bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and Accurate Identification of Human Isolates ofPasteurellaand Related Species by Sequencing thesodAGene
Authors: Gautier Anne-Lise , Dubois Damien , Escande Françoise , Avril Jean-Loup , Trieu-Cuot Patrick , Gaillot Olivier 
Published: May 2005

ABSTRACTThe identification ofPasteurellaand related bacteria remains a challenge. Here, a 449- to 473-bp fragment (sodAint) internal to thesodAgene, encoding the manganese-dependent superoxide dismutase, was amplified and sequenced with a single pair of degenerate primers from the type strains ofPasteurella(18 strains),Gallibacterium(1 strain), andMannheimia(5 strains) species. ThesodAint-based phylogenetic tree was in general agreement with that inferred from the analysis of the corresponding 16S rRNA gene sequences, with members of thePasteurellasensu stricto cluster (Pasteurella multocida,Pasteurella canis,Pasteurella dagmatis, andPasteurella stomatis) forming a monophyletic group andGallibacteriumandMannheimiabeing independent monophyletic genera. However, thesodAintsequences showed a markedly higher divergence than the corresponding 16S rRNA genes, confirming thatsodAis a potent target to differentiate related species. Thirty-three independent human clinical isolates phenotypically assigned to 13Pasteurellaspecies by a reference laboratory were successfully identified by comparing theirsodAintsequences to those of the type species. In the course of this work, we identified the firstGallibacterium anatisisolate ever reported from a human clinical specimen. ThesodAintsequences of the clinical isolates displayed less than 2.5% divergence from those of the corresponding type strains, except for thePasteurella pneumotropicaisolates, which were closely related to each other (>98%sodAintsequence identity) but shared only 92%sodAintidentity with the type strain. The method described here provides a rapid and accurate tool for species identification ofPasteurellaisolates when access to a sequencing facility is available.
Quantification of Hepatitis Delta Virus RNA in Serum by Consensus Real-Time PCR Indicates Different Patterns of Virological Response to Interferon Therapy in Chronically Infected Patients
Authors: Le Gal Frédéric , Gordien Emmanuel , Affolabi Dissou , Hanslik Thomas , Alloui Chakib , Dény Paul , Gault Elyanne 
Published: May 2005

ABSTRACTHepatitis delta virus (HDV), in association with hepatitis B virus, is responsible for severe acute and chronic hepatitis. Treatment of the infection relies on the long-term administration of high doses of alpha interferon (IFN), and the treatment efficiency is monitored by the detection of anti-HDV immunoglobulin M and HDV genome in serum. Like the case for other chronic viral infections, HDV genome quantification in serum should be useful for the follow-up of infected patients. The aims of this study were to develop a quantitative assay for the detection of any type of HDV in serum and to evaluate the benefit of HDV RNA quantification for the follow-up of chronically infected patients receiving IFN. A real-time reverse transcription-PCR assay was developed to quantify the HDV RNA load in serum. Its efficacy was evaluated with 160 serum samples, 76 of which were collected from 11 chronically infected patients who were treated with pegylated IFN. The assay was sensitive (100 copies/ml of serum) and efficient for all HDV types, including type 3 and the recently described types 5, 6, and 7. The viral load determinations for treated patients allowed us to identify different profiles of virological responses to IFN therapy with more accuracy than that attainable with the qualitative approach. In conclusion, we have developed a quantitative HDV RNA assay for serum which is adapted to the follow-up of antiviral treatment for patients infected with any HDV type. The assay will help us to understand the natural history of HDV infection and to define guidelines for the management of chronic delta hepatitis.
Loop-Mediated Isothermal Amplification Method for Rapid Detection of the Periodontopathic BacteriaPorphyromonas gingivalis,Tannerella forsythia, andTreponema denticola
Authors: Yoshida Akihiro , Nagashima Shiori , Ansai Toshihiro , Tachibana Masayo , Kato Hiroaki , Watari Hajime , Notomi Tsugunori , Takehara Tadamichi 
Published: May 2005

ABSTRACTLoop-mediated isothermal amplification (LAMP), a novel nucleic acid amplification method, was developed for the rapid detection of the major periodontal pathogensPorphyromonas gingivalis,Tannerella forsythia, andTreponema denticola. The LAMP method amplifies DNA with high specificity, efficiency, and rapidity under isothermal conditions using a set of four specially designed primers and a DNA polymerase with strand displacement activity. In this study, we initially designed the primers for LAMP assays to detect these bacteria and evaluated the specificity and sensitivity of these assays. The specificities of the primers for these bacteria were examined using various oral bacteria and various reaction times. The lower detection limits of the 60-min LAMP reaction without loop primers were 1 μg/tube forP. gingivalis, 10 fg/tube forT. forsythia, and 1 ng/tube forT. denticola. Addition of the loop primers for each bacterium improved the detection specificities and sensitivities by several magnitudes. Furthermore, LAMP assays were applied to the rapid detection of these periodontal pathogens in clinical specimens, and the results were compared with those of conventional PCR detection. The results of the LAMP assays corresponded to those of conventional PCR assays. These results indicate that the LAMP assay is an extremely rapid, highly sensitive, specific method. This method is very useful for the rapid detection of periodontopathic bacteria and the diagnosis of periodontal disease.
Development and Use of an Internal Positive Control for Detection of
Bordetella pertussis
by PCR
Authors: Herwegh Stéphanie , Carnoy Christophe , Wallet Frédéric , Loïez Caroline , Courcol René J. 
Published: May 2005

ABSTRACT

An internal control of amplification was constructed by recombinant PCR to detect PCR inhibitors. This exogenous DNA was included in the reaction mixture and coamplified with the target gene. This detection was successfully applied to the diagnosis of whooping cough by amplification of a fragment of
Bordetella pertussis
IS
481
.
Comparative Molecular Analysis of
Haemophilus influenzae
Isolates from Young Children with Acute Lower Respiratory Tract Infections and Meningitis in Hanoi, Vietnam
Authors: Watanabe Hiroshi , Kaji Chiharu , Anh Dang Duc , Huong Phan Le Thanh , Anh Nguyen Thi Hien , Huong Vu Thi , Phuong Hoang Vu Mai , Thi Ngo Thi , Suu Pham Thi , Nguyet Nguyen Thi Thu , Rusizoka Olivia Sebastian , Watanabe Kiwao , Nagatake Tsuyoshi , Oishi Kazunori 
Published: May 2005

ABSTRACT

Thirty-seven
Haemophilus influenzae
strains from nasopharyngeal swabs (NP) and 44
H. influenzae
strains from cerebrospinal fluid (CSF) were investigated. Of the 37
H. influenzae
isolates from NP, the serotypes of 30 isolates were nontypeable, 4 were type b, 2 were type c, and 1 was type a, whereas all of the 44 isolates from CSF were type b. The MICs of 16 antibiotics for the
H. influenzae
isolates from NP and CSF were similar, and no β-lactamase-negative ampicillin-resistant strain was found. Molecular typing by pulsed-field gel electrophoresis (PFGE) showed that the 37
H. influenzae
strains from NP had 22 PFGE patterns, with none predominating, and the 44
H. influenzae
strains from CSF had 9 PFGE patterns, with patterns α (22 isolates) and β (12 isolates) predominating. Our results indicate that two predominant types of
H. influenzae
type b strains have the potential to spread among children with meningitis in Hanoi, Vietnam.
Broth Microdilution and Disk Diffusion Tests for Susceptibility Testing of
Pasteurella
Species Isolated from Human Clinical Specimens
Authors: Citron Diane M. , Warren Yumi A. , Fernandez Helen T. , Goldstein Maurice A. , Tyrrell Kerin L. , Goldstein Ellie J. C. 
Published: May 2005

ABSTRACT

Broth microdilution and disk diffusion susceptibility testing were performed on 73 strains of
Pasteurella
species isolated from human infections and on five American Type Culture Collection strains of
Pasteurella
species. Both methods appear reliable for testing susceptibilities of
Pasteurella
species.
Unstable Vancomycin Heteroresistance Is Common among Clinical Isolates of Methiciliin-Resistant
Staphylococcus aureus
Authors: Plipat Nottasorn , Livni Gilat , Bertram Heidi , Thomson Richard B. 
Published: May 2005

ABSTRACT

We tested 109 unique, vancomycin-susceptible, methicillin-resistant
Staphylococcus aureus
(MRSA) strains for vancomycin heteroresistance by a selection method, i.e., step-wise exposure of large inoculums to increasing concentrations of vancomycin. Although no strains demonstrated stable heteroresistance, 81 strains (74%) demonstrated unstable heteroresistance. Unstable heteroresistance is common among clinical isolates of MRSA and may represent a cause of therapeutic failure.
Prevalence, Incidence, and Clinical Relevance of the Reverse Transcriptase V207I Mutation Outside the YMDD Motif of the Hepatitis B Virus Polymerase during Lamivudine Therapy
Authors: Zöllner B. , Sterneck M. , Wursthorn K. , Petersen J. , Schröter M. , Laufs R. , Feucht H.-H. 
Published: May 2005

ABSTRACT
The reverse transcriptase V207I mutation within the hepatitis B virus (HBV) polymerase is associated with resistance to lamivudine in vitro. The prevalence of this mutation in treatment-naïve patients was 1% (1/96). A follow-up of the patient carrying this mutation prior to treatment revealed no loss of sensitivity of HBV to lamivudine in vivo.
Routine Incubation of BacT/ALERT FA and FN Blood Culture Bottles for More than 3 Days May Not Be Necessary
Authors: Bourbeau Paul P. , Foltzer Michael 
Published: May 2005

ABSTRACT
We reviewed time to detection for 35,500 blood cultures collected in BacT/ALERT FA and FN bottles. In the first 3 days of incubation, 97.5% of the 2,609 clinically significant isolates were detected, suggesting that routine incubation for more than 3 days may not be necessary for FA and FN bottles.
In Vitro Activity of Voriconazole against
Prototheca wickerhamii
: Comparative Evaluation of Sensititre and NCCLS M27-A2 Methods of Detection
Authors: Linares Maria José , Solís Francisco , Casal Manuel 
Published: May 2005

ABSTRACT

A total of 104
Prototheca wickerhamii
isolates and two control strains were tested for susceptibility to voriconazole using the Sensititre YeastOne colorimetric antifungal plate and NCCLS reference method. Voriconazole was highly active against all isolates, with an MIC at which 90% of isolates were inhibited of ≤0.5 μg/ml. Comparison of MICs obtained with the Sensititre product and the NCCLS method demonstrated agreement (100% ± 2 log
2
dilutions) between the two methods. Voriconazole may offer an option for the treatment of
Prototheca
sp. infections, and its efficacy should be established through clinical experience.
Methods for Reducing Bacterial Contamination in the BacT/Alert Mycobacterial Culture Detection System
Authors: Dionne Kim , Sweeney Amy , Hedgepeth Annie , Carroll Karen , Parrish Nicole 
Published: May 2005

ABSTRACT

Two methods were compared for decreasing bacterial contamination in the BacT/Alert mycobacterial culture detection system. Two concentrations, 0.5 ml (standard amount) and 1.0 ml, of mycobacterial antibiotic supplement were evaluated. Contamination rates were 14% and 6% for the standard and the doubled concentrations, respectively. This difference was statistically significant (
P
< 0.005).
Listeria-Associated Arthritis in a Patient Undergoing Etanercept Therapy: Case Report and Review of the Literature
Authors: Schett Georg , Herak Petra , Graninger Winfried , Smolen Josef S. , Aringer Martin 
Published: May 2005

ABSTRACTListeriosis can be a cause of infectious arthritis. Here, we present a case of articular listeriosis in a patient with rheumatoid arthritis receiving treatment with etanercept, a tumor necrosis factor antagonist. We review the literature of articular listeriosis and discuss the role of tumor necrosis factor blockade in precipitating listeriosis.
Unusual Laboratory Findings in a Case of Norwegian Scabies Provided a Clue to Diagnosis
Authors: Wong Samson S. Y. , Woo Patrick C. Y. , Yuen Kwok-yung 
Published: May 2005

ABSTRACT
The diagnosis of Norwegian scabies was missed for a year for an elderly long-term-care facility resident. Serpiginous tracks were noted on the surface of Sabouraud dextrose agar used for fungal culture of the skin scrapings. This unusual laboratory manifestation must alert clinical microbiologists to the possible diagnosis of scabies.
Drug therapy for acute myeloid leukemia
Authors: Tallman Martin S. , Gilliland D. Gary , Rowe Jacob M. 
Published: May 2005

AbstractAlthough improvement in outcomes has occurred in younger adults with acute myeloid leukemia (AML) during the past 4 decades, progress in older adults has been much less conspicuous, if at all. Approximately 50% to 75% of adults with AML achieve complete remission (CR) with cytarabine and an anthracycline such as daunorubicin or idarubicin or the anthracenedione mitoxantrone. However, only approximately 20% to 30% of the patients enjoy long-term disease survival. Various postremission strategies have been explored to eliminate minimal residual disease. The optimal dose, schedule, and number of cycles of postremission chemotherapy for most patients are not known. A variety of prognostic factors can predict outcome and include the karyotype of the leukemic cells and the presence of transmembrane transporter proteins, which extrude certain chemotherapy agents from the cell and confer multidrug resistance and mutations in or over expressions of specific genes such as WT1, CEBPA, BAX and the ratio of BCL2 to BAX, BAALC, EVI1, KIT, and FLT3. Most recently, insights into the molecular pathogenesis of AML have led to the development of more specific targeted agents and have ushered in an exciting new era of antileukemia therapy. Such agents include the immunoconjugate gemtuzumab ozogamicin, multidrug resistance inhibitors, farnesyl transferase inhibitors, histone deacetylase and proteosome inhibitors, antiangiogenesis agents, Fms-like tyrosine kinase 3 (FLT3) inhibitors, and apoptosis inhibitors.
A novel stem-cell population in adult liver with potent hematopoietic-reconstitution activity
Authors: Kotton Darrell N. , Fabian Attila J. , Mulligan Richard C. 
Published: May 2005

Abstract
A number of recent reports have documented that cells possessing hematopoietic-reconstitution ability can be identified and isolated from a variety of solid organs in the adult animal. In all studies to date, however, purified organ-derived stem cells demonstrate a diminished repopulating capacity relative to that of purified bone marrow–derived hematopoietic stem cells (BM HSCs). It has therefore been unclear whether organ-derived HSCs possess functional properties distinct from those of BM HSCs, or simply have not been purified to a comparable extent. Here we report the identification of a rare subset of cells in adult murine liver that possess potent blood-repopulating potential, approaching that of BM HSCs. The cells, isolated on the basis of dye-efflux activity and CD45 expression (termed CD45+ liver side population [SP] tip cells), exhibit a surface phenotype similar to that of freshly isolated BM HSCs derived from normal adult animals, but are phenotypically distinct in that they do not express the stem-cell marker c-kit. Single-cell transplantation studies indicate that CD45+ liver SP tip cells can be generated from BM HSCs, suggesting a relationship between stem-cell populations in the liver and bone marrow compartments. Overall, these studies have important implications for understanding extramedullary hematopoiesis, and may be relevant to current strategies aimed at inducing tolerance to transplanted organs.
Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals
Authors: Reneker Jeff , Shyu Chi-Ren 
Published: May 2005

Abstract
Background
Searching for small tandem/disperse repetitive DNA sequences streamlines many biomedical research processes. For instance, whole genomic array analysis in yeast has revealed 22 PHO-regulated genes. The promoter regions of all but one of them contain at least one of the two core Pho4p binding sites, CACGTG and CACGTT. In humans, microsatellites play a role in a number of rare neurodegenerative diseases such as spinocerebellar ataxia type 1 (SCA1). SCA1 is a hereditary neurodegenerative disease caused by an expanded CAG repeat in the coding sequence of the gene. In bacterial pathogens, microsatellites are proposed to regulate expression of some virulence factors. For example, bacteria commonly generate intra-strain diversity through phase variation which is strongly associated with virulence determinants. A recent analysis of the complete sequences of the Helicobacter pylori strains 26695 and J99 has identified 46 putative phase-variable genes among the two genomes through their association with homopolymeric tracts and dinucleotide repeats. Life scientists are increasingly interested in studying the function of small sequences of DNA. However, current search algorithms often generate thousands of matches – most of which are irrelevant to the researcher.

Results
We present our hash function as well as our search algorithm to locate small sequences of DNA within multiple genomes. Our system applies information retrieval algorithms to discover knowledge of cross-species conservation of repeat sequences. We discuss our incorporation of the Gene Ontology (GO) database into these algorithms. We conduct an exhaustive time analysis of our system for various repetitive sequence lengths. For instance, a search for eight bases of sequence within 3.224 GBases on 49 different chromosomes takes 1.147 seconds on average. To illustrate the relevance of the search results, we conduct a search with and without added annotation terms for the yeast Pho4p binding sites, CACGTG and CACGTT. Also, a cross-species search is presented to illustrate how potential hidden correlations in genomic data can be quickly discerned. The findings in one species are used as a catalyst to discover something new in another species. These experiments also demonstrate that our system performs well while searching multiple genomes – without the main memory constraints present in other systems.

Conclusion
We present a time-efficient algorithm to locate small segments of DNA and concurrently to search the annotation data accompanying the sequence. Genome-wide searches for short sequences often return hundreds of hits. Our experiments show that subsequently searching the annotation data can refine and focus the results for the user. Our algorithms are also space-efficient in terms of main memory requirements. Source code is available upon request.
Parallel organization of contralateral and ipsilateral prefrontal cortical projections in the rhesus monkey
Authors: Barbas Helen , Hilgetag Claus C , Saha Subhash , Dermon Caterina R , Suski Joanna L 
Published: May 2005

Abstract

Background
The neocortical commissures have a fundamental role in functional integration across the cerebral hemispheres. We investigated whether commissural projections in prefrontal cortices are organized according to the same or different rules as those within the same hemisphere, by quantitatively comparing density, topography, and laminar origin of contralateral and ipsilateral projections, labeled after unilateral injection of retrograde tracers in prefrontal areas.

Results
Commissural projection neurons constituted less than one third of the ipsilateral. Nevertheless, projections from the two hemispheres were strongly correlated in topography and relative density. We investigated to what extent the distribution of contralateral projections depended on: (a) geographic proximity of projection areas to the area homotopic to the injection site; (b) the structural type of the linked areas, based on the number and neuronal density of their layers. Although both measures were good predictors, structural type was a comparatively stronger determinant of the relative distribution and density of projections. Ipsilateral projection neurons were distributed in the superficial (II-III) and deep (V-VI) layers, in proportions that varied across areas. In contrast, contralateral projection neurons were found mostly in the superficial layers, but still showed a gradient in their distribution within cortical layers that correlated significantly with cortical type, but not with geographic proximity to the homotopic area.

Conclusion
The organization of ipsilateral and contralateral prefrontal projections is similar in topography and relative density, differing only by higher overall density and more widespread laminar origin of ipsilateral than contralateral projections. The projections on both sides are highly correlated with the structural architecture of the linked areas, and their remarkable organization is likely established by punctuated development of distinct cortical types. The preponderance of contralateral projections from layer III may be traced to the late development of the callosal system, whose function may be compromised in diseases that have their root late in ontogeny.
Effects of redox cycling compounds on DT diaphorase activity in the liver of rainbow trout (Oncorhynchus mykiss)
Authors: Sturve Joachim , Stephensen Eiríkur , Förlin Lars 
Published: May 2005

Abstract
Background
DT diaphorase (DTD; NAD(P)H:quinone oxidoreductase; EC 1.6.99.2) catalyses the two electron reduction of quinones, thus preventing redox cycling and consequently quinone dependent production of reactive oxygen species. In rat and mouse, a wide range of chemicals including polyaromatic hydrocarbons, azo dyes and quinones induces DTD. Bifunctional compounds, such as β-naphthoflavone (β-NF) and benzo(a)pyrene (B(a)P), induce DTD together with CYP1A and phase II enzymes by a mechanism involving the aryl hydrocarbon receptor (AHR). Monofunctional induction of DTD is mediated through the antioxidant response element and does not lead to the induction of AHR dependent enzymes, such as CYP1A. The aim of this study was to investigate the effects of prooxidants (both bifunctional and monofunctional) on the activity of hepatic DTD in rainbow trout (Oncorhynchus mykiss) in order to evaluate DTD suitability as a biomarker. We also investigated the effect of β-NF on hepatic DTD activity in perch (Perca fluviatilis), shorthorn sculpin (Myoxocephalus scorpius), eelpout (Zoarces viviparus), brown trout (Salmo trutta) and carp (Cyprinus carpio). In addition, the effect of short term exposure to prooxidants on catalase activity was investigated.

Results
In rainbow trout, hepatic DTD activity is induced by the bifunctional AHR agonists β-NF and B(a)P and the monofunctional inducers naphthazarin, menadione and paraquat. Although exposure to both B(a)P and β-NF led to a strong 7-ethoxyresorufin-O-deethylase (EROD) induction, none of the monofunctional compounds affected the rainbow trout EROD activity. DTD was not induced by β-NF in any of the other fish species. Much higher DTD activities were observed in rainbow trout compared to the other fish species. Catalase activity was less responsive to short term exposure to prooxidants compared to DTD.

Conclusion
Since rainbow trout hepatic DTD activity is inducible by both monofunctional and bifunctional inducers, it is suggested that rainbow trout DTD may be regulated by the same mechanisms, as in mammals. The fact that DTD is inducible in rainbow trout suggests that the enzyme may be suitable as a part of a biomarker battery when rainbow trout is used in environmental studies. It appears as if DTD activity in rainbow trout is higher and inducible compared to the other fish species studied.