bluuebunny/crossref_metadata_2025 huggingface dataset:
Symmetrical Component Adaptive Beamforming
Authors: Klund William E.
Published: September 2005

The theory of symmetrical components, long used in connection with fault-current analyses of multiphase power-distribution systems, has been applied to the problem of adaptive beamforming with the result that the response of a spatially diverse array of sensors can be made virtually free of the effects of the stationary part of the surrounding noise field. The method of deriving a continually adapting set of amplitude and phase weights to be applied to the individual sensor outputs of an array to cause the cancellation of the quasistationary noise-field components is developed. This method yields beamforming weights that are similar or identical to those which are generated by the covariance-matrix-inversion techniques which have been used in adaptive beamforming; but the laborious process of matrix inversion is eliminated and replaced with an efficient, direct-approach process.
Signal and Noise Scattering by a Planar Array
Authors: Pyle Robert W. , Barger James E.
Published: September 2005

We consider here the effect of inhomogeneous surface admittance upon the performance of a planar array. We compare an acoustically “rough” array, where the interstices between adjacent transducers present a different acoustic admittance to the medium than do the transducer faces, with a “smooth” array, similar but characterized by a uniform surface admittance. Incident sound waves are scattered by the inhomogeneities of the rough array, changing its sensitivity compared with that of the smooth array. Similarly, the strong spectral components with wavenumbers ranch greater than the acoustic wavenumber ω/c, which characterize turbulent-boundary-layer wall-pressure fluctuations are partially scattered into lower-wavenumber components to which the array is more sensitive. Consequently, the self-noise of the rough array is greater than that of the smooth array. Computational results are given, comparing the response of rough and smooth arrays to acoustic signals and boundary-layer noise. [Work sponsored by Naval Undersea Warfare Center San Diego Division.]
The Weighting Game
Authors: Botsford James H.
Published: September 2005

Many systems have been developed for weighting noise data to provide meaningful indicators of human responses. Beginning with the weighting networks of the standard sound-level meter, numerous more sophisticated weighting methods have been devised to improve correlation with subjective reactions. None has proved too successful. Some of them even disagree significantly as, for example, the Stevens and Zwicker loudness calculations. Also, the proposed N weighting does not indicate PNdB accurately as intended. The calculations of these weighted levels are all too complicated for general use, but each correlates with sound levels extremely well. The reason for the high correlation becomes clear when it is realized that the octave-band SPL's of a noise are predictable from its sound levels with surprising accuracy. This fact even makes possible the expression of sound transmission loss, permissible audiometric room levels, etc., in terms of sound levels. Since searching for better weighting methods is delaying solutions of current problems and since, for practical purposes, sound levels are just as accurate, sound levels should become the preferred weighted levels for use in dealing with current problems, including the puzzles of human responses.
Discrimination of Frequency Ratios
Authors: Houtsma A. J. M.
Published: September 2005

It is well known that our natural musical scale is built up out of tones whose frequencies are related by simple whole numbers. A sequence of tones in this scale seems to sound “natural,” while sequences of tones whose frequencies form a more complicated ratio sound “strange” or “unnautral.” The purpose of this research was to determine experimentally whether or not this phenomenon is reflected in the auditory system's ability to detect small changes in frequency ratio. Specifically, an attempt was made to determine the just noticeable difference (jnd) in frequency ratio for several ratios in the vicinity of the octave. To determine the jnd, a two-alternative forced-choice method was used. The results of this experiment indicate that the jnd is independent of the ratio. [Work supported principally by a grant from the National Institutes of Health and in part by the Joint Services Electronics Program.]
Aural Harmonics: Tone-on-Tone Masking at Lower Frequencies of a Fundamental
Authors: Clack T. D.
Published: September 2005

Monaural presentation of a pure tone fundamental (f1) together with an objective second harmonic (f2) has been used to demonstrate the presence of aural harmonics. The listener's task involves tracing a Békésy-type threshold for the f2 as it is shifted through 360° relative to f1. The phase shift produces changes in threshold sensitivity described by the equation Y = A1 + A2 sin (x+φ). These results have been interpreted in terms of a model that has three major assumptions: (a) the ear generates an aural harmonic (AH); (b) the objective f2 and AH sum vectorially; (c) the listener must maintain the resultant at some perceptual threshold level. This model also successfully predicted a peculiar reversal of the usual masking effect. All previous studies have been limited, however, to f1=1000 Hz. The present experiment reports results obtained from 10 normal listeners using f1=500 Hz at intensities between 51 and 71 dB SPL. Preliminary analysis confirms that the threshold changes sinusoidally but the reversal of the usual masking effect is absent. The derived values of A1, A2, and φ will be discussed in relation to the model and previous results. [Work supported by a grant from the National Institutes of Health.]
Signal-Noise Model of Hearing
Authors: Rosenstein M. , Katz A.
Published: September 2005

A simple mathematical model of hearing is proposed in which loudness is related to signal-noise intensity. The model, in addition to conforming to empirical psychoacoustic data, has interesting physiological correlates as well. Loudness-intensity curves generated by the model closely match empirical curves over the 200- to 10 000-Hz range. The contribution of aural harmonics at high intensities is also accommodated. The model exhibits threshold shifts and recruitment effects typical of cochlear disorders, in the presence of masking noise and supplies a mechanism for low-frequency sensitivity decline in terms of internal masking. Possible physiological sources of such masking noises are discussed. The model implies some novel views of cochlear pathologies and suggests techniques for controlled simulation of such pathologies in normal ears. The utility of such simulation is discussed.
Perception of Loudness at Suprathreshold Levels during Visual Stimulation
Authors: Karlovich Raymond S.
Published: September 2005

Six observers engaged in an alternate binaural loudness balance (ABLB) task utilizing the method of adjustment to explore the perception of loudness of a 300-msec-duration 1-kHz auditory stimulus at 20 and 50 dB SL's. Conditions utilized were no visual stimulation during ABLB, visual stimulation in synchrony with the standard auditory stimulus during ABLB, and visual stimulation in synchrony with the comparison auditory stimulus during ABLB. The visual stimulus was a short-duration stroboscopic light flash. The data indicated that sensory interaction in terms of visual facilitation of auditory loudness does occur and is more apparent at higher rather than lower SL's. Observers adjusted the comparison stimulus to a higher SL when the visual stimulus was associated with the standard stimulus than they did when the visual stimulus was associated with the comparison stimulus. The magnitude of this statistically significant difference was 7 dB and it implies that information presented to the visual sensory modality can affect the perception of the magnitude of information presented to the auditory sensory modality. [Work supported by University of Wisconsin Graduate School.]
Auditory Feedback and Helium Speech
Authors: Willot James F. , Sergeant Russell L.
Published: September 2005

This study evaluated effects of auditory feedback upon production of helium speech. Recordings were made of five subjects who spoke on exhalations of air and an 80-20 mixture of He/O2, in quiet and with 95 dB SPL noise introduced to the ear via earphones. Talkers used a VU-meter to speak at a constant level throughout recording. The long-term average spectra of speech did not reveal striking differences between the two breathing mixtures as expected. Maximum energy was at 500 Hz for air and 900 Hz for He/O2. Spectrograms of vowels revealed typically reported shifts upward in the helium speech. Neither the average spectra nor the spectrograms of helium speech showed significant differences between talking in noise and quiet. Auditory feedback apparently is not utilized by talkers to change frequency characteristics of helium speech over short periods of time. On the other hand, when noise was present in air, several decibels more energy was observed at frequencies above 1300 Hz. Mean intelligibility scores significantly improved for both air and helium when noise interfered with a talker's ability to hear his speech. This improvement suggests that talkers try to compensate for their inability to hear themselves by speaking more distinctly.
Dimensional Analysis and Display of Speech Spectra
Authors: Boehm J. F. , Wright R. D.
Published: September 2005

Real-time spectrographic analysis involves processing of spectral outputs as vectors in multidimensional space. To reduce the number of dimensions and eliminate redundancy between channels, a covariance matrix can be derived and the eigenvectors calculated. Correlating the spectral cross sections with as few as three eigenvectors can account for up to 98% of the total variance. Following the theory of Yilmas [H. Yilmas, NASA Contract 12–129, Final Rept. (Dec. 1966)], a real-time display using correlations of the first three eigenvectors has been written for a PDP-1 computer. The display consists of a circle representing a cross section of a cone, and a vector representing cone height. The height represents loudness, as determined by the correlation of the first eigenvector; and the circle is analogous to a vowel circle derived from Eigenvectors 2 and 3, normalized for volume by Eigenvector 1. The display provides effective phoneme separation: display coordinates are useful for automatic phoneme identification. The eigenvectors can be quickly recalculated to accommodate variations in language or speech type.
Ultrasonic Absorption in Liquids at High Pressure
Authors: Allegra J. , Hawley S. , Holton G.
Published: September 2005

The ultrasonic absorption and velocity have been measured in a number of liquids to pressures as high as 10 000 kg/cm2. The absorption behavior observed in nonassociated liquids clearly demonstrates the presence of both thermal and structural relaxation processes. Utilizing the pressure data, the various contributions can be resolved and relevant acoustic parameters compared to those obtained by other investigators from measurements at low temperatures. Recent results in associated liquids will also be presented. [This research sponsored by U. S. Office of Naval Research.]
Acoustic Birefringence in Liquids
Authors: Klein W. R. , Riley W. A.
Published: September 2005

Observations of acoustically induced birefringence in liquids have been reported by several authors since the initial observation by Lucas in 1938. In most of these observations, a polarization analysis was performed on a collimated light beam immediately upon traversing an acoustic beam and the time-average induced birefringence calculated. Since acoustic frequencies in the low-megacycle range and acoustic pressures of the order of 0.5 atm are common, ultrasonic light-diffraction effects are significant under these experimental conditions and must be carefully considered in analyzing the experimental data. In this paper, the light distribution that results from passing a plane, linearly polarized light beam through a liquid, made optically uniaxial by an acoustic beam, is discussed for both the near- and the farfield. Experimental measurements on several liquids that exhibit large birefringence effects are reported for both the near- and farfield and the interpretation of these data discussed in terms of existing theories.
Computer Use in Parallel-Formant Speech Synthesis
Authors: Carlson Carl W. A.
Published: September 2005

The computer has been found to be an invaluable tool in the production of synthesized speech by rule, and in changing experimentally the values of the parameters in synthesized utterances in the quest for naturalness and intelligibility. Using a rules synthesis program, production time for synthesizing an utterance has been reduced to about 1 min per 10 sec of synthesized speech. With the control program, parameter values can be changed quickly and good results may be saved. A “window” program allows the operator to listen to any segment of a longer utterance in isolation. Storage of parameter values on computer tape and a program to play these back removes the problem of corespace limitations and allows synthesis of utterances of unlimited length. A display program allows use of the light pen to change any of the parameter values in an utterance and see the spectrograph of the utterance while listening to it. In these control programs, the operator gets immediate feedback from changes and can keep good ones, thus providing data for corresponding changes in the rules tables.
Transinformation Measurements on a Shallow-Water Acoustic Communication Channel
Authors: Huff Lloyd C.
Published: September 2005

Pseudorandom, binary coded, nonreturn to zero, 100% amplitude-modulated symbols have been transmitted across the USL shallow-water oceanographic/acoustic range. Symbol rates from 1 symbol/15 sec to 20 symbols/sec were transmitted during sea states 1–5. The received symbols were compared with the transmitted symbols, which had been time delayed to allow synchronous detection. The results demonstrate the presence of two noise sources. Multiplicative noise is the controlling factor for sea states less than 2, whereas the additive noise source limits the bits per symbol for higher sea states. The maximum information rate was observed at sea state 2 with 20 transmitted symbols per second.
Penetration of Sonic Booms into the Ocean
Authors: Young Robert W.
Published: September 2005

Underwater sound pressures have been measured in comparison with sound pressures in air resulting from sonic booms generated by aircraft flying near Mach 1.1. Microphones typically were mounted 1 and 12 ft (on the average) above the perturbed ocean surface, and displaced laterally at least 1000 ft; hydrophones were suspended 20, 80, and 160 ft below the surface. Sound-pressure waveforms from the two microphones, passed by octave-band filters in the lower audio-frequency range, were of comparable amplitude and approximately 10 times greater in amplitude than those from the shallow hydrophone; the waveforms were very different, however, from air and from water. In order to characterize a total pulse, the squared sound pressure within the octave was integrated in time. The resulting octave-band, pressure-squared-time levels from the two microphones agreed with each other for a given flyover and constituted a spectrum sloping downward about 4 dB/oct; the corresponding spectra from the hydrophones tended to exhibit a broad peak near 250 Hz. For a boom whose peak sound-pressure level in the octave band centered at 250 Hz was 130 dB, re 20 μN/m2, with 1 sec as the reference time, the integrated pressure-squared-time level in air was of the order of 110 dB, and the integrated level was about 90 dB, 20 ft down in the water, and less at greater depths.
Acoustic Propagation Constants in Corprene DC-100
Authors: Higgs R. W.
Published: September 2005

The acoustic propagation constants of Corprene DC-100 have been measured using impedance tube technique over a temperature range of 4°–30°C, a pressure range of 0–2000 psi and a frequency range of 8.0–40 kHz. Corprene DC-100 is a medium-firm gasket material manufactured by Armstrong Cork Co. It is a cork-polychloroprene composite. The complex reflection coefficient was the measured quantity, and this quantity was transformed to the complex acoustic impedance. Using appropriate transmission-line relations, the velocity of sound and the absorption coefficient were determined. The results showed a rapid increase in the sound velocity and a rapid decrease in attenuation with increasing hydrostatic pressure up to 500 psi. The attenuation increased with increasing frequency and increasing temperature. Density and static bulk-modulus data were also measured.
Effects of Masking Speech on the Discriminability of Elementary Consonant Attributes
Authors: Voiers William D.
Published: September 2005

The Diagnostic Rhyme Test (DRT) was used to test the effects of masking voices upon the discriminability six consonant attributes over a range of test speech-to-masking speech ratios. Pronounced qualitative differences were found between the speech-masking case and the case of bandlimited Gaussian masking noise, though some similarities were observed. Whereas Gaussian noise has relatively little effect upon the discriminability of voicing and nasality, voice maskers substantially reduce the discriminability of these attributes. Speech masking has least effect upon the discriminability of sibilation and compactness, although these attributes are among the most susceptible to noise masking. However, both types of masker exert their greatest effect upon the discriminability of sustention (i.e., the fricative-plosive opposition). In general, speech maskers tend, less than noise, to bias listener perception of the various attributes. [This research was conducted under contract with Texas Instruments, Inc., Austin, Texas.]
Some Nonlinear Phenomena in Recordings from Single Auditory-Nerve Fibers
Authors: Goldstein Julius L. , Kiang Nelson Y. S.
Published: September 2005

The phenomena of two-tone inhibition and combination tones provide experimental evidence for nonlinear processing in the peripheral auditory system. These phenomena occur within the normal operating range of the system and cannot be accounted for by overloading or saturating mechanisms. We shall review the stimulus-response characteristics of these phenomena measured in electrophysiological and psychophysical studies. We shall also present new experimental results on disinhibition and masking that can be interpreted in terms of these phenomena. To investigate the relevance of nonlinear mechanisms in frequency analysis, we have examined latency-tuning curve relations for single fibers in the auditory nerve of cats. Preliminary analysis indicates that the electrophysiological data cannot be fully accounted for on the basis of linear filtering. Theoretical implications of these results for models of auditory frequency analysis will be discussed. [Supported by NIH grants and the Joint Services Electronics Program. Part of Dr. Goldstein's work was done at the Laboratory of Psychophysics, Harvard University, supported from an NIH grant through Professor S. S. Stevens.]
Distinct Constrictive Processes, Separated in Time and Space, DivideCaulobacterInner and Outer Membranes
Authors: Judd Ellen M. , Comolli Luis R. , Chen Joseph C. , Downing Kenneth H. , Moerner W. E. , McAdams Harley H.
Published: September 2005

Cryoelectron microscope tomography (cryoEM) and a fluorescence loss in photobleaching (FLIP) assay were used to characterize progression of the terminal stages ofCaulobacter crescentuscell division. Tomographic cryoEM images of the cell division site show separate constrictive processes closing first the inner membrane (IM) and then the outer membrane (OM) in a manner distinctly different from that of septum-forming bacteria. FLIP experiments had previously shown cytoplasmic compartmentalization (when cytoplasmic proteins can no longer diffuse between the two nascent progeny cell compartments) occurring 18 min before daughter cell separation in a 135-min cell cycle so the two constrictive processes are separated in both time and space. In the very latest stages of both IM and OM constriction, short membrane tether structures are observed. The smallest observed prefission tethers were 60 nm in diameter for both the inner and outer membranes. Here, we also used FLIP experiments to show that both membrane-bound and periplasmic fluorescent proteins diffuse freely through the FtsZ ring during most of the constriction procession.
Genetic Analysis Identifies a Function for the
queC
(
ybaX
) Gene Product at an Initial Step in the Queuosine Biosynthetic Pathway in
Escherichia coli
Authors: Gaur Rahul , Varshney Umesh
Published: September 2005

Queuosine (Q), one of the most complex modifications occurring at the wobble position of tRNAs with GUN anticodons, is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. Despite these important implications, its biosynthetic pathway has remained unresolved. Earlier, we observed that a naturally occurring strain of
Escherichia coli
B105 lacked Q modification in the tRNAs. In the present study, we developed a genetic screen to map the defect in
E. coli
B105 to a single gene,
queC
(renamed from
ybaX
), predicted to code for a 231-amino-acid-long protein with a pI of 5.6. As analyzed by mobility of tRNA
Tyr
on acid urea gels and two-dimensional thin-layer chromatography of the modified nucleosides, expression of QueC from a plasmid-borne copy confers a Q
+
phenotype to
E. coli
B105. Further, analyses of tRNA
Tyr
from
E. coli
JE10651 (
queA
mutant), its derivative generated by deletion of chromosomal
queC
(
queA
Δ
queC
), and
E. coli
JE7325, deficient in converting preQ
0
to preQ
1
, have provided the first genetic evidence for the involvement of QueC at a step leading to production of preQ
0
, the first known intermediate in the generally accepted pathway that utilizes GTP as the starting molecule. In addition, we discuss the possibilities of collaboration of QueC with other cellular proteins in the production of preQ
0
.
Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon
Pyrococcus horikoshii
Authors: Keppetipola Niroshika , Shuman Stewart
Published: September 2005

Archaea encode a DNA ligase composed of a C-terminal catalytic domain typical of ATP-dependent ligases plus an N-terminal domain similar to that found in eukaryotic cellular and poxvirus DNA ligases. All archaeal DNA ligases characterized to date have ATP-dependent adenylyltransferase and nick-joining activities. However, recent reports of dual-specificity ATP/NAD
+
ligases in two
Thermococcus
species and
Pyrococcus abyssi
and an ATP/ADP ligase in
Aeropyrum pernix
raise the prospect that certain archaeal enzymes might exemplify an undifferentiated ancestral stage in the evolution of ligase substrate specificity. Here we analyze the biochemical properties of
Pyrococcus horikoshii
DNA ligase.
P. horikoshii
ligase catalyzes autoadenylylation and nick sealing in the presence of a divalent cation and ATP; it is unable to utilize NAD
+
or ADP to promote ligation in lieu of ATP.
P. horikoshii
ligase is thermophilic in vitro, with optimal adenylyltransferase activity at 90°C and nick-joining activity at 70 to 90°C.
P. horikoshii
ligase resembles the ligases of
Methanobacterium thermautotrophicum
and
Sulfolobus shibatae
in its strict specificity for ATP.
Nucleotide Excision Repair or Polymerase V-Mediated Lesion Bypass Can Act To Restore UV-Arrested Replication Forks in
Escherichia coli
Authors: Courcelle Charmain T. , Belle Jerilyn J. , Courcelle Justin
Published: September 2005

Nucleotide excision repair and translesion DNA synthesis are two processes that operate at arrested replication forks to reduce the frequency of recombination and promote cell survival following UV-induced DNA damage. While nucleotide excision repair is generally considered to be error free, translesion synthesis can result in mutations, making it important to identify the order and conditions that determine when each process is recruited to the arrested fork. We show here that at early times following UV irradiation, the recovery of DNA synthesis occurs through nucleotide excision repair of the lesion. In the absence of repair or when the repair capacity of the cell has been exceeded, translesion synthesis by polymerase V (Pol V) allows DNA synthesis to resume and is required to protect the arrested replication fork from degradation. Pol II and Pol IV do not contribute detectably to survival, mutagenesis, or restoration of DNA synthesis, suggesting that, in vivo, these polymerases are not functionally redundant with Pol V at UV-induced lesions. We discuss a model in which cells first use DNA repair to process replication-arresting UV lesions before resorting to mutagenic pathways such as translesion DNA synthesis to bypass these impediments to replication progression.
Properties of a Novel Intracellular Poly(3-Hydroxybutyrate) Depolymerase with High Specific Activity (PhaZd) in
Wautersia eutropha
H16
Authors: Abe Tomoko , Kobayashi Teruyuki , Saito Terumi
Published: September 2005

A novel intracellular poly(3-hydroxybutyrate) (PHB) depolymerase (PhaZd) of
Wautersia eutropha
(formerly
Ralstonia eutropha
) H16 which shows similarity with the catalytic domain of the extracellular PHB depolymerase in
Ralstonia pickettii
T1 was identified. The positions of the catalytic triad (Ser
190
-Asp
266
-His
330
) and oxyanion hole (His
108
) in the amino acid sequence of PhaZd deduced from the nucleotide sequence roughly accorded with those of the extracellular PHB depolymerase of
R. pickettii
T1, but a signal peptide, a linker domain, and a substrate binding domain were missing. The PhaZd gene was cloned and the gene product was purified from
Escherichia coli
. The specific activity of PhaZd toward artificial amorphous PHB granules was significantly greater than that of other known intracellular PHB depolymerase or 3-hydroxybutyrate (3HB) oligomer hydrolases of
W. eutropha
H16. The enzyme degraded artificial amorphous PHB granules and mainly released various 3-hydroxybutyrate oligomers. PhaZd distributed nearly equally between PHB inclusion bodies and the cytosolic fraction. The amount of PHB was greater in
phaZd
deletion mutant cells than the wild-type cells under various culture conditions. These results indicate that PhaZd is a novel intracellular PHB depolymerase which participates in the mobilization of PHB in
W. eutropha
H16 along with other PHB depolymerases.
Novel Pathway for Arsenic Detoxification in the Legume Symbiont
Sinorhizobium meliloti
Authors: Yang Hung-Chi , Cheng Jiujun , Finan Turlough M. , Rosen Barry P. , Bhattacharjee Hiranmoy
Published: September 2005

We report a novel pathway for arsenic detoxification in the legume symbiont
Sinorhizobium meliloti
. Although a majority of
ars
operons consist of three genes,
arsR
(transcriptional regulator),
arsB
[As(OH)
3
/H
+
antiporter], and
arsC
(arsenate reductase), the
S. meliloti ars
operon includes an aquaglyceroporin (
aqpS
) in place of
arsB
. The presence of AqpS in an arsenic resistance operon is interesting, since aquaglyceroporin channels have previously been shown to adventitiously facilitate uptake of arsenite into cells, rendering them sensitive to arsenite. To understand the role of
aqpS
in arsenic resistance,
S. meliloti aqpS
and
arsC
were disrupted individually. Disruption of
aqpS
resulted in increased tolerance to arsenite but not arsenate, while cells with an
arsC
disruption showed selective sensitivity to arsenate. The results of transport experiments in intact cells suggest that AqpS is the only protein of the
S. meliloti ars
operon that facilitates transport of arsenite. Coexpression of
S. meliloti aqpS
and
arsC
in a strain of
E. coli
lacking the
ars
operon complemented arsenate but not arsenite sensitivity. These results imply that, when
S. meliloti
is exposed to environmental arsenate, arsenate enters the cell through phosphate transport systems and is reduced to arsenite by ArsC. Internally generated arsenite flows out of the cell by downhill movement through AqpS. Thus, AqpS confers arsenate resistance together with ArsC-catalyzed reduction. This is the first report of an aquaglyceroporin with a physiological function in arsenic resistance.
Cnu, a NoveloriC-Binding Protein ofEscherichia coli
Authors: Kim Myung Suk , Bae Sung-Hun , Yun Sang Hoon , Lee Hee Jung , Ji Sang Chun , Lee Ji Hyun , Srivastava Preeti , Lee Seol-Hoon , Chae Huiseok , Lee Younghoon , Choi Byong-Seok , Chattoraj Dhruba K. , Lim Heon M.
Published: September 2005

We have found, using a newly developed genetic method, a protein (named Cnu, fororiC-bindingnucleoid-associated) that binds to a specific 26-base-pair sequence (namedcnb) in the origin of replication ofEscherichia coli, oriC. Cnu is composed of 71 amino acids (8.4 kDa) and shows extensive amino acid identity to a group of proteins belonging to the Hha/YmoA family. Cnu was previously discovered as a protein that, like Hha, complexes with H-NS in vitro. Our in vivo and in vitro assays confirm the results and further suggest that the complex formation with H-NS is involved in Cnu/Hha binding tocnb. Unlike thehnsmutants, elimination of either thecnuorhhagene did not disturb the growth rate, origin content, and synchrony of DNA replication initiation of the mutants compared to the wild-type cells. However, thecnu hhadouble mutant was moderately reduced in origin content. The Cnu/Hha complex with H-NS thus could play a role in optimal activity oforiC.
Characterization of a Novel Glucosamine-6-Phosphate Deaminase from a Hyperthermophilic Archaeon
Authors: Tanaka Takeshi , Takahashi Fumikazu , Fukui Toshiaki , Fujiwara Shinsuke , Atomi Haruyuki , Imanaka Tadayuki
Published: September 2005

A key step in amino sugar metabolism is the interconversion between fructose-6-phosphate (Fru6P) and glucosamine-6-phosphate (GlcN6P). This conversion is catalyzed in the catabolic and anabolic directions by GlcN6P deaminase and GlcN6P synthase, respectively, two enzymes that show no relationship with one another in terms of primary structure. In this study, we examined the catalytic properties and regulatory features of theglmDgene product (GlmDTk) present within a chitin degradation gene cluster in the hyperthermophilic archaeonThermococcus kodakaraensisKOD1. Although the protein GlmDTkwas predicted as a probable sugar isomerase related to the C-terminal sugar isomerase domain of GlcN6P synthase, the recombinant GlmDTkclearly exhibited GlcN6P deaminase activity, generating Fru6P and ammonia from GlcN6P. This enzyme also catalyzed the reverse reaction, the ammonia-dependent amination/isomerization of Fru6P to GlcN6P, whereas no GlcN6P synthase activity dependent on glutamine was observed. Kinetic analyses clarified the preference of this enzyme for the deaminase reaction rather than the reverse one, consistent with the catabolic function of GlmDTk. InT. kodakaraensiscells,glmDTkwas polycistronically transcribed together with upstream genes encoding an ABC transporter and a downstream exo-β-glucosaminidase gene (glmATk) within the gene cluster, and their expression was induced by the chitin degradation intermediate, diacetylchitobiose. The results presented here indicate that GlmDTkis actually a GlcN6P deaminase functioning in the entry of chitin-derived monosaccharides to glycolysis in this hyperthermophile. This enzyme is the first example of an archaeal GlcN6P deaminase and is a structurally novel type distinct from any previously known GlcN6P deaminase.
Towards the Identification of Type II Secretion Signals in a Nonacylated Variant of Pullulanase from
Klebsiella oxytoca
Authors: Francetić Olivera , Pugsley Anthony P.
Published: September 2005

Pullulanase (PulA) from the gram-negative bacterium
Klebsiella oxytoca
is a 116-kDa surface-anchored lipoprotein of the isoamylase family that allows growth on branched maltodextrin polymers. PulA is specifically secreted via a type II secretion system. PelBsp-PulA, a nonacylated variant of PulA made by replacing the lipoprotein signal peptide (sp) with the signal peptide of pectate lyase PelB from
Erwinia chrysanthemi
, was efficiently secreted into the medium. Two 80-amino-acid regions of PulA, designated A and B, were previously shown to promote secretion of β-lactamase (BlaM) and endoglucanase CelZ fused to the C terminus. We show that A and B fused to the PelB signal peptide can also promote secretion of BlaM and CelZ but not that of nuclease NucB or several other reporter proteins. However, the deletion of most of region A or all of region B, either individually or together, had only a minor effect on PelBsp-PulA secretion. Four independent linker insertions between amino acids 234 and 324 in PelBsp-PulA abolished secretion. This part of PulA, region C, could contain part of the PulA secretion signal or be important for its correct presentation. Deletion of region C abolished PelBsp-PulA secretion without dramatically affecting its stability. PelBsp-PulA-NucB chimeras were secreted only if the PulA-NucB fusion point was located downstream from region C. The data show that at least three regions of PulA contain information that influences its secretion, depending on their context, and that some reporter proteins might contribute to the secretion of chimeras of which they are a part.
Transcriptional Program of Early Sporulation and Stationary-Phase Events in
Clostridium acetobutylicum
Authors: Alsaker Keith V. , Papoutsakis Eleftherios T.
Published: September 2005

DNA microarray analysis of
Clostridium acetobutylicum
was used to examine the genomic-scale gene expression changes during the shift from exponential-phase growth and acidogenesis to stationary phase and solventogenesis. Self-organizing maps were used to identify novel expression patterns of functional gene classes, including aromatic and branched-chain amino acid synthesis, ribosomal proteins, cobalt and iron transporters, cobalamin biosynthesis, and lipid biosynthesis. The majority of pSOL1 megaplasmid genes (in addition to the solventogenic genes
aad
-
ctfA
-
ctfB
and
adc
) had increased expression at the onset of solventogenesis, suggesting that other megaplasmid genes may play a role in stationary-phase phenomena. Analysis of sporulation genes and comparison with published
Bacillus subtilis
results indicated conserved expression patterns of early sporulation genes, including
spo0A
, the
sigF
operon, and putative canonical genes of the σ
H
and σ
F
regulons. However,
sigE
expression could not be detected within 7.5 h of initial
spo0A
expression, consistent with the observed extended time between the appearance of clostridial forms and endospore formation. The results were compared with microarray comparisons of the wild-type strain and the nonsolventogenic, asporogenous M5 strain, which lacks the pSOL1 megaplasmid. While some results were similar, the expression of primary metabolism genes and heat shock proteins was higher in M5, suggesting a difference in metabolic regulation or a butyrate stress response in M5. The results of this microarray platform and analysis were further validated by comparing gene expression patterns to previously published Northern analyses, reporter assays, and two-dimensional protein electrophoresis data of metabolic genes (including all major solventogenesis genes), sporulation genes, heat shock proteins, and other solventogenesis-induced gene expression.
Site-Directed Mutagenesis and Structural Studies Suggest that the Germination Protease, GPR, in Spores ofBacillusSpecies Is an Atypical Aspartic Acid Protease
Authors: Carroll Thomas M. , Setlow Peter
Published: September 2005

Germination protease (GPR) initiates the degradation of small, acid-soluble spore proteins (SASP) during germination of spores ofBacillusandClostridiumspecies. The GPR amino acid sequence is not homologous to members of the major protease families, and previous work has not identified residues involved in GPR catalysis. The current work has focused on identifying catalytically essential amino acids by mutagenesis ofBacillus megaterium gpr. A residue was selected for alteration if it (i) was conserved among spore-forming bacteria, (ii) was a potential nucleophile, and (iii) had not been ruled out as inessential for catalysis. GPR variants were overexpressed inEscherichia coli, and the active form (P41) was assayed for activity against SASP and the zymogen form (P46) was assayed for the ability to autoprocess to P41. Variants inactive against SASP and unable to autoprocess were analyzed by circular dichroism spectroscopy and multiangle laser light scattering to determine whether the variant's inactivity was due to loss of secondary or quaternary structure, respectively. Variation of D127 and D193, but no other residues, resulted in inactive P46and P41, while variants of each form were well structured and tetrameric, suggesting that D127 and D193 are essential for activity and autoprocessing. Mapping these two aspartate residues and a highly conserved lysine onto theB. megateriumP46crystal structure revealed a striking similarity to the catalytic residues and propeptide lysine of aspartic acid proteases. These data indicate that GPR is an atypical aspartic acid protease.
Site-Directed Mutagenesis and Expression of the Soluble Form of the Family IIIa Cellulose Binding Domain from the Cellulosomal Scaffolding Protein of
Clostridium cellulovorans
Authors: Murashima Koichiro , Kosugi Akihiko , Doi Roy H.
Published: September 2005

The planar and anchoring residues of the family IIIa cellulose binding domain (CBD) from the cellulosomal scaffolding protein of
Clostridium cellulovorans
were investigated by site-directed mutagenesis and cellulose binding studies. By fusion with maltose binding protein, the family IIIa recombinant wild-type and mutant CBDs from
C. cellulovorans
were expressed as soluble forms. Cellulose binding tests of the mutant CBDs indicated that the planar strip residues played a major role in cellulose binding and that the anchoring residues played only a minor role.
Numerical Methods for the Evaluation of the Löwdin α-Function
Authors: Sovic Nemanja , Talman James D.
Published: September 2005

The problem of expanding an angular momentum wave function centered at one point in terms of angular momentum wave functions centered at another point is analysed. The emphasis is on obtaining methods that can be applied to functions that are defined numerically, in contrast to analytic methods. Three numerical approaches are described, and it is found that one leads to extremely accurate results. The question of the rate of convergence of the resulting series is discussed, and results of the application of the expansion to the calculation of nuclear attraction three-center integrals, and electron-electron four-center integrals are presented.
Commutator-Based (A)[X]n(SU(2)×Sn) NMR Cluster Systems: Establishment of the Universality of [n](Sn) Salients and Constraints on ϕ±11(1.1) Polarisations to the [1n] Salient: Permutational Spin Symmetry (PSS) Within NMR Spin Dynamics - an Analytic View
Authors: Temme Francis P.
Published: September 2005

Analytic SU(2) × Sn dual tensorial (DT) spin dynamics over uniform NMR spins is invoked in examining the modern quantum basis for the universal non-observability rule which governs dominant intracluster JXX' couplings of (A)[X]n NMR systems as a specific form of (abstract) permutational spin symmetry (PSS) with well defined properties on spin-alone space. This is shown to be linked to DT constraints that apply to the cross-product ϕ1±1(1.1) polarisation development i.e., as being confined to [1n](Sn) (Liouvillian) salient, with the existence of [n] (rotating frame) null subspaces. Both these arise within the spin dynamics of (A)[X]2 spin systems (or subsystems thereof) within (a hierarchy of) dominant JXX' governing the internal L(0); such spin systems provide analytic sequels to comparative spin dynamics studies of XX' PSS and AX broken-PSS systems in a Liouvillian coupled tensorial basis formalism, since both draw on (Sanctuary B. C.: Mol. Phys. 1985, 55, 1017), and on the realisation that proper PSS over a (uniform) spin-space L(0) = [H(0),.] zeroth-order Liouvillian and its internal (hierarchical subsets of) JXX' (Temme F. P.: J. Mol. Struct. (THEOCHEM) 2002, 547, 153) i.e., for abstract Sn ↓ G group embeddings. The present work also examines the general irrep-structure of DT spin symmetries for the extent of unit-character irreps and the role of Sn ⊃ Sn-1 ⊃ .. ⊃ [2](S2) group chains in defining the Sn multiple invariants under democratic recoupling of PSS of uniform spin systems. As group measures, these properties apply to both (A)[X]n and [AX]n PSS symmetries, with the invariant cardinality |SI|(n) being related to time-reversal invariance (TRI) and its inherent democratic recoupling (DR) over Weyl (I • I) pairs. For [X]2n uniform spin clusters, |SI|(2n) is best derived via n-fold polyhedral combinatorics of the underlying DR (Temme F. P.: Proc. R. Soc. London, Ser. A 2005, 461, 321) i.e., as an augmented post-Weyl view of the essential role of TRI in (group) invariant cardinality, with the Sn-invariants represented by certain Sn subduction properties.
Assessment of the Direct Generalized Bloch Approach B0: Application to the Li and Be Atoms and the Molecules LiH, BeH, and the Phenolate Anion
Authors: Meissner Holger
Published: September 2005

Besides the necessity of the development of sophisticated methods to calculate correlation energies - be it the coupled-cluster (CC) or the configuration-interaction (CI) methods and their various approaches - one also accentuate the need for efficient and less demanding methods in the area of medium and large molecular systems. Therefore, this article proposes a computational efficient and in our opinion reasonable approach for the calculation of correlation energies for medium and even larger molecules. This approach, named B0, based on the so-called direct generalized Bloch (DGB) equation which has already been successfully applied to small systems. Within those considerations the B0 approach showed promising results so that further investigations are worthwhile. Here, as a further step in the assessment of this method we apply the B0 approach to the Li and Be atoms as well as the LiH and BeH molecules. Molecules which show open and closed shell characteristics in the equilibrium and in the case of dissociation as well. The results are compared with CC and CI and experimental results if available. Since this results are encouraging even when considering small basis sets and with the prospect of larger molecular systems, therefore, we perform also B0 energy calculations for the low-lying states of the phenolate anion which for instance can be used in a simple model of the photoactive yellow protein (PYP) chromophore.
The challenges and ethical dilemmas of a military medical officer serving with a peacekeeping operation in regard to the medical care of the local population
Authors: Tobin J
Published: September 2005

Medical Officers serving with their national contingents in peacekeeping operations are faced with difficult ethical decisions in regard to their obligations to the local civilian population. Such populations may be under-resourced in regard to medical care, and vulnerable to abuse and exploitation. Though the medical officer may support the local medical services, he/she should never undermine these resources. Adopting a human rights approach and observing the requirements of ethical medicine, aids the doctor in prioritising his/her duties. At times there may be conflict with one’s own military superiors. It is wise to discuss potential difficulties prior to setting out on the mission. Human rights abuses cannot be ignored. The medical officer has a duty to do his/her best to report their observations so as to prevent abuse or to bring it to an end.
Emerging Therapeutics for Chronic Hepatitis B
Authors: Mailliard Mark E. , Gollan John L.
Published: September 2005

Hepatitis B is a global health problem. Patients with chronic hepatitis B (CHB) carry a significant risk to eventually develop cirrhotic liver disease. Recent therapeutic advances against CHB offer excellent potential for long-term suppression of hepatitis B virus (HBV) replication during antiviral therapy, and occasionally a durable remission off medication. Selection of appropriate patients for antiviral therapy depends on identification of HBV replication and an elevated alanine aminotransferase level or histologic liver injury. Pegylated interferon alpha offers potent immunomodulatory and antiviral activity with the potential for durability, but also with adverse effects and significant cost. The nucleoside or nucleotide analogs, lamivudine, adefovir, and entecavir, suppress HBV replication and are extremely well-tolerated, but long-term or even lifelong therapy is required. Most experience has been gained with lamivudine, but viral resistance occurs frequently. Newer analogs appear to be relatively free of this problem. Approaches using a combination of agents have promise, but have yet to be proven superior to individual drugs alone.
Emotion and Cognition: Insights from Studies of the Human Amygdala
Authors: Phelps Elizabeth A.
Published: September 2005

Traditional approaches to the study of cognition emphasize an information-processing view that has generally excluded emotion. In contrast, the recent emergence of cognitive neuroscience as an inspiration for understanding human cognition has highlighted its interaction with emotion. This review explores insights into the relations between emotion and cognition that have resulted from studies of the human amygdala. Five topics are explored: emotional learning, emotion and memory, emotion's influence on attention and perception, processing emotion in social stimuli, and changing emotional responses. Investigations into the neural systems underlying human behavior demonstrate that the mechanisms of emotion and cognition are intertwined from early perception to reasoning. These findings suggest that the classic division between the study of emotion and cognition may be unrealistic and that an understanding of human cognition requires the consideration of emotion.
Experimental colitis in mice and sensitization of converging visceral and somatic afferent pathways
Authors: Lamb Kenneth , Zhong Fang , Gebhart G. F. , Bielefeldt Klaus
Published: September 2005

Chronic pain syndromes affecting different organs often coexist. We hypothesized that sensitization of one afferent pathway may affect converging input from other areas of the body. We induced colitis in mice with 2,4,6-trinitrobenzenesulfonic acid (TNBS); control animals were treated with equal volumes of vehicle (50% ethanol) only. Visceromotor responses to graded colorectal distension, cystometrograms, and response thresholds to mechanical and thermal stimulation of both hind paws were determined on days 7 and 14. Inflammation of colon and bladder was assessed with validated histological markers and scores. TNBS caused significant colitis on day 7 that resolved by day 14; there was no evidence of bladder inflammation. There was a significant hypersensitivity to colorectal distension on day 7, which returned to normal on day 14. This was associated with bladder overactivity, as demonstrated by early onset of micturition and more frequent micturition on day 7 after TNBS administration. Colitis also significantly altered responses to mechanical and thermal stimulation of both hind paws on day 7 but not day 14. We conclude that cross talk between afferent visceral and somatic pathways may contribute to the coexistence of pain syndromes.