EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes.

Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R)

Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in many birds. Feral pigeons (Columba livia) show two major melanin-based colorations: a red coloration due to pheomelanic pigment and a black coloration due to eumelanic pigment. Furthermore, within each color type, feral pigeons display continuous variation in the amount of melanin pigment present in the feathers, with individuals varying from pure white to a full dark melanic color. Coloration is highly heritable and it has been suggested that it is under natural or sexual selection, or both. Our objective was to investigate whether MC1R allelic variants are associated with plumage color in feral pigeons.We sequenced 888 bp of the coding sequence of MC1R among pigeons varying both in the type, eumelanin or pheomelanin, and the amount of melanin in their feathers. We detected 10 non-synonymous substitutions and 2 synonymous substitution but none of them were associated with a plumage type. It remains possible that non-synonymous substitutions that influence coloration are present in the short MC1R fragment that we did not sequence but this seems unlikely because we analyzed the entire functionally important region of the gene.Our results show that color differences among feral pigeons are probably not attributable to amino acid variation at the MC1R locus. Therefore, variation in regulatory regions of MC1R or variation in other genes may be responsible for the color polymorphism of feral pigeons.

A non-linear VAD for noisy environments

This paper deals with non-linear transformations for improving the performance of an entropy-based voice activity detector (VAD). The idea to use a non-linear transformation has already been applied in the field of speech linear prediction, or linear predictive coding (LPC), based on source separation techniques, where a score function is added to classical equations in order to take into account the true distribution of the signal. We explore the possibility of estimating the entropy of frames after calculating its score function, instead of using original frames. We observe that if the signal is clean, the estimated entropy is essentially the same; if the signal is noisy, however, the frames transformed using the score function may give entropy that is different in voiced frames as compared to nonvoiced ones. Experimental evidence is given to show that this fact enables voice activity detection under high noise, where the simple entropy method fails.

Non-Linear and Non-Conventional Speech Processing: Alternative Techniques

This special issue aims to cover some problems related to non-linear and nonconventional speech processing. The origin of this volume is in the ISCA Tutorial and Research Workshop on Non-Linear Speech Processing, NOLISP’09, held at the Universitat de Vic (Catalonia, Spain) on June 25–27, 2009. The series of NOLISP workshops started in 2003 has become a biannual event whose aim is to discuss alternative techniques for speech processing that, in a sense, do not fit into mainstream approaches. A selected choice of papers based on the presentations delivered at NOLISP’09 has given rise to this issue of Cognitive Computation.

Spermatological characteristics of Pleurogenidae (Digenea) inferred from the ultrastructural study of Pleurogenes claviger, Pleurogenoides medians and Prosotocus confusus

The present work constitutes the first ultrastructural analysis of the spermatozoon in the Pleurogenidae, with the study of three species belonging to three of the 16 genera included in this family, namely Pleurogenes claviger, Pleurogenoides medians and Prosotocus confusus. The mature spermatozoa of these pleurogenids present two axonemes of the 9+'1' trepaxonematan pattern, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation, spine-like bodies and granules of glycogen. The organization of these characters in the sperm cell is similar in the three species. Thus, the anterior spermatozoon extremity is filiform and a continuous and submembranous layer of parallel cortical microtubules surrounds the axonemes at their anterior end. The posterior spermatozoon extremity exhibits the second axoneme and corresponds to the Cryptogonimidean type of Quilichini et al. (2010). Slight differences were noted between the spermatozoon of P. confusus and those of the two remaining species in the location of mitochondria.

Reducción del vector de características de reconocimiento facial

In this present work, we are proposing a characteristics reduction system for a facial biometric identification system, using transformed domains such as discrete cosine transformed (DCT) and discrete wavelets transformed (DWT) as parameterization; and Support Vector Machines (SVM) and Neural Network (NN) as classifiers. The size reduction has been done with Principal Component Analysis (PCA) and with Independent Component Analysis (ICA). This system presents a similar success results for both DWT-SVM system and DWT-PCA-SVM system, about 98%. The computational load is improved on training mode due to the decreasing of input’s size and less complexity of the classifier.

The Barcelona International Conference on Advances in Statistics (BAS 2012) : Abstracts of communications

Conferència Organitzada per l'Escola Politècnica Superior, Universitat de Vic en col·laboració amb Servei d'Estadística de la Universitat Autònoma de Barcelona i CosmoCaixa Barcelona. Celebrada del 18 al 22 de juny de 2012 a Barcelona

On cumulant techniques in speech processing

This paper analyzes applications of cumulant analysis in speech processing. A special focus is made on different second-order statistics. A dominant role is played by an integral representation for cumulants by means of integrals involving cyclic products of kernels.

Microcontroller-based interface circuit for inductive sensors

This work proposes a fully-digital interface circuit for the measurement of inductive sensors using a low-cost microcontroller (µC) and without any intermediate active circuit. Apart from the µC and the sensor, the circuit just requires an external resistor and a reference inductance so that two RL circuits with a high-pass filter (HPF) topology are formed. The µC appropriately excites such RL circuits in order to measure the discharging time of the voltage across each inductance (i.e. sensing and reference) and then it uses such discharging times to estimate the sensor inductance. Experimental tests using a commercial µC show a non-linearity error (NLE) lower than 0.5%FSS (Full-Scale Span) when measuring inductances from 1 mH to 10 mH, and from 10 mH to 100 mH.