The Inferred Cardiogenic Gene Regulatory Network in the Mammalian Heart

Cardiac development is a complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory networks was applied to time-course microarray data obtained from the developing mouse heart. Approximately 200 genes of interest were input into the algorithm to generate putative network topologies that are capable of explaining the experimental data via model simulation. To cull specious network interactions, thousands of putative networks are merged and filtered to generate scale-free, hierarchical networks that are statistically significant and biologically relevant. The networks are validated with known gene interactions and used to predict regulatory pathways important for the developing mammalian heart. Area under the precision-recall curve and receiver operator characteristic curve are 9% and 58%, respectively. Of the top 10 ranked predicted interactions, 4 have already been validated. The algorithm is further tested using a network enriched with known interactions and another depleted of them. The inferred networks contained more interactions for the enriched network versus the depleted network. In all test cases, maximum performance of the algorithm was achieved when the purely data-driven method of network inference was combined with a data-independent, functional-based association method. Lastly, the network generated from the list of approximately 200 genes of interest was expanded using gene-profile uniqueness metrics to include approximately 900 additional known mouse genes and to form the most likely cardiogenic gene regulatory network. The resultant network supports known regulatory interactions and contains several novel cardiogenic regulatory interactions. The method outlined herein provides an informative approach to network inference and leads to clear testable hypotheses related to gene regulation

Spatial fluctuations at vertices of epithelial layers: quantification of regulation by Rho pathway

In living matter, shape fluctuations induced by acto-myosin are usually studied in vitro via reconstituted gels, whose properties are controlled by changing the concentrations of actin, myosin and cross-linkers. Such an approach deliberately avoids to consider the complexity of biochemical signaling inherent to living systems. Acto-myosin activity inside living cells is mainly regulated by the Rho signaling pathway which is composed of multiple layers of coupled activators and inhibitors. We investigate how such a pathway controls the dynamics of confluent epithelial tissues by tracking the displacements of the junction points between cells. Using a phenomenological model to analyze the vertex fluctuations, we rationalize the effects of different Rho signaling targets on the emergent tissue activity by quantifying the effective diffusion coefficient, the persistence time and persistence length of the fluctuations. Our results reveal an unanticipated correlation between layers of activation/inhibition and spatial fluctuations within tissues. Overall, this work connects the regulation via biochemical signaling with mesoscopic spatial fluctuations, with potential application to the study of structural rearrangements in epithelial tissues.Comment: 8 pages, 3 figure

Propositional Dynamic Logic for Message-Passing Systems

We examine a bidirectional propositional dynamic logic (PDL) for finite and infinite message sequence charts (MSCs) extending LTL and TLC-. By this kind of multi-modal logic we can express properties both in the entire future and in the past of an event. Path expressions strengthen the classical until operator of temporal logic. For every formula defining an MSC language, we construct a communicating finite-state machine (CFM) accepting the same language. The CFM obtained has size exponential in the size of the formula. This synthesis problem is solved in full generality, i.e., also for MSCs with unbounded channels. The model checking problem for CFMs and HMSCs turns out to be in PSPACE for existentially bounded MSCs. Finally, we show that, for PDL with intersection, the semantics of a formula cannot be captured by a CFM anymore

A quantum McKay correspondence for fractional 2p-branes on LG orbifolds

We study fractional 2p-branes and their intersection numbers in non-compact orbifolds as well the continuation of these objects in Kahler moduli space to coherent sheaves in the corresponding smooth non-compact Calabi-Yau manifolds. We show that the restriction of these objects to compact Calabi-Yau hypersurfaces gives the new fractional branes in LG orbifolds constructed by Ashok et. al. in hep-th/0401135. We thus demonstrate the equivalence of the B-type branes corresponding to linear boundary conditions in LG orbifolds, originally constructed in hep-th/9907131, to a subset of those constructed in LG orbifolds using boundary fermions and matrix factorization of the world-sheet superpotential. The relationship between the coherent sheaves corresponding to the fractional two-branes leads to a generalization of the McKay correspondence that we call the quantum McKay correspondence due to a close parallel with the construction of branes on non-supersymmetric orbifolds. We also provide evidence that the boundary states associated to these branes in a conformal field theory description corresponds to a sub-class of the boundary states associated to the permutation branes in the Gepner model associated with the LG orbifold.Comment: LaTeX2e, 1+39 pages, 3 figures (v2) refs added, typos and report no. correcte

A linear programming-based method for job shop scheduling

We present a decomposition heuristic for a large class of job shop scheduling problems. This heuristic utilizes information from the linear programming formulation of the associated optimal timing problem to solve subproblems, can be used for any objective function whose associated optimal timing problem can be expressed as a linear program (LP), and is particularly effective for objectives that include a component that is a function of individual operation completion times. Using the proposed heuristic framework, we address job shop scheduling problems with a variety of objectives where intermediate holding costs need to be explicitly considered. In computational testing, we demonstrate the performance of our proposed solution approach

Distribution of finfish resources along southeast coast of India in relation to certain environmental parameters

This paper embodies the distribution pattern of major finfish resources along the southeast coast of India as observed during the cruises operated by FORV Sagar Sampada. A total of 16 cruises (1985-90) operated along latitude 7° 15'- 15°00' N and longitude 75°50'- 82°3r E hauled a total catch 37.5 tonnes with a catch rate of 537 kg/hr. The catch was constituted mainly by threadfin breams (43%), perches (14%), barracudas (9.72%), carangids (8.56%) and elasmobranchs (4.81%). Seasonally higher catch rates were obtained during July- September period. Depth range of 60 - 80 m had denser population of finfish resources. Water temperature and salinity appeared to influence the distribution of major finfishes more than dissolved oxygen. Groups such as threadfin breams were found preferring cooler waters of Wadge Bank area, while barracudas appear to occupy warmer waters of Gulf of Mannar

A green Hibiscus cannabinus oil emollient cream for potential topical applications

A green emollient cream with Hibiscus cannabinus seed oil and an alkyl polyglucoside surfactant has been formulated. It can serve as biological alternatives to synthetic formulations that normally incorporate chemical constituents as surfactants and stabilizers mainly to increase consumer compliance in terms of textural and visual aesthetics. FAME analysis of the oil showed the presence octanoic and decanoic acids. The cream after formulation and ultrasonication, presented a smooth and soft appearance with visual and textural appeal. It showed a mean particle size of 138 nm with a zeta potential of -59.2 mV and an electrophoretic mobility of -0.000459 cm2/Vs. Its SEM image projected well dispersed oil globules in water. FTIR spectrum showed extensive hydrogen bonding. Accelerated stability tests under conditions of freeze thawing, heating cooling and centrifugation revealed no cracking, creaming or phase separation. Similar results were observed during the shelf life studies. It is concluded that this Hibiscus cannabinus cream can be utilized as an emollient base for loading cosmopharmaceutic ingredients for their topical delivery, without any toxicity concerns, as it is formulated from completely natural constituents

Hedgehog Spin-texture and Berry's Phase tuning in a Magnetic Topological Insulator

Understanding and control of spin degrees of freedom on the surfaces of topological materials are key to future applications as well as for realizing novel physics such as the axion electrodynamics associated with time-reversal (TR) symmetry breaking on the surface. We experimentally demonstrate magnetically induced spin reorientation phenomena simultaneous with a Dirac-metal to gapped-insulator transition on the surfaces of manganese-doped Bi2Se3 thin films. The resulting electronic groundstate exhibits unique hedgehog-like spin textures at low energies, which directly demonstrate the mechanics of TR symmetry breaking on the surface. We further show that an insulating gap induced by quantum tunnelling between surfaces exhibits spin texture modulation at low energies but respects TR invariance. These spin phenomena and the control of their Fermi surface geometrical phase first demonstrated in our experiments pave the way for the future realization of many predicted exotic magnetic phenomena of topological origin.Comment: 38 pages, 18 Figures, Includes new text, additional datasets and interpretation beyond arXiv:1206.2090, for the final published version see Nature Physics (2012

Multimodal information processing and associative learning in the insect brain

The study of sensory systems in insects has a long-spanning history of almost an entire century. Olfaction, vision, and gustation are thoroughly researched in several robust insect models and new discoveries are made every day on the more elusive thermo- and mechano-sensory systems. Few specialized senses such as hygro- and magneto-reception are also identified in some insects. In light of recent advancements in the scientific investigation of insect behavior, it is not only important to study sensory modalities individually, but also as a combination of multimodal inputs. This is of particular significance, as a combinatorial approach to study sensory behaviors mimics the real-time environment of an insect with a wide spectrum of information available to it. As a fascinating field that is recently gaining new insight, multimodal integration in insects serves as a fundamental basis to understand complex insect behaviors including, but not limited to navigation, foraging, learning, and memory. In this review, we have summarized various studies that investigated sensory integration across modalities, with emphasis on three insect models (honeybees, ants and flies), their behaviors, and the corresponding neuronal underpinnings

Many-to-Many Information Flow Policies

Information flow techniques typically classify information according to suitable security levels and enforce policies that are based on binary relations between individual levels, e.g., stating that information is allowed to flow from one level to another. We argue that some information flow properties of interest naturally require coordination patterns that involve sets of security levels rather than individual levels: some secret information could be safely disclosed to a set of confidential channels of incomparable security levels, with individual leaks considered instead illegal; a group of competing agencies might agree to disclose their secrets, with individual disclosures being undesired, etc. Motivated by this we propose a simple language for expressing information flow policies where the usual admitted flow relation between individual security levels is replaced by a relation between sets of security levels, thus allowing to capture coordinated flows of information. The flow of information is expressed in terms of causal dependencies and the satisfaction of a policy is defined with respect to an event structure that is assumed to capture the causal structure of system computations. We suggest applications to secret exchange protocols, program security and security architectures, and discuss the relation to classic notions of information flow control