Intra- and inter-speaker variability of sibilant fricative /s/ in Argentine Spanish

En este trabajo se propone estudiar y valorizar el poder discriminativo de la fricativa sibilante /s/, de manera de incorporar este conocimiento en futuros sistemas automáticos de reconocimiento de hablantes. Se seleccionó esta fricativa por ser la principal consonante de acuerdo a la frecuencia de aparición en el corpus. Se determinó un ranking de los parámetros acústicos de dicho fonema que mejor discriminan a un hablante, teniendo en cuenta la menor variabilidad intrahablante y la máxima variabilidad inter-hablante. El material de evaluación fue extraído de la base de datos SpeechDat, con muestras de habla de telefonía fija en Español de Argentina. Los parámetros con mejor puntaje fueron: la Intensidad, el tercer formante (F3), el primer formante (F1) y el primer momento espectral o Centro de Gravedad (CG). El poder discriminante de la fricativa sibilante /s/, con respecto al resto de los fonemas, ha quedado corroborado por su importante aporte a la tasa de reconocimiento de hablantes obtenida, siendo el sexto fonema en importancia después de las vocales /e/, /a/, /o/ y /i/, y la nasal /n/. La tasa de igual error, empleando solamente este fonema, resultó un 35% menor que la media del total de los 30 fonemas involucrados.This paper focuses on the analysis of the discriminative power of the sibilant fricative /s/, in order to incorporate this knowledge in future automatic speaker recognition systems. The selected fricative is the most frequent consonant in the corpus. An acoustical parameter ranking of /s/ was performed based on minor intra-speaker variability and maximun inter-speaker variability. Evaluation is performed on Argentine-Spanish voice samples from the SpeechDat database recorded on a fixed phone environment. The intensity, the third formant (F3), the first formant (F1) and the first spectral moment or Center of Gravity (CG) were the best ranked parameters. The sibilant fricative /s/, considered in isolation, has a speaker recognition equal error rate (EER) of 35% lower than the average of the total of 30 phonemes involved, confirming the importance of this phoneme for the discrimination of speakers as the sixth phoneme in importance, preceded by the vowels /e/, /a/, /o/ and /i/, and the nasal /n/

PARCE: Protocol for Amino acid Refinement through Computational Evolution

The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their interactions with protein targets. In this work, we present PARCE, an open source Protocol for Amino acid Refinement through Computational Evolution that implements an advanced and promising method for the design of peptides and proteins. The protocol performs a random mutation in the binder sequence, then samples the bound conformations using molecular dynamics simulations, and evaluates the protein-protein interactions from multiple scoring. Finally, it accepts or rejects the mutation by applying a consensus criterion based on binding scores. The procedure is iterated with the aim to explore efficiently novel sequences with potential better affinities toward their targets. We also provide a tutorial for running and reproducing the methodology

Analysis of State-Specific Vibrations Coupled to the Unidirectional Energy Transfer in Conjugated Dendrimers

The nonadiabatic excited-state molecular dynamics (NA-ESMD) method and excited-state instantaneous normal modes (ES-INMs) analyses have been applied to describe the state-specific vibrations that participate in the unidirectional energy transfer between the coupled chromophores in a branched dendrimeric molecule. Our molecule is composed of two-, three-, and four-ring linear poly(phenyleneethynylene) (PPE) units linked through meta-substitutions. After an initial laser excitation, an ultrafast sequential S3 → S 2 → S1 electronic energy transfer from the shortest to longest segment takes place. During each Sn → Sn-1 (n = 3, 2) transition, ES-INM(Sn) and ES-INM(Sn-1) analyses have been performed on Sn and Sn-1 states, respectively. Our results reveal a unique vibrational mode localized on the Sn state that significantly matches with the corresponding nonadiabatic coupling vector dn,(n-1). This mode also corresponds to the highest frequency ES-INM(Sn) and it is seen mainly during the electronic transitions. Furthermore, its absence as a unique ES-INM(S n-1) reveals that state-specific vibrations play the main role in the efficiency of the unidirectional Sn → Sn-1 electronic and vibrational energy funneling in light-harvesting dendrimers.Fil: Soler, Miguel A.. Universidad Nacional de Quilmes; ArgentinaFil: Roitberg, Adrián E.. University of Florida; Estados UnidosFil: Nelson, Tammie. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Tretiak, Sergei. Los Alamos National High Magnetic Field Laboratory; Estados UnidosFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Hybrid Quantum/Classical simulations of the vibrational relaxation of the Amide I mode of N-methylacetamide in D2O solution

Hybrid quantum/classical molecular dynamics (MD) is applied to simulate the vibrational relaxation (VR) of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D2O) solution. A novel version of the vibrational molecular dynamics with quantum transitions (MDQT) treatment is developed in which the amide I mode is treated quantum mechanically while the remaining degrees of freedom are treated classically. The instantaneous normal modes of the initially excited NMAD molecule (INM0) are used as internal coordinates since they provide a proper initial partition of the system in quantum and classical subsystems. The evolution in time of the energy stored in each individual normal mode is subsequently quantified using the hybrid quantum-classical instantaneous normal modes (INMt). The identities of both the INM0s and the INMts are tracked using the equilibrium normal modes (ENMs) as templates. The results extracted from the hybrid MDQT simulations show that the quantum treatment of the amide I mode accelerates the whole VR process versus pure classical simulations and gives better agreement with experiments. The relaxation of the amide I mode is found to be essentially an intramolecular vibrational redistribution (IVR) process with little contribution from the solvent, in agreement with previous theoretical and experimental studies. Two well-defined relaxation mechanisms are identified. The faster one accounts for ≈40% of the total vibrational energy that flows through the NMAD molecule and involves the participation of the lowest frequency vibrations as short-life intermediate modes. The second and slower mechanism accounts for the remaining ≈60% of the energy released and is associated to the energy flow through specific mid-range and high-frequency modes.Fil: Bastida, Adolfo. Universidad de Murcia; EspañaFil: Soler, Miguel A.. Universidad de Murcia; EspañaFil: Zúñiga, José. Universidad de Murcia; EspañaFil: Requena, Alberto. Universidad de Murcia; EspañaFil: Kalstein, Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Fernández Alberti, Sebastián. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

EphrinA4 plays a critical role in α4 and αL mediated survival ofhuman CLL cells during extravasation

A role of endothelial cells in the survival of CLL cells during extravasation is presently unknown. Herein we show that CLL cells but not normal B cells can receive apoptotic signals through physical contact with TNF-α activated endothelium impairing survival in transendothelial migration (TEM) assays. In addition, the CLL cells of patients having lymphadenopathy (LApos) show a survival advantage during TEM that can be linked to increased expression of α4 and αL integrin chains. Within this context, ephrinA4 expressed on the surface of CLL cells sequestrates integrins and inactivates them resulting in reduced adhesion and inhibition of apoptotic/survival signals through them. In agreement, ephrinA4 silencing resulted in increased survival of CLL cells of LApos patients but not LA neg patients. Similarly was observed when a soluble ephrinA4 isoform was added to TEM assays strongly suggesting that accumulation of this isoform in the serum of LApos patients could contribute to CLL cells dissemination and survival in vivo. In supporting, CLL lymphadenopathies showed a preferential accumulation of apoptotic CLL cells around high endothelial venules lacking ephrinA4. Moreover, soluble ephrinA4 isolated from sera of patients increased the number and viability of CLL cells recovered from the lymph nodes of adoptively transferred mice. Finally, we present evidence suggesting that soluble ephrinA4 mediated survival during TEM could enhance a transcellular TEM route of the CLL cells. Together these findings point to an important role of ephrinA4 in the nodal dissemination of CLL cells governing extravasation and survival

Light-induced rhythmic changes in thermotolerance in stationary-phase cells of Candida utilis

In synchronized light-dark cycles, stationary-phase cultures of the budding yeast Candida utilis were able to survive heat treatment at 50ºC with an apparent circadian-like rhythm related to the onset of light. However, in continuous darkness this pattern did not run freely and was markedly dampened. We discuss these findings in terms of the potential circadian control of heat tolerance, which has been described in the fission yeast Schizosaccharomyces pombe. Our results suggest that the resistance pattern observed in C. utilis is most likely an adaptive response to the light-induced generation of reactive oxygen species rather than the occurrence of a truly endogenous circadian rhythm. [Int Microbiol 2006; 9(1):61-64

Antibody-Antigen Binding Interface Analysis in the Big Data Era

Antibodies have become the Swiss Army tool for molecular biology and nanotechnology. Their outstanding ability to specifically recognise molecular antigens allows their use in many different applications from medicine to the industry. Moreover, the improvement of conventional structural biology techniques (e.g., X-ray, NMR) as well as the emergence of new ones (e.g., Cryo-EM), have permitted in the last years a notable increase of resolved antibody-antigen structures. This offers a unique opportunity to perform an exhaustive structural analysis of antibody-antigen interfaces by employing the large amount of data available nowadays. To leverage this factor, different geometric as well as chemical descriptors were evaluated to perform a comprehensive characterization

Chloride anion effect on the advanced oxidation processes of methidathion and dimethoate: role of Cl2(center dot-) radical

NOTICE: this is the author’s version of a work that was accepted for publication in Water Research. Changes resulting from the publishing process, such as peer review, editing, corrections,structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in WATER RESEARCH [VOL 47, ISSUE 1, (January 2013)] DOI 10.1016/j.watres.2012.10.018¨ IWA Publishing : Set statement to accompany deposit, "©IWA Publishing 2013. The definitive peer-reviewed and edited version of this article is published in Water Research 47 1 351-362 2013 DOI 10.1016/j.watres.2012.10.018 and is available at www.iwapublishing.com."The reaction of phosphor-containing pesticides such as methidathion (MT) and dimethoate (DM) with dichloride radical anions (Cl-2(center dot-)) was investigated. The second order rate constants (1.3 +/- 0.4) x 10(8) and (1.1 0.4) x 10(8) M-1 s(-1) were determined for the reaction of Cl-2(center dot-) with MT and DM, respectively. A reaction mechanism involving an initial charge transfer from the sulfide groups of the insecticides to Cl-2(center dot-) is proposed and supported by the identified transient intermediates and reaction products. The formation of chlorinated byproducts was determined. The unexpected consequences of an efficient Cl-2(center dot-) activity towards MT and DM on the degradation capacity by Advanced Oxidation Procedures applied to polluted waters containing the insecticides and Cl- anions is discussed. (C) 2012 Elsevier Ltd. All rights reserved.This research was financially supported by Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Agencia Nacional de Promocion Cientifica y Tecnologica (Argentina, project PICT 2007 number 00308), and Agencia Espanola de Cooperacion Internacional (project A/8199/07). MCG, JAR and PC are research members of Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Argentina. D.O.M. is a research member of CICPBA, Argentina. This research was supported by the grant PIP 112-200801-00356 from CONICET.Caregnato, P.; Rosso, JA.; Soler Escoda, JM.; Arques Sanz, A.; Martire, DO.; González, MC. (2013). Chloride anion effect on the advanced oxidation processes of methidathion and dimethoate: role of Cl2(center dot-) radical. Water Research. 47(1):351-362. https://doi.org/10.1016/j.watres.2012.10.018S35136247

Antibody-Antigen Binding Interface Analysis in the Big Data Era

Antibodies have become the Swiss Army tool for molecular biology and nanotechnology. Their outstanding ability to specifically recognise molecular antigens allows their use in many different applications from medicine to the industry. Moreover, the improvement of conventional structural biology techniques (e.g., X-ray, NMR) as well as the emergence of new ones (e.g., Cryo-EM), have permitted in the last years a notable increase of resolved antibody-antigen structures. This offers a unique opportunity to perform an exhaustive structural analysis of antibody-antigen interfaces by employing the large amount of data available nowadays. To leverage this factor, different geometric as well as chemical descriptors were evaluated to perform a comprehensive characterization.Fil: Reis, Pedro B. P. S.. Istituto Italiano Di Technologie; Italia. Universidade Nova de Lisboa; PortugalFil: Barletta Roldan, Patricio German. The Abdus Salam; Italia. The Abdus Salam. International Centre for Theoretical Physics; Italia. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gagliardi, Lucas. Istituto Italiano Di Technologie; ItaliaFil: Fortuna, Sara. Istituto Italiano Di Technologie; ItaliaFil: Soler, Miguel A.. Istituto Italiano Di Technologie; ItaliaFil: Rocchia, Walter. Istituto Italiano Di Technologie; Itali

Cutting down on the grog: the crystallisation of Neolithic ceramic traditions at Cova d’En Pardo (Alicante, Spain) and cultural change in the western Mediterranean basin (mid-6th and 5th millennia cal. BC)

This paper presents the characterisation of 48 ceramic samples from Cova d’En Pardo (Alicante, Spain). Provenance and technology analysis are carried out on materials dated back to different Early and Middle Neolithic cultural phases, including pioneer and Epicardial levels, poorly known in the area. The techniques employed are optical petrography and scanning electron microscope. Two main fabrics were identified, characterised by the heavy presence of temper (grog and calcite), along with five minor petrographic classes, including two imports, one of them probably from southern Iberia. The comparison among occupational phases within the site reveals changes along the stratigraphic series, especially during the transition from the 6th to 5th millennia cal. BC, which is reflected in temper choice. Evidence from the earliest occupation of the site also agrees with the picture of discontinuity previously observed on nearby contexts between pioneer and traditional Cardial ceramic technology, which might be connected to neolithization routes. Firing technology is characterised by the occurrence of microstructure gradients and signs of fast heating rates.Sample preparation and analyses were funded by the projects NEOMEDPOT (Marie Skłodowska-Curie program, European Commission, grant number 659466) and Espacios sociales y espacios de frontera durante el calcolítico y la Edad del Bronce en el Levante de la península Ibérica (HAR2016-76586-P, Ministerio de Economía y Competitividad and FEDER). Miguel del Pino is a postdoctoral researcher within the Viera y Clavijo program, funded by the Universidad de Las Palmas de Gran Canaria (Spain). The initial draft of the paper was finished while a postdoctoral researcher within the APOSTD program funded by the Generalitat Valenciana and FEDER funds (Spain)