bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymer‐based S‐shaped waveguide VOA for applications in the broadband DWDM network
Authors: Lu Ying‐Tsung , Guo Huang‐Chen , Wang Hseng‐Tsong , Chi Sien 
Published: August 2003

AbstractA polymer‐based thermal‐controllable waveguide variable optical attenuator (VOA) is proposed. We numerically design an S‐shaped buried waveguide structure with a polymer core and silica cladding, which can attenuate light with satisfactory optical attenuation in the spectrum range from 1.28 to 1.58 μm. The design is suitable for the integration of VOAs with planar lightwave devices and is easy to fabricate as monolithic optical modules for application in optical communication systems. © 2003 Wiley Periodicals, Inc. Microwave Opt Technol Lett 39: 1–4, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.11108
Unequivocal total assignment of 13C and 1H NMR spectra of some pyrido[1,2‐a]pyrimidine derivatives by 2D‐NMR
Authors: Suri Krishan A. , Suri Om P. , Amina Musarat , Wakhloo Basant P. , Satti Naresh K. 
Published: August 2003

AbstractWe report the total assignments of the 13C and 1H NMR spectra of some 4‐methyl‐2‐oxo‐(2H)‐pyrido[1,2‐a]pyrimidine and 2‐methyl‐4‐oxo‐(4H)‐pyrido[1,2‐a]pyrimidine derivatives. The products were characterized by 1H and 13C NMR and reported data for similar compounds. No comparative data for the two sets of isomeric compounds with respect to 13C and 1H NMR have been reported to date. We made some detailed studies of the 2D NMR spectra of these compounds and observed that assignments made for non‐protonated carbon atoms by us and those reported in the literature for similar compounds need correction. The revised assignments were made on the basis of heteronuclear single quantum correlation (HSQC) and heteronuclear multiple bond correlation (HMBC) techniques. Copyright © 2003 John Wiley & Sons, Ltd.
Methicillin‐resistant Staphylococcus aureus in children with cystic fibrosis: An eradication protocol
Authors: Solís A. , Brown D. , Hughes J. , van Saene H.K.F. , Heaf D.P. 
Published: August 2003

AbstractA retrospective 12‐year study (May 1988–July 2000) was undertaken in children with cystic fibrosis (CF) to evaluate 1) the magnitude of methicillin‐resistant Staphylococcus aureus (MRSA) in these children; 2) the clinical impact of MRSA on CF; and 3) the efficacy of an MRSA protocol aimed at the eradication of the carrier state. The study maneuver comprised of 1) surveillance cultures of throat/rectum to detect the MRSA carrier state; 2) life‐long cephradine rather than flucloxacillin to lift selection pressure; 3) topical application of oral and nebulized vancomycin for 5 days to clear the carriage of MRSA; and 4) a strict antistaphylococcal hygiene program, including handwashing and device policy. Fifteen children with CF (11 boys, with median age 117 months) positive for MRSA were enrolled. The current prevalence of MRSA among children with CF in our hospital is 6.5%. Of 15 children identified, only 12 (18 episodes of MRSA colonization) were treated according to protocol. Median age of MRSA acquisition was 73 months (interquartile range, 43–134 months). In 7 patients (55%), MRSA was eradicated. Of a total of 18 MRSA episodes, the protocol was successful in 10 episodes. The mean period of MRSA‐free status was 12 months (range, 6–36 months). Pulmonary function (measured by FEV1) was not affected (68% of predicted before treatment, and 68% of predicted after treatment). All children were oropharyngeal carriers of both MRSA and ceftazidime‐resistant P. aeruginosa. We believe that an effort has to be made to limit MRSA in CF clinics for the following reasons: 1) MRSA carriage in any individual is an abnormal condition; 2) limitation of systemic vancomycin use is desirable; 3) MRSA carriage may be a contraindication for lung transplantation; and 4) epidemiologically, a CF unit with a substantial MRSA problem functions as a source of dissemination for other patients. Pediatr Pulmonol. 2003; 36:189–195. © 2003 Wiley‐Liss, Inc.
Flavors of protein disorder
Authors: Vucetic Slobodan , Brown Celeste J. , Dunker A. Keith , Obradovic Zoran 
Published: August 2003

AbstractIntrinsically disordered proteins are characterized by long regions lacking 3‐D structure in their native states, yet they have been so far associated with 28 distinguishable functions. Previous studies showed that protein predictors trained on disorder from one type of protein often achieve poor accuracy on disorder of proteins of a different type, thus indicating significant differences in sequence properties among disordered proteins. Important biological problems are identifying different types, or flavors, of disorder and examining their relationships with protein function. Innovative use of computational methods is needed in addressing these problems due to relative scarcity of experimental data and background knowledge related to protein disorder. We developed an algorithm that partitions protein disorder into flavors based on competition among increasing numbers of predictors, with prediction accuracy determining both the number of distinct predictors and the partitioning of the individual proteins. Using 145 variously characterized proteins with long (>30 amino acids) disordered regions, 3 flavors, called V, C, and S, were identified by this approach, with the V subset containing 52 segments and 7743 residues, C containing 39 segments and 3402 residues, and S containing 54 segments and 5752 residues. The V, C, and S flavors were distinguishable by amino acid compositions, sequence locations, and biological function. For the sequences in SwissProt and 28 genomes, their protein functions exhibit correlations with the commonness and usage of different disorder flavors, suggesting different flavor‐function sets across these protein groups. Overall, the results herein support the flavor‐function approach as a useful complement to structural genomics as a means for automatically assigning possible functions to sequences. Proteins 2003;52:573–584. © 2003 Wiley‐Liss, Inc.
Sequence analysis reveals how G protein–coupled receptors transduce the signal to the G protein
Authors: Oliveira Laerte , Paiva Paulo B. , Paiva Antonio C. M. , Vriend Gerrit 
Published: August 2003

AbstractSequence entropy—variability plots based on alignments of very large numbers of sequences—can indicate the location in proteins of the main active site and modulator sites. In the previous article in this issue, we applied this observation to a series of well‐studied proteins and concluded that it was possible to detect most of the residues with a known functional role. Here, we apply the method to rhodopsin‐like G protein–coupled receptors. Our conclusion is that G protein binding is the main evolutionary constraint on these receptors, and that other ligands, such as agonists, act as modulators. The activation of the receptors can be described as a simple, two‐step process, and the residues involved in signal transduction can be identified. Proteins 2003;52:553–560. © 2003 Wiley‐Liss, Inc.
Generation of dominant‐negative effects on the heat shock response in Arabidopsis thaliana by transgenic expression of a chimaeric HSF1 protein fusion construct
Authors: Wunderlich Markus , Werr Wolfgang , Schöffl Friedrich 
Published: August 2003

SummaryUpon heat stress, heat shock factors (HSFs) control the expression of heat shock protein (HSP) genes by transcriptional activation. The perplexing multiplicity of HSF genes in Arabidopsis– 21 potential genes have been identified – renders it difficult to identify mutant phenotypes. In this study, we have attempted to generate a transdominant‐negative mutant of HSF by transgenic expression of a protein fusion construct, EN‐HSF1, consisting of the Drosophila engrailed repressor domain (EN) and the complete Arabidopsis AtHSF1. Transgenic lines were screened for impaired ability to induce high levels of low‐molecular‐weight heat shock proteins (sHSPs). Two lines, EH14‐6 and EH16‐3, which showed quantitative differences in the expression of EN‐HSF1, were further analysed for induction of thermotolerance and heat‐stress‐dependent mRNAs of a number of different HSF target genes encoding different HSP and HSF. The mRNA levels of all genes tested were moderately downregulated in EH14‐6 but strongly reduced in EH16‐3 plants compared to wild‐type (Wt) and HSF1‐overexpressing control plants. The inhibition of the induction of heat shock response correlated with impaired basal and acquired thermotolerance of the EH16‐3 line. The kinetics of HSP expression suggest that the negative effect of EN‐HSF1 is stronger in the early phase of the heat shock response, and that the reduction in mRNA levels is partially compensated at the translational level.
Comparison of Enzyme-Linked Immunosorbent Assay, Immunoblotting, and PCR for Diagnosis of Toxoplasmic Chorioretinitis
Authors: Villard Odile , Filisetti Denis , Roch-Deries Florence , Garweg Justus , Flament Jacques , Candolfi Ermanno 
Published: August 2003

ABSTRACT

Ocular toxoplasmosis is the major cause of posterior uvetis in European populations. The clinical diagnosis of toxoplasmic chorioretinitis is based upon ophthalmoscopic findings, which are often but not always typical. Laboratory testing is therefore important to confirm the etiology of the disease. In the present 2-year prospective study, the relative diagnostic sensitivities of the three analytical techniques (enzyme-linked immunosorbent assay [ELISA], immunoblotting, and PCR) were compared by using a group of patients (
n
= 19) with suspected ocular toxoplasmosis. The relative specificities of the three techniques were assessed by including two control groups of patients: one with nontoxoplasmic and noninflammatory ocular disease (
n
= 48) and the other with nontoxoplasmic and inflammatory ocular disease (
n
= 20). All 19 of the clinically suspect patients had serological evidence of exposure to
Toxoplasma gondii
: 17 had been previously infected, and 2 had current infection. The analysis of paired aqueous humor and serum samples by ELISA and immunoblotting revealed the local production of specific antibodies of the immunoglobulin G type in 63% (12 of 19) and 53% (10 of 19) of patients, respectively. PCR analysis of aqueous humor samples confirmed the presence of
T. gondii
DNA in 28% (5 of 18) of cases. When combined, ELISA, immunoblotting, and PCR findings confirmed the toxoplasmic origin of retinal lesions in 83% (15 of 18) of patients. The relative specificities of the three techniques were 89% for ELISA and immunoblotting and 100% for PCR.
Comparison of SmartCycler Real-Time Reverse Transcription-PCR Assay in a Public Health Laboratory with Direct Immunofluorescence and Cell Culture Assays in a Medical Center for Detection of Influenza A Virus
Authors: Habib-Bein Nadia F. , Beckwith William H. , Mayo Donald , Landry Marie L. 
Published: August 2003

ABSTRACT
A single-tube real-time (fluorogenic) reverse transcription (RT)-PCR with the SmartCycler instrument (SmartCycler RT-PCR) for influenza A virus detection was evaluated with 238 respiratory specimens. Direct immunofluorescence antibody staining (DFA) and primary rhesus monkey kidney cell culture were performed on-site at Yale-New Haven Hospital. Specimens were transported to the Connecticut Department of Public Health Laboratory for real-time RT-PCR. Cell culture detected influenza A virus in all 150 influenza A virus-positive specimens, DFA detected the virus in 148 influenza A virus-positive specimens, and SmartCycler RT-PCR detected the virus 143 influenza A virus-positive specimens. The sensitivity and specificity of RT-PCR were 95.3 and 100%, respectively. The high sensitivity and specificity and the rapid turnaround time made the SmartCycler RT-PCR valuable for the rapid diagnosis of influenza A, especially in a public health laboratory. The closed real-time RT-PCR system avoided cross-contamination possible with RT-PCR and the excessive manipulations required for conventional RT-PCR analysis and saved time and labor as well. In a medical center, rapid diagnosis by DFA was labor intensive but was 98.7% sensitive and 100% specific compared to the results of culture and provided results within 2 h throughout operating hours, helping with bed allocation on admission and patient management.
Comparison of the
Bordetella pertussis
and
Bordetella parapertussis
Isolates Circulating in Saint Petersburg between 1998 and 2000 with Russian Vaccine Strains
Authors: Kourova Natacha , Caro Valérie , Weber Christian , Thiberge Sabine , Chuprinina Raisa , Tseneva Galina , Guiso Nicole 
Published: August 2003

ABSTRACT

We analyzed the
Bordetella pertussis
and
Bordetella parapertussis
isolates circulating in Saint Petersburg that were collected between 1998 and 2000 and compared them with isolates collected 40 years ago and Russian vaccine strains. The analysis involved serotyping, pulsed-field gel electrophoresis of chromosomal DNA after digestion with
Xba
I and
Spe
I, and sequencing of the
ptxS1
and
prn
genes, which encode the S1 subunit of the pertussis toxin and the major adhesin pertactin, respectively. The Russian isolates were classified in five of the six pulsed-field gel electrophoresis groups identified in other European countries. The
B. pertussis
isolates currently circulating in Saint Petersburg differed from the Russian whole-cell vaccine strains and the isolates collected in the prevaccine era. However, their repartition in the major pulsed-field gel electrophoresis groups was slightly different from that of isolates collected in countries that have had a high level of vaccine coverage for a long time, probably because the level of vaccine coverage in Saint Petersburg has increased only recently, after decreasing until the early 1990s. Most of the
B. parapertussis
isolates studied were similar to those circulating in France. However, some variants were observed, perhaps because
B. parapertussis
infections are more common in children in this area.
Virulence Genes and Neutral DNA Markers ofHelicobacter pyloriIsolates from Different Ethnic Communities of West Bengal, India
Authors: Datta Simanti , Chattopadhyay Santanu , Balakrish Nair G. , Mukhopadhyay Asish K. , Hembram Jabaranjan , Berg Douglas E. , Rani Saha Dhira , Khan Asis , Santra Amal , Bhattacharya S. K. , Chowdhury Abhijit 
Published: August 2003

ABSTRACTVirulence-associated genes and neutral DNA markers ofHelicobacter pyloristrains from the Santhal and Oroan ethnic minorities of West Bengal, India, were studied. These people have traditionally been quite separate from other Indians and differ culturally, genetically, and linguistically from mainstream Bengalis, whoseH. pyloristrains have been characterized previously.H. pyloriwas found in each of 49 study participants, although none had peptic ulcer disease, and was cultured from 31 of them. All strains carried thecagpathogenicity island and potentially toxigenic s1 alleles of vacuolating cytotoxin gene (vacA) and were resistant to at least 8 μg of metronidazole per ml. DNA sequence motifs invacAmid-region m1 alleles,cagA, and an informative insertion or deletion motif next tocagAfrom these strains were similar to those of strains from ethnic Bengalis. Three mobile elements, IS605, IS607, and ISHp608, were present in 29, 19, and 10%, respectively, of Santhal and Oroan strains, which is similar to their prevalence in BengaliH. pylori.Thus, there is no evidence that the gene pools ofH. pyloriof these ethnic minorities differ from those of Bengalis from the same region. This relatedness of strains from persons of different ethnicities bears on our understanding ofH. pyloritransmission between communities and genome evolution.
Culture of
Tropheryma whipplei
from Human Samples: a 3-Year Experience (1999 to 2002)
Authors: Fenollar Florence , Birg Marie-Laure , Gauduchon Valérie , Raoult Didier 
Published: August 2003

ABSTRACT

The culture of
Tropheryma whipplei
, the bacterium responsible for Whipple's disease, has been established only recently. Our objective is to describe, based on our experience, the culture of
T. whipplei
in HEL cells detected by immunofluorescence staining. Over 3 years, we received 18 samples for
T. whipplei
culture from 15 patients with Whipple's disease. Ten duodenal biopsy specimens from 10 patients with digestive symptoms were available. Five cardiac valves and three blood samples from five patients with endocarditis were also available. We correlated the results of culture with the type of sample and the culture procedure. Seven isolates were obtained, and three were subsequently established for more than 4 passages. The mean delay for the primary detection was 30 days. The bacterium was isolated more frequently from sterile specimens (5 of 8) than from duodenal biopsy specimens (2 of 10), but the difference (
P
= 0.14) was not significant. Decontamination of digestive samples containing colistin, amphotericin B, and cephalotin or ciprofloxacin did not impair the isolation of
T. whipplei
. The use of vancomycin precludes the primary isolation (7 of 12 versus 0 of 6;
P
= 0.08) and the establishment of
T. whipplei
(3 of 12 versus 0 of 6;
P
= 0.5). Omitting samples cultured with vancomycin, the establishment of the strain was significantly higher when antibiotics were prescribed for no more than 7 days (3 of 4 versus 0 of 8;
P
= 0.03). Our results demonstrate that samples must be collected within 1 week of an antibiotic regimen's initiation for the successful establishment of the bacterium.
Type III Secretion Genes in
Aeromonas salmonicida
subsp.
salmonicida
Are Located on a Large Thermolabile Virulence Plasmid
Authors: Stuber Katja , Burr Sarah E. , Braun Martin , Wahli Thomas , Frey Joachim 
Published: August 2003

ABSTRACT

Type III secretion genes in
Aeromonas salmonicida
subsp.
salmonicida
are located on a large plasmid of approximately 140 kb. Cultivation of this organism at elevated temperatures such as 25°C can, however, result in loss of this plasmid. This is accompanied by a loss of virulence for cultured fish cells.
Rapid Identification of
Candida glabrata
with a New Commercial Test, GLABRATA RTT
Authors: Freydiere A.-M. , Robert R. , Ploton C. , Marot-Leblond A. , Monerau F. , Vandenesch F. 
Published: August 2003

ABSTRACT

The GLABRATA RTT test (Fumouze Diagnostics, Levallois Perret, France) is based on the ability of
Candida glabrata
to hydrolyze trehalose but not maltose. It requires an inoculum of only four to six colonies, and the results are available within 20 min. We tested GLABRATA RTT with 330 stock isolates grown in subcultures on four different primary fungal isolation media and obtained a sensitivity of 94 to 98% (depending on the medium used) and a specificity of 97.3 to 98.6%. The false-positive results corresponded to
C. tropicalis
,
C. famata
, and
C. lusitaniae.
GLABRATA RTT thus offers rapid and reliable identification of
C. glabrata
.
Molecular Epidemiology of
Haemophilus influenzae
Type b Isolated from Children with Clinical Cases of Conjugate Vaccine Failures
Authors: Campos José , Aracil Belén , Román Federico , Pérez-Vázquez María 
Published: August 2003

ABSTRACT

We analyzed eight invasive
Haemophilus influenzae
strains isolated from individual children vaccinated appropriately for their ages. Five of the strains were type b and three were nontypeable strains. Children infected with nontypeable strains had a protective level of anti
-H. influenzae
type b antibodies, while only one of the children whose cases represented true vaccine failure did.
Detection of the Emerging Rotavirus G9 Serotype at High Frequency in Italy
Authors: Martella Vito , Terio Valentina , Del Gaudio Giuseppe , Gentile Mattia , Fiorente Paola , Barbuti Salvatore , Buonavoglia Canio 
Published: August 2003

ABSTRACT
Group A human rotavirus strains belonging to the unusual serotype G9 were detected at high frequency in stool specimens from infected children with acute diarrhea in Bari, Italy, during a 15-month survey from March 2001 to June 2002. This may signify a local reemergence of the G9 rotaviruses detected in Italy in the early and mid-1990s or may be related to the global emergence of G9 rotaviruses in recent years.
Severe
Serratia liquefaciens
Sepsis following Vitamin C Infusion Treatment by a Naturopathic Practitioner
Authors: Engelhart S. , Saborowski F. , Krakau M. , Scherholz-Schlösser G. , Heyer I. , Exner M. 
Published: August 2003

ABSTRACT

A 66-year-old female patient developed severe
Serratia liquefaciens
sepsis following vitamin C infusion treatment by a naturopathic practitioner. The clinical course of the infection was characterized by several complications, and the direct costs of the hospital stay amounted to about 40,000 Euro. Genotypically identical
S. liquefaciens
was isolated from the residue of the infusate given to the patient, as well as from the washbasin overflow and from two other infusion bottles. A careful inspection of the dispensing facilities and review of procedures used to prepare the infusate revealed several indications of poor hygiene. However, the source of contamination could not be fully clarified. This case report raises questions about the local facilities and personal qualifications required for naturopathic practitioners to conduct invasive procedures and demonstrates that lapses in hygiene can lead to severe morbidity and high cost.
Modeling ionic hydrogels swelling: Characterization of the non‐steady state
Authors: Traitel Tamar , Kost Joseph , Lapidot Smadar A. 
Published: August 2003

AbstractIonic hydrogels can be used as controlled release systems that respond to an external substrate or trigger by swelling or de‐swelling. One example is a glucose‐sensitive system for insulin‐controlled release based on pH‐sensitive hydrogel. To enhance understanding of non‐steady state swelling, and to facilitate design of specifications (e.g., glucose‐sensitivity) of the pH‐sensitive ionic hydrogel based on the copolymer poly (2‐hydroxyethyl methacrylate‐co‐N, N‐dimethylaminoethyl methacrylate) (poly (HEMA‐co‐DMAEMA)), we developed a mathematical compartmental model using the software SAAM II. Current analytical and computational methods focus on equilibrium swelling of hydrogels; although for many stimuli‐responsive hydrogel applications, the dynamic process is significant. We now report, using a combination of experimental data and kinetic analysis that in the poly (HEMA‐co‐DMAEMA) the rate of proton entry is governed by a different rate coefficient than water entry rate. The transport coefficient governing water uptake is dependent upon three variables: pH of external media, amine groups incorporated into the polymer, and crosslinking density of the polymer. An additional result is that swelling equilibrium is reached when all the amine groups are protonated. In this study we also demonstrate the predictive capability of the model for both interpolated and extrapolated data, and its use in design of future bench experiments. Uncovering these fundamental properties of pH‐sensitive hydrogels with the aid of a kinetic model suggests that the complexities of hydrogel research and development can be overcome by combining experimental and computational approaches. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 84: 20–28, 2003.