bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of “CandidatusThioturbo danicus,” a Microaerophilic Bacterium That Builds Conspicuous Veils on Sulfidic Sediments
Authors: Muyzer Gerard , Yildirim Esengül , van Dongen Udo , Kühl Michael , Thar Roland 
Published: December 2005

ABSTRACTMolecular analysis of bacteria enriched under in situ-like conditions and mechanically isolated by micromanipulation showed that a hitherto-uncultivated microaerophilic bacterium thriving in oxygen-sulfide counter-gradients (R. Thar and M. Kühl, Appl. Environ. Microbiol. 68:6310-6320, 2000) is affiliated with the ε-subdivision of theProteobacteria. The affiliation was confirmed by the use of whole-cell hybridization with newly designed specific oligonucleotide probes. The bacterium belongs to a new genus and received the provisional name “CandidatusThioturbo danicus.”
Analysis of
fae
and
fhcD
Genes in Mono Lake, California
Authors: Nercessian Olivier , Kalyuzhnaya Marina G. , Joye Samantha B. , Lidstrom Mary E. , Chistoserdova Ludmila 
Published: December 2005

ABSTRACT

Genes for two enzymes of the tetrahydromethanopterin-linked C
1
transfer pathway (
fae
and
fhcD
) were detected in hypersaline, hyperalkaline Mono Lake (California), via PCR amplification and analysis. Low diversity for
fae
and
fhcD
was noted, in contrast to the diversity previously detected in a freshwater lake, Lake Washington (Washington).
Molecular Forensic Profiling of
Cryptosporidium
Species and Genotypes in Raw Water
Authors: Ruecker Norma J. , Bounsombath Niravanh , Wallis Peter , Ong Corinne S. L. , Isaac-Renton Judith L. , Neumann Norman F. 
Published: December 2005

ABSTRACT

The emerging concept of host specificity of
Cryptosporidium
spp. was exploited to characterize sources of fecal contamination in a watershed. A method of molecular forensic profiling of
Cryptosporidium
oocysts on microscope slides prepared from raw water samples processed by U.S. Environmental Protection Agency Method 1623 was developed. The method was based on a repetitive nested PCR-restriction fragment length polymorphism-DNA sequencing approach that permitted the resolution of multiple species/genotypes of
Cryptosporidium
in a single water sample.
Distribution of Serotypes and Antimicrobial Resistance Genes among
Streptococcus agalactiae
Isolates from Bovine and Human Hosts
Authors: Dogan Belgin , Schukken Y. H. , Santisteban C. , Boor Kathryn J. 
Published: December 2005

ABSTRACT

To better understand the emergence and transmission of antibiotic-resistant
Streptococcus agalactiae
, we compared phenotypic and genotypic characteristics of 52 human and 83 bovine S.
agalactiae
isolates. Serotypes found among isolates from human hosts included V (48.1%), III (19.2%), Ia and Ib (13.5% each), and II (5.8%). Among isolates from bovine hosts, molecular serotypes III and II were predominant (53 and 14.5%, respectively). Four and 21 different ribotypes were found among human and bovine isolates, respectively. A combination of ribotyping and serotyping showed that two bovine isolates were indistinguishable from human isolates. Resistance to tetracycline and erythromycin was more common among human (84.6% and 26.9%, respectively) than bovine (14.5% and 3.6%, respectively) isolates.
tetM
was found in all tetracycline-resistant human isolates, while
tetO
was the predominant resistance gene among bovine isolates.
tet
genes were found among various ribotypes.
ermB
,
ermTR
, and
mefA
were detected among erythromycin-resistant human isolates, while
ermB
was the only erythromycin resistance determinant among isolates from bovine hosts. For isolates from human hosts, erythromycin resistance genes appeared to be associated with specific ribotypes. We conclude that (i) human and bovine S.
agalactiae
isolates represent distinct populations; (ii) human host-associated
S. agalactiae
subtypes may occasionally be transmitted to bovines; (iii) while emergence of erythromycin and tetracycline resistance appears to largely occur independently among human and bovine isolates, occasional cross-species transfer of resistant strains or transmission of resistance genes between human- and bovine-associated subtypes may occur; and (iv) dissemination of antibiotic-resistant
S. agalactiae
appears to include both clonal spread of resistant strains as well as horizontal gene transfer.
High Prevalence of Human Papillomavirus Infections in Urine Samples from Human Immunodeficiency Virus-Infected Men
Authors: Smits Paul H. M. , Bakker Remco , Jong Eefje , Mulder Jan Willem , Meenhorst Pieter L. , Kleter Bernhard , van Doorn Leen-Jan , Quint Wim G. V. 
Published: December 2005

ABSTRACTInfection with human immunodeficiency virus (HIV) and the resulting immunosuppression are associated with an increased risk for human papillomavirus (HPV) persistence and related malignancies. In the present study we investigated the prevalence of HPV in urine samples from 104 HIV-infected men with low CD4+cell counts (<100 per mm3) and 115 urine samples from HIV-negative men. A high prevalence of HPV DNA (39.4%) was found in the HIV patients. Most of the HPV types were high risk (81.4%), with HPV 52 as the most prevalent type (12.5%), followed by HPV 18 (6.7%), HPV 35 (5.8%), and HPV 70 (4.8%). Multiple HPV genotypes were observed in 17 (41%) of the 41 HPV- and HIV-positive men. In contrast, only 11 (9.6%) HPV DNA-positive cases were observed among the 115 HIV-uninfected men, and 3 (27.3%) contained multiple genotypes. Quantitative analyses indicated that the HPV viral load, as measured in urine samples, is significantly higher in HIV-positive men compared to HIV-negative men. In the present study we show that urine samples are useful for detecting HPV DNA, there is a high prevalence of HPV in HIV-positive men, and the HPV viral load is substantially higher in HIV-positive than in HIV-negative men. More studies are needed to evaluate the risk and natural development of HPV-related malignancies in HIV-positive men.
Comparison of Two Target Genes for Detection and Genotyping of
Giardia lamblia
in Human Feces by PCR and PCR-Restriction Fragment Length Polymorphism
Authors: Bertrand Isabelle , Albertini Laetitia , Schwartzbrod Janine 
Published: December 2005

ABSTRACT

A PCR assay targeting the
tpi
gene was developed to detect and to genotype
Giardia lamblia
in human feces. Our assay was specific and discriminated between
G. lamblia
assemblages A and B.
G. lamblia
cysts isolated from human feces were also analyzed with two previously described PCR-restriction fragment length polymorphism (RFLP) assays, which are based on the detection of
tpi
or
gdh
genes. These RFLP analyses distinguished groups I and II within assemblage A or groups III and IV within assemblage B. Among 26 fecal samples from patients with sporadic giardiasis diagnosed by hospital laboratories, the
tpi
gene was amplified from 25 (96%) with our PCR assay, whereas only 21 (81%) samples were positive when the
gdh
gene was targeted. Of the 25 positive samples, nine (36%) contained assemblage A and 16 (64%) contained assemblage B. Thus, RFLP analysis classified eight samples (32%) in assemblage A group II, eight (32%) in assemblage B group III, and five (20%) in assemblage B group IV. The group could not be specified for four samples. The
tpi
and
gdh
genes of
G. lamblia
assemblage B were amplified from 14 (93%) of 15 samples collected only from French soldiers coming back from the Ivory Coast. All of these contained assemblage B group III. The PCR method developed is sensitive, simple, and specific and shows that the
tpi
gene is well adapted for
G. lamblia
genotyping.
Evaluation of a (1→3)-β-
d
-Glucan Assay for Diagnosis of Invasive Fungal Infections
Authors: Pickering Jerry W. , Sant Howard W. , Bowles Catherine A. P. , Roberts William L. , Woods Gail L. 
Published: December 2005

ABSTRACT

The Fungitell assay (Associates of Cape Cod, Inc.) is a commercial test that detects (1-3)-β-
d
-glucan (BG) and is intended for diagnosis of invasive fungal infections. To evaluate the Fungitell assay, we tested serum and plasma samples from healthy blood donors and from patients with blood cultures positive for yeast or bacteria. All
36 blood donors were BG negative, and 13 of 15 candidemic patients were
BG positive. Of 25 bacteremic patients, 14 (10 with gram-positive
bacteremia) were BG positive. One of the latter patients with
Staphylococcus aureus
bacteremia also had invasive
candidiasis, based on histological findings in a tissue biopsy;
therefore, the BG result was a true positive. The sensitivity,
specificity, and positive and negative predictive values of the
Fungitell assay, by patient, for these three groups were 93.3%, 77.2%,
51.9%, and 97.8%, respectively. We also performed the Fungitell assay
on sera that had been tested for
Aspergillus
galactomannan or
Histoplasma
antigen. All six
Histoplasma
antigen-positive patients and 31 of 32
Aspergillus
galactomannan-positive patients were also BG positive. BG results for
the 10
Histoplasma
antigen-negative and the 32
Aspergillus
galactomannan-negative patients varied, but we
were unable to confirm many of the results. Between-run coefficients of
variance (CVs) for the assay ranged from 3.2% to 16.8%; within-run CVs
were ≤4.8%. The correlation coefficient for an interlaboratory
reproducibility study was 0.9892. Concentrations of hemoglobulin,
bilirubin, and triglycerides that caused 20% interference were 588, 72,
and 466 mg/dl, respectively. Our results suggest that the Fungitel
assay may be most useful for excluding invasive fungal
infection.
Rapid Determination of Rifampin Resistance in Clinical Isolates of
Mycobacterium tuberculosis
by Real-Time PCR
Authors: Kocagoz Tanil , Saribas Zeynep , Alp Alpaslan 
Published: December 2005

ABSTRACT

Real-time PCR was used to determine rifampin resistance in clinical isolates of
Mycobacterium tuberculosis
. Ninety-six rifampin-resistant isolates and 23 rifampin-susceptible isolates were included in the study. A 305-bp region covering the 81-bp “rifampin resistance-determining region” of
rpoB
was amplified. Two hybridization probe pairs that covered the most frequent mutation sites in
rpoB
, codon regions 526 to 531 and 513 to 516, were used. The results obtained by real-time PCR were compared to those obtained by the proportion method. For detection of rifampin resistance, the real-time PCR assay yielded a sensitivity of 92.7% and a specificity of 100%. Real-time PCR is a very rapid method, and it can be especially helpful for the reporting of resistant clinical isolates in a very short period of time.
Use of Phylogenetic and Phenotypic Analyses To Identify Nonhemolytic Streptococci Isolated from Bacteremic Patients
Authors: Hoshino Tomonori , Fujiwara Taku , Kilian Mogens 
Published: December 2005

ABSTRACTThe aim of this study was to evaluate molecular and phenotypic methods for the identification of nonhemolytic streptococci. A collection of 148 strains consisting of 115 clinical isolates from cases of infective endocarditis, septicemia, and meningitis and 33 reference strains, including type strains of all relevantStreptococcusspecies, were examined. Identification was performed by phylogenetic analysis of nucleotide sequences of four housekeeping genes,ddl,gdh,rpoB, andsodA; by PCR analysis of the glucosyltransferase (gtf) gene; and by conventional phenotypic characterization and identification using two commercial kits, Rapid ID 32 STREP and STREPTOGRAM and the associated databases. A phylogenetic tree based on concatenated sequences of the four housekeeping genes allowed unequivocal differentiation of recognized species and was used as the reference. Analysis of single gene sequences revealed deviation clustering in eight strains (5.4%) due to homologous recombination with other species. This was particularly evident inS. sanguinisand in members of the anginosus group of streptococci. The rate of correct identification of the strains by both commercial identification kits was below 50% but varied significantly between species. The most significant problems were observed withS. mitisandS. oralisand 11Streptococcusspecies described since 1991. Our data indicate that identification based on multilocus sequence analysis is optimal. As a more practical alternative we recommend identification based onsodAsequences with reference to a comprehensive set of sequences that is available for downloading from our server. An analysis of the species distribution of 107 nonhemolytic streptococci from bacteremic patients showed a predominance ofS. oralisandS. anginosuswith various underlying infections.
Use of a Commercially Available Line Probe Assay for Genotyping of Hepatitis C Virus 5a Strains
Authors: Verbeeck Jannick , Maes Piet , Wollants Elke , Van der Merwe Schalk , Song Ernie , Nevens Frederik , Van Ranst Marc 
Published: December 2005

ABSTRACT
To validate a commercially available line probe assay for samples containing the infrequently found hepatitis C virus (HCV) genotype 5a, we sequenced a 511-nucleotide fragment of the NS4b region of Belgian and South African HCV genotype 5a samples. Phylogenetic analysis of the sequence data was performed. For the 77 HCV genotype 5a samples collected, there was 100% concordance between the genotype assignment by the line probe assay and the genotyping based on nucleotide sequencing, despite sequence heterogeneity in the probe binding sites of some samples.
Broth Microdilution Susceptibility Testing of
Campylobacter jejuni
and the Determination of Quality Control Ranges for Fourteen Antimicrobial Agents
Authors: McDermott Patrick F. , Bodeis-Jones Sonya M. , Fritsche Thomas R. , Jones Ronald N. , Walker Robert D. , Campylobacter Susceptibility Testing Group the 
Published: December 2005

ABSTRACT

Quality control ranges were developed for broth microdilution testing of
Campylobacter jejuni
ATCC 33560 against 14 antimicrobials. Cation-adjusted Mueller-Hinton broth containing 2.5% laked horse blood was the preferred medium, with incubation in a microaerobic atmosphere of 10% CO
2
, 5% O
2
, and 85% N
2
at 36°C for 48 h or 42°C for 24 h.
Nocardia ignorata
, a New Agent of Human Nocardiosis Isolated from Respiratory Specimens in Europe and Soil Samples from Kuwait
Authors: Rodríguez-Nava Verónica , Couble Andrée , Khan Z. U. , Pérouse de Montclos M. , Brasme L. , Villuendas Cruz , Molinard Claudie , Boiron Patrick , Laurent Frédéric 
Published: December 2005

ABSTRACT

Nocardia ignorata
is a recently described species identified on the basis of a single isolate of unknown origin. Here we describe the epidemiological, phenotypic, and phylogenetic characteristics of this new species, based on five new clinical and soil isolates.
Thyroid Abscess Due to a Mixed Anaerobic Infection with
Fusobacterium mortiferum
Authors: Stavreas Nikolaos P. , Amanatidou Constantina D. , Hatzimanolis Emmanuel G. , Legakis Ioannis , Naoum George , Lakka-Papadodima Elli , Georgoulias George , Morfou Panagiota , Tsiodras Sotirios 
Published: December 2005

ABSTRACT

A rare case of a thyroid abscess due to mixed anaerobic flora containing
Fusobacterium mortiferum
in an immunocompetent patient is described. The patient was successfully treated with immediate surgical intervention and appropriate antimicrobial agents.
Transmission of a Panton-Valentine Leucocidin-Positive, Methicillin-Resistant
Staphylococcus aureus
Strain between Humans and a Dog
Authors: van Duijkeren E. , Wolfhagen M. J. H. M. , Heck M. E. O. C. , Wannet W. J. B. 
Published: December 2005

ABSTRACT

Panton-Valentine leucocidin-positive methicillin-resistant
Staphylococcus aureus
(MRSA) strains with identical resistance patterns were cultured from recurrent infections of a 51-year-old patient, her healthy husband, son, and dog, and pulsed-field gel electrophoresis showed that all MRSA strains were indistinguishable.
Anticipatory Gain Modulation in Preparation for Smooth Pursuit Eye Movements
Authors: Tabata Hiromitsu , Miura Kenichiro , Kawano Kenji 
Published: December 2005

Abstract
We studied the effect of the probability of required tracking on the gain of visuomotor transmission for pursuit initiation in monkeys. We recorded the ocular responses to a brief movement (perturbation) of a target located at an eccentric position from the central fixation spot. As soon as the central fixation spot went off, the animal was required to make a saccade to the target if it remained stationary or to track if it moved. The probability of an upcoming ramp motion of the target (horizontal, 200/sec), requiring pursuit, was varied (target motion probability [TMP] = 0, 0.25, 0.5, 0.75, and 1, which was fixed in a block). We found that the magnitude of the response to the perturbation increased gradually as the TMP increased. The initial pursuit response and the perturbation response showed very similar dependence on the TMP, suggesting that the response to the perturbation could be used as an index of the gain of visuomotor transmission for pursuit initiation. We also found that the changes in the ocular responses after the TMP was changed from one probability to another occurred rapidly (decay constant of only a few trials). These results suggest that the gain of visuomotor transmission in preparing for pursuit is rapidly modulated in accordance with the anticipated future need for pursuit.
Evidence That Autobiographic Memory Retrieval Does Not Become Independent of the Hippocampus: An fMRI Study Contrasting Very Recent with Remote Events
Authors: Rekkas P. V. , Constable R. Todd 
Published: December 2005

Abstract
Traditional consolidation theory, which seeks to explain how new memories are incorporated into the preexisting neural architecture, stipulates that the hippocampus plays a time-limited role in this process. However, although there is abundant research showing that the hippocampus is necessary for the initial (encoding) phase, there is very little experimental evidence with human subjects proving that the structure ceases to play a role in the retrieval of episodic items from memory stores. To test this hypothesis, we investigated recall activation associated with recent memories (2.5 days) versus remote memories (mean of 8 years) using functional magnetic resonance imaging. In accordance with the multiple memory trace theory, recall of consolidated autobiographic information, represented by the remote condition, was not independent of the hippocampus. Both types of memory retrieval produced significant activation in parahippocampal, prefrontal, and midtemporal gyri, the parietal-temporal junction, and a medial region of cortex spanning the posterior cingulate and precuneus gyri. However, where recent events activated bilateral regions of the caudate nucleus, remote events yielded significantly greater activation within the hippocampus proper. The results challenge traditional consolidation theory, which would predict greater hippocampal activity for recent events. Furthermore, they highlight the interplay between multiple memory systems in the brain. We argue that our particular question format, which encouraged depth of recall and did not require a prescan interview, as well as our delineation of the recent and remote time periods, were the determining factors for the observed pattern of hippocampal activation.
Orthographic Distinctiveness and Semantic Elaboration Provide Separate Contributions to Memory
Authors: Kirchhoff Brenda A. , Schapiro Melissa L. , Buckner Randy L. 
Published: December 2005

Abstract
Orthographic distinctiveness and semantic elaboration both enhance memory. The present behavioral and functional magnetic resonance imaging (fMRI) studies examined the relationship between the influences of orthographic distinctiveness and semantic elaboration on memory, and explored whether they make independent contributions. As is typical for manipulations of processing levels, words studied during semantic encoding were better remembered than words studied during nonsemantic encoding. Notably, orthographically distinct words were better recalled and received more remember responses on recognition memory tests than orthographically common words regardless of encoding task, suggesting that orthographic distinctiveness has an additive effect to that of semantic elaboration on memory. In the fMRI study, ortho-graphic distinctiveness and semantic elaboration engaged separate networks of brain regions. Semantic elaboration modulated activity in left inferior prefrontal and lateral temporal regions. In contrast, orthographic distinctiveness modulated activity in distinct bilateral inferior prefrontal, extrastriate, and parietal regions. Orthographic distinctiveness and semantic elaboration appear to have separate behavioral and functional-anatomic contributions to memory.
In the Nick of Time: Thoreau's "Present" Experiment as a Colloquy of East and West
Authors: Hodder Alan 
Published: December 2005

AbstractA central expression of the thematic structure of Henry David Thoreau's first two books, A Week on the Concord and Merrimack Rivers and Walden, and essential to several of the epiphanies that famously appear there, are his meditations on the nature and significance of time. Seldom, however, have these richly conceived passages been considered other than through strictly literary eyes. The objective of this essay is to examine the theological implications of Thoreau's representations of time with particular reference to two classical treatments that seem of particular relevance here: those found in Augustine's Confessions and the Hindu classic, the Bhagavad Gita. The purpose of this discussion is two-fold: to consider the theological cogency of Thoreau's treatment of time for its own sake and to reconsider Thoreau's position with respect to two theological traditions of which he was arguably an heir.
Hegemony and the International Economy
Authors: Pahre Robert 
Published: December 2005

AbstractPower and leadership are among the central features of politics. They become even more visible in an environment such as the international system that lacks strong institutions. Without legislatures or administrative organs in a normal sense, political processes such as leadership, persuasion, and coercion come to the fore.These processes, especially the question of leadership, are central to many policy questions. Is Franco-German leadership of the European Union breaking up, or will it be joined by a more Europhile Britain? How will China or Japan play a leadership role in East Asia?Nowhere is the question of leadership more discussed than in the case of the most powerful country in the world – once the United Kingdom, today the United States, perhaps one day China. For some people, the leadership of this "hegemon" helps bring peace and prosperity to the world as a whole; for others, its dominance is overbearing and illegitimate.Questions of hegemony have received significant academic attention over the past few decades. This chapter will review the North American literature on the topic, with an eye toward several questions. First, what does a hegemon do when it is being hegemonic? Second, how do non-hegemonic countries respond to its leadership? Third, and most important for the future, is hegemony good or bad for the international system? I will discuss these with reference to topics in political economy, setting aside an equally-large literature on the military consequences of hegemony. Though political economy has implications for ideology and discourse, this article will also set aside most of these issues, which have sparked a large and distinct literature of their own.