A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Background: Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results: The results shown here are for an adapted subset of a Saccharomyces cerevisiae gene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion: Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses.

CR3 (CD11b/CD18) activation of nasal neutrophils: a measure of upper airway endotoxin exposure

Inhaled endotoxin (lipopolysaccharide, LPS) initiates an inflammatory response and leads to the expression of CR3 (CD11b/CD18) receptors on polymorphonuclear leukocytes (PMNs). We determined if PMN activation in nasal lavage fluid (NLF) is a possible biomarker of occupational endotoxin exposure. Seven subjects exposed to endotoxin provided NLF samples that were split into three aliquots (negative control - 1 M nicotinamide; sham; positive control - 11 eta g of exogenous LPS) and PMN activation was measured using a chemiluminometer. Differences in mean PMN activation were apparent, negative control: 548 +/- 15.65 RLU 100 mu l(-1); sham: 11469 +/- 2582 RLU 100 mu l(-1); positive control: 42026 +/- 16659 RLU 100 mu l (n = 7; p < 0.05). This technique shows promise as a diagnostic method for measuring upper airway LPS exposure.

Gravimetric study of a potential mineral deposit in the Itapororoca region, Brazil

A semi-detailed gravity survey was carried out over an area of 650 km(2) localized in the Eo-Neoproterozoic coastal zone of Paraiba State where 548 new gravity stations were added to the existing database. Gravity measurements were made with a LaCoste and Romberg model G meter with a precision of 0.04 mGal. The altitude was determined by barometric levelling with a fixed base achieving a 1.2 m measure of uncertainty, corresponding to an overall accuracy of 0.24 mGal for the Bouguer anomaly. The residual Bouguer map for a 7th degree regional polynomial showed a circumscribed negative anomaly coincident with a localized aero-magnetic anomaly and with hydro-thermally altered outcrops, near the city of Itapororoca. The 3D gravity modelling, constrained by geologic mapping was interpreted as a low density, fractured and/or altered material with a most probable volume of approximately 23 km(3), extending to about 8,500 m depth. This result is in accordance with a volcanic body associated with hydrothermal processes accompanied by surface mineralization evidence, which may be of interest to the mining industry.

Matrix Representation of the Stationary Measure for the Multispecies TASEP

In this work we construct the stationary measure of the N species totally asymmetric simple exclusion process in a matrix product formulation. We make the connection between the matrix product formulation and the queueing theory picture of Ferrari and Martin. In particular, in the standard representation, the matrices act on the space of queue lengths. For N > 2 the matrices in fact become tensor products of elements of quadratic algebras. This enables us to give a purely algebraic proof of the stationary measure which we present for N=3.

Risk optimization of a steel frame communications tower subject to tornado winds

The structural engineering community in Brazil faces new challenges with the recent occurrence of high intensity tornados. Satellite surveillance data shows that the area covering the south-east of Brazil, Uruguay and some of Argentina is one of the world most tornado-prone areas, second only to the infamous tornado alley in central United States. The design of structures subject to tornado winds is a typical example of decision making in the presence of uncertainty. Structural design involves finding a good balance between the competing goals of safety and economy. This paper presents a methodology to find the optimum balance between these goals in the presence of uncertainty. In this paper, reliability-based risk optimization is used to find the optimal safety coefficient that minimizes the total expected cost of a steel frame communications tower, subject to extreme storm and tornado wind loads. The technique is not new, but it is applied to a practical problem of increasing interest to Brazilian structural engineers. The problem is formulated in the partial safety factor format used in current design codes, with all additional partial factor introduced to serve as optimization variable. The expected cost of failure (or risk) is defined as the product of a. limit state exceedance probability by a limit state exceedance cost. These costs include costs of repairing, rebuilding, and paying compensation for injury and loss of life. The total expected failure cost is the sum of individual expected costs over all failure modes. The steel frame communications, tower subject of this study has become very common in Brazil due to increasing mobile phone coverage. The study shows that optimum reliability is strongly dependent on the cost (or consequences) of failure. Since failure consequences depend oil actual tower location, it turn,,; out that different optimum designs should be used in different locations. Failure consequences are also different for the different parties involved in the design, construction and operation of the tower. Hence, it is important that risk is well understood by the parties involved, so that proper contracts call be made. The investigation shows that when non-structural terms dominate design costs (e.g, in residential or office buildings) it is not too costly to over-design; this observation is in agreement with the observed practice for non-optimized structural systems. In this situation, is much easier to loose money by under-design. When by under-design. When structural material cost is a significant part of design cost (e.g. concrete dam or bridge), one is likely to lose significantmoney by over-design. In this situation, a cost-risk-benefit optimization analysis is highly recommended. Finally, the study also shows that under time-varying loads like tornados, the optimum reliability is strongly dependent on the selected design life.

Classification of breast masses using a committee machine of artificial neural networks

This work proposes a new approach using a committee machine of artificial neural networks to classify masses found in mammograms as benign or malignant. Three shape factors, three edge-sharpness measures, and 14 texture measures are used for the classification of 20 regions of interest (ROIs) related to malignant tumors and 37 ROIs related to benign masses. A group of multilayer perceptrons (MLPs) is employed as a committee machine of neural network classifiers. The classification results are reached by combining the responses of the individual classifiers. Experiments involving changes in the learning algorithm of the committee machine are conducted. The classification accuracy is evaluated using the area A. under the receiver operating characteristics (ROC) curve. The A, result for the committee machine is compared with the A, results obtained using MLPs and single-layer perceptrons (SLPs), as well as a linear discriminant analysis (LDA) classifier Tests are carried out using the student's t-distribution. The committee machine classifier outperforms the MLP SLP, and LDA classifiers in the following cases: with the shape measure of spiculation index, the A, values of the four methods are, in order 0.93, 0.84, 0.75, and 0.76; and with the edge-sharpness measure of acutance, the values are 0.79, 0.70, 0.69, and 0.74. Although the features with which improvement is obtained with the committee machines are not the same as those that provided the maximal value of A(z) (A(z) = 0.99 with some shape features, with or without the committee machine), they correspond to features that are not critically dependent on the accuracy of the boundaries of the masses, which is an important result. (c) 2008 SPIE and IS&T.

AVERAGE CONTINUOUS CONTROL OF PIECEWISE DETERMINISTIC MARKOV PROCESSES

This paper deals with the long run average continuous control problem of piecewise deterministic Markov processes (PDMPs) taking values in a general Borel space and with compact action space depending on the state variable. The control variable acts on the jump rate and transition measure of the PDMP, and the running and boundary costs are assumed to be positive but not necessarily bounded. Our first main result is to obtain an optimality equation for the long run average cost in terms of a discrete-time optimality equation related to the embedded Markov chain given by the postjump location of the PDMP. Our second main result guarantees the existence of a feedback measurable selector for the discrete-time optimality equation by establishing a connection between this equation and an integro-differential equation. Our final main result is to obtain some sufficient conditions for the existence of a solution for a discrete-time optimality inequality and an ordinary optimal feedback control for the long run average cost using the so-called vanishing discount approach. Two examples are presented illustrating the possible applications of the results developed in the paper.

Differential regulation of PGC-1 alpha expression in rat liver and skeletal muscle in response to voluntary running

Background: The beneficial actions of exercise training on lipid, glucose and energy metabolism and insulin sensitivity appear to be in part mediated by PGC-1 alpha. Previous studies have shown that spontaneously exercised rats show at rest enhanced responsiveness to exogenous insulin, lower plasma insulin levels and increased skeletal muscle insulin sensitivity. This study was initiated to examine the functional interaction between exercise-induced modulation of skeletal muscle and liver PGC-1 alpha protein expression, whole body insulin sensitivity, and circulating FFA levels as a measure of whole body fatty acid (lipid) metabolism. Methods: Two groups of male Wistar rats (2 Mo of age, 188.82 +/- 2.77 g BW) were used in this study. One group consisted of control rats placed in standard laboratory cages. Exercising rats were housed individually in cages equipped with running wheels and allowed to run at their own pace for 5 weeks. At the end of exercise training, insulin sensitivity was evaluated by comparing steady-state plasma glucose (SSPG) concentrations at constant plasma insulin levels attained during the continuous infusion of glucose and insulin to each experimental group. Subsequently, soleus and plantaris muscle and liver samples were collected and quantified for PGC-1 alpha protein expression by Western blotting. Collected blood samples were analyzed for glucose, insulin and FFA concentrations. Results: Rats housed in the exercise wheel cages demonstrated almost linear increases in running activity with advancing time reaching to maximum value around 4 weeks. On an average, the rats ran a mean (Mean +/- SE) of 4.102 +/- 0.747 km/day and consumed significantly more food as compared to sedentary controls (P < 0.001) in order to meet their increased caloric requirement. Mean plasma insulin (P < 0.001) and FFA (P < 0.006) concentrations were lower in the exercise-trained rats as compared to sedentary controls. Mean steady state plasma insulin (SSPI) and glucose (SSPG) concentrations were not significantly different in sedentary control rats as compared to exercise-trained animals. Plantaris PGC-1 alpha protein expression increased significantly from a 1.11 +/- 0.12 in the sedentary rats to 1.74 +/- 0.09 in exercising rats (P < 0.001). However, exercise had no effect on PGC-1 alpha protein content in either soleus muscle or liver tissue. These results indicate that exercise training selectively up regulates the PGC-1 alpha protein expression in high-oxidative fast skeletal muscle type such as plantaris muscle. Conclusion: These data suggest that PGC-1 alpha most likely plays a restricted role in exercise-mediated improvements in insulin resistance (sensitivity) and lowering of circulating FFA levels.

Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

Direct measurement of spin correlations using magnetostriction

We demonstrate that the short-range spin correlator < S(i)center dot S(j)>, a fundamental measure of the interaction between adjacent spins, can be directly measured in certain insulating magnets. We present magnetostriction data for the insulating organic compound NiCl(2)-4SC(NH(2))(2), and show that the magnetostriction as a function of field is proportional to the dominant short-range spin correlator. Furthermore, the constant of proportionality between the magnetostriction and the spin correlator gives information about the spin-lattice interaction. Combining these results with the measured Young's modulus, we are able to extract dJ/dz, the dependence of the superexchange constant J on the Ni interionic distance z.

Alternative fidelity measure between quantum states

We propose an alternative fidelity measure (namely, a measure of the degree of similarity) between quantum states and benchmark it against a number of properties of the standard Uhlmann-Jozsa fidelity. This measure is a simple function of the linear entropy and the Hilbert-Schmidt inner product between the given states and is thus, in comparison, not as computationally demanding. It also features several remarkable properties such as being jointly concave and satisfying all of Jozsa's axioms. The trade-off, however, is that it is supermultiplicative and does not behave monotonically under quantum operations. In addition, metrics for the space of density matrices are identified and the joint concavity of the Uhlmann-Jozsa fidelity for qubit states is established.

Placebo Response of Non-Pharmacological and Pharmacological Trials in Major Depression: A Systematic Review and Meta-Analysis

Background: Although meta-analyses have shown that placebo responses are large in Major Depressive Disorder (MDD) trials; the placebo response of devices such as repetitive transcranial magnetic stimulation (rTMS) has not been systematically assessed. We proposed to assess placebo responses in two categories of MDD trials: pharmacological (antidepressant drugs) and non-pharmacological (device-rTMS) trials. Methodology/Principal Findings: We performed a systematic review and meta-analysis of the literature from April 2002 to April 2008, searching MEDLINE, Cochrane, Scielo and CRISP electronic databases and reference lists from retrieved studies and conference abstracts. We used the keywords placebo and depression and escitalopram for pharmacological studies; and transcranial magnetic stimulation and depression and sham for non-pharmacological studies. All randomized, double-blinded, placebo-controlled, parallel articles on major depressive disorder were included. Forty-one studies met our inclusion criteria-29 in the rTMS arm and 12 in the escitalopram arm. We extracted the mean and standard values of depression scores in the placebo group of each study. Then, we calculated the pooled effect size for escitalopram and rTMS arm separately, using Cohen's d as the measure of effect size. We found that placebo response are large for both escitalopram (Cohen's d-random-effects model-1.48; 95% C.I. 1.26 to 1.6) and rTMS studies (0.82; 95% C.I. 0.63 to 1). Exploratory analyses show that sham response is associated with refractoriness and with the use of rTMS as an add-on therapy, but not with age, gender and sham method utilized. Conclusions/Significance: We confirmed that placebo response in MDD is large regardless of the intervention and is associated with depression refractoriness and treatment combination (add-on rTMS studies). The magnitude of the placebo response seems to be related with study population and study design rather than the intervention itself.

Effect of crab size and habitat type on the locomotory activity of juvenile shore crabs, Carcinus maenas

Post-settlement processes are a major focus in the study of the dynamics of marine populations and communities. Post-settlement movement of juveniles is an important, but often ignored, process which affects local predator-prey and competitive interactions. We used benthic suction sampling and pitfall traps to examine density and locomotory activity of Carcinus maenas juveniles in different intertidal habitat types in the Rio Mira Estuary, Portugal, to better understand intra-specific interactions in a system where density-dependent processes are known to regulate population dynamics. As expected, significantly higher densities of juvenile shore crabs were found from bare mud compared to densely vegetated habitats. At the time of sampling, small and intermediate stages together outnumbered by far the larger juveniles. Conversely, larger crabs were much more frequent than smaller ones in traps. A locomotory index (LI), i.e. the ratio between crab catch in pitfall traps and their density within their moving range, is proposed as a measure of movement. LI analyses indicated that: (1) movement is an order of magnitude higher in large than small juveniles and much higher in sparse than dense vegetation cover; (2) activity of small juveniles is mostly crepuscular, regardless of vegetation cover; and (3) movement of large juveniles is very limited in dense Zostera patches, but very high in sparsely vegetated areas, during the day and night. These results suggest that small juveniles are relatively protected under dense vegetation cover due to lower mobility of larger crabs, and provide evidence of temporal segregation of activity windows between juvenile crabs of different sizes, which may be a key mechanism to reduce cannibalism and therefore increase the carrying capacity of nursery habitats. (C) 2008 Elsevier Ltd. All rights reserved.

Forest structure and live aboveground biomass variation along an elevational gradient of tropical Atlantic moist forest (Brazil)

Live aboveground biomass (AGB) is an important source of uncertainty in the carbon balance from the tropical regions in part due scarcity of reliable estimates of live AGB and its variation across landscapes and forest types. Studies of forest structure and biomass stocks of Neotropical forests are biased toward Amazonian and Central American sites. In particular, standardized estimates of aboveground biomass stocks for the Brazilian Atlantic forest are rarely available. Notwithstanding the role of environmental variables that control the distribution and abundance of biomass in tropical lowland forests has been the subject of considerable research, the effect of short, steep elevational gradients on tropical forest structure and carbon dynamics is not well known. In order to evaluate forest structure and live AGB variation along an elevational gradient (0-1100 m a.s.l.) of coastal Atlantic Forest in SE Brazil, we carried out a standard census of woody stems >= 4.8 cm dbh in 13 1-ha permanent plots established on four different sites in 2006-2007. Live AGB ranged from 166.3 Mg ha(-1) (bootstrapped 95% CI: 1444,187.0) to 283.2 Mg ha(-1) (bootstrapped 95% CI: 253.0,325.2) and increased with elevation. We found that local-scale topographic variation associated with elevation influences the distribution of trees >50 cm dbh and total live AGB. Across all elevations, we found more stems (64-75%) with limited crown illumination but the largest proportion of the live AGB (68-85%) was stored in stems with highly illuminated or fully exposed crowns. Topography, disturbance and associated changes in light and nutrient supply probably control biomass distribution along this short but representative elevational gradient. Our findings also showed that intact Atlantic forest sites stored substantial amounts of carbon aboveground. The live tree AGB of the stands was found to be lower than Central Amazonian forests, but within the range of Neotropical forests, in particular when compared to Central American forests. Our comparative data suggests that differences in live tree AGB among Neotropical forests are probably related to the heterogeneous distribution of large and medium-sized diameter trees within forests and how the live biomass is partitioned among those size classes, in accordance with general trends found by previous studies. In addition, the elevational variation in live AGB stocks suggests a large spatial variability over coastal Atlantic forests in Brazil, clearly indicating that it is important to consider regional differences in biomass stocks for evaluating the role of this threatened tropical biome in the global carbon cycle. (C) 2010 Elsevier B.V. All rights reserved.

Improving sample representativeness in environmental studies: a major component for the uncertainty budget

For environmental quality assessment, INAA has been applied for determining chemical elements in small (200 mg) and large (200 g) samples of leaves from 200 trees. By applying the Ingamells` constant, the expected percent standard deviation was estimated in 0.9-2.2% for 200 mg samples. Otherwise, for composite samples (200 g), expected standard deviation varied from 0.5 to 10% in spite of analytical uncertainties ranging from 2 to 30%. Results thereby suggested the expression of the degree of representativeness as a source of uncertainty, contributing for increasing of the reliability of environmental studies mainly in the case of composite samples.