bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of interleukin 28B and mutations in the core and NS5A region of hepatitis C virus with response to peg‐interferon and ribavirin therapy
Authors: Hayashi Kazuhiko , Katano Yoshiaki , Honda Takashi , Ishigami Masatoshi , Itoh Akihiro , Hirooka Yoshiki , Ishikawa Tetsuya , Nakano Isao , Yoshioka Kentaro , Toyoda Hidenori , Kumada Takashi , Goto Hidemi 
Published: June 2011

Abstract
Background and aims: Mutations in the core and NS5A region of hepatitis C virus (HCV) genotype 1b have been associated with response to interferon (IFN) therapy. Genome‐wide association studies have revealed that the single‐nucleotide polymorphism (SNP) of interleukin 28B (IL28B) contributes to IFN response. The aim of this study was to investigate whether the SNP of IL28B (rs8099917) and amino acid substitutions in the core and NS5A region affect the response to IFN therapy.
Methods: A total of 299 patients (157 men, 142 women; mean age, 55.9 ± 10.3 years) infected with HCV genotype 1b were studied. The fibrosis stage was diagnosed as F0 (n=23), F1 (n=121), F2 (n=62), F3 (n=32) and F4 (n=7) by liver biopsy.
Results: Of the 299 patients, 138 achieved sustained virological response (SVR). On univariate analysis, predictors of SVR were age <60 years, male gender, higher platelet count, lack of fibrosis, non‐Q at core 70, mutant‐type interferon sensitivity‐determining region (ISDR) and IL28B genotype TT. The factors related to SVR on multivariate analysis were IL28B (P=0.0001), fibrosis (P=0.0111) and mutations in the core region70 (P=0.0267) and ISDR (P=0.0408). The best SVR was achieved in patients with non‐Q70, mutant‐type ISDR and T allele (74.5%), and the worst was achieved in patients with Q70, wild‐type ISDR and G allele (8.1%).
Conclusions: The SNP of IL28B and mutations in the core region and NS5A are associated with IFN responsiveness. Both host and viral factors might be useful for predicting IFN response.
Acceptance of oral health promotion programmes by dental hygienists and dental nurses in public dental service
Authors: Arpalahti I , Järvinen M , Suni J , Pienihäkkinen K 
Published: June 2011

To cite this article:

Int J Dent Hygiene
10, 2012; 46–53  DOI: 10.1111/j.1601‐5037.2011.00517.x  Arpalahti I, Järvinen M, Suni J, Pienihäkkinen K. Acceptance of oral health promotion programmes by dental hygienists and dental nurses in public dental service.Abstract:Objectives:  The aim of this study was to analyse how dental hygienists and in‐service trained dental nurses accepted new health promotion programmes, how did they experience them in practice, and how did these programmes affect their attitudes to work.Methods:  The subjects were all the dental hygienists and in‐service trained dental nurses (n = 28) involved in health promotion of small children. Education and written instructions on two new programmes had been given to the professionals in two areas of Vantaa and those in the third area used the routine programme. The transtheoretical model (TTM) was selected as the theoretical framework for counselling. A structured questionnaire of 31–35 items was sent to all subjects. Independent samples Mann–Whitney U and Fisher’s exact tests were used as statistical methods.Results:  The response rate was 89%. All respondents felt that the work they had carried out had always been important during their working career. Twenty‐one of 25 respondents reported that the instructions and education were suitable for oral health promotion. The respondents within the new programmes felt they had advanced more as health professionals (P = 0.020) and acquired more confidence from the education (P = 0.018) compared with the routine programme.Conclusions:  The new programmes for small children were well accepted by the dental hygienists and the in‐service trained dental nurses, and the majority of them gained some new practices for their work.
Development of a 16S rRNA Gene Primer and PCR-Restriction Fragment Length Polymorphism Method for Rapid Detection of Members of the Genus Megasphaera and Species-Level Identification
Authors: Ohnishi Akihiro , Abe Shinko , Nashirozawa Shiho , Shimada Sayaka , Fujimoto Naoshi , Suzuki Masaharu 
Published: June 2011

ABSTRACT

The genus
Megasphaera
is relevant to the environment, human health and food, and renewable energy for the future. In this study, a primer set was designed for PCR-restriction fragment length polymorphism (RFLP) analyses to detect and identify the members of
Megasphaera
. Direct detection and identification were achieved for environmental samples and isolates.
Changes in Bacterial Diversity Associated with Epithelial Tissue in the Beef Cow Rumen during the Transition to a High-Grain Diet
Authors: Chen Yanhong , Penner Gregory B. , Li Meiju , Oba Masahito , Guan Le Luo 
Published: June 2011

ABSTRACT

Our understanding of the ruminal epithelial tissue-associated bacterial (defined as epimural bacteria in this study) community is limited. In this study, we aimed to determine whether diet influences the diversity of the epimural bacterial community in the bovine rumen. Twenty-four beef heifers were randomly assigned to either a rapid grain adaptation (RGA) treatment (
n
= 18) in which the heifers were allowed to adapt from a diet containing 97% hay to a diet containing 8% hay over 29 days or to the control group (
n
= 6), which was fed 97% hay. Rumen papillae were collected when the heifers were fed 97%, 25%, and 8% hay diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR analysis were used to characterize rumen epimural bacterial diversity and to estimate the total epimural bacterial population (copy numbers of the 16S rRNA gene). The epimural bacterial diversity from RGA heifers changed (
P
= 0.01) in response to the rapid dietary transition, whereas it was not affected in control heifers. A total of 88 PCR-DGGE bands were detected, and 44 were identified from phyla including
Firmicutes
,
Bacteroidetes
, and
Proteobacteria
. The bacteria
Treponema
sp.,
Ruminobacter
sp., and
Lachnospiraceae
sp. were detected only when heifers were fed 25% and 8% hay diets, suggesting the presence of these bacteria is the result of adaptation to the high-grain diets. In addition, the total estimated population of rumen epimural bacteria was positively correlated with molar proportions of acetate, isobutyrate, and isovalerate, suggesting that they may play a role in volatile fatty acid metabolism in the rumen.
Roles of Two Shewanella oneidensis MR-1 Extracellular Endonucleases
Authors: Gödeke Julia , Heun Magnus , Bubendorfer Sebastian , Paul Kristina , Thormann Kai M. 
Published: June 2011

ABSTRACTThe dissimilatory iron-reducing bacteriumShewanella oneidensisMR-1 is capable of using extracellular DNA (eDNA) as the sole source of carbon, phosphorus, and nitrogen. In addition, we recently demonstrated thatS. oneidensisMR-1 requires eDNA as a structural component during all stages of biofilm formation. In this study, we characterize the roles of twoShewanellaextracellular endonucleases, ExeS and ExeM. While ExeS is likely secreted into the medium, ExeM is predicted to remain associated with the cell envelope. BothexeMandexeSare highly expressed under phosphate-limited conditions. Mutants lackingexeSand/orexeMexhibit decreased eDNA degradation; however, the capability ofS. oneidensisMR-1 to use DNA as the sole source of phosphorus is only affected in mutants lackingexeM. Neither of the two endonucleases alleviates toxic effects of increased eDNA concentrations. The deletion ofexeMand/orexeSsignificantly affects biofilm formation ofS. oneidensisMR-1 under static conditions, and expression ofexeMandexeSdrastically increases during static biofilm formation. Under hydrodynamic conditions, a deletion ofexeMleads to altered biofilms that consist of densely packed structures which are covered by a thick layer of eDNA. Based on these results, we hypothesize that a major role of ExeS and, in particular, ExeM ofS. oneidensisMR-1, is to degrade eDNA as a matrix component during biofilm formation to improve nutrient supply and to enable detachment.
Role of
rpoS
in the Development of Cell Envelope Resilience and Pressure Resistance in Stationary-Phase Escherichia coli
Authors: Charoenwong Duangkamol , Andrews Simon , Mackey Bernard 
Published: June 2011

ABSTRACT

This work investigated the role of
rpoS
in the development of increased cell envelope resilience and enhanced pressure resistance in stationary-phase cells of
Escherichia coli
. Loss of both colony-forming ability and membrane integrity, measured as uptake of propidium iodide (PI), occurred at lower pressures in
E. coli
BW3709 (
rpoS
) than in the parental strain (BW2952). The
rpoS
mutant also released much higher concentrations of protein under pressure than the parent. We propose that RpoS-regulated functions are responsible for the increase in membrane resilience as cells enter stationary phase and that this plays a major role in the development of pressure resistance. Strains from the Keio collection with mutations in two RpoS-regulated genes,
cfa
(cyclopropane fatty acyl phospholipid synthase) and
osmB
(outer membrane lipoprotein), were significantly more pressure sensitive and took up more PI than the parent strain, with
cfa
having the greatest effect. Mutations in the
bolA
morphogene and other RpoS-regulated lipoprotein genes (
osmC
,
osmE
,
osmY
, and
ybaY
) had no effect on pressure resistance. The cytoplasmic membranes of the
rpoS
mutant failed to reseal after pressure treatment, and strains with mutations in
o
smB
and
nlpI
(new lipoprotein) were also somewhat impaired in the ability to reseal their membranes. The
cfa
mutant, though pressure sensitive, was unaffected in membrane resealing, implying that the initial transient permeabilization event is critical for loss of viability rather than the failure to reseal. The enhanced pressure sensitivity of
polA
,
recA
, and
xthA
mutants suggested that DNA may be a target of oxidative stress in pressure-treated cells.
An Essential Tyrosine Phosphatase Homolog Regulates Cell Separation, Outer Membrane Integrity, and Morphology in Caulobacter crescentus
Authors: Shapland Elaine B. , Reisinger Sarah J. , Bajwa Amrita K. , Ryan Kathleen R. 
Published: June 2011

ABSTRACTAlthough reversible phosphorylation on tyrosine residues regulates the activity of many eukaryotic proteins, there are few examples of this type of regulation in bacteria. We have identified the first essential tyrosine phosphatase homolog in a bacterium,Caulobacter crescentusCtpA.ctpAmutants with altered active-site residues are nonviable, and depletion of CtpA yields chains of cells with blebbed outer membranes, linked by unresolved peptidoglycan. CtpA overexpression reduces cell curvature in a manner similar to deleting the intermediate filament protein crescentin, but it does not disrupt crescentin localization or membrane attachment. Although it has no obvious signal sequence or transmembrane-spanning domains, CtpA associates with theCaulobacterinner membrane. Immunolocalization experiments suggest that CtpA accumulates at the division site during the last quarter of the cell cycle. We propose that CtpA dephosphorylates one or more proteins involved in peptidoglycan biosynthesis or remodeling, which in turn affect cell separation, cell envelope integrity, and vibrioid morphology.
Genome Sequence of Streptomyces sp. Strain Tü6071
Authors: Erxleben Anika , Wunsch-Palasis Julia , Grüning Björn A. , Luzhetska Marta , Bechthold Andreas , Günther Stefan 
Published: June 2011

ABSTRACT

Streptomyces
sp. Tü6071 is a soil-dwelling bacterium which has a highly active isoprenoid biosynthesis. Isoprenoids are important precursors for biopharmaceutical molecules such as antibiotics or anticancer agents, e.g., landomycin.
Streptomyces
sp. Tü6071 produces the industrially important terpene glycosides phenalinolactones, which have antibacterial activity against several Gram-positive bacteria. The availability of the genome sequence of
Streptomyces
sp. Tü6071 allows for understanding the biosynthesis of these pharmaceutical molecules and will facilitate rational genome modification to improve industrial use.
Draft Genome Sequence of Paenibacillus elgiiB69, a Strain with Broad Antimicrobial Activity
Authors: Ding Rui , Li Yudong , Qian Chaodong , Wu Xuechang 
Published: June 2011

ABSTRACT

Here, we report the draft genome sequence of
Paenibacillus elgii
B69, which was isolated from soil and has broad-spectrum antimicrobial activity. As far as we know, the
P. elgii
genome is the largest of the
Paenibacillus
genus for which genome sequences are available. Multiple sets of genes related to antibiotic biosynthetic pathways have been found in the genome.
Complete Genome Sequence of the Bacterium Porphyromonas gingivalis TDC60, Which Causes Periodontal Disease
Authors: Watanabe Takayasu , Maruyama Fumito , Nozawa Takashi , Aoki Akinobu , Okano Soichiro , Shibata Yasuko , Oshima Kenshiro , Kurokawa Ken , Hattori Masahira , Nakagawa Ichiro , Abiko Yoshimitsu 
Published: June 2011

ABSTRACT

Porphyromonas gingivalis
is a black-pigmented asaccharolytic anaerobe and a major causative agent of periodontitis. Here, we report the complete genome sequence of
P. gingivalis
strain TDC60, which was recently isolated from a severe periodontal lesion in a Japanese patient.
Complete Genome Sequence of Propionibacterium acnesType IB Strain 6609
Authors: Hunyadkürti Judit , Feltóti Zsófia , Horváth Balázs , Nagymihály Marianna , Vörös Andrea , McDowell Andrew , Patrick Sheila , Urbán Edit , Nagy István 
Published: June 2011

ABSTRACT

Propionibacterium acnes
is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota and is thought to play a central role in acne vulgaris, a chronic inflammatory disease of the pilosebaceous unit (I. Kurokawa et al., Exp. Dermatol.
18:
821-832, 2009). Here we present the whole genome sequence of
P. acnes
type IB strain 6609, which was recovered from a skin sample from a woman with no recorded acne history and is thus considered a nonpathogenic strain (I. Nagy, Microbes Infect.
8:
2195-2205, 2006).
Genome Sequence of the Thermophilic Strain Bacillus coagulans2-6, an Efficient Producer of High-Optical-Purity
l
-Lactic Acid
Authors: Su Fei , Yu Bo , Sun Jibin , Ou Hong-Yu , Zhao Bo , Wang Limin , Qin Jiayang , Tang Hongzhi , Tao Fei , Jarek Michael , Scharfe Maren , Ma Cuiqing , Ma Yanhe , Xu Ping 
Published: June 2011

ABSTRACT

Bacillus coagulans
2-6 is an efficient producer of lactic acid. The genome of
B. coagulans
2-6 has the smallest genome among the members of the genus
Bacillus
known to date. The frameshift mutation at the start of the
d
-lactate dehydrogenase sequence might be responsible for the production of high-optical-purity
l
-lactic acid.
Genome Analysis of a Mycoplasma hyorhinis Strain Derived from a Primary Human Melanoma Cell Line
Authors: Kornspan Jonathan D. , Lysnyansky Inna , Kahan Tamar , Herrmann Richard , Rottem Shlomo , Nir-Paz Ran 
Published: June 2011

ABSTRACT

The complete genome of
Mycoplasma hyorhinis
strain MCLD has been sequenced and annotated. This genome differs by the inversion of a 14.4-kb and a 3.7-kb fragment and the deletion of a 9.9-kb fragment from
M. hyorhinis
strain HUB-1, isolated from swine respiratory tract. The genome revealed 778 coding sequences (CDSs), with a limited number of
vlp
genes encoding variable surface lipoproteins.
Diffuse reflectance spectroscopy: diagnostic accuracy of a non-invasive screening technique for early detection of malignant changes in the oral cavity
Authors: Jayanthi J L , Nisha G U , Manju S , Philip E K , Jeemon P , Baiju K V , Beena V T , Subhash N 
Published: June 2011

BackgroundStrong proof-of-principle for utilisation of diffuse reflectance spectroscopy, a non-invasive tool for early detection of malignant changes, has emerged recently. The potential of this technique in distinguishing normal tissue from hyperplastic and dysplastic tissues was explored.MethodsDiffuse reflectance (DR) spectra in the 400–700 nm region were obtained from the buccal mucosa of 96 patients and 34 healthy volunteers. The DR spectral data were compared against the gold standard biopsy and histopathology results. A principal-component analysis was performed for dimensional reduction in the normalised spectral data with linear discriminant analysis as the classifying technique. The receiver operator characteristic curve technique was employed for evaluating the performance of the diagnostic test.ResultsDR spectral features for different lesions, such as normal/healthy, hyperplastic, dysplastic and squamous cell carcinoma (SCC), varied significantly according to the intensity of oxygenated haemoglobin absorption. While the classification based on discriminant scores provided an overall sensitivity of 98.5% and specificity of 96.0% for distinguishing SCC from dysplasia, they were 100.0% and 95.0%, respectively, for distinguishing dysplasia from hyperplasia. Similarly, the analysis yielded a sensitivity of 95.0% and specificity of 100.0% for distinguishing hyperplasia from healthy tissue. The areas under the receiver operator characteristic curves were 0.98 (95% CI 0.95 to 1.00) and 0.95 (95% CI 0.90 to 1.00) for distinguishing dysplasia from SCC and hyperplasia from dysplasia, respectively.ConclusionDR spectral data efficiently discriminate healthy tissue from oral malignant lesions. Diagnostic accuracies obtained in this study highlight the potential use of this method for routine clinical practice.
Quantitative expression study of four cytokeratins and p63 in squamous cell carcinoma of the tongue: suitability for sentinel node navigation surgery using one-step nucleic acid amplification
Authors: Yamauchi Kohichi , Fujioka Yasunori , Kogashiwa Yasunao , Kohno Naoyuki 
Published: June 2011

AimsSentinel node navigation surgery (SNNS) is currently considered to provide better staging of regional metastasis. For rapid and accurate sentinel lymph node analysis, one-step nucleic acid amplification using cytokeratin 19 (CK19) has been applied, particularly in breast cancer. On the other hand, additional quantitative reverse transcription PCR targets containing cytokeratins have been reported recently in head and neck cancer. In this report, CK19 and p63 were immunohistochemically examined in primary tumours for use as molecular markers and were compared with cytokeratin 903 (CK903), cytokeratin 8/18 (CK8/18) and cytokeratin (AE1/AE3), which are used in diagnostic immunohistochemistry for head and neck squamous cell carcinoma.MethodsThe study reviewed 17 patients with T1/T2, N0 (UICC) oral squamous cell carcinoma of the tongue who were treated surgically at Kyorin University Hospital between 2002 and 2009. The intensity and proportion of tumour cells stained for CK19, CK903, p63, CK8/18 and AE1/AE3 were evaluated.ResultsCK19 and CK8/18 staining in cytoplasm was patchy among carcinoma cells, indicating weak expression. Staining proportion for p63, CK903 and AE1/AE3 was greater than for CK19 and CK8/18, although staining intensity for CK903 was weaker than for p63 and AE1/AE3. The difference in total score between CK19 and CK8/18 staining and p63, CK903 and AE1/AE3 staining was statistically significant (p<0.001). p63 and AE1/AE3 may be better markers than CK903, CK19 and CK8/18.ConclusionsThis suggests that p63 is of clinical utility in SNNS and that CK19 is unsuitable for early tongue carcinoma. Further studies are needed before clinical application of these markers.
Republished review: Gene therapy for ocular diseases
Authors: Liu Melissa M , Tuo Jingsheng , Chan Chi-Chao 
Published: June 2011

ABSTRACT
The eye is an easily accessible, highly compartmentalised and immune-privileged organ that offers unique advantages as a gene therapy target. Significant advancements have been made in understanding the genetic pathogenesis of ocular diseases, and gene replacement and gene silencing have been implicated as potentially efficacious therapies. Recent improvements have been made in the safety and specificity of vector-based ocular gene transfer methods. Proof-of-concept for vector-based gene therapies has also been established in several experimental models of human ocular diseases. After nearly two decades of ocular gene therapy research, preliminary successes are now being reported in phase 1 clinical trials for the treatment of Leber congenital amaurosis. This review describes current developments and future prospects for ocular gene therapy. Novel methods are being developed to enhance the performance and regulation of recombinant adeno-associated virus- and lentivirus-mediated ocular gene transfer. Gene therapy prospects have advanced for a variety of retinal disorders, including retinitis pigmentosa, retinoschisis, Stargardt disease and age-related macular degeneration. Advances have also been made using experimental models for non-retinal diseases, such as uveitis and glaucoma. These methodological advancements are critical for the implementation of additional gene-based therapies for human ocular diseases in the near future.
Identification of the MEK1(F129L) Activating Mutation as a Potential Mechanism of Acquired Resistance to MEK Inhibition in Human Cancers Carrying the B-RafV600E Mutation
Authors: Wang Huisheng , Daouti Sherif , Li Wen-hui , Wen Yang , Rizzo Christine , Higgins Brian , Packman Kathryn , Rosen Neal , Boylan John F. , Heimbrook David , Niu Huifeng 
Published: June 2011

Abstract
Although targeting the Ras/Raf/MEK pathway remains a promising anticancer strategy, mitogen-activated protein/extracellular signal-regulated kinase (ERK) kinase (MEK) inhibitors in clinical development are likely to be limited in their ability to produce durable clinical responses due to the emergence of acquired drug resistance. To identify potential mechanisms of such resistance, we established MEK inhibitor–resistant clones of human HT-29 colon cancer cells (HT-29R cells) that harbor the B-RafV600E mutation. HT-29R cells were specifically resistant to MEK inhibition in vitro and in vivo, with drug-induced elevation of MEK/ERK and their downstream targets primarily accountable for drug resistance. We identified MEK1(F129L) mutation as a molecular mechanism responsible for MEK/ERK pathway activation. In an isogenic cell system that extended these findings into other cancer cell lines, the MEK1(F129L) mutant exhibited higher intrinsic kinase activity than wild-type MEK1 [MEK1(WT)], leading to potent activation of ERK and downstream targets. The MEK1(F129L) mutation also strengthened binding to c-Raf, suggesting an underlying mechanism of higher intrinsic kinase activity. Notably, the combined use of Raf and MEK inhibitors overcame the observed drug resistance and exhibited greater synergy in HT-29R cells than the drug-sensitive HT-29 parental cells. Overall, our findings suggested that mutations in MEK1 can lead to acquired resistance in patients treated with MEK inhibitors and that a combined inhibition of Raf and MEK may be potentially useful as a strategy to bypass or prevent drug resistance in the clinic. Cancer Res; 71(16); 5535–45. ©2011 AACR.