bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nasal Carriage of Methicillin-ResistantStaphylococcus aureusAmong Hospital Staff and Outpatients
Authors: Cesur Salih , Çokça Fügen 
Published: April 2006

AbstractThis study sought to determine the rate of nasal methicillin-resistantStaphylococcus aureus(MRSA) carriage among hospital staff and outpatients. Nasal swabs were obtained from 500 outpatients and 500 hospital staff. Hospital staff were 2.3-fold more likely to carry MRSA than were outpatients (6% vs 2.6%,P= .013).
Partial Shotgun Sequencing of the Boechera stricta Genome Reveals Extensive Microsynteny and Promoter Conservation with Arabidopsis
Authors: Windsor Aaron J. , Schranz M. Eric , Formanová Nataša , Gebauer-Jung Steffi , Bishop John G. , Schnabelrauch Domenica , Kroymann Juergen , Mitchell-Olds Thomas 
Published: April 2006

Abstract
Comparative genomics provides insight into the evolutionary dynamics that shape discrete sequences as well as whole genomes. To advance comparative genomics within the Brassicaceae, we have end sequenced 23,136 medium-sized insert clones from Boechera stricta, a wild relative of Arabidopsis (Arabidopsis thaliana). A significant proportion of these sequences, 18,797, are nonredundant and display highly significant similarity (BLASTn e-value ≤ 10−30) to low copy number Arabidopsis genomic regions, including more than 9,000 annotated coding sequences. We have used this dataset to identify orthologous gene pairs in the two species and to perform a global comparison of DNA regions 5′ to annotated coding regions. On average, the 500 nucleotides upstream to coding sequences display 71.4% identity between the two species. In a similar analysis, 61.4% identity was observed between 5′ noncoding sequences of Brassica oleracea and Arabidopsis, indicating that regulatory regions are not as diverged among these lineages as previously anticipated. By mapping the B. stricta end sequences onto the Arabidopsis genome, we have identified nearly 2,000 conserved blocks of microsynteny (bracketing 26% of the Arabidopsis genome). A comparison of fully sequenced B. stricta inserts to their homologous Arabidopsis genomic regions indicates that indel polymorphisms &gt;5 kb contribute substantially to the genome size difference observed between the two species. Further, we demonstrate that microsynteny inferred from end-sequence data can be applied to the rapid identification and cloning of genomic regions of interest from nonmodel species. These results suggest that among diploid relatives of Arabidopsis, small- to medium-scale shotgun sequencing approaches can provide rapid and cost-effective benefits to evolutionary and/or functional comparative genomic frameworks.
A Comparative Genomics Strategy for Targeted Discovery of Single-Nucleotide Polymorphisms and Conserved-Noncoding Sequences in Orphan Crops
Authors: Feltus F.A. , Singh H.P. , Lohithaswa H.C. , Schulze S.R. , Silva T.D. , Paterson A.H. 
Published: April 2006

AbstractCompleted genome sequences provide templates for the design of genome analysis tools in orphan species lacking sequence information. To demonstrate this principle, we designed 384 PCR primer pairs to conserved exonic regions flanking introns, using Sorghum/Pennisetum expressed sequence tag alignments to the Oryza genome. Conserved-intron scanning primers (CISPs) amplified single-copy loci at 37% to 80% success rates in taxa that sample much of the approximately 50-million years of Poaceae divergence. While the conserved nature of exons fostered cross-taxon amplification, the lesser evolutionary constraints on introns enhanced single-nucleotide polymorphism detection. For example, in eight rice (Oryza sativa) genotypes, polymorphism averaged 12.1 per kb in introns but only 3.6 per kb in exons. Curiously, among 124 CISPs evaluated across Oryza, Sorghum, Pennisetum, Cynodon, Eragrostis, Zea, Triticum, and Hordeum, 23 (18.5%) seemed to be subject to rigid intron size constraints that were independent of per-nucleotide DNA sequence variation. Furthermore, we identified 487 conserved-noncoding sequence motifs in 129 CISP loci. A large CISP set (6,062 primer pairs, amplifying introns from 1,676 genes) designed using an automated pipeline showed generally higher abundance in recombinogenic than in nonrecombinogenic regions of the rice genome, thus providing relatively even distribution along genetic maps. CISPs are an effective means to explore poorly characterized genomes for both DNA polymorphism and noncoding sequence conservation on a genome-wide or candidate gene basis, and also provide anchor points for comparative genomics across a diverse range of species.
Lung as a new target in rats of 2‐amino‐3‐methylimidazo[4,5‐f]quinoline carcinogenesis: Results of a two‐stage model initiated with N‐bis(2‐hydroxypropyl)nitrosamine
Authors: Kitamura Yasuki , Umemura Takashi , Kanki Keita , Ishii Yuji , Kuroiwa Yuichi , Masegi Toshiaki , Nishikawa Akiyoshi , Hirose Masao 
Published: April 2006

The effects of IQ on the promotion stage of DHPN‐induced lung carcinogenesis and contributions of oxidative stress were investigated in rats. Groups of 20 male 6‐week‐old F344 rats were given 0.1% DHPN in their drinking water for 2 weeks for initiation. From the age of 9 weeks, they were treated with 0, 150 and 300 p.p.m. of IQ in the diet for 27 weeks. Control rats were similarly fed 300 p.p.m. IQ or basal diet alone without the preceding initiation. IQ clearly (P < 0.01) enhanced the multiplicity of lung tumors in a dose‐dependent manner (DHPN alone, 3.63 ± 1.80; DHPN +150 p.p.m. IQ, 11.50 ± 5.04; DHPN +300 p.p.m. IQ, 18.83 ± 4.58 [no./rat]). In addition, the incidence of lung tumors in the 300 p.p.m. IQ alone group (25%) was significantly (P < 0.05) higher than that in the non‐treatment group (0%). In a second experiment, male rats were given IQ at doses of 0 and 300 p.p.m. in the diet for one week in order to analyze 8‐OHdG formation, levels of TBARS and BrdU‐LI in the lungs. There were no changes in 8‐OHdG or TBARS levels, but significant elevation of BrdU‐LI occurred in the IQ administration group. The overall data clearly indicate that IQ is a potent lung carcinogen in rats, in which oxidative stress may not be involved in lung carcinogenesis. (Cancer Sci 2006; 97: 368 –373)
Transient facilitative effects of heather on Scots pine along a grazing disturbance gradient in Scottish moorland
Authors: BROOKER R. W. , SCOTT D. , PALMER S. C. F. , SWAINE E. 
Published: April 2006

Summary
Facilitation between neighbouring plants can promote species survival and regulate community composition. However, the role of facilitation varies along environmental severity gradients. It is important to understand the shape of this relationship to improve our ability to predict the impact of a changing environment on biodiversity.
We used Scots pine saplings growing within heather to examine the shape of the relationship between facilitative interactions (protection from browsing) and the severity of the environment (deer browsing intensity). We also investigated whether protection from browsing translated into a biomass response of saplings.
In the first winter following planting heather had a facilitative effect on saplings by reducing the probability of browsing. This effect was strongest at intermediate deer browsing intensities, thus producing a hump‐backed relationship between facilitative effects and the severity of the environment.
Protection from browsing did not lead to longer‐term biomass gains for the saplings. The competitive effects of heather on sapling growth therefore outweighed the beneficial effects of protection from browsing.
These results provide much‐needed information on the shape of the severity–interactions relationship with respect to a key natural disturbance phenomenon (herbivory), and demonstrate that an observable interaction relationship does not necessarily translate into a biomass response.
This illustrates the complex and potentially transient nature of plant–plant interactions, and the potential difficulty that would be associated with using shelter effects of heather as a management tool to promote Scots pine regeneration.
Detection of infectious haematopoietic necrosis virus and infectious salmon anaemia virus by molecular padlock amplification
Authors: Millard P J , Bickerstaff L E , LaPatra S E , Kim C H 
Published: April 2006

AbstractA new method for the molecular detection of the fish pathogens, infectious haematopoietic necrosis virus (IHNV) and infectious salmon anaemia virus (ISAV), is described. By employing molecular padlock probe (MPP) technology combined with rolling circle amplification (RCA) and hyperbranching (Hbr), it is possible to detect RNA target sequence from these viruses at levels comparable with those detected by the polymerase chain reaction (PCR), but without prior reverse transcription. The use of MPP technology combined with RCA and Hbr for the detection of IHNV and ISAV in fish exhibited selectivity comparable with that of PCR while potentially reducing the time and cost required for analysis. The method described was used to detect as few as 104 DNA oligonucleotide targets and was sequence‐specific at the single base level. Viral RNA could be detected directly, either alone or in the presence of non‐viral RNA from fish tissue. This technology is applicable for detecting a variety of microbes, in addition to IHNV and ISAV, and is ideal for further integration into a biosensor platform for on‐site diagnosis of pathogen infection in fish.
Quantitative expression (Walbaum) of immunological factors in rainbow trout, Oncorhynchus mykiss (Walbaum), after infection with either Flavobacterium psychrophilum, Aeromonas salmonicida, or infectious haematopoietic necrosis virus
Authors: Overturf K , LaPatra S 
Published: April 2006

AbstractTo further enhance our understanding of immunological gene expression in rainbow trout, Oncorhynchus mykiss, after infection with naturally occurring pathogens, a series of probes and primers were developed for the quantification of immune factors. Separate groups of specific‐pathogen‐free rainbow trout were infected with either Flavobacterium psychrophilum, Aeromonas salmonicida or infectious haematopoietic necrosis virus (IHNV). Three different concentrations of each pathogen were used and samples from infected and mock‐infected fish were taken at either 1 or 5 days after infection. Ten fish were sampled at each time point for individual sections of liver, spleen and head kidney. Organ specimens from five of the fish were used to re‐isolate and quantify the pathogen at the time the samples were taken. Total RNA was extracted from the organs of the remaining five animals. Using real‐time polymerase chain reaction with fluorescent‐labelled probes, the RNA from these organs was examined for the level of expression of the following immunological factors; an interferon related protein (MX‐1), interleukin‐8 (IL‐8), the cytotoxic T‐cell marker CD‐8 and complement factor C3 (C3). They were also measured for the level of β‐actin, which was used as a standardization control for cellular RNA expression. Infection with IHNV produced the greatest change in expression level for all the immunological related factors examined in this study. IHNV elicited the best dose response profile, which was typically seen at 5‐days post‐infection for MX‐1, C3, IL‐8 and CD‐8. Infection with A. salmonicida and F. psychrophilum showed elevated, but variable expression levels for several of the genes tested.
Apoptosis in Ichthyophthirius multifiliis is associated with expression of the Fas receptor of theronts
Authors: Xu D‐H , Klesius P H , Shoemaker C A 
Published: April 2006

AbstractThe expression of type I membrane Fas receptors on the surface of Ichthyophthirius multifiliis (Ich) theronts and the possible association between Fas expression and theront apoptosis induced by the immune antibody was examined. Fas receptors were detected on the theront surface using fluorescein isothiocyanate‐conjugated mouse monoclonal antibody against Fas. Fas‐positive theronts significantly increased with time during in vitro incubation and with increasing theront concentration. Furthermore, the immune cutaneous antibody induced theront apoptosis; however, Fas ligand did not. A highly significant correlation was noted between theront Fas expression and immune cutaneous antibody‐induced theront apoptosis. Numbers of apoptotic theronts increased with increasing number of Fas‐positive theronts. The data indicated that theront apoptosis induced by immune cutaneous antibody appears to be positively correlated with the expression of Fas on the surface of Ich theronts.
Longitudinal study of a natural outbreak of heart and skeletal muscle inflammation in Atlantic salmon, Salmo salar L.
Authors: Kongtorp R T , Halse M , Taksdal T , Falk K 
Published: April 2006

AbstractHeart and skeletal muscle inflammation (HSMI) is a transmissible disease of farmed Atlantic salmon, Salmo salar L. It is characterized by significant epi‐, endo‐ and myocarditis, as well as myositis, particularly involving red skeletal muscle. The aetiology of HSMI is currently unresolved, though a viral cause is suspected. Since its discovery in 1999, HSMI has become an increasing problem for the Norwegian farming industry, with some farms experiencing yearly outbreaks and subsequent economic losses. In the present study an Atlantic salmon farm was studied from December 2003 to April 2005. Samples from apparently healthy as well as clinically diseased fish were collected monthly and examined histopathologically. The first fish to be diagnosed with HSMI was sampled in May, 8 months after transfer to sea. A clinical outbreak of HSMI followed in June, when all fish in the sample had lesions consistent with HSMI. Subsequent samples revealed that cardiac lesions decreased in severity 2 months after the start of the outbreak, but that multiple foci of cellular infiltration and necrosis persisted throughout the year. There appeared to be a shift in lesion location from being most severe in the compact myocardium in early stages of disease to a greater involvement of the atrium and spongy layer of the ventricle in later samples. Late samples also showed increased fibrosis of cardiac tissue. In conclusion, HSMI appears to be a severe disease with elevated mortality, morbidity close to 100% and prolonged duration.
Healthy eating: information and advice in primary care
Authors: Lyon Phil , Colquhoun Anne , Hillman Marjatta , Alho Eija‐Riitta 
Published: April 2006

AbstractGeneral practice surgeries and health centres often provide patients with healthy eating advice during consultation for specific problems, or in the context of general health monitoring. In some circumstances, patients will be referred for specialist dietary advice but, for most, all advice is provided from the resources of the practice. Advice about what patients should be eating or avoiding has long been a legitimate part of the consultation process for some illnesses, but diet is now seen as significant in a wider range of conditions, and in actively promoting healthy lifestyle. The research evidence as to whether primary care staff are able to effectively deliver healthy eating advice is equivocal. This paper reports Scottish data (n = 101) collected in a study of Scottish and Finnish practice nurses’ practical food knowledge conducted in 2003/2004. In this sample, practice nurses often demonstrated very good levels of nutritional knowledge to underpin basic advice, although sometimes there was considerable variation among these nurses. By comparison with earlier studies in the UK, practical cooking advice was extremely limited. This may have reflected an awareness of changed eating‐out patterns, and the increased consumption of processed foods or ready meals at home, but the need for care with snacking behaviour or the need to restrict portion size, whether eating at home or eating out, was not typically part of their healthy eating advice.
Sensory evaluation: age and gender profiling of lite, no‐sugar‐added vanilla ice creams
Authors: Stokols Jennifer , Bordi Peter , Palchak Tom , Lee H. Andy 
Published: April 2006

AbstractThis study is the third in a series of research studies aimed at profiling both genders and two distinct age groups for sensory preferences of no sugar added vanilla ice creams. A sample of two hundred participants tasted and rated three samples of market‐available lite, no‐sugar‐added vanilla ice creams (which contain a mixture, or formulation, of several sweetening agents) against the control version (which only includes maltitol as the sweetening agent). Participants used a nine‐point hedonic scale to indicate their preference for various attributes noted in both products. The four samples differed in their sugar content, fat content (though all were under 3 grams per half cup serving by definition of “lite”), and fiber content but had similar calorie and protein profiles. Participants were categorized into one of four groups for data compilation and interpretation: male students, female students, male adults, and female adults. They used computer software to complete questionnaires, and the results were tabulated by the physical attributes (i.e., taste, texture, and appearance) as well as by overall impressions of the sensory characteristics of the four samples as means for comparison. The results of the study concurred with past findings regarding overall consumer acceptability of the no‐sugar‐added ice cream. The results suggested that, for the student and adult population tested, a maltitol syrup with these characteristics is the ideal sweetener used in light no‐sugar‐added frozen desserts and would be an appropriate focus for future product manipulation by food manufacturers and marketers, alike.
Street‐level bureaucrats and the implementation of cleaning and sanitation practices in foodservice: case findings from a study in Danish hospitals and nursing homes
Authors: Mikkelsen Bent E. , Søndergård Kristine G. 
Published: April 2006

AbstractProper cleaning and sanitation that can to maintain the sanitary and hygienic level in the catering kitchens is an important routine to prevent food‐borne diseases and good management of cleaning and sanitation is an important part of any hygiene management system. But large scale industrial kitchens in general seems to be quite slow in initiating change processes required to implementing new routines and only very few large industrial kitchens in Denmark had compulsory self‐inspection programs or auto‐control operating as required. Against this background a study was carried out in Danish institutional kitchens to study the implementation process of cleaning and sanitation practices at practitioner level. The aim of the study was to study how policies aiming at improving hygiene management in foodservice have been implemented at kitchen level when it comes to cleaning and sanitation. The study was conducted as a multiple case study in nursing home and hospital kitchens. The methodology was based on individual telephone interviews in combination with a quantitative questionnaire. A total of 15 kitchens participated in the study which were based on and open‐ended interview guide, focusing on applied cleaning methods, principles for choice of cleaning procedures and methods, cleaning management, including existing documentation for cleaning quality, as well as suggestions for improvements and advancements in cleaning and sanitation. The study shows that street‐level bureaucrats responsible for cleaning and sanitation feel themselves faced with number of challenges that they don’t have the right background to be able to handle properly and this is mirrored in their views and attitudes towards cleaning and sanitation. Street‐level bureaucrats find: that cleaning and sanitation is boring, monotonous and has low status; that help and guidelines for implementing their self‐inspection program is needed; that planning and management tools and techniques are lacking; that tacit knowledge is the guiding principle rather than written procedures; and that educational opportunities are lacking and that there are few opportunities for networking and sharing of knowledge. In general street‐level bureaucrats responsible for cleaning and sanitation feel themselves faced with number of challenges that they don’t have the right background to be able to handle properly and this is mirrored in their views and attitudes towards cleaning and sanitation.
Composition-Modified Matrices Improve Identification of Homologs of
Saccharomyces cerevisiae
Low-Complexity Glycoproteins
Authors: Coronado Juan E. , Attie Oliver , Epstein Susan L. , Qiu Wei-Gang , Lipke Peter N. 
Published: April 2006

ABSTRACT

Yeast glycoproteins are representative of low-complexity sequences, those sequences rich in a few types of amino acids. Low-complexity protein sequences comprise more than 10% of the proteome but are poorly aligned by existing methods. Under default conditions, BLAST and FASTA use the scoring matrix BLOSUM62, which is optimized for sequences with diverse amino acid compositions. Because low-complexity sequences are rich in a few amino acids, these tools tend to align the most common residues in nonhomologous positions, thereby generating anomalously high scores, deviations from the expected extreme value distribution, and small
e
values. This anomalous scoring prevents BLOSUM62-based BLAST and FASTA from identifying correct homologs for proteins with low-complexity sequences, including
Saccharomyces cerevisiae
wall proteins. We have devised and empirically tested scoring matrices that compensate for the overrepresentation of some amino acids in any query sequence in different ways. These matrices were tested for sensitivity in finding true homologs, discrimination against nonhomologous and random sequences, conformance to the extreme value distribution, and accuracy of
e
values. Of the tested matrices, the two best matrices (called E and gtQ) gave reliable alignments in BLAST and FASTA searches, identified a consistent set of paralogs of the yeast cell wall test set proteins, and improved the consistency of secondary structure predictions for cell wall proteins.
Low Genetic Variation and No Detectable Population Structure in
Aspergillus fumigatus
Compared to Closely Related
Neosartorya
Species
Authors: Rydholm Carla , Szakacs George , Lutzoni François 
Published: April 2006

ABSTRACT

Aspergillus fumigatus
is an anamorphic euascomycete mold with a ubiquitous presence worldwide. Despite intensive work to understand its success as a pathogen infecting immunosuppressed patients, the population dynamics and recent evolutionary history of
A. fumigatus
remain understudied. We examined patterns of genetic variation at three intergenic loci for 70 natural isolates from Europe, North America, South America, Asia, Africa, and Australia. The same loci were used to analyze within-population genetic variation for 33 isolates obtained from five geographic locations. Neither data set detected evidence of population differentiation or found any association between the genetic and geographic distances among these isolates. No evidence for genetic differentiation within the two
A. fumigatus
mating types was detected. The genetic diversity of
A. fumigatus
, contrasted with that of its close teleomorphic relatives,
Neosartorya fischeri
and
Neosartorya spinosa
, is remarkably low.