SeLOX—a locus of recombination site search tool for the detection and directed evolution of site-specific recombination systems

Site-specific recombinases have become a resourceful tool for genome engineering, allowing sophisticated in vivo DNA modifications and rearrangements, including the precise removal of integrated retroviruses from host genomes. In a recent study, a mutant form of Cre recombinase has been used to excise the provirus of a specific HIV-1 strain from the human genome. To achieve provirus excision, the Cre recombinase had to be evolved to recombine an asymmetric locus of recombination (lox)-like sequence present in the long terminal repeat (LTR) regions of a HIV-1 strain. One pre-requisite for this type of work is the identification of degenerate lox-like sites in genomic sequences. Given their nature—two inverted repeats flanking a spacer of variable length—existing search tools like BLAST or RepeatMasker perform poorly. To address this lack of available algorithms, we have developed the web-server SeLOX, which can identify degenerate lox-like sites within genomic sequences. SeLOX calculates a position weight matrix based on lox-like sequences, which is used to search genomic sequences. For computational efficiency, we transform sequences into binary space, which allows us to use a bit-wise AND Boolean operator for comparisons. Next to finding lox-like sites for Cre type recombinases in HIV LTR sequences, we have used SeLOX to identify lox-like sites in HIV LTRs for six yeast recombinases. We finally demonstrate the general usefulness of SeLOX in identifying lox-like sequences in large genomes by searching Cre type recombination sites in the entire human genome. SeLOX is freely available at http://selox.mpi-cbg.de/cgi-bin/selox/index

Application-aware scheduling for VoIP in Wireless Mesh Networks

Wireless Mesh Networks (WMNs) are seen as a means to provide last mile connections in Next Generation Networks (NGNs). Because of their auto configuration capabilities and the low deployment cost WMNs are considered to be an efficient solution for the support of multiple voice, video and data services in NGNs. This paper looks at the optimal provision of resources in WMNs for Voice over IP (VoIP) traffic, which has strict performance requirements in terms of delay, jitter and packet loss. In WMNs, because of the challenges introduced by wireless multi hop transmissions and limited resources, providing performance quality for VoIP comparable to the voice quality in the traditional circuit switched networks is a major challenge. This paper analyses different scheduling mechanisms for TDMA based access control in mesh networks as specified in the IEEE 802.16 2004 WiMAX standard. The performance of the VoIP applications when different scheduling mechanisms are deployed is analysed on a variety of topologies using ns 2 simulation and mathematical analysis. The paper concludes that on demand scheduling of VoIP traffic typically deployed in 802.11 based WMNs is not able to provide the required VoIP quality in realistic mesh WiMAX network scenarios and is therefore not optimal from a network operator’s point of view. Instead, it is shown, that continuous scheduling is much better suited to serve VoIP traffic. The paper then proposes a new VoIP aware resource coordination scheme and shows, through simulation, that the new scheme is scalable and provides good quality for VoIP service in a wide range of network scenarios. The results shown in the paper prove that the new scheme is resilient to increasing hop count, increasing number of simultaneous VoIP sessions and the background traffic load in the network. Compared to other resource coordination schemes the VoIP aware scheduler significantly increases the number of supported calls

Complexity of coordinated beamforming and scheduling for OFDMA based heterogeneous networks

Coordination is foreseen to be an important component of future mobile radio networks. It is especially relevant in heterogeneous networks, where high power base stations produce strong interference to an underlying layer of low power base stations. This work investigates in detail the achievable performance gains for one coordination technique—coordinated beamforming. It reveals the main factors that influence the throughput of the mobile stations. These findings are combined with an analysis of the computational complexity. As a result, a heuristic algorithm is presented that achieves results close to an exhaustive search with significantly less calculations. Detailed simulation analysis is presented on a realistic network layout

Prospective evaluation of quality of life effects in patients undergoing palliative radiotherapy for brain metastases

Background: Recently published results of quality of life (QoL) studies indicated different outcomes of palliative radiotherapy for brain metastases. This prospective multi-center QoL study of patients with brain metastases was designed to investigate which QoL domains improve or worsen after palliative radiotherapy and which might provide prognostic information. Methods: From 01/2007-01/2009, n=151 patients with previously untreated brain metastases were recruited at 14 centers in Germany and Austria. Most patients (82 %) received whole-brain radiotherapy. QoL was measured with the EORTC-QLQ-C15-PAL and brain module BN20 before the start of radiotherapy and after 3 months. Results: At 3 months, 88/142 (62 %) survived. Nine patients were not able to be followed up. 62 patients (70.5 % of 3-month survivors) completed the second set of questionnaires. Three months after the start of radiotherapy QoL deteriorated significantly in the areas of global QoL, physical function, fatigue, nausea, pain, appetite loss, hair loss, drowsiness, motor dysfunction, communication deficit and weakness of legs. Although the use of corticosteroid at 3 months could be reduced compared to pre-treatment (63 % vs. 37 %), the score for headaches remained stable. Initial QoL at the start of treatment was better in those alive than in those deceased at 3 months, significantly for physical function, motor dysfunction and the symptom scales fatigue, pain, appetite loss and weakness of legs. In a multivariate model, lower Karnofsky performance score, higher age and higher pain ratings before radiotherapy were prognostic of 3-month survival. Conclusions: Moderate deterioration in several QoL domains was predominantly observed three months after start of palliative radiotherapy for brain metastases. Future studies will need to address the individual subjective benefit or burden from such treatment. Baseline QoL scores before palliative radiotherapy for brain metastases may contain prognostic information

The force of the sign. Terrorism as a symbolic phenomenon

Seit der radikalen Änderung der weltpolitischen Lage durch das Selbstmordattentat islamistischer Terroristen auf die Supermacht U.S.A. am 11.9.01 versucht die Weltöffentlichkeit, dem Phänomen des Terrorismus durch die verschiedensten Erklärungsstrategien Herr zu werden. Man führt den Kampf der Kulturen oder Religionen an, verweist auf die Ausbeutung der Peripherie des kapitalistischen Weltsystems durch den Hegemon U.S.A. oder pathologisiert bzw. dämonisiert die Taten der Terroristen. Uns scheinen diese Erklärungsstrategien den Machtkonstellationen der postmodernen Gesellschaften nicht gerecht zu werden, da sie ein zentrales soziales Phänomen der vergangenen Jahrzehnte nicht beachten: das Unbehagen an der pluralistischen Gesellschaft und der konsensuell-repräsentativen Demokratie. Um dieses Unbehagen angemessen beschreiben zu können, wollen wir uns ihm aus einer zeichentheoretischen Perspektive nähern, die soziale Formationen nicht durch (kooperative) Arbeit determiniert sieht, sondern durch die Instanz des Codes. Für Jean Baudrillard ist die Wahl des Ziels der beiden Türme bedeutend, die sich wechselseitig reflektieren und das System nach allen Seiten hin abschließen. Mit ihnen wurde das neuralgische Zentrum des Systems getroffen, das sich auf einem binären Code gründet. Die Twintowers bedeuteten nicht nur das Ende jedweder originalen Referenz, sondern auch den Abschluss des Bezeichneten durch die Wiederholung des Zeichens. Der Code führt eine symbolische Verteilung der gesellschaftlichen Körper durch und zielt auf eine möglichst genaue Übereinstimmung der Gemeinschaft mit sich selbst gemäß eines arithmetischen und geometrischen Kalküls. Die integrative Kraft dieses auf dem Identitätsprinzip basierenden Systems scheint immer häufiger nicht mehr in der Lage zu sein, das negative Potential antagonistischer Strategien binden zu können, die in Form von zivilem Ungehorsam, Politik von Minoritäten oder terroristischen Akten die symbolische Ordnung der westlichen Gesellschaften unterhöhlen. In diesem Tagungsband diskutieren wir das Ausmaß der Krise der konsensuellen Demokratie und ihrer Institutionen. Die Aufsätze behandeln folgende Themen: • Die Krise der pluralistischen Gesellschaft: Wie verständlich ist das kulturelle, politische und religiöse Unbehagen am westlichen Wertekanon? • Die Funktion der Medien in der konsensuellen Demokratie; die gesellschaftliche Wirkung der medialen Reproduktion terroristischer Akte; das Bild des Terrorismus in der Populärkultur • Ästhetischer Terror: Die Vernichtung von Sinn und Bedeutung in der zeitgenössischen Kunst und Kunsttheorie • Die politische Logik des Terrorismus (Ziele, Bedingungen u. Legitimität des Terrorismus in Abgrenzung zu alternativen politischen Ausdrucksformen wie z.B. dem zivilen Ungehorsam; die Bedeutung des terroristischen Opfertodes) • Geschichte des Terrorismus (speziell der Terrorismus der RAF) • Terror als irrationale Gewalt (der ontologische Status des Terrorismus)Since the radical changes in international politics caused by the suicide attacks on the USA by Islamic terrorists on the 11th of September in 2001, the world public tries to grasp the phenomenon of „Terrorism“ through different explanatory strategies. These include referring to the clash of cultures and of religions, to the exploitation of the periphery by the capitalist system incarnated by the USA, or pathologizing as well as demonizing the deeds of the terrorists. All these explanatory attempts do not seem to do justice to the actual constellations of power in postmodern societies, because they do not take a widespread social phenomenon of the past decades in consideration: the discomfort with the pluralistic society and with the concurrent-representative democracy. In order to describe this discomfort adequately we would like to approach the phenomenon from a semiotic perspective which does not consider social formations as determined by cooperative work but rather by the authority of the code. For Jean Baudrillard the target was meaningful since the two towers not only reflect each other but also completely close the system. With them the neuralgic center which is based upon the binary code was severely hit. The twin towers not only meant the end of every original reference but also the completion of the signified by the reduplication of the sign. The code conducts a symbolic distribution of the social bodies and aims at an as accurate as possible identification of the community with itself corresponding to an arithmetic and geometric calculus. The system which is based upon the principle of identity does not seem to have the ability to integrate antagonist energies properly. So these antagonist powers undermine the symbolic order of western societies in terms of civil disobedience, politics of minorities or terroristic acts. In this conference transcript we discuss the degree of crisis of consensual democracy and ist institutions. The essays cover the following topics: • The crisis of the pluralistic society: How comprehensible and justified is the cultural, political, and religious discomfort with western values? • The function of mass media in democratic systems: What is the impact of the reproduction of terrorist acts on society? How does popular culture deal with terrorism? • Aesthetic terror: the destruction of sense and meaning in contemporary arts and art theory • The political logic of terrorism (aims, legitimacy of terrorism as opposed to other forms of opposition like civil disobedience; the meaning of the terrorist self-sacrifice death) • History of terrorism (e.g. The German terrorism of the RAF) • Terrorism as an irrational power (ontological status of terrorism

Sistema de balance de carga para redes malladas inalámbricas multi-interfaces

Wireless mesh networks based on IEEE 802.11 have been initially designed for military purposes, but recently have been deployed widely in customer-based and industrial networks. For more than 10 years wireless mesh networks are in the focus of investigation. Still, topics on routing and quality of service (QoS) are constantly investigated and improved, especially since current wireless mesh hardware allows bigger and highly scalable mesh clouds (e.g., backbone networks). Independently of the application of mesh technology, the deployment of multi-interface nodes offers advantages in terms of capacity and network efficiency. Decreasing prices for wireless hardware benefit this trend. But multi-interface mesh networking generally comes with the cost of a higher system complexity. Especially load balancing and channel assignment have to be carefully adapted. In the presented paper a system which implements the above mentioned aspects is proposed. It includes diverse load balancing modes, taking the possibility of channel assignment algorithms into account. Included interface bundling management results in a more efficient usage of resources. Regarding components and their functionalities are described. An evaluation of the introduced system is provided in form of measurements in different mesh scenarios.Las redes malladas inalámbricas, basadas en las normas 802.11, fueron desarrolladas inicialmente con propósitos militares pero actualmente se han desplegado ampliamente en redes de usuario final e industriales. Desde hace más de diez años se realizan investigaciones en esta área. Sin embargo, los temas de enrutamiento y de calidad de servicio (QoS) no están agotados, sobre todo tomando en consideración que el tamaño de las nubes y backbones mesh ha crecido considerablemente. En estas condiciones puede ser muy beneficioso introducir nodos con múltiples interfaces inalámbricas, lo cual no representa grandes costos, por lo que el tema ha atraído el foco de atención de múltiples investigaciones en la actualidad. Esta posibilidad introduce entonces la necesidad de emplear métodos más complejos para estas redes, como el balance de carga y la asignación de canales, incluyendo la posible combinación de interfaces en cada nodo de la red. El presente artículo propone un sistema para implementar los aspectos mencionados arriba entiéndase, proveer diversos modos de balance de carga, considerando la posibilidad de asignar canales y de combinarlos en la comunicación entre nodos mesh. Esto redunda en una gestión mucho más eficiente de los recursos de las redes malladas inalámbricas. Se describen los componentes y funcionalidades más novedosos del sistema propuesto, los cuales están distribuidos en cada nodo, y se ubican en una capa intermedia entre la de enlace y la de red. Por último se presentan los resultados de las simulaciones del sistema propuesto en escenarios concretos

Sistema de gestión de recursos para mejorar la capacidad de transmisiones en redes malladas inalámbricas

With numerous active nodes in an 802.11-based wireless mesh network, operating on longer multi-hop routes, the total transmission capacity is limited and the overall network becomes unpredictable and less reliable. The presented work describes the next steps towards a more efficient resource management of a multi-radio node, in order to enhance the performance in this kind of networks. If non-overlapping channels are used for communication, the system enables an optimal usage of the available 802.11 spectrum. To manage bundles of multiple WLAN links between mesh neighbors, a modified node architecture and a novel middle-layer software module have been created. Hop-to-hop load balancing in a bundle is included in each node. In parallel, the inclusion of a distributed channel assignment protocol is foreseen. Packet scheduling is performed based on a set of pre-defined load balancing modes. The modes introduce awareness of current network conditions and cover a wide variety of requirements on mesh networks, from improved performance to robustness. Further inspiring technologies, like layer 2 forwarding and hop-to-hop priority queuing, have been tailored in the novel architecture. The achievement is a flexible platform that can be used for different purposes, ranging from a commercially oriented mesh backbone to spontaneously setting up wireless emergency networks. A set of simulator-driven measurements outlines the effectiveness of the multi-interface system.La capacidad de transmisión en una red mallada inalámbrica basada en 802.11 es limitada, si hay numerosos nodos activos que operan en largas rutas de múltiples saltos. En este caso, la red global se vuelve impredecible y menos fiable. El trabajo presentado describe los próximos pasos hacia una gestión de recursos más eficaz de un nodo con múltiples radios, con la meta de mejorar el rendimiento en este tipo de redes. Si se utilizan los canales no solapados para la comunicación, el sistema permite un uso óptimo del espectro disponible en 802.11. Para gestionar los paquetes de múltiples enlaces WLAN (bundles) entre vecinos, se han creado una arquitectura modificada de un nodo y un novedoso módulo de capa media. El balanceo de carga de salto a salto dentro de un bundle se incluye en cada nodo. En paralelo, se prevé la inclusión de un protocolo distribuido de la asignación de canales. La distribución de paquetes se realiza basada en un set de modos de balanceo de carga predefinido. Estos modos introducen la consideración de las condiciones actuales de la red y cubren una amplia variedad de requisitos de las redes malladas; de un mejor rendimiento hasta robustez. Otras tecnologías inspiradoras, como el reenvío en la capa 2 y colas de prioridad entre múltiples saltos, se han adaptado a la nueva arquitectura. Se logró crear una plataforma flexible que se puede utilizar para diferentes propósitos, que van desde una red mallada orientada comercialmente, hasta la construcción espontánea de redes inalámbricas de emergencia. Para demostrar la efectividad del sistema multi-interfaz, se usó un conjunto de mediciones en un simulador

New digital demodulator with matched filters and curve segmentation techniques for BFSK demodulation: Analytical description

The present article relates in general to digital demodulation of Binary Frequency Shift Keying (BFSK). The objective of the present research is to obtain a new processing method for demodulating BFSK-signals in order to reduce hardware complexity in comparison with other methods reported. The solution proposed here makes use of the matched filter theory and curve segmentation algorithms. This paper describes the integration and configuration of a Sampler Correlator and curve segmentation blocks in order to obtain a digital receiver for a proper demodulation of the received signal. The proposed solution is shown to strongly reduce hardware complexity. In this part a presentation of the proposed solution regarding the analytical expressions is addressed. The paper covers in detail the elements needed for properly configuring the system. In a second part it is presented the implementation of the system for FPGA technology and the simulation results in order to validate the overall performance