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PubMed2004

Entanglement as a signature of quantum chaos.

We explore the dynamics of entanglement in classically chaotic systems by considering a multiqubit system that behaves collectively as a spin system obeying the dynamics of the quantum kicked top. In the classical limit, the kicked top exhibits both regular and chaotic dynamics depending on the strength of the chaoticity parameter kappa in the Hamiltonian. We show that the entanglement of the multiqubit system, considered for both the bipartite and the pairwise entanglement, yields a signature of quantum chaos. Whereas bipartite entanglement is enhanced in the chaotic region, pairwise entanglement is suppressed. Furthermore, we define a time-averaged entangling power and show that this entangling power changes markedly as kappa moves the system from being predominantly regular to being predominantly chaotic, thus sharply identifying the edge of chaos. When this entangling power is averaged over all states, it yields a signature of global chaos. The qualitative behavior of this global entangling power is similar to that of the classical Lyapunov exponent.

Journal Article↗
PubMed2000

Signature inversion caused by triaxiality and unpaired band crossings in 72Br

High-spin states in 72Br were studied with the EUROBALL III spectrometer using the 40Ca(40Ca,alpha3p1n) reaction. The negative-parity band observed in this experiment displays a signature inversion around spin I = 16. The interpretation within the cranked Nilsson-Strutinsky approach shows that this signature pattern is a signal of a substantial triaxial shape change with increasing spin where the nucleus evolves from a triaxial shape with rotation about the intermediate axis at low spin through a collective prolate shape to a triaxial shape but with rotation about the shortest principal axis at high spin.

Journal Article↗
PubMed2003

Specific Raman signatures of a dimetallofullerene peapod.

We report on the Raman spectroscopy of a dimetallofullerene peapod, (La(2)@C(80))(m)@SWNT. Drastic changes are observed with respect to pristine nanotubes. A sharp intense line at 142 cm(-1) is interpreted as a signature of polymerization of the encapsulated metallofullerenes. Additional strong signatures appear at about 400, 520, and 640 cm(-1), respectively. Their intensity suggests the existence of an enhancement effect. The stiffening and the up-shift of the G-band modes appear to imply that a charge transfer process between the nanotube and the peas occurs.

Journal Article↗
PubMed2004

Signatures of superfluidity for Feshbach-resonant Fermi gases.

We consider atomic Fermi gases where Feshbach resonances can be used to study the whole BCS-Bose-Einstein condensate crossover. We show how a probing field transferring atoms out of the superfluid can be used to detect the onset of the superfluid transition in the high-T(c) and BCS regimes. The number of transferred atoms, as a function of the energy given by the probing field, peaks at the gap energy. The shape of the peak is asymmetric due to the single particle excitation gap. Since the excitation gap also includes a pseudogap contribution, the asymmetry alone is not a signature of superfluidity. The incoherent nature of the noncondensed pairs leads to broadening of the peak. The broadening decays below the critical temperature, causing a drastic increase in the asymmetry. This provides a signature of the transition.

Journal Article↗
PubMed2006

Rice HYDROPEROXIDE LYASES with unique expression patterns generate distinct aldehyde signatures in Arabidopsis.

HYDROPEROXIDE LYASE (HPL) genes encode enzymes that catalyze the cleavage of fatty acid hydroperoxides into aldehydes and oxoacids. There are three HPLs in rice (Oryza sativa), designated OsHPL1 through OsHPL3. To explore the possibility of differential functional activities among these genes, we have examined their expression patterns and biochemical properties of their encoded products. Transcript analysis indicates that these genes have distinct patterns and levels of expression. OsHPL1 is ubiquitously expressed, OsHPL2 is expressed in the leaves and leaf sheaths, whereas OsHPL3 is wound inducible and expressed exclusively in leaves. OsHPLs also differ in their substrate preference as determined by in vitro enzyme assays using 9-/13-hydroperoxy linolenic and 9-/13-hydroperoxy linoleic acids as substrates. OsHPL1 and OsHPL2 metabolize 9-/13-hydroperoxides, whereas OsHPL3 metabolizes 13-hydroperoxy linolenic acid exclusively. Sequence alignments of the HPL enzymes have identified signature residues potentially responsible for the substrate specificity/preference of these enzymes. All three OsHPLs are chloroplast localized as determined by chloroplast import assays and green fluorescent protein (GFP) fusion studies. Aldehyde measurements in transgenic Arabidopsis (Arabidopsis thaliana) plants overexpressing individual OsHPL-GFP fusions indicate that all rice HPLs are functional in a heterologous system, and each of them generates a distinct signature of the metabolites. Interestingly, these aldehydes were only detectable in leaves, but not in roots, despite similar levels of OsHPL-GFP proteins in both tissues. Similarly, there were undetectable levels of aldehydes in rice roots, in spite of the presence of OsHPL1 transcripts. Together, these data suggest that additional tissue-specific mechanism(s) beyond transcript and HPL enzyme abundance, regulate the levels of HPL-derived metabolites.

Aldehyde-Lyases↗
PubMed2002

Crystallization and preliminary X-ray crystallographic analysis of malonamidase E2, an amidase signature family member.

Malonamidase E2 from Bradyrhizobium japonicum catalyzes the hydrolysis of malonamate. The enzyme belongs to an amidase signature family which has a highly conserved serine- and glycine-rich sequence over a stretch of approximately 45 amino acids. More than 100 known or predicted members belonging to this family, whose biological functions vary widely, can be identified in sequence databases. Although urgently needed, no three-dimensional structure of any protein of this family is yet available. The crystallization of malonamidase E2 was undertaken as a first step toward the goal of providing information on the canonical structure of the amidase signature family. The enzyme was crystallized using the hanging-drop vapour-diffusion method at 277 K under two different conditions. One crystal form, which is easier to work with than the other form, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 104.29, b = 95.58, c = 74.90 A. The unit cell is likely to contain two molecules of MAE2, with a crystal volume per protein mass (V(M)) of 2.045 A(3)Da(-1) and solvent content of about 39.9% by volume. A native data set to 1.8 A resolution was obtained from a flash-cooled crystal using synchrotron radiation.

Amidohydrolases↗
PubMed1996

Extraction of spatio-temporal signatures from depth EEG seizure signals based on objective matching in warped vectorial observations.

In the field of epilepsy, the analysis of stereoelectroencephalographic (SEEG) signals recorded with depth electrodes provides major information on interactions between brain structures during seizures. A comprehensive methodology of comparing SEEG seizure recordings is presented. It proceeds in three steps: 1) segmentation of SEEG signals; 2) characterization and labeling of segments; and 3) comparison of observations coded as sequences of symbol vectors. The third step reports a vectorial extension of the Wagner and Fischer's algorithm to first, quantify similarities between observations and second, extract invariant sequences of events, referred to as spatiotemporal signatures. The study shows that two observations of nonequal duration can be matched by deforming the first one to optimally fit the second, under cost constraints. Results show that the methodology allows to exhibit signatures occurring during epileptic seizures and to point out different types of seizure patterns. The study brings objective results on reproducible interactions between brain structures during ictal periods and may help in the understanding of epileptogenic networks.

Algorithms↗
PubMed2001

Markov modeling of minimally invasive surgery based on tool/tissue interaction and force/torque signatures for evaluating surgical skills.

The best method of training for laparoscopic surgical skills is controversial. Some advocate observation in the operating room, while others promote animal and simulated models or a combination of surgery-related tasks. A crucial process in surgical education is to evaluate the level of surgical skills. For laparoscopic surgery, skill evaluation is traditionally performed subjectively by experts grading a video of a procedure performed by a student. By its nature, this process uses fuzzy criteria. The objective of the current study was to develop and assess a skill scale using Markov models (MMs). Ten surgeons [five novice surgeons (NS); five expert surgeons (ES)] performed a cholecystectomy and Nissen fundoplication in a porcine model. An instrumented laparoscopic grasper equipped with a three-axis force/torque (F/T) sensor was used to measure the forces/torques at the hand/tool interface synchronized with a video of the tool operative maneuvers. A synthesis of frame-by-frame video analysis and a vector quantization algorithm, allowed to define F/T signatures associated with 14 different types of tool/tissue interactions. The magnitude of F/T applied by NS and ES were significantly different (p < 0.05) and varied based on the task being performed. High F/T magnitudes were applied by NS compared with ES while performing tissue manipulation and vise versa in tasks involved tissue dissection. From each step of the surgical procedures, two MMs were developed representing the performance of three surgeons out of the five in the ES and NS groups. The data obtained by the remaining two surgeons in each group were used for evaluating the performance scale. The final result was a surgical performance index which represented a ratio of statistical similarity between the examined surgeon's MM and the MM of NS and ES. The difference between the performance index value, for a surgeon under study, and the NS/ES boundary, indicated the level of expertise in the surgeon's own group. Using this index, 87.5% of the surgical procedures were correctly classified into the NS and ES groups. The 12.5% of the procedures that were misclassified were performed by the ES and classified as NS. However in these cases the performance index values were very close to the NS/ES boundary. Preliminary data suggest that a performance index based on MM and F/T signatures provides an objective means of distinguishing NS from ES. In addition, this methodology can be further applied to evaluate haptic virtual reality surgical simulators for improving realism in surgical education.

Algorithms↗
PubMed1999

Scale-space signatures for the detection of clustered microcalculations in digital mammograms.

A method is described for the automated detection of microcalcifications in digitized mammograms. The method is based on the Laplacian scale-space representation of the mammogram only. First, possible locations of microcalcifications are identified as local maxima in the filtered image on a range of scales. For each finding, the size and local contrast is estimated, based on the Laplacian response denoted as the scale-space signature. A finding is marked as a microcalcification if the estimated contrast is larger than a predefined threshold which depends on the size of the finding. It is shown that the signature has a characteristic peak, revealing the corresponding image features. This peak can be robustly determined. The basic method is significantly improved by consideration of the statistical variation of the estimated contrast, which is the result of the complex noise characteristic of the mammograms. The method is evaluated with the Nijmegen database and compared to other methods using these mammograms. Results are presented as the free-response receiver operating characteristic (FROC) performance. At a rate of one false positive cluster per image the method reaches a sensitivity of 0.84, which is comparable to the best results achieved so far.

Algorithms↗
PubMed2004

Complex permittivity measurement as a new noninvasive tool for monitoring in vitro tissue engineering and cell signature through the detection of cell proliferation, differentiation, and pretissue formation.

In in vitro tissue engineering, microporous scaffolds are commonly used to promote cell proliferation and differentiation in three-dimensional structures. Classic measurement methods are particularly time consuming, difficult to handle, and destructive. In this study, a new nondestructive method based on complex permittivity measurement (CPM) is proposed to monitor and track the osteoblast and macrophage differentiation through their morphological variation upon cell attachment and proliferation inside the microporous scaffolds. CPM is performed using a vector network analyzer and a dielectric probe under sterile conditions in a laminar-flow hood. A suitable effective medium approximation (EMA) is applied to fit the data in order to extract the parameters of the different constituents. Our data show that the EMA depolarization factor can be monitored to assess the variation of cell morphology characterizing cell attachment. Discrimination between two batches of scaffolds seeded, respectively, with 2 million and 1 million osteoblast cells is possible; the ratio of their CPM-derived cell volume fractions is in agreement with the ratio of their cell seeding numbers. In addition, cell proliferation inside scaffolds seeded with osteoblasts cultured in alpha minimum essential medium and inside scaffolds seeded with osteoblasts cultured in alpha minimum essential medium supplemented to induce the formation of extracellular matrix is monitored via CPM over several days. CPM-determined cell volume fraction is compared to DNA assay cell counts. Extracellular matrix formation and cell presence was confirmed by scanning electron microscopy. A set of three signature parameters (epsilon'mem, epsilon'cyt, kappa'cyt) characteristic of cell line is extracted from CPM. Distinct signatures are recorded for osteoblasts and macrophages, thus confirming the ability of CPM to discriminate between different cell types. This study demonstrates the potential of CPM as a diagnostic tool to monitor quickly and noninvasively cell growth and differentiation inside microporous scaffolds. Our findings suggest that the use of CPM could be extended to many biomedical applications, such as drug detection and automation of tissue and bacterial cultures in bioreactors.

3T3 Cells↗
PubMedDate not supplied

Visual signatures in video visualization.

Video visualization is a computation process that extracts meaningful information from original video data sets and conveys the extracted information to users in appropriate visual representations. This paper presents a broad treatment of the subject, following a typical research pipeline involving concept formulation, system development, a path-finding user study, and a field trial with real application data. In particular, we have conducted a fundamental study on the visualization of motion events in videos. We have, for the first time, deployed flow visualization techniques in video visualization. We have compared the effectiveness of different abstract visual representations of videos. We have conducted a user study to examine whether users are able to learn to recognize visual signatures of motions, and to assist in the evaluation of different visualization techniques. We have applied our understanding and the developed techniques to a set of application video clips. Our study has demonstrated that video visualization is both technically feasible and cost-effective. It has provided the first set of evidence confirming that ordinary users can be accustomed to the visual features depicted in video visualizations, and can learn to recognize visual signatures of a variety of motion events.

Algorithms↗
PubMed1995

Transposon signatures: species-specific molecular markers that utilize a class of multiple-copy nuclear DNA.

Transposable elements are mobile sequences found in nuclear genomes and can potentially serve as molecular markers in various phylogenetic and population genetic investigations. A PCR-based method that utilizes restriction site variation of element copies within a genome is developed. These patterns of site variation, referred to as transposon signatures, are useful in differentiating between closely related groups. Signature data using the magellan retrotransposon, for example, is useful in examining relationships within the genus Zea and Tripsacum. This method allows transposable elements, or even other multiple-copy nuclear DNA sequences, to be generally utilized as molecular markers in discriminating between other closely related species and subspecies.

Base Sequence↗
PubMed1997

A cluster of atypical Yersinia strains with a distinctive 16S rRNA signature.

Thirty-eight bacterial isolates from raw milk samples in Queensland, Australia were identified as members of the genus Yersinia on the basis of biochemical profile, ability to hybridize with a genus-specific DNA probe, comparative 16S rDNA sequence analysis, and the presence of characteristic 16S rDNA signature nucleotides which occur in all Yersinia spp. Twenty-five of these isolates reacted with typing sera (O:22 or O:58) of Y. enterocolitica; the remainder were non-typable. None of the isolates displayed any of the phenotypic or genetic virulence-associated characteristics of Y. enterocolitica. Comparative 16S rDNA sequence analysis revealed that members of this group appear to represent a new sub-line within the genus Yersinia, most closely related to Y. frederiksenii hybridization group 2 (unnamed genomospecies 2). This findings was confirmed by DNA hybridization studies which indicated that the strains belonged to the unnamed genomospecies, Yersinia frederiksenii genomospecies 2, which is biochemically indistinguishable from Y. frederiksenii (Y. frederiksenii genomospecies 1). A 23-nucleotide 16S rDNA signature stretch which characterised these strains was identified.

Animals↗
PubMed2005

The signature amidase from Sulfolobus solfataricus belongs to the CX3C subgroup of enzymes cleaving both amides and nitriles. Ser195 and Cys145 are predicted to be the active site nucleophiles.

The signature amidase from the extremophile archeum Sulfolobus solfataricus is an enantioselective enzyme that cleaves S-amides. We report here that this enzyme also converts nitriles in the corresponding organic acid, similarly to the well characterized amidase from Rhodococcus rhodochrous J1. The archaeal and rhodococcal enzymes belong to the signature amidases and contain the typical serine-glycine rich motif. They work at different optimal temperature, share a high sequence similarity and both contain an additional CX3C motif. To explain their dual specificity, we built a 3D model of the structure of the S. solfataricus enzyme, which suggests that, in addition to the classical catalytic Ser-cisSer-Lys, a putative additional Cys-cisSer-Lys catalytic site, likely to be responsible for nitrile hydrolysis, is present in these proteins. The results of random and site-directed mutagenesis experiments, as well as inhibition studies support our hypothesis.

Amides↗
PubMed2002

Feasibility of a phased acoustic array for monitoring acoustic signatures from meshing gear teeth.

This paper investigates the feasibility of sensing damage emanating from rotating drivetrain elements such as bearings, gear teeth, and drive shafts via airborne paths. A planar phased acoustic array is evaluated as a potential fault detection scheme for detecting spatially filtered acoustic signatures radiating from gearbox components. Specifically, the use of beam focusing and steering to monitor individual tooth mesh dynamics is analyzed taking into consideration the constraints of the array/gearbox geometry and the spectral content of typical gear noise. Experimental results for a linear array are presented to illustrate the concepts of adaptive beam steering and spatial acoustic filtering. This feasibility study indicates that the planar array can be used to track the acoustic signatures at higher harmonics of the gear mesh frequency.

Journal Article↗
PubMed2000

Auditory and behavioral responses of bottlenose dolphins (Tursiops truncatus) and a beluga whale (Delphinapterus leucas) to impulsive sounds resembling distant signatures of underwater explosions.

A behavioral response paradigm was used to measure masked underwater hearing thresholds in two bottlenose dolphins and one beluga whale before and after exposure to impulsive underwater sounds with waveforms resembling distant signatures of underwater explosions. An array of piezoelectric transducers was used to generate impulsive sounds with waveforms approximating those predicted from 5 or 500 kg HBX-1 charges at ranges from 1.5 to 55.6 km. At the conclusion of the study, no temporary shifts in masked-hearing thresholds (MTTSs), defined as a 6-dB or larger increase in threshold over pre-exposure levels, had been observed at the highest impulse level generated (500 kg at 1.7 km, peak pressure 70 kPa); however, disruptions of the animals' trained behaviors began to occur at exposures corresponding to 5 kg at 9.3 km and 5 kg at 1.5 km for the dolphins and 500 kg at 1.9 km for the beluga whale. These data are the first direct information regarding the effects of distant underwater explosion signatures on the hearing abilities of odontocetes.

Animals↗
PubMed1986

Seasonal variations in the stable carbon isotopic signature of biogenic methane in a coastal sediment.

Systematic seasonal variations in the stable carbon isotopic signature of methane gas occur in the anoxic sediments of Cape Lookout Bight, a lagoonal basin on North Carolina's Outer Banks. Values for the carbon isotope ratio (delta 13C) of methane range from -57.3 per mil during summer to -68.5 per mil during winter in gas bubbles with an average methane content of 95%. The variations are hypothesized to result from changes in the pathways of microbial methane production and cycling of key substrates including acetate and hydrogen. The use of stable isotopic signatures to investigate the global methane cycle through mass balance calculations, involving various sediment and soil biogenic sources, appears to require seasonally averaged data from individual sites.

Anaerobiosis↗
PubMed2006

Development of signature-tagged mutagenesis in Burkholderia pseudomallei to identify genes important in survival and pathogenesis.

Burkholderia pseudomallei, the causative agent of melioidosis, is an important human pathogen in Southeast Asia and northern Australia for which a vaccine is unavailable. A panel of 892 double signature-tagged mutants was screened for virulence using an intranasal BALB/c mouse model of infection. A novel DNA tag microarray identified 33 mutants as being attenuated in spleens, while 6 were attenuated in both lungs and spleens. The transposon insertion sites in spleen-attenuated mutants revealed genes involved in several stages of capsular polysaccharide biosynthesis and DNA replication and repair, a putative oxidoreductase, ABC transporters, and a lipoprotein that may be important in intercellular spreading. The six mutants identified as missing in both lungs and spleens were found to have insertions in recA involved in the SOS response and DNA repair; putative auxotrophs of leucine, threonine, p-aminobenzoic acid, and a mutant with an insertion in aroB causing auxotrophy for aromatic compounds were also found. Murine challenge studies revealed partial protection in BALB/c mice vaccinated with the aroB mutant. The refined signature-tagged mutagenesis approach developed in this study was used to efficiently identify attenuating mutants from this highly pathogenic species and could be applied to other organisms.

Animals↗