SBMLToolbox: an SBML toolbox for MATLAB users

We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML

Moždana vazomotorna reaktivnost i okluzivna bolest karotidnih arterija

Cerebral autoregulation is a mechanism that enables relatively constant cerebral blood flow during variations of cerebral perfusion pressure. The differences between cerebral blood flow at rest and after administration of a potent vasodilatory stimulus test such as hypercapnia reflect cerebral vasomotor reactivity defined as the vasodilation capacity of cerebral arterioles to external stimuli, providing important information about the cerebral hemodynamic status. Cerebral vasomotor reactivity provides important information about the cerebral hemodynamic status. In this article, cerebral vasomotor reactivity assessment tests are presented, with emphasis on transcranial Doppler, as well as the use of transcranial Doppler in assessing cerebral vasomotor reactivity in carotid stenosis, occlusion, and the importance of cerebral vasomotor reactivity for carotid surgery.Moždana autoregulacija je mehanizam koji omogućava relativno ustaljeni moždani protok krvi za vrijeme promjena tlaka prokrvljenosti mozga. Razlike između moždanog protoka krvi u mirovanju i nakon testa snažne vazodilatacijske stimulacije poput hiperkapnije odražavaju moždanu vazomotornu reaktivnost definiranu kao vazodilatacijski kapacitet moždanih arteriola za vanjske poticaje, pružajući važne podatke o moždanom hemodinamskom statusu. Moždana vazomotorna reaktivnost daje važne informacije o statusu moždane hemodinamike. U članku se prikazuju testovi za procjenu moždane vazomotorne reaktivnosti s naglaskom na transkranijski Doppler, te primjena transkranijskog Dopplera u procjeni moždane vazomotorne reaktivnosti kod karotidne stenoze, okluzije, kao i važnost moždane vazomotorne reaktivnosti za kirurgiju karotidnih arterija

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Could parental rules play a role in the association between short sleep and obesity in young children?

Short sleep duration is associated with obesity in young children. This study develops the hypothesis that parental rules play a role in this association. Participants were 3-year-old children and their parents, recruited at nursery schools in socioeconomically deprived and non-deprived areas of a North-East England town. Parents were interviewed to assess their use of sleep, television-viewing and dietary rules, and given diaries to document their child's sleep for 4 days/5 nights. Children were measured for height, weight, waist circumference and triceps and subscapular skinfold thicknesses. One-hundred and eight families participated (84 with complete sleep data and 96 with complete body composition data). Parental rules were significantly associated together, were associated with longer night-time sleep and were more prevalent in the non-deprived-area compared with the deprived-area group. Television-viewing and dietary rules were associated with leaner body composition. Parental rules may in part confound the association between night-time sleep duration and obesity in young children, as rules cluster together across behavioural domains and are associated with both sleep duration and body composition. This hypothesis should be tested rigorously in large representative samples

Evaluating megaprojects: from the “iron triangle” to network mapping

Evaluation literature has paid relatively little attention to the specific needs of evaluating large, complex industrial and infrastructure projects, often called ‘megaprojects’. The abundant megaproject governance literature, in turn, has largely focused on the so-called ‘megaproject pathologies’, i.e. the chronic budget overruns, and failure of such projects to keep to timetables and deliver the expected social and economic benefits. This article draws on these two strands of literature, identifies shortcomings, and suggests potential pathways towards an improved evaluation of megaprojects. To counterbalance the current overemphasis on relatively narrowly defined accountability as the main function of megaproject evaluation, and the narrow definition of project success in megaproject evaluation, the article argues that conceptualizing megaprojects as dynamic and evolving networks would provide a useful basis for the design of an evaluation approach better able to promote learning and to address the socio economic aspects of megaprojects. A modified version of ‘network mapping’ is suggested as a possible framework for megaproject evaluation, with the exploration of the multiple accountability relationships as a central evaluation task, designed to reconcile learning and accountability as the central evaluation functions. The article highlights the role of evaluation as an ‘emergent’ property of spontaneous megaproject ‘governing’, and explores the challenges that this poses to the role of the evaluator

Neurosensory Disturbances After Apical Surgery of Mandibular Premolars and Molars: A Retrospective Analysis and Case-Control Study.

OBJECTIVE Apical surgery is an intervention to treat teeth with persistent or recurrent endodontic infection. The proximity of the mental foramen and mandibular canal may pose a risk of altered sensation when performing surgical interventions in the posterior mandible. The objective of this study was to determine the rate of neurosensory disturbances after apical surgery of mandibular premolars and molars. The secondary objective was to evaluate whether the occurrence of altered sensation correlated with the distances from the apex or the periapical lesion to the relevant anatomical structures. METHODS The charts of patients treated from September 1999 to December 2015 were retrospectively evaluated if an apical surgery had been performed in mandibular premolars or molars, and a minimum period of 1-year follow-up was documented. Patients with trauma or other surgical interventions in the same hemimandible were excluded. Cases with postsurgical altered sensation were defined as the test group. From the pool of unaffected cases, patients were selected to serve as controls. Two- or three-dimensional radiographs of test and control cases were assessed with regard to the shortest distances from the root apices/lesions to the mental foramen or mandibular canal. RESULTS The study population included 243 patients with 249 apical surgeries, of which 12.9% led to postoperative neurosensory disturbances. Sensation returned to normal within 22 days on average. The most frequent findings were hyperesthesia or paresthesia. With regard to the treated type of tooth, second premolars resulted more frequently (22.6%) in altered sensation than the other teeth (11.2 to 13.0%; p=0.310). There were no significant differences when comparing test and control cases regarding the measured distances in radiographs from the apex/lesion to the relevant anatomical structures. CONCLUSION Altered sensation may typically occur following apical surgery in posterior mandibular teeth. However, in all cases of the present study, skin sensitivity in the lip/chin region returned to normal. The clinician must be particularly careful when performing apical surgery of second premolars due to the proximity of the mental foramen

LibSBML: an API library for SBML

LibSBML is an application programming interface library for reading, writing, manipulating and validating content expressed in the Systems Biology Markup Language (SBML) format. It is written in ISO C and C++, provides language bindings for Common Lisp, Java, Python, Perl, MATLAB and Octave, and includes many features that facilitate adoption and use of both SBML and the library. Developers can embed libSBML in their applications, saving themselves the work of implementing their own SBML parsing, manipulation and validation software

Repeated Testing in Eyewitness Memory: A Means to Improve Recall of a Negative Emotional Event

Participants viewed either a violent, arousing film or a non-violent, control version of the same film. After viewing the film, they made three successive attempts to recall details of the event. Participants who were exposed to the negative emotional event were better than control participants at recalling details of the event itself, but they were worse at recalling details that preceded or followed the violence. Both groups of participants recalled significantly more information over successive recall attempts, suggesting that memory impairment due to arousal can be alleviated by repeated testing. Repeated testing was also associated with a small but reliable increase in memory intrusions. The implications of these findings for research on hypermnesia and on the relationship between arousal and memory are discussed