Effects of global atmospheric perturbations on forest ecosystems: Predictions of seasonal and cumulative effects

The physical effects of certain large events, such as giant impacts, explosive volcanism, or combined nuclear explosions, have the potential of inducing global catastrophes in our terrestrial environment. Such highly energetic events can inject substantial quantities of material into the atmosphere. In turn, this changes the amount of sunlight reaching the Earth's surface and modifies atmospheric temperatures to produce a wide range of global effects. One consequence is the introduction of serious stresses in both plants and animals throughout the Earth's biosphere. For example, recent studies predict that forest lands, crop lands, and range lands would suffer specific physical and biological degradations if major physical and chemical disruptions occurred in our atmosphere. Forests, which cover over 4 times 10 to the 9th power hectares (4 times 10 to the 7th power sq km) of our planet, or about 3 times the area now cultivated for crops, are critical to many processes in the biosphere. Forests contribute heavily to the production of atmospheric oxygen, supply the major volume of biomass, and provide a significant percentage of plant and animal habitats

SODA: an Open-Source Library for Visualizing Biological Sequence Annotation

Genome annotation is the process of identifying and labeling known genetic sequences or features within a genome. Across the various subfields within modern molecular biology, there is a common need for the visualization of such annotations. Genomic data is often visualized on web browser platforms, providing users with easy access to visualization tools without the need for installing any software or, in many cases, underlying datasets. While there exists a broad range of web-based visualization tools, there is, to my knowledge, no lightweight, modern library tailored towards the visualization of genomic data. Instead, developers charged with the task of producing a novel visualization must either adopt a complex system or fall back on general purpose visualization frameworks. Here, I present SODA, a web-based genomic annotation visualization library implemented in TypeScript as an abstraction over D3. SODA is designed to be lightweight and flexible, empowering developers with the tools to easily create customized and nuanced genomic visualizations

The association of low complement with disease activity in systemic sclerosis: a prospective cohort study

Background: In some rheumatic diseases such as systemic lupus erythematosus (SLE), low serum complement ('hypocomplementaemia') is a feature of active disease. However, the role of hypocomplementaemia in systemic sclerosis (SSc) is unknown. We sought to determine the frequency, clinical associations and relationship to disease activity of hypocomplementaemia in SSc. Methods: The study included 1140 patients fulfilling the 2013 American College of Rheumatology criteria for SSc. Demographic, serological and clinical data, obtained prospectively through annual review, were analysed using univariable methods. Linear and logistic regression, together with generalised estimating equations, were used to determine the independent correlates of hypocomplementaemia ever, and at each visit, respectively. Results: At least one episode of hypocomplementaemia (low C3 and/or low C4) occurred in 24.1 % of patients over 1893 visits; these patients were more likely to be seropositive for anti-ribonucleoprotein (OR = 3.8, p = 0.002), anti-Ro (OR = 2.2, p = 0.002), anti-Smith (OR = 6.3, p = 0.035) and anti-phospholipid antibodies (OR = 1.4, p = 0.021) and were more likely to display features of overlap connective tissue disease, in particular polymyositis (OR = 16.0, p = 0.012). However, no association was found between hypocomplementaemia and either the European Scleroderma Study Group disease activity score or any of its component variables (including erythrocyte sedimentation rate) in univariate analysis. Among patients with SSc overlap disease features, those who were hypocomplementaemic were more likely to have digital ulcers (OR = 1.6, p = 0.034), tendon friction rubs (OR = 2.4, p = 0.037), forced vital capacity <80 % predicted (OR = 2.9, p = 0.008) and lower body mass index (BMI) (OR for BMI = 0.9, p < 0.0005) at that visit, all of which are features associated with SSc disease activity and/or severity. Conclusions: While hypocomplementaemia is not associated with disease activity in patients with non-overlap SSc, it is associated with some features of increased SSc disease activity in patients with overlap disease features.James Esposito, Zoe Brown, Wendy Stevens, Joanne Sahhar, Candice Rabusa, Jane Zochling, Janet Roddy, Jennifer Walker, Susanna M. Proudman, and Mandana Nikpo

LA LOGICA DE LOS POSIBLES NARRATIVOS EN RELATOS AMAQUEMES SOBRE BRUJAS DE MARIA ISABEL CORONA VELAZQUEZ

La tesis se fundamenta en ocho relatos tomados de Relatos amaquemes que son los siguientes: “Se casó con una bruja” (1), “Esposa hechicera” (2), “Le daba de comer pura sangre” (3), “Esta es bruja” (4), “Dos luces” (5), “Se volteaban los pantalones” (6), “La bruja iba a Chalma” (7), “Dos guajolotes se peleaban” (8). (véase anexo) El planteamiento base de mi problema de investigación es el siguiente: ¿Cómo funciona la lógica de los posibles narrativos en los Relatos amaquemes? Así mismo la hipótesis que responde a mi pregunta de investigación es la siguiente: los rasgos que tienen en común los distintos relatos recopilados tienen como función caracterizar a la bruja mexicana. O particularmente caracterizar a la bruja de la región oriente del Estado de México. Mientras que los rasgos de la lógica de los posibles narrativos permiten conocer el desarrollo estructural de los relatos

Papez’s Forgotten Tract: 80 Years of Unreconciled Findings Concerning the Thalamocingulate Tract

The thalamocingulate tract is a key component of the Papez circuit that connects the anterior thalamic nucleus (ATN) to the cingulum bundle. While the other white matter connections, consisting of the fornix, cingulum bundle and mammillothalamic tract, were well defined in Papez’s original 1937 paper, the anatomy of the thalamocingulate pathway was mentioned only in passing. Subsequent research has been unable to clarify the precise anatomical trajectory of this tract. In particular, the site of thalamocingulate tract interactions with the cingulum bundle have been inconsistently reported. This review aims to synthesize research on this least studied component of the Papez circuit. A systemic approach to reviewing historical anatomical dissection and neuronal tracing studies as well as contemporary diffusion magnetic resonance imaging studies of the thalamocingulate tract was undertaken across species. We found that although inconsistent, prior research broadly encompasses two differing descriptions of how the ATN interfaces with the cingulum after passing laterally through the anterior limb of the internal capsule. The first group of studies show that the pathway turns medially and rostrally and passes to the anterior cingulate region (Brodmann areas 24, 33, and 32) only. A second group suggests that the thalamocingulate tract interfaces with both the anterior and posterior cingulate (Brodmann areas 23 and 31) and retrosplenial region (Brodmann area 29). We discuss potential reasons for these discrepancies such as altering methodologies and species differences. We also discuss how these inconsistencies may be resolved in further research with refinements of terminology for the cingulate cortex and the thalamocingulate tract. Understanding the precise anatomical course of the last remaining unresolved final white matter tract in the Papez circuit may facilitate accurate investigation of the role of the complete Papez circuit in emotion and memory

Epidemiology and disease characteristics of systemic sclerosis-related pulmonary arterial hypertension: results from a real-life screening programme

Pulmonary arterial hypertension (PAH) is the leading cause of death in systemic sclerosis (SSc). Annual screening with echocardiogram (ECHO) is recommended. We present the methodological aspects of a PAH screening programme in a large Australian SSc cohort, the epidemiology of SSc-PAH in this cohort, and an evaluation of factors influencing physician adherence to PAH screening guidelines.Patient characteristics and results of PAH screening were determined in all patients enrolled in a SSc longitudinal cohort study. Adherence to PAH screening guidelines was assessed by a survey of Australian rheumatologists. Summary statistics, chi-square tests, univariate and multivariable logistic regression were used to determine the associations of risk factors with PAH.Among 1636 patients with SSc, 194 (11.9%) had PAH proven by right-heart catheter. Of these, 160 were detected by screening. The annual incidence of PAH was 1.4%. Patients with PAH diagnosed on subsequent screens, compared with patients in whom PAH was diagnosed on first screen, were more likely to have diffuse SSc (p = 0.03), be in a better World Health Organisation (WHO) Functional Class at PAH diagnosis (p = 0.01) and have less advanced PAH evidenced by higher mean six-minute walk distance (p = 0.03), lower mean pulmonary arterial pressure (p = 0.009), lower mean pulmonary vascular resistance (p = 0.006) and fewer non-trivial pericardial effusions (p = 0.03). Adherence to annual PAH screening using an ECHO-based algorithm was poor among Australian rheumatologists, with less than half screening their patients with SSc of more than ten years disease duration.PAH is a common complication of SSc. Physician adherence to PAH screening recommendations remains poor. Identifying modifiable barriers to screening may improve adherence and ultimately patient outcomes.Kathleen Morrisroe, Wendy Stevens, Joanne Sahhar, Candice Rabusa, Mandana Nikpour, Susanna Proudman and the Australian Scleroderma Interest Group (ASIG

Survival and quality of life in incident systemic sclerosis-related pulmonary arterial hypertension

Background: Pulmonary arterial hypertension (PAH) is a leading cause of mortality in systemic sclerosis (SSc). We sought to determine survival, predictors of mortality, and health-related quality of life (HRQoL) related to PAH in a large SSc cohort with PAH. Methods: We studied consecutive SSc patients with newly diagnosed (incident) World Health Organization (WHO) Group 1 PAH enrolled in a prospective cohort between 2009 and 2015. Survival methods were used to determine age and sex-adjusted standardised mortality ratio (SMR) and years of life lost (YLL), and to identify predictors of mortality. HRQoL was measured using the Short form 36 (SF-36) instrument. Results: Among 132 SSc-PAH patients (112 female (85%); mean age 62 ± 11 years), 60 (45.5%) died, with a median (±IQR) survival time from PAH diagnosis of 4.0 (2.2-6.2) years. Median (±IQR) follow up from study enrolment was 3.8 (1.6-5.8) years. The SMR for patients with SSc-PAH was 5.8 (95% CI 4.3-7.8), with YLL of 15.2 years (95% CI 12.3-18.1). Combination PAH therapy had a survival advantage (p < 0.001) compared with monotherapy, as did anticoagulation compared with no anticoagulation (p < 0.003). Furthermore, combination PAH therapy together with anticoagulation had a survival benefit compared with monotherapy with or without anticoagulation and combination therapy without anticoagulation (hazard ratio 0.28, 95% CI 0.1-0.7). Older age at PAH diagnosis (p = 0.03), mild co-existent interstitial lung disease (ILD) (p = 0.01), worse WHO functional class (p = 0.03) and higher mean pulmonary arterial pressure at PAH diagnosis (p = 0.001), and digital ulcers (p = 0.01) were independent predictors of mortality. Conclusions: Despite the significant benefits conferred by advanced PAH therapies suggested in this study, the median survival in SSc PAH remains short at only 4 years.Kathleen Morrisroe, Wendy Stevens, Molla Huq, David Prior, Jo Sahhar, Gene-Siew Ngian, David Celermajer, Jane Zochling, Susanna Proudman, Mandana NikpourEmail author and the Australian Scleroderma Interest Group (ASIG