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

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

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

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

Streptococcus agalactiae infection in camels (Camelus dromedarius) in Kenya

Les mammites subcliniques des dromadaires dues à Streptococcus agalactiae (Lancefield type 13) ont été étudiées dans différents systèmes d'élevage camelin (Somali, Pokot, ranching). Une corrélation présumée entre le statut de porteur de S. agalactiae chez la mère et la performance du jeune a été examinée dans les ranchs. Les possibilités de détection, de traitement et de contrôle des mammites à S. agalactiae chez le dromadaire sont discutées. (Résumé d'auteur

Scleroderma and dentistry: Two case reports

© 2016 The Author(s).Background: Scleroderma is a chronic connective tissue disorder with unknown etiology. It is characterized by excessive deposition of extracellular matrix in the connective tissues causing vascular disturbances which can result in tissue hypoxia. These changes are manifested as atrophy of the skin and/or mucosa, subcutaneous tissue, muscles, and internal organs. Such changes can be classified into two types, namely, morphea (localized) and diffuse (systemic). Morphea can manifest itself as hemifacial atrophy (Parry-Romberg syndrome) although this remains debatable. Hence, we present a case of morphea, associated with Parry-Romberg syndrome, and a second case with the classical signs of progressive systemic sclerosis. Case presentation: Case one: A 20-year-old man of Dravidian origin presented to our out-patient department with a complaint of facial asymmetry, difficulty in speech, and loss of taste sensation over the last 2 years. There was no history of facial trauma. After physical and radiological investigations, we found gross asymmetry of the left side of his face, a scar on his chin, tongue atrophy, relative microdontia, thinning of the ramus/body of his mandible, and sclerotic lesions on his trunk. Serological investigations were positive for antinuclear antibody for double-stranded deoxyribonucleic acid and mitochondria. A biopsy was suggestive of morphea. Hence, our final diagnosis was mixed morphea with Parry-Romberg syndrome. Case two: A 53-year-old woman of Dravidian origin presented to our out-patient department with a complaint of gradually decreasing mouth opening over the past 7 years. Her medical history was noncontributory. On clinical examination, we found her perioral, neck, and hand skin to be sclerotic. Also, her fingers exhibited bilateral telangiectasia. An oral examination revealed completely edentulous arches as well as xerostomia and candidiasis. Her serological reports were positive for antinuclear antibodies against centromere B, Scl-70, and Ro-52. A hand and wrist radiograph revealed acro-osteolysis of the middle finger on her right hand. Hence, our final diagnosis was progressive systemic sclerosis. Conclusion: Through this article, we have tried to emphasize the importance of a general examination when diagnosing rare systemic diseases such as scleroderma and the role of the general dentist when caring for such patients, even though they can be quite rare in general practice.published_or_final_versio

Accuracy of linear measurements using three imaging modalities: two lateral cephalograms and one 3D model from CBCT data

SummaryBackground: The aim of this study was to evaluate the accuracy of linear measurements on three imaging modalities: lateral cephalograms from a cephalometric machine with a 3 m source-to-mid-sagittal-plane distance (SMD), from a machine with 1.5 m SMD and 3D models from cone-beam computed tomography (CBCT) data. Methods: Twenty-one dry human skulls were used. Lateral cephalograms were taken, using two cephalometric devices: one with a 3 m SMD and one with a 1.5 m SMD. CBCT scans were taken by 3D Accuitomo® 170, and 3D surface models were created in Maxilim® software. Thirteen linear measurements were completed twice by two observers with a 4 week interval. Direct physical measurements by a digital calliper were defined as the gold standard. Statistical analysis was performed. Results: Nasion-Point A was significantly different from the gold standard in all methods. More statistically significant differences were found on the measurements of the 3 m SMD cephalograms in comparison to the other methods. Intra- and inter-observer agreement based on 3D measurements was slightly better than others. Limitations: Dry human skulls without soft tissues were used. Therefore, the results have to be interpreted with caution, as they do not fully represent clinical conditions. Conclusions: 3D measurements resulted in a better observer agreement. The accuracy of the measurements based on CBCT and 1.5 m SMD cephalogram was better than a 3 m SMD cephalogram. These findings demonstrated the linear measurements accuracy and reliability of 3D measurements based on CBCT data when compared to 2D techniques. Future studies should focus on the implementation of 3D cephalometry in clinical practic

Reinstated episodic context guides sampling-based decisions for reward.

How does experience inform decisions? In episodic sampling, decisions are guided by a few episodic memories of past choices. This process can yield choice patterns similar to model-free reinforcement learning; however, samples can vary from trial to trial, causing decisions to vary. Here we show that context retrieved during episodic sampling can cause choice behavior to deviate sharply from the predictions of reinforcement learning. Specifically, we show that, when a given memory is sampled, choices (in the present) are influenced by the properties of other decisions made in the same context as the sampled event. This effect is mediated by fMRI measures of context retrieval on each trial, suggesting a mechanism whereby cues trigger retrieval of context, which then triggers retrieval of other decisions from that context. This result establishes a new avenue by which experience can guide choice and, as such, has broad implications for the study of decisions

Morphologic characteristics, location, and associated complications of maxillary and mandibular supernumerary teeth as evaluated using cone beam computed tomography

SUMMARYOBJECTIVES: To evaluate the location and morphologic characteristics of supernumerary teeth and to assess the frequency and extent of root resorption of adjacent teeth using cone beam computed tomography (CBCT). MATERIALS AND METHODS: CBCT scans of 82 patients with supernumerary teeth in the maxilla and mandible were evaluated by two orthodontists independently. Data regarding the type, shape, and three-dimensional (3D) location of the supernumeraries including the frequency and extent of root resorption of adjacent teeth were recorded and evaluated for possible associations. RESULTS: The study comprised a total of 101 supernumerary teeth. Most of the patients (80.5 per cent) exhibited one single supernumerary tooth, while 15.8 per cent had two and 3.7 per cent had three supernumeraries. Males were affected more than females with a ratio of 1.65:1. Mesiodentes were the most frequently diagnosed type of supernumerary teeth (48.52 per cent), followed by supernumerary premolars (23.76 per cent) and lateral incisors (18.81 per cent). Supernumeraries were most commonly conical in shape (42.6 per cent) with a normal or inclined vertical position (61.4 per cent). Root resorption of adjacent teeth was detected for 22.8 per cent of the supernumerary teeth, most frequently for supernumerary premolars. There was a significant association between root resorption of adjacent teeth and type and shape of tooth. Interrater agreement for the measurements performed showed kappa values ranging from 0.55 to 1 with a kappa value of 1 for type and shape of the supernumerary teeth. CONCLUSIONS: CBCT provides 3D information about location and shape of supernumerary teeth as well as prevalence and degree of root resorption of neighbouring teeth with moderate to high interrater correlatio

The definition and diagnosis of developmental prosopagnosia.

Over the last 20 years much attention in the field of face recognition has been directed towards the study of developmental prosopagnosia (DP), with some authors investigating the behavioural characteristics of the condition, and many others using these individuals to further our theoretical understanding of the typical face-processing system. It is broadly agreed that the term "DP" refers to people who have failed to develop the ability to recognize faces in the absence of neurological illness or injury, yet more precise terminology in relation to potential subtypes of the population are yet to be confirmed. Furthermore, specific diagnostic techniques and inclusion and exclusion criteria have yet to be uniformly accepted across the field, making cross-paper comparisons and meta-analyses very difficult. This paper presents an overview of the current challenges that face research into DP and introduces a series of papers that attempt to further our understanding of the condition's characteristics. It is hoped that this special issue will provide a springboard for further research addressing these issues, improving the current state of the art by ensuring the quality of theoretical investigations into DP, and by posing advances that will assist those who have the condition