Genome-wide transcription analysis of clinal genetic variation in Drosophila.

Clinal variation in quantitative traits is widespread, but its genetic basis awaits identification. Drosophila melanogaster shows adaptive, clinal variation in traits such as body size along latitudinal gradients on multiple continents. To investigate genome wide transcription differentiation between North and South that might contribute to the clinal phenotypic variation, we compared RNA expression patterns during development of D. melanogaster from tropical northern and temperate southern populations using whole genome tiling arrays. We found that genes that were differentially expressed between the cline ends were generally associated with metabolism and growth, and experimental alteration of expression of a sample of them generally resulted in altered body size in the predicted direction, sometimes significantly so. We further identified the serpent (srp) transcription factor binding sites to be enriched near genes up-regulated in expression in the south. Analysis of clinal populations revealed a significant cline in the expression level of srp. Experimental over-expression of srp increased body size, as predicted from its clinal expression pattern, suggesting that it may be involved in regulating adaptive clinal variation in Drosophila. This study identified a handful of genes that contributed to clinal phenotypic variation through altered gene expression level, yet misexpression of individual gene led to modest body size change

Thermodynamic analysis of black hole solutions in gravitating nonlinear electrodynamics

We perform a general study of the thermodynamic properties of static electrically charged black hole solutions of nonlinear electrodynamics minimally coupled to gravitation in three space dimensions. The Lagrangian densities governing the dynamics of these models in flat space are defined as arbitrary functions of the gauge field invariants, constrained by some requirements for physical admissibility. The exhaustive classification of these theories in flat space, in terms of the behaviour of the Lagrangian densities in vacuum and on the boundary of their domain of definition, defines twelve families of admissible models. When these models are coupled to gravity, the flat space classification leads to a complete characterization of the associated sets of gravitating electrostatic spherically symmetric solutions by their central and asymptotic behaviours. We focus on nine of these families, which support asymptotically Schwarzschild-like black hole configurations, for which the thermodynamic analysis is possible and pertinent. In this way, the thermodynamic laws are extended to the sets of black hole solutions of these families, for which the generic behaviours of the relevant state variables are classified and thoroughly analyzed in terms of the aforementioned boundary properties of the Lagrangians. Moreover, we find universal scaling laws (which hold and are the same for all the black hole solutions of models belonging to any of the nine families) running the thermodynamic variables with the electric charge and the horizon radius. These scale transformations form a one-parameter multiplicative group, leading to universal "renormalization group"-like first-order differential equations. The beams of characteristics of these equations generate the full set of black hole states associated to any of these gravitating nonlinear electrodynamics...Comment: 51 single column pages, 19 postscript figures, 2 tables, GRG tex style; minor corrections added; final version appearing in General Relativity and Gravitatio

Climate Dynamics: A Network-Based Approach for the Analysis of Global Precipitation

Precipitation is one of the most important meteorological variables for defining the climate dynamics, but the spatial patterns of precipitation have not been fully investigated yet. The complex network theory, which provides a robust tool to investigate the statistical interdependence of many interacting elements, is used here to analyze the spatial dynamics of annual precipitation over seventy years (1941-2010). The precipitation network is built associating a node to a geographical region, which has a temporal distribution of precipitation, and identifying possible links among nodes through the correlation function. The precipitation network reveals significant spatial variability with barely connected regions, as Eastern China and Japan, and highly connected regions, such as the African Sahel, Eastern Australia and, to a lesser extent, Northern Europe. Sahel and Eastern Australia are remarkably dry regions, where low amounts of rainfall are uniformly distributed on continental scales and small-scale extreme events are rare. As a consequence, the precipitation gradient is low, making these regions well connected on a large spatial scale. On the contrary, the Asiatic South-East is often reached by extreme events such as monsoons, tropical cyclones and heat waves, which can all contribute to reduce the correlation to the short-range scale only. Some patterns emerging between mid-latitude and tropical regions suggest a possible impact of the propagation of planetary waves on precipitation at a global scale. Other links can be qualitatively associated to the atmospheric and oceanic circulation. To analyze the sensitivity of the network to the physical closeness of the nodes, short-term connections are broken. The African Sahel, Eastern Australia and Northern Europe regions again appear as the supernodes of the network, confirming furthermore their long-range connection structure. Almost all North-American and Asian nodes vanish, revealing that extreme events can enhance high precipitation gradients, leading to a systematic absence of long-range patterns

Score regularization for peptide identification

<p>Abstract</p> <p>Background</p> <p>Peptide identification from tandem mass spectrometry (MS/MS) data is one of the most important problems in computational proteomics. This technique relies heavily on the accurate assessment of the quality of peptide-spectrum matches (PSMs). However, current MS technology and PSM scoring algorithm are far from perfect, leading to the generation of incorrect peptide-spectrum pairs. Thus, it is critical to develop new post-processing techniques that can distinguish true identifications from false identifications effectively.</p> <p>Results</p> <p>In this paper, we present a consistency-based PSM re-ranking method to improve the initial identification results. This method uses one additional assumption that two peptides belonging to the same protein should be correlated to each other. We formulate an optimization problem that embraces two objectives through regularization: the smoothing consistency among scores of correlated peptides and the fitting consistency between new scores and initial scores. This optimization problem can be solved analytically. The experimental study on several real MS/MS data sets shows that this re-ranking method improves the identification performance.</p> <p>Conclusions</p> <p>The score regularization method can be used as a general post-processing step for improving peptide identifications. Source codes and data sets are available at: <url>http://bioinformatics.ust.hk/SRPI.rar</url>.</p

Experimental aspects of SU(5)xU(1) supergravity

We study various aspects of $SU(5)\times U(1)$ supergravity as they relate to the experimental verification or falsification of this model. We consider two string-inspired, universal, one-parameter, no-scale soft-supersymmetry-breaking scenarios, driven by the $F$-terms of the moduli and dilaton fields. The model is described in terms of the supersymmetry mass scale (\ie, the chargino mass $m_{\chi^\pm_1}$), $\tan\beta$, and the top-quark mass. We first determine the combined effect on the parameter space of all presently available direct and indirect experimental constraints, including the LEP lower bounds on sparticle and Higgs-boson masses, the $b\to s\gamma$ rate, the anomalous magnetic moment of the muon, the high-precision electroweak parameters $\epsilon_1,\epsilon_b$ (which imply m_t\lsim180\GeV), and the muon fluxes in underground detectors (neutrino telescopes). For the still-allowed points in $(m_{\chi^\pm_1},\tan\beta)$ parameter space, we re-evaluate the experimental situation at the Tevatron, LEPII, and HERA. In the 1994 run, the Tevatron could probe chargino masses as high as 100 GeV. At LEPII the parameter space could be explored with probes of different resolutions: Higgs boson searches, selectron searches, and chargino searches. Moreover, for m_t\lsim150\GeV, these Higgs-boson searches could explore all of the allowed parameter space with \sqrt{s}\lsim210\GeV.Comment: latex, 36 pages, 25 figures (not included). Figures are available via anonymous ftp from hplaa02.cern.ch (/pub/lopez) as either 33 ps files (Easpects*.ps, 8.1MB) or one uuencoded file (AllFigures.uu, 3.7MB

Uncertainties in Coupling Constant Unification

The status of coupling constant unification in the standard model and its supersymmetric extension are discussed. Uncertainties associated with the input coupling constants, $m_{t}$, threshold corrections at the low and high scales, and possible nonrenormalizable operators are parametrized and estimated. A simple parametrization of a general supersymmetric new particle spectrum is given. It is shown that an effective scale $M_{SUSY}$ can be defined, but for a realistic spectrum it may differ considerably from the typical new particle masses. The implications of the lower (higher) values of $\alpha_{s}(M_{Z})$ suggested by low-energy ($Z$-pole) experiments are discussed.Comment: LaTex, 51 pages, 6 figures (available upon request), UPR-0513

Quality of life in patients with advanced gastric cancer: a randomized trial comparing docetaxel, cisplatin, 5-FU (TCF) with epirubicin, cisplatin, 5-FU (ECF)

BACKGROUND: Health related quality of life (HRQOL) is an important outcome after treatment for upper gastrointestinal carcinoma. This study aimed to compare HRQOL in patients with advanced gastric cancer (GC) receiving either a standard or an experimental treatment. METHODS: Seventy-one patients have been treated in Cancer Institute (Tehran, Iran) with docetaxel, cisplatin, 5 FU (TCF) or epirubicin, cisplatin, 5-FU (ECF) and were followed from Jan 2002 to Jan 2005. End points were response rate, HRQOL and survival. HRQOL was assessed using the EORCT QLQ-C30 at baseline and after the third cycle of chemotherapy. RESULTS: The baseline HRQOL scores were comparable between two groups. After treatment improvement was seen in a number of items and domains except for cognitive functioning, and diarrhoea. Pain decreased and physical functioning improved in both groups. However, only the TCF group showed statistically and clinically meaningful improvement in global QOL (P = 0.001). Surgical and pathologic response was better with TCF but there was no difference in survival rate between two groups. CONCLUSION: Docetaxel based treatment (TCF) showed better palliation and improvement of global QOL as compared with epirubicin based treatment (ECF). However, it seems that regardless of treatment offered, effective chemotherapy was the most important factor affecting QOL in these patients

Two-neutron transfer reaction mechanisms in 12^{12}C(6^6He,4^{4}He)14^{14}C using a realistic three-body 6^{6}He model

The reaction mechanisms of the two-neutron transfer reaction $^{12}$C($^6$He,$^4$He) have been studied at 30 MeV at the TRIUMF ISAC-II facility using the SHARC charged-particle detector array. Optical potential parameters have been extracted from the analysis of the elastic scattering angular distribution. The new potential has been applied to the study of the transfer angular distribution to the 2$^+_2$ 8.32 MeV state in $^{14}$C, using a realistic 3-body $^6$He model and advanced shell model calculations for the carbon structure, allowing to calculate the relative contributions of the simultaneous and sequential two-neutron transfer. The reaction model provides a good description of the 30 MeV data set and shows that the simultaneous process is the dominant transfer mechanism. Sensitivity tests of optical potential parameters show that the final results can be considerably affected by the choice of optical potentials. A reanalysis of data measured previously at 18 MeV however, is not as well described by the same reaction model, suggesting that one needs to include higher order effects in the reaction mechanism.Comment: 9 pages, 9 figure