Testing statistical hypothesis on random trees and applications to the protein classification problem

Efficient automatic protein classification is of central importance in genomic annotation. As an independent way to check the reliability of the classification, we propose a statistical approach to test if two sets of protein domain sequences coming from two families of the Pfam database are significantly different. We model protein sequences as realizations of Variable Length Markov Chains (VLMC) and we use the context trees as a signature of each protein family. Our approach is based on a Kolmogorov--Smirnov-type goodness-of-fit test proposed by Balding et al. [Limit theorems for sequences of random trees (2008), DOI: 10.1007/s11749-008-0092-z]. The test statistic is a supremum over the space of trees of a function of the two samples; its computation grows, in principle, exponentially fast with the maximal number of nodes of the potential trees. We show how to transform this problem into a max-flow over a related graph which can be solved using a Ford--Fulkerson algorithm in polynomial time on that number. We apply the test to 10 randomly chosen protein domain families from the seed of Pfam-A database (high quality, manually curated families). The test shows that the distributions of context trees coming from different families are significantly different. We emphasize that this is a novel mathematical approach to validate the automatic clustering of sequences in any context. We also study the performance of the test via simulations on Galton--Watson related processes.Comment: Published in at http://dx.doi.org/10.1214/08-AOAS218 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

New foliose and gelatinous red macroalgae (Rhodophycota) from the Azores: morphological and geographical observations.

Copyright © 2002 Published by Elsevier Science B.V.The following four species of foliose and gelatinous red algae (Rhodophycota) are newly recorded for the Azores archipelago (North Atlantic Ocean): Gracilaria multipartita (Clemente) Harvey, Meristotheca decumbens Grunow (Solieriaceae), Asteromenia peltata (W.R. Taylor) Huisman and A.J.K. Millar (Rhodymeniaceae), and Agardhinula browneae (J. Agardh) De Toni (Faucheaceae). The species are described, and information on reproductive status, ecology and biogeographical relationships is provided

Contribuição das suiniculturas na selecção e disseminação de Enterococcus spp resistentes às tetraciclinas

Apesar dos antibióticos terem sido abolidos na União Europeia como promotores de crescimento, uma elevada percentagem de Enterococcus spp resistentes às tetraciclinas e genes que lhes conferem resistência (tetM, tetL, tetS) foram detectados em amostras animais e ambientais de suiniculturas portuguesas. Estes dados são preocupantes e podem estar associados a um elevado consumo destes antibióticos em medicina veterinária. A presença de tais estirpes em amostras de ar e de estrume usado como fertilizante agrícola pode ainda promover a sua dispersão fora das explorações animais. Although antibiotics were banned from European Union as animal growth promoters, a high percentage of Enterococcus spp resistant to tetracyclines and genes conferring resistance to these agents (tetM, tetL, tetS) were detected in animal and environmental samples collected in Portuguese piggeries. These data are of concern and might be associated to the consumption of high amounts of these antibiotics in veterinary medicine. The presence of such strains in air and manure used as fertilizer in agriculture might promote their dissemination outside the animal production setting

Problemáticas da educação física I

info:eu-repo/semantics/publishedVersio

Light with tunable non-Markovian phase imprint

We introduce a simple and flexible method to generate spatially non-Markovian light with tunable coherence properties in one and two dimensions. The unusual behavior of this light is demonstrated experimentally by probing the far field and recording its diffraction pattern after a double slit: In both cases we observe instead of a central intensity maximum a line or cross shaped dark region, whose width and profile depend on the non-Markovian coherence properties. Since these properties can be controlled and easily reproduced in experiment, the presented approach lends itself to serve as a testbed to gain a deeper understanding of non-Markovian processes

Postural control is altered in females with excessive medial knee displacement

Knee valgus motion observed during landing tasks has been proposed as a predictor of future knee injury. It mainly involves excess motion in the frontal plane and is known to be greater in individuals with excessive medial knee displacement (MKD). This affects postural control during sports manoeuvres. Previous sports medicine-related research suggests that the nature of these fluctuations provide rich and more sensitive information to identify risk of (re)injury. We aimed to investigate the fluctuations of the centre of pressure (CoP) in individuals with and without excessive MKD. Twenty females (12 controls; 8 excessive MKD) were instructed to perform single-leg landing tasks from three different directions. The participants landed on a force plate and stayed still for 20 seconds. The fluctuations of the anterior-posterior and medial-lateral directions of the CoP were determined through the calculation of Sample Entropy. Mixed-model ANOVAs (3 [Landing Direction] x 2 [Group]) were used. We have found that only the entropy of the medial-lateral direction was different between groups. Individuals with excessive MKD exhibited an increase in entropy values, indicating greater randomness in CoP fluctuations. This suggests a decreased ability to adapt to environmental demands that likely result in an increased risk of injury

Beyond good intentions: the role of the building passport for the sustainable conservation of built heritage to behavioural change

Despite the recognised importance of built heritage for sustainable development, and the multiple tools, recommendations, guidelines, and policies developed in recent years to support decision-making, good sustainable conservation practices often fail to be implemented. Challenges faced by practitioners often relate to external factors, and there is a gap in the understanding of the role of the nature of the designer and the behavioural dimension of the challenges in implementation. This research applies the Theory of Planned Behaviour (TPB) to verify how a building passport for sustainable conservation (BPSC) impacts design students’ intentions and actual design decisions towards built heritage conservation. This research aims to ascertain the role of the BPSC to affect attitudes, subjective norms, and intentions and ultimately change conservation behaviours. The results show that this tool has a positive contribution to reinforce existing attitudinal beliefs. Still, no significant changes were found in the overall conservation behaviours, suggesting that beliefs hindering implementation may more often be related to aesthetic reasons, creativity and innovation, and program requirements, than with beliefs regarding the sustainable performance of the building. This study demonstrates that using the TPB to analyse design processes in the context of built heritage is an innovative methodological approach that contributes to a deeper understanding of the psychological factors affecting sustainability and built heritage conservation decisions.This research was funded by Foundation for Science and Technology (FCT), grant number PD/BD/127853/2016. The APC was funded by TU Delft Library

Chemical Abundances in Field Red Giants from High-Resolution H-Band Spectra using the APOGEE Spectral Linelist

High-resolution H-band spectra of five bright field K, M, and MS giants, obtained from the archives of the Kitt Peak National Observatory (KPNO) Fourier Transform Spectrometer (FTS), are analyzed to determine chemical abundances of 16 elements. The abundances were derived via spectrum synthesis using the detailed linelist prepared for the SDSS III Apache Point Galactic Evolution Experiment (APOGEE), which is a high-resolution near-infrared spectroscopic survey to derive detailed chemical abundance distributions and precise radial velocities for 100,000 red giants sampling all Galactic stellar populations. Measured chemical abundances include the cosmochemically important isotopes 12C, 13C, 14N, and 16O, along with Mg, Al, Si, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, and Cu. A comparison of the abundances derived here with published values for these stars reveals consistent results to ~0.1 dex. The APOGEE spectral region and linelist is, thus, well-suited for probing both Galactic chemical evolution, as well as internal nucleosynthesis and mixing in populations of red giants using high-resolution spectroscopy.Comment: Accepted for publication in The Astrophysical Journal. 42 pages, 12 figure

Behind the High Electrical Performance of Flash Sintered Potassium Sodium Niobate Piezoelectric Ceramics

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