A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data

We propose a new filter based feature selection algorithm for classification based on DNA microarray gene expression data. It utilizes null space of covariance matrix for feature selection. The algorithm can perform bulk reduction of features (genes) while maintaining the quality information in the reduced subset of features for discriminative purpose. Thus, it can be used as a pre-processing step for other feature selection algorithms. The algorithm does not assume statistical independency among the features. The algorithm shows promising classification accuracy when compared with other existing techniques on several DNA microarray gene expression datasets

Near-Optimal Scheduling for LTL with Future Discounting

We study the search problem for optimal schedulers for the linear temporal logic (LTL) with future discounting. The logic, introduced by Almagor, Boker and Kupferman, is a quantitative variant of LTL in which an event in the far future has only discounted contribution to a truth value (that is a real number in the unit interval [0, 1]). The precise problem we study---it naturally arises e.g. in search for a scheduler that recovers from an internal error state as soon as possible---is the following: given a Kripke frame, a formula and a number in [0, 1] called a margin, find a path of the Kripke frame that is optimal with respect to the formula up to the prescribed margin (a truly optimal path may not exist). We present an algorithm for the problem; it works even in the extended setting with propositional quality operators, a setting where (threshold) model-checking is known to be undecidable

Discounting in LTL

In recent years, there is growing need and interest in formalizing and reasoning about the quality of software and hardware systems. As opposed to traditional verification, where one handles the question of whether a system satisfies, or not, a given specification, reasoning about quality addresses the question of \emph{how well} the system satisfies the specification. One direction in this effort is to refine the "eventually" operators of temporal logic to {\em discounting operators}: the satisfaction value of a specification is a value in $[0,1]$, where the longer it takes to fulfill eventuality requirements, the smaller the satisfaction value is. In this paper we introduce an augmentation by discounting of Linear Temporal Logic (LTL), and study it, as well as its combination with propositional quality operators. We show that one can augment LTL with an arbitrary set of discounting functions, while preserving the decidability of the model-checking problem. Further augmenting the logic with unary propositional quality operators preserves decidability, whereas adding an average-operator makes some problems undecidable. We also discuss the complexity of the problem, as well as various extensions

Field-induced metal-insulator transition and switching phenomenon in correlated insulators

We study the nonequilibrium switching phenomenon associated with the metal-insulator transition under electric field E in correlated insulator by a gauge-covariant Keldysh formalism. Due to the feedback effect of the resistive current I, this occurs as a first-order transition with a hysteresis of I-V characteristics having a lower threshold electric field (\sim 10^4 Vcm^{-1}) much weaker than that for the Zener breakdown. It is also found that the localized mid-gap states introduced by impurities and defects act as hot spots across which the resonant tunneling occurs selectively, which leads to the conductive filamentary paths and reduces the energy cost of the switching function.Comment: 5 pages, 3 figures. A study on the metal-insulator transition in correlated insulators was adde

Formation of complex Langmuir and Langmuir-Blodgett films of water soluble rosebengal

This communication reports the formation of complex Langmuir monolayer at the air-water interface by charge transfer types of interaction with the water soluble N- cetyl N, N, N trimethyl ammonium bromide (CTAB) molecules doped with rosebengal (RB), with the stearic acid (SA) molecules of a preformed SA Langmuir monolayer. The reaction kinetics of the formation of RB-CTAB-SA complex monolayer was monitored by observing the increase in surface pressure with time while the barrier was kept fixed. Completion of interaction kinetics was confirmed by FTIR study. This complex Langmuir films at the air-water interface was transferred onto solid substrates at a desired surface pressure to form multilayered Langmuir-Blodgett films. Spectroscopic characterizations reveal some molecular level interactions as well as formation of microcrystalline aggregates depending upon the molar ratios of CTAB and RB within the complex LB films. Presence of two types of species in the complex LB films was confirmed by fluorescence spectroscopy.Comment: 13 pages, figures

CSO validator: improving manual curation workflow for biological pathways

Summary: Manual curation and validation of large-scale biological pathways are required to obtain high-quality pathway databases. In a typical curation process, model validation and model update based on appropriate feedback are repeated and requires considerable cooperation of scientists. We have developed a CSO (Cell System Ontology) validator to reduce the repetition and time during the curation process. This tool assists in quickly obtaining agreement among curators and domain experts and in providing a consistent and accurate pathway database

Ultrafast Photoinduced Formation of Metallic State in a Perovskite-type Manganite with Short Range Charge and Orbital Order

Femtosecond reflection spectroscopy was performed on a perovskite-type manganite, Gd0.55Sr0.45MnO3, with the short-range charge and orbital order (CO/OO). Immediately after the photoirradiation, a large increase of the reflectivity was detected in the mid-infrared region. The optical conductivity spectrum under photoirradiation obtained from the Kramers-Kronig analyses of the reflectivity changes demonstrates a formation of a metallic state. This suggests that ferromagnetic spin arrangements occur within the time resolution (ca. 200 fs) through the double exchange interaction, resulting in an ultrafast CO/OO to FM switching.Comment: 4 figure

Layer dynamics of a freely standing smectic-A film

We study the hydrodynamics of a freely-standing smectic-A film in the isothermal, incompressible limit theoretically by analyzing the linearized hydrodynamic equations of motion with proper boundary conditions. The dynamic properties for the system can be obtained from the response functions for the free surfaces. Permeation is included and its importance near the free surfaces is discussed. The hydrodynamic mode structure for the dynamics of the system is compared with that of bulk systems. We show that to describe the dynamic correlation functions for the system, in general, it is necessary to consider the smectic layer displacement $u$ and the velocity normal to the layers, $v_z$, together. Finally, our analysis also provides a basis for the theoretical study of the off-equilibrium dynamics of freely-standing smectic-A films.Comment: 22 pages, 4 figure

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Bacterial response to nitric oxide (NO) is of major importance since NO is an obligatory intermediate of the nitrogen cycle. Transcriptional regulation of the dissimilatory nitric oxides metabolism in bacteria is diverse and involves FNR-like transcription factors HcpR, DNR, and NnrR; two-component systems NarXL and NarQP; NO-responsive activator NorR; and nitrite-sensitive repressor NsrR. Using comparative genomics approaches, we predict DNA-binding motifs for these transcriptional factors and describe corresponding regulons in available bacterial genomes. Within the FNR family of regulators, we observed a correlation of two specificity-determining amino acids and contacting bases in corresponding DNA recognition motif. Highly conserved regulon HcpR for the hybrid cluster protein and some other redox enzymes is present in diverse anaerobic bacteria, including Clostridia, Thermotogales, and delta-proteobacteria. NnrR and DNR control denitrification in alpha- and beta-proteobacteria, respectively. Sigma-54-dependent NorR regulon found in some gamma- and beta-proteobacteria contains various enzymes involved in the NO detoxification. Repressor NsrR, which was previously known to control only nitrite reductase operon in Nitrosomonas spp., appears to be the master regulator of the nitric oxides' metabolism, not only in most gamma- and beta-proteobacteria (including well-studied species such as Escherichia coli), but also in Gram-positive Bacillus and Streptomyces species. Positional analysis and comparison of regulatory regions of NO detoxification genes allows us to propose the candidate NsrR-binding motif. The most conserved member of the predicted NsrR regulon is the NO-detoxifying flavohemoglobin Hmp. In enterobacteria, the regulon also includes two nitrite-responsive loci, nipAB (hcp-hcr) and nipC (dnrN), thus confirming the identity of the effector, i.e. nitrite. The proposed NsrR regulons in Neisseria and some other species are extended to include denitrification genes. As the result, we demonstrate considerable interconnection between various nitrogen-oxides-responsive regulatory systems for the denitrification and NO detoxification genes and evolutionary plasticity of this transcriptional network