bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid Genotyping of Hepatitis C Virus by Primer-Specific Extension Analysis
Authors: Antonishyn Nick A. , Ast Vivian M. , McDonald Ryan R. , Chaudhary Rabindra K. , Lin Lisa , Andonov Anton P. , Horsman Greg B.
Published: October 2005

Quick and accurate genotyping of hepatitis C virus (HCV) is becoming increasingly important for clinical management of chronic infection and as an epidemiological marker. Furthermore, the incidence of HCV infection with mixed genotypes has clinical significance that is not addressed by most genotyping methods. We have developed a fluorescence-based genotyping assay called primer-specific extension analysis (PSEA) for the most prevalent HCV genotypes and have demonstrated the capacity of PSEA-HCV for detecting mixed-genotype HCV infections. PSEA-HCV detects genotype-specific sequence differences in the 5′ untranslated region of HCV in products amplified by the COBAS AMPLICOR HCV Test, v2.0. Simulated mixed HCV infection of plasma with RNase-resistant RNA controls demonstrates that PSEA-HCV can detect as many as five genotypes in one specimen. Furthermore, in dual-genotype simulations, PSEA-HCV can unequivocally detect both genotypes, with one genotype representing only 3.1% of the mixture (313/10,000 IU in starting plasma). Compared to INNO-LiPA HCV II, both assays determined the same genotype for 191/199 (96%) patient specimens (175 subtype and 16 genotype-only identifications). Following the initial evaluation, PSEA-HCV was used routinely to genotype HCV from patient specimens submitted to our laboratory (
n
= 312). Seventeen (5.4%) mixed infections were identified. The distribution of single-infection HCV genotypes in our population was 60.9% type 1 (
n
= 190), 12.8% type 2 (
n
= 40), 20.2% type 3 (
n
= 63), 0.3% type 4 (
n
= 1), and 0.3% other (
n
= 1). In conclusion, PSEA-HCV provides an inexpensive, high-throughput screening tool for rapid genotyping of HCV while reliably identifying mixed HCV infections.
Characterization of New Recombinant Noroviruses
Authors: Ambert-Balay K. , Bon F. , Le Guyader F. , Pothier P. , Kohli E.
Published: October 2005

Noroviruses are important etiologic agents of acute gastroenteritis and show great genetic diversity. To characterize more fully previously detected strains that could not be assigned unequivocally to one particular genotype based on the RNA polymerase, we have sequenced a region in the capsid gene and, in some cases, in the junction between open reading frame 1 (ORF1) and ORF2. The results allowed us to identify several recombinant noroviruses: GGIIb viruses were detected for the first time in France in August 2000 and then spread through France and to Europe during the following winter. Here we present the characterization of three other probable GII recombinants which showed different phylogenetic positions depending on their ORF1 and ORF2 sequences. Analysis of the region located between ORF1 and ORF2 by a nucleotide identity window search showed a sudden shift in similarities. Moreover, recombination breakpoints were identified upstream and downstream of the beginning of ORF2 by using a statistical test, thus confirming the involvement of this region in recombination. Unlike GGIIb, the three recombinants described here do not seem to have diffused widely in the community: one was found in a waterborne outbreak, and the other two were found in sporadic cases. Recombination is important for the evolution of RNA viruses and has already been described for noroviruses. Our results suggest that recombination is not a rare phenomenon among noroviruses, but not all these presumed recombinants that formed during RNA replication are able to spread widely.
Molecular Characterization of Hand Flora and Environmental Isolates in a Community Setting
Authors: Pancholi Preeti , Healy Mimi , Bittner Tracy , Webb Renee , Wu Fan , Aiello Allison , Larson Elaine , Latta Phyllis Della
Published: October 2005

We analyzed 69 bacterial isolates, comprising seven species of gram-negative bacterial rods and three species of coagulase-negative staphylococci, recovered from both the hands of caretakers and their environment in households sampled in upper Manhattan. Repetitive sequence-based PCR and dendrogram analysis were used to determine strain similarity. Greater than 25% of individual species of
Acinetobacter
,
Enterobacter
, and coagulase-negative staphylococci recovered from the hands and immediate environment within each household shared the same genotype. This study is the first to demonstrate the frequency of bacteria shared within community households. These strains may serve as potential reservoirs for either community- or hospital-acquired infections.
Comparison of Results of Voriconazole Disk Diffusion Testing for
Candida
Species with Results from a Central Reference Laboratory in the ARTEMIS Global Antifungal Surveillance Program
Authors: Pfaller M. A. , Boyken L. , Messer S. A. , Tendolkar S. , Hollis R. J. , Diekema D. J.
Published: October 2005

The accuracy of antifungal susceptibility testing is important for reliable resistance surveillance and for the clinical management of patients with serious infections. Our primary objective was to compare the results of voriconazole disk diffusion testing of
Candida
spp. performed by centers participating in the ARTEMIS program with disk diffusion and MIC results obtained by the central reference laboratory. A total of 2,934 isolates of
Candida
spp. were tested by CLSI disk diffusion and reference broth microdilution methods in the central reference laboratory. These results were compared to the results of disk diffusion testing performed in the 54 participating centers. All tests were performed and interpreted following CLSI recommendations, as follows: susceptible (S), MIC of ≤1 μg/ml (≥17 mm); susceptible dose dependent (SDD), MIC of 2 μg/ml (14 to 16 mm); and resistant (R), MIC of ≥4 μg/ml (≤13 mm). The overall categorical agreement between participant disk diffusion test results and reference laboratory MIC results was 94.1%, with 0.1% very major errors (VME) and 3.4% major errors (ME). The categorical agreement between disk diffusion test results obtained in the reference laboratory and the MIC test results was 99.0%. Likewise, good agreement was observed between participant disk diffusion test results and reference laboratory disk diffusion test results, with an agreement of 93.8%, 0.2% VME, and 3.4% ME. The disk diffusion test was reliable for detecting those isolates of
Candida
spp. that were characterized as resistant (MIC of ≥4 μg/ml) by MIC testing. External quality assurance data obtained by surveillance programs such as the ARTEMIS Global Antifungal Surveillance Program ensure the generation of useful surveillance data and result in the continued improvement of antifungal susceptibility testing practices.
Detection of
Aspergillus
Galactomannan Antigenemia To Determine Biological and Clinical Implications of Beta-Lactam Treatments
Authors: Bart-Delabesse Emmanuelle , Basile Maria , Al Jijakli Ahmad , Souville Didier , Gay Frédérick , Philippe Bruno , Bossi Philippe , Danis Martin , Vernant Jean-Paul , Datry Annick
Published: October 2005

Detection of
Aspergillus
galactomannan (GM) in serum with the Platelia
Aspergillus
enzyme immunoassay (EIA) is useful for diagnosing invasive aspergillosis. From May 2003 to November 2004, 65 patients who did not develop aspergillosis had at least two positive sera while receiving a beta-lactam treatment (GM index [GMI], ≥0.5). Of the 69 treatment episodes scored, 41 consisted of a beta-lactam other than piperacillin-tazobactam (
n
= 29), namely, amoxicillin-clavulanate (
n
= 25), amoxicillin (
n
= 10), ampicillin (
n
= 3), or phenoxymethylpenicillin (
n
= 2). In all cases, antigenemia became negative 24 h to 120 h upon stopping the antibiotic. Monitoring of 35 patients, including 26 with hematological malignancies, revealed three antigenemia kinetic patterns: each was observed with any drug regimen and consisted of a persistent GMI of >2.0 (65.7%), >0.5, and ≤1.5 (25.7%) or a variable GMI (14.3%) from the onset of antibiotic therapy. All available drug batches given to 26 patients cross-reacted with the EIA. Galactomannan titration in batches failed to predict the GM titers in the five patients studied at cumulative doses of ampicillin or amoxicillin-clavulanate, regardless of the time lapse between serum sampling and infusion period. Our results show that beta-lactams other than piperacillin-tazobactam may lead to false presumption of aspergillosis. The resulting kinetic patterns of GM antigenemia are variable, and sampling serum prior to the next beta-lactam dose may not decrease GMI below the threshold. Consequently, testing of suspected antibiotic batches remains the only indicator of possible false EIA positivity.
Evaluation of a Rapid Direct Assay for Identification of Bacteria and the
mecA
and
van
Genes from Positive-Testing Blood Cultures
Authors: Eigner U. , Weizenegger M. , Fahr A.-M. , Witte W.
Published: October 2005

We performed the first evaluation of a DNA strip assay (GenoType blood culture; Hain Lifescience, Nehren, Germany) for the detection of the most relevant bacterial sepsis pathogens directly from positive BACTEC blood culture bottles (Becton Dickinson, Heidelberg, Germany). The test comprises two panels, one for the direct species identification of important gram-positive cocci and the other for gram-negative rods. Additionally, detection of the
mecA
and the
van
genes are implemented. The GenoType assay was validated regarding its analytical sensitivity with blood cultures spiked with reference strains. Approximately 10
4
CFU per ml were detected. Analytical specificity was calculated with a test panel of 212 reference strains. Of the strains tested, 99% were correctly identified. Additionally, 279 consecutive blood cultures signaled positive by BACTEC were processed directly, in comparison to conventional methods. The GenoType assays were performed according to Gram stain morphology. A total of 243 (87.1%) of the 279 organisms isolated were covered by specific probes. A total of 152 organisms were gram-positive cocci, of which 148 (97.4%) were correctly identified by the GenoType assay. Ninety-one organisms were gram-negative rods, of which 89 (97.8%) were correctly identified. Concerning
mecA
gene detection, GenoType assay correctly detected 12 of 13 methicillin-resistant
Staphylococcus aureus
isolates. One
Enterococcus faecium
isolate with a positive
vanA
gene isolated was correctly differentiated by the assay. All results were available 4 h after the results of microscopic analysis. The evaluated GenoType blood culture assay showed fast and reliable results in detecting the most important sepsis pathogens and the
mecA
and
van
genes directly from positive blood culture bottles.
Use of Sequence Data Generated in the Bayer TruGene Genotyping Assay To Recognize and Characterize Non-Subtype-B Human Immunodeficiency Virus Type 1 Strains
Authors: Hirigoyen Diane L. , Cartwright Charles P.
Published: October 2005

Human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) gene sequences obtained during antiretroviral resistance testing with a commercial genotyping assay (TruGene; Bayer Corp.) were analyzed to assess the utility of these data for detecting and characterizing non-subtype-B HIV-1 strains. A total of 125 viral sequences obtained from patients believed to have acquired their HIV-1 infection in Africa were analyzed, of which 121 were determined to belong to non-B subtypes. Utilizing TruGene sequence data alone, 92 (76%) of these viruses could be subtyped by conventional phylogenetic analysis. The addition of supplemental RT sequence data enabled a further 28 (23.1%) viruses to be classified, while one (0.9%) sample could not be classified conclusively. Two internet-accessible databases that generate HIV-1 subtypes from PR and RT sequences (HIV-SEQ and Geno2Pheno) were also evaluated, and both achieved 88% concordance (106/120) with phylogenetic analysis. Non-subtype-B and B-subtype HIV-1 sequences could be readily discriminated by tallying silent polymorphisms listed on the TruGene research report. The mean number of silent polymorphisms in the non-B HIV-1 sequences identified in this study was 58.3 (95% confidence interval [CI], 41.1 to 75.5), compared with 20.7 (95% CI, 9.9 to 31.5) for the four subtype B viruses in the study cohort and 118 case-matched B-subtype controls. Sequence data generated in the TruGene HIV-1 genotyping assay could, therefore, provide a ready means of tracking the prevalence and identity of non-B subtypes in HIV-1-infected populations undergoing routine antiretroviral resistance testing.
Use of the DiversiLab System for Species and Strain Differentiation of
Fusarium
Species Isolates
Authors: Healy M. , Reece K. , Walton D. , Huong J. , Frye S. , Raad I. I. , Kontoyiannis D. P.
Published: October 2005

Advances in molecular typing of fusariosis would facilitate the study of its epidemiology. We tested 26 such isolates by the commercially available DiversiLab System. The system utilizes automated repetitive sequence-based PCR (rep-PCR) and web-based data analyses. rep-PCR dendrogram cluster analysis showed agreement with species sequence identification (elongation factor 1 alpha gene). Additionally, subtype differences within the same species were noted.
Ten Cases of
Actinobaculum schaalii
Infection: Clinical Relevance, Bacterial Identification, and Antibiotic Susceptibility
Authors: Reinhard Mark , Prag Jørgen , Kemp Michael , Andresen Keld , Klemmensen Belinda , Højlyng Niels , Sørensen Susan Hildebrand , Christensen Jens Jørgen
Published: October 2005

Nine of 10 strains of
Actinobaculum schaalii
caused urinary tract infections in predisposed individuals. Identification included 16S rRNA gene sequence analysis and use of the API Coryne and Rapid ID32A test systems.
A. schaalii
is easily overlooked due to its slow growth in ambient air and its resemblance to the normal bacterial flora on skin and mucosa.
Comparison of API 50 CH Strips to Whole-Chromosomal DNA Probes for Identification of
Lactobacillus
Species
Authors: Boyd Melinda A. , Antonio May A. D. , Hillier Sharon L.
Published: October 2005

The API 50 CH identification system was evaluated for the identification of 97 strains of commensal lactobacilli. This system agreed with the species-level identifications for none of the 7 reference strains and only 4 of 90 vaginal isolates identified using whole-chromosomal DNA probes.
Prospective Comparison of Cell Cultures and Nucleic Acid Amplification Tests for Laboratory Diagnosis of
Chlamydia trachomatis
Infections
Authors: Jespersen Deborah J. , Flatten Karen S. , Jones Mary F. , Smith Thomas F.
Published: October 2005

Specimens submitted in M5 medium for cell culture detection of
Chlamydia trachomatis
were tested by nucleic acid amplification testing (NAAT) and in cell cultures. Of 35 (genital) and 26 (nongenital) specimens positive for
C. trachomatis
, 21 and 14 specimens, respectively, were detected exclusively by NAAT. NAAT is significantly (
P
< 0.0001) more sensitive than cell culture and should be considered the new “gold standard” for the laboratory diagnosis of
C. trachomatis
infections.
Sequence-Based Typing of
adeB
as a Potential Tool To Identify Intraspecific Groups among Clinical Strains of Multidrug-Resistant
Acinetobacter baumannii
Authors: Huys Geert , Cnockaert Margo , Nemec Alexandr , Swings Jean
Published: October 2005

Sequence
analysis of an 850-bp fragment internal to the aspecific drug efflux
gene
adeB
revealed 11 sequence types (STs) among a collection
of 50 multidrug-resistant
Acinetobacter baumannii
(MDRAB)
strains, including members of pan-European clones I, II, and III. The
delineation of STs conformed with the intraspecific grouping of these
strains previously determined by different DNA fingerprinting methods.
Larger strain collections need to be screened to further explore the
potential of sequence-based
adeB
typing as a universal tool
for the monitoring of MDRAB
clones.
Single Multiplex PCR Assay To Identify Simultaneously the Six Categories of Diarrheagenic
Escherichia coli
Associated with Enteric Infections
Authors: Vidal Maricel , Kruger Eileen , Durán Claudia , Lagos Rosanna , Levine Myron , Prado Valeria , Toro Cecilia , Vidal Roberto
Published: October 2005

We designed a multiplex PCR for the detection of all categories of diarrheagenic
Escherichia coli
. This method proved to be specific and rapid in detecting virulence genes from Shiga toxin-producing (
stx
1
,
stx
2
, and
eae
), enteropathogenic (
eae
and
bfp
), enterotoxigenic (
stII
and
lt
), enteroinvasive (
virF
and
ipaH
), enteroaggregative (
aafII
), and diffuse adherent (
daaE
)
Escherichia coli
in stool samples.
Endophthalmitis Caused by
Fusarium proliferatum
Authors: Ferrer Consuelo , Alio Jorge , Rodriguez Alejandra , Andreu Mariano , Colom Francisca
Published: October 2005

Fusarium proliferatum
caused endophthalmitis after cataract surgery. Diagnosis was established by classical microbiology and molecular biology methods (PCR and DNA typing). The treatment with local amphotericin B, oral ketoconazole, and topical natamycin was successful.
Bacteremia Caused by a Metronidazole-Resistant
Prevotella
sp. Strain
Authors: Mory Francine , Carlier Jean-Philippe , Alauzet Corentine , Thouvenin Maxime , Schuhmacher Hélène , Lozniewski Alain
Published: October 2005

Metronidazole resistance among
Prevotella
spp. is rare. We report here the first case of bacteremia due to a high-level metronidazole-resistant
Prevotella
sp. responsible for treatment failure.
First Case of Osteomyelitis Due to
Shewanella algae
Authors: Botelho-Nevers E. , Gouriet F. , Rovery C. , Paris P. , Roux V. , Raoult D. , Brouqui P.
Published: October 2005

Shewanella
spp. are infrequently recovered from clinical specimens. We report here on the first case of osteomyelitis due to
Shewanella algae
. This bacterium, at first misidentified by phenotypic tests as
Shewanella putrefaciens
, was subsequently identified correctly as
S. algae
by 16S rRNA gene sequence analysis.
First Report of
Salmonella enterica
Serotype Panama Meningitis Associated with Consumption of Contaminated Breast Milk by a Neonate
Authors: Chen Te-Li , Thien Peck-Foong , Liaw Shu-Chin , Fung Chang-Phone , Siu L. K.
Published: October 2005

Salmonella enterica
serotype Panama is capable of causing severe infection in children and is often transmitted via contaminated food. Here, we present the first documented case of serotype Panama infection that was acquired through the consumption of contaminated breast milk. The mother excreted the organism asymptomatically for at least 2 weeks.
VACUUM QUANTUM EFFECT FOR PARALLEL PLATES MOVING BY UNIFORM ACCELERATION IN STATIC DE SITTER SPACE
Authors: SETARE M. R.
Published: October 2005

The Casimir forces on two parallel plates moving by uniform proper acceleration in static de Sitter background due to conformally coupled massless scalar field satisfying Dirichlet boundary conditions on the plates is investigated. Static de Sitter space is conformally related to the Rindler space, as a result we can obtain vacuum expectation values of energy–momentum tensor for conformally invariant field in static de Sitter space from the corresponding Rindler counterpart by the conformal transformation.
HYPER-OPERATORS FOR NONCOMMUTATIVE CALCULUS IN QUANTUM PHYSICS
Authors: LI GENQUAN , WU ZHAOYAN
Published: October 2005

In quantum physics, one has to deal with linear operator valued functions of a linear operator argument. The derivatives and higher derivatives of such functions are no longer linear operators on state vector spaces. They are hyper-operators of various kinds. Two kinds of notations for hyper-operators are presented. We show that by using them, one can easily write down these hyper-operators, and the calculation on hyper-operators can be reduced to the calculation on ordinary operators. The hyper-operators are shown to be a powerful tool for noncommutative calculus in quantum physics.
TACHYON DYNAMICS IN OPEN STRING THEORY
Authors: SEN ASHOKE
Published: October 2005

In this review we describe our current understanding of the properties of open string tachyons on an unstable D-brane or brane–antibrane system in string theory. The various string theoretic methods used for this study include techniques of two-dimensional conformal field theory, open string field theory, boundary string field theory, noncommutative solitons, etc. We also describe various attempts to understand these results using field theoretic methods. These field theory models include toy models like singular potential models and p-adic string theory, as well as more realistic version of the tachyon effective action based on Dirac–Born–Infeld type action. Finally we study closed string background produced by the "decaying" unstable D-branes, both in the critical string theory and in the two-dimensional string theory, and describe the open string completeness conjecture that emerges out of this study. According to this conjecture the quantum dynamics of an unstable D-brane system is described by an internally consistent quantum open string field theory without any need to couple the system to closed strings. Each such system can be regarded as a part of the "hologram" describing the full string theory.
PHASE DIAGRAM OF DOUBLE EXCHANGE MODEL WITH ANTIFERROMAGNETIC COUPLING FOR LOCALIZED t2g SPINS IN ONE DIMENSION REVISITED
Authors: ZHANG Q. L.
Published: October 2005

The phase diagram of the single-orbit double exchange model for manganites with ferromagnetic Hund coupling between mobile eg electrons and spins of localized t2g electrons as well as antiferromagnetic superexchange coupling between t2g electrons is investigated with a large scale Monte Carlo simulation in one dimension. The phase boundary is determined based on the internal energy, the electron density and the structure factor. In particular, low-temperature properties at quarter filling are studied in detail.
QUANTUM DYNAMICS OF WAVE PACKET IN HARMONIC POTENTIAL
Authors: HU ZHAN-NING , KIM CHANG SUB
Published: October 2005

In this paper, the analytic solution of the time-dependent Schrödinger equation is obtained for the wave packet in two-dimensional oscillator potential. The quantum dynamics of the wave packet is investigated based on this analytic solution. To our knowledge, this is the first time we solve, analytically and exactly this kind of time-dependent Schrödinger equation in a two-dimensional system, in which the Gaussian parameters satisfy the coupled nonlinear differential equations. The coherent states and their rotations of the system are discussed in detail. We find also that this analytic solution includes four kinds of modes of the evolutions for the wave packets: rigid, rotational, vibrational states and a combination of the rotation and vibration without spreading.
Renal angiotensin II AT2receptors promote natriuresis in streptozotocin-induced diabetic rats
Authors: Hakam Amer C. , Siddiqui Athar H. , Hussain Tahir
Published: October 2005

Angiotensin II AT2receptors have been implicated to play a role in the regulation of renal/cardiovascular functions under pathological conditions. The present study is designed to investigate the function of the AT2receptors on renal sodium excretion and AT2receptor expression in the cortical membranes of streptozotocin (STZ)-induced diabetic rats. The STZ treatment led to a significant weight loss, hyperglycemia, and decrease in plasma insulin levels compared with control rats. STZ-induced diabetic rats had significantly elevated basal urine flow, urinary sodium excretion rate (UNaV), urinary fractional sodium excretion, and urinary cGMP compared with control rats. Infusion of PD-123319, an AT2receptor antagonist, caused a significant decrease in UNaV (μmol/min) in STZ-induced diabetic rats (1 ± 0.09 vs. 0.45 ± 0.1) but not in control rats (0.35 ± 0.05 vs. 0.4 ± 0.07). The decrease in UNaV was associated with a significant decrease in urinary cGMP levels (pmol/min) in STZ-induced diabetic rats (21 ± 2 vs. 10 ± 0.8) but not in control rats (11.75 ± 3 vs. 12.6 ± 2). The infusion of PD-123319 did not alter glomerular filtration rate (STZ: 0.3 ± 0.02 vs. 0.25 ± 0.03; control: 1.4 ± 0.05 vs. 1.5 ± 0.09 ml/min) or mean arterial pressure (STZ: 82 ± 3 vs. 79 ± 3.5; control: 90 ± 4 vs. 89 ± 4 mmHg), suggesting a tubular effect of the drug. Western blot analysis using an AT2receptor antibody revealed a significantly enhanced expression of the AT2receptor protein (∼45 kDa) in brush-border (∼50-fold) and basolateral membranes (∼80-fold) of STZ-induced diabetic compared with control rats. In conclusion, our data suggest that the tubular AT2receptors in diabetic rats are profoundly enhanced and possibly via a cGMP pathway promote sodium excretion in this model of diabetes.
TGF-β1 induces IL-8 and MCP-1 through a connective tissue growth factor-independent pathway
Authors: Qi Weier , Chen Xinming , Polhill Tania S. , Sumual Siska , Twigg Stephen , Gilbert Richard E. , Pollock Carol A.
Published: October 2005

Transforming growth factor-β1 (TGF-β1) functions as an important immunomodulatory cytokine in human kidney. Evidence suggests that connective tissue growth factor (CTGF) is an important downstream mediator of the profibrotic effects of TGF-β1. However, the role of CTGF in TGF-β1-induced chemokine production remains unknown. This study was undertaken to determine whether CTGF is involved in mediating TGF-β1-induced chemokine production in renal proximal tubular (HK-2) cells. Interleukin-8 (IL-8) and macrophage chemoattractant protein-1 (MCP-1) were measured. TGF-β1 induced an increase in IL-8 and MCP-1 (both P < 0.05) compared with control levels. CTGF was effectively silenced using small interference RNA (siRNA) in HK-2 cells. RT-PCR and real-time PCR confirmed a 94% reduction in CTGF mRNA. In the CTGF-silenced cells, TGF-β1-stimulated IL-8 and MCP-1 secretion was not altered compared with control cells. Similarly, basal secretion of IL-8 and MCP-1 was not changed in CTGF-silenced cells. The direct effect of CTGF (20, 200, and 400 ng/ml) on IL-8 and MCP-1 was assessed at 24-, 48-, and 72-h time points and no stimulation was observed. Our studies further demonstrate that in the CTGF gene-silenced cells, CTGF partially mediates TGF-β1-induced fibronectin and collagen IV secretion. These data suggest that TGF-β1 induced IL-8 and MCP-1 via CTGF-independent pathway. TGF-β mediates both fibrosis and chemokine production in the proximal tubule of the kidney. However, CTGF plays a more specific role as a downstream mediator of TGF-β1-induced fibrosis.
Theta Oscillations in Human Cortex During a Working-Memory Task: Evidence for Local Generators
Authors: Raghavachari S. , Lisman J. E. , Tully M. , Madsen J. R. , Bromfield E. B. , Kahana M. J.
Published: October 2005

Cortical theta appears important in sensory processing and memory. Intracanial electrode recordings provide a high spatial resolution method for studying such oscillations during cognitive tasks. Recent work revealed sites at which oscillations in the theta range (4–12 Hz) could be gated by a working-memory task: theta power was increased at task onset and continued until task offset. Using a large data set that has now been collected (10 participants/619 recording sites), we have sufficient sampling to determine how these gated sites are distributed in the cortex and how they are synchronized. A substantial fraction of sites in occipital/parietal (45/157) and temporal (23/280) cortices were gated by the task. Surprisingly, this aspect of working-memory function was virtually absent in frontal cortex (2/182). Coherence measures were used to analyze the synchronization of oscillations. We suspected that because of their coordinate regulation by the working-memory task, gated sites would have synchronized theta oscillations. We found that, whereas nearby gated sites (<20 mm) were often but not always coherent, distant gated sites were almost never coherent. Our results imply that there are local mechanisms for the generation of cortical theta.
Prefrontal Activity During Serial Probe Reproduction Task: Encoding, Mnemonic, and Retrieval Processes
Authors: Inoue Masato , Mikami Akichika
Published: October 2005

To study the prefrontal neuronal mechanism for the encoding and mnemonic processing of multiple objects, the order of object presentation, and the retrieval of an object among objects in the working memory, we recorded neuronal activity from the lateral prefrontal cortex while two monkeys performed the serial probe reproduction task. In the task, two objects (C1 and C2) were presented sequentially interleaved with a delay (D1) period, and after the second delay (D2) period, a color cue was presented. Monkeys were trained to select one target object on the basis of the color stimulus. During the C1 and C2 periods, we found responses that depended on the order of presentation (order-selective response). During the D1 and/or D2 periods, two-thirds of the neurons with object-selective delay-period activity showed order-selective activity coding either C1 or C2. Neurons with larger response magnitudes during the C2 period showed order-selective delay-period activity during the D2 period. These order-selective responses during the C2 period could also contribute to order-selective delay-period activity, and order-selective delay-period activity during the D1 and D2 periods could play an essential role in storing information on both the object and the temporal order of presentation. During the color cue period, two-thirds of the neurons with responses showed target object selectivity (CT and T responses), although the target object was not presented during this period. The CT and T responses could play a critical role in the retrieval of an item among various items in the working memory.
Control of plant-parasitic nematodes with extracts of Quillaja saponaria
Authors: Magunacelaya Juan Carlos , Martín Ricardo San
Published: October 2005

Aqueous extracts of the tree Quillaja saponaria Molina, containing triterpenoid saponins, polyphenols, salts and sugars, were tested against the most important plant-parasitic nematodes present in Chile: Xiphinema index, X. americanum s.l., Meloidogyne hapla, M. ethiopica, Pratylenchus thornei, Tylenchorhynchus sp., Criconemoides xenoplax and Helicotylenchus sp. Three different products were tested in the laboratory: i) QL 1000® (whole extract containing saponin and non-saponin fractions); ii) QL ULTRA® (saponin fraction); and iii) QL NS® (non-saponin fraction). The results showed that QL 1000® had important nematicidal effects at economically attractive doses (e.g., 100 ppm). When used separately, QL ULTRA® and QL NS® had minimum nematicidal effects. However, the combined use of both products gave similar results to QL 1000®, suggesting a synergy between the saponin and non-saponin fractions. Based on this, QL 1000® was tested in commercial vineyards and table grapes in the Central region of Chile. The use of 30 l ha−1 showed a similar control and fruit yields to synthetic chemical nematicides.
The Thelastomatoidea (Nematoda: Oxyurida) of two sympatric Panesthiinae (Insecta: Blattodea) from southeastern Queensland, Australia: taxonomy, species richness and host specificity
Authors: Schneider Margaret , Cribb Tom , Jex Aaron ,   Harley
Published: October 2005

The thelastomatoid fauna of two species of wood-burrowing cockroach (Blattodea, Blaberidae), Panesthia cribrata and Panesthia tryoni tryoni, from Lamington National Park, Australia, is described. The following eight new species and three new genera of thelastomatid are proposed: Bilobostoma exerovulva n. g., n. sp.; Cordonicola gibsoni n. sp.; Coronostoma australiae n. sp.; Desmicola ornata n. sp.; Hammerschmidtiella hochi n. sp.; Malaspinanema goateri n. g., n. sp.; Travassosinema jaidenae n. sp.; and Tsuganema cribratum n. g., n. sp. Additional data are given for Blattophila sphaerolaima and Leidynemella fusiformis. Of the 11 species reported, nine were found in P. cribrata and ten in P. tryoni tryoni. Such levels of thelastomatoid species richnessness in single host species are exceptional. Only the mole cricket, Gryllotalpa africana (23), and the domestic cockroach, Periplaneta americana (20), have higher reported richness. Three species, T. jaidenae, C. australiae and D. ornata, were found either exclusively or significantly more prevalently in P. tryoni tryoni than in P. cribrata. Species of Travassosinema, Coronostoma and Desmicola have been found previously only in millipedes (Diplopoda), a fact that suggests that there is a greater degree of niche overlap between P. tryoni tryoni and millipedes than for P. cribrata.
Comparison of the in-soil hatching responses of Globodera rostochiensis and G. pallida in the presence and absence of the host potato crop cv. British Queen
Authors: Devine Ken , Ryan Aileen
Published: October 2005

Experiments were conducted in a field in Co. Cork, Ireland, to investigate the hatching behaviour of the two potato cyst nematode (PCN) species, Globodera rostochiensis and G. pallida, in soil in the presence and absence of a host potato crop cv. British Queen. In order to compare the hatching behaviour of the two PCN species in the field, standardised populations of each PCN species (produced under identical conditions for the two previous generations and extracted without desiccation) were inserted into the field in tissue-embedding cassettes by means of a novel 'harpoon' insertion tool. Inserting cassettes of both PCN species at different distances from host potato plants and destructively sampling the contents of the cassettes over the first 8 weeks after plant emergence revealed that there was no significant difference in the hatch of either PCN species around the host plant. Hatches in excess of 80% for both PCN species were recorded 8 weeks after plant emergence over a range of depths (10-40 cm) and distances (10-50 cm) around the host potato plants. Substantial hatches of G. rostochiensis (82%) and G. pallida (88%) were also recorded at a depth of 20 cm in the furrow at harvesting. Monitoring the rate of spontaneous hatching of G. rostochiensis and G. pallida in the absence of host potato plants over the spring and summer months (a 20-week period) revealed that there was a significant difference in the rate of spontaneous hatching between the two PCN species, with G. rostochiensis juveniles hatching in greater numbers over the first 14 weeks than G. pallida juveniles. However, by mid-August the mean spontaneous hatch for both PCN species within the top 30 cm of soil was found to be 37%.
Enhancing taxonomic resolution: distribution dependent genetic diversity in populations of Meloidogyne
Authors: Navas Alfonso , Flores-Romero Pilar
Published: October 2005

Root-knot nematodes (Meloidogyne) are one of the most damaging agricultural pests. The polyploid apomictic M. arenaria, M. javanica and M. incognita are particularly ubiquitous and exhibit an extreme polyphagy. The taxonomic position of these three species remains unclear, as does the phylogenetic relationships between them. To characterise phenotype variants among these three species, allozyme electrophoresis (α-EST, MDH, CAT, GPI, DIA, GOT, and SOD) was performed in populations from the Iberian Peninsula. A total of 50 multilocus enzyme electrophoresis (MLEE) phenotype variants were detected of which, according to the esterase pattern, 24 corresponded to M. arenaria, 15 to M. javanica and 11 to M. incognita. The phylogenetic relationships of these 50 MLEE variants were studied following the Neighbour-Joining (NJ) distance method based on an allelic frequencies matrix built using two different methodologies. In addition, Maximum-Parsimony (MP) and Maximum-Likelihood (ML) phylogenetic methods were done in order to corroborate the phylogenies obtained. Our results showed a great disparity in the NJ trees obtained, thus indicating that the monophyly of the parthenogenetic Meloidogyne spp. would seem to depend on the methodology used. Evolutionary and epidemiological implications of the recovered phylogenies are discussed.
Identification of Meloidogyne spp. from North East Libya and comparison of their inter- and intra-specific genetic variation using RAPDs
Authors: Phillips Mark , Adam Mohamed , Blok Vivian
Published: October 2005

Four techniques, i.e., perineal patterns, isozymes, specific sequence characterised amplified region-polymerase chain reaction (SCAR-PCR) and random amplified polymorphic DNA (RAPD), were compared for the identification of species of root-knot nematode (RKN) from Libya. The RAPD technique proved superior for species diagnosis. A population from Massa that could not, because of atypical patterns, be identified using either perineal patterns or isozyme phenotypes, showed amplification patterns consistent with those of M. incognita. A new esterase phenotype is described for this population. Single egg mass lines from two other locations, Elhamma and Durnah, were identified as M. javanica, whereas those from Aun Mare were identified as M. incognita. RAPDs were used to examine the relationships between the Libyan isolates and isolates of Meloidogyne spp. from elsewhere. This technique revealed differences in the Libyan isolates of M. incognita that distinguished them from isolates from other geographic origins. The work demonstrates the potential to utilise the RAPD technique in an integrated programme to control RKN.
Some Effects of Model Resolution on Simulated Gravity Waves Generated by Deep, Mesoscale Convection
Authors: Lane Todd P. , Knievel Jason C.
Published: October 2005

Over the past decade, numerous numerical modeling studies have shown that deep convective clouds can produce gravity waves that induce a significant vertical flux of horizontal momentum. Such studies used models with horizontal grid spacings of O(1 km) and produced strong gravity waves with horizontal wavelengths greater than about 20 km. This paper is an examination of how simulated gravity waves and their momentum flux are sensitive to model resolution. It is shown that increases in horizontal resolution produce more power in waves with shorter horizontal wavelengths. This change in the gravity waves’ spectra influences their vertical propagation. In some cases, gravity waves that were vertically propagating in coarse simulations become vertically trapped in fine simulations, which strongly influences the vertical flux of horizontal momentum.
Downward Wave Propagation on the Polar Vortex
Authors: Scott R. K. , Dritschel D. G.
Published: October 2005

This paper considers the propagation of waves on the edge of a stratospheric polar vortex, represented by a three-dimensional patch of uniform potential vorticity in a compressible quasigeostrophic system. Waves are initialized by perturbing the vortex from axisymmetry in the center of the vortex, and their subsequent upward and downward propagation is measured in terms of a nonlinear, pseudomomentum-based wave activity. Under conditions typical of the winter stratosphere, the dominant direction of wave propagation is downward, and wave activity accumulates in the lower vortex levels. The reason for the preferred downward propagation arises from a recent result of Scott and Dritschel, which showed that the three-dimensional Green’s function in the compressible system contains an anisotropy that causes a general differential rotation in a finite volume vortex. The sense of the differential rotation is to stabilize the upper vortex and destabilize the lower vortex. This mechanism is particularly interesting in view of recent interest in the downward influence of the stratosphere on the troposphere and also provides a possible conservative, balanced explanation of the formation of the robust dome plus annulus potential vorticity structure observed in the upper stratosphere.
The Coupled Stratosphere–Troposphere Response to Impulsive Forcing from the Troposphere
Authors: Reichler Thomas , Kushner Paul J. , Polvani Lorenzo M.
Published: October 2005

A simple atmospheric general circulation model (GCM) is used to investigate the transient response of the stratosphere–troposphere system to externally imposed pulses of lower-tropospheric planetary wave activity. The atmospheric GCM is a dry, hydrostatic, global primitive-equations model, whose circulation includes an active polar vortex and a tropospheric jet maintained by baroclinic eddies. Planetary wave activity pulses are generated by a perturbation of the solid lower boundary that grow and decay over a period of 10 days. The planetary wave pulses propagate upward and break in the stratosphere. Subsequently, a zonal-mean circulation anomaly propagates downward, often into the troposphere, at lags of 30–100 days. The evolution of the response is found to be dependent on the state of the stratosphere–troposphere system at the time the pulse is generated. In particular, on the basis of a large ensemble of these simulations, it is found that the length of time the signal takes to propagate downward from the stratosphere is controlled by initial anomalies in the zonal-mean circulation and in the zonal-mean wave drag. Criteria based on these anomaly patterns can be used, therefore, to predict the long-term surface response of the stratosphere–troposphere system to a planetary wave pulse up to 90 days after the pulse is generated. In an independent test, it is verified that the initial states that most strongly satisfy these criteria respond in the expected way to the lower-tropospheric wave activity pulse.
Drizzle in Stratiform Boundary Layer Clouds. Part II: Microphysical Aspects
Authors: Wood R.
Published: October 2005

This is the second of two observational papers examining drizzle in stratiform boundary layer clouds. Part I details the vertical and horizontal structure of cloud and drizzle parameters, including some bulk microphysical variables. In this paper, the focus is on the in situ size-resolved microphysical measurements, particularly of drizzle drops (r > 20 μm). Layer-averaged size distributions of drizzle drops within cloud are shown to be well represented using either a truncated exponential or a truncated lognormal size distribution. The size-resolved microphysical measurements are used to estimate autoconversion and accretion rates by integration of the stochastic collection equation (SCE). These rates are compared with a number of commonly used bulk parameterizations of warm rain formation. While parameterized accretion rates agree well with those derived from the SCE initialized with observed spectra, the autoconversion rates seriously disagree in some cases. These disagreements need to be addressed in order to bolster confidence in large-scale numerical model predictions of the aerosol second indirect effect. Cloud droplet coalescence removal rates and mass and number fall rate relationships used in the bulk microphysical schemes are also compared, revealing some potentially important discrepancies. The relative roles of autoconversion and accretion are estimated by examination of composite profiles from the 12 flights. Autoconversion, although necessary for the production of drizzle drops, is much less important than accretion throughout the lower 80% of the cloud layer in terms of the production of drizzle liquid water. The SCE calculations indicate that the autoconversion rate depends strongly upon the cloud droplet concentration Nd such that a doubling of Nd would lead to a reduction in autoconversion rate of between 2 and 4.

Radar reflectivity–precipitation rate (Z–R) relationships suitable for radar use are derived and are shown to be significantly biased in some cases by the undersampling of large (r > 200 μm) drops with the 2D-C probe. A correction based upon the extrapolation to larger sizes using the exponential size distribution changes the Z–R relationship, leading to the conclusion that consideration should be given to sampling issues when examining higher moments of the drop size distribution in drizzling stratiform boundary layer clouds.
The Influence of Uniform Flow on Tropical Cyclone Intensity Change
Authors: Kwok Joey H. Y. , Chan Johnny C. L.
Published: October 2005

The influence of a uniform flow on the structural changes of a tropical cyclone (TC) is investigated using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5). Idealized experiments are performed on either an f plane or a β plane. A strong uniform flow on an f plane results in a weaker vortex due to the development of a vertical wind shear induced by the asymmetric vertical motion and a rotation of upper-level anticyclone. The asymmetric vertical motion also reduces the secondary circulation of the vortex.

On a β plane with no flow, a broad anticyclonic flow is found to the southeast of the vortex, which expands with time. Similar to the f-plane case, asymmetric vertical motion and vertical wind shear are also found. This beta-induced shear weakens the no-flow case significantly relative to that on an f plane. When a uniform flow is imposed on a β plane, an easterly flow produces a stronger asymmetry whereas a westerly flow reduces it. In addition, an easterly uniform flow tends to strengthen the beta-induced shear whereas a westerly flow appears to reduce it by altering the magnitude and direction of the shear vector. As a result, a westerly flow enhances TC development while an easterly flow reduces it.

The vortex tilt and midlevel warming found in this study agree with the previous investigations of vertical wind shear. A strong uniform flow with a constant f results in a tilted and deformed potential vorticity at the upper levels. For a variable f, such tilting is more pronounced for a vortex in an easterly flow, while a westerly flow reduces the tilt. In addition, the vortex tilt appears to be related to the midlevel warming such that the warm core in the lower troposphere cannot extent upward, which leads to the subsequent weakening of the TC.
Diagnosis of Subtropical Humidity Dynamics Using Tracers of Last Saturation
Authors: Galewsky Joseph , Sobel Adam , Held Isaac
Published: October 2005

A technique for diagnosing the mechanisms that control the humidity in a general circulation model (GCM) or observationally derived meteorological analysis dataset is presented. The technique involves defining a large number of tracers, each of which represents air that has last been saturated in a particular region of the atmosphere. The time-mean tracer fields show the typical pathways that air parcels take between one occurrence of saturation and the next. The tracers provide useful information about how different regions of the atmosphere influence the humidity elsewhere. Because saturation vapor pressure is a function only of temperature and assuming mixing ratio is conserved for unsaturated parcels, these tracer fields can also be used together with the temperature field to reconstruct the water vapor field. The technique is first applied to an idealized GCM in which the dynamics are dry and forced using the Held–Suarez thermal relaxation, but the model carries a passive waterlike tracer that is emitted at the surface and lost due to large-scale condensation with zero latent heat release and no condensate retained. The technique provides an accurate reconstruction of the simulated water vapor field. In this model, the dry air in the subtropical troposphere is produced primarily by isentropic transport and is moistened somewhat by mixing with air from lower levels, which has not been saturated since last contact with the surface. The technique is then applied to the NCEP–NCAR reanalysis data from December–February (DJF) 2001/02, using the offline tracer transport model MATCH. The results show that the dryness of the subtropical troposphere is primarily controlled by isentropic transport of very dry air by midlatitude eddies and that diabatic descent from the tropical upper troposphere plays a secondary role in controlling the dryness of the subtropics.