Learning Structure from Data and Its Application to Ozone Prediction

In this paper we propose an algorithm for structure learning in predictive expert systems based on a probabilistic network representation. The idea is to have the simplest structure (minimum number of links) with acceptable predictive capability. The algorithm starts by building a tree structure based on measuring mutual information between pairs of variables, and then it adds links as necessary to obtain certain predictive performance. We have applied this method for ozone prediction in México City, where the ozone level is used as a global indicator for the air quality in different parts of the city. It is important to predict the ozone level a day, or at least several hours in advance, to reduce the health hazards and industrial losses that occur when the ozone reaches emergency levels. We obtained as a first approximation a tree-structured dependency model for predicting ozone in one part of the city. We observe that even with only three parameters, its estimations are acceptable.A causal network representation and the structure learning techniques produced some very interesting results for the ozone prediction problem. Firstly, we got some insight into the dependence structure of the phenomena. Secondly, we got an indication of which are the important and not so important variables for ozone forecasting. Taking this into account, the measurement and computational costs for ozone prediction could be reduced. And thirdly, we have obtained satisfactory short term ozone predictions based on a small set of the most important parameters.     

From latex specifications to parallel codes

The advent of multicore systems, joined to the potential acceleration of the graphics processing units, has given us a low cost computation capability unprecedented. The new systems alleviate some well-known important architectural problems at the expense of a considerable increment of the programmability wall. Heterogeneity, at both the architectural and programming levels, poses a great challenge to programmers. As a contribution, we propose a development methodology for the automatic source-to-source transformation on specific domains. This methodology is successfully instantiated as a framework to solve Dynamic Programming problems. As a result of applying our framework, the end user (a physicist, a mathematician or a biologist) can express her problem through a latex equation and automatically derive efficient parallel codes for current homogeneous or heterogeneous architectures. The approach allows an easy portability to new emergent architectures.     

A cluster-DEE-based strategy to empower protein design

The Medical and Pharmaceutical industries have shown high interest in the precise engineering of protein hormones and enzymes that perform existing functions under a wide range of conditions. Proteins are responsible for the execution of different functions in the cell: catalysis in chemical reactions, transport and storage, regulation and recognition control. Computational Protein Design (CPD) investigates the relationship between 3-D structures of proteins and amino acid sequences and looks for all sequences that will fold into such 3-D structure. Many computational methods and algorithms have been proposed over the last years, but the problem still remains a challenge for Mathematicians, Computer Scientists, Bioinformaticians and Structural Biologists. In this article we present a new method for the protein design problem. Clustering techniques and a Dead-End-Elimination algorithm are combined with a SAT problem representation of the CPD problem in order to design the amino acid sequences. The obtained results illustrate the accuracy of the proposed method, suggesting that integrated Artificial Intelligence techniques are useful tools to solve such an intricate problem.     

Efficient implementation of the implicit error correction nVoD schema

Implicit Error Correction is a near Video-on-Demand (nVoD) schema that trades bandwidth utilization for initial playback delay while potentially allowing an infinite number of users. Additionally, it provides error protection without further bandwidth increase by exploiting the implicit redundancy of nVoD protocols, using linear combinations of the segments transmitted in a given time slot. This paper introduces a new implementation that outperforms the original schema by adding two new mechanisms: redundancy channels and feedback error correction.     

Development of a Real Time PCR system for detection of ochratoxin A-producing strains of the Aspergillus niger aggregate

Members of Aspergillus section Nigri are distributed worldwide, being considered as common food spoilage fungi. Some species of this section produce ochratoxin A (OTA), mainly Aspergillus carbonarius and several members of the Aspergillus niger aggregate. Detection of ochratoxigenic A. niger aggregate strains is important to prevent OTA contamination in foodstuffs. A new Real Time PCR procedure has been developed for the rapid and specific detection and quantification of ochratoxin A-producing strains of the A. niger aggregate. Two specific primers delimiting a 120 bp fragment and a probe were designed and directed to a polyketide synthase (PKS) from A. niger CBS 513.88 genome. This PKS has a strong similarity to PKS of A. ochraceus fragment involved in ochratoxin biosynthesis. Specificity was confirmed by testing primers towards purified DNA from 91 fungal strains, including reference and food isolates. The SYBR-Green and the TaqMan approaches developed allowed the specific detection only of ochratoxigenic strains of the A. niger aggregate. All other analyzed food related fungi gave negative results. This is the first report on a Real Time PCR system for the detection of OTA-producing strains of the A. niger aggregate.     

Applicability assessment of a real-time PCR assay for the specific detection of bovine,ovine and caprine material in feedstuffs

A TaqMan real-time polymerase chain reaction (PCR) method was developed for specific detection of bovine, ovine and caprine processed animal protein (PAP) in industrial feedstuffs. The method uses species-specific primers and probes targeting short mitochondrial D-loop sequences, and a positive amplification control based on 18S rRNA gene. The applicability of the real-time PCR protocol was assessed through analysis of 126 industrial feed samples that were manufactured to reproduce rendering processes of commercial feeds destined for farmed animals. The assay successfully classified samples as positive or negative according to the ruminant composition, enabling qualitative detection of banned material in feeds at levels as low as 0.1%. Although the method provides quantitative potential, results suggest that the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing treatments of the feeds, which affect the amount and quality of amplifiable DNA.     

Collagen scaffolds for orthopedic regenerative medicine

Collagen and collagen-based scaffolds offer distinct advantages when selected as biomaterials for use across a broad spectrum of regenerative medicine applications. However, relatively poor mechanical properties are often perceived to limit their usefulness for orthopedic applications. These problems can be overcome through enhanced crosslinking mechanisms or through the addition of a second, stiffer phase such as hydroxyapatite, thus allowing tailored composite scaffolds to meet specific tissue requirements. This overview will highlight the current state of the art of these scaffolds, and consider the exciting prospects and future directions of collagen-based technologies for orthopedic regenerative medicine.     

Creep behaviour of a new air-hardenable intermetallic Ti–46Al–8Ta alloy

Creep behaviour of a new cast air-hardenable intermetallic Ti–46Al–8Ta (at.%) alloy was investigated. Constant load tensile creep tests were performed at initial applied stresses ranging from 200 to 400 MPa in the temperature range from 973 to 1073 K. The minimum creep rate is found to depend strongly on the applied stress and temperature. The power law stress exponent of the minimum creep rate is n = 5.8 and the apparent activation energy for creep is calculated to be Q_a = (382.9 ± 14.5) kJ/mol. The kinetics of creep deformation of the specimens tested to a minimum creep rate (creep deformation about 2%) is suggested to be controlled by non-conservative motion of dislocations in the γ(TiAl) matrix. Besides dislocation mechanisms, deformation twinning contributes significantly to overall measured strains in the specimens tested to fracture. The initial γ(TiAl) + α₂(Ti₃Al) microstructure of the creep specimens is unstable and transforms to the γ + α₂ + τ type during creep. The particles of the τ phase are preferentially formed along the grain and lamellar colony boundaries.     

Particle Currents in a Fluid—Dynamical Description of Two Trapped Fermion Species

We apply a recent generalization of the fluid-dynamical scheme of nuclear physics that includes the pair density and current of superfluids, to trace the particle transition currents of an unpolarized fermion system in a harmonic trap. These current fluctuations are driven by the equilibrium density and gap and by the oscillations in the particle densities. We analize the velocity portraits of either species for the lowest multipolar excitations employing different equations of state of the unperturbed fluids, in order to establish the role of the equilibrium gap.