bluuebunny/crossref_metadata_2025 huggingface dataset:
Speech production in noise with and without hearing protection
Authors: Tufts Jennifer B. , Frank Tom
Published: August 2003

People working in noisy environments often complain of difficulty communicating when they wear hearing protection. It was hypothesized that part of the workers’ communication difficulties stem from changes in speech production that occur when hearing protectors are worn. To address this possibility, overall and one-third-octave-band SPL measurements were obtained for 16 men and 16 women as they produced connected speech while wearing foam, flange, or no earplugs (open ears) in quiet and in pink noise at 60, 70, 80, 90, and 100 dB SPL. The attenuation and the occlusion effect produced by the earplugs were measured. The Speech Intelligibility Index (SII) was also calculated for each condition. The talkers produced lower overall speech levels, speech-to-noise ratios, and SII values, and less high-frequency speech energy, when they wore earplugs compared with the open-ear condition. Small differences in the speech measures between the talkers wearing foam and flange earplugs were observed. Overall, the results of the study indicate that talkers wearing earplugs (and consequently their listeners) are at a disadvantage when communicating in noise.
Simultaneous reconstruction of flow and temperature cross-sections in gases using acoustic tomography
Authors: Gan Tat Hean , Hutchins David A. , Carpenter Peter W. , Wright William M. D.
Published: August 2003

This paper describes the use of air-coupled ultrasonic tomography for the simultaneous measurement of flow and temperature variations in gases. Air-coupled ultrasonic transducers were used to collect through-transmission data from a heated gas jet. A transducer pair was scanned in two-dimensional sections at an angle to the jet, and travel time and amplitude data recorded along various paths in counter-propagating directions. Parallel-beam tomographic reconstruction techniques allowed images to be formed of variations in either temperature or flow velocity. Results have been obtained using heated jets, where it has been shown that it is possible to separate the two variables successfully.
Determination of unsteady heat release distribution from acoustic pressure measurements: A reformulation of the inverse problem
Authors: Subrahmanyam P. Bala , Sujith R. I. , Ramakrishna M.
Published: August 2003

An integral method is developed to solve the inverse problem of determining the oscillatory heat release distribution from the knowledge of the acoustic pressure field within a combustor. Unlike earlier approaches, in which the problem is formulated in terms of Fredholm integral equation, the inverse problem is reformulated in terms of Volterra integral equation. This reformulation, valid for low Mach numbers (M2≪1), facilitates the recovery of heat release at all frequencies. The resulting Volterra integral equation is solved using both direct numerical method and implicit least-squares method. The results show that the implicit least-squares method is superior to the direct numerical method and yields accurate determination of heat release at all frequencies.
Some aspects of coupling-induced sound absorption in enclosures
Authors: Sum K. S. , Pan J.
Published: August 2003

It is known that the coupling between a modally reactive boundary structure of an enclosure and the enclosed sound field induces absorption in the sound field. However, the effect of this absorption on the sound-field response can vary significantly, even when material properties of the structure and dimensions of the coupled system are not changed. Although there have been numerous investigations of coupling between a structure and an enclosed sound field, little work has been done in the area of sound absorption induced by the coupling. Therefore, characteristics of the absorption are not well understood and the extent of its influence on the behavior of the sound-field response is not clearly known. In this paper, the coupling of a boundary structure and an enclosed sound field in frequency bands above the low-frequency range is considered. Three aspects of the coupling-induced sound absorption are studied namely, the effects of exciting either the structure or the sound field directly, damping in the uncoupled sound field and damping in the uncoupled structure. The results provide an understanding of some features of the coupling-induced absorption and its significance to the sound-field response.
Primary microphone calibration system stability (L)
Authors: Wong George S. K. , Wu Lixue
Published: August 2003

The stability of a primary microphone calibration system is investigated. In connection with the intercomparison on the calibration of type 4160 LS1P laboratory standard microphones involving the national laboratories of five countries, the pilot laboratory in Canada collected data over a period of 31 months. The measurements were made in a chamber with controlled environment at the reference condition of 23 °C, 101.325 kPa and 50% R.H. The microphone sensitivity levels were measured at seven frequencies from 125 to 8000 Hz. Over the above period the stability of the primary microphone calibration system was approximately 0.01 dB that included the stability of the transfer standard microphones.
Blue whale (Balaenoptera musculus) sounds from the North Atlantic
Authors: Mellinger David K. , Clark Christopher W.
Published: August 2003

Sounds of blue whales were recorded from U.S. Navy hydrophone arrays in the North Atlantic. The most common signals were long, patterned sequences of very-low-frequency sounds in the 15–20 Hz band. Sounds within a sequence were hierarchically organized into phrases consisting of one or two different sound types. Sequences were typically composed of two-part phrases repeated every 73 s: a constant-frequency tonal “A” part lasting approximately 8 s, followed 5 s later by a frequency-modulated “B” part lasting approximately 11 s. A common sequence variant consisted only of repetitions of part A. Sequences were separated by silent periods averaging just over four minutes. Two other sound types are described: a 2-5 s tone at 9 Hz, and a 5–7s inflected tone that swept up in frequency to ca. 70 Hz and then rapidly down to 25 Hz. The general characteristics of repeated sequences of simple combinations of long-duration, very-low-frequency sound units repeated every 1–2 min are typical of blue whale sounds recorded in other parts of the world. However, the specific frequency, duration, and repetition interval features of these North Atlantic sounds are different than those reported from other regions, lending further support to the notion that geographically separate blue whale populations have distinctive acoustic displays.
Reelin Promotes Peripheral Synapse Elimination and Maturation
Authors: Quattrocchi Carlo C. , Huang Cheng , Niu Sanyong , Sheldon Michael , Benhayon David , Cartwright Joiner , Mosier Dennis R. , Keller Flavio , D'Arcangelo Gabriella
Published: August 2003

Reelin is an extracellular protein that is crucial for layer formation in the embryonic brain. Here, we demonstrate that Reelin functions postnatally to regulate the development of the neuromuscular junction. Reelin is required for motor end-plate maturation and proper nerve-muscle connectivity, and it directly promotes synapse elimination. Unlike layer formation, neuromuscular junction development requires a function of Reelin that is not mediated by Disabled1 or very-low-density lipoprotein receptors and apolipoprotein E receptor 2 receptors but by a distinct mechanism involving its protease activity.
High-Density Electron Anions in a Nanoporous Single Crystal: [Ca
24
Al
28
O
64
]
4
+
(4
e
-
)
Authors: Matsuishi Satoru , Toda Yoshitake , Miyakawa Masashi , Hayashi Katsuro , Kamiya Toshio , Hirano Masahiro , Tanaka Isao , Hosono Hideo
Published: August 2003

We removed ∼100% of clathrated oxygen ions from the crystallographic cages in a single crystal of 12CaO·7Al
2
O
3
, leading to the formation of high-density (∼2 × 10
21
cm
–
3
) electrons highly localized in the cages. The resulting electron forms a structure that we interpret as an
F
+
center and migrates throughout the crystal by hopping to a neighboring cage with conductivity ∼100 siemens per centimeter, demonstrating that the encaged electron behaves as an anion. The electron anions couple antiferromagnetically with each other, forming a diamagnetic pair or singlet bipolaron. The resulting [Ca
24
Al
28
O
64
]
4
+
(4
e
–
) may be regarded as a thermally and chemically stable single crystalline “electride.”
Genome-Wide Insertional Mutagenesis of
Arabidopsis thaliana
Authors: Alonso José M. , Stepanova Anna N. , Leisse Thomas J. , Kim Christopher J. , Chen Huaming , Shinn Paul , Stevenson Denise K. , Zimmerman Justin , Barajas Pascual , Cheuk Rosa , Gadrinab Carmelita , Heller Collen , Jeske Albert , Koesema Eric , Meyers Cristina C. , Parker Holly , Prednis Lance , Ansari Yasser , Choy Nathan , Deen Hashim , Geralt Michael , Hazari Nisha , Hom Emily , Karnes Meagan , Mulholland Celene , Ndubaku Ral , Schmidt Ian , Guzman Plinio , Aguilar-Henonin Laura , Schmid Markus , Weigel Detlef , Carter David E. , Marchand Trudy , Risseeuw Eddy , Brogden Debra , Zeko Albana , Crosby William L. , Berry Charles C. , Ecker Joseph R.
Published: August 2003

Over 225,000 independent
Agrobacterium
transferred DNA (T-DNA) insertion events in the genome of the reference plant
Arabidopsis thaliana
have been created that represent near saturation of the gene space. The precise locations were determined for more than 88,000 T-DNA insertions, which resulted in the identification of mutations in more than 21,700 of the ∼29,454 predicted
Arabidopsis
genes. Genome-wide analysis of the distribution of integration events revealed the existence of a large integration site bias at both the chromosome and gene levels. Insertion mutations were identified in genes that are regulated in response to the plant hormone ethylene.
X and Y, A Wild Pair
Authors: Segal Nancy L.
Published: August 2003

The X in Sex
How the X Chromosome Controls Our Lives. by David Bainbridge. Harvard University Press, Cambridge, MA, 2003. 215 pp. $22.95, £15.50. ISBN 0-674-01028-0.

Y
The Descent of Men. by Steve Jones. Houghton Mifflin, New York, 2003. 272 pp. $25. ISBN 0-618-13930-3. Little, Brown, London, 2002. 288 pp. £14.99. ISBN 0-316-85615-0.

Writing for a popular audience, both authors use the sex chromosomes as a framework for exploring the nature, development, and evolution of sexual differences in humans. Jones takes Darwin's Descent of Man as a template for his far-ranging discussions of maleness. Bainbridge tends to stay more focused on findings from recent genomic studies of the X chromosome.
Stratospheric Memory and Skill of Extended-Range Weather Forecasts
Authors: Baldwin Mark P. , Stephenson David B. , Thompson, David W. J. , Dunkerton Timothy J. , Charlton Andrew J. , O'Neill Alan
Published: August 2003

We use an empirical statistical model to demonstrate significant skill in making extended-range forecasts of the monthly-mean Arctic Oscillation (AO). Forecast skill derives from persistent circulation anomalies in the lowermost stratosphere and is greatest during boreal winter. A comparison to the Southern Hemisphere provides evidence that both the time scale and predictability of the AO depend on the presence of persistent circulation anomalies just above the tropopause. These circulation anomalies most likely affect the troposphere through changes to waves in the upper troposphere, which induce surface pressure changes that correspond to the AO.
Mutation in the
relA
Gene of
Vibrio cholerae
Affects In Vitro and In Vivo Expression of Virulence Factors
Authors: Haralalka Shruti , Nandi Suvobroto , Bhadra Rupak K.
Published: August 2003

The
relA
gene product determines the level of (p)ppGpp, the effector nucleotides of the bacterial stringent response that are also involved in the regulation of other functions, like antibiotic production and quorum sensing. In order to explore the possible involvement of
relA
in the regulation of virulence of
Vibrio cholerae
, a
relA
homolog from the organism (
relA
VCH
) was cloned and sequenced. The
relA
VCH
gene encodes a 738-amino-acid protein having functions similar to those of other gram-negative bacteria, including
Escherichia coli
. A Δ
relA
::
kan
allele was generated by replacing ∼31% of the open reading frame of wild-type
relA
of
V. cholerae
El Tor strain C6709 with a kanamycin resistance gene. The
V. cholerae relA
mutant strain thus generated, SHK17, failed to accumulate (p)ppGpp upon amino acid deprivation. Interestingly, compared to the wild type, C6709, the mutant strain SHK17 exhibited significantly reduced in vitro production of two principal virulence factors, cholera toxin (CT) and toxin-coregulated pilus (TCP), under virulence gene-inducing conditions. In vivo experiments carried out in rabbit ileal loop and suckling mouse models also confirmed our in vitro results. The data suggest that (p)ppGpp is essential for maximal expression of CT and TCP during in vitro growth, as well as during intestinal infection by virulent
V. cholerae
. Northern blot and reverse transcriptase PCR analyses indicated significant reduction in the transcript levels of both virulence factors in the
relA
mutant strain SHK17. Such marked alteration of virulence phenotypes in SHK17 appears most likely to be due to down regulation of transcript levels of
toxR
and
toxT
, the two most important virulence regulatory genes of
V. cholerae.
In SHK17, the altered expression of the two outer membrane porin proteins, OmpU and OmpT, indicated that the
relA
mutation most likely affects the ToxR-dependent virulence regulatory pathway, because it had been shown earlier that ToxR directly regulates their expression independently of ToxT.
Mutant Analysis of the
Escherichia coli
FhuA Protein Reveals Sites of FhuA Activity
Authors: Endriß Franziska , Braun Michael , Killmann Helmut , Braun Volkmar
Published: August 2003

The FhuA outer membrane protein of
Escherichia coli
actively transports ferrichrome, albomycin, and rifamycin CGP 4832, and confers sensitivity to microcin J25, colicin M, and the phages T1, T5, and φ80. Guided by the FhuA crystal structure and derived predictions on how FhuA might function, mutants were isolated in the cork domain (residues 1 to 160) and in the β-barrel domain (residues 161 to 714). Deletion of the TonB box (residues 7 to 11) completely inactivated all TonB-dependent functions of FhuA. Fixation of the cork to turn 7 of the barrel through a disulfide bridge between introduced C27 and C533 residues abolished ferrichrome transport, which was restored by reduction of the disulfide bond. Deletion of residues 24 to 31, including the switch helix (residues 24 to 29), which upon binding of ferrichrome to FhuA undergoes a large structural transition (17 Å) and exposes the N terminus of FhuA (TonB box) to the periplasm, reduced FhuA transport activity (79% of the wild-type activity) but conferred full sensitivity to colicin M and the phages. Duplication of residues 23 to 30 or deletion of residues 13 to 20 resulted in FhuA derivatives with properties similar to those of FhuA with a deletion of residues 24 to 31. However, a frameshift mutation that changed QSEA at positions 18 to 21 to KKAP abolished almost completely most of FhuA's activities. The conserved residues R93 and R133 among energy-coupled outer membrane transporters are thought to fix the cork to the β-barrel by forming salt bridges to the conserved residues E522 and E571 of the β-barrel. Proteins with the E522R and E571R mutations were inactive, but inactivity was not caused by repulsion of R93 by R522 and R571 and of R133 by R571. Point mutations in the cork at sites that move or do not move upon the binding of ferrichrome had no effect or conferred only slightly reduced activities. It is concluded that the TonB box is essential for FhuA activity. The TonB box region has to be flexible, but its distance from the cork domain can greatly vary. The removal of salt bridges between the cork and the barrel affects the structure but not the function of FhuA.
Detachment of
Actinobacillus actinomycetemcomitans
Biofilm Cells by an Endogenous β-Hexosaminidase Activity
Authors: Kaplan Jeffrey B. , Ragunath Chandran , Ramasubbu Narayanan , Fine Daniel H.
Published: August 2003

When cultured in broth, fresh clinical isolates of the gram-negative periodontal pathogen
Actinobacillus actinomycetemcomitans
form tenaciously adherent biofilm colonies on surfaces such as plastic and glass. These biofilm colonies release adherent cells into the medium, and the released cells can attach to the surface of the culture vessel and form new colonies, enabling the biofilm to spread. We mutagenized
A. actinomycetemcomitans
clinical strain CU1000 with transposon IS
903
φ
kan
and isolated a transposon insertion mutant that formed biofilm colonies which were tightly adherent to surfaces but which lacked the ability to release cells into the medium and disperse. The transposon insertion in the mutant strain mapped to a gene, designated
dspB
, that was predicted to encode a secreted protein homologous to the catalytic domain of the family 20 glycosyl hydrolases. A plasmid carrying a wild-type
dspB
gene restored the ability of biofilm colonies of the mutant strain to disperse. We expressed
A. actinomycetemcomitans
DspB protein engineered to contain a hexahistidine metal-binding site at its C terminus in
Escherichia coli
and purified the protein by using Ni affinity chromatography. Substrate specificity studies performed with monosaccharides labeled with 4-nitrophenyl groups showed that DspB hydrolyzed the 1→4 glycosidic bond of β-substituted
N
-acetylglucosamine, which is consistent with the known functions of other family 20 glycosyl hydrolases. When added to culture medium, purified DspB protein, but not heat-inactivated DspB, restored the ability of the mutant strain to release cells and disperse. DspB protein also caused the detachment of cells from preformed biofilm colonies of strain CU1000 grown attached to plastic and the disaggregation of highly autoaggregated clumps of CU1000 cells in solution. We concluded that
dspB
encodes a soluble β-
N
-acetylglucosaminidase that causes detachment and dispersion of
A. actinomycetemcomitans
biofilm cells.
DapE Can Function as an Aspartyl Peptidase in the Presence of Mn
2+
Authors: Broder Daniel H. , Miller Charles G.
Published: August 2003

Extracts of a multiply peptidase-deficient (
pepNABDPQTE iadA iaaA
)
Salmonella enterica
serovar Typhimurium strain contain an aspartyl dipeptidase activity that is dependent on Mn
2+
. Purification of this activity followed by N-terminal sequencing of the protein suggested that the Mn
2+
-dependent peptidase is DapE (
N
-succinyl-
l
,
l
-diaminopimelate desuccinylase). A
dapE
chromosomal disruption was constructed and transduced into a multiply peptidase-deficient (MPD) strain. Crude extracts of this strain showed no aspartyl peptidase activity, and the strain failed to utilize Asp-Leu as a leucine source. The
dapE
gene was cloned into expression vectors in order to overproduce either the native protein (DapE) or a hexahistidine fusion protein (DapE-His
6
). Extracts of a strain carrying the plasmid overexpresssing native DapE in the MPD
dapE
background showed a 3,200-fold elevation of Mn
2+
-dependent aspartyl peptidase activity relative to the MPD

dapE
+

strain. In addition, purified DapE-His
6
exhibited Mn
2+
-dependent peptidase activity toward aspartyl dipeptides. Growth of the MPD strain carrying a single genomic copy of
dapE
on Asp-Leu as a Leu source was slow but detectable. Overproduction of DapE in the MPD
dapE
strain allowed growth on Asp-Leu at a much faster rate. DapE was found to be specific for N-terminal aspartyl dipeptides: no N-terminal Glu, Met, or Leu peptides were hydrolyzed, nor were any peptides containing more than two amino acids. DapE is known to bind two divalent cations: one with high affinity and the other with lower affinity. Our data indicate that the form of DapE active as a peptidase contains Zn
2+
in the high-affinity site and Mn
2+
in the low-affinity site.
In Vivo and In Vitro Evidence that TtgV Is the Specific Regulator of the TtgGHI Multidrug and Solvent Efflux Pump of
Pseudomonas putida
Authors: Rojas Antonia , Segura Ana , Guazzaroni María Eugenia , Terán Wilson , Hurtado Ana , Gallegos María Trinidad , Ramos Juan L.
Published: August 2003

The TtgGHI efflux pump of
Pseudomonas putida
DOT-T1E plays a key role in the innate and induced tolerance of this strain to aromatic hydrocarbons and antibiotics. The
ttgGHI
operon is expressed constitutively from two overlapping promoters in the absence of solvents and at a higher level in their presence, but not in response to antibiotics. Adjacent to the
ttgGHI
operon is the divergently transcribed
ttgVW
operon. In TtgV-deficient backgrounds, although not in a TtgW-deficient background, expression of the
ttgGHI
and
ttgVW
operons increased fourfold. This suggests that TtgV represses expression from the
ttgG
promoters and controls its own. TtgW plays no major role in the regulation of expression of these promoters. Primer extension revealed that the divergent
ttgG
and
ttgV
promoters overlap, and mobility shift assays indicated that TtgV binds to this region with high affinity. DNaseI footprint assays revealed that TtgV protected four DNA helical turns that include the −10 and −35 boxes of the
ttgV
and
ttgG
promoters.
Expression of the
Pseudomonas putida
OCT Plasmid Alkane Degradation Pathway Is Modulated by Two Different Global Control Signals: Evidence from Continuous Cultures
Authors: Dinamarca M. Alejandro , Aranda-Olmedo Isabel , Puyet Antonio , Rojo Fernando
Published: August 2003

Expression of the genes of the alkane degradation pathway encoded in the
Pseudomonas putida
OCT plasmid are subject to negative and dominant global control depending on the carbon source used and on the physiological status of the cell. We investigated the signals responsible for this control in chemostat cultures under conditions of nutrient or oxygen limitation. Our results show that this global control is not related to the growth rate and responds to two different signals. One signal is the concentration of the carbon source that generates the repressing effect (true catabolite repression control). The second signal is influenced by the level of expression of the cytochome
o
ubiquinol oxidase, which in turn depends on factors such as oxygen availability or the carbon source used. Since under carbon limitation conditions the first signal is relieved but the second signal is not, we propose that modulation mediated by the cytochrome
o
ubiquinol oxidase is not classical catabolite repression control but rather a more general physiological control mechanism. The two signals have an additive, but independent, effect, inhibiting induction of the alkane degradation pathway.
PorA Represents the Major Cell Wall Channel of the Gram-Positive BacteriumCorynebacterium glutamicum
Authors: Costa-Riu Noelia , Burkovski Andreas , Krämer Reinhard , Benz Roland
Published: August 2003

The cell wall of the gram-positive bacteriumCorynebacterium glutamicumcontains a channel (porin) for the passage of hydrophilic solutes. The channel-forming polypeptide PorA is a 45-amino-acid acidic polypeptide with an excess of four negatively charged amino acids, which is encoded by the 138-bp geneporA.porAwas deleted from the chromosome ofC.glutamicumwild-type strain ATCC 13032 to obtain mutant ATCC 13032ΔporA. Southern blot analysis demonstrated thatporAwas deleted. Lipid bilayer experiments revealed that PorA was not present in the cell wall of the mutant strain. Searches within the known chromosome ofC. glutamicumby using National Center for Biotechnology Information BLAST and reverse transcription-PCR showed that no other PorA-like protein is encoded on the chromosome or is expressed in the deletion strain. TheporAdeletion strain exhibited slower growth and longer growth times than theC. glutamicumwild-type strain. Experiments with different antibiotics revealed that the susceptibility of the mutant strain was much lower than that of the wild-typeC. glutamicumstrain. The results presented here suggest that PorA represents a major hydrophilic pathway through the cell wall and thatC. glutamicumcontains cell wall channels which are not related to PorA.
In Vivo Characterization of
Escherichia coli ftsZ
Mutants: Effects on Z-Ring Structure and Function
Authors: Stricker Jesse , Erickson Harold P.
Published: August 2003

We have characterized the in vivo phenotypes of 17 mutations of
Escherichia coli ftsZ
. In particular, we determined whether these mutations can complement a null
ftsZ
phenotype, and we demonstrated that two noncomplementing mutations show partial dominant-negative behavior. We performed immunofluorescence microscopy to determine whether these mutants could assemble into normal or abnormal structures in vivo. The mutants separated into four classes—those that complemented the null and formed normal FtsZ rings, those that complemented the null but formed aberrant FtsZ structures, those that formed aberrant FtsZ structures and did not complement, and those that were unable to form any FtsZ structures. We did not find any mutations that produced nonfunctional Z rings of normal appearance. Surprisingly, some mutants that produced extensively spiraled Z-ring structures divided and grew with a normal doubling time. The analysis was carried out using a complementation system based on an
ftsZ
deletion strain, a temperature-sensitive rescue plasmid, and a complementation vector that placed mutated
ftsZ
alleles under the control of the pBAD promoter, which offered several advantages over previous systems.
Molecular Analysis of Phr Peptide Processing inBacillus subtilis
Authors: Stephenson Sophie , Mueller Christian , Jiang Min , Perego Marta
Published: August 2003

InBacillus subtilis, an export-import pathway regulates production of the Phr pentapeptide inhibitors of Rap proteins. Processing of the Phr precursor proteins into the active pentapeptide form is a key event in the initiation of sporulation and competence development. The PhrA (ARNQT) and PhrE (SRNVT) peptides inhibit the RapA and RapE phosphatases, respectively, whose activity is directed toward the Spo0F∼P intermediate response regulator of the sporulation phosphorelay. The PhrC (ERGMT) peptide inhibits the RapC protein acting on the ComA response regulator for competence with regard to DNA transformation. The structural organization of PhrA, PhrE, and PhrC suggested a role for type I signal peptidases in the processing of the Phr preinhibitor, encoded by thephrgenes, into the proinhibitor form. The proinhibitor was then postulated to be cleaved to the active pentapeptide inhibitor by an additional enzyme. In this report, we provide evidence that Phr preinhibitor proteins are subject to only one processing event at the peptide bond on the amino-terminal end of the pentapeptide. This processing event is most likely independent of type I signal peptidase activity. In vivo and in vitro analyses indicate that none of the five signal peptidases ofB. subtilis(SipS, SipT, SipU, SipV, and SipW) are indispensable for Phr processing. However, we show that SipV and SipT have a previously undescribed role in sporulation, competence, and cell growth.
Temperature-Dependent Hypermutational Phenotype inrecAMutants ofThermus thermophilusHB27
Authors: Castán Pablo , Casares Lorena , Barbé Jordi , Berenguer José
Published: August 2003

TherecAgene fromThermus thermophilusHB27 was cloned and engineered to obtain insertion (recA::kat) and deletion (ΔrecA) derivatives. Transcription ofrecAin this extreme thermophile was induced by mitomycin C, leading to the synthesis of a monocistronic mRNA. This DNA damage-mediated induction was dependent on the integrity ofrecA.In addition to UV sensitivity, therecAmutants ofT. thermophilusshowed severe pleiotropic defects, ranging from irregular nucleoid condensation and segregation to a dramatic reduction in viability during culture. An increase in the frequency of both carotenoidless and auxotrophic mutants within surviving cells of the ΔrecAstrain indicated a high mutation rate. As RecA is not required for plasmid transformation, we have used the α-lacZgene fragment and the ampicillin resistance gene fromEscherichia colias passenger reporters to confirm such high mutation rates. Our data support the idea that the absence of RecA results in a hypermutational phenotype inT. thermophilus. Furthermore, a direct relationship is deduced between the growth temperature and mutation rate, which finally has a deleterious effect on cell survival in the absence of RecA.
ABurkholderia pseudomalleiType III Secreted Protein, BopE, Facilitates Bacterial Invasion of Epithelial Cells and Exhibits Guanine Nucleotide Exchange Factor Activity
Authors: Stevens Mark P. , Friebel Andrea , Taylor Lowrie A. , Wood Michael W. , Brown Philip J. , Hardt Wolf-Dietrich , Galyov Edouard E.
Published: August 2003

We report the characterization of BopE, a type III secreted protein that is encoded adjacent to theBurkholderia pseudomallei bsalocus and is homologous toSalmonellaentericaSopE/SopE2. Inactivation ofbopEimpaired bacterial entry into HeLa cells, indicating that BopE facilitates invasion. Consistent with this notion, BopE expressed in eukaryotic cells induced rearrangements in the subcortical actin cytoskeleton, and purified BopE exhibited guanine nucleotide exchange factor activity for Cdc42 and Rac1 in vitro.
ThepstOperon ofBacillus subtilisIs Specifically Induced by Alkali Stress
Authors: Atalla Akram , Schumann Wolfgang
Published: August 2003

To cope with a sudden increase in the external pH value to 8.9,Bacillus subtiliscells induce about 80 genes which can be divided into two classes. Most of these genes are members of the σWregulon, while some are under the control of so-far-unknown transcriptional regulators. The genes of thepstoperon belong to the second class. Here, we attempted to answer the questions of why and how the genes of this operon are induced. Using transcriptional fusions to two of the five genes of this operon, we confirmed their induction after alkali stress. Furthermore, a Northern blot experiment revealed that the complete operon was alkali inducible, that the transcriptional start site used was identical to that used after phosphate starvation, and that induction was prevented in aphoRbackground. Most interestingly, increasing the phosphate concentration within the medium prevented alkali induction of thepstoperon, andphoA, another member of the PhoRP regulon, did not respond to alkali stress. In the end, we showed that alkali treatment completely prevented phosphate uptake. These results are discussed to explain alkali induction of thepstoperon.
Conversion of
Lactobacillus pentosus
d
-Lactate Dehydrogenase to a
d
-Hydroxyisocaproate Dehydrogenase through a Single Amino Acid Replacement
Authors: Tokuda Chizuka , Ishikura Yoshiro , Shigematsu Mayu , Mutoh Hiroyuki , Tsuzuki Shino , Nakahira Yusaku , Tamura Yusuke , Shinoda Takeshi , Arai Kazuhito , Takahashi O , Taguchi Hayao
Published: August 2003

The single amino acid replacement of Tyr52 with Leu drastically increased the activity of
Lactobacillus pentosus
NAD-dependent
d
-lactate dehydrogenase toward larger aliphatic or aromatic 2-ketoacid substrates by 3 or 4 orders of magnitude and decreased the activity toward pyruvate by about 30-fold, converting the enzyme into a highly active
d
-2-hydroxyisocaproate dehydrogenase.
Recombinant erythropoietin in clinical practice
Authors: Ng T , Marx G , Littlewood T , Macdougall I
Published: August 2003

The introduction of recombinant human erythropoietin (RHuEPO) has revolutionised the treatment of patients with anaemia of chronic renal disease. Clinical studies have demonstrated that RHuEPO is also useful in various non-uraemic conditions including haematological and oncological disorders, prematurity, HIV infection, and perioperative therapies. Besides highlighting both the historical and functional aspects of RHuEPO, this review discusses the applications of RHuEPO in clinical practice and the potential problems of RHuEPO treatment.
Acute and chronic arsenic toxicity
Authors: Ratnaike R N
Published: August 2003

Arsenic toxicity is a global health problem affecting many millions of people. Contamination is caused by arsenic from natural geological sources leaching into aquifers, contaminating drinking water and may also occur from mining and other industrial processes. Arsenic is present as a contaminant in many traditional remedies. Arsenic trioxide is now used to treat acute promyelocytic leukaemia. Absorption occurs predominantly from ingestion from the small intestine, though minimal absorption occurs from skin contact and inhalation. Arsenic exerts its toxicity by inactivating up to 200 enzymes, especially those involved in cellular energy pathways and DNA synthesis and repair. Acute arsenic poisoning is associated initially with nausea, vomiting, abdominal pain, and severe diarrhoea. Encephalopathy and peripheral neuropathy are reported. Chronic arsenic toxicity results in multisystem disease. Arsenic is a well documented human carcinogen affecting numerous organs. There are no evidence based treatment regimens to treat chronic arsenic poisoning but antioxidants have been advocated, though benefit is not proven. The focus of management is to reduce arsenic ingestion from drinking water and there is increasing emphasis on using alternative supplies of water.
Single megadose vitamin A supplementation of Indian mothers and morbidity in breastfed young infants
Authors: Basu S , Sengupta B , Paladhi P K Roy
Published: August 2003

Background and objective

In developing countries low maternal vitamin A stores combined with increased demands of pregnancy and lactation may lead to its deficiency in breastfed infants. This study evaluates the effects of maternal supplementation with a high dose of vitamin A on the serum retinol levels of exclusively breastfed infants, and their morbidity in the first six months of life.

Setting

Hospital based.

Study design

Randomised controlled trial.

Subjects and methods

Mothers of the test group (n=150) were orally supplemented with a single dose of retinol (209 μmol) soon after delivery and were advised exclusive breastfeeding for six months. Before supplementation retinol levels were estimated in the mothers’ and newborns’ blood, and in colostrum. On follow up, breastmilk and infants’ serum retinol contents were assessed monthly for six months. Retinol level <0.7 μmol/l indicated vitamin A deficiency. Morbidity patterns like vitamin A deficiency, diarrhoea, febrile illnesses, acute respiratory infection, measles, and ear infection were also studied and compared between the two groups.

Results

Presupplement mean maternal serum retinol levels were 0.98 and 0.92 μmol/l and mean breastmilk levels were 3.85 and 3.92 μmol/l in the test and control groups respectively (p>0.05). Mean cord blood retinol levels were also comparable (0.68 v 0.64 μmol/l). After supplementation, the test group showed a rise in mean breastmilk retinol content (12.08 v 2.96 μmol/l) which remained significantly higher for four months. The infants’ mean serum retinol level, initially 322.06% of the baseline value, was significantly higher for five months. In the control group, significant numbers of mothers and infants showed deficient breastmilk and serum retinol throughout the follow up (p<0.01). Decreased incidence and duration of various diseases were also found in the test group suggesting lesser morbidity.

Conclusion

Maternal supplementation with single megadose vitamin A is an effective strategy for vitamin A prophylaxis of exclusively breastfed infants of 0–6 months.
The HIγS Facility: A Free-Electron Laser Generated Gamma-Ray Beam for Research in Nuclear Physics
Authors: Weller Henry R. , Ahmed Mohammad W.
Published: July 2003

The High Intensity Gamma-ray Source (HIγS) is a joint project between Triangle Universities Nuclear Laboratory (TUNL) and the Duke Free Electron Laser Laboratory (DFELL). This facility utilizes intra-cavity back-scattering of the FEL photons in order to produce a γ-flux enhancement of approximately 103over the existing sources. At present, gamma-ray beams with energies ranging from 2 to 50 MeV are available with intensities of 105–107γ/ s , energy spreads of 1% or better (with lower intensities), and 100% linear polarization. An upgrade is presently underway which will allow for the production of γ rays up to an energy of about 225 MeV having intensities in excess of 108γ/ sec . The primary component of the upgrade is a 1.2 GeV booster-injector which will provide for efficient injection at any chosen operating energy of the storage ring from 300 MeV to 1.2 GeV. In addition, an upgrade of the present OK-4 FEL to a helical undulator system (OK-5) is underway. This new system has many advantages over the present one, including making switchable linear and circularly polarized beams available, an increase in power and a decrease in mirror-damaging radiation. The full system, including the booster injector, is expected to be ready for use by 2006. TUNL researchers, in collaboration with outside theoretical and experimental colleagues, have proposed a broad based research program in nuclear physics which is designed to exploit the unique flux, energy resolution and polarization of the HIγS beams. A description of the presently available facility and the anticipated facility following the present upgrades will be given in this review, along with a description of recent and planned experiments.
Hamilton–Jacobi Treatment of Lagrangians with Linear Velocities
Authors: Rabei Eqab M. , Nawafleh Khaled I. , Abdelrahman Yacoub S. , Omari H. Y. Rashed
Published: July 2003

A new approach for solving mechanical problems of Linear Lagrangian systems using the Hamilton–Jacobi formulation is proposed. The equations of motion are recovered from the action integral. It has been proved that there is no need to follow the consistency conditions of the Dirac approach.
Hyperfine Splitting and Leptonic Decay Rates in Heavy Quarkonia
Authors: Ebert D. , Faustov R. N. , Galkin V. O.
Published: July 2003

The hyperfine splitting in heavy quarkonia is considered in its relation to the leptonic decay rates with the account of relativistic and radiative corrections. The calculated decay rates agree well with the available experimental data, while the predicted ηc(2S) mass is significantly smaller than the value measured recently by the Belle collaboration.
205Tl Electric Dipole Moment: Strong Versus Supersymmetric CP Problems
Authors: Boz Müge , Karagöz Nurettin
Published: July 2003

The electric dipole moment of 205Tl has been analyzed within the supersymmetric model which solves the strong CP problem via the dynamical phase of the gluino mass. It is found that the electric dipole moment of 205Tl exceeds the current experimental bounds for tan β ≳ 10 and μ ≲ 1,000 GeV, with maximal CP-violation for all phases.
N = 2 Supersymmetric Yang–Mills Theory and the Superparticle: Twistor Transform and κ-Symmetry
Authors: Uvarov D. V.
Published: July 2003

Lagrangian and Hamiltonian dynamics of de Azcarraga–Lukierski N = 2 massive superparticle is considered in the framework of twistor-like Lorentz-harmonic approach. The emphasis is on the study of the interaction with external Abelian gauge superfield. The requirement of preservation of all gauge symmetries of the free model including κ-symmetry yields correct expressions for the superfield strength constraints and determines the form of nonminimal interaction. We also show that for de Azcarraga–Lukierski N = 2 massive superparticle the pullback of field strength two-superform to the superworld line is not integrable in contrast to the massless superparticle.
Optical Unification
Authors: Giedt Joel
Published: July 2003

We discuss string scale unification facilitated by exotic matter with masses at intermediate scales, between the observable sector supersymmetry breaking scale and the string scale. We point out a mechanism by which string scale unification may occur while producing a (lower) virtual unification scale independent of the location of the intermediate scale and the value of the string coupling. The apparent unification obtained by extrapolating low energy gauge couplings is not accidental when this mechanism is invoked; virtual unification is robust.
Model of the Quark Mixing Matrix Involving its Eigenvalues
Authors: Chaturvedi S. , Gupta Virendra
Published: July 2003

A model of the 3 × 3 Cabibbo–Kobayashi–Maskawa matrix, V, is presented in which the parameters are the eigenvalues and the components of its eigenvectors. In this model, the small departure of the experimentally determined V from being moduli symmetric (i.e. |Vij|=|Vji|) is controlled by the small difference between two of the eigenvalues. In case any two eigenvalues are equal, one obtains a moduli symmetric V depending on only three parameters. Our model gives very good fits to the available data including CP-violation. Our value of sin 2β≈0.7 and other parameters associated with the ''unitarity triangle'' [Formula: see text] are in good agreement with data and other analyses.
Human Unsupervised and Supervised Learning as a Quantitative Distinction
Authors: Gureckis Todd M. , Love Bradley C.
Published: July 2003

SUSTAIN (Supervised and Unsupervised STratified Adaptive Incremental Network) is a network model of human category learning. SUSTAIN initially assumes a simple category structure. If simple solutions prove inadequate and SUSTAIN is confronted with a surprising event (e.g. it is told that a bat is a mammal instead of a bird), SUSTAIN recruits an additional cluster to represent the surprising event. Newly recruited clusters are available to explain future events and can themselves evolve into prototypes/attractors/rules. SUSTAIN has expanded the scope of findings that models of human category learning can address. This paper extends SUSTAIN to account for both supervised and unsupervised learning data through a common mechanism. The modified model, uSUSTAIN (unified SUSTAIN), is successfully applied to human learning data that compares unsupervised and supervised learning performances.18
An Intelligent Hybrid Decision Support System for the Management of Water Resources
Authors: Kazeli H. , Keravnou E. , Christofides T. C.
Published: July 2003

During the last two decades the scarcity of water resources is exponentially growing worldwide. Cyprus is one of the countries in the Mediterranean where the water shortage problem is evident and very severe. This paper describes an intelligent and flexible, hybrid decision support system for the management of water resources in the regions along the South Conveyor Project, the largest water development project in Cyprus. In particular, the paper presents the integrated system and its architecture, together with detailed descriptions of the hybrid components synthesizing it. Details on the implementation and preliminary evaluation of the system are also provided.
Turning WordNet into an Information Retrieval Resource: Systematic Polysemy and Conversion to Hierarchical Codes
Authors: Mihalcea Rada
Published: July 2003

This paper addresses the problem of transforming WordNet into a resource tailored to Information Retrieval (IR) applications. We address two of the major drawbacks pointed out in previous literature in relation to this semantic network. One is the fine granularity of senses defined in WordNet, which proves useless from an IR perspective. To solve this problem, we propose a set of methods that enable the automatic transformation of WordNet into a coarse grained dictionary. The other drawback is the encoding used in this resource, and the methods for accessing related words across the semantic net. Due to the high number of connections among concepts, the simple computation of a path in this net, or the generation of related concepts may become a computationally intensive process. This effect is highly undesirable in time sensitive applications such as IR applications. We propose a methodology for hierarchical encoding that enables increased efficiency in WordNet-based IR systems.
Using a Graph-Based Data Mining System to Perform Web Search
Authors: Cook Diane J. , Manocha Nitish , Holder Lawrence B.
Published: July 2003

The World Wide Web provides an immense source of information. Accessing information of interest presents a challenge to scientists and analysts, particularly if the desired information is structural in nature. Our goal is to design a structural search engine that uses the hyperlink structure of the Web, in addition to textual information, to search for sites of interest. Our structural search engine, called WebSUBDUE, searches not only for particular words or topics but also for a desired hyperlink structure. Enhanced by WordNet text functions, our search engine retrieves sites corresponding to structures formed by graph-based user queries. We hypothesize that this system can form the heart of a structural query engine, and demonstrate the approach on a number of structural web queries.
Analysis of Mutations in the COLIA1 Gene with Second-Order Rule Induction
Authors: Hewett Rattikorn , Leuchner John , Mooney Sean D. , Klein Teri E.
Published: July 2003

Mutations are structural changes in DNA that can cause protein malfunction and genetic disease. This paper describes a machine learning approach to analyzing mutations associated to Osteogenesis Imperfecta (OI), also known as brittle bone disease. We apply SORCER, a second-order rule induction system to predict clinical phenotypes of OI from mutation and neighboring amino acid sequences in the COLIA1 gene. On the average, over ten 10-fold cross-validations, SORCER gives more accurate results than C4.5 with average accuracy of about 81.2%. The paper discusses the advantages and limitations of SORCER and demonstrates its use to provide initial exploration of biological sequences.
Question-Driven Semantic Filters for Answer Retrieval
Authors: Paşca Marius
Published: July 2003

As part of the task of automated question answering from a large collection of text documents, the reduction of the search space to a smaller set of document passages that are actually searched for answers constitutes a difficult but rewarding research issue. We propose a set of precision-enhancing filters for passage retrieval based on semantic constraints detected in the submitted questions. The approach improves the performance of the underlying question answering system in terms of both answer accuracy and time performance.
ONASI: Online Agent Modeling Using a Scalable Markov Model
Authors: Sandanayake Priyath T. , Cook Diane J.
Published: July 2003

Human and software agents exhibit regularities in their activities. We describe our ONASI algorithm, which derives a Markov model from such observed regularities, and dynamically scales the model through merging and splitting of states. ONASI uses this model to predict the agent's next action. We evaluate ONASI's predictive accuracy on a dataset of Wumpus World games, and demonstrate from this approach that the model can correctly predict the agent's next action with adjustable computation and memory resources. These predictions can be used to imitate, assist or obstruct an agent.
Extending Dual Arc Consistency
Authors: Nagarajan S. , Goodwin S. D. , Sattar A.
Published: July 2003

Many extensions to existing binary constraint satisfaction algorithms have been proposed that directly deal with nonbinary constraints. Another choice is to perform a structural transformation of the representation of the problem, so that the resulting problem is a binary CSP except that now the original constraints which were nonbinary are replaced by binary compatibility constraints between relations. A lot of recent work has focussed on comparing different levels of local consistency enforceable in the nonbinary representation with the dual representation. In this paper we present extensions to the standard dual encoding that can compactly represent the given CSP using an equivalent dual encoding that contains all the original solutions to the CSP, using constraint coverings. We show how enforcing arc consistency in these constraint covering based encodings, strictly dominates enforcement of generalized arc consistency (GAC) on the primal nonbinary encoding.