Nonparametric Bayesian sparse factor models with application to gene expression modeling

A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data $\mathbf{Y}$ is modeled as a linear superposition, $\mathbf{G}$, of a potentially infinite number of hidden factors, $\mathbf{X}$. The Indian Buffet Process (IBP) is used as a prior on $\mathbf{G}$ to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated data sets based on a known sparse connectivity matrix for E. Coli, and on three biological data sets of increasing complexity.

Robust control of plants with saturation nonlinearity based on coprime factor representations

We consider the robust control of plants with saturation nonlinearities from an input/output viewpoint. First, we present a parameterization for anti-windup control based on coprime factorizations of the controller. Second, we propose a synthesis method which exploits the freedom to choose a particular coprime factorization.

Numerical modelling of lubricated foil rolling

A model of lubricated cold strip rolling (1, 2) is extended to the thin foil regime. The model considers the evolution of asperity geometry and lubricant pressure through the bite, treating the strip using a conventional slab model. The elastic deflections of the rolls are coupled into the problem using an elastic finite element model. Friction between the roll and the asperities on the strip is modelled using the Coulomb and Tresca friction factor approaches. The shear stress in the Coulomb friction model is limited to the shear yield stress of the strip. A novel modification to these standard friction laws is used to mimic slipping friction in the reduction regions and sticking friction in a central neutral zone. The model is able to reproduce the sticking and slipping zones predicted by Fleck et al. (3). The variation of rolling load, lubricant film thickness and asperity contact area with rolling speed is examined, for conditions typical of rolling aluminium foil from a thickness of 50 to 25 μm. T he contact area and hence friction rises as the speed drops, leading to a large increase in rolling load. This increase is considerably more marked using Coulomb friction as compared with the friction factor approach. Forward slip increases markedly as the speed falls and a significant sticking region develops.

Visualization of turbulent wedges under favourable pressure gradients using both shear-sensitive and temperature-sensitive liquid crystals

Turbulent wedges induced by a 3D surface roughness placed in a laminar boundary layer over a flat plate were visualised for the first time using both shear-sensitive and temperature-sensitive liquid crystals. The experiments were carried out at three different levels of favourable pressure gradients. The purpose of this investigation was to examine the spreading angles of the turbulent wedges indicated by their associated surface shear stresses and heat transfer characteristics and hence obtain further insight about the difference in the behaviour of transitional momentum and thermal boundary layers when a streamwise pressure gradient exists. It was shown that under a zero pressure gradient the spreading angles indicated by the two types of liquid crystals are the same, but the difference increases as the level of favourable pressure gradient increases. The result from the present study could have an important implication to the transition modelling of thermal boundary layers over gas turbine blades.

Laminar to turbulent flow transition measurements using an array of SOI-CMOS MEMS wall shear stress sensors

The successful utilization of an array of silicon on insulator complementary metal oxide semiconductor (SOICMOS) micro thermal shear stress sensors for flow measurements at macro-scale is demonstrated. The sensors use CMOS aluminum metallization as the sensing material and are embedded in low thermal conductivity silicon oxide membranes. They have been fabricated using a commercial 1 μm SOI-CMOS process and a post-CMOS DRIE back etch. The sensors with two different sizes were evaluated. The small sensors (18.5 ×18.5 μm2 sensing area on 266 × 266 μm2 oxide membrane) have an ultra low power (100 °C temperature rise at 6mW) and a small time constant of only 5.46 μs which corresponds to a cut-off frequency of 122 kHz. The large sensors (130 × 130 μm2 sensing area on 500 × 500 μm2 membrane) have a time constant of 9.82 μs (cut-off frequency of 67.9 kHz). The sensors' performance has proven to be robust under transonic and supersonic flow conditions. Also, they have successfully identified laminar, separated, transitional and turbulent boundary layers in a low speed flow. © 2008 IEEE.

Nonparametric mixtures of factor analyzers

The mixtures of factor analyzers (MFA) model allows data to be modeled as a mixture of Gaussians with a reduced parametrization. We present the formulation of a nonparametric form of the MFA model, the Dirichlet process MFA (DPMFA). The proposed model can be used for density estimation or clustering of high dimensiona data. We utilize the DPMFA for clustering the action potentials of different neurons from extracellular recordings, a problem known as spike sorting. DPMFA model is compared to Dirichlet process mixtures of Gaussians model (DPGMM) which has a higher computational complexity. We show that DPMFA has similar modeling performance in lower dimensions when compared to DPGMM, and is able to work in higher dimensions. ©2009 IEEE.

ISOLATION AND PROPERTIES OF A BLOOD-COAGULATION FACTOR-X ACTIVATOR FROM THE VENOM OF KING COBRA (OPHIOPHAGUS HANNAH)

A specific blood coagulation factor X activator was purified from the venom of Ophiophagus hannah by gel filtration and two steps of FPLC Mono-Q column ion-exchange chromatography. It showed a single protein band both in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and alkaline polyacrylamide gel electrophoresis. The mol. wt was estimated to be 62,000 in non-reducing conditions and 64,500 in reducing conditions by SDS-PAGE. The isoelectric point was found to be pH 5.6. The enzyme had weak amidolytic activities toward CBS 65-25, but it showed no activities on S-2266, S-2302, thrombin substrate S-2238, plasmin substrate S-2251 or factor Xa substrate S-2222. It had no arginine esterase activity toward substrate benzoylarginine ethylester (BAEE). The enzyme activated factor X in vitro and the effect was absolutely Ca2+ dependent, with a Hill coefficient of 6.83. It could not activate prothrombin nor had any effect on fibrinogen and thus appeared to act specifically on factor X. The procoagulant activity of the enzyme was almost completely inhibited by serine protease inhibitors like PMSF, TPCK and soybean trypsin inhibitor; partially inhibited by L-cysteine. Metal chelator EDTA did not inhibit its procoagulant activity. These results suggest that the factor X activator from O. hannah venom is a serine protease.

AN ACTIVATOR OF BLOOD-COAGULATION FACTOR-X FROM THE VENOM OF BUNGARUS-FASCIATUS

A specific activator of blood coagulation factor X was purified from the venom of Bungarus fasciatus by gel filtration and by ion-exchange chromatography on a Mono-Q column (FPLC). It consisted of a single polypeptide chain, with a mel. wt of 70,000 in reducing and non-reducing conditions. The enzyme had an amidolytic activity towards the chromogenic substrates S-2266 and S-2302 but it did not hydrolyse S-2238, S2251 or S-2222, which are specific substrates for thrombin, plasmin and factor Xa, respectively. The enzyme activated factor X in vitro and the effect was Ca2+ dependent with a Hill coefficient of 7.9. As with physiological activators, the venom activator cleaves the heavy chain of factor X, producing the activated factor Xa alpha. The purified factor X activator from B. fasciatus venom did not activate prothrombin, nor did it cleave or clot purified fibrinogen. The amidolytic activity and the factor X activation activity of the factor X activator from B. fasciatus venom were readily inhibited by serine protease inhibitors such as diisopropyl fluorophosphate (DFP), phenylmethanesulfonyl fluoride (PMSF), benzamidine and by soybean trypsin inhibitor but not by EDTA. These observations suggest that the factor X activator from B. fasciatus venom is a serine protease. It therefore differs from those of activators obtained from Vipera russelli and Bothrops atrox venoms, which are metalloproteinases.

Cloning and characterization of a blood coagulation factor IX-binding protein from the venom of Trimeresurus stejnegeri

A blood coagulation factor IX-binding protein (TSV-FIX-BP) was isolated from the snake venom of Trimeresurus stejnegeri. On SDS-polyacrylamide gel electrophoresis, TSV-FIX-BP showed a single band with an apparent molecular weight of 23,000 under non-reducing conditions. and two distinct bands with apparent molecular weights of 14,800 and 14,000 under reducing conditions. cDNA clones containing the coding sequences of TSV-FIX-BP were isolated and sequenced to determine the structure of the precusors of TSV-FIX-BP subunits. The deduced amino acid sequences of two subunits of TSV-FIX-BP were confirmed by N-terminal protein sequencing and trypsin-digested peptide mass fingerprinting. TSV-FIX-BP was a nonenzymatic C-type lectin-like anti-coagulant. The anti-coagulant activity of TSV-FIX-BP was mainly caused by its dose dependent interaction with blood coagulation factor IX but not with blood coagulation factor X. (C) 2003 Elsevier Science Ltd. All rights reserved.

Bm-TFF2, a trefoil factor protein with platelet activation activity from frog Bombina maxima skin secretions

In mammals, trefoil factor family (TFF) proteins are involved in mucosal maintenance and repair, and they are also implicated in tumor suppression and cancer progression. A novel two domain TFF protein from frog Bombina maxima skin secretions (Bm-TFF2) has been purified and cloned. It activated human platelets in a dose-dependent manner and activation of integrin a(11b)beta(3) was involved. Aspirin and apyrase did not largely reduce platelet response to Bm-TFF2 (a 30% inhibition), indicating that the aggregation is not substantially dependent on ADP and thromboxane A2 autocrine feedback. Elimination of external Ca2+ with EGTA did not influence the platelet aggregation induced by Bm-TFF2, meanwhile a strong calcium signal (cytoplasmic Ca2+ release) was detected, suggesting that activation of phospholipase C (PLC) is involved. Subsequent immunoblotting revealed that, unlike in platelets activated by stejnulxin (a glycoprotein VI agonist), PLC gamma 2 was not phosphorylated in platelets activated by Bm-TFF2. FITC-labeled Bm-TFF2 bound to platelet membranes. Bm-TFF2 is the first TFF protein reported to possess human platelet activation activity. (c) 2005 Elsevier Inc. All rights reserved.

Factor intensity and economic returns of alternate shrimp crop and shrimp-salt farming in the coastal areas of Bangladesh

The paper examines the factor intensity and economic returns of alternate shrimp-crop and shrimp-salt farming in the coastal areas of Bangladesh. Data were collected from 30 shrimp-crop and 30 shrimp-salt farmers, 30 shrimp farmers and 30 rice farmers from three selected coastal districts of Bangladesh. Cobb-Douglas production function model was used to determine the effect of various factors on alternate shrimp-crop farming. The chosen variables were stocking of juveniles, paddy seed, labour, fertilizers, feed and farm size of respective type of farming. The results indicated that the production function exhibited increasing remrns to scale for alternate shrimp-rice, alternate shrimp-salt and year round shrimp farming while it indicated decreasing returns for year round rice farming. Economic analysis of same system of farming indicated that higher amount of input use produced higher level of yield, gross return and net return for each type of production system.

Length-weight relationship and relative condition factor of pond-reared mahseer, Tor putitora(Ham.)

The study deals with the length-weight relationship and relative condition factor (Kn) of mahseer, Tor putitora reared for 150 days in ponds. The logarithmic form of equation for the relationship was found to be logW = -1.727+2.875logL or W=O.Ol875U·875 • The graphical presentation of the parabolic and logarithmic forms showed respectively the curvilinear and linear relationships between length and weight of the fish. The mean value (±sd) of relative condition factor was found to be 0.95±0.12. The exponential value 'b' was found to be 2.96 and the coefficient of correlation 'r' was 0.965, which showed strong and highly correlated relationships between length and weight of the fish.

Length-weight relationship and relative condition factor in Oreochromis mossambicus (Peters) of Bhima River

Oreochromis mossambicus (Peters), a common freshwater fish of Bhima river, has high economic value and considerable fishery importance. The length-weight relationship in the logarithmic way for this fish can be written as: Log W = - 4.50241627 + 2.884822741 log L. This is close to the cubic law indicating the isometric growth of the fish in its natural habitat. The correlation coefficient (r) was found to be 0.9865 which showed a good relationship between the two parameters. The mean relative condition factor (K sub(n)) was 1.00 suggesting the well-being of the fish.

Length-weight relationship and condition factor of Perna viridis (Linnaeus, 1758) and Meretrix meretrix (Linnaeus, 1758) from Mumbai waters

Length weight relationship of the two commercially important molluscs P. viridis and M. meretrix was found to be W=-0.40263L super(2.044719) & W=-0.04359L super(2.2315498) respectively. Condition factor was recorded to be less than 1.0 for most part of the year in P. viridis and for M. meretrix it ranged from 0.39 to 4.61. The present study reveals that there was allometric growth in both the species and the growth was not satisfactory since it showed lower K-value during most part of the year.

beta gamma-CAT, a non-lens beta gamma-crystallin and trefoil factor complex from amphibian skin secretions, caused endothelium-dependent myocardial depression in isolated rabbit hearts

Previous in vivo study demonstrated that beta gamma-CAT, a newly identified non-lens beta gamma-crystallin and trefoil factor complex from frog Bombina maxima skin secretions, possessed potent lethal toxicity on mammals resulted from hypotension and cardi