiovascular death and hospital admission. Results: A total of 9306 patients were included. The distribution of patients with no, mild, moderate and severe renal impairment at baseline were 16.9%, 49.3%, 30% and 3.8%, respectively. AF patients with impaired renal function were older, more likely to be females, had worse cardiac imaging parameters and multiple comorbidities. Among patients with an indication for anticoagulation, prescription of these agents was reduced in those with severe renal impairment, p <.001. Over 24 months, impaired renal function was associated with significantly greater incidence of the primary composite outcome and all secondary outcomes. Multivariable Cox regression analysis demonstrated an inverse relationship between eGFR and the primary outcome (HR 1.07 [95% CI, 1.01–1.14] per 10 ml/min/1.73 m2 decrease), that was most notable in patients with eGFR <30 ml/min/1.73 m2 (HR 2.21 [95% CI, 1.23–3.99] compared to eGFR ≥90 ml/min/1.73 m2). Conclusion: A significant proportion of patients with AF suffer from concomitant renal impairment which impacts their overall management. Furthermore, renal impairment is an independent predictor of major adverse events including thromboembolism, major bleeding, acute coronary syndrome and all-cause death in patients with AF

Clinical complexity and impact of the ABC (Atrial fibrillation Better Care) pathway in patients with atrial fibrillation: a report from the ESC-EHRA EURObservational Research Programme in AF General Long-Term Registry

Background: Clinical complexity is increasingly prevalent among patients with atrial fibrillation (AF). The ‘Atrial fibrillation Better Care’ (ABC) pathway approach has been proposed to streamline a more holistic and integrated approach to AF care; however, there are limited data on its usefulness among clinically complex patients. We aim to determine the impact of ABC pathway in a contemporary cohort of clinically complex AF patients. Methods: From the ESC-EHRA EORP-AF General Long-Term Registry, we analysed clinically complex AF patients, defined as the presence of frailty, multimorbidity and/or polypharmacy. A K-medoids cluster analysis was performed to identify different groups of clinical complexity. The impact of an ABC-adherent approach on major outcomes was analysed through Cox-regression analyses and delay of event (DoE) analyses. Results: Among 9966 AF patients included, 8289 (83.1%) were clinically complex. Adherence to the ABC pathway in the clinically complex group reduced the risk of all-cause death (adjusted HR [aHR]: 0.72, 95%CI 0.58–0.91), major adverse cardiovascular events (MACEs; aHR: 0.68, 95%CI 0.52–0.87) and composite outcome (aHR: 0.70, 95%CI: 0.58–0.85). Adherence to the ABC pathway was associated with a significant reduction in the risk of death (aHR: 0.74, 95%CI 0.56–0.98) and composite outcome (aHR: 0.76, 95%CI 0.60–0.96) also in the high-complexity cluster; similar trends were observed for MACEs. In DoE analyses, an ABC-adherent approach resulted in significant gains in event-free survival for all the outcomes investigated in clinically complex patients. Based on absolute risk reduction at 1 year of follow-up, the number needed to treat for ABC pathway adherence was 24 for all-cause death, 31 for MACEs and 20 for the composite outcome. Conclusions: An ABC-adherent approach reduces the risk of major outcomes in clinically complex AF patients. Ensuring adherence to the ABC pathway is essential to improve clinical outcomes among clinically complex AF patients