Ensemble and Greedy Approach for the Reconstruction of Large Gene Co-Expression Networks

In the recent years, the vast amount of genetic information generated by high-throughput approaches, have led to the need of new methods for data handling. The integrative analysis of diverse-nature gene information could provide a much-sought overview to study complex biological systems and processes. In this sense, Co-expression Gene Networks (CGN) have become a powerful tool in the comprehensive analysis of gene expression. Such networks represent relationships between genes (or gene products) by means of a graph composed of nodes and edges, where nodes represent genes and edges the relationships among them. Amongst the main features of CGN, sparseness and scale-free topology may notably affect the latter network analysis. Within this framework, structure optimization techniques are also important in the reduction of the size of the networks, not only improving their topology but also keeping a positive prediction ratio. On the other hand, ensemble strategies have significantly improved the precision of results by combining different measures or methods. In this work, we present Ensemble and Greedy networks (EnGNet), a novel two-step method for CGN inference. First, EnGNet uses an ensemble strategy for co-expression networks generation. Final score is estimated by major voting among three different methdos, i.e. Spearman and Kendall coefficients and Normalized Mutual Information. Second, a greedy algorithm optimizes both the size and the topological features of the network. Not only do achieved results show that this method is able to obtain reliable networks, but also that it significantly improves the topology of the networks. Moreover, the usefulness of the method is proven by an application to a human dataset on post-traumatic stress disorder (PTSD), revealing an innate immunity-mediated response to this pathology in accordance with previous studies. These results are indicative of the potential of CGN, and EnGNet in particular, in the unveiling of the genetic causes for complex diseases. Finally, the implications of CGN in biomarkers discovery, could lead research towards earlier detection and effective treatment of these diseases

Entanglement as a quantum order parameter

We show that the quantum order parameters (QOP) associated with the transitions between a normal conductor and a superconductor in the BCS and eta-pairing models and between a Mott-insulator and a superfluid in the Bose-Hubbard model are directly related to the amount of entanglement existent in the ground state of each system. This gives a physical meaningful interpretation to these QOP, which shows the intrinsically quantum nature of the phase transitions considered.Comment: 5 pages. No figures. Revised version. References adde

Avaliação dos recursos hospitalares para assistência perinatal em Belo Horizonte, Minas Gerais

OBJECTIVE: To verify the adequacy of hospital resources for perinatal care in Belo Horizonte, MG, Brazil in 1996. METHODS: This is a cross-sectional study conducted encompassing all the 28 maternity-hospitals in the city of Belo Horizonte, capital of the State of Minas Gerais, Brazil. A model of evaluation denominated "Níveis de Complexidade e Segurança em Potencial de Unidades Perinatais de Hospitais-Maternidade" [Levels of Complexity and Potential Safety in Maternity-Hospitals]. This model is based on the evaluation of three major areas in the hospital: general structure, perinatal clinical infra-structure and resources available in perinatal units. Two scores involving these three areas were created. When evaluating low risk perinatal care, the score may sum to a total of 1,000 points. On the other hand, when high to medium perinatal risk care is considered, the score may sum to 2,000 points. Hosptals that scored more than 500 points were classified in two levels: I-A and I-B (for low risk); and six levels I-A through III-B (for medium/high risk). RESULTS: Five hospitals were classified as level 0 according to the low risk score, that is, they were not considered adequate to assist any delivery. When the medium/high risk score was employed, a total of seven hospitals were considered inadequate to assist any delivery. CONCLUSIONS: This evaluation model was capable of classifying hospitals according to available infra-structure for perinatal care.OBJETIVO: Verificar a adequação de recursos hospitalares no atendimento às gestantes/neonatos, no ano de 1996. MÉTODOS: Trata-se de um estudo transversal abrangendo 28 hospitais-maternidade em funcionamento no município de Belo Horizonte, MG. Utilizou-se um modelo de avaliação denominado "níveis de complexidade e segurança em potencial de unidades perinatais de hospitais-maternidade", elaborado a partir da avaliação de três grandes áreas hospitalares: infra-estrutura geral, infra-estrutura clínica-perinatal e recursos das unidades perinatais. Foram desenvolvidos dois escores de pontos envolvendo essas áreas hospitalares, totalizando 1.000 pontos quando considerada a assistência perinatal de risco habitual e 2.000 pontos para assistência perinatal de médio/alto risco. A partir de 500 pontos, os hospitais foram classificados em dois níveis: I-A e I-B (para risco habitual) e seis níveis de I-A a III-B (para médio/alto risco). RESULTADOS: Na avaliação com o escore proposto para risco habitual, cinco hospitais foram considerados inadequados para realizarem atendimento a qualquer tipo de parto, classificados como nível zero; esse número aumentou para sete, quando se utilizou o escore para parto de médio/alto risco. CONCLUSÃO: O modelo de avaliação utilizado mostrou-se adequado para classificar os hospitais de acordo com a infra-estrutura disponível para assistência perinatal

Single chain magnet behaviour in an enantiopure chiral cobalt(II)–copper(II) one-dimensional compound

The self-assembly of an enantiomerically pure, chiral dianionic oxamatocopper(II) complex with cobalt(II) ions leads to neutral oxamato-bridged heterobimetallic chains that combine chirality and slow magnetic relaxation, providing thus the first example of ‘‘chiral single chain magnets (CSCMs).Ruiz Garcia, Rafael, [email protected] ; Lloret Pastor, Francisco, [email protected]

Engineering single-atom Fe-N active sites on hollow carbon spheres for oxygen reduction reaction

Seeking alternatives to noble metals-based electrocatalysts for oxygen reduction reaction (ORR), hollow carbon spheres (CSs) were finely tuned with stable single-atom Fe-N species through a synthesis methodology requiring only earth-abundant metal precursors. CSs with different sizes were synthesized by sol-gel polycondensation of resorcinol with formaldehyde over silica nanoparticles, followed by thermal annealing and silica etching. A catalyst screening revealed the positive impact of both the hollow core and structural defects of the CSs for ORR. Single-atom Fe-N active sites were introduced on the best performing CSs through simultaneous incorporation of iron and nitrogen precursors, and glucose. A significant enhancement in ORR activity was observed despite the small iron load introduced (0.12 wt%). ORR performance indicators, advanced characterization, and molecular simulation studies revealed nitrogen's crucial role in anchoring individual iron atoms and modulating the charge density nearby the active sites (increase of 80 mV in the half-wave potential). Adding glucose as a chelating agent enhances the metal-heteroatom coordination and subsequent dispersion of iron, accounting for an increase of 20 mV in the half-wave potential, an average of electrons transferred as high as 3.9 (at 0.4 V vs. RHE), and higher stability (99%) than that of a platinum-based (20 wt%) electrocatalyst (92%).11 página

Multiple Optical Elastography Techniques Reveal the Regulation of Corneal Stiffness by Collagen XII

9 pags., 5 figs., 1 tab.PURPOSE. Collagen XII plays a role in regulating the structure and mechanical properties of the cornea. In this work, several optical elastography techniques were used to investigate the effect of collagen XII deficiency on the stiffness of the murine cornea. METHODS. A three-prong optical elastography approach was used to investigate the mechanical properties of the cornea. Brillouin microscopy, air-coupled ultrasonic optical coherence elastography (OCE) and heartbeat OCE were used to assess the mechanical properties of wild type (WT) and collagen XII¿deficient (Col12a1¿/¿) murine corneas. The Brillouin frequency shift, elastic wave speed, and compressive strain were all measured as a function of intraocular pressure (IOP). RESULTS. All three optical elastography modalities measured a significantly decreased stiffness in the Col12a1¿/¿ compared to the WT (P < 0.01 for all three modalities). The optical coherence elastography techniques showed that mean stiffness increased as a function of IOP; however, Brillouin microscopy showed no discernable trend in Brillouin frequency shift as a function of IOP. CONCLUSIONS. Our approach suggests that the absence of collagen XII significantly softens the cornea. Although both optical coherence elastography techniques showed an expected increase in corneal stiffness as a function of IOP, Brillouin microscopy did not show such a relationship, suggesting that the Brillouin longitudinal modulus may not be affected by changes in IOP. Future work will focus on multimodal biomechanical models, evaluating the effects of other collagen types on corneal stiffness, and in vivo measurements.Supported by the National Institutes of Health, grant numbers R01EY022362, R01EY030063, R01EY029395, R01EY028666, and P30EY007551

Non-Invasive Assessment of Pulmonary Vasculopathy

Right heart catheterization remains necessary for the diagnosis of pulmonary hypertension and, therefore, for the prognostic evaluation of patients with chronic heart failure. The non-invaSive Assessment of Pulmonary vasculoPathy in Heart failure (SAPPHIRE) study was designed to assess the feasibility and prognostic relevance of a non-invasive evaluation of the pulmonary artery vasculature in patients with heart failure and pulmonary hypertension. Patients will undergo a right heart catheterization, cardiac resonance imaging, and a pulmonary function test in order to identify structural and functional parameters allowing the identification of combined pre- and postcapillary pulmonary hypertension, and correlate these findings with the hemodynamic dataThis research was funded by European Regional Development Fund and the Carlos III Research Institute through a grant of the Health Strategy Action (PI17/01569).S

Artículos publicados en el diario El País sobre Antonio Fernández Alba

Artículos publicados sobre Antonio Fernández Alba en el diario El Paí

How to stay together? Habitat use by three sympatric sharks in the western coast of Baja California Sur, Mexico

Sharks are top predators and play an important role in the regulation of marine ecosystems at lower trophic position. Mustelus californicus, Sphyrna zygaena, and Isurus oxyrinchus prove to be important fishery resources along the western coast of Baja California Sur and cohabit the same coastal areas, probably sharing resources. However, our knowledge about ecological dynamics of multiple species coexisting and sharing similar habitat resources is still limited, particularly for predators such as sharks. Therefore, this study focuses on the analysis of trophic ecology of the sharks species, using carbon (C) and nitrogen (N) stable isotope values in muscle tissues coupled with trace element concentration (Hg, Se, and Cd) in muscle and hepatic tissues of sharks. The values of δC (M. californicus −17.3 ± 1.1‰, S. zygaena −17.9 ± 0.5‰, and I. oxyrinchus −18.3 ± 0.3‰) and δN (M. californicus 18.2 ± 1.1‰, S. zygaena 18.4 ± 0.9‰, and I. oxyrinchus 17.8 ± 1.1‰) indicated that these species feed in the Gulf of Ulloa all throughout the year, and for extended periods with similar habitat use and trophic niche. The above-mentioned statement is also a conclusion supported by the significant correlation between isotopic and trace element concentrations in the muscular tissues in all studied species. Thus, the results of the present study emphasize the habitat and niche characteristics of three sympatric sharks off the coast of Baja California Sur, Mexico.The Instituto Politecnico Nacional (COFFA, EDI), CONA-CYT project 25370, Instituto Politecnico Nacional grants 20181417 and 20196736 and SIP20211002 and SIP2152 provided the fellowships to support this study

Erythropoietin reduces the expression of myostatin in mdx dystrophic mice

Erythropoietin (EPO) has been well characterized as a renal glycoprotein hormone regulating red blood cell production by inhibiting apoptosis of erythrocyte progenitors in hematopoietic tissues. EPO exerts regulatory effects in cardiac and skeletal muscles. Duchenne muscular dystrophy is a lethal degenerative disorder of skeletal and cardiac muscle. in this study, we tested the possible therapeutic beneficial effect of recombinant EPO (rhEPO) in dystrophic muscles in mdx mice. Total strength was measured using a force transducer coupled to a computer. Gene expression for myostatin, transforming growth factor-beta 1 (TGF-beta 1), and tumor necrosis factor-alpha (TNF-alpha) was determined by quantitative real time polymerase chain reaction. Myostatin expression was significantly decreased in quadriceps from mdx mice treated with rhEPO (rhEPO = 0.60 +/- 0.11, control= 1.07 +/- 0.11). On the other hand, rhEPO had no significant effect on the expression of TGF-beta 1 (rhEPO = 0.95 +/- 0.14, control= 1.05 +/- 0.16) and TNF-alpha (rhEPO = 0.73 +/- 0.20, control= 1.01 +/- 0.09). These results may help to clarify some of the direct actions of EPO on skeletal muscle.Fac Med ABC, BR-09060650 Santo Andre, SP, BrazilUniv São Paulo, Inst Ciencias Biomed, BR-05508 São Paulo, BrazilUniversidade Federal de São Paulo, Inst Ciencias Quim Ambientais & Farmaceut, Diadema, SP, BrazilUniversidade Federal de São Paulo, Inst Ciencias Quim Ambientais & Farmaceut, Diadema, SP, BrazilWeb of Scienc