Computationally efficient method to construct scar functions

Phys. Rev. E 85, 026214-026219 (2012) Desarrollo de un nuevo y eficiente método para la construcción de funciones de scar a lo largo de las órtbitas periódicas inestables de sistemas clásicamente caóticos

Estudio de la estructura de autofunciones de sistemas caóticos en una base de funciones de scar

El problema central que aborda esta tesis doctoral es el estudio de la correspondencia entre la mecanica clasica y la mecanica cuantica en sistemas hamiltonianos clasicamente caoticos, tema que se enmarca dentro del llamado caos cuantico. En concreto, en este trabajo proponemos un nuevo y efectivo metodo para calcular las autofunciones de sistemas caoticos usando una base de funciones de scar. Dichas funciones de scar juegan un papel fundamental en el estudio de las manifestaciones cuanticas del caos, ya que se trata de funciones de onda semiclasicas con una dispersion muy peque~na y localizadas a lo largo de las variedades invariantes de las orbitas periodicas inestables del sistema que conforman la estructura organizativa del caos clasico. El metodo de calculo desarrollado se ha denominado Metodo de Gram- Schmidt Selectivo (MGSS), dado que construye la base haciendo uso del metodo de Gram{Schmidt convencional pero teniendo en cuenta, ademas, la dispersi on de las funciones de scar y la longitud de la orbita periodica a lo largo de la cual se localizan. El MGSS nos ha permitido calcular con gran precision las 2400 autofunciones con menor energa de un oscilador cuartico altamente caotico con dos grados de libertad acoplados, as como autofunciones muy excitadas en una ventana de energa, utilizando en ambos casos una base mucho mas eciente que las descritas en la literatura. Ademas, hemos empleado el MGSS para calcular las autofunciones del sistema molecular LiNC/LiCN, que presenta un espacio de fases con zonas de regularidad y con regiones en las que el movimiento es altamente caotico; en este ultimo sistema, hemos calculado de forma muy eciente las autofunciones asociadas a las primeras 66 energas. Finalmente, hemos propuesto un metodo perturbativo para calcular velocidades de reaccion en sistemas abiertos descritos por potenciales anarmonicos. Con este metodo, hemos calculado la velocidad de reaccion de distintos potenciales de uno y dos grados de libertad, as como la velocidad de isomerizacion del sistema molecular LiNC/LiCN, tanto sometido a un ruido blanco (sin correlaciones) como en presencia de un ba~no de atomos de argon, lo que constituye un entorno con correlaciones. El metodo desarrollado es independiente de la supercie divisoria y nos ha permitido obtener correcciones analticas a la famosa formula de Kramers, lo que posibilita el calculo exacto de velocidades de reaccion en potenciales anarmonicos que interaccionan con el entorno.

Analysis of genetic variability in a sample of the durum wheat (Triticum durum Desf.) Spanish collection based on gliadin markers

In this work gliadin proteins were used to analyse the genetic variability in a sample of the durum wheat Spanish collection conserved at the CRF-INIA. In total 38 different alleles were identified at the loci Gli-A1, Gli-A3, Gli-B5, Gli-B1, Gli-A2 and Gli-B2. All the gliadin loci were polymorphic, possessed large genetic diversity and small and large differentiation within and between varieties, respectively. The Gli-A2 and Gli-B2 loci were the most polymorphic, the most fixed within varieties and the most useful to distinguish among varieties. Alternatively, Gli-B1 locus presented the least genetic variability out of the four main loci Gli-A1, Gli-B1, Gli-A2 and Gli-B2. The Gli-B1 alleles coding for the gliadin γ-45, associated with good quality, had an accumulated frequency of 69.7%, showing that the Spanish germplasm could be a good source for breeding quality. The Spanish landraces studied showed new gliadin alleles not catalogued so far. These new alleles might be associated with specific Spanish environment factors. The large number of new alleles identified also indicates that durum wheat Spanish germplasm is rather unique.

Effect of different exercise modalities plus a hypocaloric diet on inflammation markers in overweight patients

Summary Background & aims Inflammation markers (IM) have been associated with the development of chronic diseases. This study compares the effects on IM of three exercise programs combined with a hypocaloric diet. Methods 119 overweight participants (73 women, 46 men) aged 18–50 years were randomised into four treatment groups: strength training (S; n = 30), endurance training (E; n = 30), combined S + E (SE; n = 30), and a diet and physical activity recommendations group (D; n = 29). Energy intake, anthropometric variables (AV), training variables (VO2peak, strength index, dynamometric strength index [DSI]) and plasma IM were recorded at baseline and after 22 weeks of treatment. Results 84 participants completed the study. At 22 weeks, all groups showed a significantly reduced energy intake (P < 0.001) and improved AV (P < 0.001). VO2peak significantly increased in all groups (P < 0.01). DSI increased in the exercise groups only (P < 0.05). Plasma leptin fell significantly (P < 0.001) in the S and E groups, but not significantly in the SE group (P = 0.029) (no significant differences between these groups). Tumour necrosis factor-α (TNF-α), and C-reactive protein (CRP) concentrations decreased in all groups when examined together, but not when examined separately. No significant differences were seen in interleukin-6 (IL-6). Conclusions Combining strength or endurance training with a hypocaloric diet improved AV and reduced plasma leptin concentrations. No differences were seen between groups in terms of TNF-α, IL-6 or CRP reduction. This trial was registered at clinical trials.gov as NCT01116856. http://clinicaltrials.gov/.

Effectiveness of AFLPs and retrotransposon-based markers for the identification of portuguese grapevine cultivars and clones

Grapevine germplasm, including 38 of the main Portuguese cultivars and three foreign cultivars, Pinot Noir, Pinot Blanc and Chasselas, used as a reference, and 37 true-to-type clones from the Alvarinho, Arinto, Loureiro, Moscatel Galego Branco, Trajadura and Vinhão cultivars were studied using AFLP and three retrotransposon-based molecular techniques, IRAP, REMAP and SSAP. To study the retrotransposon-based polymorphisms, 18 primers based on the LTR sequences of Tvv1, Gret1 and Vine-1 were used. In the analysis of 41 cultivars, 517 IRAP, REMAP, AFLP and SSAP fragments were obtained, 83% of which were polymorphic. For IRAP, only the Tvv1Fa primer amplified DNA fragments. In the REMAP analysis, the Tvv1Fa-Ms14 primer combination only produced polymorphic bands, and the Vine-1 primers produced mainly ISSR fragments. The highest number of polymorphic fragments was found for AFLP. Both AFLP and SSAP showed a greater capacity for identifying clones, resulting in 15 and 9 clones identified, respectively. Together, all of the techniques allowed for the identification of 54% of the studied clones, which is an important step in solving one of the challenges that viticulture currently faces.

Do the spatial characteristics of myocardial scar tissue determine the risk of ventricular arrhythmias?

Sudden cardiac death is one of the main causes of mortality in patients with structural heart disease. Although an implantable cardioverter de?brillator signi?cantly reduces the mortality rate, many patients never receive a shock. Identi?cation of high-risk patients would reduce the costs associated with this therapy and prevent the deleterious effect of inappropriate discharges. As scar tissue is the substrate of ventricular arrhythmias in patients with structural heart disease, scar characterization could allow strati?cation of the risk. The objective of this article is to review the role of scar characteristics in the pathogenesis of ventricular arrhythmias in patients with structural heart disease.

Validation of microsatellite markers for cytotype discrimination in the model grass Brachypodium distachyon

Brachypodium distachyon (2n = 2x = 10) is a small annual grass species where the existence of three different cytotypes (10, 20 and 30 chromosomes) has long been regarded as a case of autopolyploid series, with x = 5. However, it has been demonstrated that the cytotypes assumed to be polyploids represent two separate Brachypodium species recently named as B. stacei (2n = 2x = 20) and B. hybridum (2n = 4x = 30). The aim of this study was to find a PCR-based alternative approach that could replace standard cytotyping methods (i. e., chromosome counting and flow cytometry) to characterize each of the three Brachypodium species. We have analyzed with four microsatellite (SSR) markers eighty-three Brachypodium distachyon-type lines from varied locations in Spain, including the Balearic and Canary Islands. Within this set of lines, 64, 4 and 15 had 10, 20 and 30 chromosomes, respectively. The surveyed markers produced cytotype-specific SSR profiles. So, a single amplification product was generated in the diploid samples, with non-overlapping allelic ranges between the 2n = 10 and 2n = 20 cytotypes, whereas two bands, one in the size range of each of the diploid cytotypes, were amplified in the 2n = 30 lines. Furthermore, the remarkable size difference obtained with the SSR ALB165 allowed the identification of the Brachypodium species by simple agarose gel electrophoresis.

Isozyme systems as markers of genetic deterioration in stored seeds of Brassicaceae species

The main objective of this study was to determine if isozyme systems can be used as markers of genetic deterioration in Brassicaceae seed accessions under different storage conditions. Seed samples of Brassica oleracea, Cardaria draba, Erysimum cheiri, Iberis sempervirens and Rapistrum rugosum were stored for periods of 9 to 30 years at -10°C and 3-4% seed moisture content (long-term or LT conditions) and at 5°C and uncontrolled relative humidity (RH) (short-term or ST conditions). Starch Gel Electrophoresis (SGE) was used to analyse six enzyme systems oriented to determine the genetic deterioration of the accessions studied. The results obtained show that long-term storage conditions (LT) were extremely effective in maintaining the viability of seeds of the five Brassicaceae species studied. The final germination percentages reached by seeds from LT samples ranged from 75 to 100%, while the germination percentages of ST samples (except for B. oleracea) were very low (from 0 to 10%). Similar conclusions were obtained studying the integrity of electrophoretic bands for several isozymes. Two enzyme systems were of special interest: malate dehydrogenase and alcohol dehydrogenase.

Merging person-specific bio-markers for predicting oral cancer recurrence through an ontology

One of the major problems related to cancer treatment is its recurrence. Without knowing in advance how likely the cancer will relapse, clinical practice usually recommends adjuvant treatments that have strong side effects. A way to optimize treatments is to predict the recurrence probability by analyzing a set of bio-markers. The NeoMark European project has identified a set of preliminary bio-markers for the case of oral cancer by collecting a large series of data from genomic, imaging, and clinical evidence. This heterogeneous set of data needs a proper representation in order to be stored, computed, and communicated efficiently. Ontologies are often considered the proper mean to integrate biomedical data, for their high level of formality and for the need of interoperable, universally accepted models. This paper presents the NeoMark system and how an ontology has been designed to integrate all its heterogeneous data. The system has been validated in a pilot in which data will populate the ontology and will be made public for further research.

Early common markers of microspore and somatic embryogenesis in Quercus suber.

Early common markers of microspore and somatic embryogenesis in Quercus suber.

Dietary and lifestyle quality indices with/without physical activity and markers of insulin resistance in European adolescents: the HELENA study

Resistencia a la insulina en adolescentes