Signatures of modulated pair interaction in cuprate superconductors

Recent low-temperature scanning tunnelling spectroscopy experiments on the surface of BSCCO-2212 have revealed a strong positive correlation between the position of localized resonances at -960 meV identified with interstitial oxygen dopants and the size of the local spectral gap. We review efforts to understand these correlations within a model where the dopants modulate the pair interaction on an atomic scale. We provide further evidence for this model by comparing the correlations between the dopants and the local density of states with experimental results.Comment: 4 pages, 2 figures, submitted to M2S-HTSC VIII, Dresden 200

Principles of resilient coding for plant ecophysiologists

Plant ecophysiology is founded on a rich body of physical and chemical theory, but it is challenging to connect theory with data in unambiguous, analytically rigorous and reproducible ways. Custom scripts written in computer programming languages (coding) enable plant ecophysiologists to model plant processes and fit models to data reproducibly using advanced statistical techniques. Since many ecophysiologists lack formal programming education, we have yet to adopt a unified set of coding principles and standards that could make coding easier to learn, use and modify. We identify eight principles to help in plant ecophysiologists without much programming experience to write resilient code: (i) standardized nomenclature, (ii) consistency in style, (iii) increased modularity/extensibility for easier editing and understanding, (iv) code scalability for application to large data sets, (v) documented contingencies for code maintenance, (vi) documentation to facilitate user understanding; (vii) extensive tutorials and (viii) unit testing and benchmarking. We illustrate these principles using a new R package, {photosynthesis}, which provides a set of analytical and simulation tools for plant ecophysiology. Our goal with these principles is to advance scientific discovery in plant ecophysiology by making it easier to use code for simulation and data analysis, reproduce results and rapidly incorporate new biological understanding and analytical tools

Variation in host susceptibility and infectiousness generated by co-infection: the myxoma–Trichostrongylus retortaeformis case in wild rabbits

One of the conditions that can affect host susceptibility and parasite transmission is the occurrence of concomitant infections. Parasites interact directly or indirectly within an individual host and often these interactions are modulated by the host immune response. We used a free-living rabbit population co-infected with the nematode Trichostrongylus retortaeformis, which appears to stimulate an acquired immune response, and the immunosuppressive poxvirus myxoma. Modelling was used to examine how myxoma infection alters the immune-mediated establishment and death/expulsion of T. retortaeformis, and consequently affects parasite intensity and duration of the infection. Simulations were based on the general TH1–TH2 immunological paradigm that proposes the polarization of the host immune response towards one of the two subsets of T helper cells. Our findings suggest that myxoma infections contribute to alter host susceptibility to the nematode, as co-infected rabbits showed higher worm intensity compared with virus negative hosts. Results also suggest that myxoma disrupts the ability of the host to clear T. retortaeformis as worm intensities were consistently high and remained high in old rabbits. However, the co-infection model has to include some immune-mediated nematode regulation to be consistent with field data, indicating that the TH1–TH2 dichotomy is not complete. We conclude that seasonal myxoma outbreaks enhance host susceptibility to the nematode and generate highly infected hosts that remain infectious for a longer time. Finally, the virus–nematode co-infection increases heterogeneities among individuals and potentially has a large effect on parasite transmission

Microwave conductivity of YBa2_2Cu3_3O6.99_{6.99} including inelastic scattering

The fluctuation spectrum responsible for the inelastic scattering in YBa$_2$Cu$_3$O$_{6.99}$ which was recently determined from consideration of the in-plane optical conductivity in the infrared, is used to calculate the temperature dependence of the microwave conductivity at several measured frequencies. Reasonable overall agreement can only be achieved if, in addition, some impurity scattering is included within a model potential intermediate between weak (Born) and strong (unitary) limit.Comment: 15 pages, 5 figures accepted for publication in Phys. Rev.

Pastoral production is associated with increased peste des petits ruminants seroprevalence in northern Tanzania across sheep, goats and cattle

Peste des petits ruminants virus (PPRV) causes a contagious disease of high morbidity and mortality in small ruminant populations globally. Using cross-sectional serosurvey data collected in 2016, our study investigated PPRV seroprevalence and risk factors among sheep, goats and cattle in 20 agropastoral (AP) and pastoral (P) villages in northern Tanzania. Overall observed seroprevalence was 21.1% (95% exact confidence interval (CI) 20.1–22.0) with 5.8% seroprevalence among agropastoral (95% CI 5.0–6.7) and 30.7% among pastoral villages (95% CI 29.3–32.0). Seropositivity varied significantly by management (production) system. Our study applied the catalytic framework to estimate the force of infection. The associated reproductive numbers (R0) were estimated at 1.36 (95% CI 1.32–1.39), 1.40 (95% CI 1.37–1.44) and 1.13 (95% CI 1.11–1.14) for sheep, goats and cattle, respectively. For sheep and goats, these R0 values are likely underestimates due to infection-associated mortality. Spatial heterogeneity in risk among pairs of species across 20 villages was significantly positively correlated (R2: 0.59–0.69), suggesting either cross-species transmission or common, external risk factors affecting all species. The non-negligible seroconversion in cattle may represent spillover or cattle-to-cattle transmission and must be investigated further to understand the role of cattle in PPRV transmission ahead of upcoming eradication efforts

Epigenome-wide SRC-1 mediated gene silencing represses cellular differentiation in advanced breast cancer

Abstract Purpose: Despite the clinical utility of endocrine therapies for estrogen receptor–positive (ER) breast cancer, up to 40% of patients eventually develop resistance, leading to disease progression. The molecular determinants that drive this adaptation to treatment remain poorly understood. Methylome aberrations drive cancer growth yet the functional role and mechanism of these epimutations in drug resistance are poorly elucidated. Experimental Design: Genome-wide multi-omics sequencing approach identified a differentially methylated hub of prodifferentiation genes in endocrine resistant breast cancer patients and cell models. Clinical relevance of the functionally validated methyl-targets was assessed in a cohort of endocrine-treated human breast cancers and patient-derived ex vivo metastatic tumors. Results: Enhanced global hypermethylation was observed in endocrine treatment resistant cells and patient metastasis relative to sensitive parent cells and matched primary breast tumor, respectively. Using paired methylation and transcriptional profiles, we found that SRC-1–dependent alterations in endocrine resistance lead to aberrant hypermethylation that resulted in reduced expression of a set of differentiation genes. Analysis of ER-positive endocrine-treated human breast tumors (n = 669) demonstrated that low expression of this prodifferentiation gene set significantly associated with poor clinical outcome (P = 0.00009). We demonstrate that the reactivation of these genes in vitro and ex vivo reverses the aggressive phenotype. Conclusions: Our work demonstrates that SRC-1-dependent epigenetic remodeling is a ’high level’ regulator of the poorly differentiated state in ER-positive breast cancer. Collectively these data revealed an epigenetic reprograming pathway, whereby concerted differential DNA methylation is potentiated by SRC-1 in the endocrine resistant setting. Clin Cancer Res; 24(15); 3692–703. ©2018 AACR.</jats:p

Keeping the herds healthy and alert: implications of predator control for infectious disease

Predator control programmes are generally implemented in an attempt to increase prey population sizes. However, predator removal could prove harmful to prey populations that are regulated primarily by parasitic infections rather than by predation. We develop models for microparasitic and macroparasitic infection that specify the conditions where predator removal will (a) increase the incidence of parasitic infection, (b) reduce the number of healthy individuals in the prey population and (c) decrease the overall size of the prey population. In general, predator removal is more likely to be harmful when the parasite is highly virulent, macroparasites are highly aggregated in their prey, hosts are long-lived and the predators select infected prey