MathSBML: a package for manipulating SBML-based biological models

Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). Math-SBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. Availability: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml. Supplementary information: Extensive online documentation is available at http://www.sbml.org/mathsbml.html. Additional examples are provided at http://www.sbml.org/software/mathsbml/bioinformatics-application-not

Tessellations and Pattern Formation in Plant Growth and Development

The shoot apical meristem (SAM) is a dome-shaped collection of cells at the apex of growing plants from which all above-ground tissue ultimately derives. In Arabidopsis thaliana (thale cress), a small flowering weed of the Brassicaceae family (related to mustard and cabbage), the SAM typically contains some three to five hundred cells that range from five to ten microns in diameter. These cells are organized into several distinct zones that maintain their topological and functional relationships throughout the life of the plant. As the plant grows, organs (primordia) form on its surface flanks in a phyllotactic pattern that develop into new shoots, leaves, and flowers. Cross-sections through the meristem reveal a pattern of polygonal tessellation that is suggestive of Voronoi diagrams derived from the centroids of cellular nuclei. In this chapter we explore some of the properties of these patterns within the meristem and explore the applicability of simple, standard mathematical models of their geometry.Comment: Originally presented at: "The World is a Jigsaw: Tessellations in the Sciences," Lorentz Center, Leiden, The Netherlands, March 200

Allogeneic Astrocytoma In Immune Competent Dogs

AbstractWe have induced in canines long-term immune tolerance to an allogeneic cell line derived from a spontaneous canine astrocytoma. Allogeneic astrocytoma cells were implanted endoscopically into the subcutaneous space of fetal dogs before the onset of immune competency (<40th gestational day). At adulthood, dogs rendered tolerant successfully serve as recipients of intracranial transplants of their growing allogeneic, subcutaneous tumor. Transplanted dogs subsequently develop a solid brain tumor with histological features similar to the original astrocytoma. This model may allow rapid development and evaluation of new therapies for brain tumors, as well as afford tumor biology studies that are untenable in smaller, immune incompetent, or inbred animals harboring less representative tumors

Measuring the Relative Phase of the Energy Gap in a High-Temperature Superconductor with EELS

A method of measuring the relative phase of the energy gap in a high-temperature superconductor is suggested for electron energy loss spectroscopy. Energy-resolved measurements of off-specular scattering should show a feature similar to the specular feature associated with the gap. Unlike the specular feature, which reflects an average of the gap over the (normal) Fermi surface, the energy loss of the off-specular feature depends on the superconducting energy gap at only two locations on the Fermi surface. The onset of the feature reflects the relative phase between these two points. This result is independent of surface characteristics. Such characteristics affect the {\it magnitude} of the off-specular feature, not its location or onset. The size of the feature is estimated for a simple surface model. Implications of specific measurements on $\rm Bi_2Sr_2CaCu_2O_8$ are discussed

Association Between Early Hyperoxia Exposure After Resuscitation From Cardiac Arrest and Neurological Disability: Prospective Multicenter Protocol-Directed Cohort Study

BACKGROUND: Studies examining the association between hyperoxia exposure after resuscitation from cardiac arrest and clinical outcomes have reported conflicting results. Our objective was to test the hypothesis that early postresuscitation hyperoxia is associated with poor neurological outcome. METHODS: This was a multicenter prospective cohort study. We included adult patients with cardiac arrest who were mechanically ventilated and received targeted temperature management after return of spontaneous circulation. We excluded patients with cardiac arrest caused by trauma or sepsis. Per protocol, partial pressure of arterial oxygen (Pao2) was measured at 1 and 6 hours after return of spontaneous circulation. Hyperoxia was defined as a Pao2 >300 mm Hg during the initial 6 hours after return of spontaneous circulation. The primary outcome was poor neurological function at hospital discharge, defined as a modified Rankin Scale score >3. Multivariable generalized linear regression with a log link was used to test the association between Pao2 and poor neurological outcome. To assess whether there was an association between other supranormal Pao2 levels and poor neurological outcome, we used other Pao2 cut points to define hyperoxia (ie, 100, 150, 200, 250, 350, 400 mm Hg). RESULTS: Of the 280 patients included, 105 (38%) had exposure to hyperoxia. Poor neurological function at hospital discharge occurred in 70% of patients in the entire cohort and in 77% versus 65% among patients with versus without exposure to hyperoxia respectively (absolute risk difference, 12%; 95% confidence interval, 1-23). Hyperoxia was independently associated with poor neurological function (relative risk, 1.23; 95% confidence interval, 1.11-1.35). On multivariable analysis, a 1-hour-longer duration of hyperoxia exposure was associated with a 3% increase in risk of poor neurological outcome (relative risk, 1.03; 95% confidence interval, 1.02-1.05). We found that the association with poor neurological outcome began at ≥300 mm Hg. CONCLUSIONS: Early hyperoxia exposure after resuscitation from cardiac arrest was independently associated with poor neurological function at hospital discharge

Plasma Levels of Mitochondrial DNA in Patients Presenting to the Emergency Department with Sepsis

Introduction Elevated levels of plasma mitochondrial DNA (mtDNA) have been reported in trauma patients, and may contribute to the systemic immune response. We sought to determine the plasma levels of mtDNA in emergency department (ED) patients with and without sepsis and evaluate their association with severity of illness. Methods Prospective observational study of patients presenting to one of three large, urban, tertiary care EDs. Patients were enrolled into one of three cohorts: 1) sepsis defined as suspected infection and two or more SIRS criteria without hypotension; 2) septic shock defined as sepsis plus hypotension despite an adequate fluid challenge; and 3) control defined as non-infected ED patients without SIRS/hypotension. Plasma levels of three mtDNAs were measured using real-time quantitative PCR. Levels of mtDNAs were compared between the three cohorts and linear regression was used to assess the association between mtDNAs, IL-6, IL-10, and sequential organ failure assessment (SOFA) scores in patients with sepsis. Results We enrolled 93 patients: 24 controls, 29 with sepsis, and 40 with septic shock. As expected, co-morbidities and SOFA score increased across categories. We found no difference in mtDNA levels between the three groups (p = 0.14-0.30). Among patients with sepsis, we found a small but significant negative association between mtDNA level and SOFA score, most clearly with cytochrome b (p=0.03). Conclusions We found no difference in mtDNA levels between controls and patients with sepsis. mtDNA levels were negatively associated with organ dysfunction, suggesting that plasma mtDNA does not significantly contribute to the pathophysiology of sepsis

A discursive psychology analysis of emotional support for men with colorectal cancer

Recent research into both masculinity and health, and the provision of social support for people with cancer has focussed upon the variations that may underlie broad assumptions about masculine health behaviour. The research reported here pursues this interest in variation by addressing the discursive properties of talk about emotional support, by men with colorectal cancer - an understudied group in the social support and cancer literature. Semi-structured interviews were conducted with eight men with colorectal cancer, and the transcripts analysed using an intensive discursive psychology approach. From this analysis two contrasting approaches to this group of men’s framing of emotional support in the context of cancer are described. First, talk about cancer was positioned as incompatible with preferred masculine identities. Second, social contact that affirms personal relationships was given value, subject to constraints arising from discourses concerning appropriate emotional expression. These results are discussed with reference to both the extant research literature on masculinity and health, and their clinical implications, particularly the advice on social support given to older male cancer patients, their families and friends

Beyond SELinux: the Case for Behavior-Based Policy and Trust Languages

Despite the availability of powerful mechanisms for security policy and access control, real-world information security practitioners---both developers and security officers---still find themselves in need of something more. We believe that this is the case because available policy languages do not provide clear and intelligible ways to allow developers to communicate their knowledge and expectations of trustworthy behaviors and actual application requirements to IT administrators. We work to address this policy engineering gap by shifting the focus of policy language design to this communication via behavior-based policies and their motivating scenarios

Human rights violations in organ procurement practice in China

Over 90% of the organs transplanted in China before 2010 were procured from prisoners. Although Chinese officials announced in December 2014 that the country would completely cease using organs harvested from prisoners, no regulatory adjustments or changes in China’s organ donation laws followed. As a result, the use of prisoner organs remains legal in China if consent is obtained