Module Anchored Network Inference: A Sequential Module-Based Approach to Novel Gene Network Construction from Genomic Expression Data on Human Disease Mechanism

Different computational approaches have been examined and compared for inferring network relationships from time-series genomic data on human disease mechanisms under the recent Dialogue on Reverse Engineering Assessment and Methods (DREAM) challenge. Many of these approaches infer all possible relationships among all candidate genes, often resulting in extremely crowded candidate network relationships with many more False Positives than True Positives. To overcome this limitation, we introduce a novel approach, Module Anchored Network Inference (MANI), that constructs networks by analyzing sequentially small adjacent building blocks (modules). Using MANI, we inferred a 7-gene adipogenesis network based on time-series gene expression data during adipocyte differentiation. MANI was also applied to infer two 10-gene networks based on time-course perturbation datasets from DREAM3 and DREAM4 challenges. MANI well inferred and distinguished serial, parallel, and time-dependent gene interactions and network cascades in these applications showing a superior performance to other in silico network inference techniques for discovering and reconstructing gene network relationships

Physical phenomena in containerless glass processing

Experiments were conducted on bubble migration in rotating liquid bodies contained in a sphere. Experiments were initiated on the migration of a drop in a slightly less dense continuous phase contained in a rotating sphere. A refined apparatus for the study of thermocapillar flow in a glass melt was built, and data were acquired on surface velocities in the melt. Similar data also were obtained from an ambient temperature fluid model. The data were analyzed and correlated with the aid of theory. Data were obtained on flow velocities in a pendant drop heated from above. The motion in this system was driven principally by thermocapillarity. An apparatus was designed for the study of volatilization from a glass melt

Project Inception Report

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Nanoscale quantum dot infrared sensors with photonic crystal cavity

We report high performance infrared sensors that are based on intersubband transitions in nanoscale self-assembled quantum dots combined with a microcavity resonator made with a high-index-contrast two-dimensional photonic crystal. The addition of the photonic crystal cavity increases the photocurrent, conversion efficiency, and the signal to noise ratio (represented by the specific detectivity D*) by more than an order of magnitude. The conversion efficiency of the detector at Vb=–2.6 V increased from 7.5% for the control sample to 95% in the PhC detector. In principle, these photonic crystal resonators are technology agnostic and can be directly integrated into the manufacturing of present day infrared sensors using existing lithographic tools in the fabrication facility

O Mediterrâneo enquanto metáfora da mestiçagem: Novas leituras sobre o modelo europeu na América Latina dos anos 1920

After the First World War, we can observe in the Latin American society a strong transformation in the perception of the Europe as a civilization model. New movements in art and literature start to rethink the National Identities in Latin America and in the whole subcontinent born a criticism against the importation of European civility concepts. This process can be deeply analyzed in Mistral’s writings that shows us the continental transformation through the Mediterranean metaphor: between a Latin space and a space of miscegenation. In Mistral’s narratives, we can notice two kinds of analytical movements between North and South relations: when the writer talks about the European contrasts, she talks also about those of the American continent. In this context, the Old World, or its Southern part, shares its Historical experience with the New World to justify the positive perception of the New Latin American men: Multiethnic

Indolicidin – Antibacterial activity against bacterial pathogens isolated from ocular infections

Indolicidin is a novel/ promising antimicrobial peptide (a 13 amino acid cationic antimicrobial residue present in the form of cytoplasmic granules of bovine neutrophils) and observed with a broad spectrum of antimicrobial activity against bacteria, fungi, protozoa & even viruses. In the present study, Escherichia coli was transformed with pET 21a+ plasmid carrying indolicidin gene and was expressed. The crude extracts of indolicidin samples induced with varying IPTG concentrations (5mM and 20 mM/ ml of the medium) in Min A medium were checked for antibacterial activities against clinically important ocular bacterial pathogens such as E. coli, Klebsiella sp,, Pseudomonas sp., Acenitobacter sp., Staphylococcus aureus, coagulase negative Staphylococcus aureus, Streptococcus viridans, S. pneumoniae and S. pyogens and its activity was evaluated.&nbsp

Experimental investigation on the influences of varying injection timing on the performance of a B20 JOME biodiesel fueled diesel engine / S. Jaichandar and K. Annamalai

This experimental study aims to optimize the injection timing to achieve higher performance from biodiesel fueled Direct Injection (DI) diesel engine. Experiments were performed using a naturally-aspirated single cylinder DI diesel engine equipped with a conventional jerk type injection system to study the effects of varying injection timing on the combustion, performance and exhaust emissions using a blend of 20% Jatropha Oil Methyl Ester (JOME) by volume with diesel. The test results showed that improvement in terms of brake thermal efficiency and specific fuel consumption for the engine operated at retarded injection timing, particularly at 21o bTDC. Substantial improvements in reduction of emission levels particularly oxides of nitrogen (NOx) were observed for retarded injection timing of 21o bTDC. Compared to the engine operated at standard injection timing of 23o bTDC, the retarded injection timing of 21o bTDC provided a better performance of 2.27% and 3.4% in terms of BTE and BSFC respectively and NOx emission level improvement of 4.5%. However, CO, UBHC and smoke emission levels were slightly deteriorated compared to standard injection timing operation. It has also been found that retarding the injection timing lowers marginally ignition delay, peak in-cylinder pressure and maximum heat release rate

Solving the initial conditions problem for modified gravity theories

Modified gravity theories such as Einstein scalar Gauss Bonnet contain higher-derivative terms in the spacetime curvature in their action, which results in modifications to the Hamiltonian and momentum constraints of the theory. In principle, such modifications may affect the principal part of the operator in the resulting elliptic equations, and so further complicate the already highly nonlinear, coupled constraints that apply to the initial data in numerical relativity simulations of curved spacetimes. However, since these are effective field theories, we expect the additional curvature terms to be small, which motivates treating them simply as an additional source in the constraints, and iterating to find a solution to the full problem. In this work we implement and test a modification to the CTT/CTTK methods of solving the constraints for the case of the most general four derivative, parity invariant scalar-tensor theory, and show that solutions can be found in both asymptotically flat/black hole and periodic/cosmological spacetimes, even up to couplings of order unity in the theory. Such methods will allow for numerical investigations of a much broader class of initial data than has previously been possible in these theories, and should be straightforward to extend to similar models in the Horndeski class

Coupled Model Simulations of Boreal Summer Intraseasonal (30-50 day) Variability, Part 1: Systematic Errors and Caution on Use of Metrics

Boreal summer intraseasonal (30-50 day) variability (BSISV) over the Asian monsoon region is more complex than its boreal winter counterpart, the Madden-Julian oscillation (MJO), since it also exhibits northward and northwestward propagating convective components near India and over the west Pacific. Here we analyze the BSISV in the CMIP3 and two CMIP2+ coupled ocean-atmosphere models. Though most models exhibit eastward propagation of convective anomalies over the Indian Ocean, difficulty remains in simulating the life cycle of the BSISV, as few represent its eastward extension into the western/central Pacific. As such, few models produce statistically significant anomalies that comprise the northwest to southeast tilted convection which results from the forced Rossby waves that are excited by the near-equatorial convective anomalies. Our results indicate that it is a necessary, but not sufficient condition, that the locations the time-mean monsoon heat sources and the easterly wind shear be simulated correctly in order for the life cycle of the BSISV to be represented realistically. Extreme caution is needed when using metrics, such as the pattern correlation, for assessing the fidelity of model performance, as models with the most physically realistic BSISV do not necessarily exhibit the highest pattern correlations with observations. Furthermore, diagnostic latitude-time plots to evaluate the northward propagation of convection from the equator to India and the Bay of Bengal also need to be used with caution. Here, incorrectly representing extratropical-tropical interactions can give rise to 'apparent' northward propagation when none exists in association with the eastward propagating equatorial convection. It is necessary to use multiple cross-checking diagnostics to demonstrate the fidelity of the simulation of the BSISV