A Tool for Integer Homology Computation: Lambda-At Model

In this paper, we formalize the notion of lambda-AT-model (where $\lambda$ is a non-null integer) for a given chain complex, which allows the computation of homological information in the integer domain avoiding using the Smith Normal Form of the boundary matrices. We present an algorithm for computing such a model, obtaining Betti numbers, the prime numbers p involved in the invariant factors of the torsion subgroup of homology, the amount of invariant factors that are a power of p and a set of representative cycles of generators of homology mod p, for each p. Moreover, we establish the minimum valid lambda for such a construction, what cuts down the computational costs related to the torsion subgroup. The tools described here are useful to determine topological information of nD structured objects such as simplicial, cubical or simploidal complexes and are applicable to extract such an information from digital pictures.Comment: Journal Image and Vision Computing, Volume 27 Issue 7, June, 200

Multiscale analysis of morphology and mechanics in tail tendon from the ZDSD rat model of type 2 diabetes

Type 2 diabetes (T2D) impacts multiple organ systems including the circulatory, renal, nervous and musculoskeletal systems. In collagen-based tissues, one mechanism that may be responsible for detrimental mechanical impacts of T2D is the formation of advanced glycation end products (AGEs) leading to increased collagen stiffness and decreased toughness, resulting in brittle tissue behavior. The purpose of this study was to investigate tendon mechanical properties from normal and diabetic rats at two distinct length scales, testing the hypothesis that increased stiffness and strength and decreased toughness at the fiber level would be associated with alterations in nanoscale morphology and mechanics. Individual fascicles from female Zucker diabetic Sprague-Dawley (ZDSD) rats had no differences in fascicle-level mechanical properties but had increased material-level strength and stiffness versus control rats (CD). At the nanoscale, collagen fibril D-spacing was shifted towards higher spacing values in diabetic ZDSD fibrils. The distribution of nanoscale modulus values was also shifted to higher values. Material-level strength and stiffness from whole fiber tests were increased in ZDSD tails. Correlations between nanoscale and microscale properties indicate a direct positive relationship between the two length scales, most notably in the relationship between nanoscale and microscale modulus. These findings indicate that diabetes-induced changes in material strength and modulus were driven by alterations at the nanoscale

The Nuclear and Circum-nuclear Stellar Population in Seyfert 2 Galaxies: Implications for the Starburst-AGN Connection

We report the results of a spectroscopic investigation of a sample of 20 of the brightest type 2 Seyfert nuclei. Our goal is to search for the direct spectroscopic signature of massive stars, and thereby probe the role of circumnuclear starbursts in the Seyfert phenomenon. The method used is based on the detection of the higher order Balmer lines and HeI lines in absorption and the Wolf-Rayet feature at $\sim$4680 \AA in emission. These lines are strong indicators of the presence of young (a few Myrs) and intermediate-age (a few 100 Myrs) stellar populations. In over half the sample, we have detected HeI and/or strong stellar absorption features in the high-order (near-UV) Balmer series together with relatively weak lines from an old stellar population. In three others we detect a broad emission feature near 4680 \AA that is most plausibly ascribed to a population of Wolf-Rayet stars (the evolved descendants of the most massive stars). We therefore conclude that the blue and near-UV light of over half of the sample is dominated by young and/or intermediate age stars. The ``young'' Seyfert 2's have have larger far-IR luminosities, cooler mid/far-IR colors, and smaller [OIII]/H$\beta$ flux ratios than the ``old'' ones. These differences are consistent with a starburst playing a significant energetic role in the former class. We consider the possibility that there may be two distinct sub-classes of Seyfert 2 nuclei (``starbursts'' and ``hidden BLR''). However, the fact that hidden BLRs have been found in three of the ``young'' nuclei argues against this, and suggests that nuclear starbursts may be a more general part of the Seyfert phenomenon.Comment: To be published in ApJ, 546, Jan 10, 200

Analysis of CMB maps with 2D wavelets

We consider the 2D wavelet transform with two scales to study sky maps of temperature anisotropies in the cosmic microwave background radiation (CMB). We apply this technique to simulated maps of small sky patches of size 12.8 \times 12.8 square degrees and 1.5' \times 1.5' pixels. The relation to the standard approach, based on the cl's is established through the introduction of the scalogram. We consider temperature fluctuations derived from standard, open and flat-Lambda CDM models. We analyze CMB anisotropies maps plus uncorrelated Gaussian noise (uniform and non-uniform) at idfferent S/N levels. We explore in detail the denoising of such maps and compare the results with other techniques already proposed in the literature. Wavelet methods provide a good reconstruction of the image and power spectrum. Moreover, they are faster than previously proposed methods.Comment: latex file 7 pages + 5 postscript files + 1 gif file; accepted for publication in A&A

Unifying phantom inflation with late-time acceleration: scalar phantom-non-phantom transition model and generalized holographic dark energy

The unifying approach to early-time and late-time universe based on phantom cosmology is proposed. We consider gravity-scalar system which contains usual potential and scalar coupling function in front of kinetic term. As a result, the possibility of phantom-non-phantom transition appears in such a way that universe could have effectively phantom equation of state at early time as well as at late time. In fact, the oscillating universe may have several phantom and non-phantom phases. As a second model we suggest generalized holographic dark energy where infrared cutoff is identified with combination of FRW parameters: Hubble constant, particle and future horizons, cosmological constant and universe life-time (if finite). Depending on the specific choice of the model the number of interesting effects occur: the possibility to solve the coincidence problem, crossing of phantom divide and unification of early-time inflationary and late-time accelerating phantom universe. The bound for holographic entropy which decreases in phantom era is also discussed.Comment: 13 pages, clarifications/refs added, to match with published versio

The Structure and Star-Formation History of NGC 5461

We compute photoionization models for the giant extragalactic H II region NGC 5461, and compare their predictions to several observational constraints. Since we aim at reproducing not only the global properties of the region, but its local structure also, the models are constrained to reproduce the observed density profile, and our analysis takes into consideration the bias introduced by the shapes and sizes of the slits used by different observers. We find that an asymmetric nebula with a gaussian density distribution, powered by a young burst of 3.1 Myr, satisfactorily reproduces most of the constraints, and that the star-formation efficiency inferred from the model agrees with current estimates. Our results strongly depend on the assumed density law, since constant density models overestimate the hardness of the ionizing field, affecting the deduced properties of the central stellar cluster. We illustrate the features of our best model, and discuss the possible sources of errors and uncertainties affecting the outcome of this type of studies.Comment: 33 pages (LaTeX), 3 .eps figures. to be published in ApJ, May 200

Low accumulation of L90M in protease from subtype FHIV-1 with resistance to protease inhibitors is caused by the L89M polymorphism

Background. This work evaluates the role of subtype F human immunodeficiency virus type 1 (HIV-1) protease ( PR) substitutions L89M and L90M in viral replication and resistance to PR inhibitors (PIs).Methods. Subtype B and F PR genes were subjected to site-directed mutagenesis, to create and reverse the methionine at positions 89 and 90. Viruses were re-created in cell culture, and their replicative capacity was assessed by fitness assay. Generated viruses were also phenotyped for PI resistance.Results. the subtype F clone (89M90L) showed a replicative capacity comparable to that of the PI-susceptible subtype B clone (89L90L) and was more fit than the L89M mutated subtype B clone ( 89M90L). Both 89M90M subtype B and F clones presented the lowest fitness s values. the L89M mutation impacted phenotypic resistance to all PIs in half of the subtype F isolates but not in the subtype B isolates. Subtype F isolates presented a phenotypic profile similar to that of subtype B isolates when the M89L mutation was introduced.Conclusion. the L89M mutation in subtype F viruses is a high genetic barrier to the accumulation of the L90M resistance mutation and can function as a resistance mutation, depending on the presence of other polymorphisms in the subtype F PR backbone.Univ Fed Rio de Janeiro, Dept Genet, Mol Virol Lab, Inst Biol, BR-21944970 Rio de Janeiro, BrazilUniv Fed Rio de Janeiro, Inst Chem, Dept Inorgan Chem, BR-21944970 Rio de Janeiro, BrazilUniv Fed Rio Grande Sul, Ctr Biotechnol, Porto Alegre, RS, BrazilUniversidade Federal de São Paulo, Retrovirol Lab, São Paulo, BrazilUniversidade Federal de São Paulo, Retrovirol Lab, São Paulo, BrazilWeb of Scienc

Broken R-parity, stop decays, and neutrino physics

We discuss the phenomenology of the lightest stop in models where R-parity is broken by bilinear superpotential terms. In this class of models we consider scenarios where the R-parity breaking two-body decay ~t_1->\tau^+b competes with the leading three-body decays such as ~t_1->W^+b~\chi^0_1. We demonstrate that the R-parity violating decay can be sizable and in some parts of the parameter space even the dominant one. Moreover we discuss the expectations for \~t_1->\mu^+b and ~t_1->e^+b. The recent results from solar and atmospheric neutrinos suggest that these are as important as the tau bottom mode. The \~t_1->l^+b decays are of particular interest for hadron colliders, as they may allow a full mass reconstruction of the lighter stop. Moreover these decay modes allow cross checks on the neutrino mixing angle involved in the solar neutrino puzzle complementary to those possible using neutralino decays. For the so--called small mixing angle or SMA solution ~t_1->e^+b should be negligible, while for the large mixing angle type solutions all ~t_1->l^+b decays should have comparable magnitude.Comment: 51 pages, 6 figures, LaTeX2e and RevTeX4, published versio

Modeling complex metabolic reactions, ecological systems, and financial and legal networks with MIANN models based on Markov-Wiener node descriptors

[Abstract] The use of numerical parameters in Complex Network analysis is expanding to new fields of application. At a molecular level, we can use them to describe the molecular structure of chemical entities, protein interactions, or metabolic networks. However, the applications are not restricted to the world of molecules and can be extended to the study of macroscopic nonliving systems, organisms, or even legal or social networks. On the other hand, the development of the field of Artificial Intelligence has led to the formulation of computational algorithms whose design is based on the structure and functioning of networks of biological neurons. These algorithms, called Artificial Neural Networks (ANNs), can be useful for the study of complex networks, since the numerical parameters that encode information of the network (for example centralities/node descriptors) can be used as inputs for the ANNs. The Wiener index (W) is a graph invariant widely used in chemoinformatics to quantify the molecular structure of drugs and to study complex networks. In this work, we explore for the first time the possibility of using Markov chains to calculate analogues of node distance numbers/W to describe complex networks from the point of view of their nodes. These parameters are called Markov-Wiener node descriptors of order kth (Wk). Please, note that these descriptors are not related to Markov-Wiener stochastic processes. Here, we calculated the Wk(i) values for a very high number of nodes (>100,000) in more than 100 different complex networks using the software MI-NODES. These networks were grouped according to the field of application. Molecular networks include the Metabolic Reaction Networks (MRNs) of 40 different organisms. In addition, we analyzed other biological and legal and social networks. These include the Interaction Web Database Biological Networks (IWDBNs), with 75 food webs or ecological systems and the Spanish Financial Law Network (SFLN). The calculated Wk(i) values were used as inputs for different ANNs in order to discriminate correct node connectivity patterns from incorrect random patterns. The MIANN models obtained present good values of Sensitivity/Specificity (%): MRNs (78/78), IWDBNs (90/88), and SFLN (86/84). These preliminary results are very promising from the point of view of a first exploratory study and suggest that the use of these models could be extended to the high-throughput re-evaluation of connectivity in known complex networks (collation)

Thermodynamics and dark energy

A significant observational effort has been directed to unveil the nature of the so-called dark energy. However, given the large number of theoretical possibilities, it is possible that such a task cannot be performed on the basis only of the observational data. In this article we discuss some thermodynamic properties of this energy component by assuming that its constituents are massless quanta with a general time-dependent equation-of-state parameter $\omega(z)=\omega_0 + \omega_a f(z)$, where $\omega_0$ and $\omega_a$ are constants and $f(z)$ may assume different forms. We show that very restrictive bounds can be placed on the $w_0$ - $w_a$ space when current observational data are combined with the thermodynamic constraints derived.Comment: 5 pages, 3 figures, LaTe