Blind reconiliation

Information reconciliation is a crucial procedure in the classical post-processing of quantum key distribution (QKD). Poor reconciliation e?ciency, revealing more information than strictly needed, may compromise the maximum attainable distance, while poor performance of the algorithm limits the practical throughput in a QKD device. Historically, reconciliation has been mainly done using close to minimal information disclosure but heavily interactive procedures, like Cascade, or using less e?cient but also less interactive ?just one message is exchanged? procedures, like the ones based in low-density parity-check (LDPC) codes. The price to pay in the LDPC case is that good e?ciency is only attained for very long codes and in a very narrow range centered around the quantum bit error rate (QBER) that the code was designed to reconcile, thus forcing to have several codes if a broad range of QBER needs to be catered for. Real world implementations of these methods are thus very demanding, either on computational or communication resources or both, to the extent that the last generation of GHz clocked QKD systems are ?nding a bottleneck in the classical part. In order to produce compact, high performance and reliable QKD systems it would be highly desirable to remove these problems. Here we analyse the use of short-length LDPC codes in the information reconciliation context using a low interactivity, blind, protocol that avoids an a priori error rate estimation. We demonstrate that 2×103 bits length LDPC codes are suitable for blind reconciliation. Such codes are of high interest in practice, since they can be used for hardware implementations with very high throughput.

A distributed end-to-end overload control mechanism for networks of SIP servers.

The Session Initiation Protocol (SIP) is an application-layer control protocol standardized by the IETF for creating, modifying and terminating multimedia sessions. With the increasing use of SIP in large deployments, the current SIP design cannot handle overload effectively, which may cause SIP networks to suffer from congestion collapse under heavy offered load. This paper introduces a distributed end-to-end overload control (DEOC) mechanism, which is deployed at the edge servers of SIP networks and is easy to implement. By applying overload control closest to the source of traf?c, DEOC can keep high throughput for SIP networks even when the offered load exceeds the capacity of the network. Besides, it responds quickly to the sudden variations of the offered load and achieves good fairness. Theoretic analysis and extensive simulations verify that DEOC is effective in controlling overload of SIP networks.

Nano-imprinted rear-side diffraction gratings for absorption enhancement in solar cells

As wafer-based solar cells become thinner, light-trapping textures for absorption enhancement will gain in importance. In this work, crystalline silicon wafers were textured with wavelength-scale diffraction grating surface textures by nanoimprint lithography using interference lithography as a mastering technology. This technique allows fine-tailored nanostructures to be realized on large areas with high throughput. Solar cell precursors were fabricated, with the surface textures on the rear side, for optical absorption measurements. Large absorption enhancements are observed in the wavelength range in which the silicon wafer absorbs weakly. It is shown experimentally that bi-periodic crossed gratings perform better than uni-periodic linear gratings. Optical simulations have been made of the fabricated structures, allowing the total absorption to be decomposed into useful absorption in the silicon and parasitic absorption in the rear reflector. Using the calculated silicon absorption, promising absorbed photocurrent density enhancements have been calculated for solar cells employing the nano-textures. Finally, first results are presented of a passivation layer deposition technique that planarizes the rear reflector for the purpose of reducing the parasitic absorption.

Probe-based end-to-end overload control for networks of SIP servers

The Session Initiation Protocol (SIP) has been adopted by the IETF as the control protocol for creating, modifying and terminating multimedia sessions. Overload occurs in SIP networks when SIP servers have insufficient resources to handle received messages. Under overload, SIP networks may suffer from congestion collapse due to current ineffective SIP overload control mechanisms. This paper introduces a probe-based end-to-end overload control (PEOC) mechanism, which is deployed at the edge servers of SIP networks and is easy to implement. By probing the SIP network with SIP messages, PEOC estimates the network load and controls the traffic admitted to the network according to the estimated load. Theoretic analysis and extensive simulations verify that PEOC can keep high throughput for SIP networks even when the offered load exceeds the capacity of the network. Besides, it can respond quickly to the sudden variations of the offered load and achieve good fairness.

Molecular tools to improve chestnut management: El Bierzo as a case study

The European chestnut (Castanea sativa Mill.) is a multipurpose species that has been widely cultivated around the Mediterranean basin since ancient times. New varieties were brought to the Iberian Peninsula during the Roman Empire, which coexist since then with native populations that survived the last glaciation. The relevance of chestnut cultivation has being steadily growing since the Middle Ages, until the rural decline of the past century put a stop to this trend. Forest fires and diseases were also major factors. Chestnut cultivation is gaining momentum again due to its economic (wood, fruits) and ecologic relevance, and represents currently an important asset in many rural areas of Europe. In this Thesis we apply different molecular tools to help improve current management strategies. For this study we have chosen El Bierzo (Castile and Leon, NW Spain), which has a centenary tradition of chestnut cultivation and management, and also presents several unique features from a genetic perspective (next paragraph). Moreover, its nuts are widely appreciated in Spain and abroad for their organoleptic properties. We have focused our experimental work on two major problems faced by breeders and the industry: the lack of a fine-grained genetic characterization and the need for new strategies to control blight disease. To characterize with sufficient detail the genetic diversity and structure of El Bierzo orchards, we analyzed DNA from 169 trees grafted for nut production covering the entire region. We also analyzed 62 nuts from all traditional varieties. El Bierzo constitutes an outstanding scenario to study chestnut genetics and the influence of human management because: (i) it is located at one extreme of the distribution area; (ii) it is a major glacial refuge for the native species; (iii) it has a long tradition of human management (since Roman times, at least); and (iv) its geographical setting ensures an unusual degree of genetic isolation. Thirteen microsatellite markers provided enough informativeness and discrimination power to genotype at the individual level. Together with an unexpected level of genetic variability, we found evidence of genetic structure, with three major gene pools giving rise to the current population. High levels of genetic differentiation between groups supported this organization. Interestingly, genetic structure does not match with spatial boundaries, suggesting that the exchange of material and cultivation practices have strongly influenced natural gene flow. The microsatellite markers selected for this study were also used to classify a set of 62 samples belonging to all traditional varieties. We identified several cases of synonymies and homonymies, evidencing the need to substitute traditional classification systems with new tools for genetic profiling. Management and conservation strategies should also benefit from these tools. The avenue of high-throughput sequencing technologies, combined with the development of bioinformatics tools, have paved the way to study transcriptomes without the need for a reference genome. We took advantage of RNA sequencing and de novo assembly tools to determine the transcriptional landscape of chestnut in response to blight disease. In addition, we have selected a set of candidate genes with high potential for developing resistant varieties via genetic engineering. Our results evidenced a deep transcriptional reprogramming upon fungal infection. The plant hormones ET and JA appear to orchestrate the defensive response. Interestingly, our results also suggest a role for auxins in modulating such response. Many transcription factors were identified in this work that interact with promoters of genes involved in disease resistance. Among these genes, we have conducted a functional characterization of a two major thaumatin-like proteins (TLP) that belongs to the PR5 family. Two genes encoding chestnut cotyledon TLPs have been previously characterized, termed CsTL1 and CsTL2. We substantiate here their protective role against blight disease for the first time, including in silico, in vitro and in vivo evidence. The synergy between TLPs and other antifungal proteins, particularly endo-p-1,3-glucanases, bolsters their interest for future control strategies based on biotechnological approaches.

CMOS integration of AlN based piezoelectric microcantilevers

El gran crecimiento de los sistemas MEMS (Micro Electro Mechanical Systems) así como su presencia en la mayoría de los dispositivos que usamos diariamente despertó nuestro interés. Paralelamente, la tecnología CMOS (Complementary Metal Oxide Semiconductor) es la tecnología más utilizada para la fabricación de circuitos integrados. Además de ventajas relacionadas con el funcionamiento electrónico del dispositivo final, la integración de sistemas MEMS en la tecnología CMOS reduce significantemente los costes de fabricación. Algunos de los dispositivos MEMS con mayor variedad de aplicaciones son los microflejes. Estos dispositivos pueden ser utilizados para la extracción de energía, en microscopios de fuerza atómica o en sensores, como por ejemplo, para biodetección. Los materiales piezoeléctricos más comúnmente utilizados en aplicaciones MEMS se sintetizan a altas temperaturas y por lo tanto no son compatibles con la tecnología CMOS. En nuestro caso hemos usado nitruro de alumino (AlN), que se deposita a temperatura ambiente y es compatible con la tecnología CMOS. Además, es biocompatible, y por tanto podría formar parte de un dispositivo que actúe como biosensor. A lo largo de esta tesis hemos prestado especial atención en desarrollar un proceso de fabricación rápido, reproducible y de bajo coste. Para ello, todos los pasos de fabricación han sido minuciosamente optimizados. Los parámetros de sputtering para depositar el AlN, las distintas técnicas y recetas de ataque, los materiales que actúan como electrodos o las capas sacrificiales para liberar los flejes son algunos de los factores clave estudiados en este trabajo. Una vez que la fabricación de los microflejes de AlN ha sido optimizada, fueron medidos para caracterizar sus propiedades piezoeléctricas y finalmente verificar positivamente su viabilidad como dispositivos piezoeléctricos. ABSTRACT The huge growth of MEMS (Micro Electro Mechanical Systems) as well as their presence in most of our daily used devices aroused our interest on them. At the same time, CMOS (Complementary Metal Oxide Semiconductor) technology is the most popular technology for integrated circuits. In addition to advantages related with the electronics operation of the final device, the integration of MEMS with CMOS technology reduces the manufacturing costs significantly. Some of the MEMS devices with a wider variety of applications are the microcantilevers. These devices can be used for energy harvesting, in an atomic force microscopes or as sensors, as for example, for biodetection. Most of the piezoelectric materials used for these MEMS applications are synthesized at high temperature and consequently are not compatible with CMOS technology. In our case we have used aluminum nitride (AlN), which is deposited at room temperature and hence fully compatible with CMOS technology. Otherwise, it is biocompatible and and can be used to compose a biosensing device. During this thesis work we have specially focused our attention in developing a high throughput, reproducible and low cost fabrication process. All the manufacturing process steps of have been thoroughly optimized in order to achieve this goal. Sputtering parameters to synthesize AlN, different techniques and etching recipes, electrode material and sacrificial layers are some of the key factors studied in this work to develop the manufacturing process. Once the AlN microcantilevers fabrication was optimized, they were measured to characterize their piezoelectric properties and to successfully check their viability as piezoelectric devices.

Compilador de consultas tipo SQL para sistema de procesamiento masivo de eventos CEP

El paradigma de procesamiento de eventos CEP plantea la solución al reto del análisis de grandes cantidades de datos en tiempo real, como por ejemplo, monitorización de los valores de bolsa o el estado del tráfico de carreteras. En este paradigma los eventos recibidos deben procesarse sin almacenarse debido a que el volumen de datos es demasiado elevado y a las necesidades de baja latencia. Para ello se utilizan sistemas distribuidos con una alta escalabilidad, elevado throughput y baja latencia. Este tipo de sistemas son usualmente complejos y el tiempo de aprendizaje requerido para su uso es elevado. Sin embargo, muchos de estos sistemas carecen de un lenguaje declarativo de consultas en el que expresar la computación que se desea realizar sobre los eventos recibidos. En este trabajo se ha desarrollado un lenguaje declarativo de consultas similar a SQL y un compilador que realiza la traducción de este lenguaje al lenguaje nativo del sistema de procesamiento masivo de eventos. El lenguaje desarrollado en este trabajo es similar a SQL, con el que se encuentran familiarizados un gran número de desarrolladores y por tanto aprender este lenguaje no supondría un gran esfuerzo. Así el uso de este lenguaje logra reducir los errores en ejecución de la consulta desplegada sobre el sistema distribuido al tiempo que se abstrae al programador de los detalles de este sistema.---ABSTRACT---The complex event processing paradigm CEP has become the solution for high volume data analytics which demand scalability, high throughput, and low latency. Examples of applications which use this paradigm are financial processing or traffic monitoring. A distributed system is used to achieve the performance requisites. These same requisites force the distributed system not to store the events but to process them on the fly as they are received. These distributed systems are complex systems which require a considerably long time to learn and use. The majority of such distributed systems lack a declarative language in which to express the computation to perform over incoming events. In this work, a new SQL-like declarative language and a compiler have been developed. This compiler translates this new language to the distributed system native language. Due to its similarity with SQL a vast amount of developers who are already familiar with SQL will need little time to learn this language. Thus, this language reduces the execution failures at the time the programmer no longer needs to know every single detail of the underlying distributed system to submit a query.

DNA typing in thirty seconds with a microfabricated device

We report the development of a practical ultrafast allelic profiling assay for the analysis of short tandem repeats (STRs) by using a highly optimized microfluidic electrophoresis device. We have achieved baseline-resolved electrophoretic separations of single-locus STR samples in 30 sec. Analyses of PCR samples containing the four loci CSF1PO, TPOX, THO1, and vWA (abbreviated as CTTv) were performed in less than 2 min. This constitutes a 10- to 100-fold improvement in speed relative to capillary or slab gel systems. The separation device consists of a microfabricated channel 45 μm × 100 μm in cross section and 26 mm in length, filled with a replaceable polyacrylamide matrix operated under denaturing conditions at 50°C. A fluorescently labeled STR ladder was used as an internal standard for allele identification. Samples were prepared by standard procedures and only 4 μl was required for each analysis. The device is capable of repetitive operation and is suitable for automated high-speed and high-throughput applications.

Fluorescence energy transfer detection as a homogeneous DNA diagnostic method

A homogeneous DNA diagnostic assay based on template-directed primer extension detected by fluorescence resonance energy transfer, named template-directed dye-terminator incorporation (TDI) assay, has been developed for mutation detection and high throughput genome analysis. Here, we report the successful application of the TDI assay to detect mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, the human leukocyte antigen H (HLA-H) gene, and the receptor tyrosin kinase (RET) protooncogene that are associated with cystic fibrosis, hemochromatosis, and multiple endocrine neoplasia, type 2, respectively. Starting with total human DNA, the samples are amplified by the PCR followed by enzymatic degradation of excess primers and deoxyribonucleoside triphosphates before the primer extension reaction is performed. All these standardized steps are performed in the same tube, and the fluorescence changes are monitored in real time, making it a useful clinical DNA diagnostic method.

Use of model plant hosts to identify Pseudomonas aeruginosa virulence factors

We used plants as an in vivo pathogenesis model for the identification of virulence factors of the human opportunistic pathogen Pseudomonas aeruginosa. Nine of nine TnphoA mutant derivatives of P. aeruginosa strain UCBPP-PA14 that were identified in a plant leaf assay for less pathogenic mutants also exhibited significantly reduced pathogenicity in a burned mouse pathogenicity model, suggesting that P. aeruginosa utilizes common strategies to infect both hosts. Seven of these nine mutants contain TnphoA insertions in previously unknown genes. These results demonstrate that an alternative nonvertebrate host of a human bacterial pathogen can be used in an in vivo high throughput screen to identify novel bacterial virulence factors involved in mammalian pathogenesis.

Serial microanalysis of renal transcriptomes

Large-scale gene expression studies can now be routinely performed on macroamounts of cells, but it is unclear to which extent current methods are valuable for analyzing complex tissues. In the present study, we used the method of serial analysis of gene expression (SAGE) for quantitative mRNA profiling in the mouse kidney. We first performed SAGE at the whole-kidney level by sequencing 12,000 mRNA tags. Most abundant tags corresponded to transcripts widely distributed or enriched in the predominant kidney epithelial cells (proximal tubular cells), whereas transcripts specific for minor cell types were barely evidenced. To better explore such cells, we set up a SAGE adaptation for downsized extracts, enabling a 1,000-fold reduction of the amount of starting material. The potential of this approach was evaluated by studying gene expression in microdissected kidney tubules (50,000 cells). Specific gene expression profiles were obtained, and known markers (e.g., uromodulin in the thick ascending limb of Henle's loop and aquaporin-2 in the collecting duct) were found appropriately enriched. In addition, several enriched tags had no databank match, suggesting that they correspond to unknown or poorly characterized transcripts with specific tissue distribution. It is concluded that SAGE adaptation for downsized extracts makes possible large-scale quantitative gene expression measurements in small biological samples and will help to study the tissue expression and function of genes not evidenced with other high-throughput methods.

Direct genetic analysis by matrix-assisted laser desorption/ionization mass spectrometry

An approach to analyzing single-nucleotide polymorphisms (SNPs) found in the human genome has been developed that couples a recently developed invasive cleavage assay for nucleic acids with detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The invasive cleavage assay is a signal amplification method that enables the analysis of SNPs by MALDI-TOF MS directly from human genomic DNA without the need for initial target amplification by PCR. The results presented here show the successful genotyping by this approach of twelve SNPs located randomly throughout the human genome. Conventional Sanger sequencing of these SNP positions confirmed the accuracy of the MALDI-TOF MS analysis results. The ability to unambiguously detect both homozygous and heterozygous genotypes is clearly demonstrated. The elimination of the need for target amplification by PCR, combined with the inherently rapid and accurate nature of detection by MALDI-TOF MS, gives this approach unique and significant advantages in the high-throughput genotyping of large numbers of SNPs, useful for locating, identifying, and characterizing the function of specific genes.

Origin of nanomechanical cantilever motion generated from biomolecular interactions

Generation of nanomechanical cantilever motion from biomolecular interactions can have wide applications, ranging from high-throughput biomolecular detection to bioactuation. Although it has been suggested that such motion is caused by changes in surface stress of a cantilever beam, the origin of the surface-stress change has so far not been elucidated. By using DNA hybridization experiments, we show that the origin of motion lies in the interplay between changes in configurational entropy and intermolecular energetics induced by specific biomolecular interactions. By controlling entropy change during DNA hybridization, the direction of cantilever motion can be manipulated. These thermodynamic principles were also used to explain the origin of motion generated from protein–ligand binding.

Diversity Arrays: a solid state technology for sequence information independent genotyping

Here we present the successful application of the microarray technology platform to the analysis of DNA polymorphisms. Using the rice genome as a model, we demonstrate the potential of a high-throughput genome analysis method called Diversity Array Technology, DArT‘. In the format presented here the technology is assaying for the presence (or amount) of a specific DNA fragment in a representation derived from the total genomic DNA of an organism or a population of organisms. Two different approaches are presented: the first involves contrasting two representations on a single array while the second involves contrasting a representation with a reference DNA fragment common to all elements of the array. The Diversity Panels created using this method allow genetic fingerprinting of any organism or group of organisms belonging to the gene pool from which the panel was developed. Diversity Arrays enable rapid and economical application of a highly parallel, solid-state genotyping technology to any genome or complex genomic mixtures.

BodyMap incorporated PCR-based expression profiling data and a gene ranking system

BodyMap is a human and mouse gene expression database that is based on site-directed 3′-expressed sequence tags generated at Osaka University. To date, it contains more than 300 000 tag sequences from 64 human and 39 mouse tissues. For the recent release, the precise anatomical expression patterns for more than half of the human gene entries were generated by introduced amplified fragment length polymorphism (iAFLP), which is a PCR-based high-throughput expression profiling method. The iAFLP data incorporated into BodyMap describe the relative contents of more than 12 000 transcripts across 30 tissue RNAs. In addition, a newly developed gene ranking system helps users obtain lists of genes that have desired expression patterns according to their significance. BodyMap supports complete transfer of unique data sets and provides analysis that is accessible through the WWW at http://bodymap.ims.u-tokyo.ac.jp.