Ontogenetic variation of plastral spotting pattern in Phrynops hilarii (Testudines, Chelidae)

The plastral spotting variation in the chelid turtle Phrynops hilarii (Duméril & Bibron, 1835) in relation to sex, size, and geographic procedence of individuals was analyzed. States for qualitative characters were analyzed using non-parametric tests. Quantitative characters (shell and scute measurements) were standardized for body size by linear regression against carapace length, and were subjected to principal components analysis and canonical discriminant function analysis. Results suggest that increased plastral spotting is a polymorphic ontogenetic trait in P. hilarii. Neither hatchlings nor juveniles have plastral pattern moderately or heavily pigmented. The simplest pattern, however, may persist without changes in some adults. There are no differences between sexes. The spatial distribution of the plastral pattern is not ordered latitudinally or longitudinally, showing no relationship with gradients of elevation, temperature, or precipitation. This pattern trait lacks of taxonomic significance. The morphometric analysis failed to reveal any character of diagnostic utility in the plastron to support the possibility that these patterns correspond to different sympatric taxa.

Species richness and community structure of arboreal spider assemblages in fragments of three vegetational types at Banhado Grande wet plain, Gravataí River, Rio Grande do Sul, Brazil

The taxonomic composition, observed and estimated species richness, and patterns of community structure of arboreal spider assemblages in eleven sites surrounding the "Banhado Grande" wet plain in the state of Rio Grande do Sul, Brazil, are presented. These sites represent three different vegetational types: hillside (four sites), riparian (five sites) and flooded forests (two sites). The spiders were captured by beating on foliage and "aerial litter". A sample was defined as the result of beating on twenty bushes, tree branches or "aerial litter" clusters, which roughly corresponds to one-hour search effort per sample. Fifty five samples (five per site) were obtained, resulting in an observed richness of 212 species present as adult or identifiable juveniles. The total richness for all samples was estimated to be between 250 (Bootstrap) to 354 species (Jackknife 2). Confidence intervals of both sample and individual-based rarefaction curves for each vegetation type clearly indicated that flooded forest is the poorest vegetation type with respect to spider species richness, with hillside and riparian forests having a similar number of species. The percentage complementarity between the eleven sites indicated that all sites contain a distinct set of species, irrespective of their vegetation types. Nevertheless, the spider assemblages in riparian and hillside forests are more similar with respect to each other than when compared to flooded forest. Both cluster and nonmetric multidimensional scaling analyses showed no strong correspondence between the spider arboreal fauna and the three vegetation types. Moreover, a Mantel test revealed no significant association between species composition and geographic distance among sites.

Dípteros ectoparasitas (Insecta, Diptera) em morcegos (Chiroptera, Mammalia) na Reserva Biológica das Perobas Paraná, Brasil

Streblidae e Nycteribiidae são encontradas exclusivamente em associação com morcegos. Este trabalho teve como objetivo investigar a diversidade de insetos ectoparasitas encontrados em morcegos da Reserva Biológica das Perobas, Estado do Paraná, Brasil. O trabalho foi realizado nos meses de maio, junho e agosto de 2008 e fevereiro, março e abril de 2009. Para a captura dos morcegos, foram utilizadas 32 redes-de-neblina, totalizando esforço de captura de 43.520m².h. A coleta de ectoparasitas foi feita manualmente ou com auxílio de pinça reta de ponta fina. Os espécimes foram conservados em álcool 70% e identificados com auxílio de microscópio estereoscópico. Os dados foram analisados por meio do estimador não paramétrico Bootstrap e estatística descritiva. As espécies de ectoparasitas identificadas foram: Aspidoptera falcata Wenzel, 1976, Megistopoda proxima (Séguy, 1926), Megistopoda aranea (Coquillett, 1899), Paratrichobius longicrus (Miranda Ribeiro, 1907), Trichobius tiptoni Wenzel, 1976 e Basilia quadrosae Graciolli & Moura, 2005. A curva de riqueza estimada indicou tendência à ocorrência de outras espécies de ectoparasitas na unidade de conservação, haja vista que não foi alcançada a assíntota horizontal. Os dados obtidos corroboram com os verificados em outras regiões do Brasil e contribuem com as informações sobre a diversidade do grupo no bioma Mata Atlântica do noroeste do Paraná.

Bird community in an Araucaria forest fragment in relation to changes in the surrounding landscape in Southern Brazil

The dynamics of the bird community in a small forest fragment was evaluated along seven years in relation to changes in the surrounding landscape. The study area is an Araucaria forest fragment in Southern Brazil (state of Paraná). The sampling period covered the years 1988 through 1994 and the mark-release-recapture method was utilized. The landscape analysis was based on Landsat TM images, and changes in exotic tree plantations, native forest, open areas (agriculture, pasture, bare soil, and abandoned field), and "capoeira"(native vegetation < 2 m) were quantified. The relationship between landscape changes and changes in abundance diversity of forest birds, open-area birds, forest-edge birds, and bamboo specialists was evaluated. Richness estimates were run for each year studied. The richness recorded in the study area comprised 96 species. The richness estimates were 114, 118 and 110 species for Chao 1, Jackknife 1 and Bootstrap, respectively. The bird community varied in species richness, abundance and diversity from year to year. As for species diversity, 1991, 1993 and 1994 were significantly different from the other years. Changes in the landscape contributed to the increase in abundance and richness for the groups of forest, open-area and bamboo-specialist species. An important factor discussed was the effect of the flowering of "taquara" (Poaceae), which contributed significantly to increasing richness of bamboo seed eaters, mainly in 1992 and 1993. In general, the results showed that landscape changes affected the dynamics and structure of the bird community of this forest fragment over time, and proved to have an important role in conservation of the avian community in areas of intensive forestry and agricultural activities.

Sexual dimorphism in Amphisbaena nigricauda (Reptilia, Squamata, Amphisbaenidae) from Southeastern Brazil

Amphisbaena nigricauda Gans, 1966 is a small, poorly known amphisbaenid endemic to the restinga of the states of Espírito Santo and Bahia, Brazil. We analyze 178 specimens collected in Vitória municipality, state of Espírito Santo, Brazil, to investigate whether this species show sexual dimorphism in pre-cloacal pores and in morphological characters. Sex was determined by a ventral incision and direct inspection of gonads. A PCA analysis was performed to generate a general body size measurement. A T test and the non-parametric Mann-Whitney test were used to assess whether this species show sexual dimorphism on five morphometric and five meristic characters, respectively. Sex could not be determined in 36 specimens because they were mutilated in the posterior portion of their bodies. The diagnosis of the species is redefined based on this sample size: the smallest number of body annuli changes from 222 to 192, the number of dorsal and ventral segments in an annulus in the middle of the body changes to 9-11/13-16 (instead of 10/16), and the autotomic tail annulus lies between annulus 7-10 (instead of 6-9). The number of tail annuli remained within the known range of variation of the species (19-24). None of the 80 females analyzed showed pre-cloacal pores, whereas within males 59 out of 62 specimens displayed four and two specimens displayed five pre-cloacal pores. A single male did not possess pre-cloacal pores, but showed irregular scales on its cloacal region. Sex-based difference based on presence or absence of pre-cloacal pores as well as males with wider head was seen in other Neotropical amphisbaenids. However, a pattern of body size differences between males and females has not been identified so far in the few amphisbaenid species studied in this regard. Further studies on this taxonomic group are still needed to elucidate the existence of general patterns of sexual dimorphism and to identify the selective pressures driving these patterns.

Creating and using a non-dedicated HPC cluster with ParallelKnoppix

This note describes ParallelKnoppix, a bootable CD that allows econometricians with average knowledge of computers to create and begin using a high performance computing cluster for parallel computing in very little time. The computers used may be heterogeneous machines, and clusters of up to 200 nodes are supported. When the cluster is shut down, all machines are in their original state, so their temporary use in the cluster does not interfere with their normal uses. An example shows how a Monte Carlo study of a bootstrap test procedure may be done in parallel. Using a cluster of 20 nodes, the example runs approximately 20 times faster than it does on a single computer.

Accuracy vs. simplicity: a complex trade-off

Inductive learning aims at finding general rules that hold true in a database. Targeted learning seeks rules for the predictions of the value of a variable based on the values of others, as in the case of linear or non-parametric regression analysis. Non-targeted learning finds regularities without a specific prediction goal. We model the product of non-targeted learning as rules that state that a certain phenomenon never happens, or that certain conditions necessitate another. For all types of rules, there is a trade-off between the rule's accuracy and its simplicity. Thus rule selection can be viewed as a choice problem, among pairs of degree of accuracy and degree of complexity. However, one cannot in general tell what is the feasible set in the accuracy-complexity space. Formally, we show that finding out whether a point belongs to this set is computationally hard. In particular, in the context of linear regression, finding a small set of variables that obtain a certain value of R2 is computationally hard. Computational complexity may explain why a person is not always aware of rules that, if asked, she would find valid. This, in turn, may explain why one can change other people's minds (opinions, beliefs) without providing new information.

Non-hyperbolic boundary equilibrium bifurcations in planar Filippov systems: a case study approach

Boundary equilibrium bifurcations in piecewise smooth discontinuous systems are characterized by the collision of an equilibrium point with the discontinuity surface. Generically, these bifurcations are of codimension one, but there are scenarios where the phenomenon can be of higher codimension. Here, the possible collision of a non-hyperbolic equilibrium with the boundary in a two-parameter framework and the nonlinear phenomena associated with such collision are considered. By dealing with planar discontinuous (Filippov) systems, some of such phenomena are pointed out through specific representative cases. A methodology for obtaining the corresponding bi-parametric bifurcation sets is developed.

A novel gene expression signature in peripheral blood mononuclear cells for early detection of colorectal cancer.

BACKGROUND: Early detection and treatment of colorectal adenomatous polyps (AP) and colorectal cancer (CRC) is associated with decreased mortality for CRC. However, accurate, non-invasive and compliant tests to screen for AP and early stages of CRC are not yet available. A blood-based screening test is highly attractive due to limited invasiveness and high acceptance rate among patients. AIM: To demonstrate whether gene expression signatures in the peripheral blood mononuclear cells (PBMC) were able to detect the presence of AP and early stages CRC. METHODS: A total of 85 PBMC samples derived from colonoscopy-verified subjects without lesion (controls) (n = 41), with AP (n = 21) or with CRC (n = 23) were used as training sets. A 42-gene panel for CRC and AP discrimination, including genes identified by Digital Gene Expression-tag profiling of PBMC, and genes previously characterised and reported in the literature, was validated on the training set by qPCR. Logistic regression analysis followed by bootstrap validation determined CRC- and AP-specific classifiers, which discriminate patients with CRC and AP from controls. RESULTS: The CRC and AP classifiers were able to detect CRC with a sensitivity of 78% and AP with a sensitivity of 46% respectively. Both classifiers had a specificity of 92% with very low false-positive detection when applied on subjects with inflammatory bowel disease (n = 23) or tumours other than CRC (n = 14). CONCLUSION: This pilot study demonstrates the potential of developing a minimally invasive, accurate test to screen patients at average risk for colorectal cancer, based on gene expression analysis of peripheral blood mononuclear cells obtained from a simple blood sample.

Benchmarking therapeutic drug monitoring software: A review of available computer tools

Therapeutic drug monitoring (TDM) aims to optimize treatments by individualizing dosage regimens based on the measurement of blood concentrations. Dosage individualization to maintain concentrations within a target range requires pharmacokinetic and clinical capabilities. Bayesian calculations currently represent the gold standard TDM approach but require computation assistance. In recent decades computer programs have been developed to assist clinicians in this assignment. The aim of this survey was to assess and compare computer tools designed to support TDM clinical activities. The literature and the Internet were searched to identify software. All programs were tested on personal computers. Each program was scored against a standardized grid covering pharmacokinetic relevance, user friendliness, computing aspects, interfacing and storage. A weighting factor was applied to each criterion of the grid to account for its relative importance. To assess the robustness of the software, six representative clinical vignettes were processed through each of them. Altogether, 12 software tools were identified, tested and ranked, representing a comprehensive review of the available software. Numbers of drugs handled by the software vary widely (from two to 180), and eight programs offer users the possibility of adding new drug models based on population pharmacokinetic analyses. Bayesian computation to predict dosage adaptation from blood concentration (a posteriori adjustment) is performed by ten tools, while nine are also able to propose a priori dosage regimens, based only on individual patient covariates such as age, sex and bodyweight. Among those applying Bayesian calculation, MM-USC*PACK© uses the non-parametric approach. The top two programs emerging from this benchmark were MwPharm© and TCIWorks. Most other programs evaluated had good potential while being less sophisticated or less user friendly. Programs vary in complexity and might not fit all healthcare settings. Each software tool must therefore be regarded with respect to the individual needs of hospitals or clinicians. Programs should be easy and fast for routine activities, including for non-experienced users. Computer-assisted TDM is gaining growing interest and should further improve, especially in terms of information system interfacing, user friendliness, data storage capability and report generation.

The Estimation of Technical Efficiency Effects Models with an Example Applied to the Thai Manufacturing Sector

This paper does two things. First, it presents alternative approaches to the standard methods of estimating productive efficiency using a production function. It favours a parametric approach (viz. the stochastic production frontier approach) over a nonparametric approach (e.g. data envelopment analysis); and, further, one that provides a statistical explanation of efficiency, as well as an estimate of its magnitude. Second, it illustrates the favoured approach (i.e. the ‘single stage procedure’) with estimates of two models of explained inefficiency, using data from the Thai manufacturing sector, after the crisis of 1997. Technical efficiency is modelled as being dependent on capital investment in three major areas (viz. land, machinery and office appliances) where land is intended to proxy the effects of unproductive, speculative capital investment; and both machinery and office appliances are intended to proxy the effects of productive, non-speculative capital investment. The estimates from these models cast new light on the five-year long, post-1997 crisis period in Thailand, suggesting a structural shift from relatively labour intensive to relatively capital intensive production in manufactures from 1998 to 2002.

Exploring Determinants of Urban Motorcycle Accident Severity: The Case of Barcelona

Public authorities and road users alike are increasingly concerned by recent trends in road safety outcomes in Barcelona, which is the European city with the highest number of registered Powered Two-Wheel (PTW) vehicles per inhabitant,. In this study we explore the determinants of motorcycle and moped accident severity in a large urban area, drawing on Barcelona’s local police database (2002-2008). We apply non-parametric regression techniques to characterize PTW accidents and parametric methods to investigate the factors influencing their severity. Our results show that PTW accident victims are more vulnerable, showing greater degrees of accident severity, than other traffic victims. Speed violations and alcohol consumption provide the worst health outcomes. Demographic and environment-related risk factors, in addition to helmet use, play an important role in determining accident severity. Thus, this study furthers our understanding of the most vulnerable vehicle types, while our results have direct implications for local policy makers in their fight to reduce the severity of PTW accidents in large urban areas.

COLOX: a new blood-based test for colorectal cancer screening

INTRODUCTION/OBJECTIVES: Detection rates for adenoma and early colorectal cancer (CRC) are insufficient due to low compliance towards invasive screening procedures, like colonoscopy.Available non-invasive screening tests have unfortunately low sensitivity and specificity performances.Therefore, there is a large unmet need calling for a cost-effective, reliable and non-invasive test to screen for early neoplastic and pre-neoplastic lesions AIMS & Methods: The objective is to develop a screening test able to detect early CRCs and adenomas.This test is based on a nucleic acids multi-gene assay performed on peripheral blood mononuclear cells (PBMCs).A colonoscopy-controlled feasibility study was conducted on 179 subjects.The first 92 subjects was used as training set to generate a statistical significant signature.Colonoscopy revealed 21 subjects with CRC,30 with adenoma bigger than 1 cm and 41 with no neoplastic or inflammatory lesions.The second group of 48 subjects (controls, CRC and polyps) was used as a test set and will be kept blinded for the entire data analysis.To determine the organ and disease specificity 38 subjects were used:24 with inflammatory bowel disease (IBD),14 with other cancers than CRC (OC).Blood samples were taken from each patient the day of the colonoscopy and PBMCs were purified. Total RNA was extracted following standard procedures.Multiplex RT-qPCR was applied on 92 different candidate biomarkers.Different univariate and multivariate statistical methods were applied on these candidates and among them 60 biomarkers with significant p-values (<0.01) were selected.These biomarkers are involved in several different biological functions as cellular movement,cell signaling and interaction,tissue and cellular development,cancer and cell growth and proliferation.Two distinct biomarker signatures are used to separate patients without lesion from those with cancer or with adenoma, named COLOX CRC and COLOX POL respectively.COLOX performances were validated using random resampling method, bootstrap. RESULTS: COLOX CRC and POL tests successfully separate patients without lesions from those with CRC (Se 67%,Sp 93%,AUC 0.87) and from those with adenoma bigger than 1cm (Se 63%,Sp 83%,AUC 0.77),respectively. 6/24 patients in the IBD group and 1/14 patients in the OC group have a positive COLOX CRC CONCLUSION: The two COLOX tests demonstrated a high sensitivity and specificity to detect the presence of CRCs and adenomas bigger than 1 cm.A prospective, multicenter, pivotal study is underway in order to confirm these promising results in a larger cohort.

Pareto or log-normal? A recursive-truncation approach to the distribution of (all) cities

Traditionally, it is assumed that the population size of cities in a country follows a Pareto distribution. This assumption is typically supported by nding evidence of Zipf's Law. Recent studies question this nding, highlighting that, while the Pareto distribution may t reasonably well when the data is truncated at the upper tail, i.e. for the largest cities of a country, the log-normal distribution may apply when all cities are considered. Moreover, conclusions may be sensitive to the choice of a particular truncation threshold, a yet overlooked issue in the literature. In this paper, then, we reassess the city size distribution in relation to its sensitivity to the choice of truncation point. In particular, we look at US Census data and apply a recursive-truncation approach to estimate Zipf's Law and a non-parametric alternative test where we consider each possible truncation point of the distribution of all cities. Results con rm the sensitivity of results to the truncation point. Moreover, repeating the analysis over simulated data con rms the di culty of distinguishing a Pareto tail from the tail of a log-normal and, in turn, identifying the city size distribution as a false or a weak Pareto law.

On the Sources of Uncertainty in Exchange Rate Predictability

We analyse the role of time-variation in coefficients and other sources of uncertainty in exchange rate forecasting regressions. Our techniques incorporate the notion that the relevant set of predictors and their corresponding weights, change over time. We find that predictive models which allow for sudden rather than smooth, changes in coefficients significantly beat the random walk benchmark in out-of-sample forecasting exercise. Using innovative variance decomposition scheme, we identify uncertainty in coefficients' estimation and uncertainty about the precise degree of coefficients' variability, as the main factors hindering models' forecasting performance. The uncertainty regarding the choice of the predictor is small.