Showing papers by "Bar-Ilan University published in 2002"

An efficient k-means clustering algorithm: analysis and implementation

Abstract: In k-means clustering, we are given a set of n data points in d-dimensional space R/sup d/ and an integer k and the problem is to determine a set of k points in Rd, called centers, so as to minimize the mean squared distance from each data point to its nearest center. A popular heuristic for k-means clustering is Lloyd's (1982) algorithm. We present a simple and efficient implementation of Lloyd's k-means clustering algorithm, which we call the filtering algorithm. This algorithm is easy to implement, requiring a kd-tree as the only major data structure. We establish the practical efficiency of the filtering algorithm in two ways. First, we present a data-sensitive analysis of the algorithm's running time, which shows that the algorithm runs faster as the separation between clusters increases. Second, we present a number of empirical studies both on synthetically generated data and on real data sets from applications in color quantization, data compression, and image segmentation.

Multifractal Detrended Fluctuation Analysis of Nonstationary Time Series

Abstract: We develop a method for the multifractal characterization of nonstationary time series, which is based on a generalization of the detrended fluctuation analysis (DFA). We relate our multifractal DFA method to the standard partition function-based multifractal formalism, and prove that both approaches are equivalent for stationary signals with compact support. By analyzing several examples we show that the new method can reliably determine the multifractal scaling behavior of time series. By comparing the multifractal DFA results for original series with those for shuffled series we can distinguish multifractality due to long-range correlations from multifractality due to a broad probability density function. We also compare our results with the wavelet transform modulus maxima method, and show that the results are equivalent.

The Genome Sequence of the Malaria Mosquito Anopheles gambiae

Abstract: Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.

Attachment-related psychodynamics

Abstract: Because there has been relatively little communication and cross-fertilization between the two major lines of research on adult attachment, one based on coded narrative assessments of defensive processes, the other on simple self-reports of 'attachment style' in close relationships, we here explain and review recent work based on a combination of self-report and other kinds of method, including behavioral observations and unconscious priming techniques. The review indicates that considerable progress has been made in testing central hypotheses derived from attachment theory and in exploring unconscious, psychodynamic processes related to affect-regulation and attachment-system activation. The combination of self-report assessment of attachment style and experimental manipulation of other theoretically pertinent variables allows researchers to test causal hypotheses. We present a model of normative and individual-difference processes related to attachment and identify areas in which further research is needed and likely to be successful. One long-range goal is to create a more complete theory of personality built on attachment theory and other object relations theories.

Operads in algebra, topology, and physics

Abstract: 'Operads are powerful tools, and this is the book in which to read about them' - ""Bulletin of the London Mathematical Society"". Operads are mathematical devices that describe algebraic structures of many varieties and in various categories. Operads are particularly important in categories with a good notion of 'homotopy', where they play a key role in organizing hierarchies of higher homotopies. Significant examples from algebraic topology first appeared in the sixties, although the formal definition and appropriate generality were not forged until the seventies. In the nineties, a renaissance and further development of the theory were inspired by the discovery of new relationships with graph cohomology, representation theory, algebraic geometry, derived categories, Morse theory, symplectic and contact geometry, combinatorics, knot theory, moduli spaces, cyclic cohomology, and, last but not least, theoretical physics, especially string field theory and deformation quantization. The book contains a detailed and comprehensive historical introduction describing the development of operad theory from the initial period when it was a rather specialized tool in homotopy theory to the present when operads have a wide range of applications in algebra, topology, and mathematical physics. Many results and applications currently scattered in the literature are brought together here along with new results and insights. The basic definitions and constructions are carefully explained and include many details not found in any of the standard literature.

Activation of the attachment system in adulthood: Threat-related primes increase the accessibility of mental representations of attachment figures.

Abstract: Three studies explored the effects of subliminal threat on the activation of representations of attachment figures. This accessibility was measured in a lexical decision task and a Stroop task following threat- or neutral-word primes, and was compared with the accessibility of representations of other close persons, known but not close persons, and unknown persons. Participants also reported on their attachment style. Threat primes led to increased accessibility of representations of attachment figures. This effect was specific to attachment figures and was replicated across tasks and experiments. Attachment anxiety heightened accessibility of representations of attachment figures even in neutral contexts, whereas attachment avoidance inhibited this activation when the threat prime was the word separation. These effects were not, explained by trait anxiety. The discussion focuses on the dynamics of attachment-system activation in adulthood.

Comparison of skin-to-skin (Kangaroo) and traditional care: Parenting outcomes and preterm infant development

Abstract: Objective. To examine whether the kangaroo care (KC) intervention in premature infants affects parent–child interactions and infant development. Methods. Seventy-three preterm infants who received KC in the neonatal intensive care unit were matched with 73 control infants who received standard incubator care for birth weight, gestational age (GA), medical severity, and demographics. At 37 weeks’ GA, mother–infant interaction, maternal depression, and mother perceptions were examined. At 3 months’ corrected age, infant temperament, maternal and paternal sensitivity, and the home environment (with the Home Observation for Measurement of the Environment [HOME]) were observed. At 6 months’ corrected age, cognitive development was measured with the Bayley-II and mother–infant interaction was filmed. Seven clusters of outcomes were examined at 3 time periods: at 37 weeks’ GA, mother–infant interaction and maternal perceptions; at 3-month, HOME mothers, HOME fathers, and infant temperament; at 6 months, cognitive development and mother–infant interaction Results. After KC, interactions were more positive at 37 weeks’ GA: mothers showed more positive affect, touch, and adaptation to infant cues, and infants showed more alertness and less gaze aversion. Mothers reported less depression and perceived infants as less abnormal. At 3 months, mothers and fathers of KC infants were more sensitive and provided a better home environment. At 6 months, KC mothers were more sensitive and infants scored higher on the Bayley Mental Developmental Index (KC: mean: 96.39; controls: mean: 91.81) and the Psychomotor Developmental Index (KC: mean: 85.47; controls: mean: 80.53). Conclusions. KC had a significant positive impact on the infant’s perceptual-cognitive and motor development and on the parenting process. We speculate that KC has both a direct impact on infant development by contributing to neurophysiological organization and an indirect effect by improving parental mood, perceptions, and interactive behavior.

Magnesium transport and function in plants: the tip of the iceberg.

Abstract: The maintenance of Mg2+ homeostasis in the plant is essential for viability. This review describes Mg2+ functions and balancing in plants, with special focus on the existing knowledge of the involved transport mechanisms. Mg2+ is essential for the function of many cellular enzymes and for the aggregation of ribosomes. Mg2+ concentrations also modulate ionic currents across the chloroplast and the vacuolar membranes, and might thus regulate ion balance in the cell and stomatal opening. The significance of Mg2+ homeostasis has been particularly established with regard to Mg2+'s role in photosynthesis. Mg2+ is the central atom of the chlorophyll molecule, and fluctuations in its levels in the chloroplast regulate the activity of key photosynthetic enzymes. Relatively little is known of the proteins mediating Mg2+ uptake and transport in plants. The plant vacuole seem to play a key role in Mg2+ homeostasis in plant cells. Physiological and molecular evidence indicate that Mg2+ entry to the vacuole is mediated by Mg2+/H+ exchangers. The Arabidopsis vacuolar Mg2+/H+ exchanger, AtMHX, is highly transcribed at the vascular tissue, apparently most abundantly at the xylem parenchyma. Inclusion of Mg2+ ions into the vacuoles of this tissue may determine their partitioning between the various plant organs. Impacts of Mg2+ imbalance are described with respect for both plant physiology and for its nutritional value to animal and human.

"On the Internet no one knows I'm an introvert": extroversion, neuroticism, and Internet interaction.

Abstract: Social communication is one of the most common reasons for using the Internet. This paper examines how the personality characteristics of the user affect the meaning and importance of Internet social interaction in comparison with "real life," face-to-face interactions. Forty subjects all of whom were familiar with using "chat" participated in this study. After a "chat" session, they were instructed to answer several questionnaires. It was found that introverted and neurotic people locate their "real me" on the Internet, while extroverts and non-neurotic people locate their "real me" through traditional social interaction. The implications of our results for understanding the user-net interaction, the "real-me" location, extroversion, neuroticism, and Internet interaction, and the treatment of social phobics are examined.

Energetics of nanocrystalline TiO2

Abstract: The energetics of the TiO2 polymorphs (rutile, anatase, and brookite) were studied by high temperature oxide melt drop solution calorimetry. Relative to bulk rutile, bulk brookite is 0.71 ± 0.38 kJ/mol (6) and bulk anatase is 2.61 ± 0.41 kJ/mol higher in enthalpy. The surface enthalpies of rutile, brookite, and anatase are 2.2 ± 0.2 J/m2, 1.0 ± 0.2 J/m2, and 0.4 ± 0.1 J/m2, respectively. The closely balanced energetics directly confirm the crossover in stability of nanophase polymorphs inferred by Zhang and Banfield (7). An amorphous sample with surface area of 34,600 m2/mol is 24.25 ± 0.88 kJ/mol higher in enthalpy than bulk rutile.

The facilitation of social-emotional understanding and social interaction in high-functioning children with autism: intervention outcomes.

Abstract: This study evaluated the effectiveness of a 7-month cognitive behavioral intervention for the facilitation of the social-emotional understanding and social interaction of 15 high-functioning children (8 to 17 years old) with autism. Intervention focused on teaching interpersonal problem solving, affective knowledge, and social interaction. Preintervention and postintervention measures included observations of social interaction, measures of problem solving and of emotion understanding, and teacher-rated social skills. Results demonstrated progress in three areas of intervention. Children were more likely to initiate positive social interaction with peers after treatment; in particular, they improved eye contact and their ability to share experiences with peers and to show interest in peers. In problem solving after treatment, children provided more relevant solutions and fewer nonsocial solutions to different social situations. In emotional knowledge, after treatment, children provided more examples of complex emotions, supplied more specific rather then general examples, and included an audience more often in the different emotions. Children also obtained higher teacher-rated social skills scores in assertion and cooperation after treatment. The implications of these findings are discussed in terms of the effectiveness of the current model of intervention for high-functioning children with autism.

Gender differences in the importance of work and family roles: Implications for work-family conflict.

Abstract: In this study we explored between- and within-gender differences in the importance of life roles and their implications for work–family conflict. In earlier research (Cinamon & Rich, 2002) we found 3 profiles of workers who differ in attributions of importance to work and family roles: persons who assigned high importance to both the work role and the family role (“Dual” profile); participants who ascribed high importance to the work role and low importance to the family role (“Work” profile); and participants who attributed high importance to the family role and low importance to the work role (“Family” profile). We used these profiles to clarify the relationship between gender and work–family conflict. Participants were 126 married men and 87 married women who were employed in computer or law firms. Significant between- and within-gender differences were found in the distribution of participants to profiles. Men were equally distributed throughout the profiles, whereas women were underrepresented in the Work category. More women than men fit the Family profile, and more men than women fit the Work profile. No gender differences were found for the Dual profile. Women reported higher parenting and work values than men did. Between-gender differences in work–family conflict were apparent, as were within-gender differences across profiles. Results demonstrate the value of examining both between- and within-gender variation in studies of gender and work–family conflict.

Reflexion and reflection: A social cognitive neuroscience approach to attributional inference

Abstract: This chapter was supported by grants from the National Science Foundation (BCS-0074562) and the James S. McDonnell Foundation (JSMF 99-25 CN-QUA.05). We gratefully acknowledge Kevin Kim for technical assistance and Naomi Eisenberger for helpful comments on previous drafts. Correspondence concerning this chapter should be addressed to Matthew Lieberman, Department of Psychology, University of California, Los Angeles, CA 900951563; email: lieber@ucla.edu. "Knowledge may give weight, but accomplishments give lustre, and many more people see than weigh." Lord Chesterfield, Letters, May 8, 1750

A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome

Abstract: The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.

Real-time fine morphology of motile human sperm cells is associated with IVF-ICSI outcome.

Abstract: The aim of the present prospective study was to determine whether subtle sperm morphological characteristics affect the outcome of intracytoplasmic sperm injection (ICSI), and if so, to identify those that are relevant. For this purpose, we developed a new method, the motile sperm organelle morphology examination (MSOME). The examination is performed in real time using an inverted light microscope equipped with high-power Nomarski optics enhanced by digital imaging to achieve a magnification up to 6300x. MSOME was applied to the leftover sperm fraction selected for microinjection in 100 random couples referred for ICSI treatment at 3 major in vitro fertilization centers. We found that the morphological normalcy of the entire sperm cell, according to MSOME criteria, was positively associated with ICSI fertilization rate (area under the receiver operating characteristics [ROC] curve, 88%) but not with pregnancy outcome. The morphological normalcy of the sperm nucleus, defined by MSOME, was significantly and positively associated with both fertilization rate and pregnancy outcome (areas under the ROC curve, 72% and 74%, respectively). These findings indicate that ICSI-associated pregnancy rate may be affected by subtle morphological malformations of the sperm nucleus, which may remain undetected by the embryologist during the routine selection procedure.

Bias in dietary-report instruments and its implications for nutritional epidemiology.

Abstract: Objective To evaluate measurement error structure in dietary assessment instruments and to investigate its implications for nutritional studies, using urinary nitrogen excretion as a reference biomarker for protein intake. Design The dietary assessment methods included different food-frequency questionnaires (FFQs) and such conventional dietary-report reference instruments as a series of 24-hour recalls, 4-day weighed food records or 7-day diaries. Setting Six original pilot validation studies within the European Prospective Investigation of Cancer (EPIC), and two validation studies conducted by the British Medical Research Council (MRC) within the Norfolk cohort that later joined as a collaborative component cohort of EPIC. Subjects A sample of approximately 100 to 200 women and men, aged 35-74 years, from each of eight validation studies. Results In assessing protein intake, all conventional dietary-report reference methods violated the critical requirements for a valid reference instrument for evaluating, and adjusting for, dietary measurement error in an FFQ. They displayed systematic bias that depended partly on true intake and partly was person-specific, correlated with person-specific bias in the FFQ. Using the dietary-report methods as reference instruments produced substantial overestimation (up to 230%) of the FFQ correlation with true usual intake and serious underestimation (up to 240%) of the degree of attenuation of FFQ-based log relative risks. Conclusion The impact of measurement error in dietary assessment instruments on the design, analysis and interpretation of nutritional studies may be much greater than has been previously estimated, at least regarding protein intake.

Perceived risks as barriers to Internet and e‐commerce usage

Abstract: Previous research suggests that perceived risk is an important ingredient in the consumer decision‐making process. The purpose of the present study is to investigate what are the perceived barriers to Internet usage and e‐marketing by both users and non‐users. By understanding these potential obstacles, more efficient marketing strategies will become available that will drive Internet use and e‐commerce. A detailed perceived risks map has been developed using a qualitative research paradigm. We suggest a model with the factors affecting the Internet’s perceived risk elements. The factors are demographic traits and usage behavior characteristics. The model is tested against a sample of 465 employed adults.

The anxiety-buffering function of close relationships: evidence that relationship commitment acts as a terror management mechanism.

Abstract: Three studies examined the terror management function of romantic commitment. In Study 1 (N = 94), making mortality salient led to higher reports of romantic commitment on the Dimensions of Commitment Inventory (J. M. Adams & W. H. Jones, 1997) than control conditions. In Study 2 (N = 60), the contextual salience of thoughts about romantic commitment reduced the effects of mortality salience on judgments of social transgressions. In Study 3 (N = 100), the induction of thoughts about problems in romantic relationships led to higher accessibility of death-related thoughts than did the induction of thoughts about either academic problems or a neutral theme. The findings expand terror management theory, emphasizing the anxiety-buffering function of close relationships.

Decoupling of Transport, Charge Storage, and Interfacial Charge Transfer in the Nanocrystalline TiO2/Electrolyte System by Impedance Methods

Abstract: Processes in the dark of electron transport and recombination in several nanoporous titanium dioxide films have been studied as a function of the applied potential, using the electrochemical impedance technique. Contact and bulk characteristics have been identified, decoupled, and interpreted, applying a transmission line model that identifies the following elements: (i) the capacitance of the interface between the exposed surface of the substrate and the electrolyte, (ii) the electron transport resistance, (iii) the charge-transfer resistance distributed in the TiO2/electrolyte interface, and (iv) a distributed capacitive element related to charging the porous matrix. The model provides a satisfactory description of the spectra in widely different conditions of conductivity of the TiO2 phase. The electron conductivity has been determined as a function of applied potential and coincides for the different samples under study. Classical electrochemical frameworks of transport and interfacial charge transfe...

Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients

Abstract: Pseudomonas aeruginosa galactose- and fucose-binding lectins (PA-IL and PA-IIL) contribute to the virulence of this pathogenic bacterium, which is a major cause of morbidity and mortality in cystic fibrosis patients. The crystal structure of PA-IIL in complex with fucose reveals a tetrameric structure. Each monomer displays a nine-stranded, antiparallel b-sandwich arrangement and contains two close calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate-protein interactions. Experimental binding studies, together with theoretical docking of fucose-containing oligosaccharides, are consistent with the assumption that antigens of the Lewis a (Le(a)) series may be the preferred ligands of this lectin. Precise knowledge of the lectin-binding site should allow a better design of new antibacterial-adhesion prophylactics.

Nanoparticles of SnO produced by sonochemistry as anode materials for rechargeable lithium batteries

Abstract: Nanoparticles of SnO were synthesized sonochemically in mildly basic SnCl2 solutions. The amorphous product thus obtained could be transformed to a nanocrystalline phase by heating to 200 °C. Composite electrodes comprised (by weight) of 80% SnO, 10% graphite flakes (conductive additive), and 10% polymeric binder (an optimal composition) were tested as anodes for rechargeable Li batteries. The nanocrystalline SnO was found to be much more effective as an active material for electrodes than the initial amorphous phase. These electrodes could reach nearly their theoretical capacity (≃790 mAh/g, SnO) in electrochemical lithiation−delithiation processes versus a Li counter electrode in nonaqueous Li salt solutions. However, there is still a long way to go to the possible use of SnO as an anode material in practical batteries. This is due to its high irreversible capacity (Li2O formation and surface film precipitation due to reactions of lithium−tin compounds with solution species) and gradual capacity decreas...

β-Aminobutyric Acid-Induced Resistance Against Plant Pathogens

Abstract: The potential of a plant to resist attack by a pathogen is enhanced after an initial inoculation with a necrotrophic pathogen. Not only the initially inoculated tissue, but also the remote organs such as leaves and roots, become resistant. Such immunization, named systemic acquired resistance (SAR), was first observed by Chester (4) with Tobacco mosaic virus (TMV) in tobacco and was further demonstrated by the pioneering work of Ross (50) and Kuc (28,29). Efforts devoted to discovering the signal translocating during SAR revealed (26,35,40) the central role of salicylic acid (SA) in activating the defense mechanisms leading to SAR. Functional analogs of SA, such as 2,6-dichloroisonicotinic acid (INA) or benzo[1,2,3] thiadiazole-7-carbothionic acid S-methyl ester (BTH or acibenzolar-Smethyl), were developed which activate the resistance mechanisms downstream of SA (16,26,35,40,57). Since the observations of Chester, little attention was given to the role of induced resistance in general, and of amino acids in particular, in plant defense (29). Kuc et al. were the first to notice in 1957 (31) and 1959 (30) that Dphenylalanine, D-alanine, and DL-tryptophan injected into apple leaves increased resistance against scab without affecting the causal pathogen in vitro. As early as 1958, Van Andel (60) examined 50 amino acids for inducing resistance against Cladosporium cucumerinum in cucumber and found only D-serine, D-threonine, and L-threo-β-phenylserine highly active in vivo but not in vitro. Interestingly, she found no activity with DL-α-aminobutyric (AABA), DL-β-aminobutyric (BABA), γaminobutyric (GABA), or their iso isomers (60). In 1960, Oort and Van Andel first noted induced resistance to tomato late blight following BABA treatment (39). In 1963, two groups reported on the activity of aminobutrates. MacLennan et al. (34) showed that D-AABA and AIB (2-aminoisobutyric acid) were active in apple leaves against scab (but not L-AABA, BABA, or isoBABA). Papavizas and Davey (45) reported on the partial activity of AABA and high activity of BABA against Aphanomyces euteiches causing root rot in peas. They also showed high SAR activity with longer, straight-chain aminobutyrates such as DL-α-aminovaleric (DL-norvaline, five carbons) and DL-α-aminocaprylic acid (eight carbons). Harnack and Schwarz (19) showed that N-substituted glycine derivatives (especially ethyl and butyl) were systemically effective against Phytophthora infestans in tomato and Septoria apii in celery without being active in vitro. The interest in amino acid–mediated induced resistance was renewed about 30 years later when we discovered a strong activity of BABA against disease in potato (10), tomato (6), and tobacco (5), and revealed some of the defense mechanisms it activates in tomato (13) and tobacco (5). In recent years, substantial evidence has been accumulated, especially in Arabidopsis mutants, showing that BABA possesses a large spectrum of activity (7,22,41), as well as multiple forms of plant activation against disease (41,55,66,67).