bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and genomic characterization of the first phage infecting Iodobacteria: ϕPLPE, a myovirus having a novel set of features
Authors: Leblanc Cécile , Caumont‐Sarcos Anne , Comeau André M. , Krisch Henry M. 
Published: July 2009

SummaryThe aquatic phage ϕPLPE infects a bacterium of the genus Iodobacter that are common inhabitants of rivers, streams and canals that produce violacein‐like pigments. Our characterization of ϕPLPE reveals it to be a small, contractile‐tailed phage whose 47.5 kb genome sequence is phylogenetically distant from all previously characterized phages. The genome has a generally modular organization (e.g. replication/recombination, structure/morphogenesis, lysis/lysogeny) and approximately half of its 84 open reading frames have no known homologues. It behaves as a virulent phage under the host growth conditions we have employed and, with the exception of an anti‐repressor (ant) homologue, the genome lacks all the genes associated with a lysogenic lifestyle. Thus, either ϕPLPE was once a temperate phage that has lost most of its lysogeny cassette or it is a virulent phage that acquired an ant‐like gene presumably for some function other than the control of lysogeny. The ϕPLPE genome has few bacterial gene homologues with the interesting exception of a putative acylhydrolase (acylase). This function has been implicated in bacterial quorum sensing since it degrades homoserine‐lactone signalling molecules and can disrupt or modulate quorum signalling from either the emitter or its competitors. ϕPLPE may be an example of a phage co‐opting components of the bacterial quorum‐sensing apparatus to its own advantage.
PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification
Authors: Siegl Alexander , Hentschel Ute 
Published: July 2009

SummaryWhole genome amplification (WGA) approaches provide genomic information on single microbial cells and hold great promise for the field of environmental microbiology. Here, the microbial consortia of the marine sponge Aplysina aerophoba were sorted by fluorescence‐activated cell sorting (FACS) and then subjected to WGA. A cosmid library was constructed from the WGA product of a sample containing two bacterial cells, one a member of the candidate phylum Poribacteria and one of a sponge‐specific clade of Chloroflexi. Library screening led to the genomic characterization of three cosmid clones, encoding a polyketide synthase (PKS), a non‐ribosomal peptide synthetase (NRPS) and the Chloroflexi 16S rRNA gene. PCR screening of WGA products from additional, FACS‐sorted single bacterial symbiont cells supports the assignment of the Sup‐PKS gene to the Poribacteria and the novel NRPS gene to the Chloroflexi. This promising single‐cell genomics approach has permitted cloning of entire gene clusters from single microbial cells of known phylogenetic origin and thus provides a sought‐after link between phylogeny and function.
ASSIGNMENT SITUATIONS WITH MULTIPLE OWNERSHIP AND THEIR GAMES
Authors: MIQUEL SILVIA , VAN VELZEN BAS , HAMERS HERBERT , NORDE HENK 
Published: July 2009

An assignment situation can be considered as a two-sided market consisting of two disjoint sets of objects. A non-negative reward matrix describes the profit if an object of one group is assigned to an object of the other group. Assuming that each object is owned by a different agent, Shapley and Shubik (1972) introduced a class of assignment games. This paper introduces assignment situations with multiple ownership (AMO). In these situations an object can be owned by several agents and an agent can participate in the ownership of more than one object. For AMO situations we introduce the class of k-AMO games. An AMO situation is called balanced if for any choice of the reward matrix the corresponding 1-AMO game is balanced. We provide necessary and sufficient conditions for balancedness of AMO situations. Moreover, sufficient conditions are provided for balancedness of k-AMO games.
Measurements and Simulations of Nadir-Viewing Radar Returns from the Melting Layer at X and W Bands
Authors: Liao Liang , Meneghini Robert , Tian Lin , Heymsfield Gerald M. 
Published: July 2009

AbstractSimulated radar signatures within the melting layer in stratiform rain—namely, the radar bright band—are checked by means of comparisons with simultaneous measurements of the bright band made by the ER-2 Doppler radar (EDOP; X band) and Cloud Radar System (CRS; W band) airborne Doppler radars during the Cirrus Regional Study of Tropical Anvils and Cirrus Layers–Florida-Area Cirrus Experiment (CRYSTAL-FACE) campaign in 2002. A stratified-sphere model, allowing the fractional water content to vary along the radius of the particle, is used to compute the scattering properties of individual melting snowflakes. Using the effective dielectric constants computed by the conjugate gradient–fast Fourier transform numerical method for X and W bands and expressing the fractional water content of a melting particle as an exponential function in particle radius, it is found that at X band the simulated radar brightband profiles are in an excellent agreement with the measured profiles. It is also found that the simulated W-band profiles usually resemble the shapes of the measured brightband profiles even though persistent offsets between them are present. These offsets, however, can be explained by the attenuation caused by cloud water and water vapor at W band. This is confirmed by comparisons of the radar profiles made in the rain regions where the unattenuated W-band reflectivity profiles can be estimated through the X- and W-band Doppler velocity measurements. The brightband model described in this paper has the potential to be used effectively for both radar and radiometer algorithms relevant to the satellite-based Tropical Rainfall Measuring Mission and Global Precipitation Measuring Mission.
Pulmonary hypertension in patients with combined pulmonary fibrosis and emphysema syndrome
Authors: Cottin V. , Le Pavec J. , Prévot G. , Mal H. , Humbert M. , Simonneau G. , Cordier J-F. ,   GERM“O”P
Published: July 2009

This study aims to describe the haemodynamic and survival characteristics of patients with pulmonary hypertension in the recently individualised syndrome of combined pulmonary fibrosis and emphysema.A retrospective multicentre study was conducted in 40 patients (38 males; age 68±9 yrs; 39 smokers) with combined pulmonary fibrosis and emphysema, and pulmonary hypertension at right heart catheterisation.Dyspnoea was functional class II in 15%, III in 55% and IV in 30%. 6-min walk distance was 244±126 m. Forced vital capacity was 86±18%, forced expiratory volume in 1 s 78±19%, and carbon monoxide diffusion transfer coefficient 28±16% of predicted. Room air arterial oxygen tension was 7.5±1.6 kPa (56±12 mmHg). Mean pulmonary artery pressure was 40±9 mmHg, cardiac index 2.5±0.7 L·min−1·m−2and pulmonary vascular resistance 521±205 dyn·s·cm−5. 1-yr survival was 60%. Higher pulmonary vascular resistance, higher heart rate, lower cardiac index and lower carbon monoxide diffusion transfer were associated with shorter survival.Patients with combined pulmonary fibrosis and emphysema syndrome and pulmonary hypertension confirmed by right heart catheterisation have a dismal prognosis despite moderately altered lung volumes and flows and moderately severe haemodynamic parameters.
Disrupted ciliated epithelium shows slower ciliary beat frequency and increased dyskinesia
Authors: Thomas B. , Rutman A. , O'Callaghan C. 
Published: July 2009

Ciliary function studies for the diagnosis of primary ciliary dyskinesia (PCD) are usually performed on nasal brush biopsy samples. It is not uncommon to find disrupted epithelial strips of tissue in these samples, and occasionally throughout a sample. The aim of the present study was to determine if cilia on disrupted ciliated epithelial edges beat with a normal pattern and frequency similar to that of cilia on undisrupted edges.Nasal brush biopsy samples from 42 children in whom the diagnosis of PCD was excluded were assessed. The epithelial strips were categorised into five groups: intact undisrupted ciliated epithelial edge, ciliated epithelial edge with minor projections, ciliated epithelial edge with major projections, an isolated ciliated cell on an epithelial edge and single unattached ciliated cells. Ciliary beat frequency and beat pattern of 50 samples from each group were determined using high speed digital video microscopy.The cilia on epithelial edges with varying degrees of disruption showed significantly reduced beat frequency and significantly increased dyskinesia compared with those on intact, undisrupted ciliated epithelial edges.Ideally, the assessment of ciliary beat pattern and frequency for PCD diagnosis should only be performed on undisrupted ciliated edges.
Toll-like receptor 7 function is reduced in adolescents with asthma
Authors: Roponen M. , Yerkovich S. T. , Hollams E. , Sly P. D. , Holt P. G. , Upham J. W. 
Published: July 2009

Anti-viral innate immune responses may be impaired in asthma, although the mechanisms are not well understood. Toll-like receptors (TLRs) 7 and 3 are particularly relevant for initiating responses to common respiratory viruses, as they recognise single-stranded viral RNA and double-stranded viral RNA, respectively. The aim of the present study was to investigate TLR7 and TLR3 function in 14-yr-old adolescents with asthma.Blood mononuclear cells obtained from 17 atopic asthmatics, 29 atopic, non-asthmatics and 21 healthy, non-atopic individuals, were stimulated with the TLR7 agonist imiquimod and the TLR3 agonist poly I:C. Expression of anti-viral molecules was measured by real-time PCR. Concentrations of interferon-γ-inducible cytokine protein (IP)-10 and interleukin (IL)-6 were measured by ELISA.TLR7-induced myxovirus resistance protein A and 2′5′ oligoadenylate synthetase mRNA expression and protein levels of IP-10 were significantly lower in asthma subjects compared with healthy subjects (p = 0.041, p = 0.003 and p = 0.001 respectively). There was a significant negative correlation between total serum immunoglobulin E and IP-10 following TLR7 stimulation. However, TLR3-induced responses did not vary with asthma or atopy. IL-10 mRNA and IL-6 protein synthesis were similar in asthmatic and control subjects. In conclusion, TLR7 function is reduced in adolescents with asthma and this may contribute to susceptibility to respiratory viral infections.
Changes in the prevalence of asthma in adults since 1966: the Busselton health study
Authors: James A. L. , Knuiman M. W. , Divitini M. L. , Hui J. , Hunter M. , Palmer L. J. , Maier G. , Musk A. W. 
Published: July 2009

Asthma prevalence has increased worldwide; although less so in developed countries recently. This study assessed changes in the prevalence of asthma and related symptoms in the Busselton community since 1966.Cross-sectional respiratory health surveys of Busselton adults were conducted in 1966, 1969, 1972, 1975, 1981, 1990 and 2005–2007. Logistic regression models were used to estimate prevalence rates of asthma, respiratory symptoms, smoking, airway hyperresponsiveness (AHR) and atopy and to make comparisons in 2005–2007 and previous survey years. Asthma was defined as ever having doctor-diagnosed asthma (DDA).The prevalence of DDA was around 6% from 1966 to 1975, 8% in 1981 and rose to 19% in 2005–2007. From 1981 to 2005–2007, smoking prevalence declined and obesity and atopy increased but changes in these variables explained only a small part of the increase in DDA. Wheeze and cough/phlegm increased but AHR, breathlessness and doctor-diagnosed bronchitis remained relatively stable over the same period.These observations indicate that the increase in DDA is partly explained by increased symptoms and atopy. The lack of changes in AHR and doctor-diagnosed bronchitis suggests that factors such as diagnostic transfer and increased awareness of asthma have also contributed to the rise in prevalence of DDA.
The scurs inheritance: new insights from the French Charolais breed
Authors: Capitan Aurélien , Grohs Cécile , Gautier Mathieu , Eggen André 
Published: July 2009

Abstract

Background
Polled animals are valued in cattle industry because the absence of horns has a significant economic impact. However, some cattle are neither polled nor horned but have so-called scurs on their heads, which are corneous growths loosely attached to the skull. A better understanding of the genetic determinism of the scurs phenotype would help to fine map the polled locus. To date, only one study has attempted to map the scurs locus in cattle. Here, we have investigated the inheritance of the scurs phenotype in the French Charolais breed and examined whether the previously proposed localisation of the scurs locus on bovine chromosome 19 could be confirmed or not.

Results
Our results indicate that the inheritance pattern of the scurs phenotype in the French Charolais breed is autosomal recessive with complete penetrance in both sexes, which is different from what is reported for other breeds. The frequency of the scurs allele (Sc) reaches 69.9% in the French Charolais population. Eleven microsatellite markers on bovine chromosome 19 were genotyped in 267 offspring (33 half-sib and full-sib families). Both non-parametric and parametric linkage analyses suggest that in the French Charolais population the scurs locus may not map to the previously identified region. A new analysis of an Angus-Hereford and Hereford-Hereford pedigree published in 1978 enabled us to calculate the frequency of the Sc allele in the Hereford breed (89.4%) and to study the penetrance of this allele in males heterozygous for both polled and scurs loci (40%). This led us to revise the inheritance pattern of the scurs phenotype proposed for the Hereford breed and to suggest that allele Sc is not fully but partially dominant in double heterozygous males while it is always recessive in females. Crossbreeding involving the Charolais breed and other breeds gave results similar to those reported in the Hereford breed.

Conclusion
Our results suggest the existence of unknown genetics factors modifying the expression of the scurs locus in double heterozygous Hereford and Angus males. The specific inheritance pattern of the scurs locus in the French Charolais breed represents an opportunity to map this gene and to identify the molecular mechanisms regulating the growth of horns in cattle.
An archived activation tagged population of Arabidopsis thalianato facilitate forward genetics approaches
Authors: Robinson Stephen J , Tang Lily H , Mooney Brent AG , McKay Sheldon J , Clarke Wayne E , Links Matthew G , Karcz Steven , Regan Sharon , Wu Yun-Yun , Gruber Margaret Y , Cui Dejun , Yu Min , Parkin Isobel AP 
Published: July 2009

Abstract

Background
Functional genomics tools provide researchers with the ability to apply high-throughput techniques to determine the function and interaction of a diverse range of genes. Mutagenised plant populations are one such resource that facilitate gene characterisation. They allow complex physiological responses to be correlated with the expression of single genes in planta, through either reverse genetics where target genes are mutagenised to assay the affect, or through forward genetics where populations of mutant lines are screened to identify those whose phenotype diverges from wild type for a particular trait. One limitation of these types of populations is the prevalence of gene redundancy within plant genomes, which can mask the affect of individual genes. Activation or enhancer populations, which not only provide knock-out but also dominant activation mutations, can facilitate the study of such genes.

Results
We have developed a population of almost 50,000 activation tagged A. thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Insertion site sequences have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes, provisional data identifying novel alleles and genes controlling steps in proanthocyanidin biosynthesis and trichome development is presented.

Conclusion
This publicly available population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterised genes annotated within the Arabidopsis genome sequence http://aafc-aac.usask.ca/FST. The presence of enhancer elements on the inserted T-DNA molecule allows both knock-out and dominant activation phenotypes to be identified for traits of interest.
Impact of supplementary private health insurance on stomach cancer care in Korea: a cross-sectional study
Authors: Shin Dong Wook , Jung Kee-Taig , Kim Sung , Bae Jae-Moon , Kim Young-Woo , Ryu Keun Won , Lee Jun Ho , Noh Jae-Hyung , Sohn Tae-Sung , Yun Young Ho 
Published: July 2009

Abstract

Background
Korea achieved universal health insurance coverage in only 12 years; however, insufficient government funding has resulted in high out-of-pocket payments and, in turn, a demand for supplementary private health insurance (PHI). Supplementary PHI provides a fixed amount of benefits in the event of critical illness (e.g., cancer or stroke), surgery, or hospitalization. In this study, we tried to identify factors that influence the decision to purchase supplementary PHI and investigate the impacts of PHI on various aspects of cancer care.

Methods
In a cross-sectional study of 391 patients with gastric cancer, we collected data on demographic and clinical variables, coverage by PHI at the time of diagnosis, and patients' cancer care experiences from surgery databases and patient questionnaires. Two separate multivariate logistic regression models were used 1) to determine whether various sociodemographic and clinical variables influence the purchase of supplementary PHI, and 2) to determine if there is a difference in various outcome measures between individuals with and without PHI.

Results
We studied 187 subjects (49.6%) who were covered under PHI at the time of diagnosis. Subjects who purchased PHI tended to be younger (aOR = 5.01, 95% C.I. = 2.05 – 12.24), and more educated (aOR = 2.67, 95% C.I. = 1.04 – 6.86). Supplementary PHI coverage was significantly associated with financial independence (aOR = 2.07, 95% CI = 1.19 – 3.61), but not with other aspects of cancer care, such as access to healthcare, quality of care, communication and patient autonomy.

Conclusion
Our findings demonstrate that supplementary PHI neither serves as a safety net for vulnerable patients nor improves cancer care experience, except for maintaining the financial independence of beneficiaries.
Photodynamic therapy inhibits p-glycoprotein mediated multidrug resistance via JNK activation in human hepatocellular carcinoma using the photosensitizer pheophorbide a
Authors: Tang Patrick Ming-Kuen , Zhang Dong-Mei , Xuan Ngoc-Ha Bui , Tsui Stephen Kwok-Wing , Waye Mary Miu-Yee , Kong Siu-Kai , Fong Wing-Ping , Fung Kwok-Pui 
Published: July 2009

Abstract

Background
Multidrug resistance (MDR) is frequently observed after prolonged treatment in human hepatoma with conventional anti-tumor drugs, and photodynamic therapy (PDT) is a recently suggested alternative to overcome MDR. The therapeutic potential of PDT was evaluated in a multidrug resistance (MDR) human hepatoma cell line R-HepG2 with photosensitizer pheophorbide a (Pa).

Results
Our results demonstrated that intracellular accumulation of Pa was not reduced by the overexpression of P-glycoprotein. Pa-based PDT (Pa-PDT) significantly inhibited the growth of R-HepG2 cells with an IC50 value of 0.6 μM. Mechanistic study demonstrated that genomic DNA fragmentation and phosphatidylserine externalization occurred where increase of intracellular singlet oxygen level triggers the phosphorylation of c-Jun N-terminal Kinase (JNK) and leads to activation of intrinsic apoptotic caspases cascade during the Pa-PDT treatment. The cytotoxicity of Pa-PDT, accumulation of sub-G1 population, and depolarization of mitochondrial membrane could be inhibited by JNK inhibitor in the Pa-PDT treated cells. Interestingly, the Pa-PDT induced JNK activation showed inhibitory effect on MDR by the down-regulation of P-glycoprotein in R-HepG2 cells in a dose-dependent manner. In addition, significant reduction of tumor size was obtained in Pa-PDT treated R-HepG2-bearing nude mice with no significant damages in liver and heart.

Conclusion
In summary, our findings provided the first evidence that PDT could inhibit the MDR activity by down-regulating the expression of P-glycoprotein via JNK activation using pheophorbide a as the photosensitizer, and our work proved that Pa-PDT inhibited the growth of MDR hepatoma cells by mitochondrial-mediated apoptosis induction.
Improved Efficacy of a Gene Optimised Adenovirus-based Vaccine for Venezuelan Equine Encephalitis Virus
Authors: Williams Amanda J , O'Brien Lyn M , Phillpotts Robert J , Perkins Stuart D 
Published: July 2009

Abstract

Background
Optimisation of genes has been shown to be beneficial for expression of proteins in a range of applications. Optimisation has increased protein expression levels through improved codon usage of the genes and an increase in levels of messenger RNA. We have applied this to an adenovirus (ad)-based vaccine encoding structural proteins (E3-E2-6K) of Venezuelan equine encephalitis virus (VEEV).

Results
Following administration of this vaccine to Balb/c mice, an approximately ten-fold increase in antibody response was elicited and increased protective efficacy compared to an ad-based vaccine containing non-optimised genes was observed after challenge.

Conclusion
This study, in which the utility of optimising genes encoding the structural proteins of VEEV is demonstrated for the first time, informs us that including optimised genes in gene-based vaccines for VEEV is essential to obtain maximum immunogenicity and protective efficacy.
Urbanicity of place of birth and symptoms of psychosis,
depression and anxiety in Uganda
Authors: Lundberg Patric , Cantor-Graae Elizabeth , Rukundo Godfrey , Ashaba Schola , Östergren Per-Olof 
Published: July 2009

BackgroundThe mechanism underlying the association between urban birth/upbringing
and increased schizophrenia risk is unknown. This study explored whether
an urban effect might be present in a low-income country setting, where
the ‘urban’ environment may have radically different components, for
example urban architecture, pollution levels or social cohesion.AimsTo investigate the potential association of urbanicity of place of birth
and symptoms of psychosis, depression and anxiety in Uganda.MethodUgandans aged 18–30 years (n = 646) were interviewed
using the Peters et al Delusions Inventory (PDI–21), the
Hopkins Symptoms Checklist (HSCL–25) and psychoticism items from the
Symptoms Checklist 90-items version (SCL–90) in Mbarara and Kampala
districts and asked about their birthplace.ResultsUrban birth (but not semi-urban) was associated with more lifetime
psychotic experiences, especially grandiosity, and more symptoms of
psychosis, depression and anxiety during the past week.ConclusionsThe urban risk factor for schizophrenia may be universally present across
different levels of human development, albeit the nature of the mechanism
remains elusive.