bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cochlear Responses to Acoustic Transients: An Interpretation of Whole-Nerve Action Potentials
Authors: Teas Donald C. , Eldredge Donald H. , Davis Hallowell 
Published: September 2005

Intracochlear electrodes in the guinea pig are used to measure the relations among cochlear potentials in response to slow acoustic transients. The traveling wave of Békésy is described in terms of cochlear-microphonic (CM) voltage as functions of time and place along the cochlear partition. The results are consistent with previous observations in the ear and on models of the basilar membrane. Interpolations of wave velocity and wave amplitudes between places used for the measurements allow continuous representations of the traveling-wave pattern of CM in either space or time. From these representations, it is clear that the duration of the stimulating phase of CM along the cochlear partition significantly exceeds the apparent duration of the whole-nerve action-potential (AP) response to these transients.
Selective changes in the waveforms of the AP responses, as opposed to simple reductions in amplitude, are observed when the transients are accompanied by bands of noise and after local chemical or mechanical injury to the organ of Corti. The selective changes in waveform allow consideration of the waveform removed from the normal AP response by the noise as well as the response remaining during noise. The responses removed by each of successive increases the bandwidth of the noise reveal the presence of AP responses at times not apparent in the normal whole-nerve AP waveform. These observations are most easily explained by assuming that the basic neural response is diphasic as conventionally recorded. When neurons become active in an orderly sequence, the positive phases of the earlier individual responses coincide with and may conceal the negative phases of later responses. The whole-nerve AP waveform is thus considered as the convolution (complex product) of two functions in time, the diphasic unit of response and the numerical sequence of newly active neurons. An empirical model for the diphasic unit of response “divided” into the AP waveform reveals patterns of neural activity that are compatible with the traveling wave of CM. The same model satisfactorily explains several details of the whole-nerve AP waveform recorded during stimulation with a burst of high-frequency tone.
Long-Range SOFAR Studies in the South Atlantic Ocean
Authors: Bryan George M. , Truchan Marek , Ewing John I. 
Published: September 2005

A study was made of the accuracy to be expected from long-range SOFAR measurements and of some of the factors which limit that accuracy. Depth charges were fired along a track across the South Atlantic and into the Indian Ocean. The signals were received on Fernando de Noronha and Ascension Island. Distances ranged from 75 to 4700 nautical miles.
The results show that it should be possible to obtain an accuracy of about 50 m in 1000 miles from a 20-shot sample. Off-axis shooting seriously affects the accuracy. Large topographic features, which do not extend into the sound channel axis itself, cut off the front of the signal, without impairing arrival-time accuracy, while continental land masses block the signal entirely. Attenuation of the peak-signal intensity with increasing range along an unimpeded path is consistent with cylindrical spreading.
Bending Wave Propagation in Rods and Plates
Authors: Lange James N. 
Published: September 2005

Rods exhibit some very complex vibrational characteristics. The ends behave like cavity resonators in a narrow frequency band and vibrate with amplitudes as much as 80 times the amplitude of the incident wave. At low frequencies, bending vibrations of rods are described by the complex Young's modulus, and the Bernoulli theory of bending leads to the same result as the exact theory. At high frequencies, bending vibrations are described by the shear modulus, and the loss factor approaches or becomes equal to that of shear waves.
Plates exhibit a behavior similar to bending vibrations in rods. At low frequencies, Young's modulus and its loss factor describe the vibrational behavior of a thin plate. As the frequency increases, the modulus approaches the shear modulus, and the loss factor approaches the loss factor for shear waves after fluctuating in a periodic manner between the loss associated with Young's modulus and that of the shear modulus. The measurement, of the loss factor by bandwidth and decay methods agree, provided a narrow bandpass filter is used so that the low-frequency modes, which are always excited by a point force, are suppressed.
Electrostatic Microphones with Electret Foil
Authors: Sessler G. M. 
Published: September 2005

In this paper the operation of electrostatic microphones with foil electrets is studied theoretically. It is assumed that a foil electret has equal (free or bound) constant charges of opposite sign on its two surfaces. A formula is obtained which shows the generated output voltage of the microphone to be a function of the surface charges of the electret, the geometrical dimensions of the microphone, and the externally connected resistance. According to this formula, typical sensitivities of a few mV/μbar can be expected.
The electret microphone is also compared theoretically to a similar system with nonelectret foil. The calculations show that a surface charge of 10−8 C/cm2 on the surface of 12-mil Mylar foil corresponds to a bias of about 45 V in the nonelectret reference system. It is pointed out in this connection that the measurement of surface charges of foil electrets by the induction method requires a correction formula.
Ultrasonic Absorption in Water Containing Plankton in Suspension
Authors: Watson John D. , Meister Robfrt 
Published: September 2005

A study is made to determine the frequency and concentration dependence of the ultrasonic absorption in aqueous suspensions of (1) scenedesmus and diatoms, two forms of algae, and (2) artemia (brine shrimp) eggs. The measurements were made over a frequency range of 125 kc/sec to 55 Mc/sec.
The excess absorption caused by scenedesmus is found to be linearly dependent on concentration and has a value of α/f2=7×10 16 m−1 sec2 for the highest concentration measured, 0.72 g/liter of water. The excess absorption caused by diatoms is also linearly dependent on concentration and has a value of 25×10−15 m−1 sec2 for 290 g/liter of water, the highest concentration measured. For both scenedesmus and diatoms, it is concluded that the normal concentration of these forms of algae found in large bodies of water causes negligible absorption compared to the absorption of the water itself.
The major portion of the excess attenuation due to the shrimp eggs in the kilocycle region is attributed to a scattering mechanism. Application of a theory for elastic scattering in this wavelength region (ka&lt;1) gave good agreement with experimental results. A phase-velocity investigation of a resonance phenomenon at 7 Mc/sec revealed a characteristic velocity dispersion.
Flip-Floating Instrument Platform
Authors: Fisher F. H. , Spiess F. N. 
Published: September 2005

A stable platform from which to perform experiments at sea has been a long-sought goal of sea-going scientists. In order to perform fine-scale experiments on fluctuations of acoustic signals in the ocean the manned buoy FLIP has been built to provide the needed stable platform for such work.
The 355-ft-long, 600-ton craft is towed to station in the horizontal position, and operates in the vertical position at a draft of 300 ft with its electronics laboratory about 30 ft above the water line.
A description is given of its development, stability, and operating characteristics, including the unique flipping operation.
Scanned Line Hydrophone Method of Determining Angle of Arrival of Sound in Water
Authors: Pigott M. T. , Whitmarsh D. C. , Brown J. L. 
Published: September 2005

A group of hydrophone elements uniformly and closely spaced along a straight line is used to measure the angle of arrival of sound waves. By sampling the outputs of these elements rapidly and in succession, one simulates single hydrophone moving relative to the sound waves. The signal measured at the output has a frequency given by the Doppler equation f=f0(1 +α cosθ), where f0 is the frequency of the sound in the water, α is the ratio of the scanning speed to the speed of sound, and θ is the bearing angle desired. The theoretical results expected along with the experimental measurements which confirm the theory and a description of the equipment used are included.
It was found that the scanned system simulates almost exactly a single moving point hydrophone, and the Doppler equation was found to hold. Pure tones and narrow-band noise signals are shifted in frequency. The angular resolution was found to be equal to the ratio of the wavelength of the sound to the component of the hydrophone length normal to the direction of sound propagation.
Stereo Geometry Measurements
Authors: Klipsch Paul W. 
Published: September 2005

Methods of evaluating accuracy of geometry of stereophonic sound reproductions involve generating sounds—such as speech or clicks—over a systematic array and then having observers attempt to locate the virtual sources of such sounds on playback over a stereo system. Multiple-row sound source arrays previously have been used. Distance and vertical localizations are poor so lateralization was evaluated with a single row of sound sources. Using the root-mean-square error divided by the array spread as a “criterion of error,” Table I evaluates direct listening (“live”) and the various reproducing systems indicated.
TABLE I.
Conditions Abbreviation Criterion of error
1. Direct listening Live 0.042
2. Stereo-directional microphone, 2 sound
tracks, 3 speakers SD-2-3 0.11
3. 3 Spaced microphones, 3 electrically
independent channels 3-3-3 0.123
4. 2 Spaced microphones, 2 sound tracks,
3 speakers 2-2-3 0.137
5. 2 Spaced microphones, 2 sound tracks,
2 speakers 2-2-2 0 30
Playback array subtended nearly 90 deg at the observer. For condition 5, errors increased grossly as the observer moved away from the axis of symmetry, only slightly for the other reproducing systems, and none for the “live” condition.
Spectrum Analysis of Earthquake T Phases and Large Underwater Shots
Authors: Northrop John 
Published: September 2005

Spectrum analysis of T phases recorded in the Atlantic for oceanic paths up to 3500 nautical miles are compared with similar recordings of large (up to 10 tons) underwater shots. In one case the T-phase energy was propagated across the Mid-Atlantic Ridge without excessive attenuation, but islands near the source or receiver do attenuate the signal. The T phases show dispersion, in the 0–35 cps range, which is proportional to the signals' duration (up to 7 min). The mid-depth shots which do not excite such low modes show comparatively little dispersion. It is possible, therefore, to establish the following criteria for differentiating shots from T phases:
Shots T-Phases
Sharp onset in the 0–150 cps Early low-frequency forerunners
range Poor reflections
Good reflections from bottom Foreshocks and aftershocks
topography P and S arrivals ahead of T
No foreshocks or aftershocks Gradual onset and decay
No early ground arrivals
Rapid onset and decay
These data are compared with those obtained from analysis of bottomed shots in the Gulf of Maine. (This work was supported by the Office of Naval Research.)
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

ABSTRACTCryoelectron 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

ABSTRACT

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

ABSTRACT

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

ABSTRACT
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

ABSTRACT

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

ABSTRACT

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

ABSTRACTWe 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

ABSTRACTA 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.