SNA--a toolbox for the stoichiometric analysis of metabolic networks

BACKGROUND: Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem. RESULTS: SNA is a interactive, high performance toolbox for analysing the possible steady state behaviour of metabolic networks by computing the generating and elementary vectors of their flux and conversions cones. It also supports analysing the steady states by linear programming. The toolbox is implemented mainly in Mathematica and returns numerically exact results. It is available under an open source license from: http://bioinformatics.org/project/?group_id=546. CONCLUSION: Thanks to its performance and modular design, SNA is demonstrably useful in analysing genome scale metabolic networks. Further, the integration into Mathematica provides a very flexible environment for the subsequent analysis and interpretation of the results.

Loss estimation for landslides in mountain areas – An integrated toolbox for vulnerability assessment and damage documentation

Global environmental change includes changes in a wide range of global scale phenomena, which are expected to affect a number of physical processes, as well as the vulnerability of the communities that will experience their impact. Decision-makers are in need of tools that will enable them to assess the loss of such processes under different future scenarios and to design risk reduction strategies. In this paper, a tool is presented that can be used by a range of end-users (e.g. local authorities, decision makers, etc.) for the assessment of the monetary loss from future landslide events, with a particular focus on torrential processes. The toolbox includes three functions: a) enhancement of the post-event damage data collection process, b) assessment of monetary loss of future events and c) continuous updating and improvement of an existing vulnerability curve by adding data of recent events. All functions of the tool are demonstrated through examples of its application.

«Toolbox Assessment» - ein hochschuldidaktischer Service im virtuellen Raum

Zeitgemäße Hochschullehre verlangt nach zeitgemäßen Prüfungsformen. Mit «Assessment», wie es hier verstanden wird, ist jedoch nicht nur die abschließende Lernerfolgskontrolle gemeint. Im Ideal der kompetenzorientierten Hochschullehre erhalten die Studierenden auch auf dem Weg zur angestrebten Handlungskompetenz immer wieder Gelegenheit zur Standortbestimmung. Eine Benotung ist dabei nicht zwingend, informierendes Feedback jedoch schon. Mit der «Toolbox Assessment» erhalten Lehrende dazu nun ein attraktives Hilfsmittel buchstäblich in die Hand.

Diagnostic microchip to assay 3D colony-growth potential of captured circulating tumor cells

Microfluidic technology has been successfully applied to isolate very rare tumor-derived epithelial cells (circulating tumor cells, CTCs) from blood with relatively high yield and purity, opening up exciting prospects for early detection of cancer. However, a major limitation of state-of-the-art CTC-chips is their inability to characterize the behavior and function of captured CTCs, for example to obtain information on proliferative and invasive properties or, ultimately, tumor re-initiating potential. Although CTCs can be efficiently immunostained with markers reporting phenotype or fate (e.g. apoptosis, proliferation), it has not yet been possible to reliably grow captured CTCs over long periods of time and at single cell level. It is challenging to remove CTCs from a microchip after capture, therefore such analyses should ideally be performed directly on-chip. To address this challenge, we merged CTC capture with three-dimensional (3D) tumor cell culture on the same microfluidic platform. PC3 prostate cancer cells were isolated from spiked blood on a transparent PDMS CTC-chip, encapsulated on-chip in a biomimetic hydrogel matrix (QGel™) that was formed in situ, and their clonal 3D spheroid growth potential was assessed by microscopy over one week in culture. The possibility to clonally expand a subset of captured CTCs in a near-physiological in vitro model adds an important element to the expanding CTC-chip toolbox that ultimately should improve prediction of treatment responses and disease progression.

Different duration of at-risk mental state associated with neurofunctional abnormalities. A multimodal imaging study

Objectives: Neurofunctional alterations are correlates of vulnerability to psychosis, as well as of the disorder itself. How these abnormalities relate to different probabilities for later transition to psychosis is unclear. We investigated vulnerability- versus disease-related versus resilience biomarkers of psychosis during working memory (WM) processing in individuals with an at-risk mental state (ARMS). Experimental design: Patients with “first-episode psychosis” (FEP, n = 21), short-term ARMS (ARMS-ST, n = 17), long-term ARMS (ARMS-LT, n = 16), and healthy controls (HC, n = 20) were investigated with an n-back WM task. We examined functional magnetic resonance imaging (fMRI) and structural magnetic resonance imaging (sMRI) data in conjunction using biological parametric mapping (BPM) toolbox. Principal observations: There were no differences in accuracy, but the FEP and the ARMS-ST group had longer reaction times compared with the HC and the ARMS-LT group. With the 2-back > 0-back contrast, we found reduced functional activation in ARMS-ST and FEP compared with the HC group in parietal and middle frontal regions. Relative to ARMS-LT individuals, FEP patients showed decreased activation in the bilateral inferior frontal gyrus and insula, and in the left prefrontal cortex. Compared with the ARMS-LT, the ARMS-ST subjects showed reduced activation in the right inferior frontal gyrus and insula. Reduced insular and prefrontal activation was associated with gray matter volume reduction in the same area in the ARMS-LT group. Conclusions: These findings suggest that vulnerability to psychosis was associated with neurofunctional alterations in fronto-temporo-parietal networks in a WM task. Neurofunctional differences within the ARMS were related to different duration of the prodromal state and resilience factors

Leaf transmission reduction using moving jaws for dynamic MLC IMRT

The aim of this work is to investigate to what extent it is possible to use the secondary collimator jaws to reduce the transmitted radiation through the multileaf collimator (MLC) during an intensity modulated radiation therapy (IMRT). A method is developed and introduced where the jaws follow the open window of the MLC dynamically (dJAW method). With the aid of three academic cases (Closed MLC, Sliding-gap, and Chair) and two clinical cases (prostate and head and neck) the feasibility of the dJAW method and the influence of this method on the applied dose distributions are investigated. For this purpose the treatment planning system Eclipse and the Research-Toolbox were used as well as measurements within a solid water phantom were performed. The transmitted radiation through the closed MLC leads to an inhomogeneous dose distribution. In this case, the measured dose within a plane perpendicular to the central axis differs up to 40% (referring to the maximum dose within this plane) for 6 and 15 MV. The calculated dose with Eclipse is clearly more homogeneous. For the Sliding-gap case this difference is still up to 9%. Among other things, these differences depend on the depth of the measurement within the solid water phantom and on the application method. In the Chair case, the dose in regions where no dose is desired is locally reduced by up to 50% using the dJAW method instead of the conventional method. The dose inside the chair-shaped region decreased up to 4% if the same number of monitor units (MU) as for the conventional method was applied. The undesired dose in the volume body minus the planning target volume in the clinical cases prostate and head and neck decreased up to 1.8% and 1.5%, while the number of the applied MU increased up to 3.1% and 2.8%, respectively. The new dJAW method has the potential to enhance the optimization of the conventional IMRT to a further step.

New molecular detection tools adapted to emerging rhinoviruses and enteroviruses

Human rhinoviruses (HRV), and to a lesser extent human enteroviruses (HEV), are important respiratory pathogens. Like other RNA viruses, these picornaviruses have an intrinsic propensity to variability. This results in a large number of different serotypes as well as the incessant discovery of new genotypes. This large and growing diversity not only complicates the design of real-time PCR assays but also renders immunofluorescence unfeasible for broad HRV and HEV detection or quantification in cells. In this study, we used the 5' untranslated region, the most conserved part of the genome, as a target for the development of both a real-time PCR assay (Panenterhino/Ge/08) and a peptide nucleic acid-based hybridization oligoprobe (Panenterhino/Ge/08 PNA probe) designed to detect all HRV and HEV species members according to publicly available sequences. The reverse transcription-PCR assay has been validated, using not only plasmid and viral stocks but also quantified RNA transcripts and around 1,000 clinical specimens. These new generic detection PCR assays overcame the variability of circulating strains and lowered the risk of missing emerging and divergent HRV and HEV. An additional real-time PCR assay (Entero/Ge/08) was also designed specifically to provide sensitive and targeted detection of HEV in cerebrospinal fluid. In addition to the generic probe, we developed specific probes for the detection of HRV-A and HRV-B in cells. This investigation provides a comprehensive toolbox for accurate molecular identification of the different HEV and HRV circulating in humans.

The Long Tail of the Rainbow Serpent: New Technologies and the Protection and Promotion of Traditional Cultural Expressions

New technologies, in particular those stemming from digitisation, allow amongst other things the production of perfect copies, instantaneous and ubiquitous distribution of and easy access to information with no real location restrictions. The effects of these technological advances have largely been perceived as negative for the protection of traditional cultural expressions (TCE), both because of the peculiarities of the digital networked environment and because of the lack of appropriate intellectual property protection models for TCE. The purpose of this article is, while accounting for the diversity and complexity of issues related to TCE, to reveal a more positive side of digital technologies. It shows the potential of these to be proactively applied and the further reaching possibilities for designing an efficient multi-level and multi-faceted toolbox for the protection and promotion of TCE in the digital ecology.

Implementing fisher Black's simple discounting rule

We propose a simple implementation of Black’s (1988) elegant rule for discounting uncertain future cash flows. Black’s rule avoids the thorny problem of estimating an appropriate risk-adjusted discount rate. Instead, the rule calls for discounting conditional mean cash flows at appropriate riskless interest rates. Our contribution in this article is to describe and illustrate a method of estimating the conditional mean cash flows called for in Black’s rule. The method is quite flexible with respect to the types of information available concerning the distributions of future cash flows. We argue that this approach to computing present values offers a theoretically sound and generally feasible addition to the toolbox of financial managers.

PolySynthesis 6.0 -- bicentennial edition

Even 197 years after its introduction, the notion of polysynthesis remains one of the most intriguing and controversial tools in the (morphological) typologist's toolbox. Several --occasionally contradictory--definitions have been proposed, employed for various purposes, and debated to this very day, but neither practitioners nor theoreticians have reached a comfortable level of consensus regarding its most effective and efficient form yet. The present talk maps the evolution of the notion, discusses its usefulness, and contends that the tool can be made better by updating it minimally with respect to its form and substantially with respect to its conceptual foundations. The former aspect of the update consists of making the notion more precise via explicit qualification; the latter bears relation to our arguably problematic understanding of the pairs lexical vs. grammatical and word vs. clause.

New Technologies and the Protection and Promotion of Traditional Cultural Expressions

New technologies, in particular those stemming from digitization, allow amongst other things the production of perfect copies, instantaneous and ubiquitous distribution of and easy access to information with no real location restrictions. The effects of these technological advances have largely been perceived as negative for the protection of Traditional Cultural Expressions (TCE), both because of the peculiarities of the digital networked environment and because of the lack of appropriate intellectual property protection models for TCE. The purpose of this article is, while accounting for the diversity and complexity of issues related to TCE, to reveal a more positive side of digital technologies. It shows the potential of these to be proactively applied and the further reaching possibilities for designing an efficient multi-level and multi-faceted toolbox for the protection and promotion of TCE in the digital ecology.

Wahrheit oder Lüge? Spielerisch zum Leistungsnachweis

Zeitgemässe Hochschullehre verlangt nach zeitgemässen Prüfungsformen. Mit der «Toolbox Assessment » erhalten die Lehrenden der Universität Bern ein praktisches Hilfsmittel, um für ihre Studierenden die beste Methode zu finden.

An automated method for mapping physical soil and water conservation structures on cultivated land using GIS and remote sensing techniques

An efficient and reliable automated model that can map physical Soil and Water Conservation (SWC) structures on cultivated land was developed using very high spatial resolution imagery obtained from Google Earth and ArcGIS, ERDAS IMAGINE, and SDC Morphology Toolbox for MATLAB and statistical techniques. The model was developed using the following procedures: (1) a high-pass spatial filter algorithm was applied to detect linear features, (2) morphological processing was used to remove unwanted linear features, (3) the raster format was vectorized, (4) the vectorized linear features were split per hectare (ha) and each line was then classified according to its compass direction, and (5) the sum of all vector lengths per class of direction per ha was calculated. Finally, the direction class with the greatest length was selected from each ha to predict the physical SWC structures. The model was calibrated and validated on the Ethiopian Highlands. The model correctly mapped 80% of the existing structures. The developed model was then tested at different sites with different topography. The results show that the developed model is feasible for automated mapping of physical SWC structures. Therefore, the model is useful for predicting and mapping physical SWC structures areas across diverse areas.