FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals

We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And Regression approach (GRAMMAR) with Model-Based MDR (MB-MDR). We focus on continuous traits, although the method is general and can be used for outcomes of any type, including binary and censored traits. When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR), which is a generalization of Multifactor Dimensionality Reduction (MDR) to continuous traits and related individuals, FAM-MDR was found to outperform PGMDR in terms of power, in most of the considered simulated scenarios. Additional simulations revealed that PGMDR does not appropriately deal with multiple testing and consequently gives rise to overly optimistic results. FAM-MDR adequately deals with multiple testing in epistasis screens and is in contrast rather conservative, by construction. Furthermore, simulations show that correcting for lower order (main) effects is of utmost importance when claiming epistasis. As Type 2 Diabetes Mellitus (T2DM) is a complex phenotype likely influenced by gene-gene interactions, we applied FAM-MDR to examine data on glucose area-under-the-curve (GAUC), an endophenotype of T2DM for which multiple independent genetic associations have been observed, in the Amish Family Diabetes Study (AFDS). This application reveals that FAM-MDR makes more efficient use of the available data than PGMDR and can deal with multi-generational pedigrees more easily. In conclusion, we have validated FAM-MDR and compared it to PGMDR, the current state-of-the-art MDR method for family data, using both simulations and a practical dataset. FAM-MDR is found to outperform PGMDR in that it handles the multiple testing issue more correctly, has increased power, and efficiently uses all available information.

The number of planar central configurations for the 4-body problem is finite when 3 mass positions are fixed

In the n{body problem a central con guration is formed when the position vector of each particle with respect to the center of mass is a common scalar multiple of its acceleration vector. Lindstrom showed for n = 3 and for n > 4 that if n ? 1 masses are located at xed points in the plane, then there are only a nite number of ways to position the remaining nth mass in such a way that they de ne a central con guration. Lindstrom leaves open the case n = 4. In this paper we prove the case n = 4 using as variables the mutual distances between the particles.

Families of periodic orbits for the spatial isosceles 3-body problem

We study the families of periodic orbits of the spatial isosceles 3-body problem (for small enough values of the mass lying on the symmetry axis) coming via the analytic continuation method from periodic orbits of the circular Sitnikov problem. Using the first integral of the angular momentum, we reduce the dimension of the phase space of the problem by two units. Since periodic orbits of the reduced isosceles problem generate invariant two-dimensional tori of the nonreduced problem, the analytic continuation of periodic orbits of the (reduced) circular Sitnikov problem at this level becomes the continuation of invariant two-dimensional tori from the circular Sitnikov problem to the nonreduced isosceles problem, each one filled with periodic or quasi-periodic orbits. These tori are not KAM tori but just isotropic, since we are dealing with a three-degrees-of-freedom system. The continuation of periodic orbits is done in two different ways, the first going directly from the reduced circular Sitnikov problem to the reduced isosceles problem, and the second one using two steps: first we continue the periodic orbits from the reduced circular Sitnikov problem to the reduced elliptic Sitnikov problem, and then we continue those periodic orbits of the reduced elliptic Sitnikov problem to the reduced isosceles problem. The continuation in one or two steps produces different results. This work is merely analytic and uses the variational equations in order to apply Poincar´e’s continuation method.

Infinitely many periodic orbits for the rhomboidal five-body problem

We prove the existence of infinitely many symmetric periodic orbits for a regularized rhomboidal five-body problem with four small masses placed at the vertices of a rhombus centered in the fifth mass. The main tool for proving the existence of such periodic orbits is the analytic continuation method of Poincaré together with the symmetries of the problem. © 2006 American Institute of Physics.

Estudi de la població de Spiraea crenata subsp. parvifolia (Rosaceae) del Collsacabra

Spiraea crenata subsp. parvifolia és un tàxon endèmic del nord-est ibèric, que té una de les escasses poblacions conegudes al Collsacabra, Osona. En aquest treball es pretén definir l’extensió d’aquesta població, caracteritzar la seva estructura demogràfica i avaluar-ne l’estat de conservació. La majoria d’individus censats viuen en un nucli principal rodejat per nuclis més petits. L’estabilitat de l’ambient que ocupa permet valorar l’evolució de la població i la categoria UICN d’amenaça, actualment considerada «en perill ». Es proposen mesures de gestió que permetin la conservació d’aquesta població.

Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

Abstract Background: Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern their function, robustness and evolution. However, one of the main limitations in using protein-protein interactions for function prediction is the availability of interaction data, especially for Mollicutes. If we could harness predicted interactions, such as those from a Protein-Protein Association Networks (PPAN), combining several protein-protein network function-inference methods with semantic similarity calculations, the use of protein-protein interactions for functional inference in this species would become more potentially useful. Results: In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in Mycoplasma genitalium. Conclusions: To our knowledge, the proposed method is the first that combines functional module detection among species, exploiting an orthology procedure and using information theory-based GO semantic similarity in PPAN of the Mycoplasma species. The results of an evaluation show a higher recall than previously reported methods that focused on only one organism network.

Do protein–protein interaction databases identify moonlighting proteins?

One of the most striking results of the human (and mammalian) genomes is the low number of protein-coding genes. To-date, the main molecular mechanism to increase the number of different protein isoforms and functions is alternative splicing. However, a less-known way to increase the number of protein functions is the existence of multifunctional, multitask, or ‘‘moonlighting’’, proteins. By and large, moonlighting proteins are experimentally disclosed by serendipity. Proteomics is becoming one of the very active areas of biomedical research, which permits researchers to identify previously unseen connections among proteins and pathways. In principle, protein–protein interaction (PPI) databases should contain information on moonlighting proteins and could provide suggestions to further analysis in order to prove the multifunctionality. As far as we know, nobody has verified whether PPI databases actually disclose moonlighting proteins. In the present work we check whether well-established moonlighting proteins present in PPI databases connect with their known partners and, therefore, a careful inspection of these databases could help to suggest their different functions. The results of our research suggest that PPI databases could be a valuable tool to suggest multifunctionality.

Malignant pheochromocytoma in a pig

Abstract. Endocrine tumors are rarely observed in pigs, and pheochromocytomas have been only punctually described. The current report describes a white and firm, 15-cm in diameter, neoplastic mass located in the adrenal gland with metastasis to regional lymph nodes in a 2.5-year-old sow. The masses had marked desmoplasia that supported a population of polygonal-tospindle– shaped neoplastic cells arranged into cords and packets within a delicate fibrovascular stroma. Immunohistochemical staining of the tumor was positive for chromogranin and negative for neurofilament protein in adrenal and lymph node masses, which was characteristic of a malignant pheochromocytoma.

Els Plans Individualitzats en les regulacions del Departament d’Educació de juny de 2008. Aplicació d’enfocaments multidimensionals en la seva elaboració

Recentment, el Departament d’Educació de la Generalitat de Catalunya ha publicat regulacions sobre els plans individuals per als alumnes considerats més vulnerables. Se n’han determinat els components i les condicions que s’han de donar per al seu inici. Aquest article considera la possibilitat de desenvolupar aquests plans individuals a partir d’enfocaments multidimensionals d’atenció a les necessitats singulars de l’alumnat de les escoles ordinàries, i presenta algunes propostes per abordar aquests procediments des de les perspectives relacionades amb els Plans Educatius Individualitzats en contextos diferents.

Creation and Validation of Chronojump-Boscosystem: A Free Tool to Measure Vertical Jumps

Measuring the height of the vertical jump is an indicator of the strength and power of the lower body. The technological tools available to measure the vertical jump are black boxes and are not open to third-party verification or adaptation. We propose the creation of a measurement system called Chronojump-Boscosystem, consisting of open hardware and free software. Methods: A microcontroller was created and validated using a square wave generator and an oscilloscope. Two types of contact platforms were developed using different materials. These platforms were validated by the minimum pressure required for activation at different points by a strain gauge, together with the on/off time of our platforms in respect of the Ergojump-Boscosystem platform by a sample of 8 subjects performing submaximal jumps with one foot on each platform. Agile methodologies were used to develop and validate the software. Results: All the tools fall under the free software / open hardware guidelines and are, in that sense, free. The microcontroller margin of error is 0.1%. The validity of the fiberglass platform is 0.95 (ICC). The management software contains nearly 113.000 lines of code and is available in 7 languages.

Educar els fills és molt complicat! Els malestars actuals de la socialització familiar

En les diferents recerques sobre la socialització familiar són cada vegada més habituals les referències dels progenitors catalans de classes mitjanes i altes a la complexitat, a les dificultats i a la tensió creixent que implica educar els fills i les filles. Sobre això, i amb la teoria de la civilització de Norbert Elias com a fil conductor, l’article es pregunta pels malestars que actualment travessa la socialització familiar i els posa en relació amb quin és l’objectiu del mateix procés en la nostra societat immersa en un capitalisme financer i flexible. Així, si la finalitat és la «socialització terciària» (Mead, 1964; Bateson, 1984), dins les famílies emergeixen un seguit de neguits i malestars lligats a l’autoritat, l’autonomia, els hàbits, els conflictes i els càstigs, les normes, les convencions i les prohibicions, etc. que, segons el parer de l’autor, cal comprendre dins del nou context social i econòmic i en relació amb els nous objectius de l’educació familiar de les famílies benestants catalanes.

Composition, nanostructure, and optical properties of silver and silver-copper lusters

Lusters are composite thin layers of coinage metal nanoparticles in glass displaying peculiar optical properties and obtained by a process involving ionic exchange, diffusion, and crystallization. In particular, the origin of the high reflectance (golden-shine) shown by those layers has been subject of some discussion. It has been attributed to either the presence of larger particles, thinner multiple layers or higher volume fraction of nanoparticles. The object of this paper is to clarify this for which a set of laboratory designed lusters are analysed by Rutherford backscattering spectroscopy, transmission electron microscopy, x-ray diffraction, and ultraviolet-visible spectroscopy. Model calculations and numerical simulations using the finite difference time domain method were also performed to evaluate the optical properties. Finally, the correlation between synthesis conditions, nanostructure, and optical properties is obtained for these materials.

Gene Promoter Evolution Targets the Center of the Human Protein Interaction Network

Assessing the contribution of promoters and coding sequences to gene evolution is an important step toward discovering the major genetic determinants of human evolution. Many specific examples have revealed the evolutionary importance of cis-regulatory regions. However, the relative contribution of regulatory and coding regions to the evolutionary process and whether systemic factors differentially influence their evolution remains unclear. To address these questions, we carried out an analysis at the genome scale to identify signatures of positive selection in human proximal promoters. Next, we examined whether genes with positively selected promoters (Prom+ genes) show systemic differences with respect to a set of genes with positively selected protein-coding regions (Cod+ genes). We found that the number of genes in each set was not significantly different (8.1% and 8.5%, respectively). Furthermore, a functional analysis showed that, in both cases, positive selection affects almost all biological processes and only a few genes of each group are located in enriched categories, indicating that promoters and coding regions are not evolutionarily specialized with respect to gene function. On the other hand, we show that the topology of the human protein network has a different influence on the molecular evolution of proximal promoters and coding regions. Notably, Prom+ genes have an unexpectedly high centrality when compared with a reference distribution (P = 0.008, for Eigenvalue centrality). Moreover, the frequency of Prom+ genes increases from the periphery to the center of the protein network (P = 0.02, for the logistic regression coefficient). This means that gene centrality does not constrain the evolution of proximal promoters, unlike the case with coding regions, and further indicates that the evolution of proximal promoters is more efficient in the center of the protein network than in the periphery. These results show that proximal promoters have had a systemic contribution to human evolution by increasing the participation of central genes in the evolutionary process.

Evolució dels nitrats analitzats a l'aigua de 87 fonts situades en 28 municipis de la comarca d'Osona

La comarca d’Osona ha disposat sempre d’aigua abundant i de bona qualitat, però en els darrers anys s’ha observat un increment del contingut de nitrats a les aigües subterrànies. Des de 1988 i fins a l’actualitat es mostreja puntualment l’aigua d’algunes fonts i se n’analitzen els nitrats. En aquest estudi s’analitza l’evolució del contingut de nitrats i com ha afectat a la mineralització de l’aigua d’aquestes fonts i en quin estat es troben actualment. La legislació actual (RD 140/2003) considera que valors de nitrats a l’aigua de consum superiors a 50 mg/l poden provocar problemes de salut pública.

El Sufragi femení a la premsa d' Osona (1931-1936)

La proclamació de la Segona República va obrir un ampli ventall de possibilitats a les dones catalanes i els va crear noves expectatives. D’entrada, la Constitució de 1931 els va atorgar el dret al vot en les mateixes condicions que als homes. Aquest article analitza el tractament del sufragi femení a tres periòdics d’Osona: el liberal Diari de Vic, el conservador la Gazeta de Vich i el setmanari obrerista Sembrar, tant des de la perspectiva dels periodistes homes, com de les dones que hi col·laboraven.