Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.

Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.

This is Release 1 of the specification for SBML Level 2 Version 4, describing the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, "http://sbml.org/":http://sbml.org/

Single particle analysis of the accumulation mode aerosol over the northeast Amazonian tropical rain forest, Surinam, South America

International audienceSingle particle analysis of aerosols particles larger than 0.2 ?m diameter was performed on 24 samples collected over Surinam tropical rain forest and in the adjacent marine boundary layer (MBL) during the LBA-CLAIRE 98 campaign in March 1998. Elemental composition and morphology of 2308 particles was determined using SEM-EDX. The aerosol particles were divided into seven groups according to their chemical composition: organic particles, mineral dust, aged mineral dust, sea salt, aged sea salt, Ca-rich, and biogenic aerosol. However the organic material in aerosol particles cannot be identified directly by SEM-EDX, we present indirect method of detection of organic material using this technique. Samples were further divided with respect to the distinct atmospheric layers present in the tropical troposphere including MBL, continental mixed layer, cloud convective layer, free troposphere and region of deep convection outflow. The organic and mineral dust particles are two major groups observed over the rainforest. In the MBL also sea salt particles represented a large fraction between 15 and 27%. The organic particles control much of the chemical characteristic of the aerosol in the continental tropical troposphere. Their abundance ranged from less than 20% in the MBL to more than 90% in the free troposphere between 4.5- and 12.6-km altitude. During the transport of the air masses from the MBL over the rain forest, fraction of organic aerosol particles more than doubled, reaching 40?60% in the continental boundary layer. This increase was attributed to direct emissions of biogenic aerosols from the tropical vegetation. The high fraction of the organic accumulation mode particles in the upper tropical troposphere could be a good indicator for the air masses originated over the tropical rain forest

A large-solid-angle X-ray Raman scattering spectrometer at ID20 of the European Synchrotron Radiation Facility

An end-station for X-ray Raman scattering spectroscopy at beamline ID20 of the European Synchrotron Radiation Facility is described. This end-station is dedicated to the study of shallow core electronic excitations using non-resonant inelastic X-ray scattering. The spectrometer has 72 spherically bent analyzer crystals arranged in six modular groups of 12 analyzer crystals each for a combined maximum flexibility and large solid angle of detection. Each of the six analyzer modules houses one pixelated area detector allowing for X-ray Raman scattering based imaging and efficient separation of the desired signal from the sample and spurious scattering from the often used complicated sample environments. This new end-station provides an unprecedented instrument for X-ray Raman scattering, which is a spectroscopic tool of great interest for the study of low-energy X-ray absorption spectra in materials under insitu conditions, such as inoperando batteries and fuel cells, insitu catalytic reactions, and extreme pressure and temperature conditions.Peer reviewe

X-ray Raman Scattering for Bulk Chemical and Structural Insight into Green Carbon

X-ray Raman scattering (XRS) spectroscopy is an emerging inelastic scattering technique which uses hard X-rays to study the X-ray absorption edges of low-Z elements (e.g. C, N, O) in bulk. This study applies XRS spectroscopy to pyrolysis and hydrothermal carbons. These materials are thermochemically-produced carbon from renewable resources and represent a route for the sustainable production of carbon materials for many applications. Results confirm local structural differences between biomass-derived (Oak, Quercus Ilex) pyrolysis and hydrothermal carbon. In comparison with NEXAFS, XRS spectroscopy has been shown to be more resilient to experimental artefacts such as self-absorption. Density functional theory XRS calculations of potential structural sub-units confirm that hydrothermal carbon is a highly disordered carbon material formed principally of furan units linked by the α carbon atoms. Comparison of two pyrolysis temperatures (450 °C and 650 °C) shows the development of an increasingly condensed carbon structure. Based on our results, we have proposed a semi-quantitative route to pyrolysis condensation

Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/

Parasitological prevalence of bovine trypanosomosis in Kindo Koisha district, Wollaita zone, south Ethiopia

A cross sectional survey to determine the distribution and prevalence of trypanosomosis was conducted in Kindo Koisha district, in the Wollaita zone in southern Ethiopia. A total of 1008 adult cattle was examined at eight different localities. Dark field examination of the buffy coat, as well as stained thin blood film examination and packed cell volume (PCV) evaluation were the diagnostic techniques used. The overall prevalence of bovine trypanosomosis was 15%. Among the positive animals, 108 (71.1%), 43 (28.4%) and 1 (0.6%) were due to Trypanosoma vivax, Trypanosoma congolense and mixed infection ( T. vivax and T. congolense), respectively. The infection rate of T. vivax and T. congolense varied significantly ( P0.05). The herd average PCV values of each site decreased with increasing proportion of the positive herds of that particular site. Of the diagnostic tests employed, the microhaematocrit buffy coat technique is relatively sensitive and it has an added advantage of indicating the general condition of the animal by haematocrit measurement. In view of the risk of trypanosomosis, a control intervention through the strategic application of appropriate trypanocidal drugs is recommended. A tsetse fly control scheme to reduce host-tsetse fly contact is equally as important as chemotherapy and chemoprophylaxis against trypanosomosis.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat v.9 was used to OCR the text and also for the merging and conversion to the final presentation PDF-format.SOS Sahel (UK) Kindo Koisha rural development project.mn201

Supercritical Fluid (SCF) Treatment: Its Effect on Bending Strength and Stiffness of Ponderosa Pine Sapwood

Adverse effects on mechanical properties from using a supercritical fluid (SCF) to increase preservative penetration of refractory woods were evaluated by treating small ponderosa pine sapwood specimens with supercritical carbon dioxide at 64 combinations of temperatures (35 to 80 C), pressure (1,000 to 4,000 psig), and time (0.5 to 2 h). Thereafter, the treated and identical untreated specimens were equilibrated to constant moisture content and tested for bending strength and stiffness. The SCF-treated and untreated specimens were not significantly different in modulus of rupture (MOR) or modulus of elasticity (MOE). Temperature, pressure, and time had no significant effect on MOR; there were interacting effects of these variables on MOE, although these interactions had no meaningful patterns

Global, regional, and national burden of chronic kidney disease, 1990–2017 : a systematic analysis for the Global Burden of Disease Study 2017

Background Health system planning requires careful assessment of chronic kidney disease (CKD) epidemiology, but data for morbidity and mortality of this disease are scarce or non-existent in many countries. We estimated the global, regional, and national burden of CKD, as well as the burden of cardiovascular disease and gout attributable to impaired kidney function, for the Global Burden of Diseases, Injuries, and Risk Factors Study 2017. We use the term CKD to refer to the morbidity and mortality that can be directly attributed to all stages of CKD, and we use the term impaired kidney function to refer to the additional risk of CKD from cardiovascular disease and gout. Methods The main data sources we used were published literature, vital registration systems, end-stage kidney disease registries, and household surveys. Estimates of CKD burden were produced using a Cause of Death Ensemble model and a Bayesian meta-regression analytical tool, and included incidence, prevalence, years lived with disability, mortality, years of life lost, and disability-adjusted life-years (DALYs). A comparative risk assessment approach was used to estimate the proportion of cardiovascular diseases and gout burden attributable to impaired kidney function. Findings Globally, in 2017, 1·2 million (95% uncertainty interval [UI] 1·2 to 1·3) people died from CKD. The global all-age mortality rate from CKD increased 41·5% (95% UI 35·2 to 46·5) between 1990 and 2017, although there was no significant change in the age-standardised mortality rate (2·8%, −1·5 to 6·3). In 2017, 697·5 million (95% UI 649·2 to 752·0) cases of all-stage CKD were recorded, for a global prevalence of 9·1% (8·5 to 9·8). The global all-age prevalence of CKD increased 29·3% (95% UI 26·4 to 32·6) since 1990, whereas the age-standardised prevalence remained stable (1·2%, −1·1 to 3·5). CKD resulted in 35·8 million (95% UI 33·7 to 38·0) DALYs in 2017, with diabetic nephropathy accounting for almost a third of DALYs. Most of the burden of CKD was concentrated in the three lowest quintiles of Socio-demographic Index (SDI). In several regions, particularly Oceania, sub-Saharan Africa, and Latin America, the burden of CKD was much higher than expected for the level of development, whereas the disease burden in western, eastern, and central sub-Saharan Africa, east Asia, south Asia, central and eastern Europe, Australasia, and western Europe was lower than expected. 1·4 million (95% UI 1·2 to 1·6) cardiovascular disease-related deaths and 25·3 million (22·2 to 28·9) cardiovascular disease DALYs were attributable to impaired kidney function. Interpretation Kidney disease has a major effect on global health, both as a direct cause of global morbidity and mortality and as an important risk factor for cardiovascular disease. CKD is largely preventable and treatable and deserves greater attention in global health policy decision making, particularly in locations with low and middle SDI

Multiplication of the V4 strain of Newcastle disease virus in Madin Derby bovine kidney cells

This study describes a reproducible cell culture system that permits the growth and secondary multiplication of the V4 strain of Newcastle disease virus. Allantoic fluid, magnesium chloride and diethylaminoethyl dextran were incorporated in Dulbecco's modified Eagle's medium to encourage secondary viral multiplication without adversely affecting healthy Madin Derby bovine kidney cell growth.The articles have been scanned in colour with a HP Scanjet 5590; 600dpi. Adobe Acrobat v.9 was used to OCR the text and also for the merging and conversion to the final presentation PDF-format.mn201

Weight gain after smoking cessation and risk of major chronic diseases and mortality

Importance: Smoking cessation is frequently followed by weight gain; however, whether weight gain after quitting reduces the health benefits of quitting is unclear. Objective: To examine the association between weight change after smoking cessation and the risk of cardiovascular diseases (CVD), type 2 diabetes, cancer, chronic obstructive pulmonary disease (COPD), and all-cause mortality. Design, Setting, and Participants: This cohort study analyzed data from a nationally representative sample of Australian adults aged 18 years or older who were studied between 2006 and 2014. Smoking status and anthropometric measurements were self-reported annually. Cox proportional hazards regressions were used to determine the hazard ratios (HRs) for the association between changes in weight and body mass index (BMI) and the risk of CVD, type 2 diabetes, cancer, COPD, and mortality. Data were analyzed in January 2019. Exposures: Annual self-reported smoking status; years since quitting. Main Outcomes and Measures: Weight gain after quitting, incident CVD, type 2 diabetes, cancer, COPD, and all-cause mortality. Results: Of a total 16663 participants (8082 men and 8581 women; mean [SD] age, 43.7 [16.3] years), those who quit smoking had greater increases in weight (mean difference [MD], 3.14 kg; 95% CI, 1.39-4.87) and BMI (MD, 0.82; 95% CI, 0.21-1.44) than continuing smokers. Compared with continuing smokers, the HRs for death were 0.50 (95% CI, 0.36-0.68) among quitters who lost weight, 0.79 (95% CI, 0.51-0.98) among quitters without weight change, 0.33 (95% CI, 0.21-0.51) among quitters who gained 0.1 to 5.0 kg, 0.24 (95% CI, 0.11-0.53) among quitters who gained 5.1 to 10 kg, and 0.36 (95% CI, 0.16-0.82) among quitters who gained more than 10 kg. The HRs for death were 0.61 (95% CI, 0.45-0.83) among quitters who lost BMI, 0.86 (95% CI, 0.51-1.44) among quitters without change in BMI, 0.32 (95% CI, 0.21-0.50) among quitters who gained up to 2 in BMI, and 0.26 (95% CI, 0.16-0.45) among quitters who gained more than 2 in BMI. Conclusions and Relevance: This cohort study found that smoking cessation was accompanied by a substantial weight gain; however, this was not associated with an increased risk of chronic diseases or an attenuation of the mortality benefit of cessation