bluuebunny/crossref_metadata_2025 huggingface dataset:
The occurrence of CH…O hydrogen bonds in α‐helices and helix termini in globular proteins
Authors: Manikandan K. , Ramakumar S.
Published: June 2004

A comprehensive database analysis of CH…O hydrogen bonds in 3124 α‐helices and their corresponding helix termini has been carried out from a nonredundant data set of high‐resolution globular protein structures resolved at better than 2.0 Å in order to investigate their role in the helix, the important protein secondary structural element. The possible occurrence of 5 → 1 CH…O hydrogen bond between the ith residue CH group and (i − 4)th residue CO with C…O ≤ 3.8 Å is studied, considering as potential donors the main‐chain Cα and the side‐chain carbon atoms Cβ, Cγ, Cδ and Cϵ. Similar analysis has been carried out for 4 → 1 CH…O hydrogen bonds, since the CH…O hydrogen bonds found in helices are predominantly of type 5 → 1 or 4 → 1. A total of 17,367 (9310 of type 5 → 1 and 8057 of type 4 → 1) CH…O hydrogen bonds are found to satisfy the selected criteria. The average stereochemical parameters for the data set suggest that the observed CH…O hydrogen bonds are attractive interactions. Our analysis reveals that the Cγ and Cβ hydrogen atom(s) are frequently involved in such hydrogen bonds. A marked preference is noticed for aliphatic β‐branched residue Ile to participate in 5 → 1 CH…O hydrogen bonds involving methylene Cγ 1 atom as donor in α‐helices. This may be an enthalpic compensation for the greater loss of side‐chain conformational entropy for β‐branched amino acids due to the constraint on side‐chain torsion angle, namely, χ1, when they occur in helices. The preference of amino acids for 4 → 1 CH…O hydrogen bonds is found to be more for Asp, Cys, and for aromatic residues Trp, Phe, and His. Interestingly, overall propensity for CH…O hydrogen bonds shows that a majority of the helix favoring residues such as Met, Glu, Arg, Lys, Leu, and Gln, which also have large side‐chains, prefer to be involved in such types of weak attractive interactions in helices. The amino acid side‐chains that participate in CH…O interactions are found to shield the acceptor carbonyl oxygen atom from the solvent. In addition, CH…O hydrogen bonds are present along with helix stabilizing salt bridges. A novel helix terminating interaction motif, X‐Gly with Gly at Ccap position having 5 → 1 CαH…O, and a chain reversal structural motif having 1 → 5 Cα‐H…O have been identified and discussed. Our analysis highlights that a multitude of local CH…O hydrogen bonds formed by a variety of amino acid side‐chains and Cα hydrogen atoms occur in helices and more so at the helix termini. It may be surmised that the main‐chain Cα and the side‐chain CH that participate in CH…O hydrogen bonds collectively augment the cohesive energy and thereby contribute together with the classical NH…O hydrogen bonds and other interactions to the overall stability of helix and therefore of proteins. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Modeling correlated main‐chain motions in proteins for flexible molecular recognition
Authors: Zavodszky Maria I. , Lei Ming , Thorpe M. F. , Day Anthony R. , Kuhn Leslie A.
Published: June 2004

We describe a new method for modeling protein and ligand main‐chain flexibility, and show its ability to model flexible molecular recognition. The goal is to sample the full conformational space, including large‐scale motions that typically cannot be reached in molecular dynamics simulations due to the computational intensity, as well as conformations that have not been observed yet by crystallography or NMR. A secondary goal is to assess the degree of flexibility consistent with protein–ligand recognition. Flexibility analysis of the target protein is performed using the graph‐theoretic algorithm FIRST, which also identifies coupled networks of covalent and noncovalent bonds within the protein. The available conformations of the flexible regions are then explored with ROCK by random‐walk sampling of the rotatable bonds. ROCK explores correlated motions by only sampling dihedral angles that preserve the coupled bond networks in the protein and generates conformers with good stereochemistry, without using a computationally expensive potential function. A representative set of the conformational ensemble generated this way can be used as targets for docking with SLIDE, which handles the flexibility of protein and ligand side‐chains. The realism of this protein main‐chain conformational sampling is assessed by comparison with time‐resolved NMR studies of cyclophilin A motions. ROCK is also effective for modeling the flexibility of large cyclic and polycyclic ligands, as demonstrated for cyclosporin and zearalenol. The use of this combined approach to perform docking with main‐chain flexibility is illustrated for the cyclophilin A–cyclosporin complex and the estrogen receptor in complex with zearalenol, while addressing the question of how much flexibility is allowed without hindering molecular recognition. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Protein unfolding at interfaces: Slow dynamics of α‐helix to β‐sheet transition
Authors: Sethuraman Ananthakrishnan , Vedantham Ganesh , Imoto Taiji , Przybycien Todd , Belfort Georges
Published: June 2004

A two‐phase sequential dynamic change in the secondary structure of hen egg lysozyme (Lys) adsorbed on solid substrates was observed. The first phase involved fast conversion of α‐helix to random/turns (within the first minute or at very low coverage or high substrate wettability) with no perceptible change in β‐sheet content. The second phase (1–1200 min), however, involved a relatively slow conversion from α‐helix to β‐sheet without a noticeable change in random/turns. An important finding of this work is that the concentration of lysozyme in the adsorbed state has a substantial effect on the fractional content of secondary structures. Attenuated total reflection Fourier transform infrared (ATR/FTIR) spectroscopy, along with a newly‐developed optimization algorithm for predicting the content of secondary structure motifs, was used to correlate the secondary structure and the amount of adsorbed lysozyme with the surface wettability of six different flat nanoporous substrates. Although three independent variables, surface wettability, solution concentration and time for adsorption, were used to follow the fractional structural changes of lysozyme, the results were all normalized onto a single plot with the amount adsorbed as the universal independent variable. Consequently, lateral interactions among proteins likely drive the transition process. Direct intermolecular force adhesion measurements between lysozyme and different functionalized self‐assembled alkanethiol monolayers confirm that hydrophobic surfaces interact strongly with proteins. The lysozyme‐unfolding pathway during early adsorption appears to be similar to that predicted by published molecular modeling results. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Structure of an anti‐DNA fab complexed with a non‐DNA ligand provides insights into cross‐reactivity and molecular mimicry
Authors: Schuermann Jonathan P. , Henzl Michael T. , Deutscher Susan L. , Tanner John J.
Published: June 2004

Antibodies that recognize DNA (anti‐DNA) are part of the autoimmune response underlying systemic lupus erythematosus. To better understand molecular recognition by anti‐DNA antibodies, crystallographic studies have been performed using an anti‐ssDNA antigen‐binding fragment (Fab) known as DNA‐1. The previously determined structure of a DNA‐1/dT5 complex revealed that thymine bases insert into a narrow groove, and that ligand recognition primarily involves the bases of DNA. We now report the 1.75‐Å resolution structure of DNA‐1 complexed with the biological buffer HEPES (4‐(2‐Hydroxyethyl)piperazine‐1‐ethanesulfonic acid). All three light chain complementarity‐determining regions (CDRs) and HCDR3 contribute to binding. The HEPES sulfonate hydrogen bonds to His L91, Asn L50, and to the backbone of Tyr H100 and Tyr H100A. The Tyr side‐chains of L32, L92, H100, and H100A form nonpolar contacts with the HEPES ethylene and piperazine groups. Comparison to the DNA‐1/dT5 structure reveals that the dual recognition of dT5 and HEPES requires a 13‐Å movement of HCDR3. This dramatic structural change converts the combining site from a narrow groove, appropriate for the edge‐on insertion of thymine bases, to one sufficiently wide to accommodate the HEPES sulfonate and piperazine. Isothermal titration calorimetry verified the association of HEPES with DNA‐1 under conditions similar those used for crystallization (2 M ammonium sulfate). Interestingly, the presence of 2 M ammonium sulfate increases the affinities of DNA‐1 for both HEPES and dT5, suggesting that non‐polar Fab–ligand interactions are important for molecular recognition in highly ionic solvent conditions. The structural and thermodynamic data suggest a molecular mimicry mechanism based on structural plasticity and hydrophobic interactions. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Nuclear moments and electron density matrices in atoms
Authors: Pavlov R. L. , Raychev P. P. , Garistov V. P. , Dimitrova‐Ivanovich M. , Maruani J.
Published: June 2004

An electron density matrix approach for the determination of nuclear multipole moments is presented. The electronic matrix elements entering the expressions of the experimentally observed hyperfine coupling constants of atoms are expressed as functionals of the electron charge or spin density matrices. In principle, the calculation of these functionals could be made using any (relativistic or not) molecular orbital (MO) or DFT method. The electronic matrix elements for all possible hyperfine interaction operators, including the yet unobserved magnetic octupole couplings, are considered. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Robust absolute stability of a class of s.i.s.o. control systems
Authors: O. Guardabassi Guido
Published: June 2004

A class of s.i.s.o. nonlinear systems rigorously linearizable by output feedback is dealt with in this paper. Any system of such a class can easily be controlled by the tandem connection of a linear controller and a linearizing compensator. The question addressed in the present paper is the robustness of such a control system against mismatched (nonlinear) compensation and linear uncertainty. Copyright © 2004 John Wiley & Sons, Ltd.
Multivariable override control for systems with output and state constraints
Authors: Turner Matthew C. , Postlethwaite Ian
Published: June 2004

An override control strategy for systems having limits on their outputs, states or linear combinations of the two, is discussed. The technique described is applicable to all nonlinear system‐controller combinations which can be written in a certain linear closed‐loop form. The discussion is first confined to the synthesis of a compensator where the limited states/outputs are perfectly known, and is then broadened to include an observer‐based compensator for the case when these measurements are not directly available. It is shown that, although a form of ‘separation principle’ indeed holds for the observer‐based problem, the type of solution available for this form of override control is not quite as strong as that available when an observer is not required. The results are illustrated using a simple multivariable example. Copyright © 2004 John Wiley & Sons, Ltd.
Immunohistochemical and electron‐microscopic identification of neuroendocrine cells in the stomach of uremic rats
Authors: Kasacka Irena
Published: June 2004

Many disturbances in electrolyte and hormonal balance in the body induced by functional impairment of renal parenchyma may affect the activity of amine precursor uptake and decarboxylation (APUD) cells, which constitute a very important link in the regulation of homeostasis. The aim of the present study was the morphological, immunohistochemical and ultrastructural estimation of enteroendocrine cells in the stomach of uremic rats. Fragments of gastric pylorus were collected 1, 2 and 4 weeks after nephrectomy. Paraffin embedded sections were stained with H + E and by silver impregnation. For identification of neuroendocrine cells, immunohistochemical reactions were performed using specific antibodies against somatostatin, synaptophysin, neuron‐specific enolase and anti‐calcitonin gene related peptide. The analysis showed an increased number of APUD cells in the stomach of uremic rats compared to control rats, which may be a morphological expression of their hyperfunction in the functional impairment of renal parenchyma. These results suggest that chronic renal failure can modulate the secretory processes of APUD cells.
Macrophage‐associated erythropoiesis and lymphocytopoiesis in mouse fetal liver: ultrastructural and ISH analysis
Authors: Li Dong , Wang Guo‐Yun , Liu Zhao‐Fen , Shi Yong‐Xiang , Zhang Hui , Bai Zeng‐Liang
Published: June 2004

To elucidate the process of fetal liver hematopoiesis, the relationships between stroma and hematopoietic cells involved in maturation were investigated. Cultured mouse fetal liver explants were established for morphological analysis of the interactions between fetal liver stroma and hematopoietic cells ex vivo. Fetal liver stroma comprised epithelial cells and macrophages, which occupied most of the culture surface. Macrophages proliferated extensively in primary culture, but almost disappeared after 3 passages. Close morphological and functional relationships were established between macrophages and hemopoietic cells, whereas epithelial cells did not interact with blood cells. Scanning electron microscopy revealed that macrophages were in close contact with erythroblasts and formed a three‐dimensional network. In each erythroblastic island, 2–3 lymphocytes were also in contact with the macrophages; erythroblasts, lymphocytes and macrophages formed close, firm associations through their cytoplasmic membranes. This cell orientation was confirmed by transmission electron microscopy of fetal liver in vivo. In situ hybridization revealed that the macrophages expressed jagged‐1, an important ligand of the Notch signaling system in hematopoiesis.
Suppressing effects of bisphenol A on the secretory function of ovine anterior pituitary cells
Authors: Katoh K. , Matsuda A , Ishigami A , Yonekura S , Ishiwata H , Chen C , Obara Y
Published: June 2004

We investigated the action of bisphenol A (BPA) on cellular GH release and content, cell number, GHmRNA expression, and concentrations of cellular cyclic AMP ([cAMP]c) and calcium ion ([Ca2+]c) in primary cultured ovine anterior pituitary cells. The following results were found: (1) BPA as well as nonylphenol (NP) at 10−6 to 10−3 M significantly and concentration‐dependently suppressed basal and GHRH‐stimulated GH release, and the cellular GH content, (2) BPA suppressed the cell number in a time‐ and concentration‐dependent manner, (3) 10−4 M BPA suppressed GHmRNA expression to 68% of control (BPA‐free), and abolished GHRH (10−8 M)‐induced increases in [cAMP]c and [Ca2+]c. From these findings we conclude that BPA possesses a suppressing action on GH synthesis and release, and this suppressing action is probably related to impairment of cellular signal transduction systems in ovine anterior pituitary cells.
Marginal blebbing during the early stages of TNF‐induced apoptosis indicates alteration in actomyosin contractility
Authors: Domnina L.V. , Ivanova O.Y. , Pletjushkina O.Y. , Fetisova E.K. , Chernyak B.V. , Skulachev V.P. , Vasiliev J.M.
Published: June 2004

Dynamics of alterations of cell surface topography during TNF‐induced apoptosis of HeLa cells was examined by phase‐contrast videomicroscopy and immunomorphological analysis. The final stage of apoptosis accompanied by cell rounding and general blebbing of the cell surface became after 4–6 h of incubation but much earlier, after 1.5–3 h, essentially flattened lamellipodia at the active edges transformed into the small blebs that were continuously extended and retracted during the next 1–2 h. This phenomenon was called “marginal blebbing”. It took place before the cytochrome c release from mitochondria to cytosol. Marginal blebbing was inhibited by drugs that depolymerized actin microfilaments (cytochalasin, latrunculin) or decreased Rho‐kinase‐dependent contractility of actin—myosin cortex (H7, HA‐1077, Y27632). A pancaspase inhibitor, zVAD‐fmk, completely prevented marginal and general blebbing, and TNF‐induced apoptosis. DEVD‐fmk, a specific inhibitor of caspase‐3, inhibited both marginal and general blebbing but not cell rounding and death. Thus, marginal blebbing is an early microfilament‐dependent apoptotic event. It is suggested that it is initiated by minimal activation of caspase‐3 and the following local Rho‐kinase‐dependent stimulation of actin—myosin cortex contractility. Localization of marginal blebs at the active edge may be associated with special organization of cortex in that zone.
Interaction of filamin A with the integrin β7 cytoplasmic domain: role of alternative splicing and phosphorylation
Authors: Travis Mark A , van der Flier Arjan , Kammerer Richard A , Paul Mould A , Sonnenberg Arnoud , Humphries Martin J
Published: June 2004

Integrin–filamin binding plays an important role in adhesion‐mediated control of the actin cytoskeleton. Here, using the interaction between recombinant fragments from the C‐terminus of filamin A and the cytoplasmic tail of integrin β7 as a model, we report a negative regulatory role for filamin alternative splicing. Splice variant forms of filamin A lacking a 41‐amino acid segment interacted more strongly than full‐length fragments. In addition, we provide evidence that phosphorylation of the splice variant region is unlikely to represent the mechanism by which binding is reduced.
A tomato lipase homologous to DAD1 (LeLID1) is induced in post‐germinative growing stage and encodes a triacylglycerol lipase
Authors: Matsui Kenji , Fukutomi Sachiko , Ishii Miho , Kajiwara Tadahiko
Published: June 2004

A tomato lipase gene homologous to Arabidopsis DAD1 (lipase homologous to DAD1; LeLID1) was cloned and characterized. The corresponding transcript increased rapidly during germination of the seeds and reached a maximum level at four days after germination. Thereafter, it decreased rapidly. Little expression could be found in flowers or fruits. Immunoblot analyses showed that the gene products could be found in the cotyledons and hypocotyls, but not in the roots. In the cotyledons most LeLID1 could be recovered in a soluble fraction. The recombinant LeLID1 protein showed maximum lipase activity at pH 8.0. It showed high activity against triacylglycerols (TAGs) with long acyl chains, but little activity with phosphatidylcholine or monogalactosyldiacylglycerol. TAGs composed of short acyl chains could not be a substrate for the enzyme. A possible involvement of LeLID1 in fat mobilization during seed germination is discussed.
NaCl‐induced phosphorylation of light harvesting chlorophyll a/b proteins in thylakoid membranes from the halotolerant green alga, Dunaliella salina
Authors: Liu Xian-De , Shen Yun-Gang
Published: June 2004

Light could induce phosphorylation of light harvesting chlorophyll a/b binding proteins (LHCII) in Dunaliella salina and spinach thylakoid membranes. We found that neither phosphorylation was affected by glycerol, whereas treatment with NaCl significantly enhanced light‐induced LHCII phosphorylation in D. salina thylakoid membranes and inhibited that in spinach. Furthermore, even in the absence of light, NaCl and several other salts induced LHCII phosphorylation in D. salina thylakoid membranes, but not in spinach thylakoid membranes. In addition, hypertonic shock induced LHCII phosphorylation in intact D. salina under dark conditions and cells adapted to different NaCl concentrations exhibited similar LHCII phosphorylation levels. Taken together, these results show for the first time that while LHCII phosphorylation of D. salina thylakoid membranes resembles that of spinach thylakoid membranes in terms of light‐mediated control, the two differ with respect to NaCl sensitivity under light and dark conditions.
Phosphorylation of the regulatory β‐subunit of protein kinase CK2 by checkpoint kinase Chk1: identification of the in vitro CK2β phosphorylation site
Authors: Kristensen Lars P , Larsen Martin R , Højrup Peter , Issinger Olaf-Georg , Guerra Barbara
Published: June 2004

The regulatory β‐subunit of protein kinase CK2 mediates the formation of the CK2 tetrameric form and it has functions independent of CK2 catalytic subunit through interaction with several intracellular proteins. Recently, we have shown that CK2β associates with the human checkpoint kinase Chk1. In this study, we show that Chk1 specifically phosphorylates in vitro the regulatory β‐subunit of CK2. Chymotryptic peptides and mutational analyses have revealed that CK2β is phosphorylated at Thr213. Formation of a stable complex between CK2β and Chk1 is not affected by the modification of Thr213 but it does require the presence of an active Chk1 kinase.
The African swine fever virus dynein‐binding protein p54 induces infected cell apoptosis
Authors: Hernáez Bruno , Dı́az-Gil Gema , Garcı́a-Gallo Mónica , Ignacio Quetglas José , Rodrı́guez-Crespo Ignacio , Dixon Linda , Escribano José M , Alonso Covadonga
Published: June 2004

A specific interaction of ASFV p54 protein with 8 kDa light chain cytoplasmic dynein (DLC8) has been previously characterized and this interaction is critical during virus internalization and transport to factory sites. During early phases of infection, the virus induces the initiation of apoptosis triggering activation of caspase‐9 and ‐3. To analyze the role of the structural protein p54 in apoptosis, transient expression experiments of p54 in Vero cells were carried out which resulted in effector caspase‐3 activation and apoptosis. Interestingly, p54 mutants, lacking the 13 aa dynein‐binding motif lose caspase activation ability and pro‐death function of p54. This is the first reported ASFV protein which induces apoptosis.
Estimating migration rates from two tag–release/one recovery experiments
Authors: Shirakihara Kunio , Kitada Shuichi
Published: June 2004

We propose a method for estimating migration (movement) rates from two tag–release/one recovery experiments, regardless of tag-shedding or incomplete tag-reporting which are major problems when tag–recovery techniques are applied to commercially exploitable populations. The entire survey area is divided into multiple strata in advance. The first release is limited to one stratum; then, the second release occurs in every stratum. Recoveries from both releases occur in every stratum. The migration rate between the time of the first and second release is estimated together with its variance. To check the applicability of our method, we applied it to tag–recovery data for skipjack tuna from various places at different times and unequal time intervals. The precision of the estimates was low and the coefficient of variation was 22.6–42.1% because of the small number of recoveries. The experimental design necessary to improve precision is discussed.
Estimation of birthdates and catch-at-age using length frequency analysis (LFA), with application for skipjack tuna (Katsuwonus pelamis) caught in the Southwest Atlantic
Authors: Andrade Humber A. , Kinas Paul G.
Published: June 2004

Converting length frequencies into age frequencies is an important component of a fisheries assessment. In this paper we use a length frequency analysis (LFA) to estimate birthdates after converting length data into catch-at-age, and use simulation studies to compare model-selection criteria and to examine the reliability of the resulting estimates. Deviance and an adaptation of the Akaike Information Criterion performed best. LFA results in useful estimates of birthdates and of catch-at-age if reliable length frequency data and estimates of growth parameters are available. The analysis is applied to skipjack tuna (Katsuwonus pelamis) caught in the Southwest Atlantic Ocean. Although spawning is reported to be seasonal in subtropical waters, the birthdates of the fish caught there were spread uniformly across the year. Young skipjack become vulnerable to fishing mainly in the first quarter of each year. Recruitment of strong year classes did not affect fishery yields equally in the Southwest Atlantic and the Caribbean Sea, so the assumption of a unit western stock for management purposes and the stock structure of skipjack in the Atlantic need further evaluation.
A quantitative study of the neuronal nitric oxide synthase expression in the superficial layers of the adult rat superior colliculus after perinatal enucleation
Authors: de Bittencourt‐Navarrete Ruben Ernesto , Giraldi‐Guimarães Arthur , Mendez‐Otero Rosalia
Published: June 2004

The level of expression of the neuronal nitric oxide synthase (nNOS) in the retinorecipient layers of rat superior colliculus (SC) was investigated in adult rats after neonatal enucleation using two biochemical methods: (1) measurement of the in vitro specific‐activity of NOS by the conversion of [3H]‐arginine to [3H]‐citrulline and (2) immunochemical analysis by western blotting and densitometry of immunoreactive bands using antibodies that recognise the three prominent isoforms of nNOS, α, β and γ. A total of 20 Lister rats were used in this study. We have shown that the deprivation of the retinocollicular projections at early postnatal ages induces no significant change in the specific‐activity of nNOS. We also have shown that the deafferentation does not significantly influence either the total amount of nNOS in the SC superficial layers or the relative contribution ratio of nNOS isoforms. In conclusion, the expression and activity of nNOS in the SC retinorecipient layers was shown not to be dependent on the presence of retinal afferents during development.
Overstretching of sarcomeres may not cause cerebral palsy muscle contracture
Authors: Smeulders Mark J. C. , Kreulen Michiel , Hage J. Joris , Huijing Peter A. , van der Horst Chantal M. A. M.
Published: June 2004

To answer the question whether the muscle contracture in patients with cerebral palsy is caused by overstretching of in‐series sarcomeres we studied the active and passive force–length relationship of the flexor carpi ulnaris muscle (FCU) in relation to its operating length range in 14 such patients with a flexion deformity of the wrist.

Force–length relationship was measured intra‐operatively using electrical stimulation, a force transducer, and a data‐acquisition system. Muscle length was measured in maximally flexed and maximally extended position of the wrist.

The spastic FCU was found to exert over 80% of its maximum active force at maximal extension of the wrist and this indicates abundant overlap of the sarcomeres. At maximal wrist extension, FCU passive force corresponded with only 0.7–18% of maximum active force. Both findings imply that the FCU sarcomeres are not overstretched when the wrist is extended. We conclude that the overstretching of in‐series sarcomeres appears not to be the cause of contracture of the spastic FCU. © 2004 Orthopaedic Research Society. Published y Elsevier Ltd. All rights reserved.
The Effectiveness of Immersion Disinfection for Flexible Fiberoptic Laryngoscopes
Authors: Bhattacharyya Neil , Kepnes Lynne J.
Published: June 2004

OBJECTIVE

We sought to determine whether highlevel disinfection renders fiberoptic laryngoscopes free of nonviral infectious microorganisms.

METHODS

Six flexible fiberoptic laryngoscopes in heavy use were subjected to surveillance cultures at the beginning, middle, and end of the clinical workday after high‐level disinfection to determine if microorganisms could be recovered. Control cultures were obtained by direct contamination of the endoscope with saliva. The rate of microorganism recovery from the endoscopes after high‐level disinfection was determined and compared with control specimens.

RESULTS

Among a total of 48 cultures submitted from in use but disinfected fiberoptic laryngoscopes, 1 positive culture (positive rate, 2.1%) for mold species was recovered. No positive bacterial cultures occurred. Eleven of 11 (100%) control cultures were positive for bacterial species (P < 0.001). The confidence interval for the risk of microorganism contamination of a disinfected laryngoscope ranged from 0.11% to 11.6%.

CONCLUSION

High‐level disinfection provides a reasonably effective method of reducing bacterial and fungal contamination of flexible fiberoptic laryngoscopes. Appropriate surveillance technique should be used in each clinical setting with flexible fiberoptic scopes to ensure adequate disinfection effectiveness. (Otolaryngol Head Neck Surg 2004; 130:681‐5.)
Popular Snore Aids: Do They Work?
Authors: Michaelson Peter G. , Mair Eric A.
Published: June 2004

OBJECTIVE

The study goal was to critically evaluate 3 popular noninvasive treatments for snoring: an oral spray lubricant applied before bedtime, a nasal strip designed to maintain nasal valve patency, and a head‐positioning pillow.

STUDY DESIGN

Prospective, randomized blinded clinical trial of 3 popular noninvasive snore aids using objective acoustic snoring analysis and subjective patient and bed‐partner questionnaires in 40 snoring patients. A digital recorder allowed snoring analysis with data collected in the home environment over 1 week.

RESULTS

There is neither objective nor subjective benefit to the use of tested popular noninvasive snore aids. Palatal snoring, palatal loudness, average loudness of snoring, averaged palatal flutter frequency, and respiratory disturbance index did not significantly change when comparing the 3 snoring aids with no treatment. Subjective comments and complications are reviewed as well.

CONCLUSION

This is the first prospective comparison trial of popular noninvasive snoring aids. There is no significant objective or subjective snoring improvement in the anti‐snoring aids studied compared with the use of no aid.

SIGNIFICANCE

Outcome studies aid in verifying or refuting claims made by popular noninvasive snore aids. (Otolaryngol Head Neck Surg 2004;130: 649‐58.)
Nasal Mucociliary Clearance in Coal Mine Workers
Authors: Çinar Fikret , Beder Levent
Published: June 2004

OBJECTIVE

The purpose of this study was to analyze the effect of coal dust particles on nasal mucociliary function in coal mine workers.

METHOD

Using the saccharin method, nasal mucociliary clearance was determined for 77 subjects, of which 39 who worked in a coal mine were actively exposed to coal dust whereas 38 were unexposed control subjects. The measurements were performed in the coal mine, at the level of 170 m below sea level.

RESULTS

The average saccharin nasal transit time in coal mine workers, 12.61 (SD: 4.30) minutes, is longer than that of the control subjects, 10.97 (SD: 3.22).

CONCLUSION: Although the findings of this study demonstrate that the coal particles affect the nasal mucociliary clearance, the difference in saccharin nasal transit time between the two groups (exposed vs unexposed) is not statistically significant (P = 0.063). (Otolaryngol Head Neck Surg 2004;130: 767‐9.)
The Role of Food Allergy in Otitis Media with Effusion
Authors: Aydoğan Barlas , Kiroğlu Mete , Altintas Derya , Yilmaz Mustafa , Yorgancilar Ediz , Tuncer Ülkü
Published: June 2004

OBJECTIVE

To detect the relationship between food allergy and otitis media with effusion (OME).

MATERIALS AND METHODS

This study was performed on three different groups. The patient group was made up of 56 patients with OME (group I). There were 28 patients with food allergy in group II and these patients were investigated for OME. The control group consisted of 28 patients without any complaints concerning food allergy or OME (group III).

RESULTS

Food allergy was detected in 25 patients with OME (44.6%) (group I). In patients with food allergy (group II), OME was detected in 7 patients (25%). In the control group (group III) food allergy was diagnosed in 5 patients (18%) and OME in 1 patient (3%). The incidence of food allergy in OME group was statistically significant when compared to the normal group (P > 0.05).

CONCLUSIONS: This study demonstrates that food allergy may play a role in the etiopathogenesis of OME. (Otolaryngol Head Neck Surg 2004;130: 747‐50.)
Topical Ciprofloxacin/Dexamethasone Otic Suspension is Superior to Ofloxacin Otic Solution in the Treatment of Granulation Tissue in Children with Acute Otitis Media With Otorrhea Through Tympanostomy Tubes
Authors: Roland Peter S. , Dohar Joseph E. , Lanier Brent J. , Hekkenburg Robert , Lane Edward M. , Conroy Peter J. , Wall G. Michael , Dupre Sheryl J. , Potts Susan L. ,   THE CIPRODEX AOMT STUDY GROUP
Published: June 2004

OBJECTIVE

Comparison of topical ciprofloxacin/dexamethasone otic suspension (CIP/DEX) to ofloxacin otic solution (OFL) for treatment of granulation tissue in children with AOMT.

STUDY DESIGN

599 children aged ≥6 months to 12 years with AOMT of up to 3 weeks' duration were enrolled. Patients received either CIP/DEX 4 drops twice daily for 7 days or OFL 5 drops twice daily for 10 days. Granulation tissue severity was graded at clinic visits on days 1, 3, 11, and 18.

RESULTS

Granulation tissue was present in 90 of 599 AOMT patients (15.0%) at baseline. CIP/DEX treatment was superior to OFL for reduction of granulation tissue at the day 11 visit (81.3% compared with 56.1%, P = 0.0067) and the day 18 visit (91.7% compared with 73.2%, P = 0.0223). Both topical otic preparations are safe and well tolerated in pediatric patients.

CONCLUSION: CIP/DEX was superior to OFL in the treatment of granulation tissue in children with AOMT. (Otolaryngol Head Neck Surg 2004;130: 736‐41.)
Immigration Law Information Sources – Databases and the Internet
Authors: Ogden David
Published: June 2004

Before 1905 there were no immigration laws in the UK. The first system of appeals in immigration cases was introduced by the Immigration Appeals Act 1969. Since then it has been subject to numerous changes. A full right of appeal to an adjudicator in asylum cases was first created by the Asylum and Immigration Appeals Act 1993. Immigration law is governed by the Immigration Act 1971, with changes made by Immigration Acts in 1993, 1996, 1999, and most recently with the Nationality, Immigration and Asylum Act 2002.
Nottingham Law School's Post-graduate Diploma in Know-How Management for Legal Practice
Authors: Battersby Karen
Published: June 2004

In September 2003, Nottingham Law School launched its innovative Postgraduate Diploma in Know-How Management for Legal Practice, the first course of its kind in the UK providing professional development and training for those engaged in knowledge management in legal organisations. Now nearing completion of a successful first year, with students from both private practice and in-house legal departments, and from a range of backgrounds in knowledge management, including librarians, professional support lawyers, heads of knowledge management, managing partners and in-house counsel, the Law School is currently in the process of recruiting intake for the second running of the course commencing in September 2004.
Current Awareness
Authors: Sands Gillian , Weston-Smith Sam
Published: June 2004

This Current Awareness column, and previous Current Awareness columns, are now fully searchable in the new caLIM database (Current Awareness for Legal Information Managers). The caLIM database is available on the Institute of Advanced Legal Studies website at: http://ials.sas.ac.uk/library/caware/caware.htm
The Role of Executive Director in National Professional Associations
Authors: Fox Susan
Published: June 2004

I am always at something of a loss when a new acquaintance asks, “So, what do you do?” Should I go for the straightforward, “I am Executive Director of the American Association of Law Libraries”? Should I go for the more general, “I am the CEO of a national professional association”? Or, more general still, “I am an association executive”?
Re‐quantifying the emission factors based on field measurements and estimating the direct N2O emission from Chinese croplands
Authors: Zheng Xunhua , Han Shenghui , Huang Yao , Wang Yuesi , Wang Mingxing
Published: June 2004

The authors collect 54 direct N2O emission factors (EFds) obtained from 12 sites of Chinese croplands, of which 60% are underestimated by 29% and 30% are overestimated by 50% due to observation shortages. The biases of EFds are corrected and their uncertainties are re‐estimated. Of the 31 site‐scale EFds, 42% are lower by 58% and 26% are higher by 143% than the Intergovernmental Panel on Climate Change default. Periodically wetting/drying the fields or doubling nitrogen fertilizers may double or even triple an EFd. The direct N2O emission from Chinese croplands is estimated at 275 × 109 g N2O‐N yr−1 in the 1990s, of which ∼20% is due to vegetable cultivation. The great uncertainty of this estimate, −79% to 135%, is overwhelmingly due to the huge uncertainty in estimating EFds (−78 ± 15% to 129 ± 62%). Direct N2O emission intensities significantly depend upon the economic situation of the region, implicating a larger potential emission in the future.
Meteorological forcing of sea ice concentrations in the southern Beaufort Sea over the period 1979 to 2000
Authors: Barber David G. , Hanesiak John M.
Published: June 2004

Northern Hemisphere sea ice areal extent, and perhaps thickness, have shown a detectable reduction over the past several decades. This situation is particularly apparent in the southern Beaufort Sea. The region encompassing the Mackenzie Shelf, the Cape Bathurst Polynya, and the Canada Basin mobile pack ice all occur in a region referred to here as the Canadian Arctic Shelf Exchange study area (CASES). In this paper we present results from an analysis of atmosphere, sea ice, and ocean coupling over the period 1979 to 2000 as a means of setting a physical science context for the CASES research network (operating over the period 2001–2005). Results show that the Cape Bathurst Polynya complex can be considered as a recurrent polynya; particularly the flaw leads associated with the early opening of the polynya. The Polynya appears to be a consequence of the Beaufort Sea Gyre acting like an ice bridge and a series of flaw leads creating conditions conducive to oceanic upwelling. The sea ice average areal extent has been decreasing in this region over the period 1979 to 2000. Large regional reductions are found (1) north of the Yukon and Alaska Coasts in the region between the Canada Basin pack ice and the landfast sea ice and (2) at the eastern limit of the Cape Bathurst Polynya in Amundsen Gulf. The meteorological forcing of sea ice anomalies occurs through a full range of timescales and space scales. At hemispheric scales a statistical cross‐correlation analysis between weekly sea ice concentration anomalies and the Arctic Oscillation accounts for a maximum of about 25 percent of the explained variance and show a surprising spatial coherence in correlation magnitudes both within the study area and northward along the Canadian Archipelago coast. At local scales, positive and negative concentration anomaly periods can be explained through local‐scale advective processes associated with regional‐scale sea level pressure, 500 hPa geopotential heights, and surface temperature anomalies.
Statistical classification of buried objects from spatially sampled time or frequency domain electromagnetic induction data
Authors: Tarokh Ashley B. , Miller Eric L. , Won I. J. , Huang Haoping
Published: June 2004

Methods for classifying objects based on spatially sampled electromagnetic induction data taken in the time or frequency domain are developed and analyzed. To deal with nuisance parameters associated with the position of the object relative to the sensor as well as the object orientation, a computationally tractable physical model explicit in these unknowns is developed. The model is also parameterized by a collection of decay constants (or equivalently Laplace‐plane poles) whose values in theory are independent of object position and orientation. These poles are used as features for classification. The overall algorithm consists of two stages. First, we estimate the values of the unknown parameters and then we do classification. Classification is done by comparing either the raw data or some low‐dimensional collection of features extracted from the data to entries in a library. The library can be constructed using either simulated or calibration data. A maximum likelihood method is developed and analyzed for the problem of joint pole, location, and orientation parameter determination. Here we examine and compare two classification schemes. The first classification method is based on data residuals generated from estimated signal parameters. This scheme performs well in low SNR cases. The second is based on estimated pole values themselves, which performs well in high SNR cases. We validate our methods on both simulated and field data taken from frequency and time domain sensors.
Analysis of water resources variability in the Yellow River of China during the last half century using historical data
Authors: Yang Dawen , Li Chong , Hu Heping , Lei Zhidong , Yang Shixiu , Kusuda Tetsuya , Koike Toshio , Musiake Katumi
Published: June 2004

The river discharges have decreased continuously during the last half century in the Yellow River, the second‐largest river basin in China. In particular, a drying up of the main river along the lower reach has occurred since 1972, and the situation has become more and more serious during the 1990s. Using 50 years of meteorological data from 108 stations together with a collection of irrigation data, the long‐term changes in the river discharge have been investigated with a view to identifying the reason for the drying up of the Yellow River. It was found that the annual precipitation generally decreased (−45.3 mm/50 yr) while the air temperature generally increased (+1.28°C/50 yr). From the 1960s to the 1970s the precipitation decreased by 29.6 mm/10 yr, the evaporation increased by 7 mm/10 yr (for pan evaporation), and the irrigation water usage increased by 10.5 mm/10 yr. As a consequence the drying up of the Yellow River has occurred since 1972. Irrigation was developed continuously in the 1980s, but the drying‐up situation maintained at the same level as during the 1970s. The reason for this was the increase in precipitation (by 10.3 mm/10 yr) and the sharp decrease in the evaporation (by 133 mm/10 yr for pan evaporation). During the 1990s the irrigation was maintained at a level similar to that during the 1980s, but the drying‐up situation was greatly aggravated. The reason for this was found to be a result of the decrease in precipitation (by 38.2 mm/10 yr) and the increase in evaporation (by 52 mm/10 yr for pan evaporation).
Tidal modulation of the gravity‐wave momentum flux in the Antarctic mesosphere
Authors: Espy P. J. , Jones G. O. L. , Swenson G. R. , Tang J. , Taylor M. J.
Published: June 2004

Airglow imager and dynasonde/IDI radar wind measurements at Halley Station, Antarctica (76°S, 27°W) have been used to estimate the diurnal variation of the vertical fluxes of horizontal momentum carried by high‐frequency atmospheric gravity waves. The cross‐correlation coefficients between the vertical and horizontal wind perturbations were calculated from the sodium airglow imager data collected during four consecutive nights of near total darkness during July of 2000. These were combined with wind‐velocity variances from coincident radar measurements to estimate the upper limit of the vertical flux of horizontal momentum during three‐hour intervals throughout the period. The resulting momentum flux showed a marked semi‐diurnal oscillation in the zonal and meridional components. Calculations of the momentum flux through the Na airglow show variations in period and phase consistent with the observations, implying that tidal propagation and modulated gravity‐wave forcing may both affect observed wind variations.
PDF model based on Langevin equation for polydispersed two-phase flows applied to a bluff-body gas-solid flow
Authors: Minier Jean-Pierre , Peirano Eric , Chibbaro Sergio
Published: June 2004

The aim of the paper is to discuss the main characteristics of a complete theoretical and numerical model for turbulent polydispersed two-phase flows, pointing out some specific issues. The theoretical details of the model have already been presented [Minier and Peirano, Phys. Rep. 352, 1 (2001)]. Consequently, the present work is mainly focused on complementary aspects that are often overlooked and that require particular attention. In particular, the following points are analyzed: the necessity to add an extra term in the equation for the velocity of the fluid seen in the case of two-way coupling, the theoretical and numerical evaluations of particle averages and the fulfillment of the particle mass-continuity constraint. The theoretical model is developed within the probability density function (PDF) formalism. The important physical choice of the state vector variables is first discussed and the model is then expressed as a stochastic differential equation written in continuous time (Langevin equations) for the velocity of the fluid seen. The interests and limitations of Langevin equations, compared to the single-phase case, are reviewed. From the numerical point of view, the model corresponds to a hybrid Eulerian/Lagrangian approach where the fluid and particle phases are simulated by different methods. Important aspects of the Monte Carlo particle/mesh numerical method are emphasized. Finally, the complete model is validated and its performance is assessed by simulating a bluff-body case with an important recirculation zone and in which two-way coupling is noticeable.
Self-acceleration and fractal structure of outward freely propagating flames
Authors: Liberman Michael A. , Ivanov Mikhail F. , Peil Oleg E. , Valiev Damir M. , Eriksson Lars-Erik
Published: June 2004

Flame acceleration associated with development of the Landau–Darrieus hydrodynamic instability is studied by means of direct numerical simulation of the Navier–Stokes equations including chemical kinetics in the form of the Arrhenius law. The fractal excess for radially expanding flames in cylindrical geometry is evaluated. Two-dimensional (2-D) simulation of radially expanding flames in cylindrical geometry displays a radial growth with 1.25 power law temporal behavior after some transient time. It is shown that the fractal excess for 2-D geometry obtained in the numerical simulation is in good agreement with theoretical predictions. The difference in fractal dimension between 2-D cylidrical and three-dimensional spherical radially expanding flames is outlined. Extrapolation of the obtained results for the case of spherical expanding flames gives a radial growth power law that is consistent with temporal behavior obtained in the survey of experimental data.