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.

EXPLOITING A GENERIC APPROACH TO CONSTRUCT COMPONENT-BASED SYSTEMS SOFTWARE IN LINUX ENVIRONMENTS

Component-based software engineering has recently emerged as a promising solution to the development of system-level software. Unfortunately, current approaches are limited to specific platforms and domains. This lack of generality is particularly problematic as it prevents knowledge sharing and generally drives development costs up. In the past, we have developed a generic approach to component-based software engineering for system-level software called OpenCom. In this paper, we present OpenComL an instantiation of OpenCom to Linux environments and show how it can be profiled to meet a range of system-level software in Linux environments. For this, we demonstrate its application to constructing a programmable router platform and a middleware for parallel environments.

PAIN IN FIBROMYALGIA AND DISCRIMINATIVE POWER OF THE INSTRUMENTS: VISUAL ANALOG SCALE, DOLORIMETRY AND THE MCGILL PAIN QUESTIONNAIRE

Objective: The aim of this study was to verify the discriminative power of the most widely used pain assessment instruments. Methods: The sample consisted of 279 subjects divided into Fibromyalgia Group (FM- 205 patients with fibromyalgia) and Control Group (CG-74 healthy subjects), mean age 49.29 +/- 10.76 years. Only 9 subjects were male, 6 in FM and 3 in CG. FM were outpatients from the Rheumatology Clinic of the University of Sao Paulo - Hospital das Clinicas (HCFMUSP); the CG included people accompanying patients and hospital staff with similar socio-demographic characteristics. Three instruments were used to assess pain: the McGill Pain Questionnaire (MPQ), the Visual Analog Scale (VAS), and the Dolorimetry, to measure pain threshold on tender points (generating the TP index). In order to assess the discriminative power of the instruments, the measurements obtained were submitted to descriptive analysis and inferential analysis using ROC Curve - sensibility (S), specificity (S I) and area under the curve (AUC) - and Contingence tables with Chi-square Test and odds ratio. Significance level was 0.05. Results: Higher sensibility, specificity and area under the curve was obtained by VAS (80%, 80% and 0.864, respectively), followed by Dolorimetry (S 77%, S177% and AUC 0.851), McGill Sensory (S 72%, S167% and AUC 0.765) and McGill Affective (S 69%, S1 67% and AUC 0.753). Conclusions: VAS presented the higher sensibility, specificity and AUC, showing the greatest discriminative power among the instruments. However, these values are considerably similar to those of Dolorimetry.

Center for the Study of Free Reed Instruments Collection, 1947-2011 Finding Aid

The Center for the Study of Free-Reed Instruments Collection is an archival collection at the City University of New York Graduate Center’s Mina Rees Library which contains materials donated by Professor Allan W. Atlas, related to free-reed instruments and the International Concertina Association.

Möjligheten till att utveckla en generiskt användbar applikation för e-guider - The possibility to develop a generic useful application for e-guides

En e-guide är ett fenomen som kan ge mervärde för besökaren. Det innebär en övergång ifrån en mänsklig guide till en digitaliserad. Det har tidigare skapats e-guider som inte har haft de tekniska aspekterna som krävs för att kunna framföra informationen till besökaren på det sätt utvecklarna och andra inblandade har önskat. Vi har undersökt och utvärderat en av dessa eguiderför att skapa en prototyp för en e-guide över Elsborg, som är en del av Världsarvet Falun. Prototypen utgår ifrån smartphones och operativsystemet Android. Utifrån tidigare och nutida eguider och prototypen, har vi analyserat resultaten och därigenom undersökt möjligheten för att skapa en generisk arkitektur, i form av en applikation för en e-guide som ska kunna appliceras på olika sammanhang oberoende av dess innehåll. Våra efterforskningar har dock visat att det ärsvårt att skapa en så pass generaliserad mall att den direkt går att implementera utan vissa justeringar.

Policy instruments to improve energy efficiency in buildings

The newly adopted energy efficiency directive (2012/27/EU) highlights the importance of energy efficiency in reaching the Union’s 2020 targets. The directive commits member states to defining national energy efficiency targets (art. 3), achieving yearly energy savings of 1.5% of the annual energy sales through the energy efficiency obligation scheme (art. 7), and providing a long-term strategy for the building sector that aims at a 3% refurbishment rate for public buildings (art. 4+5). Buildings currently account for 40% of energy use in most countries, putting them among the largest end-use sectors. This report takes a closer look at the best practices for implementing increasing energy efficiency in different regions and countries in Europe. The final aim is to identify some policy tools to be suggested to the region of Dalarna (Dalarna having been chosen as the pilot county in Sweden) as a means of implementing energy efficiency in the building sector. The final objective is to give analysts and decision-makers a better analytical foundation to explore future policy development in the area of buildings to be proposed and tested at the regional level in Dalarna and later at the national level in Sweden.

Wald tests for IV regression with weak instruments

This dissertation deals with the problem of making inference when there is weak identification in models of instrumental variables regression. More specifically we are interested in one-sided hypothesis testing for the coefficient of the endogenous variable when the instruments are weak. The focus is on the conditional tests based on likelihood ratio, score and Wald statistics. Theoretical and numerical work shows that the conditional t-test based on the two-stage least square (2SLS) estimator performs well even when instruments are weakly correlated with the endogenous variable. The conditional approach correct uniformly its size and when the population F-statistic is as small as two, its power is near the power envelopes for similar and non-similar tests. This finding is surprising considering the bad performance of the two-sided conditional t-tests found in Andrews, Moreira and Stock (2007). Given this counter intuitive result, we propose novel two-sided t-tests which are approximately unbiased and can perform as well as the conditional likelihood ratio (CLR) test of Moreira (2003).

Generic-branded drug competition and the price for pharmaceuticals in procurement auctions

This paper studies the effects of generic drug’s entry on bidding behavior of drug suppliers in procurement auctions for pharmaceuticals, and the consequences on procurer’s price paid for drugs. Using an unique data set on procurement auctions for off-patent drugs organized by Brazilian public bodies, we surprisingly find no statistically difference between bids and prices paid for generic and branded drugs. On the other hand, some branded drug suppliers leave auctions in which there exists a supplier of generics, whereas the remaining ones lower their bidding price. These findings explain why we find that the presence of any supplier of generic drugs in a procurement auction reduces the price paid for pharmaceuticals by 7 percent. To overcome potential estimation bias due to generic’s entry endogeneity, we exploit variation in the number of days between drug’s patent expiration date and the tendering session. The two-stage estimations document the same pattern as the generalized least square estimations find. This evidence indicates that generic competition affects branded supplier’s behavior in public procurement auctions differently from other markets.

The distortion of currencies misalignments on trade Instruments: or why currencies wars are not over

The negotiations of mega agreements between the US and the Pacific countries (TPP) and between the US and the EU (TTIP) are raising the attention of experts on international trade law and economics. TPP and TTIP are proclaimed to be the designers of the rules for the XXI Century. Old trade instruments such as tariffs are said to be no more important for TTIP because tariffs are negligible among those partners but significant to for TPP. Another relevant agreement in negotiation is between the EU and Mercosul, where tariffs are the most important issue in discussion. The main purpose of this paper is to shows that tariff are important for all these agreements, not because of its nominal value, but because the impacts of exchange rate misalignments on tariffs are so significant that all concessions can be distorted by overvalued and by devaluated currencies. The article is divided into several sections: the first gives an introduction to the issue; the second explains the methodologies used to determine exchange rate misalignments and also presents some results for Brazil, US and China; the third summarizes the methodology applied to calculate the impacts of exchange rate misalignments on the level of tariff protection through an exercise of “misalignment tariffication” and examines the effects of exchange rate variations on tariffs and their consequences for the multilateral trading system; the fourth creates a methodology to estimate exchange rates against a basket of currencies (a virtual currency of the World) and a proposal to deal with persistent and significant misalignments related to trade rules. The fifth presents some estimates for the main PTAs. The conclusions are present in the last section

Description of a new species of skate of the genus Malacoraja Stehmann, 1970: the first species from the southwestern Atlantic Ocean, with notes on generic monophyly and composition (Chondrichthyes: Rajidae)

O primeiro registro para o Atlântico Sul ocidental de uma espécie do gênero Malacoraja Stehmann, 1970 é feita com base na descrição de Malacoraja obscura, espécie nova, proveniente do talude continental do Sudeste brasileiro dos estados do Espírito Santo e Rio de Janeiro em profundidades de 808-1105 m. A espécie nova é conhecida através de cinco exemplares e é distinta de seus congêneres pela sua coloração dorsal composta por numerosas manchas esbranquiçadas e pequenas na região do disco e nadadeiras pélvicas, por apresentar uma fileira irregular de espinhos ao longo da superfície dorsal mediana da cauda a qual persiste em espécimes maiores (desde a base da cauda até dois-terços do seu comprimento numa fêmea de 680 mm de comprimento total, CT) e uma região pequena desprovida de dentículos na base ventral da cauda (estendendo somente até a margem distal da nadadeira pélvica). Outros caracteres diagnósticos em combinação incluem a ausência de espinhos escapulares em indivíduos maiores, número elevado de fileiras dentárias (64/62 fileiras num macho subadulto de 505 mm de CT e 76/74 numa fêmea de 680 mm de CT) e de vértebras (27-28 Vtr, 68-75 Vprd), coloração ventral do disco uniformemente castanha escura, duas fenestras pós-ventrais na cintura escapular, fenestra pós-ventral posterior grande, forame magno circular e dois forames para a carótida interna na placa basal ventral do neurocrânio. Machos adultos não são conhecidos, porém uma descrição anatômica de M. obscura, sp. nov., é fornecida. Comparações são realizadas com todo o material conhecido de M. kreffti, com a literatura sobre M. senta e com material abundante de M. spinacidermis da África do Sul; M. obscura, sp. nov., assemelha-se mais a M. spinacidermis do Atlântico Sul oriental em esqueleto dérmico, coloração e tamanho. Malacoraja é monofilético devido à sua espinulação e apêndices rostrais conspícuos e é aparentemente composta por dois grupos de espécies, um para M. obscura e M. spinacidermis e outro para M. kreffti e M. senta, porém a elucidação das relações filogenéticas entre as espécies necessita de mais informações anatômicas, principalmente das duas últimas espécies.

Calibração de um equipamento de TDR para medida de umidade de solos

Este estudo visou à obtenção das curvas de calibração de um equipamento de TDR (Time Domain Reflectometry) em cinco solos da região de Piracicaba, SP, e testou a adequação da calibração interna do equipamento e das curvas genéricas de calibração. As curvas ajustadas, em cada solo separadamente, apresentaram coeficientes de determinação (R²) da ordem de 0,99, e a curva ajustada para o conjunto de dados dos cinco solos apresentou R² = 0,976. A análise de erros-padrão de estimativa mostrou que as curvas genéricas não se prestam às aplicações mais sensíveis, tais como na determinação absoluta do conteúdo de água do solo. Os testes de comparação entre as curvas ajustadas, a curva genérica e a curva embutida no equipamento mostraram que a primeira é superior às demais. O estudo mostrou, também, que a curva de calibração embutida no equipamento é inadequada para as determinações de umidade nos cinco solos estudados.

Generic Bifurcations of Planar Filippov Systems via Geometric Singular Perturbations

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Disclosing the generic behavior of topological solutions: An orbit-based approach

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Alcohol screening instruments in elderly male: a population-based survey in metropolitan São Paulo, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)