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PubMed2006

Emergence of hexatic and threefold hidden order in two-dimensional smectic liquid crystals: A Monte Carlo study.

Using a high resolution Monte Carlo simulation technique based on a multihistogram method and cluster algorithm, we have investigated the critical properties of a coupled XY model, consisting of a sixfold symmetric hexatic and a hidden order parameter of threefold symmetry in two dimensions. The simulation results demonstrate a series of continuous transitions in which both kinds of orderings are established simultaneously. It is found that the specific-heat anomaly exponents for some regions in coupling constants space are in excellent agreement with the experimentally measured exponents extracted from heat-capacity data near the smectic- A -hexatic- B transition of two-layer free standing films.

Journal Article↗

PubMed2001

Simulations on infinite-size lattices.

We introduce a Monte Carlo method, as a modification of existing cluster algorithms, which allows simulations directly on systems of infinite size, and for quantum models also at beta = infinity. All two-point functions can be obtained, including dynamical information. When the number of iterations is increased, correlation functions at larger distances become available. Limits q-->0 and omega-->0 can be approached directly. As examples we calculate spectra for the d = 2 Ising model and for Heisenberg quantum spin ladders with two and four legs.

Journal Article↗

PubMed2001

Anisotropic scaling and generalized conformal invariance at Lifshitz points.

The behaviour of the 3D axial next-nearest-neighbor Ising model at the uniaxial Lifshitz point is studied using Monte Carlo techniques. A new variant of the Wolff cluster algorithm permits the analysis of systems far larger than in previous studies. The Lifshitz point critical exponents are alpha = 0.18(2), beta = 0.238(5), and gamma = 1.36(3). Data for the spin-spin correlation function are shown to be consistent with the explicit scaling function derived from the assumption of local scale invariance, which is a generalization of conformal invariance to the anisotropic scaling at the Lifshitz point.

Journal Article↗

PubMed2002

Integral equation generates high-temperature expansion of the Heisenberg chain.

Recently a new integral equation describing the thermodynamics of the 1D Heisenberg model was discovered by Takahashi. Using the integral equation we have succeeded in obtaining the high-temperature expansion of the specific heat and the magnetic susceptibility up to O[(J/T)(100)]. This is much higher than those obtained so far by the standard methods such as the linked-cluster algorithm. Our results will be useful to examine various approximation methods to extrapolate the high-temperature expansion to the low temperature region.

Journal Article↗

PubMed2004

Hidden neuronal correlations in cultured networks.

Utilization of a clustering algorithm on neuronal spatiotemporal correlation matrices recorded during a spontaneous activity of in vitro networks revealed the existence of hidden correlations: the sequence of synchronized bursting events (SBEs) is composed of statistically distinguishable subgroups each with its own distinct pattern of interneuron spatiotemporal correlations. These findings hint that each of the SBE subgroups can serve as a template for coding, storage, and retrieval of a specific information.

Algorithms↗

PubMed2005

Study of CP(N-1) theta-vacua by cluster simulation of SU(N) quantum spin ladders.

D-theory provides an alternative lattice regularization of the 2D CP(N-1) quantum field theory in which continuous classical fields emerge from the dimensional reduction of discrete SU(N) quantum spins. Spin ladders consisting of n transversely coupled spin chains lead to a CP(N-1) model with a vacuum angle theta=npi. In D-theory no sign problem arises and an efficient cluster algorithm is used to investigate theta-vacuum effects. At theta=pi there is a first order phase transition with spontaneous breaking of charge conjugation symmetry for CP(N-1) models with N>2.

Journal Article↗

PubMed2005

Efficient simulation of resistively shunted Josephson junctions.

We present a cluster algorithm for resistively shunted Josephson junctions or similar physical systems, which dramatically improves sampling efficiency, and apply it to the superconductor-to-metal transition in a single junction. Measuring the temperature dependence of the zero bias resistance, we confirm that the critical point does not depend on the strength of the Josephson coupling. However, we find that the correlation exponents vary continuously along the phase boundary, indicating that the Schmid-Bulgadaev transition is a line of fixed points.

Journal Article↗

PubMed2006

Simulation of phase transitions in highly asymmetric fluid mixtures.

We present a novel method for the accurate numerical determination of the phase behavior of fluid mixtures having large particle-size asymmetries. By incorporating the recently developed geometric cluster algorithm within a restricted Gibbs ensemble, we are able to probe directly the density and concentration fluctuations that drive phase transitions, but that are inaccessible to conventional simulation algorithms. We develop a finite-size scaling theory that relates these density fluctuations to those of the grand-canonical ensemble, thereby enabling accurate location of critical points and coexistence curves of multicomponent fluids. Several illustrative examples are presented.

Journal Article↗

PubMed1996

Approaches to very low resolution phasing of the ribosome 50S particle from Thermus thermophilus by the few-atoms-models and molecular-replacement methods.

Estimates for the phases of the X-ray diffraction data from the 50S ribosomal particle of Thermus thermophilus has been made to an effective resolution around 80 A using the few-atoms-modes ab initio technique [Lunin, Lunina, Petrova, Vernoslova, Urzhumtsev & Podjarny (1995). Acta Cryst. D51, 896-903]. This technique models the density with a small number of Gaussian spheres to generate a large number of possible phase sets and then uses clustering algorithms to identify the best ones. Independently, an envelope obtained from electron-micrograph image reconstruction [Yonath, Leonard & Wittmann (1987). Science, 236, 813-816] was oriented and positioned using the molecular-replacement technique, specially adapted to the very low resolution case [Urzhumtsev & Podjarny (1995). Acta Cryst. D51, 888-895]. The two methods show similar packing arrangements. The electron density calculated by the few-atoms-models technique without any assumption on the number of molecules in asymmetric unit or on their shape shows recognizable features of the particle.

Journal Article↗

PubMed2003

A software package for the decomposition of long-term multichannel EMG signals using wavelet coefficients.

This paper presents a method to decompose multichannel long-term intramuscular electromyogram (EMG) signals. In contrast to existing decomposition methods which only support short registration periods or single-channel recordings of signals of constant muscle effort, the decomposition software EMG-LODEC (ElectroMyoGram LOng-term DEComposition) is especially designed for multichannel long-term recordings of signals of slight muscle movements. A wavelet-based, hierarchical cluster analysis algorithm estimates the number of classes [motor units (MUs)], distinguishes single MUAPs from superpositions, and sets up the shape of the template for each class. Using three channels and a weighted averaging method to track action potential (AP) shape changes improve the analysis. In the last step, nonclassified segments, i.e., segments containing superimposed APs, are decomposed into their units using class-mean signals. Based on experiments on simulated and long-term recorded EMG signals, our software is capable of providing reliable decompositions with satisfying accuracy. EMG-LODEC is suitable for the study of MU discharge patterns and recruitment order in healthy subjects and patients during long-term measurements.

Action Potentials↗

PubMedDate not supplied

Correlation between gene expression and GO semantic similarity.

This research analyzes some aspects of the relationship between gene expression, gene function, and gene annotation. Many recent studies are implicitly based on the assumption that gene products that are biologically and functionally related would maintain this similarity both in their expression profiles as well as in their Gene Ontology (GO) annotation. We analyze how accurate this assumption proves to be using real publicly available data. We also aim to validate a measure of semantic similarity for GO annotation. We use the Pearson correlation coefficient and its absolute value as a measure of similarity between expression profiles of gene products. We explore a number of semantic similarity measures (Resnik, Jiang, and Lin) and compute the similarity between gene products annotated using the GO. Finally, we compute correlation coefficients to compare gene expression similarity against GO semantic similarity. Our results suggest that the Resnik similarity measure outperforms the others and seems better suited for use in Gene Ontology. We also deduce that there seems to be correlation between semantic similarity in the GO annotation and gene expression for the three GO ontologies. We show that this correlation is negligible up to a certain semantic similarity value; then, for higher similarity values, the relationship trend becomes almost linear. These results can be used to augment the knowledge provided by clustering algorithms and in the development of bioinformatic tools for finding and characterizing gene products.

Algorithms↗

PubMed2006

Halftone visual cryptography.

Visual cryptography encodes a secret binary image (SI) into n shares of random binary patterns. If the shares are xeroxed onto transparencies, the secret image can be visually decoded by superimposing a qualified subset of transparencies, but no secret information can be obtained from the superposition of a forbidden subset. The binary patterns of the n shares, however, have no visual meaning and hinder the objectives of visual cryptography. Extended visual cryptography [1] was proposed recently to construct meaningful binary images as shares using hypergraph colourings, but the visual quality is poor. In this paper, a novel technique named halftone visual cryptography is proposed to achieve visual cryptography via halftoning. Based on the blue-noise dithering principles, the proposed method utilizes the void and cluster algorithm [2] to encode a secret binary image into n halftone shares (images) carrying significant visual information. The simulation shows that the visual quality of the obtained halftone shares are observably better than that attained by any available visual cryptography method known to date.

Algorithms↗

PubMed2004

Approaching the Ocean Color problem using fuzzy rules.

In this paper, we propose a fuzzy logic-based approach which exploits remotely sensed multispectral measurements of the reflected sunlight to estimate the concentration of optically active constituents of the sea water. The relation between the concentrations of interest and the subsurface reflectances is modeled by a set of fuzzy rules extracted automatically from the data through a two-step procedure. First, a compact initial rule base is generated by projecting onto the input variables the clusters produced by a fuzzy clustering algorithm. Then, a genetic algorithm is applied to optimize the rules. Appropriate constraints maintain the semantic properties of the initial model during the genetic evolution. Results of the application of the fuzzy model obtained from data simulated with an ocean color model over the channels of the Medium Resolution Imaging Spectrometer are shown and discussed.

Algorithms↗

PubMed2006

Determination of network of residues that regulate allostery in protein families using sequence analysis.

Allosteric interactions between residues that are spatially apart and well separated in sequence are important in the function of multimeric proteins as well as single-domain proteins. This observation suggests that, among the residues that are involved in long-range communications, mutation at one site should affect interactions at a distant site. By adopting a sequence-based approach, we present an automated approach that uses a generalization of the familiar sequence entropy in conjunction with a coupled two-way clustering algorithm, to predict the network of interactions that trigger allosteric interactions in proteins. We use the method to identify the subset of dynamically important residues in three families, namely, the small PDZ family, G protein-coupled receptors (GPCR), and the Lectins, which are cell-adhesion receptors that mediate the tethering and rolling of leukocytes on inflamed endothelium. For the PDZ and GPCR families, our procedure predicts, in agreement with previous studies, a network containing a small number of residues that are involved in their function. Application to the Lectin family reveals a network of residues interspersed throughout the C-terminal end of the structure that are responsible for binding to ligands. Based on our results and previous studies, we propose that functional robustness requires that only a small subset of distantly connected residues be involved in transmitting allosteric signals in proteins.

Algorithms↗

PubMed1990

Relative changes in LH pulsatility during the menstrual cycle: using data from hypogonadal women as a reference point.

The basic premise of this study is that the GnRH-LH pulsatile activity, particularly its frequency characteristics, constitutes, in the absence of any considerable ovarian feedback, the intrinsic rhythm of the hypothalamic-pituitary unit at its maximal rate. Thus, LH pulse attributes determined in postpubertal hypogonadal subjects may be used as a reference in assessing the degree of influence exerted by endocrine factors that modulate GnRH-LH pulses. Accordingly, serum LH levels were determined in samples obtained at 15-min intervals for 24 h in 20 hypogonadal women: 13 postmenopausal women (PMW) and seven women with premature ovarian failure (POF). Similar measurements were performed in 60 normally cycling women: 25 in the early follicular phase (EFP), 13 in the late follicular phase (LFP), seven at midcycle surge (LH surge) and 15 in the midluteal phase (MLP). Significant pulses were identified by the cluster algorithm utilizing factors appropriate for 24 h data series of a sampling frequency of 15-min intervals. The results show a 24-h mean (+/- SE) LH pulse frequency of 78.2 +/- 2.8 and 85.5 +/- 2.4 min per pulse for young (POF) and older (PMW) hypogonadal women, respectively. During the follicular phase of the cycle, the LH pulse frequency is not significantly different from that of hypogonadal women, but there is a significant (P less than 0.05) increase from early to late follicular phases (95.4 +/- 3.3 vs 78.8 +/- 2.2 min per pulse). However, when the sleep periods are excluded from the 24-h data series because of the associated decrease of LH pulse frequency in EFP women, the resulting pulse frequencies are almost identical for EFP, LFP and PMW. An elevation beyond the basic pulse rhythm determined in PMW or POF is not observed in any phase of the menstrual cycle studied, including the midcycle surge. The decrease in LH pulse frequency during the luteal phase of the cycle (151.8 +/- 8.0 min per pulse, P less than 0.001 vs hypogonadal women) beyond the reference pulse frequency of hypogonadal women is unequivocal. By contrast, the pulse amplitude varies markedly among the groups with the largest found in POF (36.6 +/- 4.5 IU/l). It follows, in descending order, PMW (22.7 +/- 3.1 IU/l), midcycle surge (17.3 +/- 2.8 IU/l), MLP women (7.0 +/- 1.3 IU/l) and the EFP (4.9 +/- 0.3 IU/l) and LFP (4.0 +/- 0.4 IU/l).(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1992

Pulsatile growth hormone release in normal women during the menstrual cycle.

OBJECTIVE: We sought to characterize pulsatile growth hormone (GH) release in normal women during the menstrual cycle and to document possible relationships between such characteristics and concentrations of 17 beta-oestradiol and progesterone. SUBJECTS: Fifteen women with ostensibly normal menstrual function were studied during the early follicular phase, 15 during the late follicular phase and 15 during the mid-luteal phase of the menstrual cycle. DESIGN: The phase of the menstrual cycle having been documented, blood samples were obtained from each woman every 10 minutes for 24 hours. MEASUREMENTS: Serum GH was measured in each sample by immunoradiometric assay. Pulsatile GH release was appraised utilizing the objective, statistically-based pulse detection algorithm Cluster. RESULTS: The mean (+/- SEM) integrated serum GH concentration (mU/l min) in late follicular phase women (5335 +/- 848) was higher than that observed in early follicular phase women (3156 +/- 322; P = 0.032). The integrated GH concentration calculated for mid-luteal phase women (3853 +/- 788) was intermediate between but not statistically different from that observed in early follicular (P = 0.48) and late follicular (P = 0.14) phase women. No differences in GH pulse frequency (pulses/24 hours) were found among early follicular (8.27 +/- 0.55), late follicular (7.93 +/- 0.91) or mid-luteal (8.47 +/- 0.66) phase women. Mean maximal GH pulse amplitude (mU/l) was higher in late follicular phase (8.93 +/- 1.00) than early follicular phase (5.74 +/- 0.67; P = 0.008) and mid-luteal phase (5.76 +/- 0.74; P = 0.008) women. Similarly, incremental GH pulse amplitude (mU/l) was higher in late follicular phase (7.33 +/- 0.83) than early follicular phase (4.68 +/- 0.58; P = 0.005) and mid-luteal phase (4.36 +/- 0.39; P = 0.002) women. No differences in mean pulse widths or in the interpeak valley mean GH concentrations were found among the groups. Multiple regression of each pulse parameter against serum concentrations of testosterone, 17 beta-oestradiol and progesterone revealed a significant (P = 0.045) positive correlation between maximum GH pulse amplitude and oestradiol and a significant (P = 0.04) negative correlation between maximal GH pulse amplitude and progesterone (r = 0.41). CONCLUSION: These results suggest that late follicular phase concentrations of oestradiol may enhance circulating GH via an amplitude-modulated rather than a frequency-modulated effect on the endogenous GH pulse. Progesterone may blunt this oestrogen-associated effect, thus resulting in the observed mid-luteal phase concentrations of GH. Whether these gonadal hormones act primarily at the hypothalamus and/or anterior pituitary gland remains to be clarified, but the present observations indicate that pulsatile GH release throughout the normal menstrual cycle is significantly amplitude regulated.

Adult↗

PubMed1992

The pulsatile GH secretion in acromegaly: hypothalamic or pituitary origin?

OBJECTIVE: We studied the effects of different modes of octreotide therapy on the pulsatile pattern of GH release in an attempt to define better its regulation by growth hormone-releasing hormone (GHRH) and somatostatin and its effects on IGF-I plasma levels in acromegaly. DESIGN: In six acromegalic patients not cured by previous treatment we compared the 24-hour GH secretion profiles under basal conditions with subcutaneous (s.c.) bolus injections of 100 micrograms octreotide every 8 hours and with continuous s.c. infusions of the same daily dose. Blood samples were taken every 10 minutes over 24 hours followed by a GHRH test (100 micrograms GHRH i.v.) with blood sampling every 15 minutes for another 2 hours. After a 4-week interval all patients were treated either by the bolus or continuous mode of octreotide application in a randomized cross-over design. On day 4 of treatment blood sampling and GHRH test were repeated. Octreotide treatment was withdrawn for another 4 weeks; all patients then received the alternate application mode and were measured under similar conditions. MEASUREMENTS: Serum GH and plasma IGF-I concentrations were analysed by serial array averaging. IGF-I levels were measured in two different assays with and without previous protein extraction. For GH pulse detection three different algorithms (Cluster, Pulsar, Desade) were applied. RESULTS: With both treatments, the initially elevated basal 24-hour mean serum GH concentrations (58.0 +/- 9.7 mU/l mean +/- SEM) decreased significantly (bolus: 11.5 +/- 4.9 mU/l, P < 0.001 vs basal; continuous infusion: 7.6 +/- 1.9 mU/l, P < 0.001 vs basal) after 4 days. GH suppression was significantly more pronounced following continuous infusion than bolus (P < 0.05). IGF-I plasma concentrations were lowered significantly (P < 0.05) with both forms of treatment which did not differ between themselves. Bolus and continuous infusion treatment significantly inhibited (P < 0.05) the amplitudes of pulsatile GH release, but did not change the pulse frequency. In two of the patients, GHRH stimulation did not increase GH serum levels suggesting a constitutive activation of adenylyl cyclase. CONCLUSION: Continuous subcutaneous octreotide treatment in acromegaly suppresses mean GH levels better than bolus injection. The number of GH pulses remains unaffected by both modes of treatment providing evidence against a somatostatinergic mechanism of pulsatile GH secretion in these patients. The unchanged frequency of pulsatile GH release in the patients unresponsive to exogenous GHRH indicates that this pattern might be independent of hypothalamic GHRH and somatostatin and suggests a pituitary-derived mechanism for GH pulse generation in acromegaly.

Acromegaly↗

PubMed2006

Microsatellite variation and differentiation in African and non-African populations of Drosophila simulans.

Drosophila simulans originated in sub-Saharan Africa or Madagascar and colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic history, sub-Saharan African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, only limited information is available on the population structure of D. simulans. Here, we analysed X-linked and autosomal microsatellite loci in four sub-Saharan African, one North African, one Israeli, and two European D. simulans populations. Bayesian clustering algorithms combined the North African, Israeli, and European populations into a single cosmopolitan group. The four sub-Saharan populations were split into two separate groups. Pairwise F(ST) analysis, however, indicated significant population differentiation between all eight populations surveyed. A significant signal for population reduction in cosmopolitan populations was found only for X-linked loci.

Africa↗