Study of meta-analysis strategies for network inference using information-theoretic approaches

© 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Reverse engineering of gene regulatory networks (GRNs) from gene expression data is a classical challenge in systems biology. Thanks to high-throughput technologies, a massive amount of gene-expression data has been accumulated in the public repositories. Modelling GRNs from multiple experiments (also called integrative analysis) has; therefore, naturally become a standard procedure in modern computational biology. Indeed, such analysis is usually more robust than the traditional approaches focused on individual datasets, which typically suffer from some experimental bias and a small number of samples. To date, there are mainly two strategies for the problem of interest: the first one (”data merging”) merges all datasets together and then infers a GRN whereas the other (”networks ensemble”) infers GRNs from every dataset separately and then aggregates them using some ensemble rules (such as ranksum or weightsum). Unfortunately, a thorough comparison of these two approaches is lacking. In this paper, we evaluate the performances of various metaanalysis approaches mentioned above with a systematic set of experiments based on in silico benchmarks. Furthermore, we present a new meta-analysis approach for inferring GRNs from multiple studies. Our proposed approach, adapted to methods based on pairwise measures such as correlation or mutual information, consists of two steps: aggregating matrices of the pairwise measures from every dataset followed by extracting the network from the meta-matrix.Peer ReviewedPostprint (author's final draft

Entanglement Dynamics in 1D Quantum Cellular Automata

Several proposed schemes for the physical realization of a quantum computer consist of qubits arranged in a cellular array. In the quantum circuit model of quantum computation, an often complex series of two-qubit gate operations is required between arbitrarily distant pairs of lattice qubits. An alternative model of quantum computation based on quantum cellular automata (QCA) requires only homogeneous local interactions that can be implemented in parallel. This would be a huge simplification in an actual experiment. We find some minimal physical requirements for the construction of unitary QCA in a 1 dimensional Ising spin chain and demonstrate optimal pulse sequences for information transport and entanglement distribution. We also introduce the theory of non-unitary QCA and show by example that non-unitary rules can generate environment assisted entanglement.Comment: 12 pages, 8 figures, submitted to Physical Review

Nudging Students Beyond the FAFSA: The Impact of University Outreach on Financial Aid Behaviors and Outcomes

A growing body of research indicates that proactive outreach from high schools and college access organizations about college preparation tasks, and specifically focusing on completing the Free Application for Federal Student Aid (FAFSA), results in increased college enrollment. Comparatively less attention has been paid to the role of colleges and universities in this outreach and outreach relating to additional financial aid barriers that students face while applying to college, such as the CSS PROFILE form. In this article we investigated, through an inter-university collaboration, the effect of sending targeted, semi-personalized text messages to students during the college application process about important financial aid deadlines, making salient the specific forms required and prompting students to plan specific times to complete these tasks. The intervention increased CSS PROFILE filing by 3.1-4.3 percentage points, where the estimates and their significance varied depending on the comparison group. Impacts on student enrollment did not accompany these filing impacts. Results from our collaboration support the idea that colleges and universities have an important role to play in outreach to applicants relating to important financial aid tasks. The paper includes a discussion of the promises and challenges of this outreach with recommendations for practitioners

Multi-Player Quantum Games

Recently the concept of quantum information has been introduced into game theory. Here we present the first study of quantum games with more than two players. We discover that such games can possess a new form of equilibrium strategy, one which has no analogue either in traditional games or even in two-player quantum games. In these `pure' coherent equilibria, entanglement shared among multiple players enables new kinds of cooperative behavior: indeed it can act as a contract, in the sense that it prevents players from successfully betraying one-another.Comment: 5 pages, 2 figs. Substantial revisons inc. new result

An Analysis of the Quantum Penny Flip Game using Geometric Algebra

We analyze the quantum penny flip game using geometric algebra and so determine all possible unitary transformations which enable the player Q to implement a winning strategy. Geometric algebra provides a clear visual picture of the quantum game and its strategies, as well as providing a simple and direct derivation of the winning transformation, which we demonstrate can be parametrized by two angles. For comparison we derive the same general winning strategy by conventional means using density matrices.Comment: 8 Pages, 1 Figure, accepted for publication in the Journal of Physical Society of Japa

Agl24 is an ancient archaeal homolog of the eukaryotic N-glycan chitobiose synthesis enzymes

Protein N-glycosylation is a post-translational modification found in organisms of all domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in Eukaryotes, although the enzyme catalyzing this reaction remains unknown. Here, we report the identification of a thermostable archaeal β-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed its function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its functional importance for Agl24. Furthermore, bioinformatics and structural modeling revealed similarities of Agl24 to the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which are catalyzing the same or a similar reaction, respectively. Phylogenetic analysis of Alg14/13 homologs indicates that they are ancient in Eukaryotes, either as a lateral transfer or inherited through eukaryogenesis.</p

Loss of CCR7 Expression on CD56brightCD56^{bright} NK Cells Is Associated with a CD56dimCD16+CD56^{dim}CD16^{+} NK Cell-Like Phenotype and Correlates with HIV Viral Load

NK cells are pivotal sentinels of the innate immune system and distinct subpopulations in peripheral blood have been described. A number of studies addressed HIV-induced alterations of NK cell phenotype and functionality mainly focusing on $CD56^{dim}CD16^{+}$ and $CD56^{-} CD16^{+}$ NK cells. However, the impact of HIV-infection on $CD56^{bright}$ NK cells is less well understood. Here we report a rise of $CD56^{bright}$ NK cells in HIV-infected individuals, which lack CCR7-expression and strongly correlate with HIV viral load. $CCR7^{−} CD56^{bright}$ NK cells were characterized by increased cytolytic potential, higher activation states and a more differentiated phenotype. These cells thus acquired a number of features of $CD56^{dim}CD16^{+}$ NK cells. Furthermore, $CD56^{bright}$ NK cells from HIV patients exhibited higher degranulation levels compared to uninfected individuals. Thus, chronic HIV-infection is associated with a phenotypic and functional shift of $CD56^{bright}$ NK cells, which provides a novel aspect of HIV-associated pathogenesis within the NK cell compartment

Near-infrared spectroscopy in NGC 7538

The characterisation of the stellar population toward young high-mass star-forming regions allows to constrain fundamental cluster properties like distance and age. These are essential when using high-mass clusters as probes to conduct Galactic studies. NGC 7538 is a star-forming region with an embedded stellar population only unearthed in the near-infrared. We present the first near-infrared spectro-photometric study of the candidate high-mass stellar content in NGC 7538. We obtained H and K spectra of 21 sources with both the multi-object and long-slit modes of LIRIS at the WHT, and complement these data with sub-arcsecond JHKs photometry of the region using the imaging mode of the same instrument. We find a wide variety of objects within the studied stellar population of NGC 7538. Our results discriminate between a stellar population associated to the HII region, but not contained within its extent, and several pockets of more recent star formation. We report the detection of CO bandhead emission toward several sources as well as other features indicative of a young stellar nature. We infer a spectro-photometric distance of 2.7+-0.5 kpc, an age spread in the range 0.5-2.2 Myr and a total mass ~1.7x10^3 Msun for the older population.Comment: 11 pages, 8 figures, 1 table, accepted by A&

Quantum Matching Pennies Game

A quantum version of the Matching Pennies (MP) game is proposed that is played using an Einstein-Podolsky-Rosen-Bohm (EPR-Bohm) setting. We construct the quantum game without using the state vectors, while considering only the quantum mechanical joint probabilities relevant to the EPR-Bohm setting. We embed the classical game within the quantum game such that the classical MP game results when the quantum mechanical joint probabilities become factorizable. We report new Nash equilibria in the quantum MP game that emerge when the quantum mechanical joint probabilities maximally violate the Clauser-Horne-Shimony-Holt form of Bell's inequality.Comment: Revised in light of referees' comments, submitted to Journal of the Physical Society of Japan, 14 pages, 1 figur