How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Signal set design for full-diversity low-decoding-complexity differential scaled-unitary STBCs

The problem of designing high rate, full diversity noncoherent space-time block codes (STBCs) with low encoding and decoding complexity is addressed. First, the notion of g-group encodable and g-group decodable linear STBCs is introduced. Then for a known class of rate-1 linear designs, an explicit construction of fully-diverse signal sets that lead to four-group encodable and four-group decodable differential scaled unitary STBCs for any power of two number of antennas is provided. Previous works on differential STBCs either sacrifice decoding complexity for higher rate or sacrifice rate for lower decoding complexity.

Gene modulation and immunoregulatory roles of Interferon gamma

Interferon-gamma (IFN gamma) is a central regulator of the immune response and signals via the Janus Activated Kinase (JAK)-Signal Transducer and Activator of Transcription (STAT) pathway. Phosphorylated STAT1 homodimers translocate to the nucleus, bind to Gamma Activating Sequence (GAS) and recruit additional factors to modulate gene expression. A bioinformatics analysis revealed that greater number of putative promoters of immune related genes and also those not directly involved in immunity contain GAS compared to response elements (RE) for Interferon Regulatory Factor (IRF)1, Nuclear factor kappa B (NF kappa B) and Activator Protein (AP)1. GAS is present in putative promoters of well known IFN gamma-induced genes, IRF1, GBP1, CXCL10, and other genes identified were TLR3, VCAM1, CASP4, etc. Analysis of three microarray studies revealed that the expression of asubset of only GAS containing immune genes were modulated by IFN gamma. As a significant correlation exists between GAS containing immune genes and IFN gamma-regulated gene expression, this strategy may identify novel IFN gamma-responsive immune genes. This analysis is integrated with the literature on the roles of IFN gamma in mediating a plethoraof functions: anti-microbial responses, antigen processing,inflammation, growth suppression, cell death, tumor immunity and autoimmunity. Overall, this review summarizes our present knowledge onIFN gamma mediated signaling and functions. (C) 2009 Elsevier Ltd. All rights reserved.

Response time measurement in flow induced signal generation on semiconductors

Measurable electrical signal is generated when a gas flows over a variety of solids, including doped semiconductors, even at the modest speed of a few meters per second. The underlying mechanism is an interesting interplay of Bernoulli's principle and the Seebeck effect. The electrical signal depends on the square of Mach number (M) and is proportional to the Seebeck coefficient (S) of the solids. Here we present experimental estimate of the response time of the signal rise and fall process, i.e. how fast the semiconductor materials respond to a steady flow as soon as it is set on or off. A theoretical model is also presented to understand the process and the dependence of the response time on the nature and physical dimensions of the semiconductor material used and they are compared with the experimental observations. (c) 2007 Elsevier B.V. All rights reserved.

Signal set design for full-diversity low-decoding-complexity differential scaled-unitary STBCs

The problem of designing high rate, full diversity noncoherent space-time block codes (STBCs) with low encoding and decoding complexity is addressed. First, the notion of g-group encodable and g-group decodable linear STBCs is introduced. Then for a known class of rate-1 linear designs, an explicit construction of fully-diverse signal sets that lead to four-group encodable and four-group decodable differential scaled unitary STBCs for any power of two number of antennas is provided. Previous works on differential STBCs either sacrifice decoding complexity for higher rate or sacrifice rate for lower decoding complexity.

Detection of a periodic structure hidden in random background: the role of signal amplitude in the matched filter detection method

The matched filter method for detecting a periodic structure on a surface hidden behind randomness is known to detect up to (r(0)/Lambda) gt;= 0.11, where r(0) is the coherence length of light on scattering from the rough part and 3 is the wavelength of the periodic part of the surface-the above limit being much lower than what is allowed by conventional detection methods. The primary goal of this technique is the detection and characterization of the periodic structure hidden behind randomness without the use of any complicated experimental or computational procedures. This paper examines this detection procedure for various values of the amplitude a of the periodic part beginning from a = 0 to small finite values of a. We thus address the importance of the following quantities: `(a)lambda) `, which scales the amplitude of the periodic part with the wavelength of light, and (r(0))Lambda),in determining the detectability of the intensity peaks.

A non-orthogonal distributed space-time coded protocol - Part 1:Signal model and design criteria

In this two-part series of papers, a generalized non-orthogonal amplify and forward (GNAF) protocol which generalizes several known cooperative diversity protocols is proposed. Transmission in the GNAF protocol comprises of two phases - the broadcast phase and the cooperation phase. In the broadcast phase, the source broadcasts its information to the relays as well as the destination. In the cooperation phase, the source and the relays together transmit a space-time code in a distributed fashion. The GNAF protocol relaxes the constraints imposed by the protocol of Jing and Hassibi on the code structure. In Part-I of this paper, a code design criteria is obtained and it is shown that the GNAF protocol is delay efficient and coding gain efficient as well. Moreover GNAF protocol enables the use of sphere decoders at the destination with a non-exponential Maximum likelihood (ML) decoding complexity. In Part-II, several low decoding complexity code constructions are studied and a lower bound on the Diversity-Multiplexing Gain tradeoff of the GNAF protocol is obtained.

Transient signal detection using wigner-ville distribution and wavelet denoising

The problem of detecting an unknown transient signal in noise is considered. The SNR of the observed data is first enhanced using wavelet domain filter The output of the wavelet domain filter is then transformed using a Wigner-Ville transform,which separates the spectrum of the observed signal into narrow frequency bands. Each subband signal at the output of the Wigner-ville block is subjected kto wavelet based level dependent denoising (WBLDD)to supress colored noise A weighted sum of the absolute value of outputs of WBLDD is passed through an energy detector, whose output is used as test statistic to take the final decision. By assigning weights proportional to the energy of the corresponding subband signals, the proposed detector approximates a frequency domain matched filter Simulation results are presented to show that the performance of the proposed detector is better than that of the wavelet packet transform based detector.

Coding for Two-User Gaussian MAC with PSK and PAM Signal Sets

Constellation Constrained (CC) capacity regions of a two-user Gaussian Multiple Access Channel(GMAC) have been recently reported. For such a channel, code pairs based on trellis coded modulation are proposed in this paper with MPSK and M-PAM alphabet pairs, for arbitrary values of M,toachieve sum rates close to the CC sum capacity of the GMAC. In particular, the structure of the sum alphabets of M-PSK and M-PAMmalphabet pairs are exploited to prove that, for certain angles of rotation between the alphabets, Ungerboeck labelling on the trellis of each user maximizes the guaranteed squared Euclidean distance of the sum trellis. Hence, such a labelling scheme can be used systematically,to construct trellis code pairs to achieve sum rates close to the CC sum capacity. More importantly, it is shown for the first time that ML decoding complexity at the destination is significantly reduced when M-PAM alphabet pairs are employed with almost no loss in the sum capacity.

Regulation of cytochrome P-450b/e gene expression by a heme- and phenobarbitone-modulated transcription factor

The cloned DNA fragment of the cytochrome P-450b/e gene containing the upstream region from position -179 through part of the first exon is faithfully transcribed in freeze-thawed rat liver nuclei. Phenobarbitone treatment of the animal strikingly increases this transcription, and the increase is blocked by cycloheximide (protein synthesis inhibitor) or CoCl2 (heme biosynthetic inhibitor) treatment of animals. This picture correlates very well with the reported cytochrome P-450b/e mRNA levels in vivo and run-on transcription rates in vitro under these conditions. The upstream region (from position -179) was assessed for protein binding with nuclear extracts by nitrocellulose filter binding, gel retardation, DNase I treatment ("footprinting"), and Western blot analysis. Phenobarbitone treatment dramatically increases protein binding to the upstream region, an increase once again blocked by cycloheximide or CoCl2 treatments. Addition of heme in vitro to heme-deficient nuclei and nuclear extracts restores the induced levels of transcription and protein binding to the upstream fragment, respectively. Thus, drug-mediated synthesis and heme-modulated binding of a transcription factor(s) appear involved in the transcriptional activation of the cytochrome P-450b/e genes, and an 85-kDa protein may be a major factor in this regard.

A Ca2+-sensitive cyclic-3',5'-nucleotide phosphodiesterase from sheep lung modulated by a tightly bound endogenous calmodulin.

Highly purified sheep lung cyclic-3',5'-nucleotide phosphodiesterase was sensitive to Ca2+/EGTA but insensitive to exogenous calmodulin. The Ca2+-sensitivity was inhibited by trifluoperazine. Heat-treated enzyme could activate a calmodulin-deficient phosphodiesterase, suggesting the presence of endogenous calmodulin in sheep lung cyclic-3',5'-nucleotide phosphodiesterase, possibly associated with the enzyme in a Ca2+-independent manner.

Wave propagation analysis in carbon nanotube embedded composite using wavelet based spectral finite elements

In this paper, elastic wave propagation is studied in a nanocomposite reinforced with multiwall carbon nanotubes (CNTs). Analysis is performed on a representative volume element of square cross section. The frequency content of the exciting signal is at the terahertz level. Here, the composite is modeled as a higher order shear deformable beam using layerwise theory, to account for partial shear stress transfer between the CNTs and the matrix. The walls of the multiwall CNTs are considered to be connected throughout their length by distributed springs, whose stiffness is governed by the van der Waals force acting between the walls of nanotubes. The analyses in both the frequency and time domains are done using the wavelet-based spectral finite element method (WSFEM). The method uses the Daubechies wavelet basis approximation in time to reduce the governing PDE to a set of ODEs. These transformed ODEs are solved using a finite element (FE) technique by deriving an exact interpolating function in the transformed domain to obtain the exact dynamic stiffness matrix. Numerical analyses are performed to study the spectrum and dispersion relations for different matrix materials and also for different beam models. The effects of partial shear stress transfer between CNTs and matrix on the frequency response function (FRF) and the time response due to broadband impulse loading are investigated for different matrix materials. The simultaneous existence of four coupled propagating modes in a double-walled CNT-composite is also captured using modulated sinusoidal excitation.

Unified large and small signal non-quasi-static model for long channel symmetric DG MOSFET

We propose a unified model for large signal and small signal non-quasi-static analysis of long channel symmetric double gate MOSFET. The model is physics based and relies only on the very basic approximation needed for a charge-based model. It is based on the EKV formalism Enz C, Vittoz EA. Charge based MOS transistor modeling. Wiley; 2006] and is valid in all regions of operation and thus suitable for RF circuit design. Proposed model is verified with professional numerical device simulator and excellent agreement is found. (C) 2010 Elsevier Ltd. All rights reserved.

Composite signal decomposition by digital inverse filtering

Inverse filters are conventionally used for resolving overlapping signals of identical waveshape. However, the inverse filtering approach is shown to be useful for resolving overlapping signals, identical or otherwise, of unknown waveshapes. Digital inverse filter design based on autocorrelation formulation of linear prediction is known to perform optimum spectral flattening of the input signal for which the filter is designed. This property of the inverse filter is used to accomplish composite signal decomposition. The theory has been presented assuming constituent signals to be responses of all-pole filters. However, the approach may be used for a general situation.