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At least 883 records · Page 49Linked to original sources
PubMed2005

Nonlinear transport and heat dissipation in metallic carbon nanotubes.

We show that the local temperature dependence of thermalized electron and phonon populations along metallic carbon nanotubes is the main reason behind the nonlinear transport characteristics in the high bias regime. Our model is based on the solution of the Boltzmann transport equation considering both optical and zone boundary phonon emission as well as absorption by charge carriers. It also assumes a local temperature along the nanotube, determined self-consistently with the heat transport equation. By using realistic transport parameters, our results not only reproduce experimental data for electronic transport but also provide a coherent interpretation of thermal breakdown under electric stress. In particular, electron and phonon thermalization prohibits ballistic transport in short nanotubes.

Journal Article↗
PubMed2006

Ferroelectricity induced by acentric spin-density waves in YMn2O5.

The commensurate and incommensurate magnetic structures of the magnetoelectric system YMn2O5, as determined from neutron diffraction, were found to be spin-density waves lacking a global center of symmetry. We propose a model, based on a simple magnetoelastic coupling to the lattice, which enables us to predict the polarization based entirely on the observed magnetic structure. Our data accurately reproduce the temperature dependence of the spontaneous polarization, particularly its sign reversal at the commensurate-incommensurate transition.

Journal Article↗
PubMed2006

Clustering of polarity reversals of the geomagnetic field.

Often in nature the temporal distribution of inhomogeneous stochastic point processes can be modeled as a realization of renewal Poisson processes with a variable rate. Here we investigate one of the classical examples, namely, the temporal distribution of polarity reversals of the geomagnetic field. In spite of the commonly used underlying hypothesis, we show that this process strongly departs from a Poisson statistics, the origin of this failure stemming from the presence of temporal clustering. We find that a Lévy statistics is able to reproduce paleomagnetic data, thus suggesting the presence of long-range correlations in the underlying dynamo process.

Journal Article↗
PubMed2006

Structural depinning of Ne monolayers on Pb at T < 6/5 K.

We have studied the nanofriction of Ne monolayers with a quartz-crystal microbalance technique at temperatures below 6.5 K and in ultrahigh-vacuum conditions. Very homogeneous and smooth lead electrodes have been physically deposited on a quartz blank at 150 K and then annealed at room temperatures. With such a Pb-plated quartz-crystal microbalance, we have observed a pronounced depinning transition separating a low-coverage region, where the film is nearly locked to the oscillating electrode, from a high-coverage region characterized by slippage at the solid-fluid boundary. Such a behavior has been found to be very reproducible. These data are suggestive of a structural depinning of the solid Ne film when it becomes incommensurate with the lead substrate, in agreement with the results of an extensive molecular-dynamics study.

Journal Article↗
PubMed2006

Vibrationally induced two-level systems in single-molecule junctions.

Single-molecule junctions are found to show anomalous spikes in dI/dV spectra. The position in energy of the spikes is related to local vibration mode energies. A model of vibrationally induced two-level systems reproduces the data very well. This mechanism is expected to be quite general for single-molecule junctions. It acts as an intrinsic amplification mechanism for local vibration mode features and may be exploited as a new spectroscopic tool.

Journal Article↗
PubMed2005

Whole-genome validation of high-information-content fingerprinting.

Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the construction of a whole-genome HICF FPC map for maize (Zea mays subsp. mays cv B73), using a variant of HICF in which a type IIS restriction enzyme is used to generate the fluorescently labeled fragments. The HICF maize map was constructed from the same three maize bacterial artificial chromosome libraries as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end-merging of contigs to reduce the effects of contamination and repetitive bands. Several new features in FPC v7.2 are presented, including shared-memory multiprocessing, which allows dramatically faster assemblies, and automatic end-merging, which permits more accurate assemblies. It is further shown that sequenced clones may be digested in silico and located accurately on the HICF assembly, despite size deviations that prevent the precise prediction of experimental fingerprints. Finally, repetitive bands are isolated, and their effect on the assembly is studied.

DNA Fingerprinting↗
PubMed1979

Incorporation of [S]Sulfate and [C]Bicarbonate into Karyotype-specific Polysaccharides of Chondrus crispus.

Gametophytic and sporophytic tissues of Chondrus crispus (Stackhouse) cultured in vitro were labeled with (35)S and (14)C. The major sulfated polysccharides isolated from the two karyotypes were characterized by KCI fractionation, immunoprecipitation, and infrared spectroscopy. Reproducibility of data has been demonstrated by an experiment using gametophytic T(4) strain with five replicates per time point. The rate of sulfate uptake was similar in haploid and diploid plants from a given area cultured for a similar time. Cultures from different sources cultured for different times showed different uptake and incorporation levels. Although sulfate uptake did not appear to be karyotype-related, the pattern of incorporation of (35)S and (14)C into polysaccharides was ploidy-specific.

Journal Article↗
PubMed1999

X-ray phase determination by the principle of minimum charge.

When the electron density in a crystal or a quasicrystal is reconstructed from its Fourier modes, the global minimum value of the density is sensitively dependent on the relative phases of the modes. The set of phases that maximizes the value of the global minimum corresponds, by positivity of the density, to the density having the minimum total charge that is consistent with the measured Fourier amplitudes. Phases that minimize the total electronic charge (i.e. the average electron density) have the additional property that the lowest minima of the electron density become exactly degenerate and proliferate within the unit cell. The large number of degenerate minima have the effect that density maxima are forced to occupy ever smaller regions of the unit cell. Thus, by minimization of the electronic charge, the atomicity of the electron density is enhanced as well. Charge minimization applied to simulated crystalline and quasicrystalline diffraction data successfully reproduces the correct phases starting from random initial phases.

Journal Article↗
PubMed1998

X-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form.

beta-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to beta-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-beta-lactamase from Bacillus cereus, has been solved at 2.5 A resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914-4921]. Recently, the crystal structure of the metallo-beta-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823-836]. The structure of the metallo-beta-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 A resolution is reported here. The final crystallographic R is 0.196 for all the 32501 observed reflections in the range 10-2.0 A. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-beta-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.

Amino Acid Sequence↗
PubMed1994

An automated film reader for DNA sequencing based on homomorphic deconvolution.

An automated reader for electrophoresis based DNA sequencing methods is described that provides fast and accurate sequence determination. Digitized sequencing lanes are processed with homomorphic blind deconvolution in preparation for peak detection, interlane alignment, peak refinement and base calling. Initial reads from direct blot sequencing films have error rates of about 1% at the rate of 5 nucleotides/s. Typical read lengths are 500-600 nucleotides. The described reader is a significant improvement over existing readers and could be an essential component in the sequencing efforts of the Human Genome Project.

Base Sequence↗
PubMedDate not supplied

Open magnetic and electric graphic analysis.

The OMEGA software provides an analysis platform for user-independent, fast, and reproducible multimodal data analysis in one single software environment. Synergetic interactions pursued between the two functional imaging techniques fMRI and MEG use the morphological MRI recording as a basis for a common coordinate frame. In this way, direct interchange, comparison, and integration among the results of the different modalities have become feasible. The fMRI data analysis provides information about the localization of functional activity with low temporal resolution, whereas the MEG recording complements the corresponding time evolution with a high temporal resolution. The implementation of OMEGA allows the analyst to receive comprehensive MEG/fMRI results in a matter of minutes after the measurements have been completed. With OMEGA, the clinical researcher gets comprehensive information in a quick and standardized approach about the sites and the time course of neurological activation, which is useful for clinical applications and diagnostics.

Algorithms↗
PubMedDate not supplied

Improved gapped alignment in BLAST.

Homology search is a key tool for understanding the role, structure, and biochemical function of genomic sequences. The most popular technique for rapid homology search is BLAST, which has been in widespread use within universities, research centers, and commercial enterprises since the early 1990s. In this paper, we propose a new step in the BLAST algorithm to reduce the computational cost of searching with negligible effect on accuracy. This new step-semigapped alignment-compromises between the efficiency of ungapped alignment and the accuracy of gapped alignment, allowing BLAST to accurately filter sequences with lower computational cost. In addition, we propose a heuristic-restricted insertion alignment-that avoids unlikely evolutionary paths with the aim of reducing gapped alignment cost with negligible effect on accuracy. Together, after including an optimization of the local alignment recursion, our two techniques more than double the speed of the gapped alignment stages in BLAST. We conclude that our techniques are an important improvement to the BLAST algorithm. Source code for the alignment algorithms is available for download at http://www.bsg.rmit.edu.au/iga/.

Algorithms↗
PubMed1993

A comparison of the concentration-effect relationships of midazolam for EEG-derived parameters and saccadic peak velocity.

1. Concentration-effect relationships of midazolam were assessed in an open study in six healthy volunteers. Saccadic eye movements and EEG parameters derived by fast Fourier transform (FFT) and aperiodic analysis (AP) were used to quantify drug effects. 2. Midazolam was infused at a rate of 0.6 mg kg-1 h-1 for a maximum of 15 min. Hypnotic effects were avoided by terminating infusions when subjects could no longer perform the eye movement test properly. 3. Wake-sleep transitions could be recognized through frequent observation of eye movements. The dose needed to reach maximum conscious sedation averaged 0.10 mg kg-1, ranging from 0.06 to 0.13 mg kg-1. 4. Sigmoidal concentration-effect relationships were found for EEG beta-amplitudes in five of six subjects, with average EC50 values (+/- s.d.) of 120 +/- 54 ng ml-1 for FFT and 104 +/- 40 ng ml-1 for AP. For the 'total number of waves' in the beta frequency range (AP) an average (n = 6) EC50 of 63 +/- 37 ng ml-1 was found. Changes in EEG alpha-amplitudes were found in three subjects, resulting in an average EC50 value of 55 +/- 32 ng ml-1. 5. For saccadic peak velocity (PV) concentration-effect relationships were linear in five subjects and sigmoidal in one. The maximal measured decrease in PV averaged -44 +/- 9%. 6. The differences in concentration-effect relationships for various effect parameters call for further studies with emphasis on the external validity and reproducibility of data. In such studies the dose needed to reach wake-sleep transition may be used as a relevant clinical end-point.

Adult↗
PubMed1992

Salivary anti-candidal assays.

Inhibition of Candida albicans blastospore viability by parotid, submandibular-sublingual and whole salivas could not be determined by direct assay of yeast cells in each respective saliva. Determination of antifungal activity could, however, be carried out if saliva was first preincubated with Candida cells and this was immediately followed by removal of saliva and resuspension of yeast cells in nonenriched buffers of pH 5-7 for appropriate incubation periods. To attain accurate reproducible quantitative data, parotid, submandibular-sublingual and whole salivas each required different preincubation times with C. albicans as well as prior acidification and boiling. Acidification was also necessary for optimizing the germ tube assay although, in contrast to blastospore viability, inhibition of blastospore-germ tube conversion could be determined directly in saliva. Salivary antifungal effects on blastospore division were negligible at yeast cell concentrations greater than 10(6) colony-forming units per ml and were found to be independent of pH, whereas salivary inhibition of germ tube formation was significant only at pH 5 in the assay systems employed. The requirement for acidification and an observed enhancement of antifungal activity on aqueous dilution of the saliva suggested that only a fraction of the salivary antifungal components present in saliva were available in the free form to exert their biological activity. These results open up the possibility of investigating salivary antifungal activity in human health and disease.

Antifungal Agents↗
PubMed2006

Microelectrode array studies of basal and potassium-evoked release of L-glutamate in the anesthetized rat brain.

L-glutamate (Glu) is the predominant excitatory neurotransmitter in the mammalian central nervous system. It plays major roles in normal neurophysiology and many brain disorders by binding to membrane-bound Glu receptors. To overcome the spatial and temporal limitations encountered in previous in vivo extracellular Glu studies, we employed enzyme-coated microelectrode arrays to measure both basal and potassium-evoked release of Glu in the anesthetized rat brain. We also addressed the question of signal identity, which is the predominant criticism of these recording technologies. In vivo self-referencing recordings demonstrated that our Glu signals were both enzyme- and voltage-dependent, supporting the identity of L-glutamate. In addition, basal Glu was actively regulated, tetrodotoxin (TTX)-dependent, and measured in the low micromolar range (approximately 2 microm) using multiple self-referencing subtraction approaches for identification of Glu. Moreover, potassium-evoked Glu release exhibited fast kinetics that were concentration-dependent and reproducible. These data support the hypothesis that Glu release is highly regulated, requiring detection technologies that must be very close to the synapse and measure on a second-by-second basis to best characterize the dynamics of the Glu system.

Anesthetics↗
PubMed2007

Numerical simulation of hemodynamic changes during beating-heart surgery: analysis of the effects of cardiac position alteration in an animal model.

Hemodynamic instability, mostly due to vertical lifting of the heart, is usually observed during beating-heart surgical procedures. However, some hemodynamic parameters, such as coronary blood flow, are not routinely measured. A digital computer model of the circulation able to simulate and analyze the effects of heart lifting and the Trendelenburg maneuver, and thus supply detailed hemodynamic information to the clinicians would provide a useful analytical tool. A lumped parameters model of the circulation was applied to both beta-blocked and not beta-blocked pigs. The results confirmed a drop of cardiac output and coronary flow during heart lifting and a rise of both variables after the Trendelenburg maneuver for beta-blocked animals. In not beta-blocked pigs, the analysis was more complex but the model reproduced experimental data and permitted coronary flow to be estimated. These results showed the feasibility of numerical simulation for specific circulatory conditions encountered during beating-heart surgery.

Animals↗