P Systems with Minimal Left and Right Insertion and Deletion

In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol

P Systems with Minimal Left and Right Insertion and Deletion

Summary. In this article we investigate the operations of insertion and deletion performed at the ends of a string. We show that using these operations in a P systems framework (which corresponds to using specific variants of graph control), computational completeness can even be achieved with the operations of left and right insertion and deletion of only one symbol.

Link IDE : A Real Time Collaborative Development Environment

While working on large scale development projects all software engineers find themselves, at some point, working with a source control system in order to add or re-vert changes to code. With software projects involving a multitude of programmers this is a crucial part of successful development. When working on a smaller project howev-er, with a tight knit group, setting up and dealing with such a system can become more work than it is worth. To solve this problem a real time collaborative integrated devel-opment environment could be used. The IDE’s focus would be on providing a collabora-tive setting for programming teams or pair programming by taking advantage of real time text editing, the ability to build and run code, chat, and various other team and task oriented features. Instead of running into code conflicts at check-in time, users would be able to see conflicts appearing in real-time. This would allow small programming teams to bypass source control, avoid wasting time, and spend more time collaborating. Real time text editing has recently become popular with its appearance in Google Docs. There are a number of open source applications that support real time text editing. Real time editing by multiple users allows not only for excellent collaborative programming but can also be very effective in teaching sessions of programming. Other features such as chatting and task lists would also help to create a fully immersive and organized col-laborative environment where users do not need outside tools in order to collaborate

Detecting Manipulations in Video

This chapter presents the techniques researched and developed within InVID for the forensic analysis of videos, and the detection and localization of forgeries within User-Generated Videos (UGVs). Following an overview of state-of-the-art video tampering detection techniques, we observed that the bulk of current research is mainly dedicated to frame-based tampering analysis or encoding-based inconsistency characterization. We built upon this existing research, by designing forensics filters aimed to highlight any traces left behind by video tampering, with a focus on identifying disruptions in the temporal aspects of a video. As for many other data analysis domains, deep neural networks show very promising results in tampering detection as well. Thus, following the development of a number of analysis filters aimed to help human users in highlighting inconsistencies in video content, we proceeded to develop a deep learning approach aimed to analyze the outputs of these forensics filters and automatically detect tampered videos. In this chapter, we present our survey of the state of the art with respect to its relevance to the goals of InVID, the forensics filters we developed and their potential role in localizing video forgeries, as well as our deep learning approach for automatic tampering detection. We present experimental results on benchmark and real-world data, and analyze the results. We observe that the proposed method yields promising results compared to the state of the art, especially with respect to the algorithm’s ability to generalize to unknown data taken from the real world. We conclude with the research directions that our work in InVID has opened for the future

Frontiers of Membrane Computing: Open Problems and Research Topics

This is a list of open problems and research topics collected after the Twelfth Conference on Membrane Computing, CMC 2012 (Fontainebleau, France (23 - 26 August 2011), meant initially to be a working material for Tenth Brainstorming Week on Membrane Computing, Sevilla, Spain (January 30 - February 3, 2012). The result was circulated in several versions before the brainstorming and then modified according to the discussions held in Sevilla and according to the progresses made during the meeting. In the present form, the list gives an image about key research directions currently active in membrane computing

RPA and PCNA suppress formation of large deletion errors by yeast DNA polymerase δ

In fulfilling its biosynthetic roles in nuclear replication and in several types of repair, DNA polymerase δ (pol δ) is assisted by replication protein A (RPA), the single-stranded DNA-binding protein complex, and by the processivity clamp proliferating cell nuclear antigen (PCNA). Here we report the effects of these accessory proteins on the fidelity of DNA synthesis in vitro by yeast pol δ. We show that when RPA and PCNA are included in reactions containing pol δ, rates for single base errors are similar to those generated by pol δ alone, indicating that pol δ itself is by far the prime determinant of fidelity for single base errors. However, the rate of deleting multiple nucleotides between directly repeated sequences is reduced by ∼10-fold in the presence of either RPA or PCNA, and by ≥90-fold when both proteins are present. We suggest that PCNA and RPA suppress large deletion errors by preventing the primer terminus at a repeat from fraying and/or from relocating and annealing to a downstream repeat. Strong suppression of deletions by PCNA and RPA suggests that they may contribute to the high replication fidelity needed to stably maintain eukaryotic genomes that contain abundant repetitive sequences

Implementation of a digital workspace

Projecte de final de master realitzat en col.laboració amb l'empresa Bull s.aThis document is the summary of my final assignment project report. In this report, I described my internship, the problems encountered and the solutions chosen. It includes also an analysis of my planning and the budget involved. This project aimed at producing a digital workspace which will provide for all pedagogical and management needs in the educational context. This digital workspace is designed to propose a unique and secure gateway to all on line services offered to the users. It will respect the single authentication principle and each application will manage by itself its own access right to its services. Within the team of developers, I was in charge of the data integration. It included the introduction of new data in the main database through an automated process, the management of data modification and the data forwarding to other application. This central process allows all the application to be synchronized at any moment with the data provided by the government. In the report, I present the functionality expected from the portal, and the requisite express by the client. Then, from a technical point of view, I introduce different portals and explain the reason behind our choice within all available. I also highlight a few technical points about the authentication system and the users management system. In another section of the report, I present my own work related to the data integration. From the extraction by the government to the transfer into the different applications, the data are passed from an application to another through different applications I designed and developed. A presented in-depth analysis of the requisites explains the reason of the design used. In the last part, the Gantt diagram and the budget presentation achieves the presentation of my internship

Genome Editing for the Production of Natural Products in Escherichia coli

Natural products such as secondary metabolites (e.g., plant terpenoids) are found to be a major source of bioactive compounds. These natural products accumulate as complex mixtures with other related compounds and this chemical complexity adds cost to the downstream recovery and purification of natural products from plant biomass. One aim of synthetic biology and metabolic engineering programmes is to produce such compounds from synthetic gene clusters in heterologous hosts and thereby achieve more targeted and affordable production. Both fungi and bacteria are common hosts for metabolic engineering in industry. Fungal hosts include Penicillium chrysogenum, Saccharomyces cerevisiae, Aspergillus niger and the bacterial hosts Escherichia coli, Bacillus subtilis, Corynebacterium glutamicum. E. coli is often selected as a host given the ease of its genetic manipulation and the long history of using this organism in laboratory‐based bioengineering. The bioengineering of E. coli extends also to feedstock pathways to interface and optimize the production of high value compounds from widely available and inexpensive carbon sources. Genome editing is important in these microbial bioengineering programmes and is needed to isolate stable strains and to optimize production. Herein, this review discusses frequently used methods for genome editing in E. coli in relation to the production of natural compounds and chemicals