Evaluation of algorithms used to order markers on genetic maps

When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results. Heredity (2009) 103, 494-502; doi:10.1038/hdy.2009.96; published online 29 July 2009

Generation and Analysis of Interaction Energy Maps of p-Substituted Benzoic Acid [(5-Nitro-thiophen-2-yl)-methylene]-Hydrazides Active against MRSA

In this preliminary study eighteen p-substituted benzoic acid [(5-nitro-thiophen-2-yl)-methylene]-hydrazides with antimicrobial activity were evaluated against multidrug-resistant Staphylococcus aureus, correlating the three-dimensional characteristics of the ligands with their respective bioactivities. The computer programs Sybyl and CORINA were used, respectively, for the design and three-dimensional conversion of the ligands. Molecular interaction fields were calculated using GRID program. Calculations using Volsurf resulted in a statistically consistent model with 48 structural descriptors showing that hydrophobicity is a fundamental property in the analyzed biological response.

Application of thermal sums concept to estimate the time to harvest new banana hybrids for export

Application of the thermal sum concept was developed to determine the optimal harvesting stage of new banana hybrids to be grown for export. It was tested on two triploid hybrid bananas, FlhorBan 916 (F916) and FlhorBan 918 (F918), created by CIRAD`s banana breeding programme, using two different approaches. The first approach was used with F916 and involved calculating the base temperature of bunches sampled at two sites at the ripening stage, and then determining the thermal sum at which the stage of maturity would be identical to that of the control Cavendish export banana. The second approach was used to assess the harvest stage of F918 and involved calculating the two thermal parameters directly, but using more plants and a longer period. Using the linear regression model, the estimated thermal parameters were a thermal sum of 680 degree-days (dd) at a base temperature of 17.0 degrees C for cv. F916, and 970 dd at 13.9 degrees C for cv. F918. This easy-to-use method provides quick and reliable calculations of the two thermal parameters required at a specific harvesting stage for a given banana variety in tropical climate conditions. Determining these two values is an essential step for gaining insight into the agronomic features of a new variety and its potential for export. (C) 2011 Elsevier B.V. All rights reserved.

Self-Organizing Maps as a New Tool for Classification of Plants at Lower Hierarchical Levels

A chemotaxonomic analysis is described of a database containing various types of compounds from the Heliantheae tribe (Asteraceae) using Self-Organizing Maps (SOM). The numbers of occurrences of 9 chemical classes in different taxa of the tribe were used as variables. The study shows that SOM applied to chemical data can contribute to differentiate genera, subtribes, and groups of subtribes (subtribe branches), as well as to tribal and subtribal classifications of Heliantheae, exhibiting a high hit percentage comparable to that of an expert performance, and in agreement with the previous tribe classification proposed by Stuessy.

Stability property of matchings is a natural solution concept in coalitional market games

Stability of matchings was proved to be a new cooperative equilibrium concept in Sotomayor (Dynamics and equilibrium: essays in honor to D. Gale, 1992). That paper introduces the innovation of treating as multi-dimensional the payoff of a player with a quota greater than one. This is done for the many-to-many matching model with additively separable utilities, for which the stability concept is defined. It is then proved, via linear programming, that the set of stable outcomes is nonempty and it may be strictly bigger than the set of dual solutions and strictly smaller than the core. The present paper defines a general concept of stability and shows that this concept is a natural solution concept, stronger than the core concept, for a much more general coalitional game than a matching game. Instead of mutual agreements inside partnerships, the players are allowed to make collective agreements inside coalitions of any size and to distribute his labor among them. A collective agreement determines the level of labor at which the coalition operates and the division, among its members, of the income generated by the coalition. An allocation specifies a set of collective agreements for each player.

The pareto-stability concept is a natural solution concept for discrete matching markets with indifferences

In a decentralized setting the game-theoretical predictions are that only strong blockings are allowed to rupture the structure of a matching. This paper argues that, under indifferences, also weak blockings should be considered when these blockings come from the grand coalition. This solution concept requires stability plus Pareto optimality. A characterization of the set of Pareto-stable matchings for the roommate and the marriage models is provided in terms of individually rational matchings whose blocking pairs, if any, are formed with unmatched agents. These matchings always exist and give an economic intuition on how blocking can be done by non-trading agents, so that the transactions need not be undone as agents reach the set of stable matchings. Some properties of the Pareto-stable matchings shared by the Marriage and Roommate models are obtained.

Pentafecta: A New Concept for Reporting Outcomes of Robot-Assisted Laparoscopic Radical Prostatectomy

Background: Widespread use of prostate-specific antigen screening has resulted in younger and healthier men being diagnosed with prostate cancer. Their demands and expectations of surgical intervention are much higher and cannot be adequately addressed with the classic trifecta outcome measures. Objective: A new and more comprehensive method for reporting outcomes after radical prostatectomy, the pentafecta, is proposed. Design, setting, and participants: From January 2008 through September 2009, details of 1111 consecutive patients who underwent robot-assisted radical prostatectomy performed by a single surgeon were retrospectively analyzed. Of 626 potent men, 332 who underwent bilateral nerve sparing and who had 1 yr of follow-up were included in the study group. Measurements: In addition to the traditional trifecta outcomes, two perioperative variables were included in the pentafecta: no postoperative complications and negative surgical margins. Patients who attained the trifecta and concurrently the two additional outcomes were considered as having achieved the pentafecta. A logistic regression model was created to evaluate independent factors for achieving the pentafecta. Results and limitations: Continence, potency, biochemical recurrence-free survival, and trifecta rates at 12 mo were 96.4%, 89.8%, 96.4%, and 83.1%, respectively. With regard to the perioperative outcomes, 93.4% had no postoperative complication and 90.7% had negative surgical margins. The pentafecta rate at 12 mo was 70.8%. On multivariable analysis, patient age (p = 0.001) was confirmed as the only factor independently associated with the pentafecta. Conclusions: A more comprehensive approach for reporting prostate surgery outcomes, the pentafecta, is being proposed. We believe that pentafecta outcomes more accurately represent patients` expectations after minimally invasive surgery for prostate cancer. This approach may be beneficial and may be used when counseling patients with clinically localized disease. (C) 2011 European Association of Urology. Published by Elsevier B. V. All rights reserved.

XMM-Newton temperature maps for five intermediate redshift clusters of galaxies

We have analyzed XMM-Newton archive data for five clusters of galaxies (redshifts 0.223-0.313) covering a wide range of dynamical states, from relaxed objects to clusters undergoing several mergers. We present here temperature maps of the X-ray gas together with a preliminary interpretation of the formation history of these clusters. (c) 2007 COSPAR. Published by Elsevier Ltd. All rights reserved.

A two-armed pattern in flickering maps of the nova-like variable UU aquarii

We report the analysis of a uniform sample of 31 light curves of the nova-like variable UU Aqr with eclipse-mapping techniques. The data were combined to derive eclipse maps of the average steady-light component, the long-term brightness changes, and the low- and high-frequency flickering components. The long-term variability responsible for the ""low-brightness`` and ""high-brightness`` states is explained in terms of the response of a viscous disk to changes of 20%-50% in the mass transfer rate from the donor star. Low- and high-frequency flickering maps are dominated by emission from two asymmetric arcs reminiscent of those seen in the outbursting dwarf nova IP Peg, and they are similarly interpreted as manifestations of a tidally induced spiral shock wave in the outer regions of a large accretion disk. The asymmetric arcs are also seen in the map of the steady light aside from the broad brightness distribution of a roughly steady-state disk. The arcs account for 25% of the steady-light flux and are a long-lasting feature in the accretion disk of UU Aqr. We infer an opening angle of 10 degrees +/- 3 degrees for the spiral arcs. The results suggest that the flickering in UU Aqr is caused by turbulence generated after the collision of disk gas with the density-enhanced spiral wave in the accretion disk.

A novel locus for split-hand/foot malformation associated with tibial hemimelia (SHFLD syndrome) maps to chromosome region 17p13.1-17p13.3

Split-hand/foot malformation (SHFM) associated with aplasia of long bones, SHFLD syndrome or Tibial hemimelia-ectrodactyly syndrome is a rare condition with autosomal dominant inheritance, reduced penetrance and an incidence estimated to be about 1 in 1,000,000 liveborns. To date, three chromosomal regions have been reported as strong candidates for harboring SHFLD syndrome genes: 1q42.2-q43, 6q14.1 and 2q14.2. We characterized the phenotype of nine affected individuals from a large family with the aim of mapping the causative gene. Among the nine affected patients, four had only SHFM of the hands and no tibial defects, three had both defects and two had only unilateral tibial hemimelia. In keeping with previous publications of this and other families, there was clear evidence of both variable expression and incomplete penetrance, the latter bearing hallmarks of anticipation. Segregation analysis and multipoint Lod scores calculations (maximum Lod score of 5.03 using the LINKMAP software) using all potentially informative family members, both affected and unaffected, identified the chromosomal region 17p13.1-17p13.3 as the best and only candidate for harboring a novel mutated gene responsible for the syndrome in this family. The candidate gene CRK located within this region was sequenced but no pathogenic mutation was detected.

Neuronal Expression of Cd36, Cd44, and Cd83 Antigen Transcripts Maps to Distinct and Specific Murine Brain Circuits

Cells recruited by the innate immune response rely on surface-expressed molecules in order to receive signals from the local environment and to perform phagocytosis, cell adhesion, and others processes linked to host defense. Hundreds of surface antigens designated through a cluster of differentiation (CD) number have been used to identify particular populations of leukocytes. Surprisingly, we verified that the genes that encode Cd36 and Cd83 are constitutively expressed in specific neuronal cells. For instance, Cd36 mRNA is expressed in some regions related to circuitry involved in pheromone responses and reproductive behavior. Cd44 expression, reanalyzed and detailed here, is associated with the laminar formation and midline thalamic nuclei in addition to striatum, extended amygdala, and a few hypothalamic, cortical, and hippocampal regions. A systemic immune challenge was able to increase Cd44 expression quickly in the area postrema and motor nucleus of the vagus but not in regions presenting expressive constitutive expression. In contrast to Cd36 and Cd44, Cd83 message was widely distributed from the olfactory bulb to the brain stem reticular formation, sparing the striatopallidum, olivary region, and cerebellum. Its pattern of expression nevertheless remained strongly associated with hypothalamic, thalamic, and hindbrain nuclei. Unlike the other transcripts, Cd83 mRNA was rapidly modulated by restraint stress. Our results indicate that these molecules might play a role in specific neural circuits and present functions other than those attributed to leukocyte biology. The data also suggest that these surface proteins, or their associated mRNA, could be used to label neurons in specific circuits/regions. J. Comp. Neurol. 517:906-924, 2009. (C) 2009 Wiley-Liss, Inc.

ROOT PROBLEM FOR CONVENIENT MAPS

In this paper we study when the minimal number of roots of the so-called convenient maps horn two-dimensional CW complexes into closed surfaces is zero We present several necessary and sufficient conditions for such a map to be root free Among these conditions we have the existence of specific fittings for the homomorphism induced by the map on the fundamental groups, existence of the so-called mutation of a specific homomorphism also induced by the map, and existence of particular solutions of specific systems of equations on free groups over specific subgroups

Strong surjectivity of maps from 2-complexes into the 2-sphere

Given a model 2-complex K(P) of a group presentation P, we associate to it an integer matrix Delta(P) and we prove that a cellular map f : K(P) -> S(2) is root free (is not strongly surjective) if and only if the diophantine linear system Delta(P) Y = (deg) over right arrow (f) has an integer solution, here (deg) over right arrow (f) is the so-called vector-degree of f

An extension of the concept of gradient semigroups which is stable under perturbation

In this article we introduce the concept of a gradient-like nonlinear semigroup as an intermediate concept between a gradient nonlinear semigroup (those possessing a Lyapunov function, see [J.K. Hale, Asymptotic Behavior of Dissipative Systems, Math. Surveys Monogr., vol. 25, Amer. Math. Soc., 1989]) and a nonlinear semigroup possessing a gradient-like attractor. We prove that a perturbation of a gradient-like nonlinear semigroup remains a gradient-like nonlinear semigroup. Moreover, for non-autonomous dynamical systems we introduce the concept of a gradient-like evolution process and prove that a non-autonomous perturbation of a gradient-like nonlinear semigroup is a gradient-like evolution process. For gradient-like nonlinear semigroups and evolution processes, we prove continuity, characterization and (pullback and forwards) exponential attraction of their attractors under perturbation extending the results of [A.N. Carvalho, J.A. Langa, J.C. Robinson, A. Suarez, Characterization of non-autonomous attractors of a perturbed gradient system, J. Differential Equations 236 (2007) 570-603] on characterization and of [A.V. Babin, M.I. Vishik, Attractors in Evolutionary Equations, Stud. Math. Appl.. vol. 25, North-Holland, Amsterdam, 1992] on exponential attraction. (C) 2009 Elsevier Inc. All rights reserved.

Integrable maps with non-trivial topology: application to divertor configurations

We explore a method for constructing two-dimensional area-preserving, integrable maps associated with Hamiltonian systems, with a given set of fixed points and given invariant curves. The method is used to find an integrable Poincare map for the field lines in a large aspect ratio tokamak with a poloidal single-null divertor. The divertor field is a superposition of a magnetohydrodynamic equilibrium with an arbitrarily chosen safety factor profile, with a wire carrying an electric current to create an X-point. This integrable map is perturbed by an impulsive perturbation that describes non-axisymmetric magnetic resonances at the plasma edge. The non-integrable perturbed map is applied to study the structure of the open field lines in the scrape-off layer, reproducing the main transport features obtained by integrating numerically the magnetic field line equations, such as the connection lengths and magnetic footprints on the divertor plate.