Decreasing the number of false positives in sequence classification

Abstract Background A large number of probabilistic models used in sequence analysis assign non-zero probability values to most input sequences. To decide when a given probability is sufficient the most common way is bayesian binary classification, where the probability of the model characterizing the sequence family of interest is compared to that of an alternative probability model. We can use as alternative model a null model. This is the scoring technique used by sequence analysis tools such as HMMER, SAM and INFERNAL. The most prevalent null models are position-independent residue distributions that include: the uniform distribution, genomic distribution, family-specific distribution and the target sequence distribution. This paper presents a study to evaluate the impact of the choice of a null model in the final result of classifications. In particular, we are interested in minimizing the number of false predictions in a classification. This is a crucial issue to reduce costs of biological validation. Results For all the tests, the target null model presented the lowest number of false positives, when using random sequences as a test. The study was performed in DNA sequences using GC content as the measure of content bias, but the results should be valid also for protein sequences. To broaden the application of the results, the study was performed using randomly generated sequences. Previous studies were performed on aminoacid sequences, using only one probabilistic model (HMM) and on a specific benchmark, and lack more general conclusions about the performance of null models. Finally, a benchmark test with P. falciparum confirmed these results. Conclusions Of the evaluated models the best suited for classification are the uniform model and the target model. However, the use of the uniform model presents a GC bias that can cause more false positives for candidate sequences with extreme compositional bias, a characteristic not described in previous studies. In these cases the target model is more dependable for biological validation due to its higher specificity.

Automatic lumen segmentation in IVOCT images using binary morphological reconstruction

Abstract Background Atherosclerosis causes millions of deaths, annually yielding billions in expenses round the world. Intravascular Optical Coherence Tomography (IVOCT) is a medical imaging modality, which displays high resolution images of coronary cross-section. Nonetheless, quantitative information can only be obtained with segmentation; consequently, more adequate diagnostics, therapies and interventions can be provided. Since it is a relatively new modality, many different segmentation methods, available in the literature for other modalities, could be successfully applied to IVOCT images, improving accuracies and uses. Method An automatic lumen segmentation approach, based on Wavelet Transform and Mathematical Morphology, is presented. The methodology is divided into three main parts. First, the preprocessing stage attenuates and enhances undesirable and important information, respectively. Second, in the feature extraction block, wavelet is associated with an adapted version of Otsu threshold; hence, tissue information is discriminated and binarized. Finally, binary morphological reconstruction improves the binary information and constructs the binary lumen object. Results The evaluation was carried out by segmenting 290 challenging images from human and pig coronaries, and rabbit iliac arteries; the outcomes were compared with the gold standards made by experts. The resultant accuracy was obtained: True Positive (%) = 99.29 ± 2.96, False Positive (%) = 3.69 ± 2.88, False Negative (%) = 0.71 ± 2.96, Max False Positive Distance (mm) = 0.1 ± 0.07, Max False Negative Distance (mm) = 0.06 ± 0.1. Conclusions In conclusion, by segmenting a number of IVOCT images with various features, the proposed technique showed to be robust and more accurate than published studies; in addition, the method is completely automatic, providing a new tool for IVOCT segmentation.

Influence of the substitutional solute on the mechanical properties of Ti-Nb binary alloys for biomedical use

Titanium alloys are widely used in the manufacture of biomedical implants because they possess an excellent combination of physical properties and outstanding biocompatibility. Today, the most widely used alloy is Ti-6Al-4V, but some studies have reported adverse effects with the long-term presence of Al and V in the body, without mentioning that the elasticity modulus value of this alloy is far superior to the bone. Thus, there is a need to develop new Ti-based alloys without Al and V that have a lower modulus, greater biocompatibility, and similar mechanical strength. In this paper, we investigated the effect of Nb as a substitutional solute on the mechanical properties of Ti-Nb alloys, prepared in an arc-melting furnace and characterized by density, X-ray diffraction, optical microscopy, hardness and elasticity modulus measurements. The X-ray and microscopy measurements show a predominance of the α phase. The microhardness values showed a tendency to increase with the concentration of niobium in the alloy. Regarding the elasticity modulus, it was observed a nonlinear behavior with respect to the concentration of niobium. This behavior is associated with the presence of the α phase.

Effects of visual and auditory stimuli in a choice reaction time task

The effect produced by a warning stimulus(i) (WS) in reaction time (RT) tasks is commonly attributed to a facilitation of sensorimotor mechanisms by alertness. Recently, evidence was presented that this effect is also related to a proactive inhibition of motor control mechanisms. This inhibition would hinder responding to the WS instead of the target stimulus (TS). Some studies have shown that auditory WS produce a stronger facilitatory effect than visual WS. The present study investigated whether the former WS also produces a stronger inhibitory effect than the latter WS. In one session, the RTs to a visual target in two groups of volunteers were evaluated. In a second session, subjects reacted to the visual target both with (50% of the trials) and without (50% of the trials) a WS. During trials, when subjects received a WS, one group received a visual WS and the other group was presented with an auditory WS. In the first session, the mean RTs of the two groups did not differ significantly. In the second session, the mean RT of the two groups in the presence of the WS was shorter than in their absence. The mean RT in the absence of the auditory WS was significantly longer than the mean RT in the absence of the visual WS. Mean RTs did not differ significantly between the present conditions of the visual and auditory WS. The longer RTs of the auditory WS group as opposed to the visual WS group in the WS-absent trials suggest that auditory WS exert a stronger inhibitory influence on responsivity than visual WS.

Stability and dynamics of terrestrial planets in binary star systems: application on Alpha Centauri

Binary stars are frequent in the universe, with about 50% of the known main sequence stars being located at a multiple star system (Abt, 1979). Even though, they are universally thought as second rate sites for the location of exo-planets and the habitable zone, due to the difficulties of detection and high perturbation that could prevent planet formation and long term stability. In this work we show that planets in binary star systems can have regular orbits and remain on the habitable zone. We introduce a stability criterium based on the solution of the restricted three body problem and apply it to describe the short period planar and three-dimentional stability zones of S-type orbits around each star of the Alpha Centauri system. We develop as well a semi-analytical secular model to study the long term dynamics of fictional planets in the habitable zone of those stars and we verify that planets on the habitable zone would be in regular orbits with any eccentricity and with inclination to the binary orbital plane up until 35 degrees. We show as well that the short period oscillations on the semi-major axis is 100 times greater than the Earth's, but at all the time the planet would still be found inside the Habitable zone.

Transformaciones basadas en el algoritmo Local Binary Pattern de imágenes capturadas con la Kinect para clasificación facial

Máster Universitario en Sistemas Inteligentes y Aplicaciones Numéricas en Ingeniería (SIANI)

Liquid-liquid equilibria in binary solutions formed by [Pyridinium-Derived][F4B] ionic liquids and alkanols:new experimental data and validation of a multiparametric model for correlating LLE data

[EN]Experimental solubility data are presented for a set of binary systems composed of ionic liquids (IL) derived from pyridium, with the tetrafluoroborate anion, and normal alcohols ranging from ethanol to decanol, in the temperature interval of 275 420 K, at atmospheric pressure. For each case, the miscibility curve and the upper critical solubility temperature (UCST) values are presented. The effects of the ILs on the behavior of solutions with alkanols are analyzed, paying special attention to the pyridine derivatives, and considering a series of structural characteristics of the compounds involved.

Correlation and prediction of mixing thermodynamic properties of ester-containing systems Ester+alkane and ester+ester binary systems and the ternary dodecane+ethyl pentonoate+ethyl ethanoate

[EN]Excess thermodynamic properties VE m and HE m, have been measured for the ternary mixture dodecane + ethyl pentanoate + ethyl ethanoate and for the corresponding binaries dodecane + ethyl pentanoate, dodecane + ethyl ethanoate, ethyl pentanoate + ethyl ethanoate at 298.15 K. All mixtures show endothermic and expansive effects. Experimental results are correlated with a suitable equation whose final form for the excess ternary quantity ME contains the particular contributions of the three binaries (i–j) and a last term corresponding to the ternary, all of them obtained considering fourth-order interactions.

Measurements and correlations of the isobaric vapor-liquid equilibria of binary mixtures and excess properties for mixtures containing and alkyl (Methyl, Ethyl) butanoate with an alkane (Heptane, Nonane) at 101.32 kPa.

[EN]In this work, the measurements of the isobaric vapor−liquid equilibrium (VLE) data at 101.32 kPa and the excess molar volumes (vE), obtained at 10 K intervals of temperature in the range (288.15 to 328.15) K, for four binary systems comprised of methyl or ethyl butanoate with two alkanes (heptane and nonane) are presented.

Multiproperty modeling for a set of binary systems. Evaluation of a model to correlate simultaneously several mixing properties of methyl ethanoate+alkanes and new experimental data

[EN] This work makes a theoretical–experimental contribution to the study of ester and alkane solutions. Experimental data of isobaric vapor–liquid equilibria (VLE) are presented at 101.3 kPa for binary systems of methyl ethanoate with six alkanes (from C5 to C10), and of volumes and mixing enthalpies, vE and hE.

Binary liquid-liquid equilibria for systems of mono or disubstituted haloakanes (Cl,Br) and pyiridinium based ionic liquids. Advances in the experimentation and interpretation of results

[EN]This work presents the measurements made to define the temperature−composition curves for a set of binary systems composed of several pyridinium-based ionic liquids (ILs) [bpy][BF4] and [bYmpy][BF4] (Y = 2,3,4) with mono- and dihaloalkanes (Cl and Br) in the temperature interval [280−473] K and at atmospheric pressure. With the exception of the short chain dichloroalkanes (1,1- and 1,2-), all the compounds present some degree of immiscibility with the ionic liquids selected.

Exploring the use of local binary patterns as focus measure

[EN]In this work local binary patterns based focus measures are presented. Local binary patterns (LBP) have been introduced in computer vision tasks like texture classification or face recognition. In applications where recognition is based on LBP, a computational saving can be achieved with the use of LBP in the focus measures. The behavior of the proposed measures is studied to test if they fulfill the properties of the focus measures and then a comparison with some well know focus measures is carried out in different scenarios.

Analysis of preferences for freight transport using advanced choice models

Programa de doctorado: Perspectivas científicas sobre el turismo y la dirección de empresas turísticas

Per un'etica della letteratura: la cornice il doppio legame nell'opera di J. M. Coetzee

The elusive fiction of J. M. Coetzee is not a work in which you can read fixed ethical stances. I suggest testing the potentialities of a logic based on frames and double binds in Coetzee's novels. A double bind is a dilemma in communication which consists on tho conflicting messages, with the result that you can’t successfully respond to neither. Jacques Derrida highlighted the strategic value of a way of thinking based on the double bind (but on frames as well), which enables to escape binary thinking and so it opens an ethical space, where you can make a choice out of a set of fixed rules and take responsibility for it. In Coetzee’s fiction the author himself can be considered in a double bind, seeing that he is a white South African writer who feels that his “task” can’t be as simply as choosing to represent faithfully the violence and the racism of the apartheid or of choosing to give a voice to the oppressed. Good intentions alone do not ensure protection against entering unwittingly into complicity with the dominant discourse, and this is why is important to make the frame in which one is always situated clearly visible and explicit. The logic of the double bind becomes the way in which moral problem are staged in Coetzee’s fiction as well: the opportunity to give a voice to the oppressed through the same language which co-opted to serve the cause of oppression, a relation with the otherness never completed, or the representability of evil in literature, of the secret and of the paradoxical implications of confession and forgiveness.