bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of Novel Conformational and Genotype-Specific Antigens for Improving Sensitivity of Immunoassays for Hepatitis C Virus-Specific Antibodies
Authors: Lin Sansan , Arcangel Phillip , Medina-Selby Angelica , Coit Doris , Ng Philip , Nguyen Steve , McCoin Colin , Gyenes Alex , Hu Celine , Tandeske Laura , Phelps Bruce , Chien David 
Published: August 2005

ABSTRACT
The current commercially licensed enzyme-linked immunosorbent assays (ELISAs) for hepatitis C virus (HCV) mainly use recombinant proteins containing linear epitopes. There is evidence, however, that conformational epitopes of HCV are more immunoreactive. Thus, we have designed an HCV antibody assay that employs a conformational protein, NS3NS4a PI (with functional protease and helicase activities), and a linear fusion protein, multiple-epitope fusion antigen 7.1 (MEFA 7.1) or MEFA 7.2. We have shown that NS3NS4a PI detects early-seroconversion conformation-sensitive antibodies better than c33c antigen. The correct conformation of NS3NS4a PI also cross-reacts with different genotype samples better than the c33c antigen. MEFA 7.1 and MEFA 7.2 incorporate all the major immunodominant and genotype-specific epitopes of HCV core, E1, E2 hypervariable region 1 (HVR1), E2 HVR1-plus-HVR2 consensus, NS3, NS4, and NS5. Since MEFA 7.1 is degraded by the active NS3NS4a PI protease, we designed a second MEFA 7.2 construct in which the six protease cleavage sites found in MEFA 7.1 were eliminated by amino acid mutation. We demonstrate here that MEFA 7.2 remains intact in the presence of NS3NS4a PI and preserves the epitopes present in MEFA 7.1. Compared to currently licensed assays, an ELISA incorporating a combination of the two antigens NS3NS4a PI and MEFA 7.1 or 7.2 demonstrates better serotype sensitivity and detects seroconversion earlier in many commercially available panels. We believe that an assay using NS3NS4a PI and MEFA 7.1 or 7.2 may have the potential to replace current HCV immunoassays for better sensitivity.
Comparison of
Staphylococcus aureus
Genotypes Recovered from Cases of Bovine, Ovine, and Caprine Mastitis
Authors: Mørk T. , Tollersrud T. , Kvitle B. , Jørgensen H. J. , Waage S. 
Published: August 2005

ABSTRACT

Staphylococcus aureus
is an important pathogen in domestic ruminants. The main objective of this study was to determine the similarity of epidemiologically unrelated
S. aureus
isolates from bovine, ovine, and caprine mastitis. By pulsed-field gel electrophoresis, 160 different pulsotypes (PTs) were identified among 905 isolates recovered from 588 herds in 12 counties in Norway. Based on estimates of similarity, using an 80% cluster cutoff, the isolates were assigned to 47 clusters. One cluster included 62% of all the isolates and more than 45% of the isolates from each host species. Twenty-three PTs included isolates from more than one host species; these 23 PTs represented 72% of all the isolates. The six most prevalent PTs included isolates from all host species and contained 45% of the bovine isolates, 54% of the ovine isolates, and 37% of the caprine isolates. Antimicrobial susceptibility testing of 373 of the isolates revealed resistance to penicillin in 2.9% and to streptomycin in 2.4%; only 1.9% were resistant to 1 of the other 11 antimicrobials tested. The results of this study suggest that a small number of closely related genotypes are responsible for a great proportion of
S. aureus
mastitis cases in cows, ewes, and goats in Norway and that these genotypes exhibit little or no host preference among these species. Selection due to antimicrobial resistance appears not to have contributed to the predominance of these genotypes.
Biochemical Differentiation and Comparison ofDesulfovibrioSpecies and Other Phenotypically Similar Genera
Authors: Warren Yumi A. , Citron Diane M. , Merriam C. Vreni , Goldstein Ellie J. C. 
Published: August 2005

ABSTRACTSeventeen human clinical isolates representing four species ofDesulfovibriowere characterized using 16S rRNA gene sequences and tests for catalase, indole, nitrate, bile, urease, formate-fumarate stimulation, desulfoviridin, motility, and hydrogen sulfide production, plus susceptibility to antimicrobial agents. Eighty additional strains representing 10 phenotypically similar genera (Bilophila,Selenomonas,Capnocytophaga,Campylobacter,Bacteroides,Sutterella,Anaerobiospirillum,Dialister,Veillonella, andMobiluncus) were included for comparison. AllDesulfovibriospecies produced H2S and were desulfoviridin positive, and allDesulfovibriospecies exceptD. pigerwere motile. The fourDesulfovibriospecies could be distinguished from each other using tests for catalase, indole, nitrate, urease, and growth on bile, with the following results (positive [+], negative [−], growth [G], and no growth [NG]): forD. piger, −,− , −, −, and G, respectively; forD.fairfieldensis, +, −, +, −, and G, respectively; forD. desulfuricans, −,− , +, +, and NG, respectively; and forD. vulgaris, −, +, −,− , and G, respectively. Resistance to the 10-μg colistin disk separated theDesulfovibriospecies from most of the other genera, which were usually susceptible. These simple tests were useful for characterizing theDesulfovibriospecies and differentiating them from other phenotypically similar genera.
Detection of
toxB
, a Plasmid Virulence Gene of
Escherichia coli
O157, in Enterohemorrhagic and Enteropathogenic
E. coli
Authors: Tozzoli Rosangela , Caprioli Alfredo , Morabito Stefano 
Published: August 2005

ABSTRACT

The virulence plasmid of
Escherichia coli
O157 strain EDL933 carries a 10-kb putative virulence gene designated
toxB
. Little is known about the distribution of this gene among
E. coli
O157 strains or its presence in other enterohemorrhagic
E. coli
(EHEC) and enteropathogenic
E. coli
(EPEC) strains. We developed PCR and hybridization tools for the detection of the entire
toxB
sequence and investigated its presence in a collection of EHEC O157 strains and other EHEC and EPEC strains belonging to different serogroups and isolated from different sources. The EHEC O157 strains reacted with all of the PCR primers and probes used, thus indicating the presence of a complete
toxB
gene regardless of the human or bovine origin of the isolates. Similar positive reactions were observed for about 50% of the EHEC O26 strains tested and a few other EHEC and EPEC strains. However, the size of the DNA fragments hybridizing with the
toxB
probes differed from that of the positive fragments from EHEC O157, suggesting a polymorphism in the
toxB
genes present in the different
E. coli
serogroups. Moreover, several EHEC and EPEC strains belonging to different serogroups reacted with only some of the genetic tools used, suggesting either the existence of major variants of
toxB
or the presence of fragments of the gene. Southern blotting analysis showed that
toxB
sequences were located on large plasmids in EHEC and EPEC O26 as well.
Superiority of Molecular Techniques for Identification of Gram-Negative, Oxidase-Positive Rods, Including Morphologically Nontypical
Pseudomonas aeruginosa
, from Patients with Cystic Fibrosis
Authors: Wellinghausen Nele , Köthe Juliane , Wirths Beate , Sigge Anja , Poppert Sven 
Published: August 2005

ABSTRACT

Phenotypic identification of gram-negative bacteria from Cystic Fibrosis (CF) patients carries a high risk of misidentification. Therefore, we compared the results of biochemical identification by API 20NE with 16S rRNA gene sequencing in 88 gram-negative, oxidase-positive rods, other than morphologically and biochemically typical
P. aeruginosa
, from respiratory secretions of CF patients. The API 20NE allowed correct identification of the bacterial species in 15 out of 88 (17%) isolates investigated. Agreement between the API and the 16S rRNA gene sequencing results was high only in isolates with an API result classified as “excellent identification.” Even API results classified as “very good identification” or “good identification” showed a high rate of misidentification (67% and 84%). Fifty-two isolates of morphological and biochemical nontypical
Pseudomonas aeruginosa
, representing 59% of all isolates investigated, were not identifiable or misidentified in the API 20NE. Therefore, rapid molecular diagnostic techniques like real-time PCR and fluorescence in situ hybridization (FISH) were evaluated in this particular group of bacteria for identification of the clinically most relevant pathogen,
P. aeruginosa
. The LightCycler PCR assay with a
P. aeruginosa
-specific probe showed a sensitivity and specificity of 98.1% and 100%, respectively. For FISH analysis, a newly designed
P. aeruginosa
-specific probe had a sensitivity and specificity of 100%. In conclusion, molecular methods are superior over biochemical tests for identification of gram-negative, oxidase-positive rods in CF patients. In addition, real-time PCR and FISH allowed identification of morphologically nontypical isolates of
P. aeruginosa
within a few hours.
Enhanced Expression of an α2,6-Linked Sialic Acid on MDCK Cells Improves Isolation of Human Influenza Viruses and Evaluation of Their Sensitivity to a Neuraminidase Inhibitor
Authors: Hatakeyama Shuji , Sakai-Tagawa Yuko , Kiso Maki , Goto Hideo , Kawakami Chiharu , Mitamura Keiko , Sugaya Norio , Suzuki Yasuo , Kawaoka Yoshihiro 
Published: August 2005

ABSTRACT

The extensive use of neuraminidase (NA) inhibitors to treat influenza virus infections mandates close monitoring for resistant variants. Cultured cells do not provide a reliable means of evaluating the susceptibility of human influenza virus isolates to NA inhibitors. That is, the growth of such viruses in cell lines (e.g., Madin-Darby canine kidney [MDCK] cells) is not inhibited by these drugs, even though their sialidase activity is drug-sensitive. Matrosovich et al. (J. Virol.
77:
8418-8425, 2003) showed that an MDCK cell line overexpressing the human β-galactoside α2,6-sialyltransferase I (ST6Gal I) gene has the potential to assess the sensitivity of human influenza virus isolates to NA inhibitors, based on studies with a limited number of viruses. Here, we asked whether clinical isolates of influenza virus are universally sensitive to an NA inhibitor (oseltamivir) in an MDCK cell line expressing the ST6Gal I gene. The sensitivity of viruses to oseltamivir correlated with the sensitivity of viral sialidase to the compound, demonstrating the potential utility of this modified cell line for detecting NA inhibitor-resistant viruses. Moreover, in ST6Gal I-overexpressing cells, the growth of human influenza viruses was up to 2 logs higher than in MDCK cells. We conclude that the human ST6Gal I-expressing MDCK cell line is useful not only for evaluating their sensitivity to NA inhibitors, but also for isolation of influenza viruses from clinical samples.
Novel Application of the Masson-Fontana Stain for Demonstrating
Malassezia
Species Melanin-Like Pigment Production In Vitro and in Clinical Specimens
Authors: Gaitanis George , Chasapi Vassiliki , Velegraki Aristea 
Published: August 2005

ABSTRACT

Melanin-like pigment produced in vitro and in vivo by
Malassezia
yeasts has not been described before. Masson-Fontana staining confirmed accumulation of black pigment on the cell walls of
l
-dihydroxyphenylalaline (
l
-DOPA)-cultured
Malassezia
species. Black pigment was also observed in cells and hyphae from hyperpigmented patient lesions with culture-confirmed pityriasis versicolor and seborrheic dermatitis.
Approaches to Bacterial RNA Isolation and Purification for Microarray Analysis of
Escherichia coli
K1 Interaction with Human Brain Microvascular Endothelial Cells
Authors: Di Cello Francescopaolo , Xie Yi , Paul-Satyaseela Maneesh , Kim Kwang Sik 
Published: August 2005

ABSTRACT

We established a protocol for isolation of microarray-grade bacterial RNA from
Escherichia coli
K1 interacting with human brain microvascular endothelial cells. The extracted RNA was free of human RNA contamination. More importantly, microarray analysis demonstrated that no bias was introduced in the gene expression pattern during the RNA isolation procedure.
Affordable, Abbreviated Roche Monitor Assay for Quantification of Human Immunodeficiency Virus Type 1 RNA in Plasma
Authors: Fiscus Susan A. , Chen Shu , Hoover Donald , Kerkau Melissa G. , Alabanza Paul , Siharath Som , Schmitz John , Kumwenda Newton , Taha Taha E. 
Published: August 2005

ABSTRACT
The cost for the Roche Monitor assay kit can be reduced 50% by using only the 1:1, 1:25, and 1:625 human immunodeficiency virus (HIV) and the 1:1 quantitation standard dilutions. This abbreviated test applied to 1,774 mostly African samples had results nearly identical to those obtained following the package insert instructions. To make this approach feasible, Roche would have to provide additional lysis buffer and master mix.
Dissemination ofSalmonella entericasubsp.entericaSerovar Typhimurium var. Copenhagen Clonal Types through a Contract Heifer-Raising Operation
Authors: Hegde Narasimha V. , Cook Michelle L. , Wolfgang David R. , Love Brenda C. , Maddox Carol C. , Jayarao Bhushan M. 
Published: August 2005

ABSTRACTSalmonella entericasubsp.entericaserovar Typhimurium var. Copenhagen isolates from a heifer-raising operation and from 11 dairy herds that had their calves contracted to the heifer-raising operation were examined for their phenotypic and genotypic characteristics. Results of the study showed that the heifer-raising operation could serve as a clearinghouse forSalmonellaserovar Typhimurium var. Copenhagen and perhaps otherSalmonellaserotypes.
Pathogen Evolution In Vivo: Genome Dynamics of Two Isolates Obtained 9 Years Apart from a Duodenal Ulcer Patient Infected with a Single
Helicobacter pylori
Strain
Authors: Prouzet-Mauléon Valérie , Hussain M. Abid , Lamouliatte Hervé , Kauser Farhana , Mégraud Francis , Ahmed Niyaz 
Published: August 2005

ABSTRACT

The survival and microevolution of
Helicobacter pylori
strains in the niches of the stomach after eradication therapy have largely been unexplored. We analyzed genomic signatures for two successive isolates obtained 9 years apart from a duodenal ulcer patient who underwent eradication therapy for
H. pylori
. These isolates were genotyped based on 50 different parameters involving three different fingerprinting approaches and several evolutionarily significant and virulence-associated landmarks in the genome, including nine informative gene loci, the
cag
pathogenicity island and its right junction, members of the plasticity region cluster, and
vacA
and
iceA
alleles. Our observations reveal that the two isolates were derived from the same strain that colonized the patient for almost a decade and were almost identical. Microevolution, however, was observed in the
cagA
gene and its right junction, the
vacA
m1 allele, and a member of the plasticity region cluster (JHP926). These results suggest that
H. pylori
has a great ability to survive and reemerge as a microevolved strain posteradication, thereby hinting at the requirement for follow-up of patients after therapy.
Microbiology of Bartholin's Gland Abscess in Japan
Authors: Tanaka Kaori , Mikamo Hiroshige , Ninomiya Mochiyoshi , Tamaya Teruhiko , Izumi Koji , Ito Kunihiko , Yamaoka Kazukiyo , Watanabe Kunitomo 
Published: August 2005

ABSTRACT

This study was conducted to determine the current epidemiology concerning the causative organisms for Bartholin's gland abscess in Japan. Microbiological examination of 224 cases showed positive results in 219 cases and negative results in 5 cases. Of all of the bacterial isolates, 307 and 118 were aerobes and anaerobes, respectively. The most frequently isolated bacterium was
Escherichia coli
. Of the anaerobes, the most frequently isolated organism was
Bacteroides
species, followed by
Prevotella
species. The organisms related to respiratory infectious diseases, such as
Streptococcus pneumoniae
and
Haemophilus influenzae
, including resistant bacteria, were sometimes involved between 2000 and 2004.
Molecular Detection of
Cellulosimicrobium cellulans
as the Etiological Agent of a Chronic Tongue Ulcer in a Human Immunodeficiency Virus-Positive Patient
Authors: Heym Beate , Gehanno Pierre , Friocourt Véronique , Bougnoux Marie-Elisabeth , Le Moal Michèle , Husson Corinne , Leibowitch Jacques , Nicolas-Chanoine Marie-Hélène 
Published: August 2005

ABSTRACT

Ulcerations appeared on the tongue of a 48-year-old human immunodeficiency virus-positive man. Histological findings of the biopsy specimen and the fact that the patient had resided in Louisiana led us to suspect “American histoplasmosis.” A new ulcer appeared while the patient was being treated with itraconazole, and the gene for 16S rRNA of
Cellulosimicrobium cellulans
was amplified. The lesions healed during treatment with oral penicillin and azithromycin.
First Case of Infant Botulism Caused by
Clostridium baratii
Type F in California
Authors: Barash Jason R. , Tang Tania W. H. , Arnon Stephen S. 
Published: August 2005

ABSTRACT

In late 2003 a severely hypotonic neonate, just 38 h old at onset of illness, was found to have infant botulism caused by neurotoxigenic
Clostridium baratii
type F. Environmental investigations failed to identify a source of this strain. This is the youngest patient reported to have infant botulism and the fifth instance of infant botulism caused by
C. baratii
type F.
Phase II Study of Weekly Paclitaxel and 24-Hour Infusion of High-Dose 5-Fluorouracil and Leucovorin in the Treatment of Recurrent or Metastatic Gastric Cancer
Authors: Yeh Kun-Huei , Lu Yen-Shen , Hsu Chih-Hung , Lin Jing-Fang , Hsu Chiun , Kuo Sung-Hsin , Li Shiou-Jr , Cheng Ann-Lii 
Published: August 2005

To investigate the efficacy and safety of combining weekly paclitaxel with weekly 24-hour infusion of high-dose 5-fluorouracil (5-FU) and leucovorin (LV, folinic acid) in the treatment of patients with advanced gastric cancer. Patients with histologically confirmed recurrent or metastatic gastric cancer were studied. Paclitaxel 80 mg/m<sup>2</sup> 3-hour intravenous infusion was given on days 1, 8, and 15, and high-dose 5-FU 2,600 mg/m<sup>2</sup> plus LV 300 mg/m<sup>2</sup> 24-hour intravenous infusion (HDFL) was given on days 2, 9, and 16, repeated every 4 weeks. Between August 1997 and August 2003, 30 patients were enrolled. The median age was 58 years (range: 37–70). Eighteen patients (60.0%) had recurrent or metastatic disease and 12 patients had de novo metastatic disease. Among the 27 patients evaluable for tumor response, 2 achieved complete response and 9 achieved partial response, with an overall response rate of 40.7% (95% confidence interval, CI: 22–61%). Eleven of the 21 patients without prior exposure to HDFL-containing regimens responded (response rate: 52.4%, 95% CI: 29–74%), while none of the 6 patients who had previously failed HDFL-containing regimens responded (p value = 0.054 by Fisher’s exact test). All 30 patients were evaluated for survival and toxicities. Median time to progression and overall survival were 6 and 10 months, respectively. Major grade 3–4 toxicities were neutropenia in 12 patients (40.0%), diarrhea in 10 patients (33.3%), and stomatitis in 3 patients (10.0%). Grade 1–2 and 3–4 paclitaxel-related neuropathy developed in 16 (53.3%) and 2 (6.7%) patients, respectively. None of the patients discontinued protocol treatment because of paclitaxel-related neuropathy or developed HDFL-related hyperammonemic encephalopathy. This paclitaxel-HDFL regimen is effective and well tolerated in the treatment of advanced gastric cancer.
Diagnosing Heat and Vorticity Budgets of Annual Coupled Rossby Waves
Authors: White Warren B. , Annis Jeffrey L. 
Published: August 2005

Abstract
Annual coupled Rossby waves are generated at the west coast of Australia and propagate westward across the eastern Indian Ocean from 10° to 30°S in covarying sea level height (SLH), sea surface temperature (SST), and meridional surface wind (MSW) residuals, generally traveling slower than uncoupled Rossby waves while increasing amplitude. The waves decouple in the western Indian Ocean as SST and SLH residuals become decorrelated, with wave amplitudes decreasing and westward phase speeds increasing. Here, the ocean and atmosphere thermal and vorticity budgets of the coupled Rossby waves in the eastern Indian Ocean along 20°S are diagnosed. In the upper ocean, these diagnostics find the residual SST tendency driven by the residual meridional geostrophic advection of mean temperature with warm SST residuals dissipated by upward latent heat flux to the atmosphere. In the troposphere, these upward latent heat fluxes drive mid-to-upper-level residual diabatic heating via excess condensation, balanced there by upward residual vertical thermal advection. The resulting upward residual vertical velocity drives residual upper-level divergence and lower-level convergence, the latter balanced in the troposphere vorticity budget by the residual meridional advection of planetary vorticity. This yields poleward MSW residuals collocated with warm SST residuals, as observed. The SLH tendency is modified by a positive feedback from wind stress curl residuals, the latter acting to increase the amplitude and decrease the westward phase speed of the wave. These diagnostics allow a more exact analytical model for coupled Rossby waves to be constructed, yielding wave characteristics as observed.
Squid – a simple bioinformatics grid
Authors: Carvalho Paulo C , Glória Rafael V , de Miranda Antonio B , Degrave Wim M 
Published: August 2005

Abstract
Background
BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers.

Results
Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer.

Conclusion
Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example.