bluuebunny/crossref_metadata_2025_split huggingface dataset:
One Group of Genetically Similar
Listeria monocytogenes
Strains Frequently Dominates and Persists in Several Fish Slaughter- and Smokehouses
Authors: Wulff Gitte , Gram Lone , Ahrens Peter , Vogel Birte Fonnesbech 
Published: June 2006

ABSTRACT

Contamination of foods with the human pathogen
Listeria monocytogenes
may occur during processing, and the purpose of this study was to determine whether genetically similar strains colonize different processing plants or whether specific persistent strains are unique to each processing plant. We hypothesized that specific
L. monocytogenes
strains may be better adapted to specific environmental niches in the processing environment.
L. monocytogenes
contamination patterns were identified by the collection of 686 and 267 samples from the processing environments: raw fish and products of four fish smokehouses and four fish slaughterhouses, respectively. Samples were collected both during production and after cleaning and disinfection. Typically, these samplings were separated by 1 to 3 months. Sampling sites were targeted toward areas likely to harbor the bacterium.
L. monocytogenes
was isolated from 213 samples, and one strain from each positive sample was typed by RAPD (random amplified polymorphic DNA) analysis with four different primers. The 213 strains were divided into 37 RAPD types. One RAPD type was predominant; 86 of 213 strains belonged to this type. This type was found in three smokehouses and two slaughterhouses and was predominant in three of these plants. A subset of 35 strains was also analyzed by amplified fragment length polymorphism typing, which confirmed the genetic similarity of the groups. Moreover, strains of the dominant RAPD type were indistinguishable from strains isolated frequently from smoked fish products 10 years ago. One smokehouse was surveyed for a year and a half, and the dominant RAPD type persisted throughout the survey period and accounted for 94 of 118 isolates. Our study indicates that strains of
L. monocytogenes
that are genetically very closely related may be especially adapted to colonizing the processing equipment or especially resistant to cleaning and disinfection.
Biotic and Abiotic Factors Influencing In Vitro Growth of
Escherichia coli
O157:H7 in Ruminant Digestive Contents
Authors: Chaucheyras-Durand Frédérique , Madic Jordan , Doudin Florent , Martin Christine 
Published: June 2006

ABSTRACT

The gastrointestinal tract (GIT) of ruminants is the main reservoir of enterohemorrhagic
Escherichia coli
, which is responsible for food-borne infections in humans that can lead to severe kidney disease. Characterization of biotic and abiotic factors that influence the carriage of these pathogens by the ruminant would help in the development of ecological strategies to reduce their survival in the GIT and to decrease the risk of contamination of animal products. We found that growth of
E. coli
O157:H7 in rumen fluid was inhibited by the autochthonous microflora. Growth was also reduced when rumen fluid came from sheep fed a mixed diet composed of 50% wheat and 50% hay, as opposed to a 100% hay diet. In fecal suspensions,
E. coli
O157:H7 growth was not suppressed by the autochthonous flora. However, a probiotic strain of
Lactobacillus acidophilus
inhibited
E. coli
O157:H7 growth in fecal suspensions. The inhibitory effect was dose dependent. These lactic acid bacteria could be a relevant tool for controlling O157:H7 development in the terminal part of the ruminant GIT, which has been shown to be the main site of colonization by these pathogenic bacteria.
Energetic Consequences of Nitrite Stress in
Desulfovibrio vulgaris
Hildenborough, Inferred from Global Transcriptional Analysis
Authors: He Qiang , Huang Katherine H. , He Zhili , Alm Eric J. , Fields Matthew W. , Hazen Terry C. , Arkin Adam P. , Wall Judy D. , Zhou Jizhong 
Published: June 2006

ABSTRACT

Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in
Desulfovibrio
spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts,
Desulfovibrio vulgaris
Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.
Ca
2+
-Dependent Maturation of Subtilisin from a Hyperthermophilic Archaeon,
Thermococcus kodakaraensis
: the Propeptide Is a Potent Inhibitor of the Mature Domain but Is Not Required for Its Folding
Authors: Pulido Marian , Saito Kenji , Tanaka Shun-Ichi , Koga Yuichi , Morikawa Masaaki , Takano Kazufumi , Kanaya Shigenori 
Published: June 2006

ABSTRACT

Subtilisin from the hyperthermophilic archaeon
Thermococcus kodakaraensis
KOD1 is a member of the subtilisin family.
T. kodakaraensis
subtilisin in a proform (
T. kodakaraensis
pro-subtilisin), as well as its propeptide (
T. kodakaraensis
propeptide) and mature domain (
T. kodakaraensis
mat-subtilisin), were independently overproduced in
E. coli
, purified, and biochemically characterized.
T. kodakaraensis
pro-subtilisin was inactive in the absence of Ca
2+
but was activated upon autoprocessing and degradation of propeptide in the presence of Ca
2+
at 80°C. This maturation process was completed within 30 min at 80°C but was bound at an intermediate stage, in which the propeptide is autoprocessed from the mature domain (
T. kodakaraensis
mat-subtilisin*) but forms an inactive complex with
T. kodakaraensis
mat-subtilisin*, at lower temperatures. At 80°C, approximately 30% of
T. kodakaraensis
pro-subtilisin was autoprocessed into
T. kodakaraensis
propeptide and
T. kodakaraensis
mat-subtilisin*, and the other 70% was completely degraded to small fragments. Likewise,
T. kodakaraensis
mat-subtilisin was inactive in the absence of Ca
2+
but was activated upon incubation with Ca
2+
at 80°C. The kinetic parameters and stability of the resultant activated protein were nearly identical to those of
T. kodakaraensis
mat-subtilisin*, indicating that
T. kodakaraensis
mat-subtilisin does not require
T. kodakaraensis
propeptide for folding. However, only ∼5% of
T. kodakaraensis
mat-subtilisin was converted to an active form, and the other part was completely degraded to small fragments.
T. kodakaraensis
propeptide was shown to be a potent inhibitor of
T. kodakaraensis
mat-subtilisin* and noncompetitively inhibited its activity with a

K
i

of 25 ± 3.0 nM at 20°C.
T. kodakaraensis
propeptide may be required to prevent the degradation of the
T. kodakaraensis
mat-subtilisin molecules that are activated later by those that are activated earlier.
Immobilization and Detection of
Listeria monocytogenes
Authors: Schindler B. D. , Shelef L. A. 
Published: June 2006

ABSTRACT

A procedure was developed for immobilization of
Listeria monocytogenes
cells on metal hydroxides coupled with detection and enumeration using an automated optical system. The results of the immobilization procedure (<1 h) and detection during overnight incubation agreed with calculated plate counts, and this technique is simple and rapid and provides samples that are ready for confirmation of the presence of the pathogen by rapid methods.
High-Resolution Fluorometer for Mapping Microscale Phytoplankton Distributions
Authors: Doubell Mark J. , Seuront Laurent , Seymour Justin R. , Patten Nicole L. , Mitchell James G. 
Published: June 2006

ABSTRACT
A new high-resolution, in situ profiling fluorometer maps fluorescence distributions with a spatial resolution of 0.5 to 1.5 mm to a depth of 70 m in the open ocean. We report centimeter-scale patterns for phytoplankton distributions associated with gradients exhibiting 10- to 30-fold changes in fluorescence in contrasting marine ecosystems.
Use of the modified Delphi technique to identify and rate home injury hazard risks and prevention methods for young children
Authors: Katcher M L , Meister A N , Sorkness C A , Staresinic A G , Pierce S E , Goodman B M , Peterson N M , Hatfield P M , Schirmer J A 
Published: June 2006

Objective:For children aged 1–5 years, the authors used the Delphi method to determine (1) the most important injury hazards in each area of the home; (2) the most important injury prevention behaviors; and (3) feasible and efficacious safety devices and behaviors to reduce injury risks.Design:The authors used a modified Delphi method to prioritize home injury hazards for children 1–5 years of age. The Delphi method is an indirect, anonymous, iterative process aimed at achieving consensus among experts; in this study, the authors queried key informants electronically. Thirty four key informants, primarily from the United States, participated in at least one of the three rounds of questionnaires. Responses were submitted by email or fax. Participants identified, rated, and ranked home injury hazards and prevention methods.Results:The overall response rate for each survey ranged from 82% to 97%. Initially, 330 unique hazards and prevention behaviors/devices were identified in seven areas of the home. The 126 home injury hazards were rated based on frequency, severity, and preventability of injury; and the 204 behaviors and devices were rated by efficacy and feasibility. These experts rated firearms and pools as the most significant hazards, and smoke alarms and safe water temperature as the most important preventions.Conclusions:The modified Delphi method of consensus was useful to prioritize home injury hazards and prevention methods for children under the age of 6 years.
Changes in traffic crash mortality rates attributed to use of alcohol, or lack of a seat belt, air bag, motorcycle helmet, or bicycle helmet, United States, 1982–2001
Authors: Cummings P , Rivara F P , Olson C M , Smith K M 
Published: June 2006

Objective:To estimate the contributions of five risk factors to changes in US traffic crash mortality: (1) alcohol use by drivers and pedestrians, (2) not wearing a seat belt, (3) lack of an air bag, (4) not wearing a motorcycle helmet, and (5) not wearing a bicycle helmet.Design:Longitudinal study of deaths; attributable deaths were estimated using data from other studies.Setting:US traffic crashes in 1982–2001.Subjects:People who died in a crash.Main outcome measures:Counts of deaths attributed to each risk factor, change in rates of deaths, and counts of lives saved by changes in risk factor prevalence.Results:There were 858 741 traffic deaths during the 20 year period. Estimated deaths attributed to each factor were: (1) alcohol use, 366 606; (2) not wearing a seat belt, 259 239; (3) lack of an air bag, 31 377; (4) no motorcycle helmet, 12 095; (5) no bicycle helmet, 10 552. Over the 20 years, mortality rates attributed to each risk factor declined: alcohol by 53%; not wearing a seat belt by 49%; lack of an air bag by 17%; no motorcycle helmet by 74%; no bicycle helmet by 39%. There were 153 168 lives saved by decreased drinking and driving, 129 297 by increased use of seat belts, 4305 by increased air bag prevalence, 6475 by increased use of motorcycle helmets, and 239 by increased use of bicycle helmets.Conclusions:Decreased alcohol use and increased use of seat belts were associated with substantial reductions in crash mortality from 1982 through 2001. Increased presence of air bags, motorcycle helmets, and bicycle helmets were associated with smaller reductions.
Novel Candidate Genes in Unstable Areas of Human Atherosclerotic Plaques
Authors: Papaspyridonos Marianna , Smith Alberto , Burnand Kevin G. , Taylor Peter , Padayachee Soundrie , Suckling Keith E. , James Christian H. , Greaves David R. , Patel Lisa 
Published: June 2006

Objective—Comparison of gene expression in stable versus unstable atherosclerotic plaque may be confounded by interpatient variability. The aim of this study was to identify differences in gene expression between stable and unstable segments of plaque obtained from the same patient.Methods and Results—Human carotid endarterectomy specimens were segmented and macroscopically classified using a morphological classification system. Two analytical methods, an intraplaque and an interplaque analysis, revealed 170 and 1916 differentially expressed genes, respectively using Affymetrix gene chip analysis. A total of 115 genes were identified from both analyses. The differential expression of 27 genes was also confirmed using quantitative-polymerase chain reaction on a larger panel of samples. Eighteen of these genes have not been associated previously with plaque instability, including the metalloproteinase, ADAMDEC1 (≈37-fold), retinoic acid receptor responder-1 (≈5-fold), and cysteine protease legumain (≈3-fold). Matrix metalloproteinase-9 (MMP-9), cathepsin B, and a novel gene, legumain, a potential activator of MMPs and cathepsins, were also confirmed at the protein level.Conclusions—The differential expression of 18 genes not previously associated with plaque rupture has been confirmed in stable and unstable regions of the same atherosclerotic plaque. These genes may represent novel targets for the treatment of unstable plaque or useful diagnostic markers of plaque instability.
Conditional Nonlinear Optimal Perturbations of a Two-Dimensional Quasigeostrophic Model
Authors: Mu Mu , Zhang Zhiyue 
Published: June 2006

Abstract
Conditional nonlinear optimal perturbations (CNOPs) of a two-dimensional quasigeostrophic model are obtained numerically. The CNOP is the initial perturbation whose nonlinear evolution attains the maximum value of the cost function, which is constructed according to the physical problems of interests with physical constraint conditions. The difference between the CNOP and a linear singular vector is compared. The results demonstrate that CNOPs catch the nonlinear effects of the model on the evolutions of the initial perturbations. These results suggest that CNOPs are applicable to the study of predictability and sensitivity analysis when nonlinearity is of importance.
MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution
Authors: Wang Jun , Keightley Peter D , Johnson Toby 
Published: June 2006

Abstract

Background
Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are able to align non-coding DNA sequences. However, the alignment of non-coding DNA sequences is more difficult than aligning protein-coding sequences.

Results
Here we present an improved pair-hidden-Markov-Model (pair HMM) based method for performing global pairwise alignment of non-coding DNA sequences. The method uses an explicit model of indel length frequency distribution which can be specified, and allows any time reversible model of nucleotide substitution. The method uses a deterministic global optimiser to find the alignment with the highest posterior probability. We test MCALIGN2 in simulations, and compare it to a previous Monte Carlo based method (MCALIGN), to the pair HMM method of Knudsen and Miyamoto, and to a heuristic method (AVID) that performed very well in a previous simulation study. We show that the pair HMM methods have excellent performance for all combinations of parameter values we have considered. MCALIGN2 is up to ten times faster than MCALIGN. MCALIGN2 is more accurate in resolving indels given an accurate explicit model than heuristic methods, but is computationally slower.

Conclusion
MCALIGN2 produces better quality alignments by explicitly using biological knowledge about the indel length distribution and time reversible models of nucleotide substitution. As a result, it can outperform other available sequence alignment methods for the cases we have considered to align non-coding DNA sequences.
Patterns of inflammation and the use of reversibility testing in smokers with airway complaints
Authors: Chavannes Niels H , Vernooy Juanita HJ , Schermer Tjard RJ , Jacobs Jan A , Dentener Mieke A , van Weel Chris , van Schayck Onno CP , Wouters Emiel FM 
Published: June 2006

AbstractBackgroundAlthough both smoking and respiratory complaints are very common, tools to improve diagnostic accuracy are scarce in primary care. This study aimed to reveal what inflammatory patterns prevail in clinically established diagnosis groups, and what factors are associated with eosinophilia.MethodInduced sputum and blood plasma of 59 primary care patients with COPD (n = 17), asthma (n = 11), chronic bronchitis (CB, n = 14) and smokers with no respiratory complaints ('healthy smokers', n = 17) were collected, as well as lung function, smoking history and clinical work-up. Patterns of inflammatory markers per clinical diagnosis and factors associated with eosinophilia were analyzed by multiple regression analyses, the differences expressed in odds ratios (OR) with 95% confidence intervals.ResultsMultivariately, COPD was significantly associated with raised plasma-LBP (OR 1.2 [1.04–1.37]) and sTNF-R55 in sputum (OR 1.01 [1.001–1.01]), while HS expressed significantly lowered plasma-LBP (OR 0.8 [0.72–0.95]). Asthma was characterized by higher sputum eosinophilic counts (OR 1.3 [1.05–1.54]), while CB showed a significantly higher proportion of sputum lymphocytic counts (OR 1.5 [1.12–1.9]). Sputum eosinophilia was significantly associated with reversibility after adjusting for smoking, lung function, age, gender and allergy.ConclusionPatterns of inflammatory markers in a panel of blood plasma and sputum cells and mediators were discernable in clinical diagnosis groups of respiratory disease. COPD and so-called healthy smokers showed consistent opposite associations with plasma LBP, while chronic bronchitics showed relatively predominant lymphocytic inflammation compared to other diagnosis groups. Only sputum eosinophilia remained significantly associated with reversibility across the spectrum of respiratory disease in smokers with airway complaints.
Gene expression in cortex and hippocampus during acute pneumococcal meningitis
Authors: Coimbra Roney S , Voisin Veronique , de Saizieu Antoine B , Lindberg Raija LP , Wittwer Matthias , Leppert David , Leib Stephen L 
Published: June 2006

AbstractBackgroundPneumococcal meningitis is associated with high mortality (~30%) and morbidity. Up to 50% of survivors are affected by neurological sequelae due to a wide spectrum of brain injury mainly affecting the cortex and hippocampus. Despite this significant disease burden, the genetic program that regulates the host response leading to brain damage as a consequence of bacterial meningitis is largely unknown.We used an infant rat model of pneumococcal meningitis to assess gene expression profiles in cortex and hippocampus at 22 and 44 hours after infection and in controls at 22 h after mock-infection with saline. To analyze the biological significance of the data generated by Affymetrix DNA microarrays, a bioinformatics pipeline was used combining (i) a literature-profiling algorithm to cluster genes based on the vocabulary of abstracts indexed in MEDLINE (NCBI) and (ii) the self-organizing map (SOM), a clustering technique based on covariance in gene expression kinetics.ResultsAmong 598 genes differentially regulated (change factor ≥ 1.5; p ≤ 0.05), 77% were automatically assigned to one of 11 functional groups with 94% accuracy. SOM disclosed six patterns of expression kinetics. Genes associated with growth control/neuroplasticity, signal transduction, cell death/survival, cytoskeleton, and immunity were generally upregulated. In contrast, genes related to neurotransmission and lipid metabolism were transiently downregulated on the whole. The majority of the genes associated with ionic homeostasis, neurotransmission, signal transduction and lipid metabolism were differentially regulated specifically in the hippocampus. Of the cell death/survival genes found to be continuously upregulated only in hippocampus, the majority are pro-apoptotic, while those continuously upregulated only in cortex are anti-apoptotic.ConclusionTemporal and spatial analysis of gene expression in experimental pneumococcal meningitis identified potential targets for therapy.
Comparison of Venae Sectio vs. modified Seldinger Technique for Totally Implantable Access Ports; Portas-trial [ISRCTN:52368201]
Authors: Knebel P , Fröhlich B , Knaebel H-P , Kienle P , Luntz S , Buchler MW , Seiler CM 
Published: June 2006

Abstract

Background
The insertion of a Totally Implantable Access Port (TIAP) is a routinely employed technique in patients who need a safe and permanent venous access. The number of TIAP implantations is increasing constantly mainly due to advanced treatment options for malignant diseases. Therefore it is important to identify the implantation technique which has the optimal benefit/risk ratio for the patient.

Study design
A single-centre, randomized, controlled superiority trial to compare two different TIAP implantation techniques. Sample size: 160 patients will be included and randomized intra-operatively. Eligibility criteria: Age equal or older than 18 years, patients scheduled for primary elective implantation of a TIAP in local anaesthesia and a signed informed consent. Primary endpoint: Primary success rate of the randomized technique. Intervention: Venae Sectio in combination with the Seldinger Technique (guide wire and a peel away sheath) will be used to place a TIAP. Reference treatment: Conventional Venae Sectio will be used with a direct insertion of the TIAP without guide wire or peel away sheath. Duration of study: Approximately 20 months.

Organisation/Responsibility
The trial will be conducted in compliance with the protocol and in accordance with the moral, ethical, and scientific principles governing clinical research as set out in the Declaration of Helsinki (1989) and Good Clinical Practice (GCP). The trial will also be carried out in keeping with local and regulatory requirements. The Klinisches Studienzentrum Chirurgie (KSC) – Centre of Clinical Trials in Surgery at the Department of Surgery, University Hospital Heidelberg is responsible for planning and conduction of the trial. Documentation of patient's data will be accomplished via electronical Case Report Files (eCRF) with MACRO®-Software by the KSC. Randomization, data management, monitoring and biometry are provided by the independent Koordinierungszentrum für Klinische Studien (KKS) – Coordination Centre for Clinical Trails at the University of Heidelberg.