Gene filtering with optimal threshold selection

Gene filtering is a useful preprocessing technique often applied to microarray datasets. However, it is no common practice because clear guidelines are lacking and it bears the risk of excluding some potentially relevant genes. In this work, we propose to model microarray data as a mixture of two Gaussian distributions that will allow us to obtain an optimal filter threshold in terms of the gene expression level.

Optimal Exchange Rate Policy in a Growing Semi-Open Economy

This paper considers an alternative perspective to China's exchange rate policy. It studies a semi-open economy where the private sector has no access to international capital markets but the central bank has full access. Moreover, it assumes limited financial development generating a large demand for saving instruments by the private sector. The paper analyzes the optimal exchange rate policy by modeling the central bank as a Ramsey planner. Its main result is that in a growth acceleration episode it is optimal to have an initial real depreciation of the currency combined with an accumulation of reserves, which is consistent with the Chinese experience. This depreciation is followed by an appreciation in the long run. The paper also shows that the optimal exchange rate path is close to the one that would result in an economy with full capital mobility and no central bank intervention.

Causality and contagion in peripheral EMU public debt markets: a dynamic approach

Our research aims to analyze the causal relationships in the behavior of public debt issued by peripheral member countries of the European Economic and Monetary Union -EMU-, with special emphasis on the recent episodes of crisis triggered in the eurozone sovereign debt markets since 2009. With this goal in mind, we make use of a database of daily frequency of yields on 10-year government bonds issued by five EMU countries -Greece, Ireland, Italy, Portugal and Spain-, covering the entire history of the EMU from its inception on 1 January 1999 until 31 December 2010. In the first step, we explore the pair-wise causal relationship between yields, both for the whole sample and for changing subsamples of the data, in order to capture the possible time-varying causal relationship. This approach allows us to detect episodes of contagion between yields on bonds issued by different countries. In the second step, we study the determinants of these contagion episodes, analyzing the role played by different factors, paying special attention to instruments that capture the total national debt -domestic and foreign- in each country.

Identifying Individual T Cell Receptors of Optimal Avidity for Tumor Antigens.

Cytotoxic T cells recognize, via their T cell receptors (TCRs), small antigenic peptides presented by the major histocompatibility complex (pMHC) on the surface of professional antigen-presenting cells and infected or malignant cells. The efficiency of T cell triggering critically depends on TCR binding to cognate pMHC, i.e., the TCR-pMHC structural avidity. The binding and kinetic attributes of this interaction are key parameters for protective T cell-mediated immunity, with stronger TCR-pMHC interactions conferring superior T cell activation and responsiveness than weaker ones. However, high-avidity TCRs are not always available, particularly among self/tumor antigen-specific T cells, most of which are eliminated by central and peripheral deletion mechanisms. Consequently, systematic assessment of T cell avidity can greatly help distinguishing protective from non-protective T cells. Here, we review novel strategies to assess TCR-pMHC interaction kinetics, enabling the identification of the functionally most-relevant T cells. We also discuss the significance of these technologies in determining which cells within a naturally occurring polyclonal tumor-specific T cell response would offer the best clinical benefit for use in adoptive therapies, with or without T cell engineering.

Graduating 4th year radiology residents' perception of optimal imaging modalities for neoplasm and trauma: a pilot study from four U.S. universities

OBJECTIVE: Our purpose was to assess 4th year radiology residents' perception of the optimal imaging modality to investigate neoplasm and trauma. MATERIALS AND METHODS: Twenty-seven 4th year radiology residents from four residency programs were surveyed. They were asked about the best imaging modality to evaluate the brain and spine, lungs, abdomen, and the musculoskeletal system. Imaging modalities available were MRI, CT, ultrasound, PET, and X-ray. All findings were compared to the ACR appropriateness criteria. RESULTS: MRI was chosen as the best imaging modality to evaluate brain, spine, abdominal, and musculoskeletal neoplasm in 96.3%, 100%, 70.4%, and 63% of residents, respectively. CT was chosen by 88.9% to evaluate neoplasm of the lung. Optimal imaging modality to evaluate trauma was CT for brain injuries (100%), spine (92.6%), lung (96.3%), abdomen (92.6%), and major musculoskeletal trauma (74.1%); MRI was chosen for sports injury (96.3%). There was agreement with ACR appropriateness criteria. CONCLUSION: Residents' perception of the best imaging modalities for neoplasm and trauma concurred with the appropriateness criteria by the ACR.

Life span and reproductive cost explain interspecific variation in the optimal onset of reproduction.

Fitness can be profoundly influenced by the age at first reproduction (AFR), but to date the AFR-fitness relationship only has been investigated intraspecifically. Here, we investigated the relationship between AFR and average lifetime reproductive success (LRS) across 34 bird species. We assessed differences in the deviation of the Optimal AFR (i.e., the species-specific AFR associated with the highest LRS) from the age at sexual maturity, considering potential effects of life history as well as social and ecological factors. Most individuals adopted the species-specific Optimal AFR and both the mean and Optimal AFR of species correlated positively with life span. Interspecific deviations of the Optimal AFR were associated with indices reflecting a change in LRS or survival as a function of AFR: a delayed AFR was beneficial in species where early AFR was associated with a decrease in subsequent survival or reproductive output. Overall, our results suggest that a delayed onset of reproduction beyond maturity is an optimal strategy explained by a long life span and costs of early reproduction. By providing the first empirical confirmations of key predictions of life-history theory across species, this study contributes to a better understanding of life-history evolution.

Optimal slopes and speeds in uphill ski mountaineering: a laboratory study.

The purpose of this study was to estimate the energy cost of linear (EC) and vertical displacement (ECvert), mechanical efficiency and main stride parameters during simulated ski mountaineering at different speeds and gradients, to identify an optimal speed and gradient that maximizes performance. 12 subjects roller skied on a treadmill at three different inclines (10, 17 and 24 %) at three different speeds (approximately 70, 80 and 85 % of estimated peak heart rate). Energy expenditure was calculated by indirect calorimetry, while biomechanical parameters were measured with an inertial sensor-based system. At 10 % there was no significant change with speed in EC, ECvert and mechanical efficiency. At 17 and 24 % the fastest speed was significantly more economical. There was a significant effect of gradient on EC, ECvert and mechanical efficiency. The most economical gradient was the steepest one. There was a significant increase of stride frequency with speed. At steep gradients only, relative thrust phase duration decreased significantly, while stride length increased significantly with speed. There was a significant effect of gradient on stride length (decrease with steepness) and relative thrust phase duration (increase with steepness). A combination of a decreased relative thrust phase duration with increased stride length and frequency decreases ECvert. To minimize the energy expenditure to reach the top of a mountain and to optimize performance, ski-mountaineers should choose a steep gradient (~24 %) and, provided they possess sufficient metabolic scope, combine it with a fast speed (~6 km h(-1)).

Analyse de réseau piéton et gestion scolaire: sinuosité, centricité et transport optimal régularisé

Que ce soit d'un point de vue, urbanistique, social, ou encore de la gouvernance, l'évolution des villes est un défi majeur de nos sociétés contemporaines. En offrant la possibilité d'analyser des configurations spatiales et sociales existantes ou en tentant de simuler celles à venir, les systèmes d'information géographique sont devenus incontournables dans la gestion et dans la planification urbaine. En cinq ans la population de la ville de Lausanne est passée de 134'700 à 140'570 habitants, alors que les effectifs de l'école publique ont crû de 12'200 à 13'500 élèves. Cet accroissement démographique associé à un vaste processus d'harmonisation de la scolarité obligatoire en Suisse ont amené le Service des écoles à mettre en place et à développer en collaboration avec l'université de Lausanne des solutions SIG à même de répondre à différentes problématiques spatiales. Établies en 1989, les limites des établissements scolaires (bassins de recrutement) ont dû être redéfinies afin de les réadapter aux réalités d'un paysage urbain et politique en pleine mutation. Dans un contexte de mobilité et de durabilité, un système d'attribution de subventions pour les transports publics basé sur la distance domicile-école et sur l'âge des écoliers, a été conçu. La réalisation de ces projets a nécessité la construction de bases de données géographiques ainsi que l'élaboration de nouvelles méthodes d'analyses exposées dans ce travail. Cette thèse s'est ainsi faite selon une dialectique permanente entre recherches théoriques et nécessités pratiques. La première partie de ce travail porte sur l'analyse du réseau piéton de la ville. La morphologie du réseau est investiguée au travers d'approches multi-échelles du concept de centralité. La première conception, nommée sinuo-centralité ("straightness centrality"), stipule qu'être central c'est être relié aux autres en ligne droite. La deuxième, sans doute plus intuitive, est intitulée centricité ("closeness centrality") et exprime le fait qu'être central c'est être proche des autres (fig. 1, II). Les méthodes développées ont pour but d'évaluer la connectivité et la marchabilité du réseau, tout en suggérant de possibles améliorations (création de raccourcis piétons). Le troisième et dernier volet théorique expose et développe un algorithme de transport optimal régularisé. En minimisant la distance domicile-école et en respectant la taille des écoles, l'algorithme permet de réaliser des scénarios d'enclassement. L'implémentation des multiplicateurs de Lagrange offre une visualisation du "coût spatial" des infrastructures scolaires et des lieux de résidence des écoliers. La deuxième partie de cette thèse retrace les aspects principaux de trois projets réalisés dans le cadre de la gestion scolaire. À savoir : la conception d'un système d'attribution de subventions pour les transports publics, la redéfinition de la carte scolaire, ou encore la simulation des flux d'élèves se rendant à l'école à pied. *** May it be from an urbanistic, a social or from a governance point of view, the evolution of cities is a major challenge in our contemporary societies. By giving the opportunity to analyse spatial and social configurations or attempting to simulate future ones, geographic information systems cannot be overlooked in urban planning and management. In five years, the population of the city of Lausanne has grown from 134'700 to 140'570 inhabitants while the numbers in public schools have increased from 12'200 to 13'500 students. Associated to a considerable harmonisation process of compulsory schooling in Switzerland, this demographic rise has driven schooling services, in collaboration with the University of Lausanne, to set up and develop GIS capable of tackling various spatial issues. Established in 1989, the school districts had to be altered so that they might fit the reality of a continuously changing urban and political landscape. In a context of mobility and durability, an attribution system for public transport subventions based on the distance between residence and school and on the age of the students was designed. The implementation of these projects required the built of geographical databases as well as the elaboration of new analysis methods exposed in this thesis. The first part of this work focuses on the analysis of the city's pedestrian network. Its morphology is investigated through multi-scale approaches of the concept of centrality. The first conception, named the straightness centrality, stipulates that being central is being connected to the others in a straight line. The second, undoubtedly more intuitive, is called closeness centrality and expresses the fact that being central is being close to the others. The goal of the methods developed is to evaluate the connectivity and walkability of the network along with suggesting possible improvements (creation of pedestrian shortcuts).The third and final theoretical section exposes and develops an algorithm of regularised optimal transport. By minimising home to school distances and by respecting school capacity, the algorithm enables the production of student allocation scheme. The implementation of the Lagrange multipliers offers a visualisation of the spatial cost associated to the schooling infrastructures and to the student home locations. The second part of this thesis recounts the principal aspects of three projects fulfilled in the context of school management. It focuses namely on the built of an attribution system for public transport subventions, a school redistricting process and on simulating student pedestrian flows.

Optimal Traffic Grooming in WDM using Lighttours

Recent developments in optical communications have allowed simpler optical devices to improve network resource utilization. As such, we propose adding a lambda-monitoring device to a wavelength-routing switch (WRS) allowing better performance when traffic is routed and groomed. This device may allow a WRS to aggregate traffic over optical routes without incurring in optical-electrical-optical conversion for the existing traffic. In other words, optical routes can be taken partially to route demands creating a sort of "lighttours". In this paper, we compare the number of OEO conversions needed to route a complete given traffic matrix using either lighttours or lightpaths

Improving the efficiency of PV low-power processing circuits by selecting an optimal inductor current of the DC/DC converter

In the context of autonomous sensors powered by small-size photovoltaic (PV) panels, this work analyses how the efficiency of DC/DC-converter-based power processing circuits can be improved by an appropriate selection of the inductor current that transfers the energy from the PV panel to a storage unit. Each component of power losses (fixed, conduction and switching losses) involved in the DC/DC converter specifically depends on the average inductor current so that there is an optimal value of this current that causes minimal losses and, hence, maximum efficiency. Such an idea has been tested experimentally using two commercial DC/DC converters whose average inductor current is adjustable. Experimental results show that the efficiency can be improved up to 12% by selecting an optimal value of that current, which is around 300-350 mA for such DC/DC converters.

Capital Structure of Finnish SMEs and Financial Constraints

This thesis studies capital structure of Finnish small and medium sized enterprises. The specific object of the study is to test whether financial constraints have an effect on capital structure. In addition influences of several other factors were studied. Capital structure determinants are formulated based on three capital structure theories. The tradeoff theory and the agency theory concentrate on the search of optimal capital structure. The pecking order theory concerns favouring on financing source over another. The data of this study consists of financial statement data and results of corporate questionnaire. Regression analysis was used to find out the effects of several determinants. Regression models were formed based on the presented theories. Short and long term debt ratios were considered separately. The metrics of financially constrained firms was included in all models. It was found that financial constrains have a negative and significant effect to short term debt ratios. The effect was negative also to long term debt ratio but not statistically significant. Other considerable factors that influenced debt ratios were fixed assets, age, profitability, single owner and sufficiency of internal financing.

Optimal latent period in a bacteriophage population model structured by infection-age

We study the lysis timing of a bacteriophage population by means of a continuously infection-age-structured population dynamics model. The features of the model are the infection process of bacteria, the death process, and the lysis process which means the replication of bacteriophage viruses inside bacteria and the destruction of them. The time till lysis (or latent period) is assumed to have an arbitrary distribution. We have carried out an optimization procedure, and we have found that the latent period corresponding to maximal fitness (i.e. maximal growth rate of the bacteriophage population) is of fixed length. We also study the dependence of the optimal latent period on the amount of susceptible bacteria and the number of virions released by a single infection. Finally, the evolutionarily stable strategy of the latent period is also determined as a fixed period taking into account that super-infections are not considered