A comparative study of Gaussian Graphical Model approaches for genomic data

The inference of networks of dependencies by Gaussian Graphical models on high-throughput data is an open issue in modern molecular biology. In this paper we provide a comparative study of three methods to obtain small sample and high dimension estimates of partial correlation coefficients: the Moore-Penrose pseudoinverse (PINV), residual correlation (RCM) and covariance-regularized method $(\ell_{2C})$. We first compare them on simulated datasets and we find that PINV is less stable in terms of AUC performance when the number of variables changes. The two regularized methods have comparable performances but $\ell_{2C}$ is much faster than RCM. Finally, we present the results of an application of $\ell_{2C}$ for the inference of a gene network for isoprenoid biosynthesis pathways in Arabidopsis thaliana.Comment: 7 pages, 1 figure, RevTex4, version to appear in the proceedings of 1st International Workshop on Pattern Recognition, Proteomics, Structural Biology and Bioinformatics: PR PS BB 2011, Ravenna, Italy, 13 September 201

Two-photon decay of heavy quarkonium from heavy-quark spin symmetry

With the recent measurements on $\eta_{c}$ and $\eta_{c}^{\prime}$ at CLEO, Babar and Belle, and with the prospect of finding the $\eta_{b}$ at the Tevatron, it seems appropriate to have another look at the two-photon decay of heavy quarkonium from the standpoint of an effective Lagrangian based on local operator expansion and heavy-quark spin symmetry. In this talk, I would like to discuss a recent work on the two-photon decay rates of ground states and excited states of $\eta_c$ and $\eta_b$ using the local operator expansion approach and heavy-quark spin symmetry and taking into account the binding-energy. We find that the predicted two-photon width for $\eta_c$ agrees well with experiment, but the predicted value for $\eta_c(2S)$ is twice larger than the CLEO estimation. We point out that the essentially model-independent ratio of $\eta_b$ two-photon width to the $\Upsilon$ leptonic width and the $\eta_b$ two-photon width could be used to extract the strong coupling constant $\alpha_s$ .Comment: 9 pages, Talk given at the QCD@Work 2007 International Workshop on QCD: Theory and Experiment}, Martina Franca, Italy, 16--20 June 200

Signals of Warped Extra Dimensions at the LHC

We discuss the signatures of the spin-2 graviton excitations predicted by the Randall-Sundrum model with one warped extra dimension, in dilepton and diphoton production at LHC. By using a specific angular analysis, we assess the ranges in mass and coupling constant where such gravitons can be discriminated against competitor spin-1 and spin-0 objects, that potentially could manifest themselves in these processes with the same mass and rate of events. Depending on the value of the coupling constant to quarks and leptons, the numerical results indicate graviton identification mass ranges up to 1.1-2.4 TeV and 1.6-3.2 TeV for LHC nominal energy of 14 TeV and time-integrated luminosity of 10 and 100~${\rm fb}^{-1}$, respectively.Comment: 8 pages, Talk given at QCD@Work - International Workshop on QCD - Theory and Experiment, 20 - 23 June, 2010, Martina Franca Ital

Linking the genomic signatures of human beat synchronization and learned song in birds

The development of rhythmicity is foundational to communicative and social behaviours in humans and many other species, and mechanisms of synchrony could be conserved across species. The goal of the current paper is to explore evolutionary hypotheses linking vocal learning and beat synchronization through genomic approaches, testing the prediction that genetic underpinnings of birdsong also contribute to the aetiology of human interactions with musical beat structure. We combined state-of-the-art-genomic datasets that account for underlying polygenicity of these traits: birdsong genome-wide transcriptomics linked to singing in zebra finches, and a human genome-wide association study of beat synchronization. Results of competitive gene set analysis revealed that the genetic architecture of human beat synchronization is significantly enriched for birdsong genes expressed in songbird Area X (a key nucleus for vocal learning, and homologous to human basal ganglia). These findings complement ethological and neural evidence of the relationship between vocal learning and beat synchronization, supporting a framework of some degree of common genomic substrates underlying rhythm-related behaviours in two clades, humans and songbirds (the largest evolutionary radiation of vocal learners). Future cross-species approaches investigating the genetic underpinnings of beat synchronization in a broad evolutionary context are discussed

Some topics in theoretical population genetics: Editorial commentaries on a selection of Marc Feldman's TPB papers.

This article consists of commentaries on a selected group of papers of Marc Feldman published in Theoretical Population Biology from 1970 to the present. The papers describe a diverse set of population-genetic models, covering topics such as cultural evolution, social evolution, and the evolution of recombination. The commentaries highlight Marc Feldman's role in providing mathematically rigorous formulations to explore qualitative hypotheses, in many cases generating surprising conclusions

Genome-wide association study of musical beat synchronization demonstrates high polygenicity

Moving in synchrony to the beat is a fundamental component of musicality. Here we conducted a genome-wide association study to identify common genetic variants associated with beat synchronization in 606,825 individuals. Beat synchronization exhibited a highly polygenic architecture, with 69 loci reaching genome-wide significance (P < 5 × 10−8) and single-nucleotide-polymorphism-based heritability (on the liability scale) of 13%–16%. Heritability was enriched for genes expressed in brain tissues and for fetal and adult brain-specific gene regulatory elements, underscoring the role of central-nervous-system-expressed genes linked to the genetic basis of the trait. We performed validations of the self-report phenotype (through separate experiments) and of the genome-wide association study (polygenic scores for beat synchronization were associated with patients algorithmically classified as musicians in medical records of a separate biobank). Genetic correlations with breathing function, motor function, processing speed and chronotype suggest shared genetic architecture with beat synchronization and provide avenues for new phenotypic and genetic explorations

Charge collection measurements with p-type Magnetic Czochralski silicon single pad detectors

Abstract The charge collected from beta source particles in single pad detectors produced on p-type Magnetic Czochralski (MCz) silicon wafers has been measured before and after irradiation with 26 MeV protons. After a 1 MeV neutron equivalent fluence of 1 × 10 15 cm - 2 the collected charge is reduced to 77% at bias voltages below 900 V. This result is compared with previous results from charge collection measurements

Charge collection and capacitance–voltage analysis in irradiated n-type magnetic Czochralski silicon detectors

Abstract The depletion depth of irradiated n-type silicon microstrip detectors can be inferred from both the reciprocal capacitance and from the amount of collected charge. Capacitance voltage ( C – V ) measurements at different frequencies and temperatures are being compared with the bias voltage dependence of the charge collection on an irradiated n-type magnetic Czochralski silicon detector. Good agreement between the reciprocal capacitance and the median collected charge is found when the frequency of the C – V measurement is selected such that it scales with the temperature dependence of the leakage current. Measuring C – V characteristics at prescribed combinations of temperature and frequency allows then a realistic estimate of the depletion characteristics of irradiated silicon strip detectors based on C – V data alone

Behavioral Modernity and the Cultural Transmission of Structured Information: The Semantic Axelrod Model

Cultural transmission models are coming to the fore in explaining increases in the Paleolithic toolkit richness and diversity. During the later Paleolithic, technologies increase not only in terms of diversity but also in their complexity and interdependence. As Mesoudi and O'Brien (2008) have shown, selection broadly favors social learning of information that is hierarchical and structured, and multiple studies have demonstrated that teaching within a social learning environment can increase fitness. We believe that teaching also provides the scaffolding for transmission of more complex cultural traits. Here, we introduce an extension of the Axelrod (1997} model of cultural differentiation in which traits have prerequisite relationships, and where social learning is dependent upon the ordering of those prerequisites. We examine the resulting structure of cultural repertoires as learning environments range from largely unstructured imitation, to structured teaching of necessary prerequisites, and we find that in combination with individual learning and innovation, high probabilities of teaching prerequisites leads to richer cultural repertoires. Our results point to ways in which we can build more comprehensive explanations of the archaeological record of the Paleolithic as well as other cases of technological change.Comment: 24 pages, 7 figures. Submitted to "Learning Strategies and Cultural Evolution during the Paleolithic", edited by Kenichi Aoki and Alex Mesoudi, and presented at the 79th Annual Meeting of the Society for American Archaeology, Austin TX. Revised 5/14/1

Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV

A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7 TeV is presented. The data were collected at the LHC, with the CMS detector, and correspond to an integrated luminosity of 4.6 inverse femtobarns. No significant excess is observed above the background expectation, and upper limits are set on the Higgs boson production cross section. The presence of the standard model Higgs boson with a mass in the 270-440 GeV range is excluded at 95% confidence level.Comment: Submitted to JHE