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/

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

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

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

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

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

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

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

Governments' policy response to drought in Eswatini and Lesotho : a systematic review of the characteristics, comprehensiveness, and quality of existing policies to improve community resilience to drought hazards

The southern African kingdoms of Eswatini and Lesotho experience recurrent drought-induced disasters. Policies have been enacted, but no attempt has been made to synthesise the effects on disaster resilience. This review analyses the characteristics, quality, and comprehensiveness of drought-resilience policies in Eswatini and Lesotho. We have systematically reviewed public policies that shape responses to disaster resilience published between 1 January 1980 and 30 June 2019. A combination of keywords was used to search electronic bibliographic databases, multidisciplinary databases, key organisational websites, and the first 20 pages of Google for policies that addressed disaster and/or drought resilience. Identified documents were downloaded into an EndNote database and screened for eligibility using predetermined criteria. The logic of events framework was used for quality assessment, and a metaethnographic approach was applied for data synthesis. Three broad categories of characteristics, thematic outcomes and quality, and comprehensiveness of policy documents emerged and are presented. Policy responses contributing to disaster resilience were found in n = 32 out of 13,700 documents. Three (n = 3/32) policies were statutory, and the rest were nonstatutory. Eleven (n = 11/32) were assessed to be of high quality. Policy responses relating to drought resilience focused on reducing vulnerability to recurrent disasters; promoting drought and climate change adaptation; improving agriculture and food security; safeguarding cultural heritage; and preventing gender inequality and gender-based violence as well as improving disaster governance. However, the construct of drought resilience was not strongly articulated as a major policy goal across policy documents. There is an urgent need to promote better understanding of drought resilience in order to motivate policymakers to steer away from reactive interventions and position resilience as a major national policy goal in both countries to expedite inclusive growth and safeguard development gains and the health and wellbeing of the majority of their populations who are rural-based populations

Assessing temperature effects on multipole contributions and angular dependence in core-level spectroscopies

This study aims at assessing the thermal nuclei motion effects on the multipole transition channels involved in two core-level spectroscopies, x-ray absorption spectroscopy (XAS) and x-ray Raman scattering (XRS). Temperature effects on the 1s -> s monopole, 1s -> p dipole, and 1s -> d quadrupole transitions are investigated using two reference systems for which we present original experimental data: alpha-Al2O3 at the Al K edge probed by XRS at room temperature and rutile TiO2 at the Ti K pre-edge probed by XAS at temperatures ranging from 6 to 700 K. Through the latter, this work enlightens the part of the pre-edge peak enhancement due to temperature in the K pre-edge region of 3d transition metal, which is known to be routinely used to determine the concentration, valence or symmetry of the probed element in a given sample. Nuclear thermal fluctuations are taken into account using a method based on density functional theory that consists in averaging spectra over atomic configurations, generated within the harmonic approximation and obeying quantum statistics at finite temperature. Since only a finite number of such configurations are used, the numerically averaged spectra generally lose the symmetry of the equilibrium crystal positions. In this paper, we demonstrate that the physical average has to be symmetric and propose a method to restore the physical angular dependence of the spectra. The approach is successfully applied to investigate the angular dependent XAS spectra in rutile as a function of temperature. The two systems under study allow to draw general conclusions regarding the effect of nuclear quantum fluctuations on the different transition channels available to both core-level spectroscopies.Peer reviewe