bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterisation of cucumber leaf spot virus isolated from recycled irrigation water of soil‐less cucumber cultures
Authors: Rosner A. , Lachman O. , Pearlsman M. , Feigelson L. , Maslenin L. , Antignus Y. 
Published: November 2006

AbstractGreenhouse‐grown cucumber plants showed mosaic‐type symptoms and irregular yellow spots on their leaves. The disease did not affect plant growth and the fruits remained symptom free. A virus having isometric particles, 30 nm in size, was isolated from the infected tissues and from recycled drainage water collected from tuff (volcanic rock) raised beds on which plants were grown. The virus was identified as a variant of cucumber leaf spot virus (CLSV) that has a host range similar but not identical to that of a previously described CLSV isolate. The overall nucleotide sequence identity between the RNAs of the Israeli isolate and the type isolate virus (accession numbers: DQ227315 and AY571334, respectively) amounts to 96%.
Long‐term outcome of therapy for 59 cats and 11 dogs with cryptococcosis
Authors: O’Brien CR , Krockenberger MB , Martin P , Wigney DI , Malik R 
Published: November 2006

Objective  To determine the outcome of therapy in cats and dogs with naturally occurring cryptococcosis.Design  Retrospective study of 59 cats and 11 dogs at the University Veterinary Centre Sydney from 1986 to 2004.Method  Following detailed analysis of case notes potential associations between patient characteristics, cryptococcal species, retroviral status (cats), disease severity and type of therapy were examined in relation to duration and success of therapy. Treatment protocols based on amphotericin B, fluconazole and itraconazole were compared.Results  Seventy‐six percent of feline patients were successfully treated. For cats, the presence of central nervous system disease was the only factor found to influence outcome. Cats with neurological involvement, disseminated disease or refractory disease treated with amphotericin B containing protocols did as well, on average, as cats with less severe disease treated with azole monotherapy. Amphotericin B was thus an effective agent for treating severe cases of cryptococcosis. The median cumulative dose of amphotericin B for cats cured at the first attempt was 16 mg/kg (range 7 to 23 mg/kg). The median duration of treatment required to effect a cure at first attempt was significantly shorter for fluconazole (4 months; range 1 to 8 months) than for itraconazole (9 months; range 3 to 24 months; P = 0. 0191; Mann Whitney U test). The success rate for treatment of canine cases was 55%. No factor appeared to influence disease outcome in dogs. Large cumulative doses of amphotericin B could be administered via the subcutaneous route in both species and generally with minimal nephrotoxicity. Recrudescence occurred in a significant proportion of animals, in some cases despite a reduction of serum latex cryptococcal antigen agglutination test to zero.Conclusion  Although the prognosis of cryptococcosis should be described as guarded, a majority of the canine and especially feline patients can be expected to be cured, although treatment is protracted and expensive.
Reference limits for urinary fractional excretion of electrolytes in adult non‐racing Greyhound dogs
Authors: Bennett SL , Abraham LA , Anderson GA , Holloway SA , Parry BW 
Published: November 2006

Objective To determine reference limits for urinary fractional excretion of electrolytes in Greyhound dogs.Methods Urinary fractional excretion was calculated using a spot clearance method preceded by a 16 to 20 hour fast in 48 Greyhound dogs. Raw data analysed using the bootstrap estimate was used to calculate the reference limits.Results The observed range for urinary fractional excretion in Greyhound dogs was 0.0 to 0.77% for sodium, 0.9 to 14.7% for potassium, 0 to 0.66% for chloride, 0.03 to 0.22% for calcium and 0.4 to 20.1% for phosphate. Expressed as percentages, the suggested reference limits for fractional excretion in Greyhound dogs are as follows: sodium ≤ 0.72, potassium ≤ 12.2, chloride ≤ 0.55, calcium ≤ 0.13 and phosphate ≤ 16.5.Clinical significance Veterinary practitioners may use these reference limits for urinary electrolyte fractional excretion when investigating renal tubular disease in Greyhound dogs.
Dynamics of the Immune Response against Extracellular Products of Group A Streptococci during Infection
Authors: Maripuu Linda , Eriksson Anna , Eriksson Björn , Pauksen Karlis , Holm Stig , Norgren Mari 
Published: November 2006

ABSTRACT

The immune response against the infecting group A streptococcus (GAS) extracellular products (EP) was determined in acute- and convalescent-phase sera from 75 patients with different clinical manifestations of GAS infection. All EP elicited a high proliferative response in human peripheral blood mononuclear cells. In patients with bacteremia, low neutralization in acute-phase sera was associated with development of streptococcal toxic shock syndrome. Lack of neutralization in acute-phase sera was more common in patients infected with the T1
emm1
serotype. The majority of patients did not develop the ability to neutralize the mitogenic activity of their infecting isolate despite a significant increase in enzyme-linked immunosorbent assay titer in early convalescent-phase sera. In patients with the ability to neutralize GAS EP, the immune response remained high over at least 3 years. In contrast, the neutralization capacity conferred by intravenous immunoglobulin and/or plasma treatment disappeared within 3 months.
Comparative Evaluation of Löwenstein-Jensen Proportion Method, BacT/ALERT 3D System, and Enzymatic Pyrazinamidase Assay for Pyrazinamide Susceptibility Testing of
Mycobacterium tuberculosis
Authors: Singh Pushpendra , Wesley Clement , Jadaun G. P. S. , Malonia Sunil Kumar , Das R. , Upadhyay P. , Faujdar J. , Sharma P. , Gupta P. , Mishra Abhay Kumar , Singh Kalpana , Chauhan D. S. , Sharma V. D. , Gupta U. D. , Venkatesan K. , Katoch V. M. 
Published: November 2006

ABSTRACT

Pyrazinamide (PZA) is an important first-line antituberculosis drug because of its sterilizing activity against semidormant tubercle bacilli. In spite of its very high in vivo activity, its in vitro activity is not apparent unless an acidic environment is available, which makes PZA susceptibility testing difficult by conventional methods. The present study was, therefore, planned to assess the performance of the colorimetric BacT/ALERT 3D system and compare the results with those from conventional tests, i.e., the Löwenstein-Jensen (LJ) proportion method (pH 4.85) and Wayne's pyrazinamidase (PZase) assay, using 107 clinical isolates. The concordance among all of these tests was 89.71% after the first round of testing and reached 92.52% after resolution of the discordant results by retesting. Prolonged incubation of the PZase tube for up to 10 days was found to increase the specificity of the PZase test. The concordances between LJ proportion and BacT/ALERT 3D, LJ proportion and the PZase assay, and BacT/ALERT 3D and the PZase assay were found to be 99.06%, 93.46%, and 92.52%, respectively. Using the LJ results as the gold standard, the sensitivities of BacT/ALERT 3D and the PZase assay were 100 and 82.85%, respectively, while the specificity was 98.61% for both of the tests. The difference between the sensitivities of BacT/ALERT 3D and the PZase assay was significant (
P
= 0.025). The mean turnaround times for the detection of resistant and susceptible results by BacT/ALERT 3D were 8.04 and 11.32 days, respectively. While the major limitations associated with the PZase assay and the LJ proportion method are lower sensitivity in previously treated patients and a longer time requirement, respectively, the BacT/ALERT 3D system was found to be rapid, highly sensitive, and specific.
Combined Use of Pastorex Staph-Plus and Either of Two New Chromogenic Agars, MRSA ID and CHROMagar MRSA, for Detection of Methicillin-Resistant
Staphylococcus aureus
Authors: Compernolle Veerle , Verschraegen Gerda , Claeys Geert 
Published: November 2006

ABSTRACT

We describe the search toward a fast and reliable strategy to detect and confirm the presence of methicillin-resistant
Staphylococcus aureus
(MRSA) in screening samples. First, we evaluated the sensitivities and specificities of oxacillin resistance screening agar (ORSA) with enrichment (tryptic soy broth [TSB] and ORSA [TSB-ORSA]) and without enrichment (ORSA), MRSA ID (MRSA_ID) plates, and CHROMagar MRSA (C_MRSA) plates, all of which were inoculated with equal volumes of a suspension made by emulsifying screening swabs. Whereas the sensitivities after 48 h were similar for all media tested (77% for MRSA_ID and ORSA; 73% for C_MRSA and ORSA after enrichment [TSB-ORSA]), the specificities of MRSA_ID (98% after 24 h and 94% after 48 h) and C_MRSA (98% after 24 h and 90% after 48 h) were superior to the specificities of ORSAs (92% after 24 h and 83% after 48 h) and TSB-ORSA (86% after 24 h and 81% after 48 h). Subsequently, the performance of the Pastorex Staph-Plus agglutination test with presumptive MRSA isolates taken directly from chromogenic agars (direct_Pastorex agglutination) was compared to that of the Pastorex Staph-Plus agglutination test with isolates from blood agar subcultures (conventional_Pastorex agglutination). When the direct_Pastorex agglutination test on MRSA_ID plates was combined with Gram staining, the direct_Pastorex agglutination test with samples from MRSA_ID plates was as reliable as the conventional_Pastorex agglutination test with samples from blood agar subcultures from MRSA_ID plates. In contrast, the direct_Pastorex agglutination test with samples from C_MRSA plates gave false-negative results. Finally, we calculated the processing times of the four different strategies, namely, (i) enrichment in TSB supplemented with NaCl, subsequent culture on ORSA, and the conventional_Pastorex agglutination test; (ii) direct inoculation of ORSA combined with conventional_Pastorex agglutination test; (iii) direct inoculation of MRSA_ID plates combined with Gram staining and the direct_Pastorex agglutination test; and (iv) direct inoculation of C_MRSA plates combined with Gram staining and the direct_Pastorex agglutination test. We concluded that the use of MRSA_ID in combination with Gram staining and the direct_Pastorex agglutination test is faster and more specific than the other strategies tested.
Penile, Urethral, and Seminal Sampling for Diagnosis of Human Papillomavirus Infection in Men
Authors: Giovannelli Lucia , Migliore Maria Colomba , Capra Giuseppina , Caleca Maria Pia , Bellavia Carmelina , Perino Antonio , Viviano Enza , Matranga Domenica , Ammatuna Pietro 
Published: November 2006

ABSTRACT
Methods that used specimens from three genital sites (penile brushing [PB], urethral brushing [UB], and the retrieval of semen [SE]) from 50 men were examined for human papillomavirus (HPV) DNA detection. The rates of detection by PB, UB, SE, PB and UB, and PB and SE were 88.9%, 50.0%, 33.3%, 100%, and 97.2%, respectively. The use of PB and UB appears to be the most accurate method; as an alternative to UB, the use of SE with PB could be used to improve the rate of HPV DNA detection in men.
Quantitative Detection of Plasma Human Immunodeficiency Virus Type 2 Subtype A RNA by the Nuclisens EasyQ Assay (Version 1.1)
Authors: Rodés Berta , Sheldon Julie , Toro Carlos , Cuevas Laureano , Pérez-Pastrana Esperanza , Herrera Inmaculada , Soriano Vincent 
Published: November 2006

ABSTRACT

No commercial viral load assay has yet been approved for use for measurement of human immunodeficiency virus type 2 (HIV-2) RNA levels in plasma. We assessed the performance of the NucliSens EasyQ (version 1.1) assay (EasyQ; bioMérieux, Boxtel, The Netherlands) to quantify HIV-2 viremia. A viral stock was prepared from an HIV-2 (subtype A)-infected patient. Culture supernatant was subjected to viral particle counting by electron microscopy. Serial dilutions of the viral stock were made in HIV-negative plasma and were used to test EasyQ for its sensitivity, linearity, and reproducibility. RNA was quantified by the NucliSens EasyQ (version 1.1) assay. Plasma samples from 75 HIV-2-infected patients were further tested. EasyQ was able to quantify HIV-2 RNA in a reproducible manner. Overall, estimates of the number of HIV-2 RNA copies/ml obtained with EasyQ were lower than those obtained by electron microscopy; however, the differences were always less than 0.7 log (mean, 0.55 ± 0.19 log
10
). The assay showed good linearity (
r
2
= 0.964;
P
< 0.0001). The agreement between both measures was assessed by use of a Bland-Altman plot; the narrow limits (0.158 to 0.952), defined as the mean difference ± 2 standard deviations, indicated good agreement. The reproducibility was also good, since the between-run coefficients of variation were 1.49, 3.60, and 12.25% for samples containing 6.30, 4.30, and 2.30 log
10
HIV-2 RNA copies/ml, respectively. HIV-2 RNA was detected in 34 of 75 (45%) plasma specimens (mean, 2.72 log RNA copies/ml; range, 1.74 to 4.11 log RNA copies/ml); the rest of the specimens were considered to have undetectable viremia. A negative correlation was found between the number of HIV-2 RNA copies/ml and CD4 counts. In summary, EasyQ was shown to be reliable for the measurement of plasma HIV-2 subtype A RNA levels and may be a feasible tool for routine clinical monitoring of HIV-2 subtype A-infected patients.
Characterization of In Vitro Biofilm-Associated Pneumococcal Phase Variants of a Clinically Relevant Serotype 3 Clone
Authors: McEllistrem M. Catherine , Ransford Jennifer V. , Khan Saleem A. 
Published: November 2006

ABSTRACT

An increasing proportion of children with acute otitis media due to
Streptococcus pneumoniae
have serotype 3 infections since licensure of the seven-valent pneumococcal conjugate vaccine. These serotype 3 strains are genetically related by molecular subtyping. During otitis media with effusion and recurrent otitis media, biofilms commonly develop. Pneumococcal in vitro biofilms are comprised of phase variants that differ in colony morphology. By using a representative strain of the mucoid serotype 3 clone, rough phase variants with a diverse array of mutations were detected in biofilms formed in vitro. Most phase variants had mutations in the
cps3D
gene, the first gene of the capsular operon. Eleven had single nucleotide polymorphisms (SNPs) in the
cps3D
gene, one had an SNP in the −10 promoter, and three had large deletions in the
cps3D
gene. Reversion to the mucoid phenotype was associated with reversion of the mutation in the
cps3D
gene. Unlike the phase variants detected in the nasopharynx, which have at least 20% of the parental amount of capsule, the in vitro biofilm-associated phase variants had ≤12% of the parental amount of capsule, as determined by capsule enzyme-linked immunosorbent assays. Using real-time reverse transcription-PCR, we determined that capsule expression in the phase variants was likely regulated at multiple levels. These in vitro phase variation data, which underscore the plasticity of the pneumococcus, need to be confirmed with in vivo analyses of the middle ear mucosa during otitis media.
Validation of Pulsed-Field Gel Electrophoresis and
spa
Typing for Long-Term, Nationwide Epidemiological Surveillance Studies of
Staphylococcus aureus
Infections
Authors: Hallin M. , Deplano A. , Denis O. , De Mendonça R. , De Ryck R. , Struelens M. J. 
Published: November 2006

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) of genomic macrorestriction fragments has been used by the Belgian Reference Laboratory for Staphylococci for national hospital surveys of methicillin-resistant
Staphylococcus aureus
since 1992. The sequencing of the polymorphic X region of the protein A gene (
spa
typing) offers significant advantages over PFGE in terms of speed, ease of interpretation, and exportability. To validate its potential use for national surveillance, we evaluated the robustness of
spa
typing compared with that of PFGE based on a collection of 217
S. aureus
strains representative of the Belgian
S. aureus
epidemiology during the last 13 years.
spa
typing and PFGE both showed high discriminatory power (discriminatory indexes of 0.98 and 0.96, respectively) and achieved high concordance (95.9%) in type classification. Both methods also showed good concordance with multilocus sequence typing (MLST) (95.5%). However, we observed occasional “violations” of MLST clonal complex assignment by
spa
typing. Our results suggest that both PFGE and
spa
typing are reliable methods for long-term, nationwide epidemiological surveillance studies. We suggest that
spa
typing, which is a single-locus-based method, should preferably be used in combination with additional markers, such as staphylococcal cassette chromosome
mec
typing or resistance or virulence gene detection.
Mutational Analysis of Aminopeptidase N, a Receptor for Several Group 1 Coronaviruses, Identifies Key Determinants of Viral Host Range
Authors: Tusell Sonia M. , Schittone Stephanie A. , Holmes Kathryn V. 
Published: November 2006

ABSTRACT
Feline coronavirus (FCoV), porcine transmissible gastroenteritis coronavirus (TGEV), canine coronavirus (CCoV), and human coronavirus HCoV-229E, which belong to the group 1 coronavirus, use aminopeptidase N (APN) of their natural host and feline APN (fAPN) as receptors. Using mouse-feline APN chimeras, we identified three small, discontinuous regions, amino acids (aa) 288 to 290, aa 732 to 746 (called R1), and aa 764 to 788 (called R2) in fAPN that determined the host ranges of these coronaviruses. Blockade of infection with anti-fAPN monoclonal antibody RG4 suggested that these three regions lie close together on the fAPN surface. Different residues in fAPN were required for infection with each coronavirus. HCoV-229E infection was blocked by an N-glycosylation sequon present between aa 288 to 290 in murine APN. TGEV required R1 of fAPN, while FCoV and CCoV required both R1 and R2 for entry. N740 and T742 in fAPN and the homologous R741 in human APN (hAPN) were key determinants of host range for FCoV, TGEV, and CCoV. Residue N740 in fAPN was essential only for CCoV receptor activity. A conservative T742V substitution or a T742R substitution in fAPN destroyed receptor activity for the pig, dog, and cat coronaviruses, while a T742S substitution retained these receptor activities. Thus, the hydroxyl on T742 is required for the coronavirus receptor activity of fAPN. In hAPN an R741T substitution caused a gain of receptor activity for TGEV but not for FCoV or CCoV. Therefore, entry and host range of these group 1 coronaviruses depend on the ability of the viral spike glycoproteins to recognize small, species-specific amino acid differences in the APN proteins of different species.
GB Virus B Disrupts RIG-I Signaling by NS3/4A-Mediated Cleavage of the Adaptor Protein MAVS
Authors: Chen Zihong , Benureau Yann , Rijnbrand Rene , Yi Jianzhong , Wang Ting , Warter Lucile , Lanford Robert E. , Weinman Steven A. , Lemon Stanley M. , Martin Annette , Li Kui 
Published: November 2006

ABSTRACT
Understanding the mechanisms of hepatitis C virus (HCV) pathogenesis and persistence has been hampered by the lack of small, convenient animal models. GB virus B (GBV-B) is phylogenetically the closest related virus to HCV. It causes generally acute and occasionally chronic hepatitis in small primates and is used as a surrogate model for HCV. It is not known, however, whether GBV-B has evolved strategies to circumvent host innate defenses similar to those of HCV, a property that may contribute to HCV persistence in vivo. We show here in cultured tamarin hepatocytes that GBV-B NS3/4A protease, but not a related catalytically inactive mutant, effectively blocks innate intracellular antiviral responses signaled through the RNA helicase, retinoic acid-inducible gene I (RIG-I), an essential sensor molecule that initiates host defenses against many RNA viruses, including HCV. GBV-B NS3/4A protease specifically cleaves mitochondrial antiviral signaling protein (MAVS; also known as IPS-1/Cardif/VISA) and dislodges it from mitochondria, thereby disrupting its function as a RIG-I adaptor and blocking downstream activation of both interferon regulatory factor 3 and nuclear factor kappa B. MAVS cleavage and abrogation of virus-induced interferon responses were also observed in Huh7 cells supporting autonomous replication of subgenomic GBV-B RNAs. Our data indicate that, as in the case of HCV, GBV-B has evolved to utilize its major protease to disrupt RIG-I signaling and impede innate antiviral defenses. These data provide further support for the use of GBV-B infection in small primates as an accurate surrogate model for deciphering virus-host interactions in hepacivirus pathogenesis.
Biochemical and Genetic Analysis of the Vaccinia Virus D5 Protein: Multimerization-Dependent ATPase Activity Is Required To Support Viral DNA Replication
Authors: Boyle Kathleen A. , Arps Lisa , Traktman Paula 
Published: November 2006

ABSTRACT

The vaccinia virus-encoded D5 protein is an essential ATPase involved in viral DNA replication. We have expanded the genotypic and phenotypic analysis of six temperature-sensitive (
ts
) D5 mutants (C
ts
17, C
ts
24, E
ts
69, D
ts
6389 [also referred to as D
ts
38], D
ts
12, and D
ts
56) and shown that at nonpermissive temperature all of the
ts
D5 viruses exhibit a dramatic reduction in DNA synthesis and virus production. For C
ts
17 and C
ts
24, this restriction reflects the thermolability of the D5 proteins. The D
ts
6389, D
ts
12, and D
ts
56 D5 proteins become insoluble at 39.7°C, while the E
ts
69 D5 protein remains stable and soluble and retains the ability to oligomerize and hydrolyze ATP when synthesized at 39.7°C. To investigate which structural features of D5 are important for its biological and biochemical activities, we generated targeted mutations in invariant residues positioned within conserved domains found within D5. Using a transient complementation assay that assessed the ability of D5 variants to sustain ongoing DNA synthesis during nonpermissive C
ts
24 infections, only a
wt
D5 allele supported DNA synthesis. Alleles of D5 containing targeted mutations within the Walker A or B domains, the superfamily III helicase motif C, or the AAA+ motif lacked biological competency. Furthermore, purified preparations of these variant proteins revealed that they all were defective in ATP hydrolysis. Multimerization of D5 appeared to be a prerequisite for enzymatic activity and required the Walker B domain, the AAA+ motif, and a region located upstream of the catalytic core. Finally, although multimerization and enzymatic activity are necessary for the biological competence of D5, they are not sufficient.
A cosmology with variable c
Authors: Shojaie H , Farhoudi M 
Published: November 2006

A new varying-c cosmological model, constructed using two additional assumptions, which was introduced in our previous work, is briefly reviewed and the dynamic equation of the model is derived distinctly from a semi-Newtonian approach. The results of this model, using a [Formula: see text] term and an extra energy-momentum tensor, are considered separately. It is shown that the Universe began from a hot Big Bang and expands forever with a constant deceleration parameter regardless of its curvature. Finally, the age, the radius, and the energy content of the Universe are estimated and some discussion about the type of the geometry of the Universe is provided. PACS Nos.: 98.80.Bp, 98.80.Jk