Iterative optimization of high-affinity proteases inhibitors using phage display. 1. Plasmin

We generated a series of libraries having variants of the first Kunitz domain of human lipoprotein-associated coagulation inhibitor (LACI-D1, also known as tissue-factor pathway inhibitor-I) displayed on bacteriophage M13 as pIII-fusions. We varied LACI-DI iteratively in two regions: the P1 region (positions 10-21) and the "second loop", (positions 31-39), which together form one end of the domain. Display-phage library Lib#1 allows 31 200 amino-acid sequences in P1 region (residues 13, 16-19). Preliminary, we screened Lib#1 against human plasmin (PLA, EC 3.4.21.7) immobolized on agarose to enrich for phage displaying variants with PLA affinity. We introduced a 1600-fold increase in second-loop diversity (residues 31, 32, 34, 39) into the population of selectants from Lib#1, yielding Lib#2. Lib#2 (allowing approximately 50 million amino-acid sequences) was screened against PLA-agarose to isolate highest affinity binders. Protein EPI-P211, derived from the best isolate of Lib#2, inhibits PLA with Ki = 2 nM (at least 500-fold better than LACI-D1) and with high specificity. We used amino-acid sequences of PLA-binding selectants to design a PLA-biased library (Lib#3) which we screened against PLA. The protein EPI-P302 (derived from the best binder obtained from Lib#3) has Ki for PLA inhibition of 87 pM, which is 25-fold better than the first-round best binder and > or = 12 500-fold better than LACI-D1. EPI-P302 also shows very high specificity for PLA vs other human proteases and is resistant to inactivation by oxidants and extremes of temperature or pH. Thus, one can use selectants from one library to design target-tailored combinatorial libraries and obtain quite stable, highly specific, very high-affinity binding molecules while maintaining an essentially human framework.     

Hybrid phenol biosensor based on modified phenoloxidase electrode

Electrolytic deposition has been widely used to immobilize biomacromolecules, and it is always the most important factor to preserve or even increase an activity of the immobilized protein. We report here simple and rather universal method for the highly efficient immobilization of laccase for amperometric biosensing. Laccase from Cerrena unicolor has been successfully immobilized (electrolytic deposition) on the surface of thin, ordered polythiophene films (3-methylthiophene/3-thiopheneacetic acid/N-heptyl-3,6-bis(2-thiophene)carbazole). Two different compounds capable of mediating laccase-catalyzed reactions have been tested by cyclic voltammetry. They exhibited quasi-reversible electrodic behaviour with formal redox potentials ranging from 68 and 918 mV (E⁰vs. SCE). The immersion of the laccase-coated electrode in solution with substrate generated large catalytic currents easily recorded by cyclic voltammetry at low potential scan rates. Considering the fact, that immobilization strategy showed high efficiency, obtained results suggest that method for phenoloxidase immobilization has a great potential of enabling high throughput fabrication of bioelectronics’ devices.     

Soft set theory applied to p-ideals of BCI-algebras related to fuzzy points

The notions of $(\overline{\in}, \overline{\in} \vee \overline{\hbox{q}})The notions of ([`( ? )],[`( ? )] ú[`q])(\overline{\in}, \overline{\in} \vee \overline{\hbox{q}})-fuzzy p-ideals and fuzzy p-ideals with thresholds related to soft set theory are discussed. Relations between ([`( ? )],[`( ? )] ú[`q])(\overline{\in}, \overline{\in} \vee \overline{\hbox{q}})-fuzzy ideals and ([`( ? )],[`( ? )] ú[`q])(\overline{\in}, \overline{\in} \vee \overline{\hbox{q}})-fuzzy p-ideals are investigated. Characterizations of an ([`( ? )],[`( ? )] ú[`q])(\overline{\in}, \overline{\in} \vee \overline{\hbox{q}})-fuzzy p-ideal and a fuzzy p-ideal with thresholds are displayed. Implication-based fuzzy p-ideals are discussed.     

Robust portfolio optimization via solution to the Hamilton–Jacobi–Bellman equation

We consider a problem of dynamic stochastic portfolio optimization modelled by a fully non-linear Hamilton–Jacobi–Bellman (HJB) equation. Using the Riccati transformation, the HJB equation is transformed to a simpler quasi-linear partial differential equation. An auxiliary quadratic programming problem is obtained, which involves a vector of expected asset returns and a covariance matrix of the returns as input parameters. Since this problem can be sensitive to the input data, we modify the problem from fixed input parameters to worst-case optimization over convex or discrete uncertainty sets both for asset mean returns and their covariance matrix. Qualitative as well as quantitative properties of the value function are analysed along with providing illustrative numerical examples. We show application to robust portfolio optimization for the German DAX30 Index.     

A flexible encapsulated MEMS pressure sensor system for biomechanical applications

 The use of pressure sensors made of conductive polymers is common in biomechanical applications. Unfortunately, hysteresis, nonlinearity, non-repeatability and creep have a significant effect on the pressure readings when such conductive polymers are used. The objective of this paper is to explore the potential of a new flexible encapsulated micro electromechanical system (MEMS) pressure sensor system as an alternative for human interface pressure measurement. A prototype has been designed, fabricated, and characterized. Testing has shown that the proposed packaging approach shows very little degradation in the performance characteristics of the original MEMS pressure sensor. The much-needed characteristics of repeatability, linearity, low hysteresis, temperature independency are preserved. Thus the flexible encapsulated MEMS pressure sensor system is very promising and shows superiority over the commercially available conductive polymer film sensors for pressure measurement in biomechanical applications. Received: 1 December 1999/Accepted: 17 August 2000     

A low cost, non-individualized surround sound system based upon head related transfer functions: an ergonomics study and prototype development

This paper reports on the types and magnitudes of localization errors of simulated binaural direction cues generated using non-individualized, head-related transfer functions (HRTFs) with different levels of complexity. Four levels of complexity, as represented by the number of non-zero coefficients of the associated HRTF filters (128, 64, 32, 18 non-zero coefficients), were studied. Experiment 1 collected 1728 data runs that were exhaustive combinations of the four levels of complexity, nine simulated directions of sound (no direction (i.e., diotical-mono), 0 degrees , 45 degrees , 90 degrees , 135 degrees , 180 degrees , 225 degrees , 270 degrees , and 315 degrees azimuth angles at 0 degrees elevation), two repetitions, and 24 participants). Binaural cues generated from HRTFs of reduced complexity (from 128 to 18 non-zero coefficients) produced significantly higher localization errors for the directions of 45 degrees , 135 degrees , 225 degrees , and 315 degrees azimuth angles (p<0.01). From the directions of 0 degrees , 90 degrees , and 270 degrees azimuth angles, the cues produced by HRTFs with reduced complexity did not affect the localization error (p>0.2). Surprisingly, cues produced by HRTFs of 128 non-zero coefficients did not have the lowest number of errors. From 45 degrees , 135 degrees , 225 degrees , and 315 degrees , the lowest numbers of errors were obtained from cues produced by HRTFs of 64, 32, 32, and 64 non-zero coefficients, respectively. Based on these findings, a prototype virtual headphone-based surround-sound (VHSS) system was developed. A double-blind usability experiment with 32 participants indicated that the prototype VHSS system received significantly better surround-sound ratings than did a Dolby stereo system (p<0.02). This paper reports results from an original ergonomics study and the application of these results to the design of a consumer product.     

Computation of madalines' sensitivity to input and weight perturbations

The sensitivity of a neural network's output to its input and weight perturbations is an important measure for evaluating the network's performance. In this letter, we propose an approach to quantify the sensitivity of Madalines. The sensitivity is defined as the probability of output deviation due to input and weight perturbations with respect to overall input patterns. Based on the structural characteristics of Madalines, a bottom-up strategy is followed, along which the sensitivity of single neurons, that is, Adalines, is considered first and then the sensitivity of the entire Madaline network. By means of probability theory, an analytical formula is derived for the calculation of Adalines' sensitivity, and an algorithm is designed for the computation of Madalines' sensitivity. Computer simulations are run to verify the effectiveness of the formula and algorithm. The simulation results are in good agreement with the theoretical results.     

The course of geriatric depression with "reversible dementia": a controlled study

OBJECTIVE: The goals of this longitudinal investigation were 1) to study the rate of development of irreversible dementia in elderly depressed patients with a dementia syndrome that subsided after improvement of depression and 2) to compare it with that of depressed, never-demented patients. METHOD: The subjects were 57 elderly patients consecutively hospitalized for major depression. At entry into the study, 23 subjects also met criteria for "reversible dementia," while 34 were without dementia. After a systematic clinical evaluation, the subjects were followed up at approximately yearly intervals for an average of 33.8 months. RESULTS: Irreversible dementia developed significantly more frequently in the depressed group with reversible dementia (43%) than in the group with depression alone (12%). Survival analysis showed that the group with reversible dementia had a 4.69-times higher chance of having developed dementia at follow-up than the patients with depression alone. No clinical characteristics at entry into the study were found to discriminate the subjects who developed irreversible dementia during the follow-up period from those who remained nondemented. CONCLUSIONS: These findings suggest that geriatric depression with reversible dementia is a clinical entity that includes a group of patients with early-stage dementing disorders. Therefore, identification of a reversible dementia syndrome is an indication for a thorough diagnostic workup and frequent follow-ups in order to identify treatable neurological disorders.     

Modeling and measurement of simultaneous switching noise coupling through signal via transition

The signal via is a heavily utilized interconnection structure in high-density System-on-Package (SoP) substrates and printed circuit boards (PCBs). Vias facilitate complicated routings in these multilayer structures. Significant simultaneous switching noise (SSN) coupling occurs through the signal via transition when the signal via suffers return current interruption caused by reference plane exchange. The coupled SSN decreases noise and timing margins of digital and analog circuits, resulting in reduction of achievable jitter performance, bit error ratio (BER), and system reliability. We introduce a modeling method to estimate SSN coupling based on a balanced transmission line matrix (TLM) method. The proposed modeling method is successfully verified by a series of time-domain and frequency-domain measurements of several via transition structures. First, it is clearly verified that SSN coupling causes considerable clock waveform distortion, increases jitter and noise, and reduces margins in pseudorandom bit sequence (PRBS) eye patterns. We also note that the major frequency spectrum component of the coupled noise is one of the plane pair resonance frequencies in the PCB power/ground pair. Furthermore, we demonstrate that the amount of SSN noise coupling is strongly dependent not only on the position of the signal via, but also on the layer configuration of the multilayer PCB. Finally, we have successfully proposed and confirmed a design methodology to minimize the SSN coupling based on an optimal via positioning approach.