Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

Rapid assessment of fruit-color selection by birds using artificial fruits at local scale in Central Amazonia

Modeling clays have been used in several ecological experiments and have proved to be an important tool to variables control. The objective of our study was to determine if fruit color in isolated and grouped displays influences the fruit selection by birds in the field using artificial fruits. Data were collected in six plots distributed homogeneously in 3 km long trails with a minimum distance of 0.5 km. We used a paired experimental design to establish our experiments, so that all treatments were available to the local bird community in each plot. Overall, red was more pecked than brown and white. Isolated red and brown displays were significantly more pecked than others display. Even though our study was conducted in small spatial scales, artificial fruits appeared to be efficient in register fruit consumption attempts by bird. Although inconclusive about selective forces that sharp the dynamics of fruit color polymorphisms and choice by frugivorous birds, our findings corroborate recent studies wherein birds showed preferences by high- over low-contrast fruit signals.

Three essays in financial economics: asset pricing, optimal portfolio selection and financial integration

Executive Summary The unifying theme of this thesis is the pursuit of a satisfactory ways to quantify the riskureward trade-off in financial economics. First in the context of a general asset pricing model, then across models and finally across country borders. The guiding principle in that pursuit was to seek innovative solutions by combining ideas from different fields in economics and broad scientific research. For example, in the first part of this thesis we sought a fruitful application of strong existence results in utility theory to topics in asset pricing. In the second part we implement an idea from the field of fuzzy set theory to the optimal portfolio selection problem, while the third part of this thesis is to the best of our knowledge, the first empirical application of some general results in asset pricing in incomplete markets to the important topic of measurement of financial integration. While the first two parts of this thesis effectively combine well-known ways to quantify the risk-reward trade-offs the third one can be viewed as an empirical verification of the usefulness of the so-called "good deal bounds" theory in designing risk-sensitive pricing bounds. Chapter 1 develops a discrete-time asset pricing model, based on a novel ordinally equivalent representation of recursive utility. To the best of our knowledge, we are the first to use a member of a novel class of recursive utility generators to construct a representative agent model to address some long-lasting issues in asset pricing. Applying strong representation results allows us to show that the model features countercyclical risk premia, for both consumption and financial risk, together with low and procyclical risk free rate. As the recursive utility used nests as a special case the well-known time-state separable utility, all results nest the corresponding ones from the standard model and thus shed light on its well-known shortcomings. The empirical investigation to support these theoretical results, however, showed that as long as one resorts to econometric methods based on approximating conditional moments with unconditional ones, it is not possible to distinguish the model we propose from the standard one. Chapter 2 is a join work with Sergei Sontchik. There we provide theoretical and empirical motivation for aggregation of performance measures. The main idea is that as it makes sense to apply several performance measures ex-post, it also makes sense to base optimal portfolio selection on ex-ante maximization of as many possible performance measures as desired. We thus offer a concrete algorithm for optimal portfolio selection via ex-ante optimization over different horizons of several risk-return trade-offs simultaneously. An empirical application of that algorithm, using seven popular performance measures, suggests that realized returns feature better distributional characteristics relative to those of realized returns from portfolio strategies optimal with respect to single performance measures. When comparing the distributions of realized returns we used two partial risk-reward orderings first and second order stochastic dominance. We first used the Kolmogorov Smirnov test to determine if the two distributions are indeed different, which combined with a visual inspection allowed us to demonstrate that the way we propose to aggregate performance measures leads to portfolio realized returns that first order stochastically dominate the ones that result from optimization only with respect to, for example, Treynor ratio and Jensen's alpha. We checked for second order stochastic dominance via point wise comparison of the so-called absolute Lorenz curve, or the sequence of expected shortfalls for a range of quantiles. As soon as the plot of the absolute Lorenz curve for the aggregated performance measures was above the one corresponding to each individual measure, we were tempted to conclude that the algorithm we propose leads to portfolio returns distribution that second order stochastically dominates virtually all performance measures considered. Chapter 3 proposes a measure of financial integration, based on recent advances in asset pricing in incomplete markets. Given a base market (a set of traded assets) and an index of another market, we propose to measure financial integration through time by the size of the spread between the pricing bounds of the market index, relative to the base market. The bigger the spread around country index A, viewed from market B, the less integrated markets A and B are. We investigate the presence of structural breaks in the size of the spread for EMU member country indices before and after the introduction of the Euro. We find evidence that both the level and the volatility of our financial integration measure increased after the introduction of the Euro. That counterintuitive result suggests the presence of an inherent weakness in the attempt to measure financial integration independently of economic fundamentals. Nevertheless, the results about the bounds on the risk free rate appear plausible from the view point of existing economic theory about the impact of integration on interest rates.

Biometrical analysis and selection of tetraploid progenies of Panicum maximum using mixed model methods

The objectives of this work were to estimate the genetic and phenotypic parameters and to predict the genetic and genotypic values of the selection candidates obtained from intraspecific crosses in Panicum maximum as well as the performance of the hybrid progeny of the existing and projected crosses. Seventy-nine intraspecific hybrids obtained from artificial crosses among five apomictic and three sexual autotetraploid individuals were evaluated in a clonal test with two replications and ten plants per plot. Green matter yield, total and leaf dry matter yields and leaf percentage were evaluated in five cuts per year during three years. Genetic parameters were estimated and breeding and genotypic values were predicted using the restricted maximum likelihood/best linear unbiased prediction procedure (REML/BLUP). The dominant genetic variance was estimated by adjusting the effect of full-sib families. Low magnitude individual narrow sense heritabilities (0.02-0.05), individual broad sense heritabilities (0.14-0.20) and repeatability measured on an individual basis (0.15-0.21) were obtained. Dominance effects for all evaluated characteristics indicated that breeding strategies that explore heterosis must be adopted. Less than 5% increase in the parameter repeatability was obtained for a three-year evaluation period and may be the criterion to determine the maximum number of years of evaluation to be adopted, without compromising gain per cycle of selection. The identification of hybrid candidates for future cultivars and of those that can be incorporated into the breeding program was based on the genotypic and breeding values, respectively. The prediction of the performance of the hybrid progeny, based on the breeding values of the progenitors, permitted the identification of the best crosses and indicated the best parents to use in crosses.

Selection via simulated individual BLUP based on family genotypic effects in sugarcane

The objective of this work was to propose a new selection strategy for the initial stages of sugarcane improvement, based on the methodology 'simulated individual BLUP (BLUPIS)', which promotes a dynamic allocation of individuals selected in each full-sib family, using BLUP as a base for both the genotypic effects of the referred families and plot effects. The method proposed applies to single full-sib families or those obtained from unbalanced or balanced diallel crosses, half-sib families and self-pollinated families. BLUPIS indicates the number of individuals to be selected within each family, the total number of clones to be advanced, and the number of families to contribute with selected individuals. Correlation between BLUPIS and true BLUP was 0.96, by method validation. Additionally, BLUPIS allows the identification of which replication contains the best individuals of each family.

Allohexaploid pearl millet x elephantgrass population potential for a recurrent selection program

The objective of this work was to evaluate the potential of allohexaploid pearl millet x elephantgrass (HGL) population for a recurrent selection program through open-pollinated progenies. Seventy-eight progenies, one representative sample of the population, and two commercial cultivars, Pioneiro and Paraíso, were evaluated in a 9x9 triple lattice design, in two sites. Plant height and dry matter yield were evaluated in three and four cuts, respectively. For plant height, the 17 best progenies were similar to both commercial controls, while for dry matter yield they were higher than 'Paraíso' and lower than 'Pioneiro'. The correlation between progenies and cuts indicated that the fourth cut represents the mean of all cuts, and the possibility of using early selection. Heritability estimates considering cuts and sites were 56.9% for plant height and 58.8% for dry matter yield, and the expected response to selection was 23.4% for dry matter yield and 18.1% for plant height. These results demonstrate the promising HGL population potential for a recurrent selection program.

Habitat selection of three rodents in a frequently burned boreal environment : productivity and habitat diversity

How does fire affect the plant and animal community of the boreal forest? This study attempted to examine the changes in plant composition and productivity, and small mammal demography brought about by fire in the northern boreal environment at Chick Lake, N.W.T. (65053fN, 128°14,W). Two 5*6 ha plots measuring 375m x 150m were selected for study during the summers of 1973 and 197^. One had been unburned for 120 years, the other was part of a fire which burned in the spring of 1969. Grids of 15m x 15m were established in each plot and meter square quadrats taken at each of the 250 grid intersections in order to determine plant composition and density. Aerial primary production was assessed by clipping and drying 80 samples of terminal new production for each species under investigation. Small mammal populations were sampled by placing a Sherman live trap at each grid intersection for ten days in every month. The two plots were similar in plant species composition which suggested that most regrowth in the burned area was from rootstocks which survived the fire. The plant data were submitted to a cluster analysis that revealed nine separate species associations, six of which occured in the burned area and eight of which occured in the control. These were subsequently treated as habitats for purposes of comparison with small mammal distributions. The burned area showed a greater productivity in flowers and fruits although total productivity in the control area was higher due to a large contribution from the non-vascular component. Maximum aerial productivity as dry wieght was measured at 157.1 g/m and 207.8 g/m for the burn and control respectively. Microtus pennsylvanicus and Clethrionomys rutilus were the two most common small mammals encountered; Microtus xanthognathus, Synaptomys borealis, and Phenacomys intermedius also occured in the area. Populations of M. pennsylvanicus and C. rutilus were high during the summer of 1973; however, M. pennsylvanicus was rare on the control but abundant on the burn, while C. rutilus was rare on the burn but abundant in the control. During the summer of 197^ populations declined, with the result that few voles of any species were caught in the burn while equal numbers of the two species were caught in the control. During the summer of 1973 M. pennsylvanicus showed a positive association to the most productive habitat type in the burn which was avoided by C. rutilus. In the control £• rutilus showed a similar positive association to the most productive habitat type which was avoided by M. pennsylvanicus. In all cases for the high population year of 1973# the two species never overlapped in habitat preference. When populations declined in 197^f "both species showed a strong association for the most productive habitat in the control. This would suggest that during a high population year, an abundant species can exclude competitors from a chosen habitat, but that this dominance decreases as population levels decrease. It is possible that M. pennsylvanicus is a more efficient competitor in a recently burned environment, while C. rutilus assumes this role once non-vascular regrowth becomes extensive.

Numerical Response of Breeding Birds Following Experimental Selection Harvesting in Northern Hardwood Forests

Silvicultural treatments have been shown to alter the composition of species assemblages in numerous taxa. However, the intensity and persistence of these effects have rarely been documented. We used a before-after, control-impact (BACI) paired design, i.e., five pairs of 25-ha study plots, 1-control and 1-treated plot, to quantify changes in the density of eight forest bird species in response to selection harvesting over six breeding seasons, one year pre- and five years postharvest. Focal species included mature forest associates, i.e., Northern Parula (Setophaga americana) and Black-throated Green Warbler (Setophaga virens), forest generalists, i.e., Yellow-bellied Sapsucker (Sphyrapicus varius) and Swainson’s Thrush (Catharus ustulatus), early-seral specialists, i.e., Mourning Warbler (Geothlypis philadelphia) and Chestnut-sided Warbler (Setophaga pensylvanica), species associated with shrubby forest gaps, i.e., Black-throated Blue Warbler (Setophaga caerulescens), and mid-seral species, i.e., American Redstart (Setophaga ruticilla). As predicted, we found a negative numerical response to the treatment in the Black-throated Green Warbler, no treatment effect in the Yellow-bellied Sapsucker, and a positive treatment effect in early-seral specialists. We only detected a year effect in the Northern Parula and the American Redstart. There was evidence for a positive treatment effect on the Swainson’s Thrush when the regeneration started to reach the pole stage, i.e., fifth year postharvest. These findings suggest that selection harvesting has the potential to maintain diverse avian assemblages while allowing sustainable management of timber supply, but future studies should determine whether mature-forest associates can sustain second- and third-entry selection harvest treatments.

Modelling habitat selection and distribution of the critically endangered Jerdon's courser Rhinoptilus bitorquatus in scrub jungle: an application of a new tracking method

1. Jerdon's courser Rhinoptilus bitorquatus is a nocturnally active cursorial bird that is only known to occur in a small area of scrub jungle in Andhra Pradesh, India, and is listed as critically endangered by the IUCN. Information on its habitat requirements is needed urgently to underpin conservation measures. We quantified the habitat features that correlated with the use of different areas of scrub jungle by Jerdon's coursers, and developed a model to map potentially suitable habitat over large areas from satellite imagery and facilitate the design of surveys of Jerdon's courser distribution. 2. We used 11 arrays of 5-m long tracking strips consisting of smoothed fine soil to detect the footprints of Jerdon's coursers, and measured tracking rates (tracking events per strip night). We counted the number of bushes and trees, and described other attributes of vegetation and substrate in a 10-m square plot centred on each strip. We obtained reflectance data from Landsat 7 satellite imagery for the pixel within which each strip lay. 3. We used logistic regression models to describe the relationship between tracking rate by Jerdon's coursers and characteristics of the habitat around the strips, using ground-based survey data and satellite imagery. 4. Jerdon's coursers were most likely to occur where the density of large (>2 m tall) bushes was in the range 300-700 ha(-1) and where the density of smaller bushes was less than 1000 ha(-1). This habitat was detectable using satellite imagery. 5. Synthesis and applications. The occurrence of Jerdon's courser is strongly correlated with the density of bushes and trees, and is in turn affected by grazing with domestic livestock, woodcutting and mechanical clearance of bushes to create pasture, orchards and farmland. It is likely that there is an optimal level of grazing and woodcutting that would maintain or create suitable conditions for the species. Knowledge of the species' distribution is incomplete and there is considerable pressure from human use of apparently suitable habitats. Hence, distribution mapping is a high conservation priority. A two-step procedure is proposed, involving the use of ground surveys of bush density to calibrate satellite image-based mapping of potential habitat. These maps could then be used to select priority areas for Jerdon's courser surveys. The use of tracking strips to study habitat selection and distribution has potential in studies of other scarce and secretive species.

Modelling habitat selection and distribution of the critically endangered Jerdon's courser Rhinoptilus bitorquatus in scrub jungle: an application of a new tracking method

1. Jerdon's courser Rhinoptilus bitorquatus is a nocturnally active cursorial bird that is only known to occur in a small area of scrub jungle in Andhra Pradesh, India, and is listed as critically endangered by the IUCN. Information on its habitat requirements is needed urgently to underpin conservation measures. We quantified the habitat features that correlated with the use of different areas of scrub jungle by Jerdon's coursers, and developed a model to map potentially suitable habitat over large areas from satellite imagery and facilitate the design of surveys of Jerdon's courser distribution. 2. We used 11 arrays of 5-m long tracking strips consisting of smoothed fine soil to detect the footprints of Jerdon's coursers, and measured tracking rates (tracking events per strip night). We counted the number of bushes and trees, and described other attributes of vegetation and substrate in a 10-m square plot centred on each strip. We obtained reflectance data from Landsat 7 satellite imagery for the pixel within which each strip lay. 3. We used logistic regression models to describe the relationship between tracking rate by Jerdon's coursers and characteristics of the habitat around the strips, using ground-based survey data and satellite imagery. 4. Jerdon's coursers were most likely to occur where the density of large (>2 m tall) bushes was in the range 300-700 ha(-1) and where the density of smaller bushes was less than 1000 ha(-1). This habitat was detectable using satellite imagery. 5. Synthesis and applications. The occurrence of Jerdon's courser is strongly correlated with the density of bushes and trees, and is in turn affected by grazing with domestic livestock, woodcutting and mechanical clearance of bushes to create pasture, orchards and farmland. It is likely that there is an optimal level of grazing and woodcutting that would maintain or create suitable conditions for the species. Knowledge of the species' distribution is incomplete and there is considerable pressure from human use of apparently suitable habitats. Hence, distribution mapping is a high conservation priority. A two-step procedure is proposed, involving the use of ground surveys of bush density to calibrate satellite image-based mapping of potential habitat. These maps could then be used to select priority areas for Jerdon's courser surveys. The use of tracking strips to study habitat selection and distribution has potential in studies of other scarce and secretive species.

Mean-tracking clustering algorithm for radial basis function centre selection

Radial basis functions can be combined into a network structure that has several advantages over conventional neural network solutions. However, to operate effectively the number and positions of the basis function centres must be carefully selected. Although no rigorous algorithm exists for this purpose, several heuristic methods have been suggested. In this paper a new method is proposed in which radial basis function centres are selected by the mean-tracking clustering algorithm. The mean-tracking algorithm is compared with k means clustering and it is shown that it achieves significantly better results in terms of radial basis function performance. As well as being computationally simpler, the mean-tracking algorithm in general selects better centre positions, thus providing the radial basis functions with better modelling accuracy

U-curve: A branch-and-bound optimization algorithm for U-shaped cost functions on Boolean lattices applied to the feature selection problem

This paper presents the formulation of a combinatorial optimization problem with the following characteristics: (i) the search space is the power set of a finite set structured as a Boolean lattice; (ii) the cost function forms a U-shaped curve when applied to any lattice chain. This formulation applies for feature selection in the context of pattern recognition. The known approaches for this problem are branch-and-bound algorithms and heuristics that explore partially the search space. Branch-and-bound algorithms are equivalent to the full search, while heuristics are not. This paper presents a branch-and-bound algorithm that differs from the others known by exploring the lattice structure and the U-shaped chain curves of the search space. The main contribution of this paper is the architecture of this algorithm that is based on the representation and exploration of the search space by new lattice properties proven here. Several experiments, with well known public data, indicate the superiority of the proposed method to the sequential floating forward selection (SFFS), which is a popular heuristic that gives good results in very short computational time. In all experiments, the proposed method got better or equal results in similar or even smaller computational time. (C) 2009 Elsevier Ltd. All rights reserved.

Is what you say what you do? Analyzing and comparing the effect of buyer-supplier relationship in the Brazilian and Chinese supplier selection criteria

Choosing properly and efficiently a supplier has been challenging practitioners and academics since 1960’s. Since then, countless studies had been performed and relevant changes in the business scenario were considered such as global sourcing, quality-orientation, just-in-time practices. It is almost consensus that quality should be the selection driver, however, some polemical findings questioned this general agreement. Therefore, one of the objectives of the study was to identify the supplier selection criteria and bring this discussion back again. Moreover, Dickson (1966) suggested existing business relationship as selection criterion, then it was reviewed the importance of business relationship for the company and noted a set of potential negative effects that could rise from it. By considering these side effects of relationship, this research aimed to investigate how the relationship could influence the supplier selection and how its harmful effects could affect the selection process. The impact of this phenomenon was investigated cross-nationally. The research strategy adopted was a controlled experiment via vignette combined with discrete choice analysis. The data collections were performed in China and Brazil. By examining the results, it could be drawn five major findings. First, when purchasers were asked to declare their supplier selection priorities, quality was stated as the most important independently of country and relationship. This result was consistent with diverse studies since 60’s. However, when purchasers were exposed to a multi-criteria trade-off situation, their actual selection priorities deviate from what they had declared. In the actual decision-making without influence of buyer-supplier relationship, Brazilian purchasers focused on price and Chinese buyers prioritized delivery then price. This observation reinforced some controversial prior studies of Verma & Pullman (1998) and Hirakubo & Kublin (1998). Second, through the introduction of the buyer-supplier relationship (operationalized via relational capital) in the supplier selection process, this research extended the existing studies and found that Brazilian buyers still focused on price. The relationship became just another criterion for supplier selection such as quality and delivery. However, from the Chinese sample, the results suggested that quality was totally discarded and the decision was majorly made through price and relationship. The third finding suggested that relational capital could legitimate the quality and sustainability of the supplier and replaces these selection criteria and made the decisional task less complex. Additionally, with the relational capital, the decision-makings were associated to few biases such as availability cognition, commitment, confirmatory and perceived biases. By analyzing the purchasers’ behavior, relational capital inducted buyers of both countries to relax in their purchasing requirements (quality, delivery and sustainability) leading to potential negative effects. In the Brazilian sample, the phenomenon of willing to pay a higher price for a lower quality offer demonstrated to be a potential counterproductive and suboptimal decision. Finally, the last finding was associated to the cultural effect on the buyers’ decisions. From the outcome, it is possible to observe that if a purchaser’s cultural background is more relation-oriented, the more he will tend to use relational capital as a decision heuristic, thus, the purchaser will be more susceptible to the potential relationship’s side effects

Selection for bulb maturity in onion

Embora seja possível produzir cebola (Allium cepa) o ano inteiro no Brasil, a maioria dos cultivares nacionais apresentam bulbos com baixa qualidade, o que proporcionou grande importação de cebola da Argentina, do tipo Valenciana, que não bulbifica no Brasil, mas que agradou os consumidores brasileiros. Para estudar o efeito da seleção para maturidade de bulbos baseada em progênies de meios irmãos obtidas do híbrido triplo intervarietal [Crioula x (Pira Ouro x Valenciana Sintética 14)] foram semeadas 17 progênies selecionadas para maturidade precoce e 25 para tardia, além da geração F1 e dos cultivares Pira Ouro (dias curtos), Crioula (intermediários) e Armada (dias longos), totalizando 46 tratamentos. O delineamento foi em blocos ao acaso, com três repetições de 32 plantas por parcela, cultivadas em bandejas de isopor. As progênies precoces apresentaram ciclo médio variando de 67 a 83 dias e as tardias de 85 a 103 dias. Na comparação da porcentagem de plantas improdutivas esta diferença também foi evidente, variando de 0,0% a 6,2% nas precoces e de 8,1% a 59,5% nas tardias. Os coeficientes de herdabilidades obtidos foram elevados, variando de 0,65 (porcentagem de plantas improdutivas, na seleção tardia) a 0,80 (peso médio de bulbo, na seleção precoce), sendo, em média, superiores na população selecionada para maturidade precoce. Foram obtidas progênies com peso de bulbo superior às testemunhas 'Pira Ouro' e 'Crioula' e com ciclo que não diferia destas. A seleção para maturidade foi altamente eficiente e a população selecionada para maturidade precoce apresenta grande potencial de originar cultivares adaptados, com produção e qualidade de bulbos superiores às disponíveis no mercado brasileiro.

Optimal conductor size selection and reconductoring in radial distribution systems using a mixed-integer LP approach

This paper presents a mixed-integer linear programming model to solve the conductor size selection and reconductoring problem in radial distribution systems. In the proposed model, the steady-state operation of the radial distribution system is modeled through linear expressions. The use of a mixed-integer linear model guarantees convergence to optimality using existing optimization software. The proposed model and a heuristic are used to obtain the Pareto front of the conductor size selection and reconductoring problem considering two different objective functions. The results of one test system and two real distribution systems are presented in order to show the accuracy as well as the efficiency of the proposed solution technique. © 1969-2012 IEEE.