bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructural Characterization of Cyanobacterial Mats from the McMurdo Ice Shelf, Antarctica
Authors: de los Ríos Asunción , Ascaso Carmen , Wierzchos Jacek , Fernández-Valiente Eduardo , Quesada Antonio
Published: January 2004

The three-dimensional structures of two types of cyanobacterium-dominated microbial mats from meltwater ponds on the McMurdo Ice Shelf were as determined by using a broad suite of complementary techniques, including optical and fluorescence microscopy, confocal scanning laser microscopy, scanning electron microscopy with back-scattered electron-imaging mode, low-temperature scanning electron microscopy, and microanalyitical X-ray energy dispersive spectroscopy. By using a combination of the different in situ microscopic techniques, the Antarctic microbial mats were found to be structures with vertical stratification of groups of cyanobacteria and mineral sediments, high contents of extracellular polymeric substances, and large void spaces occupied by water. In cyanobacterium-rich layers, heterocystous nostocalean and nonheterocystous oscillatorialean taxa were the most abundant taxa and appeared to be intermixed with fine-size deposits of epicellular silica and calcium carbonate. Most of the cyanobacterial filaments had similar orientations in zones without sediment particles, but thin filaments were tangled among thicker filaments. The combination of the microscopic techniques used showed the relative positions of biological and mineral entities within the microbial mats and enabled some speculation about their interactions.
Development of Genetic Techniques for the Psychrotrophic Fish Pathogen
Flavobacterium psychrophilum
Authors: Alvarez B. , Secades P. , McBride M. J. , Guijarro J. A.
Published: January 2004

Flavobacterium psychrophilum
, a member of the
Cytophaga-Flavobacterium-Bacteroides
group, is an important pathogen of salmonid fish. Previous attempts to develop genetic techniques for this fastidious, psychrotrophic bacterium have met with failure. Here we describe the development of techniques for the genetic manipulation of
F. psychrophilum
and the identification of plasmids, selectable markers, a reporter system, and a transposon that function in several isolates of this fish pathogen. The antibiotic resistance genes
ermF
,
cfxA
, and
tetQ
function in
F. psychrophilum
. Cloning vectors based on the
F. psychrophilum
cryptic plasmid pCP1 which carried these selectable markers were introduced by conjugation from
E. coli
, resulting in antibiotic-resistant colonies of
F. psychrophilum
. Conjugative transfer of DNA into
F. psychrophilum
was strain dependent. Efficient transfer was observed for two of the seven strains tested (THC02-90 and THC04-90).
E. coli lacZY
functioned in
F. psychrophilum
when expressed from a pCP1 promoter, allowing its development as a reporter for studies of gene expression. Plasmids isolated from
F. psychrophilum
were efficiently introduced into
F. psychrophilum
by electroporation, but plasmids isolated from
E. coli
were not suitable for transfer by this route, suggesting the presence of a restriction barrier. DNA isolated from
F. psychrophilum
was resistant to digestion by
Sau
3AI and
Bam
HI, indicating that a
Sau
3AI-like restriction modification system may constitute part of this barrier. Tn
4351
was introduced into
F. psychrophilum
from
E. coli
and transposed with apparent randomness, resulting in erythromycin-resistant colonies. The techniques developed in this study allow for genetic manipulation and analysis of this important fish pathogen.
Use of Stable-Isotope Probing, Full-Cycle rRNA Analysis, and Fluorescence In Situ Hybridization-Microautoradiography To Study a Methanol-Fed Denitrifying Microbial Community
Authors: Ginige Maneesha P. , Hugenholtz Philip , Daims Holger , Wagner Michael , Keller Jürg , Blackall Linda L.
Published: January 2004

A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source and nitrate as the electron acceptor. The SBR was inoculated with sludge from a biological nutrient removal activated sludge plant exhibiting good denitrification. The SBR denitrification rate improved from less than 0.02 mg of NO
3
−
-N mg of mixed-liquor volatile suspended solids (MLVSS)
−1
h
−1
to a steady-state value of 0.06 mg of NO
3
−
-N mg of MLVSS
−1
h
−1
over a 7-month operational period. At this time, the enriched microbial community was subjected to stable-isotope probing (SIP) with [
13
C]methanol to biomark the DNA of the denitrifiers. The extracted [
13
C]DNA and [
12
C]DNA from the SIP experiment were separately subjected to full-cycle rRNA analysis. The dominant 16S rRNA gene phylotype (group A clones) in the [
13
C]DNA clone library was closely related to those of the obligate methylotrophs
Methylobacillus
and
Methylophilus
in the order
Methylophilales
of the
Betaproteobacteria
(96 to 97% sequence identities), while the most abundant clone groups in the [
12
C]DNA clone library mostly belonged to the family
Saprospiraceae
in the
Bacteroidetes
phylum. Oligonucleotide probes for use in fluorescence in situ hybridization (FISH) were designed to specifically target the group A clones and
Methylophilales
(probes DEN67 and MET1216, respectively) and the
Saprospiraceae
clones (probe SAP553). Application of these probes to the SBR biomass over the enrichment period demonstrated a strong correlation between the level of SBR denitrification and relative abundance of DEN67-targeted bacteria in the SBR community. By contrast, there was no correlation between the denitrification rate and the relative abundances of the well-known denitrifying genera
Hyphomicrobium
and
Paracoccus
or the
Saprospiraceae
clones visualized by FISH in the SBR biomass. FISH combined with microautoradiography independently confirmed that the DEN67-targeted cells were the dominant bacterial group capable of anoxic [
14
C]methanol uptake in the enriched biomass. The well-known denitrification lag period in the methanol-fed SBR was shown to coincide with a lag phase in growth of the DEN67-targeted denitrifying population. We conclude that
Methylophilales
bacteria are the dominant denitrifiers in our SBR system and likely are important denitrifiers in full-scale methanol-fed denitrifying sludges.
Quantum Dots as a Novel Immunofluorescent Detection System for
Cryptosporidium parvum
and
Giardia lamblia
Authors: Zhu Liang , Ang Simon , Liu Wen-Tso
Published: January 2004

Semiconductor quantum dot-conjugated antibodies were successfully developed to label
Cryptosporidium parvum
and
Giardia lamblia
. This novel fluorescence system exhibited superior photostability, gave 1.5- to 9-fold-higher signal-to-noise ratios than traditional organic dyes in detecting
C. parvum
, and allowed dual-color detection for
C. parvum
and
G. lamblia
.
Analysis of the
gyrA
Gene of Clinical
Yersinia ruckeri
Isolates with Reduced Susceptibility to Quinolones
Authors: Gibello Alicia , Porrero M. Concepción , Blanco M. Mar , Vela Ana I. , Liébana Pilar , Moreno Miguel A. , Fernández-Garayzábal José F. , Domínguez Lucas
Published: January 2004

Antimicrobial susceptibility of seven clinical strains of
Yersinia ruckeri
representative of those isolated between 1994 and 2002 from a fish farm with endemic enteric redmouth disease was studied. All isolates displayed indistinguishable pulsed-field gel electrophoresis restriction patterns, indicating that they represented a single strain. However, considering both inhibition zone diameters (IZD) and MICs, the isolates recovered in 2001-2002 formed a separate cluster with lower levels of susceptibility to all the quinolones tested, especially nalidixic acid (NA) and oxolinic acid (OA), compared with the isolates recovered between 1994 and 1998. Analysis of the PCR product of the quinolone resistance-determining region of the
gyr
A gene from clinical isolates of
Y. ruckeri
with reduced susceptibility to OA and NA revealed a single amino acid substitution, Ser-83 to Arg-83 (
Escherichia coli
numbering). Identical substitution was observed in induced OA-resistant mutant strains, which displayed IZD and MICs of quinolones similar to those of the clinical isolates of
Y. ruckeri
with reduced susceptibility to these antimicrobial agents. These data indicate in that for
Y. ruckeri
, the substitution of Ser by Arg at position 83 of the
gyr
A gene is associated with reduced susceptibility to quinolones.
Cloning and Heterologous Expression of Hematin-Dependent Catalase Produced by
Lactobacillus plantarum
CNRZ 1228
Authors: Abriouel Hikmate , Herrmann Anette , Stärke Joachim , Yousif Nuha M. K. , Wijaya Agus , Tauscher Bernhard , Holzapfel Wilhelm , Franz Charles M. A. P.
Published: January 2004

Lactobacillus plantarum
CNRZ 1228 exhibited heme-dependent catalase activity under environmental conditions similar to those encountered during sausage fermentation. The 1,455-bp catalase gene (
katL
) was cloned and encoded a protein of 484 amino acids. Expression of
katL
in a heterologous host showed that
katL
encodes a functional catalase. PCR screening of selected strains of lactic acid bacteria for
katL
indicated the presence of similar genes in other strains of lactobacilli.
A Complete Library of Amino Acid Alterations at N304 in
Streptomyces clavuligerus
Deacetoxycephalosporin C Synthase Elucidates the Basis for Enhanced Penicillin Analogue Conversion
Authors: Chin Hong Soon , Goo Kian Sim , Sim T. S.
Published: January 2004

N304 of
Streptomyces clavuligerus
deacetoxycephalosporin C synthase was mutagenized to alter its catalytic ability. Given that N304A, N304K, N304L, and N304R mutant enzymes exhibited significant improvements in penicillin analogue conversions, we advocate that replacement of N304 with residues with aliphatic or basic side chains is preferable for engineering of a hypercatalytic enzyme.
Localization of the Insertion Site and Pathotype Determination of the Locus of Enterocyte Effacement of Shiga Toxin-Producing
Escherichia coli
Strains
Authors: Bertin Yolande , Boukhors Karima , Livrelli Valerie , Martin Christine
Published: January 2004

Of 220 Shiga toxin-producing
Escherichia coli
(STEC) strains collected in central France from healthy cattle, food samples, and asymptomatic children, 12 possessed the
eae
gene included in the locus of enterocyte effacement (LEE) pathogenicity island. Based on gene typing, we observed 7 different
eae espA espB tir
pathotypes among the 12 STEC strains and described the new
espA
βv variant. As previously observed, the O157 serogroup is associated with
eae
γ, O26 is associated with
eae
β, and O103 is associated with
eae
ε. However, the unexpected
eae
ζ allele was detected in 5 of the 12 isolates. PCR amplification and pulsed-field gel electrophoresis using the I-
Ceu
I endonuclease followed by Southern hybridization indicated that the LEE was inserted in the vicinity of the
selC
(three isolates),
pheU
(two isolates), or
pheV
(six isolates) tRNA gene. Six isolates harbored two or three of these tRNA loci altered by the insertion of integrase genes (CP4-
int
and/or
int-phe
), suggesting the insertion of additional foreign DNA fragments at these sites. In spite of great genetic diversity of LEE pathotypes and LEE insertion sites, bovine strains harbor alleles of LEE genes that are frequently found in clinical STEC strains isolated from outbreaks and sporadic cases around the world, underscoring the potential risk of the bovine strains on human health.
Simple and Reliable Method To Precipitate Proteins from Bacterial Culture Supernatant
Authors: Caldwell Randolph B. , Lattemann Claus T.
Published: January 2004

A simple and reliable method for precipitating protein from bacterial culture supernatants based on a pyrogallol red-molybdate-methanol (PRMM) protocol has been developed and applied for the analysis of proteins secreted by a bacterial type III secretion system. PRMM-based precipitation has been shown to be more efficient and robust than are conventional protocols.
Pet Snakes as a Reservoir for
Salmonella enterica
subsp.
diarizonae
(Serogroup IIIb): a Prospective Study
Authors: Schröter Matthias , Roggentin Peter , Hofmann Jörg , Speicher Angelika , Laufs Rainer , Mack Dietrich
Published: January 2004

Reptile-associated
Salmonella
infections are an increasing problem for humans. We have prospectively screened two breeding groups of 16 pet snakes for colonization with
Salmonella
species. Various serovars of
S. enterica
subsp.
diarizonae
were found in 81% of the snakes. To avoid transmission, strict hygienic precautions should be applied when reptiles are handled.
Intracellular Symbionts and Other Bacteria Associated with Deer Ticks (Ixodes scapularis) from Nantucket and Wellfleet, Cape Cod, Massachusetts
Authors: Benson Micah J. , Gawronski Jeffrey D. , Eveleigh Douglas E. , Benson David R.
Published: January 2004

The diversity of bacteria associated with the deer tick (Ixodes scapularis) was assessed using PCR amplification, cloning, and sequencing of 16S rRNA genes originating from seven ticks collected from Nantucket Island and Wellfleet, Cape Cod, Mass. The majority of sequences obtained originated from gram-negative proteobacteria. Four intracellular bacteria were detected including strains ofEhrlichia,Rickettsia, andWolbachiaand an organism related to intracellular insect symbionts from theCytophaga-Flavobacterium-Bacteroidesgroup. Several strains of members of theSphingomonadaceaewere also detected in all but one tick. The results provide a view of the diversity of bacteria associated withI. scapularisticks in the field.
Sensitive and Rapid Detection of Edwardsiellosis in Fish by a Loop-Mediated Isothermal Amplification Method
Authors: Savan Ram , Igarashi Arisa , Matsuoka Satoru , Sakai Masahiro
Published: January 2004

Here we report a rapid and sensitive method (using loop-mediated isothermal amplification [LAMP]) for the diagnosis of edwardsiellosis, a fish disease caused by
Edwardsiella tarda
, in Japanese flounder. A set of four primers was designed, and conditions for the detection were optimized for the detection of
E. tarda
in 45 min at 65°C. No amplification of the target hemolysin gene was detected in other related bacteria. When the LAMP primers were used, detection of edwardsiellosis in infected Japanese flounder kidney, and spleen and seawater cultures was possible. We have developed a rapid and sensitive diagnostic protocol for edwardsiellosis detection in fish. This is the first report of the application of LAMP for the diagnosis of a fish pathogen.
Molecular Cloning, Purification, and Biochemical Characterization of Hydantoin Racemase from the Legume Symbiont
Sinorhizobium meliloti
CECT 4114
Authors: Martínez-Rodríguez Sergio , Las Heras-Vázquez Francisco Javier , Mingorance-Cazorla Lydia , Clemente-Jiménez Josefa María , Rodríguez-Vico Felipe
Published: January 2004

Hydantoin racemase from
Sinorhizobium meliloti
was functionally expressed in
Escherichia coli
. The native form of the enzyme was a homotetramer with a molecular mass of 100 kDa. The optimum temperature and pH for the enzyme were 40°C and 8.5, respectively. The enzyme showed a slight preference for hydantoins with short rather than long aliphatic side chains or those with aromatic rings. Substrates, which showed no detectable activity toward the enzyme, were found to exhibit competitive inhibition.
Identification of Bacilysin, Chlorotetaine, and Iturin A Produced by
Bacillus
sp. Strain CS93 Isolated from Pozol, a Mexican Fermented Maize Dough
Authors: Phister Trevor G. , O'Sullivan Daniel J. , McKay Larry L.
Published: January 2004

Three antimicrobial compounds produced by
Bacillus
sp. strain CS93 isolated from pozol were identified by using high-performance liquid chromatography and mass spectrometry. The three compounds were iturin, bacilysin, and chlorotetaine. Production of these compounds by CS93 could account for the medicinal properties attributed to pozol.
Combined Effects of High Hydrostatic Pressure and Temperature for Inactivation of
Bacillus anthracis
Spores
Authors: Cléry-Barraud Cécile , Gaubert Agnès , Masson Patrick , Vidal Dominique
Published: January 2004

Spores of
Bacillus anthracis
are known to be extremely resistant to heat treatment, irradiation, desiccation, and disinfectants. To determine inactivation kinetics of spores by high pressure,
B. anthracis
spores of a Sterne strain-derived mutant deficient in the production of the toxin components (strain RP42) were exposed to pressures ranging from 280 to 500 MPa for 10 min to 6 h, combined with temperatures ranging from 20 to 75°C. The combination of heat and pressure resulted in complete destruction of
B. anthracis
spores, with a
D
value (exposure time for 90% inactivation of the spore population) of approximately 4 min after pressurization at 500 MPa and 75°C, compared to 160 min at 500 MPa and 20°C and 348 min at atmospheric pressure (0.1 MPa) and 75°C. The use of high pressure for spore inactivation represents a considerable improvement over other available methods of spore inactivation and could be of interest for antigenic spore preparation.
Role of Aminotransferase IlvE in Production of Branched-Chain Fatty Acids by
Lactococcus lactis
subsp.
lactis
Authors: Ganesan Balasubramanian , Weimer Bart C.
Published: January 2004

The objective of this study was to determine the role of a lactococcal branched-chain amino acid aminotransferase gene,
ilvE
, in the production of branched-chain fatty acids.
Lactococcus lactis
subsp.
lactis
LM0230 and an
ilvE
deletion mutant, JLS450, produced branched-chain fatty acids from amino and α-keto acids at levels above α-keto acid spontaneous degradation and the fatty acids' flavor thresholds. The deletion mutant produced the same amounts of branched-chain fatty acids from precursor amino acids as did the parent. This was not the case, however, for the production of branched-chain fatty acids from the corresponding precursor α-keto acids. The deletion mutant produced a set of fatty acids different from that produced by the parent. We concluded from these observations that
ilvE
plays a role in the specific type of fatty acids produced but has little influence on the total amount of fatty acids produced by lactococci.
Neonatal-Mouse Infectivity of IntactCryptosporidium parvumOocysts Isolated after Optimized In Vitro Excystation
Authors: Hou L. , Li X. , Dunbar L. , Moeller R. , Palermo B. , Atwill E. R.
Published: January 2004

We reexamined the finding of Neumann et al. (10) that intactCryptosporidium parvumoocysts obtained after in vitro excystation were infectious for neonatal CD-1 mice. We used both established excystation protocols and our own protocol that maximized excystation (2). Although intact oocysts isolated after any of three protocols were infectious for neonatal CD-1 mice, the infectivity of intact oocysts isolated with our optimized excystation protocol was significantly lower than the infectivity of intact oocysts isolated after established protocols or from fresh oocysts. Excystation should not be considered a valid measure ofC. parvumviability, given that it is biologically implausible for oocysts to be nonviable and yet infectious.
Rapid and Specific Detection ofSalmonellaspp. in Animal Feed Samples by PCR after Culture Enrichment
Authors: Löfström Charlotta , Knutsson Rickard , Axelsson Charlotta Engdahl , Rådström Peter
Published: January 2004

A PCR procedure has been developed for routine analysis of viableSalmonellaspp. in feed samples. The objective was to develop a simple PCR-compatible enrichment procedure to enable DNA amplification without any sample pretreatment such as DNA extraction or cell lysis. PCR inhibition by 14 different feed samples and natural background flora was circumvented by the use of the DNA polymeraseTth. This DNA polymerase was found to exhibit a high level of resistance to PCR inhibitors present in these feed samples compared to DyNAzyme II, FastStartTaq, PlatinumTaq,Pwo, rTth,Taq, andTfl. The specificity of theTthassay was confirmed by testing 101Salmonellaand 43 non-Salmonellastrains isolated from feed and food samples. A sample preparation method based on culture enrichment in buffered peptone water and DNA amplification withTthDNA polymerase was developed. The probability of detecting small numbers of salmonellae in feed, in the presence of natural background flora, was accurately determined and found to follow a logistic regression model. From this model, the probability of detecting 1 CFU per 25 g of feed in artificially contaminated soy samples was calculated and found to be 0.81. The PCR protocol was evaluated on 155 naturally contaminated feed samples and compared to an established culture-based method, NMKL-71. Eight percent of the samples were positive by PCR, compared with 3% with the conventional method. The reasons for the differences in sensitivity are discussed. Use of this method in the routine analysis of animal feed samples would improve safety in the food chain.
Utilization of
Escherichia coli
Outer-Membrane Endoprotease OmpT Variants as Processing Enzymes for Production of Peptides from Designer Fusion Proteins
Authors: Okuno Kazuaki , Yabuta Masayuki , Ooi Toshihiko , Kinoshita Shinichi
Published: January 2004

Escherichia coli
outer-membrane endoprotease OmpT has suitable properties for processing fusion proteins to produce peptides and proteins. However, utilization of this protease for such production has been restricted due to its generally low cleavage efficiency at Arg (or Lys)-Xaa, where Xaa is a nonbasic N-terminal amino acid of a target polypeptide. The objective of this study was to generate a specific and efficient OmpT protease and to utilize it as a processing enzyme for producing various peptides and proteins by converting its substrate specificity. Since OmpT Asp
97
is proposed to interact with the P1′ amino acid of its substrates, OmpT variants with variations at Asp
97
were constructed by replacing this amino acid with 19 natural amino acids to alter the cleavage specificity at Arg (P1)-Xaa (P1′). The variant OmpT that had a methionine at this position, but not the wild-type OmpT, efficiently cleaved a fusion protein containing the amino acid sequence -Arg-Arg-Arg-Ala-Arg↓motilin, in which motilin is a model peptide with a phenylalanine at the N terminus. The OmpT variants with leucine and histidine at position 97 were useful in releasing human adrenocorticotropic hormone (1-24) (serine at the N terminus) and human calcitonin precursor (cysteine at the N terminus), respectively, from fusion proteins. Motilin was produced by this method and was purified up to 99.0% by two chromatographic steps; the yield was 160 mg/liter of culture. Our novel method in which the OmpT variants are used could be employed for production of various peptides and proteins.
Saccharomyces cerevisiae JEN1Promoter Activity Is Inversely Related to Concentration of Repressing Sugar
Authors: Chambers Prima , Issaka Aminatu , Palecek Sean P.
Published: January 2004

When carbon sources are changed,Saccharomyces cerevisiaetranscriptional patterns drastically change. To identify genes whose transcription can be used to quantitatively measure sugar concentrations, we searched genomic expression databases for a set of genes that are highly induced during the diauxic shift, and we used the promoters from these genes to drive expression of green fluorescent protein (GFP). Certain sugars, including glucose, fructose, and mannose, repress the promoter ofJEN1, which encodes a lactate-pyruvate transporter, in a dose-dependent manner. Nonrepressing carbon sources include galactose, raffinose, ethanol, lactate, and glycerol.JEN1promoter activity is a linear function of glucose concentration when organisms are grown at a steady-state glucose concentration below 1 g/liter.JEN1promoter repression is specific to carbon source; heat or cold shock, osmotic stress, DNA damage, and nitrogen starvation do not significantly affect promoter activity. Activation of theJEN1promoter requires the Snf1 protein kinase, but multiple regulatory elements most likely combine to provide the linear relationship betweenJEN1promoter activity and sugar concentration. Thus, aJEN1promoter-reporter system appears to provide a good living cell biosensor for the concentration of certain sugars. TheJEN1promoter also permits quantitative regulation of cellular functions not normally controlled by sugar concentrations. For example, a strain expressingFLO1under control of theJEN1promoter flocculates at a low glucose concentration.
Campylobacter
spp.
, Giardia
spp.
, Cryptosporidium
spp., Noroviruses, and Indicator Organisms in Surface Water in Southwestern Finland, 2000-2001
Authors: Hörman Ari , Rimhanen-Finne Ruska , Maunula Leena , von Bonsdorff Carl-Henrik , Torvela Niina , Heikinheimo Annamari , Hänninen Marja-Liisa
Published: January 2004

A total of 139 surface water samples from seven lakes and 15 rivers in southwestern Finland were analyzed during five consecutive seasons from autumn 2000 to autumn 2001 for the presence of various enteropathogens (
Campylobacter
spp.,
Giardia
spp
., Cryptosporidium
spp., and noroviruses) and fecal indicators (thermotolerant coliforms,
Escherichia coli
,
Clostridium perfringens
, and F-RNA bacteriophages) and for physicochemical parameters (turbidity and temperature); this was the first such systematic study. Altogether, 41.0% (57 of 139) of the samples were positive for at least one of the pathogens; 17.3% were positive for
Campylobacter
spp. (45.8% of the positive samples contained
Campylobacter jejuni
, 25.0% contained
Campylobacter lari
, 4.2% contained
Campylobacter coli
, and 25.0% contained
Campylobacter
isolates that were not identified), 13.7% were positive for
Giardia
spp., 10.1% were positive for
Cryptosporidium
spp., and 9.4% were positive for noroviruses (23.0% of the positive samples contained genogroup I and 77.0% contained genogroup II). The samples were positive for enteropathogens significantly (
P
< 0.05) less frequently during the winter season than during the other sampling seasons. No significant differences in the prevalence of enteropathogens were found when rivers and lakes were compared. The presence of thermotolerant coliforms,
E. coli
, and
C. perfringens
had significant bivariate nonparametric Spearman's rank order correlation coefficients (
P
< 0.001) with samples that were positive for one or more of the pathogens analyzed. The absence of these indicators in a logistic regression model was found to have significant predictive value (odds ratios, 1.15 × 10
8
, 7.57, and 2.74, respectively;
P
< 0.05) for a sample that was negative for the pathogens analyzed. There were no significant correlations between counts or count levels for thermotolerant coliforms or
E. coli
or the presence of F-RNA phages and pathogens in the samples analyzed.
Mur-LH, the Broad-Spectrum Endolysin of
Lactobacillus helveticus
Temperate Bacteriophage φ-0303
Authors: Deutsch Stéphanie-Marie , Guezenec Stéphane , Piot Michel , Foster Simon , Lortal Sylvie
Published: January 2004

φ-0303 is a temperate bacteriophage isolated from
Lactobacillus helveticus
CNRZ 303 strain after mitomycin C induction. In this work, the gene coding for a lytic protein of this bacteriophage was cloned using a library of φ-0303 in
Escherichia coli
DH5α. The lytic activity was detected by its expression, using whole cells of the sensitive strain
L. helveticus
CNRZ 892 as the substrate. The lysin gene was within a 4.1-kb DNA fragment of φ-0303 containing six open reading frames (ORFs) and two truncated ORFs. No sequence homology with holin genes was found within the cloned fragment. An integrase-encoding gene was also present in the fragment, but it was transcribed in a direction opposite that of the lysin gene. The lysin-encoding
lys
gene was verified by PCR amplification from the total phage DNA and subcloned. The
lys
gene is a 1,122-bp sequence encoding a protein of 373 amino acids (Mur-LH), whose product had a deduced molecular mass of 40,207 Da. Comparisons with sequences in sequence databases showed homology with numerous endolysins of other bacteriophages. Mur-LH was expressed in
E. coli
BL21, and by renaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis with
L. helveticus
CNRZ 892 as the substrate, the recombinant protein showed an apparent molecular mass of 40 kDa. The N-terminal sequence of the protein confirmed the start codon. Hydrolysis of cell walls of
L. helveticus
CNRZ 303 by the endolysin and biochemical analysis of the residues produced demonstrated that Mur-LH has
N
-acetylmuramidase activity. Last, the endolysin exhibited a broad spectrum of lytic activity, as it was active on different species, mainly thermophilic lactobacilli but also lactococci, pediococci,
Bacillus subtilis
,
Brevibacterium linens
, and
Enterococcus faecium
.
A PARALLEL CELL-BY-CELL AMR METHOD FOR THE PPM HYDRODYNAMICS CODE
Authors: DINGE DENNIS C. , WOODWARD PAUL R.
Published: January 2004

The Piecewise Parabolic Method (PPM) hydrodynamics code and other codes based on the PPM technique have been used extensively for the simulation of astrophysical phenomena. A new version of the PPM hydrodynamics code under development at the Laboratory for Computational Science and Engineering (LCSE) at the University of Minnesota is described. This new code incorporates a version of dynamic local adaptive mesh refinement (AMR) targeted specifically at improving the treatment of shocks and contact discontinuities. This AMR technique is not intended to increase grid resolution in entire regions of the problem for which standard techniques of nonuniform grids and simple grid motion are adequate. Because the AMR is targeted at surfaces within a flow that can develop complex shapes, a cell-by-cell approach to the grid refinement is adopted in order to minimize the number of refined grid cells, with the hope of controlling the computational cost. As a result of this approach, the number of refined cells needed across a given shock or captured contact discontinuity is modest (< 10). Because the PPM method is very complex, ordinarily its wide difference stencil demands that a relatively large number of extra grid cells need to be added to each end of a grid strip, even when adapting to a thin feature of the flow. To avoid the work associated in handling these extra cells, only to conveniently produce valid data in the thin strip of actual interest, we have used intermediate results of the coarse grid calculation in order to eliminate the need for all but two of these extra cells at each end of the refined grid strip. The benefits of this approach will be described through sample results in 2D, and the method for handling the boundaries of the refined grid strips efficiently will be discussed. The data structures in this method are being carefully designed to permit efficient implementation of the algorithm on clusters of shared memory machines, with automatic dynamic balancing of computational loads over the cluster members.
BRAIN NEURONS AS QUANTUM COMPUTERS: IN VIVO SUPPORT OF BACKGROUND PHYSICS
Authors: BERSHADSKII A. , DREMENCOV E. , BERSHADSKII J. , YADID G.
Published: January 2004

The question: whether quantum coherent states can sustain decoherence, heating and dissipation over time scales comparable to the dynamical timescales of brain neurons, has been actively discussed in the last years. A positive answer on this question is crucial, in particular, for consideration of brain neurons as quantum computers. This discussion was mainly based on theoretical arguments. In the present paper nonlinear statistical properties of the Ventral Tegmental Area (VTA) of genetically depressive limbic brain are studied in vivo on the Flinders Sensitive Line of rats (FSL). VTA plays a key role in the generation of pleasure and in the development of psychological drug addiction. We found that the FSL VTA (dopaminergic) neuron signals exhibit multifractal properties for interspike frequencies on the scales where healthy VTA dopaminergic neurons exhibit bursting activity. For high moments the observed multifractal (generalized dimensions) spectrum coincides with the generalized dimensions spectrum calculated for a spectral measure of a quantum system (so-called kicked Harper model, actively used as a model of quantum chaos). This observation can be considered as a first experimental (in vivo) indication in the favor of the quantum (at least partially) nature of brain neurons activity.
ANOMALOUS DIFFUSION AT PERCOLATION THRESHOLD IN HIGH DIMENSIONS ON 1018 SITES
Authors: OSTERKAMP DIRK , STAUFFER DIETRICH , AHARONY AMNON
Published: January 2004

Using an inverse of the standard linear congruential random number generator, large randomly occupied lattices can be visited by a random walker without having to determine the occupation status of every lattice site in advance. In seven dimensions, at the percolation threshold with L7 sites and L≤420, we confirm the expected time-dependence of the end-to-end distance (including the corrections to the asymptotic behavior).
SATO–CRUTCHFIELD FORMULATION FOR SOME EVOLUTIONARY GAMES
Authors: AHMED E. , HEGAZI A. S. , ELGAZZAR A. S.
Published: January 2004

The Sato–Crutchfield equations are analytically and numerically studied. The Sato–Crutchfield formulation corresponds to losing memory. Then the Sato–Crutchfield formulation is applied for some different types of games including hawk–dove, prisoner's dilemma and the battle of the sexes games. The Sato–Crutchfield formulation is found not to affect the evolutionarily stable strategy of the ordinary games. But choosing a strategy becomes purely random, independent of the previous experiences, initial conditions, and the rules of the game itself. The Sato–Crutchfield formulation for the prisoner's dilemma game can be considered as a theoretical explanation for the existence of cooperation in a population of defectors.
SELF-ORGANIZED PHASE SEGREGATION IN A DRIVEN FLOW OF DISSIMILAR PARTICLES MIXTURES
Authors: PANDEY R. B. , GETTRUST J. F. , SEYFARTH RAY , CUEVA-PARRA LUIS A.
Published: January 2004

Self-organized patterns in an immiscible fluid mixture of dissimilar particles driven from a source at the bottom are examined as a function of hydrostatic pressure bias by a Monte Carlo computer simulation. As the upward pressure bias competes with sedimentation due to gravity, a multi-phase system emerges: a dissociating solid phase from the source is separated from a migrating gas phase towards the top by an interface of mixed (bi-continuous) phase. Scaling of solid-to-gas phase with the altitude is nonuniversal and depends on both the range of the height/depth and the magnitude of the pressure bias. Onset of phase separation and layering is pronounced at low bias range.
A FAST AND EFFECTIVE CONFORMATIONAL SEARCH METHOD FOR PEPTIDES
Authors: ARKIN HANDAN , ÇELIK TARIK
Published: January 2004

We propose a hybrid algorithm, which combines the features of the energy landscape paving (ELP) and Monte Carlo Minimization (MCM) methods. We have tested its performance in studying the low-energy conformations of the heptapeptide deltorphin.
TAYLOR SERIES EXPANSION AND LEAST SQUARES-BASED LATTICE BOLTZMANN METHOD: THREE-DIMENSIONAL FORMULATION AND ITS APPLICATIONS
Authors: SHU C. , NIU X. D. , CHEW Y. T.
Published: January 2004

The two-dimensional form of the Taylor series expansion- and least square-based lattice Boltzmann method (TLLBM) was recently presented by Shu et al.8 TLLBM is based on the standard lattice Boltzmann method (LBM), Taylor series expansion and the least square optimization. The final formulation is an algebraic form and essentially has no limitation on the mesh structure and lattice model. In this paper, TLLBM is extended to the three-dimensional case. The resultant form keeps the same features as the two-dimensional one. The present form is validated by its application to simulate the three-dimensional lid-driven cavity flow at Re=100, 400 and 1000. Very good agreement was achieved between the present results and those of Navier–Stokes solvers.
OPTIMIZING THE SUBDIVISION OF ELEMENTS IN DISCONTINUITY MESHING FOR HIERARCHICAL RADIOSITY
Authors: PANTAZOPOULOS IOANNIS A. , TZAFESTAS SPYROS G.
Published: January 2004

This paper presents a new topological structure for use in the context of hierarchical radiosity combined with discontinuity meshing. This is most useful for a new strategy adopted for subdividing the elements of a scene consisting of convex polygons. The subdivision is done in a local optimization manner keeping the aspect ratios of produced polygons low. The generated meshes give high visual accuracy.
INCREMENTAL CASE-BASED PLAN RECOGNITION WITH LOCAL PREDICTIONS
Authors: KERKEZ BORIS , COX MICHAEL T.
Published: January 2004

We present a novel case-based plan recognition method that interprets observations of plan behavior using an incrementally constructed case library of past observations. The technique is novel in several ways. It combines plan recognition with case-based reasoning and leverages the strengths of both. The representation of a plan is a sequence of action-state pairs rather than only the actions. The technique compensates for the additional complexity with a unique abstraction scheme augmented by pseudo-isomorphic similarity relations to represent indices into the case base. Past cases are used to predict subsequent actions by adapting old actions and their arguments. Moreover, the technique makes predictions despite observations of unknown actions. This paper evaluates the algorithms and their implementation both analytically and empirically. The evaluation criteria include prediction accuracy at both an abstract and a concrete level and across multiple domains with and without case-adaptation. In each domain the system starts with an empty case base that grows to include thousands of past observations. Results demonstrate that this new method is accurate, robust, scalable, and general across domains.
INTELLIGENT DATA ANALYSIS OF BREAST CANCER BASED ON ROUGH SET THEORY
Authors: HASSANIEN ABOUL ELLA
Published: January 2004

Extensive amounts of knowledge and data stored in medical databases require the development of specialized tools for storing, accessing, analysis, and effectiveness usage of stored knowledge and data. Intelligent methods such as neural networks, fuzzy sets, decision trees, and expert systems are, slowly but steadily, applied in the medical fields. Recently, rough set theory is a new intelligent technique was used for the discovery of data dependencies, data reduction, approximate set classification, and rule induction from databases.

In this paper, we present a rough set method for generating classification rules from a set of observed 360 samples of the breast cancer data. The attributes are selected, normalized and then the rough set dependency rules are generated directly from the real value attribute vector. Then the rough set reduction technique is applied to find all reducts of the data which contains the minimal subset of attributes that are associated with a class label for classification. Experimental results from applying the rough set analysis to the set of data samples are given and evaluated. In addition, the generated rules are also compared to the well-known ID3 classifier algorithm. The study showed that the theory of rough sets seems to be a useful tool for inductive learning and a valuable aid for building expert systems.
SPEAKER-INDEPENDENT SPEECH RECOGNITION BASED ON FAST NEURAL NETWORK
Authors: TAO CUI , ZHANG TAIYI
Published: January 2004

This paper presents a fast Neural Network algorithm, in which the step is regarded as the function of the error and the output function of network node, and weight is calculated by different step. By adopting the fast NN algorithm, we developed a speaker-independent speech recognition system. The experiment shows that the new algorithm is over 10 times faster than the traditional BP algorithm and has better performance and spreading ability.
A QUASILINEAR CLASSIFIER FOR COMPLETE SEPARATION OF A DICHOTOMY
Authors: PRABHU N.
Published: January 2004

We present a new classifier, which given any two distinct finite sets P, Q ⊂ R n can construct a closed-form expression of a quasilinear surface that completely separates P and Q. The new classifier, which is based on gauged Lie groups, has low-polynomial space and time complexities and is particularly efficient on large sets P and Q wherein, modulo small subsets of P and Q, the sets P and Q are linearly separable.
MUTATING REAL-VALUED VECTORS USING ANGULAR DISPLACEMENT
Authors: ZMUDA MICHAEL A. , RIZKI MATEEN M. , TAMBURINO LOUIS A.
Published: January 2004

A new self-adaptive mutation operator, Angular Displacement, for optimizing real-valued vectors is presented. This is designed for applications, called directional problems, where the quality of a solution vector is based exclusively on the direction of the vector and not the length of the vector. Angular Displacement maintains one control parameter that stochastically governs the amount of angular displacement, θ, induced by a single mutation. After θ is chosen, a random vector is selected that forms an angle of θ radians with the input vector. This approach contrasts the standard mutation operator that maintains one extra parameter for each vector component to control the displacement of the vector's head. Experiments show Angular Displacement is superior to the standard mutation operator in a directional problem involving the optimization of a hyperplane's parameters.
DECISION TREES FOR PERNICIOUS PAGES DETECTION
Authors: PABARSKAITE ZIDRINA , LONG JAMES ALLEN
Published: January 2004

An application framework to perform web usage analysis using advanced data mining methodology is presented. The investigation proposes decision trees for web user behavior analysis. This includes prediction of user future actions and the typical pages leading to browsing termination. The widely known decision tree package C4.5 was used in this study. In the new area of web log mining decision trees showed reasonable computational performance and accuracy. Experiments showed that it is possible to predict future user actions with reasonable misclassification error as well as to find combinations of sequential pages resulting in browsing termination. In addition to this, decision trees generate human understandable rules which can be used to analyze further for web site improvement.
A BIG-STEPPED PROBABILITY APPROACH FOR DISCOVERING DEFAULT RULES
Authors: BENFERHAT SALEM , DUBOIS DIDIER , LAGRUE SYLVAIN , PRADE HENRI
Published: January 2004

This paper deals with the extraction of default rules from a database of examples. The proposed approach is based on a special kind of probability distributions, called "big-stepped probabilities", which are known to provide a semantics for non-monotonic reasoning. The rules which are learnt are genuine default rules, which could be used (under some conditions) in a non-monotonic reasoning system and can be encoded in possibilistic logic.
CLOSED SET BASED DISCOVERY OF MAXIMAL COVERING RULES
Authors: KRYSZKIEWICZ MARZENA
Published: January 2004

Many knowledge discovery tasks consist in mining databases. Nevertheless, there are cases in which a user is not allowed to access the database and can deal only with a provided fraction of knowledge. Still, the user hopes to find new interesting relationships. Surprisingly, a small number of patterns can be augmented into new knowledge so considerably that its analysis may become infeasible. In the article, we offer a method of inferring the concise lossless and sound representation of association rules in the form of maximal covering rules from a concise lossless representation of all derivable patterns. The respective algorithm is offered as well.
QUERYING FUZZY MULTIDIMENSIONAL DATABASES: UNARY OPERATORS AND THEIR PROPERTIES
Authors: LAURENT ANNE
Published: January 2004

In this paper, we study the properties of flexible queries in the OLAP (On-Line Analytical Processing) framework, focusing on unary operators. For this purpose, we consider the model we have defined for fuzzy multidimensional databases. This model provides means to handle fuzzy data and flexible queries. The operators defined in this model are closed on the set of fuzzy hypercubes (hereafter cubes), which means that the result of each operator on a fuzzy cube is a cube. Thus, these operators can be nested into expressions. In this paper, the combination of several queries is investigated in order to study the possibility for the definition of an algebra to manipulate fuzzy cubes. This would provide a framework for query rewriting and, as a result, for query optimization.
A TUPLE-ORIENTED ALGORITHM FOR DEDUCTION IN A FUZZY RELATIONAL DATABASE
Authors: BLANCO IGNACIO J. , MARTIN-BAUTISTA MARIA J. , PONS OLGA , VILA M. AMPARO
Published: January 2004

In this paper, we define the concept of generalized rule for making classical deduction with imprecise data, stored both data and rules in a fuzzy relational database represented in the GEFRED model. We propose a way of measuring the imprecision related to the calculation of a fact based on the matching degree of the facts in the database and the facts calculated while expanding the rules. In order to achieve this, classical algorithms for deduction are not appropriated and we propose the modifications that have to be applied on a classical tuple-oriented algorithm in order to design a new algorithm for deducing from imprecise data with generalized rules.
EFFICIENT ANDNESS-DIRECTED IMPORTANCE WEIGHTED AVERAGING OPERATORS
Authors: LARSEN HENRIK LEGIND
Published: January 2004

Importance weighted averaging is a central information processing task in multicriteria decision problems of many kinds, such that selection, classification, object recognition, query answering, and information retrieval. These problems are characterized by a query, i.e., a set of importance weighted criteria, and a set of options queried. While each criterion determines a ranking of the options, the task of the averaging operator is essentially to aggregate these rankings into an overall ranking under the consideration of the criterion importance. We present a class of such operators, based on the power means, namely the Andness-directed Importance Weighted Averaging (AIWA) operators. The operators are equipped with an approximate andness measure allowing an easy, direct control of the andness in the unit interval. The aggregation behavior of the operators appears to be similar to that of importance weighted maximum entropy OWA operators. However, AIWA operators aggregates n arguments (criterion satisfaction values) in O(n) time as opposed to O(n log n) time for OWA operators. An interesting property provided by AIWA operators is decomposability, allowing us to consider new or improved criteria without recomputing with all arguments. Overall, the AIWA operators appear to be effective as andness controlled, importance weighted averaging operators, as well as easy to apply and computationally efficient.
DISTRIBUTED INFORMATION RETRIEVAL: A MULTI-OBJECTIVE RESOURCE SELECTION APPROACH
Authors: WU SHENGLI , CRESTANI FABIO
Published: January 2004

Information retrieval is becoming increasingly concerned with resource selection and data fusion for distributed archives. In distributed information retrieval, a user submits a query to a broker, which determines a solution for how to yield a given number of documents from all available resources. In this paper, we present a multi-objective model for resource selection, in which four aspects: a document's relevance to the given query, time, monetary cost, and the chance of getting document duplicates from resources, are considered simultaneously. Some variants of this multi-objective model, aimed at achieving better implementation efficiency, are also proposed.