EthoSeq: A tool for phylogenetic analysis and data mining in behavioral sequences

This article introduces the software program called EthoSeq, which is designed to extract probabilistic behavioral sequences (tree-generated sequences, or TGSs) from observational data and to prepare a TGS-species matrix for phylogenetic analysis. The program uses Graph Theory algorithms to automatically detect behavioral patterns within the observational sessions. It includes filtering tools to adjust the search procedure to user-specified statistical needs. Preliminary analyses of data sets, such as grooming sequences in birds and foraging tactics in spiders, uncover a large number of TGSs which together yield single phylogenetic trees. An example of the use of the program is our analysis of felid grooming sequences, in which we have obtained 1,386 felid grooming TGSs for seven species, resulting in a single phylogeny. These results show that behavior is definitely useful in phylogenetic analysis. EthoSeq simplifies and automates such analyses, uncovers much of the hidden patterns of long behavioral sequences, and prepares this data for further analysis with standard phylogenetic programs. We hope it will encourage many empirical studies on the evolution of behavior.

Chemical Composition and fermentative characteristics of Elephant grass (Pennisetum purpureum Schum.) silages added of increasing levels of mango (Mangifera indica L.) byproducts

Aiming at evaluating the use of those byproducts on ruminant feeding an experiment has been carried out in the Forage Research department (www.npf.ufc.br), in order to evaluate the effects of addition of increasing levels of mango processing byproducts (MB) in Elephant grass silages. Twenty experimental silos made of PVC pipe (100 x 340 mm), in a completely randomized design with 5 levels of addition (0; 5; 10; 15; and 20%) of MB and 4 replications. Upon 32 days of ensilage, samples were collected for determination of levels of dry Matter (DM), crude protein (CP), ethereal extract (EE), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicelluloses (HC), ammonia nitrogen (N-NH3), and pH values. Data were evaluated by analyses of variance and regression analyses using the F test at the 5% level. The levels of DM and CP increased of 0.50 and 0.03 percentage units, respectively, for every 1% of MB added. The levels of NDF and ADF decreased of 0.51 and 0.24 percentage units, respectively, for every 1% of MB added. The levels of N-NH3 decreased from 4 to 23 percentage units while pH values remained constant (p>0.05), with average values of 3.29. Addition of 20% of MB improved silages chemical composition by promoting an increase in the levels of MS and reduction in the levels of fiber.

The effects of anxiety on visual search, movement kinematics, and performance in table tennis: A test of Eysenck and Calvo's processing efficiency theory

Processing efficiency theory predicts that anxiety reduces the processing capacity of working memory and has detrimental effects on performance. When tasks place little demand on working memory, the negative effects of anxiety can be avoided by increasing effort. Although performance efficiency decreases, there is no change in performance effectiveness. When tasks impose a heavy demand on working memory, however, anxiety leads to decrements in efficiency and effectiveness. These presumptions were tested using a modified table tennis task that placed low (LWM) and high (HWM) demands on working memory. Cognitive anxiety was manipulated through a competitive ranking structure and prize money. Participants' accuracy in hitting concentric circle targets in predetermined sequences was taken as a measure of performance effectiveness, while probe reaction time (PRT), perceived mental effort (RSME), visual search data, and arm kinematics were recorded as measures of efficiency. Anxiety had a negative effect on performance effectiveness in both LWM and HWM tasks. There was an increase in frequency of gaze and in PRT and RSME values in both tasks under high vs. low anxiety conditions, implying decrements in performance efficiency. However, participants spent more time tracking the ball in the HWM task and employed a shorter tau margin when anxious. Although anxiety impaired performance effectiveness and efficiency, decrements in efficiency were more pronounced in the HWM task than in the LWM task, providing support for processing efficiency theory.

Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa

Xylella fastidiosa is a xylem-dwelling, insect-transmitted, gamma-proteobacterium that causes diseases in many plants, including grapevine, citrus, periwinkle, almond, oleander, and coffee. X. fastidiosa has an unusually broad host range, has an extensive geographical distribution throughout the American continent, and induces diverse disease phenotypes. Previous molecular analyses indicated three distinct groups of X.fastidiosa isolates that were expected to be genetically divergent. Here we report the genome sequence of X. fastidiosa (Temecula strain), isolated from a naturally infected grapevine with Pierce's disease (PD) in a wine-grape-growing region of California. Comparative analyses with a previously sequenced X.fastidiosa strain responsible for citrus variegated chlorosis (CVC) revealed that 98% of the PD X.fastidiosa Temecula genes are shared with the CVC X. fastidiosa strain 9a5c genes. Furthermore, the average amino acid identity of the open reading frames in the strains is 95.7%. Genomic differences are limited to phage-associated chromosomal rearrangements and deletions that also account for the strain-specific genes present in each genome. Genomic islands, one in each genome, were identified, and their presence in other X.fastidiosa strains was analyzed. We conclude that these two organisms have identical metabolic functions and are likely to use a common set of genes in plant colonization and pathogenesis, permitting convergence of functional genomic strategies.

Molecular phylogeny of the green lacewings (Neuroptera : Chrysopidae)

The first quantitative analysis of phylogenetic relationships of green lacewings (Chrysopidae) is presented based on DNA sequence data. A single nuclear and two mitochondrial genes are used in the analysis: carbomoylphosphate synthase (CPS) domain of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase (CAD) (i.e. rudimentary locus), large subunit ribosomal gene (16S) and cytochrome oxidase I (COI). This study represents the first use of the CAD gene to investigate phylogenetic relationships of the lacewings. DNA sequences for 33 chrysopid species from 18 genera, representing all subfamilies and tribes, were compared with outgroups sampled from families Hemerobiidae, Osmylidae and Polystoechotidae. Parsimony analyses of the combined data set recovered all of the previously established subfamilial and tribal groups as monophyletic clades (although relatively weakly supported) except Apochrysinae sensu lato. The enigmatic Nothancyla verreauxi Navas has historically been difficult to place in a subfamily group based on morphological characteristics; molecular data presented herein do not adequately resolve this problem.

Chain sequences and symmetric generalized orthogonal polynomials

in this paper, we derive an explicit expression for the parameter sequences of a chain sequence in terms of the corresponding orthogonal polynomials and their associated polynomials. We use this to study the orthogonal polynomials K-n((lambda.,M,k)) associated with the probability measure dphi(lambda,M,k;x), which is the Gegenbauer measure of parameter lambda + 1 with two additional mass points at +/-k. When k = 1 we obtain information on the polynomials K-n((lambda.,M)) which are the symmetric Koornwinder polynomials. Monotonicity properties of the zeros of K-n((lambda,M,k)) in relation to M and k are also given. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Increasing the dielectric breakdown strength of poly(ethylene terephthalate) films using a coated polyaniline layer

The dielectric strength of films made from poly(ethylene terephthalate) (PET) coated with a thin layer of polyaniline (PANI) was studied. The PANI layer was deposited on the PET films by the 'in situ' chemical polymerization method. The PANI layer of the PANI/PET films was undoped in NH4OH 0.1 M solution and re-doped with aqueous HCl solution under different pH values varying from 1 to 10. Electric breakdown measurements were performed by applying a voltage ramp and the results showed a dependence of the dielectric strength on the pH of the doping solution due to the changes in the electrical conductivity of the PANI layer. The dielectric strength of PET/PANI films treated under higher pH conditions showed an electric strength about 30% larger than the PET films, since it leads to a non-conductive PANI layer.

Demographic of short gut syndrome: Increasing demand is not followed by referral of potential candidates for small bowel transplantation

Background. Despite improvements in small bowel transplantation (SBTx), early referral of patients with irreversible intestinal failure (IF) remains a major obstacle. In this study we evaluated the demand for SBTx among seven surgical pediatric centers located at least 200 km from our center.Methods. From 1997 to 2001, 640 patients have been treated for neonatal diseases, including 248 who underwent a minor or major intestinal resection. Twenty-four patients with major resections presented with short gut syndrome, requiring total parenteral nutrition (TPN). The greatest demand was in postsurgical neonates with necrotizing enterocolitis, gastroschiesis, onphalocoeles, or midgut volvulus, and in three adults with postradiotherapy arteritis (n = 2) and mesenteric vein thromboses (n = 1). The median length of residual bowel after resection was 20 to 30 cm, without an ileocecal valve. Four patients were referred for SBTx evaluation; three died while awaiting a donor; 20 were not referred, among whom 14 died of TPN complications.Results. Approximately 62 children per year require nutritional support for IF, most of whom develop complications related to TPN. Because many patients who are TPN-dependent develop complications, we believe that early referral would reduce mortality.Conclusions. Greater medical awareness about the feasibility of SBTx procedures and earlier referral may improve results and quality of life after transplant.

Gelation and drying of weakly bonded silica-PPO nanocomposites

Silica-poly(oxypropylene) (PPO) nanocomposites containing PPO with weak physical bonds between the organic (PPO) and inorganic (silica) phases were obtained by the sol-gel procedure. Three precursor sols containing silica and PPO with molecular weights of 1000, 2000 and 4000g/mol were prepared. The structure changes during the whole sol-gel process, i.e. sol formation, sol-gel transition and gel aging and drying were investigated in situ by small angle X-ray scattering (SAXS). The experimental SAXS curves corresponding to sols and wet gels containing PPO of molecular weight 1000g/mol indicate that the aggregates formed during the studied process are fractal objects. Close to the sol-gel transition and during gel aging the fractal dimension is D=2.5. A clearly different structure evolution occurs in samples prepared with PPO with molecular weights 2000 and 4000 g/mol. Our SAXS results indicate the presence of two coexisting and well-defined structure levels, one of them corresponding to small silica clusters and the other to large silica aggregates. These two levels remain along the whole transformation. The SAXS curves of all dry samples are similar to those of the corresponding wet gels suggesting that no significant changes at nanoscopic scale occur during the drying process.

On the effects of system parameters on the response of a harmonically excited system consisting of weakly coupled nonlinear and linear oscillators

This paper discusses the dynamic behaviour of a nonlinear two degree-of-freedom system consisting of a harmonically excited linear oscillator weakly connected to a nonlinear attachment having linear and cubic restoring forces. The effects of the system parameters on the shape of the frequency-response curve are investigated, in particular those yielding the appearance and disappearance of outer and inner detached resonance curves. In contrast to the case when the linear stiffness of the attachment is zero, it is found that multivaluedness occurs at low frequencies as the resonant peak bends to the right. It is also found that as the coefficient of the linear term increases, the range of parameters yielding detached curves reduces. Compared to the case when the attached system has no linear stiffness term, this range of parameters corresponds to smaller values of the damping and nonlinear coefficients. Approximate analytical expressions for the jump-up and jump-down frequencies of the system under investigation are also derived. (C) 2011 Elsevier Ltd. All rights reserved.

Aging reduces complexity of heart rate variability assessed by conditional entropy and symbolic analysis

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