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

Prevalence of baseline polymorphisms for potential resistance to NS5A inhibitors in drug-naive individuals infected with hepatitis C genotypes 1–4

Background: The non-structural 5A (NS5A) protein of HCV is a multifunctional phosphoprotein involved in regulation of viral replication and virion assembly. NS5A inhibitors targeting domain I of NS5A protein have demonstrated high potency and pan-genotypic antiviral activity, however they possess a low genetic barrier to resistance. At present, only genotype 1, the most prevalent HCV genotype has been studied in detail for resistant variants. Methods: Utilising a panel of genotypic-specific resistance assays, population sequencing was performed on plasma derived viral RNA isolated from 138 patients infected with HCV genotypes 1-4 and not treated with directly acting anti-viral agents (DAAs). Amino acid changes in HCV NS5A domain I at codon positions 28, 30, 31, 32 and 93, reported to confer reduced susceptibility to certain NS5A inhibitors were examined. Additionally, genotypic outcome based on NS5A sequences were compared with LiPA and Abbott® real time. Results: Amino acid substitutions associated with moderate to high level resistance to NS5A inhibitors were detected in 2/42 (4.76%) HCV-1a, 3/23 (13.04%) HCV-1b, 4/26 ( 15.38% ) HCV-2, 1/24 (4.17%) HCV-3 and 1/23 (4.35%) HCV-4 infected patients who had not been treated with NS5A inhibitors. Genotype prediction based on NS5A sequences were concordant with LiPA and/or Abbott® real-time for 97.10% of cases. Conclusion: Primary resistance mutations associated with resistance to first generation NS5A inhibitors such as Daclatasvir (DCV) were observed in all genotypes, albeit at low frequencies. An excellent correlation based on NS5A genotyping and LiPA or Abbott® real-time was achieved

Semiparametric theory and empirical processes in causal inference

In this paper we review important aspects of semiparametric theory and empirical processes that arise in causal inference problems. We begin with a brief introduction to the general problem of causal inference, and go on to discuss estimation and inference for causal effects under semiparametric models, which allow parts of the data-generating process to be unrestricted if they are not of particular interest (i.e., nuisance functions). These models are very useful in causal problems because the outcome process is often complex and difficult to model, and there may only be information available about the treatment process (at best). Semiparametric theory gives a framework for benchmarking efficiency and constructing estimators in such settings. In the second part of the paper we discuss empirical process theory, which provides powerful tools for understanding the asymptotic behavior of semiparametric estimators that depend on flexible nonparametric estimators of nuisance functions. These tools are crucial for incorporating machine learning and other modern methods into causal inference analyses. We conclude by examining related extensions and future directions for work in semiparametric causal inference

Chain Homotopies for Object Topological Representations

This paper presents a set of tools to compute topological information of simplicial complexes, tools that are applicable to extract topological information from digital pictures. A simplicial complex is encoded in a (non-unique) algebraic-topological format called AM-model. An AM-model for a given object K is determined by a concrete chain homotopy and it provides, in particular, integer (co)homology generators of K and representative (co)cycles of these generators. An algorithm for computing an AM-model and the cohomological invariant HB1 (derived from the rank of the cohomology ring) with integer coefficients for a finite simplicial complex in any dimension is designed here. A concept of generators which are "nicely" representative cycles is also presented. Moreover, we extend the definition of AM-models to 3D binary digital images and we design algorithms to update the AM-model information after voxel set operations (union, intersection, difference and inverse)

Radiative Mechanism to Light Fermion Masses in the MSSM

In a previous work we have showed that the ${\cal Z}_{2}^{\prime}$ Symmetry, imply that the light fermions, the electron and the quarks, $u,d$ and $s$, get their masses only at one loop level. Here, we considere the more general hypothesis for flavour mixing in the sfermion sector in the MSSM. Then, we present our results to the masses of these light fermions and as a final result we can explain why the $s$ quark is heavier than the $u,d$ quarks. This mechanism is in agrement with the experimental constraint on the sfermion's masses values.Comment: 22 pages, 8 figures, TeX mistakes corrected, accepted for publication in JHE

PAMELA, DAMA, INTEGRAL and Signatures of Metastable Excited WIMPs

Models of dark matter with ~ GeV scale force mediators provide attractive explanations of many high energy anomalies, including PAMELA, ATIC, and the WMAP haze. At the same time, by exploiting the ~ MeV scale excited states that are automatically present in such theories, these models naturally explain the DAMA/LIBRA and INTEGRAL signals through the inelastic dark matter (iDM) and exciting dark matter (XDM) scenarios, respectively. Interestingly, with only weak kinetic mixing to hypercharge to mediate decays, the lifetime of excited states with delta < 2 m_e is longer than the age of the universe. The fractional relic abundance of these excited states depends on the temperature of kinetic decoupling, but can be appreciable. There could easily be other mechanisms for rapid decay, but the consequences of such long-lived states are intriguing. We find that CDMS constrains the fractional relic population of ~100 keV states to be <~ 10^-2, for a 1 TeV WIMP with sigma_n = 10^-40 cm^2. Upcoming searches at CDMS, as well as xenon, silicon, and argon targets, can push this limit significantly lower. We also consider the possibility that the DAMA excitation occurs from a metastable state into the XDM state, which decays via e+e- emission, which allows lighter states to explain the INTEGRAL signal due to the small kinetic energies required. Such models yield dramatic signals from down-scattering, with spectra peaking at high energies, sometimes as high as ~1 MeV, well outside the usual search windows. Such signals would be visible at future Ar and Si experiments, and may be visible at Ge and Xe experiments. We also consider other XDM models involving ~ 500 keV metastable states, and find they can allow lighter WIMPs to explain INTEGRAL as well.Comment: 22 pages, 7 figure

A hypothesis of a redistribution of North Atlantic swordfish based on changing ocean conditions

Conflicting trends in indices of abundance for North Atlantic swordfish starting in the mid-to late 1990s, in the form of fleet specific catch-per-unit-effort (CPUE), suggest the possibility of a spatial shift in abundance to follow areas of preferred temperature. The observed changes in the direction of the CPUEs correspond with changes in trends in the summer Atlantic Multidecadal Oscillation (AMO), a long term mode of variability of North Atlantic sea surface temperature. To test the hypothesis of a relation between the CPUE and the AMO, the CPUEs were made spatially explicit by re-estimating using an “areas-as-fleets” approach. These new CPUEs were then used to create alternative stock histories. The residuals of the fit were then regressed against the summer AMO. Significant, and opposite, relations were found in the regressions between eastern and western Atlantic areas. When the AMO was in a warm phase, the CPUEs in the western (eastern) areas were higher (lower) than predicted by the assessment model fit. Given the observed temperature tolerance limits of swordfish, it is possible that either their preferred habitat, prey species, or both have shifted spatial distributions resulting in conflicting CPUE indices. Because the available CPUE time series only overlaps with one change in the sign of the AMO (~1995), it is not clear whether this is a directional or cyclical trend. Given the relatively localized nature of many of the fishing fleets, and the difficulty of separating fleet effects from changes in oceanography we feel that it is critical to create CPUE indices by combining data across similar fleets that fish in similar areas. This approach allowed us to evaluate area-specific catch rates which provided the power to detect basin-wide responses to changing oceanography, a critical step for providing robust management advice in a changing climate.Postprin

Flavor changing single top quark production channels at e^+e^- colliders in the effective Lagrangian description

We perform a global analysis of the sensitivity of LEP2 and e^+e^- colliders with a c.m. energy in the range 500 - 2000 GeV to new flavor-changing single top quark production in the effective Lagrangian approach. The processes considered are sensitive to new flavor-changing effective vertices such as Ztc, htc, four-Fermi tcee contact terms as well as a right-handed Wtb coupling. We show that e^+ e^- colliders are most sensitive to the physics responsible for the contact tcee vertices. For example, it is found that the recent data from the 189 GeV LEP2 run can be used to rule out any new flavor physics that can generate these four-Fermi operators up to energy scales of \Lambda > 0.7 - 1.4 TeV, depending on the type of the four-Fermi interaction. We also show that a corresponding limit of \Lambda > 1.3 - 2.5 and \Lambda > 17 - 27 TeV can be reached at the future 200 GeV LEP2 run and a 1000 GeV e^+e^- collider, respectively. We note that these limits are much stronger than the typical limits which can be placed on flavor diagonal four-Fermi couplings. Similar results hold for \mu^+\mu^- colliders and for tu(bar) associated production. Finally we briefly comment on the necessity of measuring all flavor-changing effective vertices as they can be produced by different types of heavy physics.Comment: 34 pages, plain latex, 7 figures embadded in the text using epsfig. Added new references and discussions regarding their relevance to the paper. Added more comments on the comparison between flavor-changing and flavor-diagonal contact terms and on the importance of measuring the Ztc verte

The VLT-FLAMES survey of massive stars: observations in the Galactic clusters NGC3293, NGC4755 and NGC6611

We introduce a new survey of massive stars in the Galaxy and the Magellanic Clouds using the Fibre Large Array Multi-Element Spectrograph (FLAMES) instrument at the Very Large Telescope (VLT). Here we present observations of 269 Galactic stars with the FLAMES-Giraffe Spectrograph (R ~ 25,000), in fields centered on the open clusters NGC 3293, NGC 4755 and NGC 6611. These data are supplemented by a further 50 targets observed with the Fibre-Fed Extended Range Optical Spectrograph (FEROS, R = 48,000). Following a description of our scientific motivations and target selection criteria, the data reduction methods are described; of critical importance the FLAMES reduction pipeline is found to yield spectra that are in excellent agreement with less automated methods. Spectral classifications and radial velocity measurements are presented for each star, with particular attention paid to morphological peculiarities and evidence of binarity. These observations represent a significant increase in the known spectral content of NGC 3293 and NGC 4755, and will serve as standards against which our subsequent FLAMES observations in the Magellanic Clouds will be compared.Comment: 26 pages, 9 figures (reduced size). Accepted for publication in A&A. A copy with full res. figures is available from http://www.ing.iac.es/~cje/flames_mw.ps.gz. Minor changes following correction of proof