Gene Set Analysis for improving genetic association studies

Introduction. Genetic epidemiology is focused on the study of the genetic causes that determine health and diseases in populations. To achieve this goal a common strategy is to explore differences in genetic variability between diseased and nondiseased individuals. Usual markers of genetic variability are single nucleotide polymorphisms (SNPs) which are changes in just one base in the genome. The usual statistical approach in genetic epidemiology study is a marginal analysis, where each SNP is analyzed separately for association with the phenotype. Motivation. It has been observed, that for common diseases the single-SNP analysis is not very powerful for detecting genetic causing variants. In this work, we consider Gene Set Analysis (GSA) as an alternative to standard marginal association approaches. GSA aims to assess the overall association of a set of genetic variants with a phenotype and has the potential to detect subtle effects of variants in a gene or a pathway that might be missed when assessed individually. Objective. We present a new optimized implementation of a pair of gene set analysis methodologies for analyze the individual evidence of SNPs in biological pathways. We perform a simulation study for exploring the power of the proposed methodologies in a set of scenarios with different number of causal SNPs under different effect sizes. In addition, we compare the results with the usual single-SNP analysis method. Moreover, we show the advantage of using the proposed gene set approaches in the context of an Alzheimer disease case-control study where we explore the Reelin signal pathway.

Diverse set of Turing nanopatterns coat corneae across insect lineages.

Nipple-like nanostructures covering the corneal surfaces of moths, butterflies, and Drosophila have been studied by electron and atomic force microscopy, and their antireflective properties have been described. In contrast, corneal nanostructures of the majority of other insect orders have either been unexamined or examined by methods that did not allow precise morphological characterization. Here we provide a comprehensive analysis of corneal surfaces in 23 insect orders, revealing a rich diversity of insect corneal nanocoatings. These nanocoatings are categorized into four major morphological patterns and various transitions between them, many, to our knowledge, never described before. Remarkably, this unexpectedly diverse range of the corneal nanostructures replicates the complete set of Turing patterns, thus likely being a result of processes similar to those modeled by Alan Turing in his famous reaction-diffusion system. These findings reveal a beautiful diversity of insect corneal nanostructures and shed light on their molecular origin and evolutionary diversification. They may also be the first-ever biological example of Turing nanopatterns.

A novel set of DIP-STR markers for improved analysis of challenging DNA mixtures.

Currently available molecular biology tools allow forensic scientists to characterize DNA evidence found at crime scenes for a large variety of samples, including those of limited quantity and quality, and achieve high levels of individualization. Yet, standard forensic markers provide limited or no results when applied to mixed DNA samples where the contributors are present in very different proportions (unbalanced DNA mixtures). This becomes an issue mostly for the analysis of trace samples collected on the victim or from touched objects. To this end, we recently proposed an innovative type of genetic marker, named DIP-STR that relies on pairing deletion/insertion polymorphisms (DIP) with standard short tandem repeats (STR). This novel compound marker allows detection of the minor DNA contributor in a DNA mixture of any gender and cellular origin with unprecedented resolution (beyond a DNA ratio of 1:1000). To provide a novel analytical tool useful in practice to common forensic laboratories, this article describes the first set of 10 DIP-STR markers selected according to forensic technical standards. The novel DIP-STR regions are short (between 146 and 271 bp), include only highly polymorphic tri-, tetra- and pentanucleotide tandem repeats and are located on different chromosomes or chromosomal arms to provide statistically independent results. This novel set of DIP-STR can target the amplification of 0.03-0.1 ng of DNA when mixed with a 1000-fold excess of major DNA. DIP-STR relative allele frequencies are estimated based on a survey of 103 Swiss individuals. Finally, this study provides an estimate of the occurrence of informative alleles and a calculation of the corresponding random match probability of the detected minor DIP-STR genotype assessed across 10,506 pairwise conceptual mixtures.

A minimal set of coordinates for describing humanoid shoulder motion

The kinematics of the anatomical shoulder are analysed and modelled as a parallel mechanism similar to a Stewart platform. A new method is proposed to describe the shoulder kinematics with minimal coordinates and solve the indeterminacy. The minimal coordinates are defined from bony landmarks and the scapulothoracic kinematic constraints. Independent from one another, they uniquely characterise the shoulder motion. A humanoid mechanism is then proposed with identical kinematic properties. It is then shown how minimal coordinates can be obtained for this mechanism and how the coordinates simplify both the motion-planning task and trajectory-tracking control. Lastly, the coordinates are also shown to have an application in the field of biomechanics where they can be used to model the scapulohumeral rhythm.

Llegint Cinema. Anàlisi de la representació de la malaltia mental en el setè art

El present treball és un estudi sobre l'estigma social en la malaltia mental i la representació d'aquest al cinema. Aquesta anàlisi s'ha portat a terme a partir de dues línies de treball. Per una banda amb l'anàlisi interpretativa de dotze pel·lícules utilitzant els indicadors de 'perillositat'; 'incapacitat per a la vida'; 'incurabilitat'; 'pèrdua de rols socials'; 'por al rebuig i/o por a les relacions socials'; i per l'altra banda a partir d'un grup de discussió, en el qual s'han visionat fragments de cinc pel·lícules amb set estudiants del Grau d'Educació Social de la Universitat de Vic. Dels resultats obtinguts es desprèn que la pel·lícula és un mitjà de comunicació mitjançant el qual els estereotips són usats en favor de l'espectacle, estigmatitzant així les persones diagnosticades de malaltia mental. Aquest és un dels motius que fan valorar el cinema com un recurs educatiu a considerar tant en la formació d'educadors i educadores socials com en els projectes d'intervenció socioeducativa.

Set-up of a method using LC-UV to assay mometasone furoate in pharmaceutical dosage forms

A reliable method using LC-UV to assay mometasone furoate (MF) in creams or nasal sprays using the same chromatographic conditions was set up. Methanol:water 80:20 (v/v) (1.0 mL min-1) was used as mobile phase. MF was detected at 248 nm and analyzed in a concentration range from 1.0 to 20.0 µg mL-1. The method provided acceptable theoretical plates, peak simmetry, peak tailing factor and peak resolution a short run (5 min). The method showed specificity, good linearity (r = 0.9999) and the quantification limit was 0.379 µg mL-1. Furthermore, the method was precise (RSD < 2.0%), accurate (recovery > 97%) and robust.

Conditions for different autonomy regimes in the world : a fuzzy-set application

Avhandlingen behandlar temat territoriell autonomi ur ett globalt perspektiv. Syftet är dels att kartlägga de territoriella autonomierna i världen och dels att visa hur en ny metod som fuzzy-set kan användas inom ämnesområdet jämförande politik. Forskningsproblemet är att försöka finna de bakgrundsfaktorer som förklarar uppkomsten av territoriell autonomi som sådant. Territoriella autonomier ses som särlösningar inom stater. Dessa regioner har erhållit en specialställning i förhållande till andra regioner inom respektive stat och även i förhållande till centralmakten i övrigt. Regionerna kan därför ses som undantag inom det enhetliga federala, regionala eller decentraliserade systemet inom en viss stat ifråga. En kartläggning visar att det finns 65 specialregioner fördelade på 25 stater i världen. De flesta av dessa utgörs av öar. Resultaten visar att det finns två vägar vilka leder till territoriell autonomi i allmänhet. Den ena vägen är en kombination av etnisk särprägel och liten befolkningsmängd, medan den andra vägen utgörs av kombinationen av historiska orsaker och geografiskt avstånd. Båda vägar är lika giltiga och förutsättningen är en demokratisk miljö.

Water application uniformity and fertigation in a dripping irrigation set

The purpose of this study was to evaluate the uniformity of distribution coefficient (UDC) and coefficient of variation (CV) of a familiar set of irrigation, classifying it the ASAE standard. The irrigation and fertigation are determined by two methods the KELLER & KARMELI and DENÍCULI . The two experiments were subjected to varying pressures: 12, 14, 16 and 18 kPa, in a completely randomized design of twenty samples composed of flows with three replications. Urea, potassium chloride (KCl) and ammonium phosphate (MAP) were the elements used for fertigation. The system consisted of a 200 L tank, which supplied another container of 30 L, it was moved vertically to control the pressure. The data was statistically compared between treatments for each methodology. In fertigation the best pressure was 16 kPa and was classified as "excellent" for UDC (91.03%) and "marginal" for C.V. (7.47%). For the irrigation treatment, the best pressure was 16 kPa rated "excellent" for UDC (91.2%) and "marginal" for C.V. (7.68%). The DENÍCULI et al. (1980) methodology proved more reliable for the evaluation of drip systems. It was observed that this set has good uniformity of distribution, but with great variability in flows.

Method adjustment and equation set of maximum rainfall intensity, duration and frequency in the Mato Grosso do Sul State

Due to the lack of information concerning maximum rainfall equations for most locations in Mato Grosso do Sul State, the alternative for carrying out hydraulic work projects has been information from meteorological stations closest to the location in which the project is carried out. Alternative methods, such as 24 hours rain disaggregation method from rainfall data due to greater availability of stations and longer observations can work. Based on this approach, the objective of this study was to estimate maximum rainfall equations for Mato Grosso do Sul State by adjusting the 24 hours rain disaggregation method, depending on data obtained from rain gauge stations from Dourado and Campo Grande. For this purpose, data consisting of 105 rainfall stations were used, which are available in the ANA (Water Resources Management National Agency) database. Based on the results we concluded: the intense rainfall equations obtained by pluviogram analysis showed determination coefficient above 99%; and the performance of 24 hours rain disaggregation method was classified as excellent, based on relative average error WILMOTT concordance index (1982).

Fast pyrolysis in circulating fluidized bed: feasibility study

Today the limitedness of fossil fuel resources is clearly realized. For this reason there is a strong focus throughout the world on shifting from fossil fuel based energy system to biofuel based energy system. In this respect Finland with its proven excellent forestry capabilities has a great potential to accomplish this goal. It is regarded that one of the most efficient ways of wood biomass utilization is to use it as a feedstock for fast pyrolysis process. By means of this process solid biomass is converted into liquid fuel called bio-oil which can be burnt at power plants, used for hydrogen generation through a catalytic steam reforming process and as a source of valuable chemical compounds. Nowadays different configurations of this process have found their applications in several pilot plants worldwide. However the circulating fluidized bed configuration is regarded as the one with the highest potential to be commercialized. In the current Master’s Thesis a feasibility study of circulating fluidized bed fast pyrolysis process utilizing Scots pine logs as a raw material was conducted. The production capacity of the process is 100 000 tonne/year of bio-oil. The feasibility study is divided into two phases: a process design phase and economic feasibility analysis phase. The process design phase consists of mass and heat balance calculations, equipment sizing, estimation of pressure drops in the pipelines and development of plant layout. This phase resulted in creation of process flow diagrams, equipment list and Microsoft Excel spreadsheet that calculates the process mass and heat balances depending on the bio-oil production capacity which can be set by a user. These documents are presented in the current report as appendices. In the economic feasibility analysis phase there were at first calculated investment and operating costs of the process. Then using these costs there was calculated the price of bio-oil which is required to reach the values of internal rate of return of 5%, 10%, 20%, 30%, 40%, and 50%.

The Shadow Moiré method using the phase shifting technique and digital image processing: computational implementation and application to the 3D-reconstruction of a buckled plate

The Shadow Moiré fringe patterns are level lines of equal depth generated by interference between a master grid and its shadow projected on the surface. In simplistic approach, the minimum error is about the order of the master grid pitch, that is, always larger than 0,1 mm, resulting in an experimental technique of low precision. The use of a phase shift increases the accuracy of the Shadow Moiré technique. The current work uses the phase shifting method to determine the surfaces three-dimensional shape using isothamic fringe patterns and digital image processing. The current study presents the method and applies it to images obtained by simulation for error evaluation, as well as to a buckled plate, obtaining excellent results. The method hands itself particularly useful to decrease the errors in the interpretation of the Moiré fringes that can adversely affect the calculations of displacements in pieces containing many concave and convex regions in relatively small areas.

Phenology, fruit set and dispersal of Cordia multispicata Cham., an important weed shrub of abandoned pastures in eastern Amazonia

ABSTRACT - (Phenology, fruit set and dispersal of Cordia multispicata Cham., an important weed shrub of abandoned pastures in eastern Amazonia). The reproductive ecology of the distylous tropical shrub Cordia multispicata was studied in an abandoned pasture in Paragominas County , Pará state, Brazil. It is a common species in the Amazon basin where it occurs as a weed in open and disturbed habitats. C. multispicata has many flowers per inflorescence (85 ± 12) but 84% abort before fertilization. Flowering occurs throughout the year. Fruits are small, with a red fleshy pericarp (skin-pulp) attractive to birds. Fruit set is lower during the dry season (less than 30%) and higher during the rainy season when there are many visits of insects to the flowers. Fruiting has a peak between the end of the dry season and the middle of the rainy season. Nineteen bird species were observed foraging for the fruits of C. multispicata, and 79% of those species can be considered as potential dispersal agents. The efficient seed dispersal and aggregated spatial distribution associated with some characteristics of the dispersors greatly contributed to the success of this species in abandoned pastures of eastern Amazonia.

Flowering phenology, seed set and arthropod guilds in Trichogoniopsis adenantha (DC) (Asteraceae) in south-east Brazil

and glades. This species blooms throughout the year, attracting arthropods of various guilds, including herbivores, pollinators and predators. In this study, done over a two year period, we described the phenology of T. adenantha and assessed the seasonal variation in arthropod numbers of different guilds. We also determined the periods of lowest and highest seed set. T. adenantha population showed a peak in flowering in March-April (rainy season) with greater production of achenes in December-April. April and October had respectively highest and lowest number of fertilized, undamaged ovules, and this pattern is possibly related with population dynamics of pollinators and herbivores. In August, which was the period of greatest damage to the stigma (by geometrid larvae), there was a positive relationship between the proportion of unfertilized ovules and flowers with damaged stigma, suggesting that floral herbivory may affect reproduction in T. adenantha. We discuss the complex dynamics of the beneficial and harmful interactions between arthropods and the host plant.