Novel developments in SBGN-ED and applications

Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.
We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3].
As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants, and RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development, http://rimas.ipk-gatersleben.de) [5], an information portal that provides a comprehensive overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development. 

[1] Le Novère, N. et al. (2009) The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741.
[2] Czauderna, T., Klukas, C., Schreiber, F. (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26 (18), 2340-2341.
[3] Junker, B.H., Klukas, C., Schreiber, F. (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109+.
[4] Grafahrend-Belau, E., Weise, S., Koschützki, D., Scholz, U., Junker, B.H., Schreiber, F. (2008) MetaCrop - A detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-D958.
[5] Junker, A., Hartmann, A., Schreiber, F., Bäumlein, H. (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6), 303-307.
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Überlegungen zu einer entrepreneur-orientierten Ausbildung an gewerblichen Fachschulen : eine Bestandsaufnahme mit Vorschlägen für eine Ergänzung des Curriculums

In der Arbeit wird untersucht ob eine Ausbildung zum Entrepreneur, also zur Selbständigkeit möglich ist und es wird ein geeigneter curricularer Ansatz gesucht eine Entrepreneurship Education in die Ausbildung zum staatlich geprüften Techniker Maschinentechnik zu integriereren

Überlegungen zu einer entrepreneur-orientierten Ausbildung an gewerblichen Fachschulen: eine Bestandsaufnahme mit Vorschlägen für eine Ergänzung des Curriculums

In der Arbeit wird untersucht ob eine Ausbildung zum Entrepreneur, also zur Selbständigkeit möglich ist und es wird ein geeigneter curricularer Ansatz gesucht eine Entrepreneurship Education in die Ausbildung zum staatlich geprüften Techniker Maschinentechnik zu integriereren

Molekulare Grundlagen der Regulation und Modulation der Motorfunktion von Myosinen

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HTPheno: An image analysis pipeline for high-throughput plant phenotyping

<p>Abstract</p> <p>Background</p> <p>In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image acquisition techniques. During such screening different images of each plant are recorded and must be analysed by applying sophisticated image analysis algorithms.</p> <p>Results</p> <p>This paper presents an image analysis pipeline (HTPheno) for high-throughput plant phenotyping. HTPheno is implemented as a plugin for ImageJ, an open source image processing software. It provides the possibility to analyse colour images of plants which are taken in two different views (top view and side view) during a screening. Within the analysis different phenotypical parameters for each plant such as height, width and projected shoot area of the plants are calculated for the duration of the screening. HTPheno is applied to analyse two barley cultivars.</p> <p>Conclusions</p> <p>HTPheno, an open source image analysis pipeline, supplies a flexible and adaptable ImageJ plugin which can be used for automated image analysis in high-throughput plant phenotyping and therefore to derive new biological insights, such as determination of fitness.</p

Risiken in der Softwareentwicklung

The overall costs of software production are of crucial importance to many companies, as software is involved in a constantly increasing number of business processes and products. On the other hand, the completion of software projects in accordance with defined quality, time and cost requirements involves a high level risk. This paper enumerates specific risks within software development, outlines possibilities for risk prevention and illustrates the treatment of risks within the software development process. The increasing application of software within embedded systems also founds a necessity of knowledge concerning the risks in software development for the established engineering disciplines.Die Kosten der Softwareproduktion sind für viele Firmen von entscheidender Bedeutung, da Software in einer ständig wachsenden Anzahl von Firmenprozessen und Produkten eingesetzt wird und immer mehr Anwendungsbereiche durchdringt. Allerdings birgt die qualitäts-, zeit- und kostengerechte Fertigstellung von Softwareprojekten enorme Risiken. Dieses Papier nennt spezifische Risiken der Softwareentwicklung anhand von fehlgeschlagenen Projekten, skizziert die Möglichkeiten der Risikovermeidung in der Softwareentwicklung und die Behandlung des Risikomanagements im Prozess der Softwareentwicklung. Der zunehmende Einsatz von Software in eingebetteten Systemen begründet die Notwendigkeit des Wissens um Risiken der Softwareentwicklung auch in den klassischen Ingenieurdisziplinen

Canine Brucellosis: Insights Into the Epidemiologic Situation in Europe

Brucella canis is one of many responsible pathogens of discospondylitis in dogs and infections require specific management. Little is known about the epidemiologic situation in Europe. The purpose of the study was to get insights into the occurrence of brucellosis in dogs in Europe. The database of a European veterinary laboratory was screened for Brucella positive samples. Additionally, medical records of a veterinary hospital in Germany were screened for diagnosis of discospondylitis and brucellosis. The laboratory received samples from 20 European countries for Brucella testing in dogs: 3.7% of submitted samples were Brucella spp. PCR-positive (61/1,657), and Brucella canis antibodies were identified in 5.4% of submitted samples (150/2,764). Brucella spp. PCR-positive samples originated from Spain (11.1% of submitted samples), Poland (6.7% of submitted samples) and rarely from Italy and France. Samples with Brucella canis antibodies originated from 13 European countries (Sweden, Belgium, Austria, Switzerland, Italy, Finland, Germany, Denmark, Hungary, Norway, Poland, France, Netherlands). Young dogs (0-24 months) had a 5.4-fold increased risk of PCR positive samples. The supplementary medical records search identified four young female dogs (7-30 months) with Brucella canis discospondylitis in Germany. The four dogs had been imported to Germany from Eastern European countries (Moldavia, Romania, Macedonia). In conclusion, infection with Brucella canis needs to be considered in dogs in Europe and diagnostics for Brucella canis infection appear indicated in young dogs with discospondylitis

FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks

<p>Abstract</p> <p>Background</p> <p>The quantification of metabolic fluxes is gaining increasing importance in the analysis of the metabolic behavior of biological systems such as organisms, tissues or cells. Various methodologies (wetlab or drylab) result in sets of fluxes which require an appropriate visualization for interpretation by scientists. The visualization of flux distributions is a necessary prerequisite for intuitive flux data exploration in the context of metabolic networks.</p> <p>Results</p> <p>We present FluxMap, a tool for the advanced visualization and exploration of flux data in the context of metabolic networks. The template-based flux data import assigns flux values and optional quality parameters (e. g. the confidence interval) to biochemical reactions. It supports the discrimination between mass and substance fluxes, such as C- or N-fluxes. After import, flux data mapping and network-based visualization allow the interactive exploration of the dataset. Various visualization options enable the user to adapt layout and network representation according to individual purposes.</p> <p>Conclusions</p> <p>The Vanted add-on FluxMap comprises a comprehensive set of functionalities for visualization and advanced visual exploration of flux distributions in biological networks. It is available as a Java open source tool from http://www.vanted.org/fluxmap.</p

Genomic analysis of single cytokeratin-positive cells from bone marrow reveals early mutational events in breast cancer

SummaryChromosomal instability in human breast cancer is known to take place before mammary neoplasias display morphological signs of invasion. We describe here the unexpected finding of a tumor cell population with normal karyotypes isolated from bone marrow of breast cancer patients. By analyzing the same single cells for chromosomal aberrations, subchromosomal allelic losses, and gene amplifications, we confirmed their malignant origin and delineated the sequence of genomic events during breast cancer progression. On this trajectory of genomic progression, we identified a subpopulation of patients with very early HER2 amplification. Because early changes have the highest probability of being shared by genetically unstable tumor cells, the genetic characterization of disseminated tumor cells provides a novel rationale for selecting patients for targeted therapies

Digital Behavior Change Interventions for the Prevention and Management of Type 2 Diabetes: Systematic Market Analysis

Background Advancements in technology offer new opportunities for the prevention and management of type 2 diabetes. Venture capital companies have been investing in digital diabetes companies that offer digital behavior change interventions (DBCIs). However, little is known about the scientific evidence underpinning such interventions or the degree to which these interventions leverage novel technology-driven automated developments such as conversational agents (CAs) or just-in-time adaptive intervention (JITAI) approaches. Objective Our objectives were to identify the top-funded companies offering DBCIs for type 2 diabetes management and prevention, review the level of scientific evidence underpinning the DBCIs, identify which DBCIs are recognized as evidence-based programs by quality assurance authorities, and examine the degree to which these DBCIs include novel automated approaches such as CAs and JITAI mechanisms. Methods A systematic search was conducted using 2 venture capital databases (Crunchbase Pro and Pitchbook) to identify the top-funded companies offering interventions for type 2 diabetes prevention and management. Scientific publications relating to the identified DBCIs were identified via PubMed, Google Scholar, and the DBCIs’ websites, and data regarding intervention effectiveness were extracted. The Diabetes Prevention Recognition Program (DPRP) of the Center for Disease Control and Prevention in the United States was used to identify the recognition status. The DBCIs’ publications, websites, and mobile apps were reviewed with regard to the intervention characteristics. Results The 16 top-funded companies offering DBCIs for type 2 diabetes received a total funding of US $2.4 billion as of June 15, 2021. Only 4 out of the 50 identified publications associated with these DBCIs were fully powered randomized controlled trials (RCTs). Further, 1 of those 4 RCTs showed a significant difference in glycated hemoglobin A1c (HbA1c) outcomes between the intervention and control groups. However, all the studies reported HbA1c improvements ranging from 0.2% to 1.9% over the course of 12 months. In addition, 6 interventions were fully recognized by the DPRP to deliver evidence-based programs, and 2 interventions had a pending recognition status. Health professionals were included in the majority of DBCIs (13/16, 81%,), whereas only 10% (1/10) of accessible apps involved a CA as part of the intervention delivery. Self-reports represented most of the data sources (74/119, 62%) that could be used to tailor JITAIs. Conclusions Our findings suggest that the level of funding received by companies offering DBCIs for type 2 diabetes prevention and management does not coincide with the level of evidence on the intervention effectiveness. There is considerable variation in the level of evidence underpinning the different DBCIs and an overall need for more rigorous effectiveness trials and transparent reporting by quality assurance authorities. Currently, very few DBCIs use automated approaches such as CAs and JITAIs, limiting the scalability and reach of these solutions