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

Rapid prototyping of plastic lab-on-a-chip by femtosecond laser micromachining and removable insert microinjection molding

We have introduced a new hybrid fabrication method for lab-on-a-chip devices through the combination of femtosecond laser micromachining and removable insert micro-injection molding. This method is particularly suited for the fast prototyping of new devices, while maintaining a competitive low cost. To demonstrate the effectiveness of our approach, we designed, fabricated, and tested a completely integrated flow cytometer coupled to a portable media device. The system operation was tested with fluorescent plastic micro-bead solutions ranging from 100 beads/?L to 500 beads/?L. We demonstrated that this hybrid lab-on-a-chip fabrication technology is suitable for producing low-cost and portable biological microsystems and for effectively bridging the gap between new device concepts and their mass production

Behavioral types in programming languages

A recent trend in programming language research is to use behav- ioral type theory to ensure various correctness properties of large- scale, communication-intensive systems. Behavioral types encompass concepts such as interfaces, communication protocols, contracts, and choreography. The successful application of behavioral types requires a solid understanding of several practical aspects, from their represen- tation in a concrete programming language, to their integration with other programming constructs such as methods and functions, to de- sign and monitoring methodologies that take behaviors into account. This survey provides an overview of the state of the art of these aspects, which we summarize as the pragmatics of behavioral types

Nyquist method for Wigner-Poisson quantum plasmas

By means of the Nyquist method, we investigate the linear stability of electrostatic waves in homogeneous equilibria of quantum plasmas described by the Wigner-Poisson system. We show that, unlike the classical Vlasov-Poisson system, the Wigner-Poisson case does not necessarily possess a Penrose functional determining its linear stability properties. The Nyquist method is then applied to a two-stream distribution, for which we obtain an exact, necessary and sufficient condition for linear stability, as well as to a bump-in-tail equilibrium.Comment: 6 figure

The boundary Riemann solver coming from the real vanishing viscosity approximation

We study a family of initial boundary value problems associated to mixed hyperbolic-parabolic systems: v^{\epsilon} _t + A (v^{\epsilon}, \epsilon v^{\epsilon}_x ) v^{\epsilon}_x = \epsilon B (v^{\epsilon} ) v^{\epsilon}_{xx} The conservative case is, in particular, included in the previous formulation. We suppose that the solutions $v^{\epsilon}$ to these problems converge to a unique limit. Also, it is assumed smallness of the total variation and other technical hypotheses and it is provided a complete characterization of the limit. The most interesting points are the following two. First, the boundary characteristic case is considered, i.e. one eigenvalue of $A$ can be $0$. Second, we take into account the possibility that $B$ is not invertible. To deal with this case, we take as hypotheses conditions that were introduced by Kawashima and Shizuta relying on physically meaningful examples. We also introduce a new condition of block linear degeneracy. We prove that, if it is not satisfied, then pathological behaviours may occur.Comment: 84 pages, 6 figures. Text changes in Sections 1 and 3.2.3. Added Section 3.1.2. Minor changes in other section

Celecoxib for the prevention of nonmuscle invasive bladder cancer: Results from a matched control study

New targets and approaches are under investigation for the treatment of nonmuscle invasive bladder cancer (NMIBC). Preclinical data suggest cyclooxygenase-2 (COX-2) as a promising target. Celecoxib, a COX-2 selective inhibitor, inhibits tumor development and enhances survival, both in vitro and in vivo models of bladder cancer. Therefore, we conducted a pilot study of celecoxib to prevent recurrence in patients with intermediate risk NMIBC

An efficient semiparametric maxima estimator of the extremal index

The extremal index $\theta$, a measure of the degree of local dependence in the extremes of a stationary process, plays an important role in extreme value analyses. We estimate $\theta$ semiparametrically, using the relationship between the distribution of block maxima and the marginal distribution of a process to define a semiparametric model. We show that these semiparametric estimators are simpler and substantially more efficient than their parametric counterparts. We seek to improve efficiency further using maxima over sliding blocks. A simulation study shows that the semiparametric estimators are competitive with the leading estimators. An application to sea-surge heights combines inferences about $\theta$ with a standard extreme value analysis of block maxima to estimate marginal quantiles.Comment: 17 pages, 7 figures. Minor edits made to version 1 prior to journal publication. The final publication is available at Springer via http://dx.doi.org/10.1007/s10687-015-0221-

Hardy's inequality for functions vanishing on a part of the boundary

We develop a geometric framework for Hardy's inequality on a bounded domain when the functions do vanish only on a closed portion of the boundary.Comment: 26 pages, 2 figures, includes several improvements in Sections 6-8 allowing to relax the assumptions in the main results. Final version published at http://link.springer.com/article/10.1007%2Fs11118-015-9463-