Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets

Motivation: Recently, many univariate and several multivariate approaches have been suggested for testing differential expression of gene sets between different phenotypes. However, despite a wealth of literature studying their performance on simulated and real biological data, still there is a need to quantify their relative performance when they are testing different null hypotheses.

Results: In this article, we compare the performance of univariate and multivariate tests on both simulated and biological data. In the simulation study we demonstrate that high correlations equally affect the power of both, univariate as well as multivariate tests. In addition, for most of them the power is similarly affected by the dimensionality of the gene set and by the percentage of genes in the set, for which expression is changing between two phenotypes. The application of different test statistics to biological data reveals that three statistics (sum of squared t-tests, Hotelling's T2, N-statistic), testing different null hypotheses, find some common but also some complementing differentially expressed gene sets under specific settings. This demonstrates that due to complementing null hypotheses each test projects on different aspects of the data and for the analysis of biological data it is beneficial to use all three tests simultaneously instead of focusing exclusively on just one.

Sets of p-multiplicity in locally compact groups

We initiate the study of sets of p-multiplicity in locally compact groups and their operator versions. We show that a closed subset E of a second countable locally compact group G is a set of p-multiplicity if and only if E∗={(s,t):ts−1∈E} is a set of operator p-multiplicity. We exhibit examples of sets of p-multiplicity, establish preservation properties for unions and direct products, and prove a p-version of the Stone–von Neumann Theorem.

Simultaneous Embeddings Of Graphs As Median And Antimedian Subgraphs

The distance DG(v) of a vertex v in an undirected graph G is the sum of the distances between v and all other vertices of G. The set of vertices in G with maximum (minimum) distance is the antimedian (median) set of a graph G. It is proved that for arbitrary graphs G and J and a positive integer r 2, there exists a connected graph H such that G is the antimedian and J the median subgraphs of H, respectively, and that dH(G, J) = r. When both G and J are connected, G and J can in addition be made convex subgraphs of H.

The future of veterinarians in dairy herd health management

The future of the Veterinary Practice in Dairy Health Management has changed and will change more drastically from our point of view in the next years. The consumer’s pressure and the Media are more and more concerned about animal welfare, traceability of animal products and safety of products of animal origin. On the other hand the Farmers in Europe have to produce under strong rules (competing with other countries outside Europe), which are normally very expensive to put in practice, and the veterinarians should adapt their knowledge to the new challenges, because without their work and cooperation, dairy farming will have no future. In that sense, the old veterinary practice has to go in other ways, otherwise the Veterinarians will loose clients and the animal population in Europe will be reduced. The Dairy farmers will ask for support in other areas besides clinical: efficacy, management, welfare, profitability, nutrition, prophylaxis, economics, reproduction, environmental protection, grassland management, etc. Cattle practitioners should be able to give answers in several subjects and this sets the challenge to our profession - Veterinary preparation has to be very strong in single animal species, particularly in Dairy or beef cows. The cattle practitioner has to look beyond, but he should never forget that “the single animal” has to be looked at as one unit of the herd, which means that without a very good knowledge of the single animal he will be insufficiently prepared to solve herd problems, and the Herd is the sum of several animals. We all know that very often one single animal allows us to implement herd strategies and develop prophylactic programs. We are convinced that the veterinary profession, and in our case the Cattle Medicine should have the ability to evolve, otherwise the Veterinarian as we know him will miss the train in the next years.

On the spectra of certain integro-differential-delay problems with applications in neurodynamics

We investigate the spectrum of certain integro-differential-delay equations (IDDEs) which arise naturally within spatially distributed, nonlocal, pattern formation problems. Our approach is based on the reformulation of the relevant dispersion relations with the use of the Lambert function. As a particular application of this approach, we consider the case of the Amari delay neural field equation which describes the local activity of a population of neurons taking into consideration the finite propagation speed of the electric signal. We show that if the kernel appearing in this equation is symmetric around some point a= 0 or consists of a sum of such terms, then the relevant dispersion relation yields spectra with an infinite number of branches, as opposed to finite sets of eigenvalues considered in previous works. Also, in earlier works the focus has been on the most rightward part of the spectrum and the possibility of an instability driven pattern formation. Here, we numerically survey the structure of the entire spectra and argue that a detailed knowledge of this structure is important within neurodynamical applications. Indeed, the Amari IDDE acts as a filter with the ability to recognise and respond whenever it is excited in such a way so as to resonate with one of its rightward modes, thereby amplifying such inputs and dampening others. Finally, we discuss how these results can be generalised to the case of systems of IDDEs.

Separating the dynamical effects of climate change and ozone depletion. Part I: Southern Hemisphere stratosphere

A version of the Canadian Middle Atmosphere Model that is coupled to an ocean is used to investigate the separate effects of climate change and ozone depletion on the dynamics of the Southern Hemisphere (SH) stratosphere. This is achieved by performing three sets of simulations extending from 1960 to 2099: 1) greenhouse gases (GHGs) fixed at 1960 levels and ozone depleting substances (ODSs) varying in time, 2) ODSs fixed at 1960 levels and GHGs varying in time, and 3) both GHGs and ODSs varying in time. The response of various dynamical quantities to theGHGand ODS forcings is shown to be additive; that is, trends computed from the sum of the first two simulations are equal to trends from the third. Additivity is shown to hold for the zonal mean zonal wind and temperature, the mass flux into and out of the stratosphere, and the latitudinally averaged wave drag in SH spring and summer, as well as for final warming dates. Ozone depletion and recovery causes seasonal changes in lower-stratosphere mass flux, with reduced polar downwelling in the past followed by increased downwelling in the future in SH spring, and the reverse in SH summer. These seasonal changes are attributed to changes in wave drag caused by ozone-induced changes in the zonal mean zonal winds. Climate change, on the other hand, causes a steady decrease in wave drag during SH spring, which delays the breakdown of the vortex, resulting in increased wave drag in summer

Large Changes of Static Electric Properties Induced by Hydrogen Bonding: An ab Initio Study of Linear HCN Oligomers

We report the partitioning of the interaction-induced static electronic dipole (hyper)polarizabilities for linear hydrogen cyanide complexes into contributions arising from various interaction energy terms. We analyzed the nonadditivities of the studied properties and used these data to predict the electric properties of an infinite chain. The interaction-induced static electric dipole properties and their nonadditivities were analyzed using an approach based on numerical differentiation of the interaction energy components estimated in an external electric field. These were obtained using the hybrid variational-perturbational interaction energy decomposition scheme, augmented with coupled-cluster calculations, with singles, doubles, and noniterative triples. Our results indicate that the interaction-induced dipole moments and polarizabilities are primarily electrostatic in nature; however, the composition of the interaction hyperpolarizabilities is much more complex. The overlap effects substantially quench the contributions due to electrostatic interactions, and therefore, the major components are due to the induction and exchange induction terms, as well as the intramolecular electron-correlation corrections. A particularly intriguing observation is that the interaction first hyperpolarizability in the studied systems not only is much larger than the corresponding sum of monomer properties, but also has the opposite sign. We show that this effect can be viewed as a direct consequence of hydrogen-bonding interactions that lead to a decrease of the hyperpolarizability of the proton acceptor and an increase of the hyperpolarizability of the proton donor. In the case of the first hyperpolarizability, we also observed the largest nonadditivity of interaction properties (nearly 17%) which further enhances the effects of pairwise interactions.

Mining allocating patterns in one-sum weighted items

An Association Rule (AR) is a common knowledge model in data mining that describes an implicative cooccurring relationship between two disjoint sets of binary-valued transaction database attributes (items), expressed in the form of an "antecedent⇒ consequent" rule. A variant of the AR is the Weighted Association Rule (WAR). With regard to a marketing context, this paper introduces a new knowledge model in data mining -ALlocating Pattern (ALP). An ALP is a special form of WAR, where each rule item is associated with a weighting score between 0 and 1, and the sum of all rule item scores is 1. It can not only indicate the implicative co-occurring relationship between two (disjoint) sets of items in a weighted setting, but also inform the "allocating" relationship among rule items. ALPs can be demonstrated to be applicable in marketing and possibly a surprising variety of other areas. We further propose an Apriori based algorithm to extract hidden and interesting ALPs from a "one-sum" weighted transaction database. The experimental results show the effectiveness of the proposed algorithm. © 2008 IEEE.

Kinetic energy sum spectra in nonmesonic weak decay of hypernuclei

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

On the Betti number of the union of two generic map images

Let f: M --> N and g: K --> N be generic differentiable maps of compact manifolds without boundary into a manifold such that their intersection satisfies a certain transversality condition. We show, under a certain cohomological condition, that if the images f(M) and g(K) intersect, then the (upsilon + 1)th Betti number of their union is strictly greater than the sum of their (upsilon + 1)th Betti numbers, where upsilon = dim M + dim K - dim N. This result is applied to the study of coincidence sets and fixed point sets. (C) 1999 Elsevier B.V. B.V. All rights reserved.

An assessment of the economic impact of climate change on the water sector in the Turks and Caicos Islands

The best description of water resources for Grand Turk was offered by Pérez Monteagudo (2000) who suggested that rain water was insufficient to ensure a regular water supply although water catchment was being practised and water catchment possibilities had been analysed. Limestone islands, mostly flat and low lying, have few possibilities for large scale surface storage, and groundwater lenses exist in very delicate equilibrium with saline seawater, and are highly likely to collapse due to sea level rise, improper extraction, drought, tidal waves or other extreme event. A study on the impact of climate change on water resources in the Turks and Caicos Islands is a challenging task, due to the fact that the territory of the Islands covers different environmental resources and conditions, and accurate data are lacking. The present report is based on collected data wherever possible, including grey data from several sources such as the Intergovernmental Panel on Climate Change (IPCC) and Cuban meteorological service data sets. Other data were also used, including the author’s own estimates and modelling results. Although challenging, this was perhaps the best approach towards analysing the situation. Furthermore, IPCC A2 and B2 scenarios were used in the present study in an effort to reduce uncertainty. The main conclusion from the scenario approach is that the trend observed in precipitation during the period 1961 - 1990 is decreasing. Similar behaviour was observed in the Caribbean region. This trend is associated with meteorological causes, particularly with the influence of the North Atlantic Anticyclone. The annual decrease in precipitation is estimated to be between 30-40% with uncertain impacts on marine resources. After an assessment of fresh water resources in Turks and Caicos Islands, the next step was to estimate residential water demand based on a high fertility rate scenario for the Islands (one selected from four scenarios and compared to countries having similar characteristics). The selected scenario presents higher projections on consumption growth, enabling better preparation for growing water demand. Water demand by tourists (stopover and excursionists, mainly cruise passengers) was also obtained, based on international daily consumption estimates. Tourism demand forecasts for Turks and Caicos Islands encompass the forty years between 2011 and 2050 and were obtained by means of an Artificial Neural Networks approach. for the A2 and B2 scenarios, resulting in the relation BAU>B2>A2 in terms of tourist arrivals and water demand levels from tourism. Adaptation options and policies were analysed. Resolving the issue of the best technology to be used for Turks and Caicos Islands is not directly related to climate change. Total estimated water storage capacity is about 1, 270, 800 m3/ year with 80% capacity load for three plants. However, almost 11 desalination plants have been detected on Turks and Caicos Islands. Without more data, it is not possible to estimate long term investment to match possible water demand and more complex adaptation options. One climate change adaptation option would be the construction of elevated (30 metres or higher) storm resistant water reservoirs. The unit cost of the storage capacity is the sum of capital costs and operational and maintenance costs. Electricity costs to pump water are optional as water should, and could, be stored for several months. The costs arising for water storage are in the range of US$ 0.22 cents/m3 without electricity costs. Pérez Monteagudo (2000) estimated water prices at around US$ 2.64/m3 in stand points, US$ 7.92 /m3 for government offices, and US$ 13.2 /m3for cistern truck vehicles. These data need to be updated. As Turks and Caicos Islands continues to depend on tourism and Reverse Osmosis (RO) for obtaining fresh water, an unavoidable condition to maintaining and increasing gross domestic product(GDP) and population welfare, dependence on fossil fuels and vulnerability to increasingly volatile prices will constitute an important restriction. In this sense, mitigation supposes a synergy with adaptation. Energy demand and emissions of carbon dioxide (CO2) were also estimated using an emissions factor of 2. 6 tCO2/ tonne of oil equivalent (toe). Assuming a population of 33,000 inhabitants, primary energy demand was estimated for Turks and Caicos Islands at 110,000 toe with electricity demand of around 110 GWh. The business as usual (BAU), as well as the mitigation scenarios were estimated. The BAU scenario suggests that energy use should be supported by imported fossil fuels with important improvements in energy efficiency. The mitigation scenario explores the use of photovoltaic and concentrating solar power, and wind energy. As this is a preliminary study, the local potential and locations need to be identified to provide more relevant estimates. Macroeconomic assumptions are the same for both scenarios. By 2050, Turks and Caicos Islands could demand 60 m toe less than for the BAU scenario.

Improvements in the sensibility of MSA-GA tool using COFFEE objective function

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

Sets of probability distributions, independence, and convexity

This paper analyzes concepts of independence and assumptions of convexity in the theory of sets of probability distributions. The starting point is Kyburg and Pittarelli's discussion of "convex Bayesianism" (in particular their proposals concerning E-admissibility, independence, and convexity). The paper offers an organized review of the literature on independence for sets of probability distributions; new results on graphoid properties and on the justification of "strong independence" (using exchangeability) are presented. Finally, the connection between Kyburg and Pittarelli's results and recent developments on the axiomatization of non-binary preferences, and its impact on "complete" independence, are described.

The importance of visual and olfactory stimuli during flower visits in Apis mellifera

Flowers attract honeybees using colour and scent signals. Bimodality (having both scent and colour) in flowers leads to increased visitation rates, but how the signals influence each other in a foraging situation is still quite controversial. We studied four basic questions: When faced with conflicting scent and colour information, will bees choose by scent and ignore the “wrong” colour, or vice versa? To get to the bottom of this question, we trained bees on scent-colour combination AX (rewarded) versus BY (unrewarded) and tested them on AY (previously rewarded colour and unrewarded scent) versus BX (previously rewarded scent and unrewarded colour). It turned out that the result depends on stimulus quality: if the colours are very similar (unsaturated blue and blue-green), bees choose by scent. If they are very different (saturated blue and yellow), bees choose by colour. We used the same scents, lavender and rosemary, in both cases. Our second question was: Are individual bees hardwired to use colour and ignore scent (or vice versa), or can this behaviour be modified, depending on which cue is more readily available in the current foraging context? To study this question, we picked colour-preferring bees and gave them extra training on scent-only stimuli. Afterwards, we tested if their preference had changed, and if they still remembered the scent stimulus they had originally used as their main cue. We came to the conclusion that a colour preference can be reversed through scent-only training. We also gave scent-preferring bees extra training on colour-only stimuli, and tested for a change in their preference. The number of animals tested was too small for statistical tests (n = 4), but a common tendency suggested that colour-only training leads to a preference for colour. A preference to forage by a certain sensory modality therefore appears to be not fixed but flexible, and adapted to the bee’s surroundings. Our third question was: Do bees learn bimodal stimuli as the sum of their parts (elemental learning), or as a new stimulus which is different from the sum of the components’ parts (configural learning)? We trained bees on bimodal stimuli, then tested them on the colour components only, and the scent components only. We performed this experiment with a similar colour set (unsaturated blue and blue-green, as above), and a very different colour set (saturated blue and yellow), but used lavender and rosemary for scent stimuli in both cases. Our experiment yielded unexpected results: with the different colours, the results were best explained by elemental learning, but with the similar colour set, bees exhibited configural learning. Still, their memory of the bimodal compound was excellent. Finally, we looked at reverse-learning. We reverse-trained bees with bimodal stimuli to find out whether bimodality leads to better reverse-learning compared to monomodal stimuli. We trained bees on AX (rewarded) versus BY (unrewarded), then on AX (unrewarded) versus BY (rewarded), and finally on AX (rewarded) and BY (unrewarded) again. We performed this experiment with both colour sets, always using the same two scents (lavender and rosemary). It turned out that bimodality does not help bees “see the pattern” and anticipate the switch. Generally, bees trained on the different colour set performed better than bees trained on the similar colour set, indicating that stimulus salience influences reverse-learning.

Selection of body fat distribution indices in adults and associations with plasma lipid metabolism variables

Body fat distribution is a cardiovascular health risk factor in adults. Body fat distribution can be measured through various methods including anthropometry. It is not clear which anthropometric index is suitable for epidemiologic studies of fat distribution and cardiovascular disease. The purpose of the present study was to select a measure of body fat distribution from among a series of indices (those traditionally used in the literature and others constructed from the analysis) that is most highly correlated with lipid-related variables and is independent of overall fatness. Subjects were Mexican-American men and women (N = 1004) from a study of gallbladder disease in Starr County, Texas. Multivariate associations were sought between lipid profile measures (lipids, lipoproteins, and apolipoproteins) and two sets of anthropometric variables (4 circumferences and 6 skinfolds). This was done to assess the association between lipid-related measures and the two sets of anthropometric variables and guide the construction of indices.^ Two indices emerged from the analysis that seemed to be highly correlated with lipid profile measures independent of obesity. These indices are: 2*arm circumference-thigh skinfold in pre- and post-menopausal women and arm/thigh circumference ratio in men. Next, using the sum of all skinfolds to represent obesity and the selected body fat distribution indices, the following hypotheses were tested: (1) state of obesity and centrally/upper distributed body fat are equally predictive of lipids, lipoproteins and apolipoproteins, and (2) the correlation among the lipid-related measures is not altered by obesity and body fat distribution.^ With respect to the first hypothesis, the present study found that most lipids, lipoproteins and apolipoproteins were significantly associated with both overall fatness and anatomical location of body fat in both sex and menopausal groups. However, within men and post-menopausal women, certain lipid profile measures (triglyceride and HDLT among post-menopausal women and apos C-II, CIII, and E among men) had substantially higher correlation with body fat distribution as compared with overall fatness.^ With respect to the second hypothesis, both obesity and body fat distribution were found to alter the association among plasma lipid variables in men and women. There was a suggestion from the data that the pattern of correlations among men and post-menopausal women are more comparable. Among men correlations involving apo A-I, HDLT, and HDL$\sb2$ seemed greatly influenced by obesity, and A-II by fat distribution; among post-menopausal women correlations involving apos A-I and A-II were highly affected by the location of body fat.^ Thus, these data point out that not only can obesity and fat distribution affect levels of single measures, they also can markedly influence the pattern of relationship among measures. The fact that such changes are seen for both obesity and fat distribution is significant, since the indices employed were chosen because they were independent of one another. ^