Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

Performance Improvement of Tomographic Image Reconstruction Based on DSP Processors

This paper presents the use of a multiprocessor architecture for the performance improvement of tomographic image reconstruction. Image reconstruction in computed tomography (CT) is an intensive task for single-processor systems. We investigate the filtered image reconstruction suitability based on DSPs organized for parallel processing and its comparison with the Message Passing Interface (MPI) library. The experimental results show that the speedups observed for both platforms were increased in the same direction of the image resolution. In addition, the execution time to communication time ratios (Rt/Rc) as a function of the sample size have shown a narrow variation for the DSP platform in comparison with the MPI platform, which indicates its better performance for parallel image reconstruction.

Accurate velocity reconstruction for Discontinuous Galerkin approximations of two-phase porous media flows

We consider Discontinuous Galerkin approximations of two-phase, immiscible porous media flows in the global pressure/fractional flow formulation with capillary pressure. A sequential approach is used with a backward Euler step for the saturation equation, equal-order interpolation for the pressure and the saturation, and without any limiters. An accurate total velocity field is recovered from the global pressure equation to be used in the saturation equation. Numerical experiments show the advantages of the proposed reconstruction. To cite this article: A. Ern et al., C R. Acad. Sci. Paris, Ser. 1347 (2009). (C) 2009 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

The mitochondrial transcription factor A functions in mitochondrial base excision repair

Mitochondrial transcription factor A (TFAM) is an essential component of mitochondrial nucleoids TFAM plays an important role in mitochondrial transcription and replication TFAM has been previously reported to inhibit nucleotide excision repair (NER) in vitro but NER has not yet been detected in mitochondria, whereas base excision repair (BER) has been comprehensively characterized in these organelles The BER proteins are associated with the inner membrane in mitochondria and thus with the mitochondrial nucleoid, where TFAM is also situated However, a function for TFAM in BER has not yet been investigated This study examines the role of TFAM in BER In vitro studies with purified recombinant TFAM indicate that it preferentially binds to DNA containing 8-oxoguanines, but not to abasic sites, uracils, or a gap in the sequence TFAM inhibited the in vitro incision activity of 8-oxoguanine DNA glycosylase (OGG1), uracil-DNA glycosylase (UDG), apurinic endonuclease 1 (APE1), and nucleotide incorporation by DNA polymerase gamma (pol gamma) On the other hand, a DNA binding-defective TFAM mutant, L58A, showed less inhibition of BER in vitro Characterization of TFAM knockdown (KD) cells revealed that these lysates had higher 8oxoG incision activity without changes in alpha OGG1 protein levels TFAM KD cells had mild resistance to menadione and increased damage accumulation in the mtDNA when compared to the control cells In addition, we found that the tumor suppressor p53, which has been shown to interact with and alter the DNA binding activity of TFAM, alleviates TFAM-Induced inhibition of BER proteins Together, the results suggest that TFAM modulates BER in mitochondria by virtue of its DNA binding activity and protein interactions Published by Elsevier B V

Asymmetrical awnings : a way to increase daylight in buildings without increasing the overheating

Different shapes of asymmetric awnings for east and west windows are investigated mathematically as well as by measurement in a model. A box with 90 cm side and a 30x30 cm window was placed outdoor in overcast weather and the daylight factor was measured at the bottom of the box when the window was unshaded or equipped with different awnings. The average daylight factor in the box decreased from 4.6% for the unshaded window to 1.0% when a full awning was used. With “the best” asymmetrical awning, the average daylight factor was 80% larger than with the full awing. Using Dutch climate, calculation of the energy from direct radiation transmitted through the window during the cooling season showed that this was decreased from 100% as an annual mean for the unshaded window down 22% with a full awing. With “the best” asymmetrical awning, 26% of the energy was transmitted. Calculation of the indoor temperature in a hypothetical row house in Netherlands show that the use of either normal or asymmetrical awnings considerable decrease the indoor temperature during the hot season. Therefore the use of asymmetrical awnings for east or west faced windows considerable can increase the daylight in buildings, with almost no change in overheating, compared to if traditional awnings are used.

Improved Road Design for Future Maintenance - Analysis of Road Barrier Repair Costs

The cost of a road construction over its service life is a function of the design, quality of construction, maintenance strategies and maintenance operations. Unfortunately, designers often neglect a very important aspect which is the possibility to perform future maintenance activities. The focus is mainly on other aspects such as investment costs, traffic safety, aesthetic appearance, regional development and environmental effects. This licentiate thesis is a part of a Ph.D. project entitled “Road Design for lower maintenance costs” that aims to examine how the life-cycle costs can be optimized by selection of appropriate geometrical designs for the roads and their components. The result is expected to give a basis for a new method used in the road planning and design process using life-cycle cost analysis with particular emphasis on road maintenance. The project started with a review of literature with the intention to study conditions causing increased needs for road maintenance, the efforts made by the road authorities to satisfy those needs and the improvement potential by consideration of maintenance aspects during planning and design. An investigation was carried out to identify the problems which obstruct due consideration of maintenance aspects during the road planning and design process. This investigation focused mainly on the road planning and design process at the Swedish Road Administration. However, the road planning and design process in Denmark, Finland and Norway were also roughly evaluated to gain a broader knowledge about the research subject. The investigation was carried out in two phases: data collection and data analysis. Data was collected by semi-structured interviews with expert actors involved in planning, design and maintenance and by a review of design-related documents. Data analyses were carried out using a method called “Change Analysis”. This investigation revealed a complex combination of problems which result in inadequate consideration of maintenance aspects. Several urgent needs for changes to eliminate these problems were identified. Another study was carried out to develop a model for calculation of the repair costs for damages of different road barrier types and to analyse how factors such as road type, speed limits, barrier types, barrier placement, type of road section, alignment and seasonal effects affect the barrier damages and the associated repair costs. This study was carried out using a method called the “Case Study Research Method”. Data was collected from 1087 barrier repairs in two regional offices of the Swedish Road Administration, the Central Region and the Western Region. A table was established for both regions containing the repair cost per vehicle kilometre for different combinations of barrier types, road types and speed limits. This table can be used by the designers in the calculation of the life-cycle costs for different road barrier types.

Electricity Supply Solutions for an Educational Center in Tanzania

The aim of this study was to investigate electricity supply solutions for an educationalcenter that is being built in Chonyonyo Tanzania. Off-grid power generation solutions andfurther optimization possibilities were studied for the case.The study was done for Engineers Without Borders in Sweden. Who are working withMavuno Project on the educational center. The school is set to start operating in year 2015with 40 girl students in the beginning. The educational center will help to improve genderequality by offering high quality education in a safe environment for girls in rural area.It is important for the system to be economically and environmentally sustainable. Thearea has great potential for photovoltaic power generation. Thus PV was considered as theprimary power generation and a diesel generator as a reliable backup. The system sizeoptimization was done with HOMER. For the simulations HOMER required componentdata, weather data and load data. Common components were chose with standardproperties, the loads were based on load estimations from year 2011 and the weather datawas acquired from NASA database. The system size optimization result for this base casewas a system with 26 kW PW; 5.5 kW diesel generator, 15 kW converter and 112 T-105batteries. The initial cost of the system was 55 875 €, the total net present cost 92 121 €and the levelized cost of electricity 0.264 €/kWh.In addition three optimization possibilities were studied. First it was studied how thesystem should be designed and how it would affect the system size to have night loads(security lights) use DC and could the system then be extended in blocks. As a result it wasfound out that the system size could be decreased as the inverter losses would be avoided.Also the system extension in blocks was found to be possible. The second study was aboutinverter stacking where multiple inverters can work as one unit. This type of connectionallows only the required number of inverters to run while shutting down the excess ones.This would allow the converter-unit to run with higher efficiency and lower powerconsumption could be achieved. In future with higher loads the system could be easilyextendable by connecting more inverters either in parallel or series depending on what isneeded. Multiple inverters would also offer higher reliability than using one centralizedinverter. The third study examined how the choice of location for a centralized powergeneration affects the cable sizing for the system. As a result it was found that centralizedpower generation should be located close to high loads in order to avoid long runs of thickcables. Future loads should also be considered when choosing the location. For theeducational center the potential locations for centralized power generation were found outto be close to the school buildings and close to the dormitories.

Passive crosslaminated timber buildings : Final report Cerbof-project no. 76

In this project, Stora Enso’s newly developed building system has been further developed to allow building to the Swedish passive house standard for the Swedish climate. The building system is based on a building framework of CLT (Cross laminated timber) boards. The concept has been tested on a small test building. The experience gained from this test building has also been used for planning a larger building (two storeys with the option of a third storey) with passive house standard with this building system. The main conclusions from the project are:  It is possible to build airtight buildings with this technique without using traditional vapour barriers. Initial measurements show that this can be done without reaching critical humidity levels in the walls and roof, at least where wood fibre insulation is used, as this has a greater capacity for storing and evening out the moisture than mineral wool. However, the test building has so far not been exposed to internal generation of moisture (added moisture from showers, food preparation etc.). This needs to be investigated and this will be done during the winter 2013-14.  A new fixing method for doors and windows has been tested without traditional fibre filling between them and the CLT panel. The door or window is pressed directly on to the CLT panel instead, with an expandable sealing strip between them. This has been proved to be successful.  The air tightness between the CLT panels is achieved with expandable sealing strips between the panels. The position of the sealing strips is important, both for the air tightness itself and to allow rational assembly.  Recurrent air tightness measurements show that the air tightness decreased somewhat during the first six months, but not to such an extent that the passive house criteria were not fulfilled. The reason for the decreased air tightness is not clear, but can be due to small movements in the CLT construction and also to the sealing strips being affected by changing outdoor temperatures.  Long term measurements (at least two years) have to be carried out before more reliable conclusions can be drawn regarding the long term effect of the construction on air tightness and humidity in the walls.  An economic analysis comparing using a concrete frame or the studied CLT frame for a three storey building shows that it is probably more expensive to build with CLT. For buildings higher than three floors, the CLT frame has economic advantages, mainly because of the shorter building time compared to using concrete for the frame. In this analysis, no considerations have been taken to differences in the influence on the environment or the global climate between the two construction methods.

Product verification and defect repair - status and considerations

Product verifications have become a cost-intensive and time-consuming aspect of modern electronics production, but with the onset of an ever-increasing miniaturisation, these aspects will become even more cumbersome. One may also go as far as to point out that certain precision assembly, such as within the biomedical sector, is legally bound to have 0 defects within production. Since miniaturisation and precision assembly will soon become a part of almost any product, the verifications phases of assembly need to be optimised in both functionality and cost. Another aspect relates to the stability and robustness of processes, a pre-requisite for flexibility. Furthermore, as the re-engineering cycle becomes ever more important, all information gathered within the ongoing process becomes vital. In view of these points, product, or process verification may be assumed to be an important and integral part of precision assembly. In this paper, product verification is defined as the process of determining whether or not the products, at a given phase in the life-cycle, fulfil the established specifications. Since the product is given its final form and function in the assembly, the product verification normally takes place somewhere in the assembly line which is the focus for this paper.

An approach to evaluate product verifications

Companies implement a module product assortment as a part of their strategy to, among others, shorten lead-times, increase the product quality and to create more product variants with fever parts. However, the increased number of variants becomes a challenging task for the personnel responsible for the product verifications. By implementing verifications at module level, so called MPV (Module Property Verification) several advantages ensue. The advantages is not only a decrease in cost of verifications, but also a decrease in repair times, occupied space, storages with spare parts, and repair tools. Further, MPV also give an increased product quality due to an increased understanding of which defects that may occur. As an approach to implement MPV, this paper discusses defects and verification processes based on a study at a Swedish company. It also describes a matrix which is used to map relations between company specific cost drivers and so called verification factors. The matrix may indicate cost drivers which have a large impact on the total cost of product verifications.

Energy efficient and economic renovation of residential buildings with low-temperature heating and air heat recovery

With the building sector accounting for around 40% of the total energy consumption in the EU, energy efficiency in buildings is and continues to be an important issue. Great progress has been made in reducing the energy consumption in new buildings, but the large stock of existing buildings with poor energy performance is probably an even more crucial area of focus. This thesis deals with energy efficiency measures that can be suitable for renovation of existing houses, particularly low-temperature heating systems and ventilation systems with heat recovery. The energy performance, environmental impact and costs are evaluated for a range of system combinations, for small and large houses with various heating demands and for different climates in Europe. The results were derived through simulation with energy calculation tools. Low-temperature heating and air heat recovery were both found to be promising with regard to increasing energy efficiency in European houses. These solutions proved particularly effective in Northern Europe as low-temperature heating and air heat recovery have a greater impact in cold climates and on houses with high heating demands. The performance of heat pumps, both with outdoor air and exhaust air, was seen to improve with low-temperature heating. The choice between an exhaust air heat pump and a ventilation system with heat recovery is likely to depend on case specific conditions, but both choices are more cost-effective and have a lower environmental impact than systems without heat recovery. The advantage of the heat pump is that it can be used all year round, given that it produces DHW. Economic and environmental aspects of energy efficiency measures do not always harmonize. On the one hand, lower costs can sometimes mean larger environmental impact; on the other hand there can be divergence between different environmental aspects. This makes it difficult to define financial subsidies to promote energy efficiency measures.

Terapia das construções de concreto : metodologia de avaliação de sistemas epoxi destinadas a injeção de fissuras passivas das estruturas de concreto

A perda do desempenho de uma edificação está associada ao aparecimento de patologias. A escolha de uma adequada terapia para os problemas encantrados, depende de um diagnóstico preciso do caso. A fissuração do concreto é alvo deste trabalho, por ser ela uma das manifestacoes patológicas mais incidentes nas edificacões, tanto a nível nacional como mundial. Nesse trabaho os diversos tipos de fissuras verificadas no concreto são agrupadas em ativas e passivas. Apresenta-se,H ainda, os materiais e técnicas de recuperacão para corrigir as fissuras dos dois grupos. Entre as soluções mais adotadas para recuperar as problemas patológicos, as que utilizam sistemas de base epóxi possuem destaque. O trabalho faz uma discussão sobre os fatores que influenciam o desempenho de sistemas epóxi destinados à injeção de fiissuras passivas do concreto e apresenta ensaios que podem ser realizados para garantir o sucesso da técnica. Ao final, apresenta um exemplo de avaliação de sistemas epóxi, encontradas no mercado nacional, destinados à injecão de fissuras e uma análise dos resultados obtidos.

A contribuição de técnicas modernas de reabilitação estrutural para autenticidade e integridade de edificações patrimoniais

This work discusses the study of the application of structural reinforcement and rehabilitation using modern techniques for interventions in repair works of historical buildings as well as the verification of the behavior of works that have already undergone different structural intervention techniques, with the objective of obtaining data to allow a comparative analysis of the advantages/disadvantages of techniques adapted in each case, regarding the interferences related the authenticity and integrity of the buildings belong to the constructed patrimony so as to obtain a basis for the theoretical foundation for choosing the best solution to be adopted in the case study which consists in an intervention of structural rehabilitation of the old historic building in the primary school "Augusto Severo"

Desenvolvimento de argamassa para restauração utilizando resíduo do polimento do porcelanato

The coatings mortars are essential elements of building structures because they execute an important role in protecting walls and are particularly exposed to aggressive action responsible for its degradation over time. The importance of wall coverings has been the subject of discussion and analysis in the conservation and rehabilitation of old buildings. Are sometimes removed and replaced with inappropriate solutions of constructive point of view or architecture. The most commonly used coatings on walls of old buildings is based on traditional hydraulic lime mortars. The present study aims at the formulation of new lime- based mortars and aerial fine aggregate, in order to contribute to a better field of conservation and restoration mortar coating of old buildings. Residue was used for polishing porcelain as fine aggregate, replacing the aggregate (sand), in percentages 05-30% by mass. We conducted a thorough evaluation of the mortar properties in fresh and hardened state by comparing the performance of the same with a reference mortar. The residue used was characterized as the density, bulk density, and particle size laser, scanning electron microscopy, X-ray diffraction and X-ray fluorescence. Formulations were produced 7, 6 with residue and one commonly used formulation, which served as a reference. In the formulations of lime mortars air (hydrated lime powder CH-I) has been adopted a stroke volume (1:3) with constant binder, was varied and the water / binder and aggregate and waste. For evaluation of mortars fresh, proceeded to consistency analysis, specific gravity, water retention and air content embedded. In the hardened state assays were performed in specific gravity, water retention, modulus of elasticity, tensile strength in bending, compressive strength, water absorption by capillary action, adhesion, tensile strength, resistance to shrinkage and salts by of crystallization trials with resources chloride solution, nitrate and sulfate all sodium in prismatic at 90 days of age, in addition to the micro structural analysis of mortars. Based on the results we can see that the mortar formulated with 10% content of waste and the reference free retraction feature more stable closer to neutrality. The composition of 10% was obtained better performance against the action of the salt crystallization. The mortar with 15% residue obtained better density, lower air content embedded and high capacity for water retention developing good workability. The replacement of 20% of waste generates a satisfactory utilization of resistance to compression, flexion and traction grip the base. And, finally, it can be seen that the mortar with 10, 15 and 20% residual show, in principle, good suitability as coatings, thus enabling a final result consistent with durability, workability and aesthetics developing therefore a material with better performance to repair or replace existing mortars in old buildings

Xylella fastidiosa: An in vivo system to study possible survival strategies within citrus xylem vessels based on global gene expression analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)