bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gastroduodenal Lesions and Helicobacter pylori Infection in Dyspeptic Patients With and Without Chronic Renal Failure
Authors: Nardone Gerardo , Rocco Alba , Fiorillo Maria , Del Pezzo Mariassunta , Autiero Giovanni , Cuomo Rosario , Sarnelli Giovanni , Lambiase Antonietta , Budillon Gabriele , Cianciaruso Bruno 
Published: February 2005

ABSTRACTBackground.  Patients with chronic renal failure (CRF) often have dyspeptic symptoms and may develop peptic disease or digestive disorders leading to severe gastrointestinal complications. The primary aim of this study was to evaluate the prevalence of peptic lesions and Helicobacter pylori infection, and the severity of dyspeptic symptoms, in dyspeptic patients with and without CRF. Our secondary aim was to investigate whether uremic status may affect the diagnostic efficiency of the [13]C‐urea breath test ([13]C‐UBT).Patients and Methods.  We consecutively enrolled in the study 50 dyspeptic patients with chronic kidney failure (mean age 52 ± 5 years), of whom 11 were on hemodialysis treatment (HD), and 93 subjects (mean age 54 ± 7 years) with chronic dyspepsia and normal renal function (NRF). All patients completed an oriented and validated questionnaire scoring the severity of nine dyspeptic symptoms (i.e. epigastric pain, epigastric burning, postprandial fullness, early satiety, bloating, belching, nausea and vomiting) and underwent upper endoscopy with multiple bioptic sampling for rapid urease test and histological examination, [13]C‐UBT and HpSA test.Results.  The prevalences of peptic lesions and H. pylori infection and mean symptom score were 74%, 52% and 3.5 ± 3, respectively, in dyspeptic patients with CRF and 18%, 36% and 8 ± 5, respectively, in dyspeptic patients with NRF. The diagnostic accuracy of [13]C‐UBT with respect to histological diagnosis was 94% and 97% for dyspeptic patients with and without renal failure, respectively.Conclusions.  1, A high frequency of peptic lesions and low symptom scores were observed in uremic patients in spite of H. pylori infection; 2, uremic status did not affect the diagnostic accuracy of [13]C‐UBT.
A Novel Enterohepatic Helicobacter Species ‘Helicobacter mastomyrinus’ Isolated from the Liver and Intestine of Rodents
Authors: Shen Zeli , Xu Shilu , Dewhirst Floyd E. , Paster Bruce J. , Pena Jeremy A. , Modlin Irvin M. , Kidd Mark , Fox James G. 
Published: February 2005

ABSTRACTBackground.  A number of novel Helicobacter species have been isolated from both animals and humans. Many of these helicobacters colonize the lower gastrointestinal tract and hepatobiliary tract and are associated with diseases.Methods.  A spiral‐shaped bacterium, with bipolar single‐sheathed flagella, was isolated from the liver and cecum of mastomys (the African rodent, Mastomys natalenis), from the feces and ceca of normal mice, and also from the cecum of a mouse with proctitis. 16S ribosomal RNA gene sequence analysis, restriction fragment length polymorphism (RFLP) and fluorophore‐enhanced repetitive element polymerase chain reaction (FERP or rep‐PCR) analysis were used to classify the organism.Results.  The bacterium grew at 37 and 42°C under microaerobic conditions, rapidly hydrolyzed urea, and was catalase and oxidase positive. It did not reduce nitrate to nitrite, and was resistant to cephalothin and nalidixic acid. Like many other enterohepatic Helicobacter species, this organism expressed cytolethal distending toxin and causes cell distention.Conclusions.  The organism was classified as a novel Helicobacter species for which we propose the name ‘Helicobacter mastomyrinus’. Although ‘H. mastomyrinus’, like Helicobacter hepaticus and Helicobacter bilis, colonizes the liver of rodents, the pathogenic potential of this novel helicobacter is unknown.
Template DNA Ratio can Affect Detection by Genus‐Specific PCR–Denaturing Gradient Gel Electrophoresis of Bacteria Present at Low Abundance in Mixed Populations
Authors: Zhang Li , Danon Stephen , Grehan Martin , Lee Adrian , Mitchell Hazel 
Published: February 2005

ABSTRACTThe detection of Helicobacter species by genus‐specific polymerase chain reaction–denaturing gradient gel electrophoresis (PCR‐DGGE) was compared with that by species‐specific PCR in murine intestinal samples. Results suggest that, in samples containing multiple Helicobacter species, genus‐specific PCR‐DGGE may fail to detect all Helicobacter species present and that this relates to the initial template DNA ratio.
The Effect of Ascorbic Acid on Helicobacter pylori Induced Cyclooxygenase 2 Expression and Prostaglandin E2 Production by Gastric Epithelial Cells in vitro
Authors: Smith Geoff V. , Farthing Michael J. G. 
Published: February 2005

ABSTRACTBackground.  Cyclooxygenase 2 (COX‐2) is induced by the presence of Helicobacter pylori (H. pylori) on the gastric mucosa as part of the inflammatory response; this results in the synthesis of prostaglandins that amplify the local inflammatory response. The presence of H. pylori inhibits the secretion of ascorbate into the gastric lumen. Interestingly, ascorbate inhibits the growth of H. pylori and low dietary levels are associated with an increased risk of gastric adenocarcinoma. We therefore investigated the effect of ascorbate on H. pylori mediated COX‐2 induction and prostaglandin production in vitro.Methods.  H. pylori was cocultured with gastric epithelial cells in the presence of ascorbate at physiological concentrations. The expression of COX‐2 was assessed by Western blotting and prostaglandin E2 (PGE2) was assessed by ELISA.Results.  Ascorbate inhibited gastric cell PGE2 synthesis but not in COX‐2 expression in response to H. pylori. In the absence of the organism, ascorbate also reduced PGE2 expression in cells that constitutively express COX‐2, again with no reduction of COX‐2 protein expression.Conclusions.  Physiological concentrations of ascorbate inhibit PGE2 but not COX‐2 expression in response to H. pylori in gastric epithelial cells.
Experimental deformation of partially melted granite revisited: implications for the continental crust
Authors: ROSENBERG C. L. , HANDY M. R. 
Published: February 2005

AbstractA review and reinterpretation of previous experimental data on the deformation of partially melted crustal rocks reveals that the relationship of aggregate strength to melt fraction is non‐linear, even if plotted on a linear ordinate and abscissa. At melt fractions, Φ < 0.07, the dependence of aggregate strength on Φ is significantly greater than at Φ > 0.07. This melt fraction (Φ = 0.07) marks the transition from a significant increase in the proportion of melt‐bearing grain boundaries up to this point to a minor increase thereafter. Therefore, we suggest that it is the increase of melt‐interconnectivity that causes the dramatic strength drop between the solidus and a melt fraction of 0.07. We term this drop the ‘melt connectivity transition’ (MCT). A second, less‐pronounced strength drop occurs at higher melt fractions and corresponds to the breakdown of the solid (crystal) framework. This is the ‘solid‐to‐liquid transition’ (SLT), corresponding to the well known ‘rheologically critical melt percentage’. Although the strength drop at the SLT is about four orders of magnitude, the absolute value of this drop is small compared with the absolute strength of the unmelted aggregate, rendering the SLT invisible in a linear aggregate strength v. melt‐fraction diagram. On the other hand, the more important MCT has been overlooked in previous work because experimental data usually are plotted in logarithmic strength v. melt‐fraction diagrams, obscuring large strength drops at high absolute strength values. We propose that crustal‐scale localization of deformation effectively coincides with the onset of melting, pre‐empting attainment of the SLT in most geological settings. The SLT may be restricted to controlling flow localization within magmatic bodies, especially where melt accumulates.
Melting and melt segregation in the aureole of the Glenmore Plug, Ardnamurchan
Authors: HOLNESS M. B. , DANE K. , SIDES R. , RICHARDSON C. , CADDICK M. 
Published: February 2005

AbstractContact metamorphism caused by the Glenmore plug in Ardnamurchan, a magma conduit active for 1 month, resulted in partial melting, with melt now preserved as glass. The pristine nature of much of the aureole provides a natural laboratory in which to investigate the distribution of melt. A simple thermal model, based on the first appearance of melt on quartz–feldspar grain boundaries, the first appearance of quartz paramorphs after tridymite and a plausible magma intrusion temperature, provides a time‐scale for melting. The onset of melting on quartz–feldspar grain boundaries was initially rapid, with an almost constant further increase in melt rim thickness at an average rate of 0.5–1.0 × 10−9 cm s−1. This rate was most probably controlled by the distribution of limited amounts of H2O on the grain boundaries and in the melt rims.The melt in the inner parts of the aureole formed an interconnected grain‐boundary scale network, and there is evidence for only limited melt movement and segregation. Layer‐parallel segregations and cross‐cutting veins occur within 0.6 m of the contact, where the melt volume exceeded 40%. The coincidence of the first appearance of these signs of the segregation of melt in parts of the aureole that attained the temperature at which melting in the Qtz–Ab–Or system could occur, suggests that internally generated overpressure consequent to fluid‐absent melting was instrumental in the onset of melt movement.
Neurological toxicity of long‐term (>1 yr) thalidomide therapy in patients with multiple myeloma
Authors: Tosi Patrizia , Zamagni Elena , Cellini Claudia , Plasmati Rosaria , Cangini Delia , Tacchetti Paola , Perrone Giulia , Pastorelli Francesca , Tura Sante , Baccarani Michele , Cavo Michele 
Published: February 2005

Abstract: Objective: Thalidomide is remarkably active in advanced relapsed and refractory multiple myeloma (MM), so that its use has been recently proposed either in newly diagnosed patients or as maintenance treatment after conventional or high‐dose therapy. This latter therapeutic approach has risen the concern of side‐effects of long‐term therapy with this drug. Methods: We analysed long‐term toxicity of 40 patients (27 M, 13 F, median age = 61.5 yr) who received salvage therapy with thalidomide ± dexamethasone for longer than 12 months (median 15, range 12–44) at our centre. All the patients had achieved at least a stable disease upon treatment with thalidomide alone (200–400 mg/d, n = 20) or thalidomide (200 mg/d) and dexamethasone (40 mg/d for 4 d every 4 wk) (n = 20). Results and conclusions: Neurotoxicity was the most troublesome and frequent toxic effect that was observed after long‐term treatment, the incidence averaging 75%. Among these 30 patients symptoms included paraesthesias, tremor and dizziness. Neurotoxicity was grade 1 in six patients (15%); grade 2 in 13 patients (32.5%), thus determining thalidomide dose reduction to 100 mg/d; and grade 3 in 11 patients (27.5%) who had subsequently to interrupt therapy despite their response. Electromyographic study, performed in patients with grade ≥2 neurotoxicity, revealed a symmetrical, mainly sensory peripheral neuropathy, with minor motor involvement. The severity of neurotoxicity was not related to cumulative or daily thalidomide dose, but only to the duration of the disease prior to thalidomide treatment, although no patients presented neurological symptoms at study entry. These results suggest that long‐term thalidomide therapy in MM may be hampered by the remarkable neurotoxicity of the drug, and that a neurological evaluation should be mandatory prior to thalidomide treatment, in order to identify patients at risk of developing a peripheral neuropathy.
Use of Ethidium Monoazide and PCR in Combination for Quantification of Viable and Dead Cells in Complex Samples
Authors: Rudi Knut , Moen Birgitte , Drømtorp Signe Marie , Holck Askild L. 
Published: February 2005

ABSTRACT

The distinction between viable and dead cells is a major issue in many aspects of biological research. The current technologies for determining viable versus dead cells cannot readily be used for quantitative differentiation of specific cells in mixed populations. This is a serious limitation. We have solved this problem by developing a new concept with the viable/dead stain ethidium monoazide (EMA) in combination with real-time PCR (EMA-PCR). A dynamic range of approximately 4 log
10
was obtained for the EMA-PCR viable/dead assay. Viable/dead differentiation is obtained by covalent binding of EMA to DNA in dead cells by photoactivation. EMA penetrates only dead cells with compromised membrane/cell wall systems. DNA covalently bound to EMA cannot be PCR amplified. Thus, only DNA from viable cells can be detected. We evaluated EMA-PCR with the major food-borne bacterium
Campylobacter jejuni
as an example. Traditional diagnosis of this bacterium is very difficult due to its specific growth requirements and because it may enter a state where it is viable but not cultivable. The conditions analyzed included detection in mixed and natural samples, survival in food, and survival after disinfection or antibiotic treatment. We obtained reliable viable/dead quantifications for all conditions tested. Comparison with standard fluorescence-based viable/dead techniques showed that the EMA-PCR has a broader dynamic range and enables quantification in mixed and complex samples. In conclusion, EMA-PCR offers a novel real-time PCR method for quantitative distinction between viable and dead cells with potentially very wide application.
Transcriptional Organization of Genes for Protocatechuate and Quinate Degradation from
Acinetobacter
sp. Strain ADP1
Authors: Dal Süreyya , Trautwein Gaby , Gerischer Ulrike 
Published: February 2005

ABSTRACT

Quinate and protocatechuate are both abundant plant products and can serve, along with a large number of other aromatic or hydroaromatic compounds, as growth substrates for
Acinetobacter
sp. strain ADP1. The respective genes are part of the chromosomal
dca-pca-qui-pob-hca
cluster encoding these pathways. The adjacent
pca
and
qui
gene clusters, which encode enzymes for protocatechuate breakdown via the β-ketoadipate pathway and for the conversion of quinate or shikimate to protocatechuate, respectively, have the same direction of transcription and are both expressed inducibly in response to protocatechuate. The
pca
genes are governed by the transcriptional activator-repressor PcaU. The mechanism governing
qui
gene expression was previously unknown. Here we report data suggesting the existence of a large 14-kb primary transcript covering the
pca
and
qui
genes. The area between the
pca
and
qui
genes contains no promoter activity, whereas a weak, constitutive promoter was identified upstream of
quiA
(
quiAp
). The 5′ end of the
quiA
transcript was mapped. Northern blot analysis allowed the identification of a 12-kb transcript spanning
pcaI
to
quiX
. An analysis of the
pca
and
qui
gene transcripts in a strain missing the structural gene promoter
pcaIp
led to the identification of two
pcaIp
-independent transcripts (4 and 2.4 kb). The 2.4-kb transcript makes up about 25% of the total transcript abundance of
quiA
, and thus the majority of transcription of the last gene of the area is also driven by
pcaIp
. This report strongly supports the organization of the
pca
and
qui
genes as a
pca-qui
operon and, furthermore, suggests that PcaU is the regulator governing its expression.
Desulfitobacterium hafniense
Is Present in a High Proportion within the Biofilms of a High-Performance Pentachlorophenol-Degrading, Methanogenic Fixed-Film Reactor
Authors: Lanthier M. , Juteau P. , Lépine F. , Beaudet R. , Villemur R. 
Published: February 2005

ABSTRACT

We developed a pentachlorophenol (PCP)-degrading, methanogenic fixed-film reactor by using broken granular sludge from an upflow anaerobic sludge blanket reactor. This methanogenic consortium was acclimated with increasing concentrations of PCP. After 225 days of acclimation, the reactor was performing at a high level, with a PCP removal rate of 1,173 μM day
−1
, a PCP removal efficiency of up to 99%, a degradation efficiency of approximately 60%, and 3-chlorophenol as the main chlorophenol residual intermediate. Analyses by PCR-denaturing gradient gel electrophoresis (DGGE) showed that
Bacteria
and
Archaea
in the reactor stabilized in the biofilms after 56 days of operation. Important modifications in the profiles of
Bacteria
between the original granular sludge and the reactor occurred, as less than one-third of the sludge DGGE bands were still present in the reactor. Fluorescence in situ hybridization experiments with probes for
Archaea
or
Bacteria
revealed that the biofilms were composed mostly of
Bacteria
, which accounted for 70% of the cells. With PCR species-specific primers, the presence of the halorespiring bacterium
Desulfitobacterium hafniense
in the biofilm was detected very early during the reactor acclimation period.
D. hafniense
cells were scattered in the biofilm and accounted for 19% of the community. These results suggest that the presence of PCP-dehalogenating
D. hafniense
in the biofilm was crucial for the performance of the reactor.
Propionate Oxidation by and Methanol Inhibition of Anaerobic Ammonium-Oxidizing Bacteria
Authors: Güven Didem , Dapena Ana , Kartal Boran , Schmid Markus C. , Maas Bart , van de Pas-Schoonen Katinka , Sozen Seval , Mendez Ramon , Op den Camp Huub J. M. , Jetten Mike S. M. , Strous Marc , Schmidt Ingo 
Published: February 2005

ABSTRACT

Anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. Anammox bacteria have been described as obligate chemolithoautotrophs. However, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. In this study, the effect of organic compounds on anammox bacteria was investigated. It was shown that alcohols inhibited anammox bacteria, while organic acids were converted by them. Methanol was the most potent inhibitor, leading to complete and irreversible loss of activity at concentrations as low as 0.5 mM. Of the organic acids acetate and propionate, propionate was consumed at a higher rate (0.8 nmol min
−1
mg of protein
−1
) by Percoll-purified anammox cells. Glucose, formate, and alanine had no effect on the anammox process. It was shown that propionate was oxidized mainly to CO
2
, with nitrate and/or nitrite as the electron acceptor. The anammox bacteria carried out propionate oxidation simultaneously with anaerobic ammonium oxidation. In an anammox enrichment culture fed with propionate for 150 days, the relative amounts of anammox cells and denitrifiers did not change significantly over time, indicating that anammox bacteria could compete successfully with heterotrophic denitrifiers for propionate. In conclusion, this study shows that anammox bacteria have a more versatile metabolism than previously assumed.
Association ofCryptosporidium parvumwith Suspended Particles: Impact on Oocyst Sedimentation
Authors: Searcy Kristin E. , Packman Aaron I. , Atwill Edward R. , Harter Thomas 
Published: February 2005

ABSTRACTThe association ofCryptosporidium parvumoocysts with suspended particles can alter the oocysts' effective physical properties and influence their transport in aquatic systems. To assess this behavior,C. parvumoocysts were mixed with various suspended sediments under a variety of water chemical conditions, and the resulting settling of the oocysts was observed. Direct microscopic observations showed that oocysts attached to suspended sediments. Settling column and batch experiments demonstrated that oocysts are removed from suspension at a much higher rate when associated with sediments. The rate of oocyst sedimentation depended primarily on the type of sediment with which the oocysts were mixed. Changes in background water conditions had a relatively small impact on the extent of oocyst-particle association and the resulting oocyst deposition. We believe that the ubiquitous association ofC. parvumoocysts with suspended particles enhances the sedimentation of oocysts in natural waters and that this interaction should generally be considered when predicting the migration of pathogens in the environment.
Phylogenetic Characterization of 16S rRNA Gene Clones from Deep-Groundwater Microorganisms That Pass through 0.2-Micrometer-Pore-Size Filters
Authors: Miyoshi Tatsuo , Iwatsuki Teruki , Naganuma Takeshi 
Published: February 2005

ABSTRACT

A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-μm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-μm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-μm-pore-size filters were largely affiliated with
Betaproteobacteria
.
Discovery of
glpC
, an Organic Solvent Tolerance-Related Gene in
Escherichia coli
, Using Gene Expression Profiles from DNA Microarrays
Authors: Shimizu Kazunori , Hayashi Shuhei , Kako Takeshi , Suzuki Maiko , Tsukagoshi Norihiko , Doukyu Noriyuki , Kobayashi Takeshi , Honda Hiroyuki 
Published: February 2005

ABSTRACT

Gene expression profiles were collected from
Escherichia coli
strains (OST3410, TK33, and TK31) before and after exposure to organic solvents, and the six genes that showed higher gene expression were selected. Among these genes,
glpC
encoding the anaerobic glycerol-3-phosphate dehydrogenase subunit C remarkably increased the organic solvent tolerance.
Complexity of Bacterial Communities in a River-Floodplain System (Danube, Austria)
Authors: Besemer Katharina , Moeseneder Markus M. , Arrieta Jesus M. , Herndl Gerhard J. , Peduzzi Peter 
Published: February 2005

ABSTRACT
Natural floodplains play an essential role in the processing and decomposition of organic matter and in the self-purification ability of rivers, largely due to the activity of bacteria. Knowledge about the composition of bacterial communities and its impact on organic-matter cycling is crucial for the understanding of ecological processes in river-floodplain systems. Particle-associated and free-living bacterial assemblages from the Danube River and various floodplain pools with different hydrological characteristics were investigated using terminal restriction fragment length polymorphism analysis. The particle-associated bacterial community exhibited a higher number of operational taxonomic units (OTUs) and was more heterogeneous in time and space than the free-living community. The temporal dynamics of the community structure were generally higher in isolated floodplain pools. The community structures of the river and the various floodplain pools, as well as those of the particle-associated and free-living bacteria, differed significantly. The compositional dynamics of the planktonic bacterial communities were related to changes in the algal biomass, temperature, and concentrations of organic and inorganic nutrients. The OTU richness of the free-living community was correlated with the concentration and origin of organic matter and the concentration of inorganic nutrients, while no correlation with the OTU richness of the particle-associated assemblage was found. Our results demonstrate the importance of the river-floodplain interactions and the influence of damming and regulation on the bacterial-community composition.