Showing papers by "Technion – Israel Institute of Technology published in 1994"

Oxidative damage to proteins : spectrophotometric method for carbonyl assay

Abstract: Publisher Summary Oxygen radicals are implicated as an important cause of oxidative modification of proteins which may lead to their rapid degradation. Among the various oxidative modifications of amino acids in proteins, carbonyl formation may be an early marker for protein oxidation. This type of alteration is characterized as metal-catalyzed oxidation of proteins. The molecular mechanisms of this type of protein oxidation are discussed in this chapter. Redox cycling cations, such as Fe 2+ or Cu 2+ can bind to cation binding locations on proteins and with the aid of further attack by H 2 O 2 or O 2 can transform side-chain amine groups on several amino acids into carbonyls. The most likely amino acid residues to form carbonyl derivatives are lysine, arginine, proline, and histidine. Metal-catalyzed oxidation of proteins is not necessarily the only mechanism by which carbonyls are introduced into proteins. The chapter discusses the physiological importance of protein oxidation. Increases in carbonyl levels are examined in several diseases, such as rheumatoid arthritis, ischemia-reperfusion injury to heart muscles, and muscle damage caused by exhaustive exercise.

Model checking and abstraction

Abstract: We describe a method for using abstraction to reduce the complexity of temporal-logic model checking. Using techniques similar to those involved in abstract interpretation, we construct an abstract model of a program without ever examining the corresponding unabstracted model. We show how this abstract model can be used to verify properties of the original program. We have implemented a system based on these techniques, and we demonstrate their practicality using a number of examples, including a program representing a pipelined ALU circuit with over 101300 states.

Information theoretic considerations for cellular mobile radio

Abstract: We present some information-theoretic considerations used to determine upper bounds on the information rates that can be reliably transmitted over a two-ray propagation path mobile radio channel model, operating in a time division multiplex access (TDMA) regime, under given decoding delay constraints. The sense in which reliability is measured is addressed, and in the interesting eases where the decoding delay constraint plays a significant role, the maximal achievable rate (capacity), is specified in terms of capacity versus outage. In this case, no coding capacity in the strict Shannon sense exists. Simple schemes for time and space diversity are examined, and their potential benefits are illuminated from an information-theoretic stand point. In our presentation, we chose to specialize to the TDMA protocol for the sake of clarity and convenience. Our main arguments and results extend directly to certain variants of other multiple access protocols such as code division multiple access (CDMA) and frequency division multiple access (FDMA), provided that no fast feedback from the receiver to the transmitter is available. >

Traveling wave solutions of parabolic systems

Abstract: Part I. Stationary waves: Scalar equation Leray-Schauder degree Existence of waves Structure of the spectrum Stability and approach to a wave Part II. Bifurcation of waves: Bifurcation of nonstationary modes of wave propagation Mathematical proofs Part III. Waves in chemical kinetics and combustion: Waves in chemical kinetics Combustion waves with complex kinetics Estimates and asymptotics of the speed of combustion waves Asymptotic and approximate analytical methods in combustion problems (supplement) Bibliography.

Model checking and modular verification

Abstract: We describe a framework for compositional verification of finite-state processes. The framework is based on two ideas: a subset of the logic CTL for which satisfaction is preserved under composition, and a preorder on structures which captures the relation between a component and a system containing the component. Satisfaction of a formula in the logic corresponds to being below a particular structure (a tableau for the formula) in the preorder. We show how to do assume-guarantee-style reasoning within this framework. Additionally, we demonstrate efficient methods for model checking in the logic and for checking the preorder in several special cases. We have implemented a system based on these methods, and we use it to give a compositional verification of a CPU controller.

Residues in chaperonin GroEL required for polypeptide binding and release

Abstract: Chaperonins are ring-shaped protein complexes that are essential in the cell, mediating ATP-dependent polypeptide folding in a variety of compartments. Recent studies suggest that they function through multiple rounds of binding and release of non-native proteins: with each round of ATP-driven release into the bulk solution, a substrate protein kinetically partitions between folding to the native state or rebinding to another chaperonin molecule. To gain further insight into the mechanism of polypeptide binding and release by the chaperonin GroEL from Escherichia coli, we have undertaken a mutational analysis that relates the functional properties of GroEL to its crystal structure. Our functional tests identify a putative polypeptide-binding site on the inside surface of the apical domain, facing the central channel, consisting of hydrophobic residues. These same residues are essential for binding of the co-chaperonin GroES, which is required for productive polypeptide release. A highly conserved residue, Asp 87, positioned within a putative nucleotide-binding pocket in the top of the equatorial domain, is essential for ATP hydrolysis and polypeptide release.

The soft x-ray properties of a complete sample of optically selected quasars. 1: First results

Abstract: We present the results of ROSAT position sensitive proportional counter (PSPC) observations of 10 quasars. These objects are part of our ROSAT program to observe a complete sample of optically selected quasars. This sample includes all 23 quasars from the bright quasar survey with a redshift z less than or = 0.400 and a Galactic H I column density N(sup Gal sub H I) less than 1.9 x 10(exp 20)/sq cm. These selection criteria, combined with the high sensitivity and improved energy resolution of the PSPC, allow us to determine the soft (approximately 0.2-2 keV) X-ray spectra of quasars with about an order of magnitude higher precision compared with earlier soft X-ray observations. The following main results are obtained: Strong correlations are suggested between the soft X-ray spectral slope alpha(sub x) and the following emission line parameters: H beta Full Width at Half Maximum (FWHM), L(sub O III), and the Fe II/H beta flux ratio. These correlations imply the following: (1) The quasar's environment is likely to be optically thin down to approximately 0.2 keV. (2) In most objects alpha(sub x) varies by less than approximately 10% on timescales shorter than a few years. (3) alpha(sub x) might be a useful absolute luminosity indicator in quasars. (4) The Galactic He I and H I column densities are well correlated. Most spectra are well characterized by a simple power law, with no evidence for either significant absorption excess or emission excess at low energies, to within approximately 30%. We find mean value of alpha(sub x) = -1.50 +/- 0.40, which is consistent with other ROSAT observations of quasars. However, this average is significantly steeper than suggested by earlier soft X-ray observations of the Einstein IPC. The 0.3 keV flux in our sample can be predicted to better than a factor of 2 once the 1.69 micrometer(s) flux is given. This implies that the X-ray variability power spectra of quasars flattens out between f approximately 10(exp -5) and f approximately 10(exp -8) Hz. A steep alpha(sub x) is mostly associated with a weak hard X-ray component, relative to the near-IR and optical emission, rather than a strong soft excess, and the scatter in the normalized 0.3 keV flux is significantly smaller than the scatter in the normalized 2 keV flux. This argues against either thin or thick accretion disks as the origin of the soft X-ray emission. Further possible implications of the results found here are briefly discussed.

Definitions and properties of zero-knowledge proof systems

Abstract: In this paper we investigate some properties of zero-knowledge proofs, a notion introduced by Goldwasser, Micali, and Rackoff. We introduce and classify two definitions of zero-knowledge: auxiliary-input zero-knowledge and blackbox-simulation zero-knowledge. We explain why auxiliary-input zero-knowledge is a definition more suitable for cryptographic applications than the original [GMR1] definition. In particular, we show that any protocol solely composed of subprotocols which are auxiliary-input zero-knowledge is itself auxiliary-input zero-knowledge. We show that blackbox-simulation zero-knowledge implies auxiliary-input zero-knowledge (which in turn implies the [GMR1] definition). We argue that all known zero-knowledge proofs are in fact blackbox-simulation zero-knowledge (i.e., we proved zero-knowledge using blackbox-simulation of the verifier). As a result, all known zero-knowledge proof systems are shown to be auxiliary-input zero-knowledge and can be used for cryptographic applications such as those in [GMW2]. We demonstrate the triviality of certain classes of zero-knowledge proof systems, in the sense that only languages in BPP have zero-knowledge proofs of these classes. In particular, we show that any language having a Las Vegas zero-knowledge proof system necessarily belongs to RP. We show that randomness of both the verifier and the prover, and nontriviality of the interaction are essential properties of (nontrivial) auxiliary-input zero-knowledge proofs.

New types of cryptanalytic attacks using related keys

Abstract: In this paper we study the influence of key-scheduling algorithms on the strength of blockciphers. We show that the key-scheduling algorithms of many blockciphers inherit obvious relationships between keys, and use these key relations to attack the blockciphers. Two new types of attacks are described: New chosen plaintext reductions of the complexity of exhaustive search attacks (and the faster variants based on complementation properties), and new low-complexity chosen key attacks. These attacks are independent of the number of rounds of the cryptosystems and of the details of the F-function and may have very small complexities. These attacks show that the key-scheduling algorithm should be carefully designed and that its structure should not be too simple. These attacks are applicable to both variants of LOKI and to Lucifer. DES is not vulnerable to the related keys attacks since the shift pattern in the key-scheduling algorithm is not the same in all the rounds.

Transfer of Skill from a Computer Game Trainer to Flight

Abstract: An experimental study was conducted to test the transfer of skills from a complex computer game to the flight performance of cadets in the Israeli Air Force flight school. The context relevance of the game to flight was argued on the basis of a skill-oriented task analysis, using the framework provided by contemporary models of the human processing system. The influence of two embedded training strategies was compared, one focusing on the specific skills involved in performing the game, the other designed to improve the general ability of trainees to cope with the high processing and response demands of the flight task and teach better strategies of attention control. Efficient control and management of attention under high task load are argued to be skills that can improve with proper training and generalize to new situations. Flight performance scores of two groups of cadets who received 10 h of training in the computer game were compared with those of a matched group without game experience. Both game ...

Recent developments in modeling heat transfer in blood perfused tissues

Abstract: Successful hyperthermia treatment of tumors requires understanding the attendant thermal processes in both diseased and healthy tissue. Accordingly, it is essential for developers and users of hyperthermia equipment to predict, measure and interpret correctly the tissue thermal and vascular response to heating. Modeling of heat transfer in living tissues is a means towards this end. Due to the complex morphology of living tissues, such modeling is a difficult task and some simplifying assumptions are needed. Some investigators have recently argued that Pennes' interpretation of the vascular contribution to heat transfer in perfused tissues fails to account for the actual thermal equilibration process between the flowing blood and the surrounding tissue and proposed new models, presumably based on a more realistic anatomy of the perfused tissue. The present review compares and contrasts several of the new bio-heat transfer models, emphasizing the problematics of their experimental validation, in the absence of measuring equipment capable of reliable evaluation of tissue properties and their variations that occur in the spatial scale of blood vessels with diameters less than about 0.2 mm. For the most part, the new models still lack sound experimental grounding, and in view of their inherent complexity, the best practical approach for modeling bio-heat transfer during hyperthermia may still be the Pennes model, providing its use is based on some insights gained from the studies described here. In such cases, these models should yield a more realistic description of tissue locations and/or thermal conditions for which the Pennes model might not apply. >

The Role of pH and Temperature in the Development of Leishmania Parasites

Abstract: Protozoans of the genus Leishmania are obligate intracellular parasites that cycle between the midgut of sandflies and the phagolysosomes of mammalian macrophages and therefore are exposed to extreme environmental changes. Recent evidence obtained from in vitro experiments indicate that such environmental changes trigger a developmental program in the parasites. Thus, following heat shock, promastigotes from certain Leishmania species differentiate to amastigotes. Promastigotes also respond to acidification of their environment by changing the expression of a number of genes. However, the combination of both low pH and high temperature induces the transformation of the promastigote to the amastigote in all Leishmania species examined to date. This review discusses the role of pH and heat shock in gene regulation and its contribution to the differentiation processes in Leishmania spp. Cycling between cold-blooded insect vectors and the warm-blooded mammalian host is not unique to Leishmania spp., but typical to most parasitic protozoa. It is therefore likely that the mechanism of stress-induced differentiation is shared by other mammalian parasites.

Structural investigation of xenon-ion-beam-irradiated glassy carbon

Abstract: Raman spectroscopy, cross-sectional transmission electron microscopy, and electron-energy-loss spectroscopy have been used to monitor the ion-beam-induced transformation in glassy carbon irradiated with 320-keV Xe ions to doses between 5\ifmmode\times\else\texttimes\fi{}${10}^{12}$ and 6\ifmmode\times\else\texttimes\fi{}${10}^{16}$ ions/${\mathrm{cm}}^{2}$. It was found that (i) the ion beam amorphizes the glassy carbon structure; (ii) the amorphization is accompanied by a compaction of the glassy carbon from an initial density of 1.55 to 2.2\ifmmode\pm\else\textpm\fi{}0.2 g/${\mathrm{cm}}^{3}$; and (iii) approximately 15% of the graphitelike bonds in glassy carbon are converted to diamondlike bonds in the amorphization process. The transformation of glassy carbon to an amorphous state occurs in two distinct stages as a function of ion dose. For damage levels up to 0.2 displacements per atom (dpa) the effect of the ion beam is to decrease the average graphitic crystallite size. Above 0.2 dpa, disorder in bond length and bond angle away from ideal graphitic threefold coordination occurs leading to complete amorphization at high doses. The amorphization, compaction, and presence of \ensuremath{\approxeq}15% ${\mathit{sp}}^{3}$ bonds in the implanted layer of glassy carbon results in a surface layer which is significantly more resistant to abrasion than as-grown glassy carbon.

Word sense disambiguation using a second language monolingual corpus

Abstract: This paper presents a new approach for resolving lexical ambiguities in one language using statistical data from a monolingual corpus of another language. This approach exploits the differences between mappings of words to senses in different languages. The paper concentrates on the problem of target word selection in machine translation, for which the approach is directly applicable. The presented algorithm identifies syntactic relations between words, using a source language parser, and maps the alternative interpretations of these relations to the target language, using a bilingual lexicon. The preferred senses are then selected according to statistics on lexical relations in the target language. The selection is based on a statistical model and on a constraint propagation algorithm, which simultaneously handles all ambiguities in the sentence. The method was evaluated using three sets of Hebrew and German examples and was found to be very useful for disambiguation. The paper includes a detailed comparative analysis of statistical sense disambiguation methods.

The fragile X syndrome d(CGG)n nucleotide repeats form a stable tetrahelical structure

Abstract: The fragile X mental retardation syndrome is associated with the expansion of trinucleotide 5'-d(CGG)-3' repeats within the FMR1 gene and with hypermethylation of the cytosine residues of these repeats The expansion and hypermethylation may account for the suppression of the transcription of the FMR1 gene and for the delay of its replication during the cell cycle Here we show that d(CGG)n oligomers can form a stable Hoogsteen-bonded structure that exhibits properties consistent with those of tetraplex DNA Oligomers, d(mCGG)n, (n = 4, 5, or 7), at pH 80 and in the presence of an alkali metal ion form stable species exhibiting a reduced electrophoretic mobility in nondenaturing polyacrylamide gels These species are denatured by heating at 90 degrees C for 10 min With a short d(mCGG)5 oligomer, the slowly migrating species is formed only when the cytosine residue is 5-methylated, whereas with the longer d(CGG)7 it is generated whether or not cytosine is 5-methylated By contrast, complementary cytosine-rich oligomers do not form analogous complexes The second-order association kinetics of the formation of the slowly migrating species of d(mCGG)5 suggests that it is an interstrand complex Formation of intermediate-size complexes between d(mCGG)5 and d(mCGG)7 indicates that the stoichiometry of the slowly migrating structures is tetramolecular Protection of the complex from methylation by dimethyl sulfate indicates the involvement of the N-7 positions of the guanine residues in Hoogsteen hydrogen bonding, a characteristic of quadruplex structures If formed in vivo along the expanded and hypermethylated d(mCGG)n stretch, this tetraplex structure could suppress transcription and replication of the FMR1 gene in the fragile X syndrome cells

Sleep disorders and melatonin rhythms in elderly people.

Abstract: Biological aging is often associated with problems with sleep and daytime napping.1 There is considerable evidence linking melatonin, produced by the pineal gland, with the sleep-wake cycle. When administered orally to humans or animals it enhances sleep2 and has a synchronising effect on circadian rhythms. Circulating melatonin concentrations decrease in old age, and its time of secretion is delayed.3 We examined whether sleep disorders in old age were associated with changes in concentration of 6-sulphatoxymelatonin, the major urinary measure of melatonin. The study population comprised four groups: (a) eight independently living patients with insomnia (four men, four women, mean age 73.1 (SD 3.9)); (b) 15 patients with insomnia (five men, 10 women, mean age 82.1 (8.8)) who had lived a minimum of six months in a nursing home; (c) 25 elderly patients without sleep disorders (19 …

Sequential consistency versus linearizability

Abstract: The power of two well-known consistency conditions for shared-memory multiprocessors, sequential consistency and linearizability, is compared. The cost measure studied is the worst-case response time in distributed implementations of virtual shared memory supporting one of the two conditions. Three types of shared-memory objects are considered: read/write objects, FIFO queues, and stacks. If clocks are only approximately synchronized (or do not exist), then for all three object types it is shown that linearizability is more expensive than sequential consistency. We show that, for all three data types, the worst-case response time is very sensitive to the assumptions that are made about the timing information available to the system. Under the strong assumption that processes have perfectly synchronized clocks, it is shown that sequential consistency and linearizability are equally costly. We present upper bounds for linearizability and matching lower bounds for sequential consistency. The upper bounds are shown by presenting algorithms that use atomic broadcast in a modular fashion. The lower-bound proofs for the approximate case use the technique of “shifting,” first introduced for studying the clock synchronization problem.

On the power of randomization in on-line algorithms

Abstract: Against in adaptive adversary, we show that the power of randomization in on-line algorithms is severely limited! We prove the existence of an efficient "simulation" of randomized on-line algorithms by deterministic ones, which is best possible in general. The proof of the upper bound is existential. We deal with the issue of computing the efficient deterministic algorithm, and show that this is possible in very general cases.

Nonlinear dispersion and compact structures

Abstract: Relaxing the distinguished ordering underlying the derivation of soliton supporting equations leads to new equations endowed with nonlinear dispersion crucial for the formation and coexistence of compactons, solitons with a compact support, and conventional solitons. Vibrations of the anharmonic mass-spring chain lead to a new Boussinesq equation admitting compactons and compact breathers. The model equation ${u}_{t}+{[\frac{\ensuremath{\delta}u+3\ensuremath{\gamma}{u}^{2}}{2+{u}^{1\ensuremath{-}\ensuremath{\omega}}{({u}^{\ensuremath{\omega}}{u}_{x})}_{x}}]}_{x}+\ensuremath{ u}{u}_{\mathrm{txx}}=0(\ensuremath{\omega},\ensuremath{ u},\ensuremath{\delta},\ensuremath{\gamma} \mathrm{const})$ admits compactons and for $2\ensuremath{\omega}=\ensuremath{ u}\ensuremath{\gamma}=1$ has a bi-Hamiltonian structure. The infinite sequence of commuting flows generates an integrable, compacton's supporting variant of the Harry Dym equation.

Optimization Methods for Truss Geometry and Topology Design

Abstract: Truss topology design for minimum external work (compliance) can be expressed in a number of equivalent potential or complementary energy problem formulations in terms of member forces, displacements and bar areas. Using duality principles and non-smooth analysis we show how displacements only as well as stresses only formulations can be obtained and discuss the implications these formulations have for the construction and implementation of efficient algorithms for large-scale truss topology design. The analysis covers min-max and weighted average multiple load designs with external as well as self-weight loads and extends to the topology design of reinforcement and the topology design of variable thickness sheets and sandwich plates. On the basis of topology design as an inner problem in a hierarchical procedure, the combined geometry and topology design of truss structures is also considered. Numerical results and illustrative examples are presented.

Realtime curve interpolators

Abstract: The amount of geometric information that must be transferred between a cad system and a computerized numerical control system creates a conflict between part precision on the one hand and feedrate fidelity and communications load on the other. This is the motivation for the development of new curve interpolation algorithms for CNC. The interpolation depends on the method of curve representation, i.e. the use of an implicit or a parametric from. Accordingly, the paper presents two realtime interpolation algorithms and compares them with existing cad interpolators. With the new interpolators, the amount of geometric information transferred from the cad system to the CNC system is reduced by orders of magnitude. Moreover, the contour errors caused by the new interpolators are much smaller than those caused by conventional cad interpolators.

Isolation of the tomato AGAMOUS gene TAG1 and analysis of its homeotic role in transgenic plants.

Abstract: To understand the details of the homeotic systems that govern flower development in tomato and to establish the ground rules for the judicious manipulation of this floral system, we have isolated the tomato AGAMOUS gene, designated TAG1, and examined its developmental role in antisense and sense transgenic plants. The AGAMOUS gene of Arabidopsis is necessary for the proper development of stamens and carpels and the prevention of indeterminate growth of the floral meristem. Early in flower development, TAG1 RNA accumulates uniformly in the cells fated to differentiate into stamens and carpels and later becomes restricted to specific cell types within these organs. Transgenic plants that express TAG1 antisense RNA display homeotic conversion of third whorl stamens into petaloid organs and the replacement of fourth whorl carpels with pseudocarpels bearing indeterminate floral meristems with nested perianth flowers. A complementary phenotype was observed in transgenic plants expressing the TAG1 sense RNA in that first whorl sepals were converted into mature pericarpic leaves and sterile stamens replaced the second whorl petals.