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Biomedical subjects

C W Clark

Publications and source records attributed to C W Clark.

At least 19 recordsLinked to original sources
PubMed2001

Superfluid-to-solid crossover in a rotating Bose-Einstein condensate.

The properties of a rotating Bose-Einstein condensate confined in a prolate cylindrically symmetric trap are explored both analytically and numerically. As the rotation frequency increases, an ever greater number of vortices are energetically favored. Though the cloud anisotropy and moment of inertia approach those of a classical fluid at high frequencies, the observed vortex density is consistently lower than the solid-body estimate. Furthermore, the vortices are found to arrange themselves in highly regular triangular arrays, with little distortion even near the condensate surface. These results are shown to be a direct consequence of the inhomogeneous confining potential.

Journal Article↗
PubMed2001

Biogenetically inspired approach to the Strychnos alkaloids. Concise syntheses of (+/-)-akuammicine and (+/-)-strychnine.

A linear synthesis of the indole alkaloid (+/-)-akuammicine (2) was completed by a novel sequence of reactions requiring only 10 steps from commercially available starting materials. The approach features a tandem vinylogous Mannich addition and an intramolecular hetero Diels-Alder reaction to rapidly assemble the pentacyclic heteroyohimboid derivative 8 from the readily available hydrocarboline 6. Oxidation of the E ring of 8 gave the lactone 9 that was converted into deformylgeissoschizine (11). The subsequent elaboration of 11 into 2 was effected by a biomimetically patterned transformation that involved sequential oxidation and base-induced skeletal reorganization. A variation of these tactics was then applied to the synthesis of the C(18) hydroxylated akuammicine derivative 36. Because 36 had previously been converted into strychnine (1) in four steps, its preparation constitutes a concise, formal synthesis of this complex alkaloid.

Alkaloids↗
PubMed2001

Watching dark solitons decay into vortex rings in a Bose-Einstein condensate.

We have created spatial dark solitons in two-component Bose-Einstein condensates in which the soliton exists in one of the condensate components and the soliton nodal plane is filled with the second component. The filled solitons are stable for hundreds of milliseconds. The filling can be selectively removed, making the soliton more susceptible to dynamical instabilities. For a condensate in a spherically symmetric potential, these instabilities cause the dark soliton to decay into stable vortex rings. We have imaged the resulting vortex rings.

Journal Article↗
PubMed2001

Anomalous modes drive vortex dynamics in confined Bose-Einstein condensates.

The dynamics of vortices in trapped Bose-Einstein condensates are investigated both analytically and numerically. In axially symmetric traps, the critical rotation frequency for metastability of an isolated vortex coincides with the largest vortex precession frequency (or anomalous mode) in the Bogoliubov excitation spectrum. The number of anomalous modes increases for an elongated condensate. The largest mode frequency exceeds the thermodynamic critical frequency and the nucleation frequency at which vortices are created dynamically. Thus, anomalous modes describe both vortex precession and the critical rotation frequency for creation of the first vortex in an elongated condensate.

Journal Article↗
PubMed2000

The use of biomagnetic separation to recover DNA suitable for PCR from Claviceps species.

DNA analysis of agriculturally important fungi using polymerase chain reaction (PCR)-based methods is becoming routine in research and for diagnostic purposes. Rapid, small-scale DNA isolation methods that take advantage of the sensitivity, speed and automation potential of PCR technology are needed for timely analysis of important plant pathogens. DNA isolated from Claviceps africana (causal agent of ergot of sorghum) using several standard DNA extraction protocols was found to be unamplifiable using PCR. The standard methods apparently failed to separate DNA from substances inhibitory to the Taq polymerase enzyme. We obtained DNA amenable to PCR analysis using a novel method involving magnetic beads and high salt extraction buffer. The biomagnetic purification method allowed us to obtain reliable PCR amplification of the internal transcribed spacer (ITS) regions of rDNA of Claviceps africana, making genetic comparisons possible.

Claviceps↗
PubMed2000

Behavioral responses of humpback whales (Megaptera novaeangliae) to full-scale ATOC signals.

Loud (195 dB re 1 microPa at 1 m) 75-Hz signals were broadcast with an ATOC projector to measure ocean temperature. Respiratory and movement behaviors of humpback whales off North Kauai, Hawaii, were examined for potential changes in response to these transmissions and to vessels. Few vessel effects were observed, but there were fewer vessels operating during this study than in previous years. No overt responses to ATOC were observed for received levels of 98-109 dB re 1 microPa. An analysis of covariance, using the no-sound behavioral rate as a covariate to control for interpod variation, found that the distance and time between successive surfacings of humpbacks increased slightly with an increase in estimated received ATOC sound level. These responses are very similar to those observed in response to scaled-amplitude playbacks of ATOC signals [Frankel and Clark, Can. J. Zool. 76, 521-535 (1998)]. These similar results were obtained with different sound projectors, in different years and locations, and at different ranges creating a different sound field. The repeatability of the findings for these two different studies indicates that these effects, while small, are robust. This suggests that at least for the ATOC signal, the received sound level is a good predictor of response.

Animals↗
PubMed2000

Calibration and comparison of the acoustic location methods used during the spring migration of the bowhead whale, Balaena mysticetus, off Pt. Barrow, Alaska, 1984-1993.

Between 1984 and 1993, visual and acoustic methods were combined to census the Bering-Chukchi-Beaufort bowhead whale, Balaena mysticetus, population. Passive acoustic location was based on arrival-time differences of transient bowhead sounds detected on sparse arrays of three to five hydrophones distributed over distances of 1.5-4.5 km along the ice edge. Arrival-time differences were calculated from either digital cross correlation of spectrograms (old method), or digital cross correlation of time waveforms (new method). Acoustic calibration was conducted in situ in 1985 at five sites with visual site position determined by triangulation using two theodolites. The discrepancy between visual and acoustic locations was <1%-5% of visual range and less than 0.7 degrees of visual bearing for either method. Comparison of calibration results indicates that the new method yielded slightly more precise and accurate positions than the old method. Comparison of 217 bowhead whale call locations from both acoustic methods showed that the new method was more precise, with location errors 3-4 times smaller than the old method. Overall, low-frequency bowhead transients were reliably located out to ranges of 3-4 times array size. At these ranges in shallow water, signal propagation appears to be dominated by the fundamental mode and is not corrupted by multipath.

Acoustics↗
PubMed2000

Recognizing transient low-frequency whale sounds by spectrogram correlation.

A method is described for the automatic recognition of transient animal sounds. Automatic recognition can be used in wild animal research, including studies of behavior, population, and impact of anthropogenic noise. The method described here, spectrogram correlation, is well-suited to recognition of animal sounds consisting of tones and frequency sweeps. For a sound type of interest, a two-dimensional synthetic kernel is constructed and cross-correlated with a spectrogram of a recording, producing a recognition function--the likelihood at each point in time that the sound type was present. A threshold is applied to this function to obtain discrete detection events, instants at which the sound type of interest was likely to be present. An extension of this method handles the temporal variation commonly present in animal sounds. Spectrogram correlation was compared to three other methods that have been used for automatic call recognition: matched filters, neural networks, and hidden Markov models. The test data set consisted of bowhead whale (Balaena mysticetus) end notes from songs recorded in Alaska in 1986 and 1988. The method had a success rate of about 97.5% on this problem, and the comparison indicated that it could be especially useful for detecting a call type when relatively few (5-200) instances of the call type are known.

Animals↗
PubMed1998

The differentiation of Phytophthora species that are pathogenic on potatoes by an asymmetric PCR combined with single-strand conformation polymorphism analysis.

The goal of this study was to develop a polymerase chain reaction (PCR) capable of differentiating Phytophthora species that are pathogenic on potatoes using a single primer pair. To achieve this objective, primers were derived from conserved regions flanking variable sequences in the internal transcribed spacer 1 (ITS1) of Phytophthora species. One primer pair produced a 140 bp product from P. infestans, P. erythroseptica and P. nicotianae. The PCR products were purified and used in an asymmetric PCR (A-PCR) protocol to generate single-strand DNA (ssDNA). The ssDNA of the Phytophthora potato pathogens reproducibly migrated in non-denaturing polyacrylamide gels in a species-specific manner.

Base Sequence↗
PubMed1996

Characterization of bacterial cell membrane attachment sites of plasmid R6K.

In vitro binding studies revealed that plasmid R6K could attach to both inner and outer membrane fractions of its host cell, Escherichia coli. Derivatives of R6K carrying one or two of its three origins of replication could not bind stably to the same membrane fractions in the presence of salt. However, the derivative, pRK35, carrying the intact three origins of replication could bind stably to membrane fractions from its host in the presence or absence of salt. These observations suggest that the three origins of DNA replication must be contiguous for stable binding of the plasmid to the cell membrane. The results of binding experiments showed that plasmid R6K bound competitively with pRK35 as well as the heterologous plasmid, pl524.

Binding, Competitive↗
PubMed1995

Identification of the central regulatory segment of plasmid R6K complexed with the membranes of Escherichia coli.

Understanding the mechanisms which control replication of chromosomes with multiple origins of replication have been the subject of many investigations. The plasmid, R6K, has three origins of replication, alpha, beta, and gamma. In vivo, alpha and beta are utilized with equal frequencies while the gamma origin is rarely used in the parental plasmid, or remains silent in several miniplasmids. Hence, in the present study, the multiple origin plasmid, R6K, was utilized as a model system to investigate DNA replication. A 1.6 kb PCR (polymerase chain reaction) amplified region of R6K containing the central regulatory segment (CRS) was examined to determine if membrane complexing is required for maintenance. Crude membrane extracts from exponentially growing cultures were prepared and sedimented through 30-50% (w/v) linear sucrose gradients. Fractions collected were probed using quantitative PCR which revealed two fractions containing CRS DNA. These complexes were localized in a region between the inner and outer membranes of Escherichia coli.

Base Sequence↗
PubMed1994

Population dynamics of sexual and resource competition.

Interspecific competition is usually thought of in terms of resource competition. Closely related species, however, may often compete also for a "sexual niche," a sexual resource. Both sexual and resource competition are likely to affect the dynamics of closely related sympatric species. Here, a combined model of sexual and resource competition is developed and analyzed in terms of phase planes. Population dynamics involving sexual competition alone are characterized by competitive exclusion and dependence on relative initial population size of the competing species. This dependence on initial population size is due to the nonlinear equilibrium isoclines of sexual competition, which contrast with the linear isoclines of the Lotka-Volterra competition equations. Dependence on initial population size is stronger when sexual competition is severe and/or when growth rates of the two species are low. Additional dynamic possibilities arise under combined sexual and resource competition. If the sexual competition is strong, competitive exclusion is the only outcome. But if sexual competition is weak, and if stable coexistence would occur without sexual competition, then both stable coexistence and competitive exclusion may occur simultaneously. A species that is relatively rare initially may be excluded, but when both species are initially of comparable abundance both will persist. Adding sexual competition to resource competition thus introduces additional uncertainty concerning the outcome of competition between two sympatric species.

Animals↗
PubMed1994

Marine mammal call discrimination using artificial neural networks.

Recent work has applied a linear spectrogram correlator filter (SCF) to detect bowhead whale (Balaena mysticetus) song notes, outperforming both a time-series-matched filter and a hidden Markov model. The method relies on an empirical weighting matrix. An artificial neural net (ANN) may be better yet, since it offers two advantages; (i) the equivalent weighting matrix is determined by training and can converge to a more optimal solution and (ii) an ANN is a nonlinear estimator and can embody more sophisticated responses. A three-layer feed-forward ANN is ideally suited to this application and has been implemented on 1475 sounds, of which 54% were used for training and 46% kept as "unseen" test data. The trained ANN error rate was 1.5%, a twofold improvement over previous methods. It is shown that ANN hidden neurons can be interrogated to reveal the operating paradigm developed during training. The function of each of these neurons can be determined in terms of spectrographic features of the training calls. Furthermore, the operating paradigm can be controlled and training time reduced by assigning specific recognition tasks to hidden neurons prior to training, rather than initiating training with randomized weights. The ANN is compared to the SCF and the role of the "hidden" neurons and equivalent weighting matrices are discussed.

Animals↗
PubMed1987

Relationship between canine transthoracic impedance and defibrillation threshold. Evidence for current-based defibrillation.

The electrical parameter used to define defibrillation strength is energy. Peak current, however, may more accurately reflect the field quantities (i.e., electric field strength and current density) that mediate defibrillation and therefore should be a better clinical descriptor of threshold than energy. Though transthoracic impedance is a major determinant of energy-based threshold and is sensitive to operator-dependent changes in impedance (electrode-subject interface), an ideal threshold descriptor should be invariant with respect to these changes in impedance. We therefore compared the relative invariance of energy- and current-based thresholds when transthoracic impedance was altered by one of two methods: (a) change in electrode size (protocol A) or (b) change in electrode force (protocol B). In protocol A, impedance was altered in each dog by a mean of 95%. Energy thresholds determined at both low and high impedance were 44 +/- 21 J (mean +/- SD) and 105 +/- 35 J, respectively, P less than 0.0001. In contrast, peak current (A) thresholds were independent of transthoracic impedance, 22 +/- 5 A (low impedance) vs. 24 +/- 6 A (high impedance), P = NS. Energy and current thresholds showed a similar relationship for animals tested in protocol B. Therefore, current-based thresholds, in contrast to energy thresholds are independent of operator-dependent variables of transthoracic impedance and are invariant for a given animal. These results suggest that redefining defibrillation threshold in terms of peak current rather than energy provides a superior method of defibrillation.

Animals↗
PubMed1986

Isolated dissecting aneurysm of the renal artery.

A 40-year-old man with a history of renal stone formation was evaluated for left flank pain. An excretory urogram failed to show any renal calculi. However, renal arteriography and computerized tomography studies demonstrated a primary dissection of the left renal artery with resulting decreased perfusion to the lower pole of the left kidney.

Adult↗
PubMed1978

Relationship of R6K replicating forms to the folded chromosome of Escherichia coli.

An examination of the relationship of both nonreplicating and replicating forms of R6K plasmid DNA to the Escherichia coli folded chromosome showed that both forms cosediment with the chromosome in neutral sucrose gradients. Approximately 20% of the nonreplicatin molecules was found as freely sedimenting forms when the folded-configuration of the chromosomes was preserved. However, under the same conditions negligible amounts of the replicating forms were found as freely sedimenting molecules. Thus, it is concluded that the replicating forms, when compared with nonreplicating molecules, are preferentially associated with the folded chromosomal structure. Exposure of the folded chromosomal structure to RNase resulted in an unfolding of the chromosome and a concomitant increase in the amount of freely sedimenting replicating and nonreplicating forms of R6K DNA. Analyses of the single-stranded length of RNase-released nascent molecules suggest that they replicate in continuous association with the folded chromsome complex. Nonenzymatic unfolding of the chromosomes by progressively lowering the sodium ion concentration during lysis resulted in a progressive increase in the release of nonreplicating molecules. Replicating molecules wer not released by unfolding the chromosome in this fashion.

Centrifugation, Density Gradient↗