bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of forest grazing as a management practice to utilize and control Miscanthus sinensis in a young tree plantation in southern Kyushu, Japan
Authors: Hirata Masahiko , Hasegawa Nobumi , Nogami Kangoro , Sonoda Tatsunobu 
Published: September 2007

Abstract Miscanthus sinensis, a tall cespitose warm‐season perennial grass, occurs widely in tree plantations across Japan as a major weed. A 4‐year grazing trial was conducted in a young Chamaecyparis obtusa (an evergreen conifer) plantation in south‐western Japan, in an effort to evaluate forest grazing as a management practice to utilize and control M. sinensis and to deepen a mechanistic understanding of the responses of this grass to herbivory. The plantation was continuously stocked by Japanese Black cattle during the grazing season from May–November (July–November in the first year) at rates of 0.38–0.63 animals ha−1. M. sinensis was always the major species selected by animals, with most of the plants (80–90%) in the paddocks being defoliated during the grazing season. Reflecting these, M. sinensis plants declined with time under grazing, mainly in shoot number per tuft and partly in leaf appearance rate and the weight of the youngest fully expanded leaf, leading to a drastic decrease in production of leaves (laminae) as a photosynthetic organ and a main feed component for animals. Animals did little fatal damage to C. obtusa trees. Performance of animals was acceptable for cows that had experienced forest grazing in preceding years, but needed improvement for inexperienced heifers and calves. The results demonstrate the potential value of cattle grazing in utilizing and controlling M. sinensis in young tree plantations, which enables multifunctional land use linking forest and animal industries. Further studies are necessary to explore the optimum grazing intensity that balances effective control and extended utilization of the grass.
Development and public release of a comprehensive hepatitis virus database
Authors: Shin‐i Tadasu , Tanaka Yasuhito , Tateno Yoshio , Mizokami Masashi 
Published: September 2007

Aim:  Currently, approximately 44 000 hepatitis C virus (HCV), 11 000 hepatitis B virus (HBV), and 1600 hepatitis E virus (HEV) sequences are available at the International Nucleotide Sequence Database Collaboration (INSDC, previously known as DDBJ/EMBL/GenBank), and the number of these virus sequences is growing rapidly. However, since INDSC is not specialized to hepatitis viruses, it is difficult to retrieve information of virological or clinical interests from it. Thus, it is quite worthwhile to construct a specialized database for the hepatitis virus sequences and to make it accessible to researchers worldwide.Methods:  We developed a WWW‐based database hepatitis virus database (HVDB), which contains all the HCV, HBV, and HEV sequences available at INSDC. In the HVDB, all piece sequences obtained from INSDC are arranged to the genomesequence of each virus. Also given in the database are the phylogenetic relationships of each locus on the genome among variants for each virus.Results:  Users of the database can easily retrieve entries (sequences with annotations) of the specific genotype by referring to the phylogenetic relationships or those of specific loci by referring to the genome map information. HVDB provides users with a tool for phylogenetic analysis that can be used in combination with the data retrieval tools.Conclusion:  The latest release is publicly accessible at the HVDB website: http://s2as02.genes.nig.ac.jp.
Forced
Convective Heat Transfer in Parallel Flow Multilayer
Microchannels
Authors: Saidi M.
H. , Khiabani Reza
H. 
Published: September 2007

Abstract
In this paper, the effect of increasing the number of layers on improving the thermal performance of microchannel heat sinks is studied. In this way, both numerical and analytical methods are utilized. The analytical method is based on the porous medium assumption. Here, the modified Darcy equation and the energy balance equations are used. The method has led to an analytical expression presenting the average dimensionless temperature field in the multilayer microchannel heat sink. The effects of different parameters such as aspect ratio, porosity, channel width, and the solid properties on the thermal resistance are described. The results for single layer and multilayer heat sinks are compared to show the effectiveness of using multilayer microchannels.
Determination of the Fractal Scaling Parameter From Simulated
Fractal-Regular Surface Profiles Based on the Weierstrass-Mandelbrot
Function
Authors: Wang Shao , Shen Ji , Kin Chan Wai 
Published: September 2007

Abstract
A fractal dimension and a fractal roughness parameter are usually used to characterize a fractal surface. For a fractal-regular surface, a fractal domain length is also included. Such a formulation is based on an approximation using a constant value of the fractal scaling parameter that represents the ratio of the spatial frequencies of adjacent harmonic components in the Weierstrass–Mandelbrot (W-M) function. Although there were some reasons for assuming a constant value of 1.5 for the fractal scaling parameter, it is still left more or less arbitrary to adopt this assumption in fractal modeling of solid contact. In the present study, the fractal scaling parameter was treated as a variable rather than a constant by using a form of the W-M function with randomized phases based on a random walk formulation. A simple numerical scheme with clear graphical interpretation was developed to determine the value of the fractal scaling parameter. The fractal dimension, fractal roughness parameter, and fractal scaling parameter were all recovered with reasonable accuracy from numerically generated surface profiles.
Use of Antibody Avidity Assays for Diagnosis of Severe Acute Respiratory Syndrome Coronavirus Infection
Authors: Chan K. H. , Sonnenberg K. , Niedrig M. , Lam S. Y. , Pang C. M. , Chan K. M. , Ma S. K. , Seto W. H. , Peiris J. S. M. 
Published: September 2007

ABSTRACT
An indirect immunofluorescent assay (Euroimmun AG, Luebeck, Germany) was used to investigate the avidity of immunoglobulin G (IgG), IgM, IgA, and total Ig (IgGAM) antibody responses to severe acute respiratory syndrome coronavirus (SARS CoV) infections. Serial serum samples from eight patients collected during the first, third, and ninth months after the onset of infection were evaluated. It was found that low-avidity IgG antibodies were detected in 15/15 (100%), 1/5 (20%), and 0/8 (0%) serum samples collected during the first, third, and ninth months after the onset of symptoms, respectively. Low-avidity antibodies of IgA and IgM subclasses were detected in 14/14 (100%) and 3/14 (21%) serum samples, respectively, collected in the first month after the onset of infection. However, IgA antibodies remained low in avidity in a proportion of patients even during late convalescence. As a consequence, IgG antibody avidity assays gave better discrimination between acute-phase and late-convalescent-phase serum samples than IgM, IgA, or IgGAM assays. In two of these patients, sequential serum samples were also tested for IgG avidity against human CoV strains OC43 and 229E in parallel. While SARS CoV infections induced an anamnestic IgG antibody response to the 229E and OC43 viruses, these cross-reactive antibodies remained of high avidity from early (the first month) postinfection. The results showed that assays to detect low-avidity antibody may be useful for discriminating early from late antibody responses and also for distinguishing anamnestic cross-reactive antibody responses from primary specific responses. This may be useful in some clinical situations.
Dried Blood Spots versus Sera for Detection of Rubella Virus-Specific Immunoglobulin M (IgM) and IgG in Samples Collected during a Rubella Outbreak in Peru
Authors: Helfand Rita F. , Cabezas Cesar , Abernathy Emily , Castillo-Solorzano Carlos , Ortiz Ana Cecilia , Sun Hong , Osores Fernando , Oliveira Lucia , Whittembury Alvaro , Charles Myrna , Andrus Jon , Icenogle Joe 
Published: September 2007

ABSTRACT

Most persons with rubella virus-specific immunoglobulin M (IgM)- or IgG-positive sera tested positive (98% [
n
= 178] and 99% [
n
= 221], respectively) using paired filter paper dried blood spot (DBS) samples, provided that DBS indeterminate results were called positive. For persons with IgM- or IgG-negative sera, 97% and 98%, respectively, were negative using DBS.
Serum Reactivity against
Borrelia burgdorferi
OspA in Patients with Rheumatoid Arthritis
Authors: Hsieh Yu-Fan , Liu Han-Wen , Hsu Tsai-Ching , Wei James C.-C. , Shih Chien-Ming , Krause Peter J. , Tsay Gregory J. 
Published: September 2007

ABSTRACT

Lyme arthritis and rheumatoid arthritis share common clinical features and synovial histology. It is unclear whether they also share similar pathogenesis. Previous studies have shown that the severity and duration of Lyme arthritis correlate directly with serum concentrations of antibody against outer surface protein A (OspA) of the causative pathogen
Borrelia burgdorferi
. We tested the sera of 68 subjects with rheumatoid arthritis, 147 subjects with other autoimmune diseases, and 44 healthy subjects who had never had Lyme disease, as well as sera of 16 patients who had Lyme disease, for reactivity against the
B. burgdorferi
OspA protein. The sera of about a quarter of the rheumatoid arthritis patients and a 10th of the autoimmune disease and Lyme disease patients reacted against OspA antigen. Of 50 rheumatoid arthritis patients who could be evaluated for disease severity, a 28-joint count disease activity score of >2.6 was noted for 11 of 15 (73%) patients whose sera reacted against OspA antigen and 13 of 35 (37%;
P
< 0.05) whose sera were nonreactive. Serum reactivity against OspA antigen is associated with the pathogenesis of rheumatoid arthritis.
Age-Stratified Prevalences of Pneumococcal-Serotype-Specific Immunoglobulin G in England and Their Relationship to the Serotype-Specific Incidence of Invasive Pneumococcal Disease Prior to the Introduction of the Pneumococcal 7-Valent Conjugate Vaccine
Authors: Balmer Paul , Borrow Ray , Findlow Jamie , Warrington Rosalind , Frankland Sarah , Waight Pauline , George Robert , Andrews Nick , Miller Elizabeth 
Published: September 2007

ABSTRACT
Recent changes to the childhood immunization schedule in the United Kingdom have resulted in the inclusion of the 7-valent pneumococcal conjugate vaccine. However, the seroprevalence of pneumococcal antibodies in the population was unknown. To address this, we measured pneumococcal, age-specific immunoglobulin G (IgG) concentrations specific for nine serotypes by an assay run on the Bioplex platform, using 2,664 serum samples collected in England from 2000 to 2004. The lowest concentrations of IgG specific to all serotypes and the proportions of serotype-specific IgG concentrations of ≥0.35 μg/ml were observed in children aged <1 year. From 1 year on, there was a general increase in antibody levels with increasing age, and they remained high in adults. Maternal antibody was detected in young children aged <36 days but waned rapidly. Comparison of the age-specific seroprevalence of serotype-specific IgG to the serotype-specific incidence of invasive pneumococcal disease demonstrated a general inverse relationship for all age groups except the elderly. These data provide a baseline for natural immunity to the pneumococcal serotypes analyzed prior to the introduction of pneumococcal conjugate vaccine in the United Kingdom.
Enhancement of the Sensitivity of the Whole-Blood Gamma Interferon Assay for Diagnosis ofMycobacterium bovisInfections in Cattle
Authors: Denis Michel , Wedlock D. Neil , McCarthy Allison R. , Parlane Natalie A. , Cockle Paul J. , Vordermeier H. Martin , Hewinson R. Glyn , Buddle Bryce M. 
Published: September 2007

ABSTRACTIn this study, we determined if the sensitivity of the currently available in vitro test to detect bovine tuberculosis could be enhanced by adding the following immunomodulators: interleukin-2 (IL-2); granulocyte-macrophage colony-stimulating factor (GM-CSF); antibodies neutralizing IL-10 and transforming growth factor β (TGF-β); mono-methyl-l-arginine, which blocks nitric oxide production; andl-methyl-tryptophan, which interferes with the indoleamine dioxygenase pathway. Blood was obtained from uninfected control cattle, experimentally infected cattle, cattle responding positively to the skin test in tuberculosis-free areas (false positives), and cattle naturally infected withMycobacterium bovisfrom New Zealand and Great Britain. Gamma interferon (IFN-γ) responses to bovine purified protein derivative (PPD-b), avian purified protein derivative, and a fusion protein of ESAT-6 and CFP-10 were measured. Mono-methyl-l-arginine,l-methyl-tryptophan, or an antibody neutralizing TGF-β had minimal impact on IFN-γ production. IL-2 and GM-CSF promoted IFN-γ release whether antigen was present or not. In contrast, adding an antibody against IL-10 enhanced only antigen-specific responses. In particular, addition of anti-IL-10 to ESAT-6/CFP-10-stimulated blood cultures enhanced the test sensitivity. Furthermore, whole blood cells from field reactors produced substantial amounts of IL-10 upon stimulation with PPD-b or ESAT-6/CFP-10. Testing “false-positive” cattle from tuberculosis-free areas of New Zealand revealed that addition of anti-IL-10 did not compromise the test specificity. Therefore, the use of ESAT-6/CFP-10 with anti-IL-10 could be useful to detect cattle potentially infected with tuberculosis, which are not detected using current procedures.
Antiplatelet Drug Therapy Moderates Immune-Mediated Liver Disease and Inhibits Viral Clearance in Mice Infected with a Replication-Deficient Adenovirus
Authors: Iannacone Matteo , Sitia Giovanni , Narvaiza Iñigo , Ruggeri Zaverio M. , Guidotti Luca G. 
Published: September 2007

ABSTRACT

Treatment with a low dose of combined aspirin and clopidogrel, two antiplatelet drugs widely used in humans, markedly reduced the homing of virus-specific cytotoxic T lymphocytes and virus-nonspecific inflammatory leukocytes to the liver of mice acutely infected with a hepatotropic, replication-deficient,
lacZ
-expressing adenovirus (RAd35). Consequently, aspirin/clopidogrel-induced platelet dysfunction greatly diminished liver disease severity and inhibited viral clearance. Along with the finding that aspirin/clopidogrel caused neither bleeding nor anemia, our results suggest that antiplatelet drugs may be considered to limit excessive liver immunopathology and/or to facilitate the persistence of hepatotropic viral vectors utilized in gene therapy.
Preliminary Evaluation of a Multiplex Reverse Transcription-PCR Assay Combined with a New DNA Chip Hybridization Assay for Detecting Respiratory Syncytial Virus
Authors: Causse Manuel , García-Mayorgas Ángel D. , Gutiérrez Juan B. , Casal Manuel 
Published: September 2007

ABSTRACT
DNA chips represent a major advance in microbiology laboratories, enabling the detection of a wide range of possible pathogens using a single test. This study compared a multiplex reverse transcription-PCR combined with DNA chip hybridization (ProDect BCS RV chip; bcs Biotech) with the indirect immunofluorescence test commonly used to detect respiratory viruses. A total of 39 respiratory viruses (38 respiratory syncytial viruses [RSVs] and 1 influenza A virus) were detected in samples from 96 patients using the immunofluorescence test, while 36 viruses (34 RSV, 1 influenza A virus, and 1 influenza B virus) were detected by the DNA chip technique. Results showed a good level of agreement between the two tests for RSV detection; the incidence of other viruses was low, since samples were taken from patients with suspected bronchiolitis. DNA chips displayed high sensitivity (94.6%) and specificity (100%).
Multilocus Sequence Typing Compared to Pulsed-Field Gel Electrophoresis for Molecular Typing of
Pseudomonas aeruginosa
Authors: Johnson Jennifer K. , Arduino Sonia M. , Stine O. Colin , Johnson Judith A. , Harris Anthony D. 
Published: September 2007

ABSTRACT

For hospital epidemiologists, determining a system of typing that is discriminatory is essential for measuring the effectiveness of infection control measures. In situations in which the incidence of resistant
Pseudomonas aeruginosa
is increasing, the ability to discern whether it is due to patient-to-patient transmission versus an increase in patient endogenous strains is often made on the basis of molecular typing. The present study compared the discriminatory abilities of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for 90
P. aeruginosa
isolates obtained from cultures of perirectal surveillance swabs from patients in an intensive care unit. PFGE identified 85 distinct types and 76 distinct groups when similarity cutoffs of 100% and 87%, respectively, were used. By comparison, MLST identified 60 sequence types that could be clustered into 11 clonal complexes and 32 singletons. By using the Simpson index of diversity (
D
), PFGE had a greater discriminatory ability than MLST for
P. aeruginosa
isolates (
D
values, 0.999 versus 0.975, respectively). Thus, while MLST was better for detecting genetic relatedness, we determined that PFGE was more discriminatory than MLST for determining genetic differences in
P. aeruginosa
.
MP1
Homologue-Based Multilocus Sequence System for Typing the Pathogenic Fungus
Penicillium marneffei
: a Novel Approach Using Lineage-Specific Genes
Authors: Woo Patrick C. Y. , Lau Candy C. Y. , Chong Ken T. K. , Tse Herman , Tsang Dominic N. C. , Lee Rodney A. , Tse Cindy W. S. , Que Tak-lun , Chung Liliane M. W. , Ngan Antonio H. Y. , Hui Wai-ting , Wong Samson S. Y. , Lau Susanna K. P. , Yuen Kwok-yung 
Published: September 2007

ABSTRACT

A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of
Penicillium marneffei
, the most important thermal dimorphic fungus causing respiratory, skin, and systemic mycosis in Southeast Asia. The sequences of 11 housekeeping genes were identical among 10 strains of
P. marneffei
, but those of
MP1
and its 13 homologues, a novel superfamily of mannoproteins in the subdivision Pezizomycotina of Ascomycetes, mostly species of
Penicillium
and
Aspergillus
, showed significant variations. Therefore, a multilocus sequence typing (MLST) system for
P. marneffei
was constructed using
MP1
(549 bp) and the four of its homologues (
MPLP4
[337 bp],
MPLP7
[347 bp],
MPLP10
[546 bp], and
MPLP13
[422 bp]) that showed the greatest variations. Among the 2,201 bp of the five loci, 183 polymorphic sites were observed in 44 strains of
P. marneffei
. The median number of alleles at each locus was five (range, 5 [
MPLP4
,
MPLP7
, and
MPLP13
] to 15 [
MPLP10
]). Four of the five genes had nonsynonymous substitution/synonymous substitution (

d
n

/

d
s

) ratios of >1. A total of 35 different sequence types (STs) were assigned to the 44
P. marneffei
isolates, with 28 of the 35 STs identified only once. The discriminatory power was 0.9884.
MP1
and its homologues were better than housekeeping genes for MLST in
P. marneffei
. Due to their more rapid evolutionary rates, lineage-specific genes may be better candidates than housekeeping genes for sequence-based typing, especially in microbes that evolve slowly or have evolved recently.
Quantitative Detection of
Staphylococcus aureus
and
Enterococcus faecalis
DNA in Blood To Diagnose Bacteremia in Patients in the Intensive Care Unit
Authors: Peters Remco P. H. , van Agtmael Michiel A. , Gierveld Sonja , Danner Sven A. , Groeneveld A. B. Johan , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M. 
Published: September 2007

ABSTRACT

Direct detection of bacterial DNA in blood offers a fast alternative to blood culture and is presumably unaffected by the prior use of antibiotics. We evaluated the performance of two real-time PCR assays for the quantitative detection of
Staphylococcus aureus
bacteremia and for
Enterococcus faecalis
bacteremia directly in blood samples, without prior cultivation. Whole-blood samples for PCR were obtained simultaneously with blood cultures from patients admitted to the intensive care unit of our hospital. After the extraction of DNA from 200 μl of blood, real-time PCR was performed for the specific detection and quantification of
S. aureus
and
E. faecalis
DNA. The sensitivity for bacteremia of the
S. aureus
PCR was 75% and that of the
E. faecalis
PCR was 73%, and both tests had high specificity values (93 and 96%, respectively). PCR amplification reactions were positive for
S. aureus
for 10 (7%) blood samples with negative blood cultures, and 7 (4%) PCR reactions were positive for
E. faecalis
. The majority of these PCR results were likely (50%) or possibly (42%) related to infection with the specific microorganism, based on clinical data and radiological and microbiological investigations. PCR results were concordant for 95% of paired whole-blood samples, and blood culture results were concordant for 97% of the paired samples. We conclude that the detection of
S. aureus
and
E. faecalis
DNA in blood by real-time PCR enables a rapid diagnosis of bacteremia and that a positive DNAemia is related to proven or possible infection with the specific microorganism in the majority of patients with negative blood cultures.
Revised Culture-Based System for Identification of
Malassezia
Species
Authors: Kaneko Takamasa , Makimura Koichi , Abe Michiko , Shiota Ryoko , Nakamura Yuka , Kano Rui , Hasegawa Atsuhiko , Sugita Takashi , Shibuya Shuichi , Watanabe Shinichi , Yamaguchi Hideyo , Abe Shigeru , Okamura Noboru 
Published: September 2007

ABSTRACT

Forty-six strains of
Malassezia
spp. with atypical biochemical features were isolated from 366 fresh clinical isolates from human subjects and dogs. Isolates obtained in this study included 2 (4.7%) lipid-dependent
M. pachydermatis
isolates; 1 (2.4%) precipitate-producing and 6 (14.6%) non-polyethoxylated castor oil (Cremophor EL)-assimilating
M. furfur
isolates; and 37 (34.3%)
M. slooffiae
isolates that were esculin hydrolyzing, 17 (15.7%) that were non-tolerant of growth at 40°C, and 2 (1.9%) that assimilated polyethoxylated castor oil. Although their colony morphologies and sizes were characteristic on CHROMagar
Malassezia
medium (CHROM), all strains of
M. furfur
developed large pale pink and wrinkled colonies, and all strains of
M. slooffiae
developed small (<1 mm) pale pink colonies on CHROM. These atypical strains were distinguishable by the appearance of their colonies grown on CHROM. Three clinically important
Malassezia
species,
M. globosa, M. restricta
, and
M. furfur
, were correctly identified by their biochemical characteristics and colony morphologies. The results presented here indicate that our proposed identification system will be useful as a routine tool for the identification of clinically important
Malassezia
species in clinical laboratories.
Validation of a PCR-Oligochromatography Test for Detection of
Trypanozoon
Parasites in a Multicenter Collaborative Trial
Authors: Claes F. , Deborggraeve S. , Verloo D. , Mertens P. , Crowther J. R. , Leclipteux T. , Büscher P. 
Published: September 2007

ABSTRACT
A PCR-oligochromatography test for diagnosis of human and animal trypanosomiasis was evaluated through a multicenter ring trial with six laboratories testing a set of 21 blinded samples, resulting in qualitative data (positive or negative). Results showed an intralaboratory repeatability (accordance) of 88.7% (credible interval [CI], 84.4 to 92.5%) and an interlaboratory repeatability (concordance) of 88.1% (CI, 84.3 to 92.3%).