Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

Abstract Background Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies. Results We propose here a computational method for optimizing the choice of primer sets, based on multi-objective optimization, which simultaneously: 1) maximizes efficiency and specificity of target amplification; 2) maximizes the number of different bacterial 16S sequences matched by at least one primer; 3) minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any desired amplicon length without affecting computational performance. The source code of the developed algorithm is released as the mopo16S software tool (Multi-Objective Primer Optimization for 16S experiments) under the GNU General Public License and is available at http://sysbiobig.dei.unipd.it/?q=Software#mopo16S. Conclusions Results show that our strategy is able to find better primer pairs than the ones available in the literature according to all three optimization criteria. We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to different genera and phyla. Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers

Internationales Kolloquium über Anwendungen der Informatik und Mathematik in Architektur und Bauwesen : 20. bis 22.7. 2015, Bauhaus-Universität Weimar

The 20th International Conference on the Applications of Computer Science and Mathematics in Architecture and Civil Engineering will be held at the Bauhaus University Weimar from 20th till 22nd July 2015. Architects, computer scientists, mathematicians, and engineers from all over the world will meet in Weimar for an interdisciplinary exchange of experiences, to report on their results in research, development and practice and to discuss. The conference covers a broad range of research areas: numerical analysis, function theoretic methods, partial differential equations, continuum mechanics, engineering applications, coupled problems, computer sciences, and related topics. Several plenary lectures in aforementioned areas will take place during the conference. We invite architects, engineers, designers, computer scientists, mathematicians, planners, project managers, and software developers from business, science and research to participate in the conference

A Way Out of the Quantum Trap

We review Event Enhanced Quantum Theory (EEQT). In Section 1 we address the question "Is Quantum Theory the Last Word". In particular we respond to some of recent challenging staments of H.P. Stapp. We also discuss a possible future of the quantum paradigm - see also Section 5. In Section 2 we give a short sketch of EEQT. Examples are given in Section 3. Section 3.3 discusses a completely new phenomenon - chaos and fractal-like phenomena caused by a simultaneous "measurement" of several non-commuting observables (we include picture of Barnsley's IFS on unit sphere of a Hilbert space). In Section 4 we answer "Frequently Asked Questions" concerning EEQT.Comment: Replacement. Corrected affiliation. Latex, one .jpg figure. To appear in Proc. Conf. Relativistic Quantum Measurements, Napoli 1998, Ed. F. Petruccion

G-CSC Report 2010

The present report gives a short summary of the research of the Goethe Center for Scientific Computing (G-CSC) of the Goethe University Frankfurt. G-CSC aims at developing and applying methods and tools for modelling and numerical simulation of problems from empirical science and technology. In particular, fast solvers for partial differential equations (i.e. pde) such as robust, parallel, and adaptive multigrid methods and numerical methods for stochastic differential equations are developed. These methods are highly adanvced and allow to solve complex problems.. The G-CSC is organised in departments and interdisciplinary research groups. Departments are localised directly at the G-CSC, while the task of interdisciplinary research groups is to bridge disciplines and to bring scientists form different departments together. Currently, G-CSC consists of the department Simulation and Modelling and the interdisciplinary research group Computational Finance

Numerical Simulations

This book will interest researchers, scientists, engineers and graduate students in many disciplines, who make use of mathematical modeling and computer simulation. Although it represents only a small sample of the research activity on numerical simulations, the book will certainly serve as a valuable tool for researchers interested in getting involved in this multidisciplinary field. It will be useful to encourage further experimental and theoretical researches in the above mentioned areas of numerical simulation

Collaborative and adaptive supply chain planning

Dans le contexte industriel d'aujourd'hui, la compétitivité est fortement liée à la performance de la chaîne d'approvisionnement. En d'autres termes, il est essentiel que les unités d'affaires de la chaîne collaborent pour coordonner efficacement leurs activités de production, de façon a produire et livrer les produits à temps, à un coût raisonnable. Pour atteindre cet objectif, nous croyons qu'il est nécessaire que les entreprises adaptent leurs stratégies de planification, que nous appelons comportements, aux différentes situations auxquelles elles font face. En ayant une connaissance de l'impact de leurs comportements de planification sur la performance de la chaîne d'approvisionnement, les entreprises peuvent alors adapter leur comportement plutôt que d'utiliser toujours le même. Cette thèse de doctorat porte sur l'adaptation des comportements de planification des membres d'une même chaîne d'approvisionnement. Chaque membre pouvant choisir un comportement différent et toutes les combinaisons de ces comportements ayant potentiellement un impact sur la performance globale, il est difficile de connaître à l'avance l'ensemble des comportements à adopter pour améliorer cette performance. Il devient alors intéressant de simuler les différentes combinaisons de comportements dans différentes situations et d'évaluer les performances de chacun. Pour permettre l'utilisation de plusieurs comportements dans différentes situations, en utilisant la technologie à base d'agents, nous avons conçu un modèle d'agent à comportements multiples qui a la capacité d'adapter son comportement de planification selon la situation. Les agents planificateurs ont alors la possibilité de se coordonner de façon collaborative pour améliorer leur performance collective. En modélisant les unités d'affaires par des agents, nous avons simulé avec la plateforme de planification à base d'agents de FORAC des agents utilisant différents comportements de planification dits de réaction et de négociation. Cette plateforme, développée par le consortium de recherche FORAC de l'Université Laval, permet de simuler des décisions de planification et de planifier les opérations de la chaîne d'approvisionnement. Ces comportements de planification sont des métaheurisciques organisationnelles qui permettent aux agents de générer des plans de production différents. La simulation est basée sur un cas illustrant la chaîne d'approvisionnement de l'industrie du bois d'œuvre. Les résultats obtenus par l'utilisation de multiples comportements de réaction et de négociation montrent que les systèmes de planification avancée peuvent tirer avantage de disposer de plusieurs comportements de planification, en raIson du contexte dynamique des chaînes d'approvisionnement. La pertinence des résultats de cette thèse dépend de la prémisse que les entreprises qui adapteront leurs comportements de planification aux autres et à leur environnement auront un avantage concurrentiel important sur leurs adversaires

Mining Safety and Sustainability I

Safety and sustainability are becoming ever bigger challenges for the mining industry with the increasing depth of mining. It is of great significance to reduce the disaster risk of mining accidents, enhance the safety of mining operations, and improve the efficiency and sustainability of development of mineral resource. This book provides a platform to present new research and recent advances in the safety and sustainability of mining. More specifically, Mining Safety and Sustainability presents recent theoretical and experimental studies with a focus on safety mining, green mining, intelligent mining and mines, sustainable development, risk management of mines, ecological restoration of mines, mining methods and technologies, and damage monitoring and prediction. It will be further helpful to provide theoretical support and technical support for guiding the normative, green, safe, and sustainable development of the mining industry

View on 5G Architecture: Version 2.0

The 5G Architecture Working Group as part of the 5GPPP Initiative is looking at capturing novel trends and key technological enablers for the realization of the 5G architecture. It also targets at presenting in a harmonized way the architectural concepts developed in various projects and initiatives (not limited to 5GPPP projects only) so as to provide a consolidated view on the technical directions for the architecture design in the 5G era. The first version of the white paper was released in July 2016, which captured novel trends and key technological enablers for the realization of the 5G architecture vision along with harmonized architectural concepts from 5GPPP Phase 1 projects and initiatives. Capitalizing on the architectural vision and framework set by the first version of the white paper, this Version 2.0 of the white paper presents the latest findings and analyses with a particular focus on the concept evaluations, and accordingly it presents the consolidated overall architecture design