bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enterotoxigenic
Escherichia coli
with STh and STp Genotypes Is Associated with Diarrhea Both in Children in Areas of Endemicity and in Travelers
Authors: Bölin Ingrid , Wiklund Gudrun , Qadri Firdausi , Torres Olga , Bourgeois A. Louis , Savarino Stephen , Svennerholm Ann-Mari 
Published: November 2006

ABSTRACT

Enterotoxigenic
Escherichia coli
(ETEC) is an important cause of diarrhea among children in developing countries and in travelers to areas of ETEC endemicity. ETEC strains isolated from humans may produce a heat-labile enterotoxin (LT) and two types of the heat-stable enterotoxin STa, called STh and STp, encoded by the
estA
gene. Two commonly used assay methods for the detection of STa, the infant mouse assay or different enzyme-linked immunosorbent assays, are unable to distinguish between the two subtypes of ST. Different genotypic methods, such as DNA probes or PCR assays, may, however, allow such discrimination. Using gene probes, it has recently been reported that ETEC strains producing STp as the only enterotoxin are not associated with diarrhea. In this study, we have used highly specific PCR methods, including newly designed primers for STh together with previously described STp primers, to compare the relative distribution of STh and STp in ETEC isolated from children with diarrhea in three different geographically distinct areas, i.e., Bangladesh, Egypt, and Guatemala, and from travelers to Mexico and Guatemala. It was found that ETEC strains producing STp were as commonly isolated from cases of diarrhea as strains producing STh both in Egypt and Guatemala, whereas STp strains were considerably less common in Bangladesh. No difference was found in the relative distribution of STh and STp in ETEC strains isolated from travelers with diarrhea and from asymptomatic carriers. Irrespective of ST genotype, the disease symptoms were also similar in both children and travelers.
Pregnancy and Human Herpesvirus 8 Reactivation in Human Immunodeficiency Virus Type 1-Infected Women
Authors: Lisco Andrea , Barbierato Massimo , Fiore Josè R. , Gasperini Paola , Favia Anna , Volpe Anna , Chironna Maria , Pastore Giuseppe , Chieco-Bianchi Luigi , Calabrò Maria Luisa 
Published: November 2006

ABSTRACT
To investigate the impact of pregnancy on human herpesvirus 8 (HHV-8) reactivation in human immunodeficiency virus type 1 (HIV-1)-infected women, the HHV-8 DNA presence and load were analyzed in peripheral blood mononuclear cells (PBMCs) and cervicovaginal secretions (CVSs) from 15 pregnant women coinfected with HIV-1 and HHV-8. HHV-8 detection was analyzed in relation to anti-HHV-8 antibodies and HIV-1-related parameters. Nucleotide sequence analysis of an ORFK1 hypervariable region of the HHV-8 strains was performed. HHV-8 was detected in maternal PBMCs (5/15 women) from the second trimester and in CVSs (5/15 women) mainly from the third trimester. The HHV-8 load significantly increased late in pregnancy in both maternal compartments and was associated with a significant increase in HIV-1 shedding in the genital tract. Antilytic antibodies were significantly more common in HHV-8 DNA-positive women. An elevated HHV-8 load was found in the PBMCs of an infant born to a mother with large amounts of HHV-8 in both compartments at delivery. Different ORFK1 subtypes were found in maternal samples, whereas the same subtype was identified in the mother-child pair. These data suggest that pregnancy may induce HHV-8 replication in HIV-1-infected women. An augmented HHV-8 load may, in turn, influence mother-to-child transmission, since one of the HIV-1-infected mothers with HHV-8 reactivation transmitted her ORFK1 subtype to the infant, who showed a high level of HHV-8 viremia indicative of a primary infection. This finding documents for the first time the perinatal transmission of a specific HHV-8 subtype. Vertical transmission may thus play a role in HHV-8 spread also in areas of subendemicity among HIV-1-infected women.
Optimal Surveillance Culture Sites for Detection of Methicillin-Resistant
Staphylococcus aureus
in Newborns
Authors: Rosenthal Alana , White Diane , Churilla Sheila , Brodie Sandra , Katz Kevin C. 
Published: November 2006

ABSTRACT

We describe two outbreaks among newborns, one caused by community-associated methicillin-resistant
Staphylococcus aureus
(MRSA) and the other by hospital-associated MRSA. The umbilicus, rectum, and nares were tested for colonization. We found that no single body site had optimal sensitivity when tested alone. The combination of umbilical and nasal swabs achieved a sensitivity of >90%.
What Does Detection of
Mycobacterium ulcerans
DNA in the Margin of an Excised Buruli Ulcer Lesion Tell Us?
Authors: Rondini Simona , Mensah-Quainoo Ernestina , Junghanss Thomas , Pluschke Gerd 
Published: November 2006

ABSTRACT

We determined by real-time PCR the distribution of
Mycobacterium ulcerans
DNA in the excised lesion of a Buruli ulcer patient. A new lesion developed adjacent to the site of excision in the patient. The excised margin around the primary lesion contained a small amount of mycobacterial DNA in the area where the secondary lesion developed. These results suggest that a relatively small number of infiltrating mycobacteria can lead to the development of a recurrence.
Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and Ulcerative Colitis
Authors: Gophna Uri , Sommerfeld Katrin , Gophna Sharon , Doolittle W. Ford , Veldhuyzen van Zanten Sander J. O. 
Published: November 2006

ABSTRACT

A leading hypothesis for the role of bacteria in inflammatory bowel diseases is that an imbalance in normal gut flora is a prerequisite for inflammation. Testing this hypothesis requires comparisons between the microbiota compositions of ulcerative colitis and Crohn's disease patients and those of healthy individuals. In this study, we obtained biopsy samples from patients with Crohn's disease and ulcerative colitis and from healthy controls. Bacterial DNA was extracted from the tissue samples, amplified using universal bacterial 16S rRNA gene primers, and cloned into a plasmid vector. Insert-containing colonies were picked for high-throughput sequencing, and sequence data were analyzed, yielding species-level phylogenetic data. The clone libraries yielded 3,305 sequenced clones, representing 151 operational taxonomical units. There was no significant difference between floras from inflamed and healthy tissues from within the same individual.
Proteobacteria
were significantly (
P
= 0.0007) increased in Crohn's disease patients, as were
Bacteroidetes
(
P
< 0.0001), while
Clostridia
were decreased in that group (
P
< 0.0001) in comparison with the healthy and ulcerative colitis groups, which displayed no significant differences. Thus, the bacterial flora composition of Crohn's patients appears to be significantly altered from that of healthy controls, unlike that of ulcerative colitis patients. Imbalance in flora in Crohn's disease is probably not sufficient to cause inflammation, since microbiotas from inflamed and noninflamed tissues were of similar compositions within the same individual.
Characterization of Atypical Enteropathogenic
Escherichia coli
Strains That Express Typical Localized Adherence in HeLa Cells in the Absence of the Bundle-Forming Pilus
Authors: Hernandes Rodrigo Tavanelli , Vieira Mônica Aparecida Midolli , Carneiro Sylvia Mendes , Salvador Fábia Andréia , Gomes Tânia Aparecida Tardelli 
Published: November 2006

ABSTRACT

The characterization of nine atypical enteropathogenic
Escherichia coli
strains expressing localized adherence in HeLa cells in the absence of the bundle-forming pilus revealed a diversity of serotypes, plasmids, and virulence genes. Although the strains lacked known
E. coli
adhesin genes, the identification of new adhesins could contribute to the characterization of similar enteropathogenic
E. coli
isolates.
Rapid Identification of Pathogens in Blood Cultures with a Modified Fluorescence In Situ Hybridization Assay
Authors: Peters Remco P. H. , van Agtmael Michiel A. , Simoons-Smit Alberdina M. , Danner Sven A. , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M. 
Published: November 2006

ABSTRACT
We evaluated a modified fluorescence in situ hybridization (FISH) assay for rapid (<1 h) identification of microorganisms in growth-positive blood cultures. The results were compared to those of the standard FISH technique and conventional culturing. The rapid identification of microorganisms with modified FISH can have important effects on clinical management of patients with bloodstream infections.
Comparative Genomic Analysis of
Campylobacter jejuni
Strains Reveals Diversity Due to Genomic Elements Similar to Those Present in
C. jejuni
Strain RM1221
Authors: Parker Craig T. , Quiñones Beatriz , Miller William G. , Horn Sharon T. , Mandrell Robert E. 
Published: November 2006

ABSTRACT

Analysis of the complete genomic sequence of
Campylobacter jejuni
strain RM1221 identified four large genomic elements,
Campylobacter jejuni
-
i
ntegrated
e
lements (CJIEs), that were absent from
C. jejuni
strain NCTC 11168. To further investigate the genomic diversity of
Campylobacter
, we conducted a comparative genomic analysis from a collection of 67
C. jejuni
and 12
Campylobacter coli
strains isolated from various geographical locations and clinical and veterinary sources. Utilizing PCR, we demonstrated that 55% of the
C. jejuni
strains examined were positive for at least one RM1221-like genomic element and 27% were positive for two or more of these CJIEs. Furthermore, many
C. coli
strains were positive for either genomic element CJIE1 or CJIE3. To simultaneously assess for the presence or absence of several genes that comprise the various CJIEs, we developed a multistrain
C. jejuni
DNA microarray that contained most of the putative coding sequences for strains NCTC 11168 and RM1221. A comparative genomic hybridization (CGH) analysis of 35 of the 67
C. jejuni
strains confirmed the presence of genomic elements similar to those in strain RM1221. Interestingly, the DNA microarray analysis demonstrated that these genomic elements in the other
C. jejuni
strains often exhibited modular patterns with some regions of the CJIEs present and other regions either absent or highly divergent compared to strain RM1221. Our CGH method also identified 18 other intraspecies hypervariable regions, such as the capsule and lipooligosaccharide biosynthesis regions. Thus, the inclusion of genes from these integrated genomic elements and the genes from the other intraspecies hypervariable regions contributes to a better assessment of the diversity in
C. jejuni
and may increase the usefulness of DNA microarrays as an epidemiological genotyping tool. Finally, we also showed that in CJIE1, a
Campylobacter
Mu-like phage, is located differentially in other strains of
C. jejuni
, suggesting that it may integrate essentially randomly.
Use of the
Coccidioides posadasii
Δchs5 Strain for Quality Control in the ACCUPROBE Culture Identification Test for
Coccidioides immitis
Authors: McGinnis Michael R. , Smith Michael B. , Hinson Elizabeth 
Published: November 2006

ABSTRACT

Coccidioides posadasii
Δchs5 is a strain that is excluded from the select agent list. Sixteen assays using test reagents from three different ACCUPROBE
Coccidioides immitis
culture identification test lots had an average of 132,998 relative light units (RLU), which is well beyond the 50,000-RLU positive cutoff value for the test.
Coccidioides posadasii
Δchs5 is a satisfactory quality control isolate in the ACCUPROBE culture identification test for
Coccidioides immitis
.
Performance of Rapid Streptococcal Antigen Testing Varies by Personnel
Authors: Fox James W. , Cohen Daniel M. , Marcon Mario J. , Cotton William H. , Bonsu Bema K. 
Published: November 2006

ABSTRACT

Rapid carbohydrate antigen tests are frequently used to diagnose group A streptococcal (GAS) pharyngitis. Despite evidence of modest sensitivity in medical settings, rapid antigen tests are available to the public for self-testing. We sought to determine if the personnel performing a rapid streptococcal antigen test influence the test's performance characteristics. Throat swabs of pediatric patients performed for GAS pharyngitis in a tertiary-care children's hospital network were included during two study periods in 2004 and 2005. The performance characteristics of a rapid carbohydrate antigen test were evaluated in three clinical settings against a nucleic acid probe test method according to the personnel performing the test (laboratory technologist versus nonlaboratory personnel). Between the study periods, nonlaboratory personnel from one site underwent retraining. Subsequently, the performance characteristics of the rapid antigen test were reassessed. The sensitivity of the rapid antigen test varied widely among the different testing sites (56 to 90%). Notably, test sensitivity was consistently greater when the test was performed by laboratory technologists than when it was performed by nonlaboratory personnel (
P
< 0.0001). Although the rapid antigen test sensitivity significantly improved after nonlaboratory personnel at one testing site were retrained (sensitivity before versus after retraining;
P
< 0.0001), the sensitivity remained greater in the laboratory technologist cohort (
P
< 0.0001). These data confirm the important relationship of the operator performing a rapid streptococcal antigen test with the test's accuracy, even in a clinical setting, where operator training is mandated. Therefore, its use outside the medical setting by lay persons cannot be recommended without culture backup.
Production of Monoclonal Antibodies toTropheryma whippleiand Identification of Recognized Epitopes by Two-Dimensional Electrophoresis and Mass Spectrometry
Authors: Yu Yuefei , Kowalczewska Malgorzata , Decloquement Philippe , Nappez Claude , La Scola Bernard 
Published: November 2006

ABSTRACTTropheryma whipplei, the agent of Whipple's disease, is a gram-positive rod-shaped bacterium that belongs to the group of actinobacteria. In order to produce monoclonal antibodies (MAbs) against this bacterium, we inoculated mice with two different strains, Slow2 and Endo5. We produced 13 and 10 MAbs against Slow2 and Endo5, respectively. Nine of the Slow2 MAbs and seven of the Endo5 MAbs recognized a 58-kDa epitope. In addition, three other Endo5 MAbs detected a unique 84-kDa epitope. These MAbs were species specific, as they did not react with a selection of 22 different bacterial species, but they were not strain specific, as they did react with six other strains ofT. whipplei. Two-dimensional gel electrophoresis (2-DE) was combined with mass spectrometry (MS) to identify the 58-kDa and 84-kDa epitopes recognized by MAbs. After trypsin in-gel digestion of the spot, the 58-kDa protein was identified as an ATP synthase F1 complex beta chain, whereas the 84-kDa protein was identified as a polyribonucleotide nucleotidyltransferase by MS with matrix-assisted laser desorption ionization-time of flight. In an in vitro model, one of these MAbs allowed good detection ofT. whippleiin stool samples, contrary to a rabbit polyclonal antibody, which led to high fluorescent background. In the prospective studies, the produced MAb will be tested for detection ofT. whippleiin clinical samples, and the gene coding for identified 58-kDa and 84-kDa antigens will be tentatively cloned and then tested for its use in a diagnostic enzyme-linked immunosorbent assay for Whipple's disease.
Using Climate Forecasts for Drought Management
Authors: Steinemann Anne C. 
Published: November 2006

Abstract
Drought hazards, and the ability to mitigate them with advance warning, offer potentially valuable applications of climate forecast products. Yet the value is often untapped, owing to the gap between climate science and societal decisions. This study bridged that gap; it determined forecast needs among water managers, translated forecasts to meet those needs, and shaped drought decision making to take advantage of forecasts. NOAA Climate Prediction Center (CPC) seasonal precipitation outlooks were converted into a forecast precipitation index (FPI) tailored for water managers in the southeastern United States. The FPI expresses forecasts as a departure from the climatological normal and is consistent with other drought indicators. Evaluations of CPC seasonal forecasts issued during 1995–2000 demonstrated positive skill for drought seasons in the Southeast. In addition, using evaluation criteria of water managers, 88% of forecasts for drought seasons would have appropriately prompted drought responses. Encouraged by these evaluations, and the understandability of the FPI, state water managers started using the forecasts in 2001 for deciding whether to pay farmers to suspend irrigation. Economic benefits of this forecast information were estimated at $100–$350 million in a state-declared drought year (2001, 2002) and $5–$30 million in the other years (2003, 2004). This study provides four main contributions: 1) an investigation of the needs and potential benefits of seasonal forecast information for water management, 2) a method for translating the CPC forecasts into a format needed by water managers, 3) the integration of forecast information into agency decision making, and 4) the economic valuation of that forecast information.
The Modified Palmer Drought Severity Index Based on the NCEP North American Regional Reanalysis
Authors: Mo Kingtse C. , Chelliah Muthuvel 
Published: November 2006

Abstract
A 32-km high-resolution modified Palmer drought severity index (MPDSI) based on the National Centers for Environmental Prediction (NCEP) North American Regional Reanalysis (RR) from 1979 to 2004 is presented. The assumptions of Palmer, such as the water balance equation, the difference between observed precipitation and the climatologically expected precipitation over the maximum conditions, and the changes of the index as a function of the current index, are preserved. Many deficiencies of the original PDSI are eliminated by taking fields directly from the RR or by making better estimates. For example, fields such as potential evapotranspiration, evaporation, runoff, total soil moisture, and soil moisture change in a given month are obtained directly from the RR. The potential recharge is defined as the total soil moisture needed to reach the maximum total soil moisture at each grid point for each calendar month. The potential precipitation is defined as the maximum precipitation at each grid point for a given calendar month. The underground volumetric soil moisture includes both frozen and liquid form. Therefore, the contribution of snowmelt is taken into account inexplicitly. The questionable assumptions of two-layer soil model and the available soil moisture capacity are no longer needed. Overall, the MPDSI, when averaged over a large area and long time, often resembles the traditional PDSI based on the Palmer formula and the climate-division data. The MPDSI obeys Gaussian distribution, and so it can also be used to assess the potential for floods. Together with a consistent suite of soil moisture, surface energy, and atmospheric terms from the RR, the MPDSI can be used to monitor and diagnose drought and floods.
The Successive-Order-of-Interaction Radiative Transfer Model. Part II: Model Performance and Applications
Authors: O’Dell Christopher W. , Heidinger Andrew K. , Greenwald Thomas , Bauer Peter , Bennartz Ralf 
Published: November 2006

Abstract
Radiative transfer models for scattering atmospheres that are accurate yet computationally efficient are required for many applications, such as data assimilation in numerical weather prediction. The successive-order-of-interaction (SOI) model is shown to satisfy these demands under a wide range of conditions. In particular, the model has an accuracy typically much better than 1 K for most microwave and submillimeter cases in precipitating atmospheres. Its speed is found to be comparable to or faster than the commonly used though less accurate Eddington model. An adjoint has been written for the model, and so Jacobian sensitivities can be quickly calculated. In addition to a conventional error assessment, the correlation between errors in different microwave channels is also characterized. These factors combine to make the SOI model an appealing candidate for many demanding applications, including data assimilation and optimal estimation, from microwave to thermal infrared wavelengths.
Comparisons of Transport and Dispersion Model Predictions of the Mock Urban Setting Test Field Experiment
Authors: Warner Steve , Platt Nathan , Heagy James F. , Jordan Jason E. , Bieberbach George 
Published: November 2006

Abstract
The potential effects of a terrorist attack involving the atmospheric release of chemical, biological, radiological, nuclear, or other hazardous materials continue to be of concern to the United States. The Defense Threat Reduction Agency has developed a Hazard Prediction Assessment Capability (HPAC) that includes initial features to address hazardous releases within an urban environment. Improved characterization and understanding of urban transport and dispersion are required to allow for more robust modeling. In 2001, a scaled urban setting was created in the desert of Utah using shipping containers, and tracer gases were released. This atmospheric tracer and meteorological study is known as the Mock Urban Setting Test (MUST). This paper describes the creation of sets of HPAC predictions and comparisons with the MUST field experiment. Strong consistency between the conclusions of this study and a previously reported HPAC evaluation that relied on urban tracer observations within the downtown area of Salt Lake City was found. For example, in both cases, improved predictions were associated with the inclusion of a simple empirically based urban dispersion model within HPAC, whereas improvements associated with the inclusion of a more computationally intensive wind field module were not found. The use of meteorological observations closest to the array and well above the obstacle array—the sonic anemometer measurements 16 m above ground level—resulted in predictions with the best fit to the observed tracer concentrations. The authors speculate that including meteorological observations or vertical wind profiles above or upwind of an urban region might be a sufficient input to create reasonable HPAC hazard-area predictions.
Thieno[3,4-d]imidazolium-containing Molecular Wire: Switching Behavior of Photoinduced Intramolecular Electron Transfer
Authors: Ie Yutaka , Kawabata Tetsuro , Kaneda Takahiro , Aso Yoshio 
Published: November 2006

Abstract
Zinc–porphyrin–oligothiophene–fullerene triad, where diethynylthieno[3,4-d]imidazolium is incorporated as a central unit of oligothiophene, has been synthesized. A dramatic enhancement of fluorescence from the zinc–porphyrin unit was observed on displacing counter anion from I− to F− in the imidazolium salt, indicating that photoinduced intramolecular electron transfer is controllable by the electronic perturbation to this unit.
Lower Temperature Dehydrogenation of Methylcyclohexane by Membrane-assisted Equilibrium Shift
Authors: Gora Artur , Tanaka David A Pacheco , Mizukami Fujio , Suzuki Toshishige M 
Published: November 2006

Abstract
Selective removal of hydrogen by the palladium membrane of novel configuration shifts the equilibrium in the dehydrogenation of methylcyclohexane allowing a continuous operation at below the critical temperature of palladium α–β phase transition.