bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of Railway-Induced Ground Vibrations in Tunnels
Authors: Lai Carlo G. , Callerio Alberto , Faccioli Ezio , Morelli Vittorio , Romani Pietro 
Published: September 2005

AbstractThe authors of this paper present the results of a study concerned with the assessment of the vibrational impact induced by the passage of commuter trains running in a tunnel placed underground the city of Rome. Since the railway line is not yet operational, it was not possible to make a direct measurement of the ground vibrations induced by the railway traffic and the only way to make predictions was by means of numerical simulations. The numerical model developed for the analyses was calibrated using the results of a vibration measurement campaign purposely performed at the site using as a vibration source a sinusoidal vibration exciter operating in a frequency-controlled mode. The problem of modeling the vibrational impact induced by the passage of a train moving in a tunnel is rather complex because it requires the solution of a boundary value problem of three-dimensional elastodynamics in a generally heterogeneous, nonsimply connected continuum with a moving source. The subject is further complicated by the difficulties of modeling the source mechanism, which constitutes itself a challenge even in the case of railway lines running at the surface. At last, the assessment of the vibrational impact at a receiver placed inside a building (e.g., a human individual or a sensitive instrument) requires an evaluation of the role played by the structure in modifying the computed free-field ground motion. So far, few attempts have been made to model the whole vibration chain (from the source to the receiver) of railway-induced ground vibrations, with results that have been only moderately successful. The numerical simulations performed in this study were made by using a simplified numerical model aimed to capture the essence of the physical phenomena involved in the above vibration chain including the influence of the structural response as well as the dependence of the predicted vibration spectra on the train speed.
Dissimilatory Iron Reduction and Odor Indicator Abatement by Biofilm Communities in Swine Manure Microcosms
Authors: Castillo-Gonzalez Hugo A. , Bruns Mary Ann 
Published: September 2005

ABSTRACTAnimal waste odors arising from products of anaerobic microbial metabolism create community relations problems for livestock producers. We investigated a novel approach to swine waste odor reduction: the addition of FeCl3, a commonly used coagulant in municipal wastewater treatment, to stimulate degradation of odorous compounds by dissimilatory iron-reducing bacteria (DIRB). Two hypotheses were tested: (i) FeCl3is an effective source of redox-active ferric iron (Fe3+) for dissimilatory reduction by bacteria indigenous to swine manure, and (ii) dissimilatory iron reduction results in significant degradation of odorous compounds within 7 days. Our results demonstrated that Fe3+from FeCl3was reduced biologically as well as chemically in laboratory microcosms prepared with prefiltered swine manure slurry and limestone gravel, which provided pH buffering and a substrate for microbial biofilm development. Addition of a 1-g liter−1equivalent concentration of Fe3+from FeCl3, but not from presynthesized ferrihydrite, caused initial, rapid solids flocculation, chemical Fe3+reduction, and Ehincrease, followed by a 2-day lag period. Between 2 and 6 days of incubation, increases in Fe2+concentrations were accompanied by significant reductions in concentrations of volatile fatty acids used as odor indicators. Increases in Fe2+concentrations between 2 and 6 days did not occur in FeCl3-treated microcosms that were sterilized by gamma irradiation or amended with NaN3, a respiratory inhibitor. DNA sequences obtained from rRNA gene amplicons of bacterial communities in FeCl3-treated microcosms were closely related toDesulfitobacteriumspp., which are known representatives of DIRB. Use of iron respiration to abate wastewater odors warrants further investigation.
Changes in Antimicrobial Susceptibility of Native
Enterococcus faecium
in Chickens Fed Virginiamycin
Authors: McDermott Patrick F. , Cullen Patti , Hubert Susannah K. , McDermott Shawn D. , Bartholomew Mary , Simjee Shabbir , Wagner David D. 
Published: September 2005

ABSTRACT

The extent of transfer of antimicrobial resistance from agricultural environments to humans is controversial. To assess the potential hazard posed by streptogramin use in food animals, this study evaluated the effect of virginiamycin exposure on antimicrobial resistance in
Enterococcus faecium
recovered from treated broilers. Four consecutive broiler feeding trials were conducted using animals raised on common litter. In the first three trials, one group of birds was fed virginiamycin continuously in feed at 20 g/ton, and a second group served as the nontreated control. In the fourth trial, antimicrobial-free feed was given to both groups. Fecal samples were cultured 1 day after chickens hatched and then at 1, 3, 5, and 7 weeks of age. Isolates from each time point were tested for susceptibility to a panel of different antimicrobials. Quinupristin/dalfopristin-resistant
E. faecium
appeared after 5 weeks of treatment in trial 1 and within 7 days of trials 2 to 4. Following removal of virginiamycin in trial 4, no resistant isolates were detected after 5 weeks. PCR failed to detect
vat
,
vgb
, or
erm
(B) in any of the streptogramin-resistant
E. faecium
isolates, whereas the
msr
(C) gene was detected in 97% of resistant isolates. In an experimental setting using broiler chickens, continuous virginiamycin exposure was required to maintain a stable streptogramin-resistant population of
E. faecium
in the animals. The bases of resistance could not be explained by known genetic determinants.
Heterogeneity of Times Required for Germination and Outgrowth from Single Spores of Nonproteolytic
Clostridium botulinum
Authors: Stringer Sandra C. , Webb Martin D. , George Susan M. , Pin Carmen , Peck Michael W. 
Published: September 2005

ABSTRACT

Knowledge of the distribution of growth times from individual spores and quantification of this biovariability are important if predictions of growth in food are to be improved, particularly when, as for
Clostridium botulinum
, growth is likely to initiate from low numbers of spores. In this study we made a novel attempt to determine the distributions of times associated with the various stages of germination and subsequent growth from spores and the relationships between these stages. The time to germination (
t
germ
), time to emergence (
t
emerg
), and times to reach the lengths of one (
t
C1
) and two (
t
C2
) mature cells were quantified for individual spores of nonproteolytic
C. botulinum
Eklund 17B using phase-contrast microscopy and image analysis. The times to detection for wells inoculated with individual spores were recorded using a Bioscreen C automated turbidity reader and were compatible with the data obtained microscopically. The distributions of times to events during germination and subsequent growth showed considerable variability, and all stages contributed to the overall variability in the lag time. The times for germination (
t
germ
), emergence (
t
emerg
−
t
germ
), cell maturation (
t
C1
−
t
emerg
), and doubling (
t
C2
−
t
C1
) were not found to be correlated. Consequently, it was not possible to predict the total duration of the lag phase from information for just one of the stages, such as germination. As the variability in postgermination stages is relatively large, the first spore to germinate will not necessarily be the first spore to produce actively dividing cells and start neurotoxin production. This information can make a substantial contribution to improved predictive modeling and better quantitative microbiological risk assessment.
Bacterial Community Composition in Lake Tanganyika: Vertical and Horizontal Heterogeneity
Authors: De Wever Aaike , Muylaert Koenraad , Van der Gucht Katleen , Pirlot Samuel , Cocquyt Christine , Descy Jean-Pierre , Plisnier Pierre-Denis , Vyverman Wim 
Published: September 2005

ABSTRACTVertical and latitudinal differences in bacterial community composition (BCC) in Lake Tanganyika were studied during the dry season of 2002 by means of denaturing gradient gel electrophoresis analysis of PCR-amplified 16S RNA fragments. Dominant bands were sequenced and identified as members of theCyanobacteria,Actinobacteria,Nitrospirae, green nonsulfur bacteria, andFirmicutesdivisions and theGamma- andDeltaproteobacteriasubdivisions. The BCC in the lake displayed both vertical and latitudinal variation. Vertical changes in BCC were related to the thermal water column stratification, which influences oxygen and nutrient concentrations. Latitudinal variation was related to upwelling of deep water and increased primary production in the south of the lake. The number of bands per sample increased with bacterial production in the epilimnion of the lake, suggesting a positive diversity-productivity relationship.
Maltotriose Utilization by Industrial
Saccharomyces
Strains: Characterization of a New Member of the α-Glucoside Transporter Family
Authors: Salema-Oom Madalena , Valadão Pinto Vera , Gonçalves Paula , Spencer-Martins Isabel 
Published: September 2005

ABSTRACT

Maltotriose utilization by
Saccharomyces cerevisiae
and closely related yeasts is important to industrial processes based on starch hydrolysates, where the trisaccharide is present in significant concentrations and often is not completely consumed. We undertook an integrated study to better understand maltotriose metabolism in a mixture with glucose and maltose. Physiological data obtained for a particularly fast-growing distiller's strain (PYCC 5297) showed that, in contrast to what has been previously reported for other strains, maltotriose is essentially fermented. The respiratory quotient was, however, considerably higher for maltotriose (0.36) than for maltose (0.16) or glucose (0.11). To assess the role of transport in the sequential utilization of maltose and maltotriose, we investigated the presence of genes involved in maltotriose uptake in the type strain of
Saccharomyces carlsbergensis
(PYCC 4457). To this end, a previously constructed genomic library was used to identify maltotriose transporter genes by functional complementation of a strain devoid of known maltose transporters. One gene, clearly belonging to the
MAL
transporter family, was repeatedly isolated from the library. Sequence comparison showed that the novel gene (designated
MTY1
) shares 90% and 54% identity with
MAL31
and
AGT1
, respectively. However, expression of Mty1p restores growth of the
S. cerevisiae
receptor strain on both maltose and maltotriose, whereas the closely related Mal31p supports growth on maltose only and Agt1p supports growth on a wider range of substrates, including maltose and maltotriose. Interestingly, Mty1p displays higher affinity for maltotriose than for maltose, a new feature among all the α-glucoside transporters described so far.
Amylomaltase ofPyrobaculum aerophilumIM2 Produces Thermoreversible Starch Gels
Authors: Kaper Thijs , Talik Boguslawa , Ettema Thijs J. , Bos Herman , van der Maarel Marc J. E. C. , Dijkhuizen Lubbert 
Published: September 2005

ABSTRACTAmylomaltases are 4-α-glucanotransferases (EC 2.4.1.25) of glycoside hydrolase family 77 that transfer α-1,4-linked glucans to another acceptor, which can be the 4-OH group of an α-1,4-linked glucan or glucose. The amylomaltase-encoding gene (PAE1209) from the hyperthermophilic archaeonPyrobaculum aerophilumIM2 was cloned and expressed inEscherichia coli, and the gene product (PyAMase) was characterized. PyAMase displays optimal activity at pH 6.7 and 95°C and is the most thermostable amylomaltase described to date. The thermostability of PyAMase was reduced in the presence of 2 mM dithiothreitol, which agreed with the identification of two possible cysteine disulfide bridges in a three-dimensional model of PyAMase. The kinetics for the disproportionation of malto-oligosaccharides, inhibition by acarbose, and binding mode of the substrates in the active site were determined. Acting on gelatinized food-grade potato starch, PyAMase produced a thermoreversible starch product with gelatin-like properties. This thermoreversible gel has potential applications in the food industry. This is the first report on an archaeal amylomaltase.
Phylogeny and Molecular Identification of Vibrios on the Basis of Multilocus Sequence Analysis
Authors: Thompson F. L. , Gevers D. , Thompson C. C. , Dawyndt P. , Naser S. , Hoste B. , Munn C. B. , Swings J. 
Published: September 2005

ABSTRACTWe analyzed the usefulness ofrpoA,recA, andpyrHgene sequences for the identification of vibrios. We sequenced fragments of these loci from a collection of 208 representative strains, including 192 well-documentedVibrionaceaestrains and 16 presumptiveVibrioisolates associated with coral bleaching. In order to determine the intraspecies variation among the three loci, we included several representative strains per species. The phylogenetic trees constructed with the different genetic loci were roughly in agreement with former polyphasic taxonomic studies, including the 16S rRNA-based phylogeny of vibrios. The familiesVibrionaceae,Photobacteriaceae,Enterovibrionaceae, andSalinivibrionaceaewere all differentiated on the basis of each genetic locus. Each species clearly formed separated clusters with at least 98, 94, and 94%rpoA,recA, andpyrHgene sequence similarity, respectively. The genusVibriowas heterogeneous and polyphyletic, withVibrio fischeri,V. logei, andV. wodanisgrouping closer to thePhotobacteriumgenus.V. halioticoli-,V. harveyi-,V. splendidus-, andV. tubiashii-related species formed groups within the genusVibrio. Overall, the three genetic loci were more discriminatory among species than were 16S rRNA sequences. In some cases, e.g., within theV. splendidusandV. tubiashiigroup,rpoAgene sequences were slightly less discriminatory thanrecAandpyrHsequences. In these cases, the combination of several loci will yield the most robust identification. We can conclude that strains of the same species will have at least 98, 94, and 94%rpoA,recA, andpyrHgene sequence similarity, respectively.
Longitudinal Study of Microbial Diversity and Seasonality in the Mexico City Metropolitan Area Water Supply System
Authors: Mazari-Hiriart Marisa , López-Vidal Yolanda , Ponce-de-León Sergio , Calva Juan José , Rojo-Callejas Francisco , Castillo-Rojas Gonzalo 
Published: September 2005

ABSTRACT

In the Mexico City metropolitan area (MCMA), 70% of the water for 18 million inhabitants is derived from the Basin of Mexico regional aquifer. To provide an overview of the quality of the groundwater, a longitudinal study was conducted, in which 30 sites were randomly selected from 1,575 registered extraction wells. Samples were taken before and after chlorine disinfection during both the rainy and dry seasons (2000-2001). Microbiological parameters (total coliforms, fecal coliforms, streptococci, and
Vibrio
spp.), the presence of
Helicobacter pylori
, and physicochemical parameters, including the amount of trihalomethanes (THMs), were determined. Although microorganisms and inorganic and organic compounds were evident, they did not exceed current permissible limits. Chlorine levels were low, and the bacterial counts were not affected by chlorine disinfection. Eighty-four bacterial species from nine genera normally associated with fecal contamination were identified in water samples.
H. pylori
was detected in at least 10% of the studied samples. About 40% of the samples surpassed the THM concentration allowed by Mexican and U.S. regulations, with levels of chloroform being high. The quality of the water distributed to the MCMA varied between the rainy and dry seasons, with higher levels of pH, nitrates, chloroform, bromodichloromethane, total organic carbon, and fecal streptococci during the dry season. This study showed that the groundwater distribution system is susceptible to contamination and that there is a need for a strict, year-round disinfection strategy to ensure adequate drinking-water quality. This situation in one of the world's megacities may reflect what is happening in large urban centers in developing countries which rely on a groundwater supply.
Fate of
Escherichia coli
during Ensiling of Wheat and Corn
Authors: Chen Y. , Sela S. , Gamburg M. , Pinto R. , Weinberg Z. G. 
Published: September 2005

ABSTRACT

A recombinant
Escherichia coli
strain carrying a plasmid with an antibiotic resistance marker and expressing the green fluorescent protein was inoculated at a concentration of 3.8 × 10
8
CFU/g into direct-cut wheat (348 g of dry matter kg
−1
), wilted wheat (450 g of dry matter kg
−1
), and corn (375 g of dry matter kg
−1
). The forages were ensiled in mini-silos. The treatments included control (no
E. coli
added), application of tagged
E. coli
, and delayed sealing of the inoculated wheat. Three silos per treatment were sampled on predetermined dates, and the numbers of
E. coli
were determined on Chromocult TBX medium with or without kanamycin. Colonies presumptively identified as
E. coli
were also tested for fluorescence activity. Addition of
E. coli
at the time of ensiling resulted in a more rapid decrease in the pH but had almost no effect on the chemical composition of the final silages or their aerobic stability.
E. coli
disappeared from the silages when the pH decreased below 5.0. It persisted longer in silages of wilted wheat, in which the pH declined more slowly. Control silages of all crops also contained bacteria, presumptively identified as
E. coli
, that were resistant to the antibiotic, which suggests that some epiphytic strains are naturally resistant to antibiotics.
Novel Lectin-Like Bacteriocins of Biocontrol Strain
Pseudomonas fluorescens
Pf-5
Authors: Parret Annabel H. A. , Temmerman Koen , De Mot René 
Published: September 2005

ABSTRACT

Bacteriocin LlpA, produced by
Pseudomonas
sp. strain BW11M1, is a peculiar antibacterial protein due to its homology to mannose-binding lectins mostly found in monocots (A. H. A. Parret, G. Schoofs, P. Proost, and R. De Mot, J. Bacteriol.
185:
897-908, 2003). Biocontrol strain
Pseudomonas fluorescens
Pf-5 contains two
llpA
-like genes, named
llpA1
Pf-5
and
llpA2
Pf-5
. Recombinant
Escherichia coli
cells expressing
llpA1
Pf-5
or
llpA2
Pf-5
acquired bacteriocin activity and secreted a 31-kDa protein cross-reacting with LlpA
BW11M1
antibodies. Antibacterial activity of the recombinant proteins was evidenced by gel overlay assays. Analysis of the antimicrobial spectrum indicated that LlpA1
Pf-5
and LlpA2
Pf-5
are able to inhibit
P. fluorescens
strains, as well as the related mushroom pathogen
Pseudomonas tolaasii
. LlpA-type bacteriocins are characterized by a domain structure consisting of tandem monocot mannose-binding lectin (MMBL) domains. Molecular phylogeny of these MMBL domains suggests that the individual MMBL domains within an LlpA protein have evolved separately toward a specific, as yet unknown, function or, alternatively, were acquired from different ancestral sources. Our observations are consistent with earlier observations, which hinted that MMBL-like bacteriocins represent a new family of antibacterial proteins, probably with a novel mode of action.
Artificial Neural Network Prediction of Viruses in Shellfish
Authors: Brion Gail , Viswanathan Chandramouli , Neelakantan T. R. , Lingireddy Srinivasa , Girones Rosina , Lees David , Allard Annika , Vantarakis Apostolos 
Published: September 2005

ABSTRACT
A database was probed with artificial neural network (ANN) and multivariate logistic regression (MLR) models to investigate the efficacy of predicting PCR-identified human adenovirus (ADV), Norwalk-like virus (NLV), and enterovirus (EV) presence or absence in shellfish harvested from diverse countries in Europe (Spain, Sweden, Greece, and the United Kingdom). The relative importance of numerical and heuristic input variables to the ANN model for each country and for the combined data was analyzed with a newly defined relative strength effect, which illuminated the importance of bacteriophages as potential viral indicators. The results of this analysis showed that ANN models predicted all types of viral presence and absence in shellfish with better precision than MLR models for a multicountry database. For overall presence/absence classification accuracy, ANN modeling had a performance rate of 95.9%, 98.9%, and 95.7% versus 60.5%, 75.0%, and 64.6% for the MLR for ADV, NLV, and EV, respectively. The selectivity (prediction of viral negatives) was greater than the sensitivity (prediction of viral positives) for both models and with all virus types, with the ANN model performing with greater sensitivity than the MLR. ANN models were able to illuminate site-specific relationships between microbial indicators chosen as model inputs and human virus presence. A validation study on ADV demonstrated that the MLR and ANN models differed in sensitivity and selectivity, with the ANN model correctly identifying ADV presence with greater precision.
Adhesion of the Entomopathogenic Fungus
Beauveria
(
Cordyceps
)
bassiana
to Substrata
Authors: Holder Diane J. , Keyhani Nemat O. 
Published: September 2005

ABSTRACT

The entomopathogenic fungus
Beauveria bassiana
produces at least three distinct single-cell propagules, aerial conidia, vegetative cells termed blastospores, and submerged conidia, which can be isolated from agar plates, from rich broth liquid cultures, and under nutrient limitation conditions in submerged cultures, respectively. Fluorescently labeled fungal cells were used to quantify the kinetics of adhesion of these cell types to surfaces having various hydrophobic or hydrophilic properties. Aerial conidia adhered poorly to weakly polar surfaces and rapidly to both hydrophobic and hydrophilic surfaces but could be readily washed off the latter surfaces. In contrast, blastospores bound poorly to hydrophobic surfaces, forming small aggregates, bound rapidly to hydrophilic surfaces, and required a longer incubation time to bind to weakly polar surfaces than to hydrophilic surfaces. Submerged conidia displayed the broadest binding specificity, adhering to hydrophobic, weakly polar, and hydrophilic surfaces. The adhesion of the
B. bassiana
cell types also differed in sensitivity to glycosidase and protease treatments, pH, and addition of various carbohydrate competitors and detergents. The outer cell wall layer of aerial conidia contained sodium dodecyl sulfate-insoluble, trifluoroacetic acid-soluble proteins (presumably hydrophobins) that were not present on either blastospores or submerged conidia. The variations in the cell surface properties leading to the different adhesion qualities of
B. bassiana
aerial conidia, blastospores, and submerged conidia could lead to rational design decisions for improving the efficacy and possibly the specificity of entomopathogenic fungi for host targets.