bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of physical and chemical immobilization on hematologic and biochemical variables in captive brown brocket deer (Mazama gouazoubira)
Authors: Munerato Marina Salles , Duarte José Maurício Barbanti , Pereira Gener Tadeu , Marques José Antônio 
Published: October 2010

Background: Alterations in cellular and chemical constituents in blood are indicators of physical or chemical restraint in deer.Objectives: The aim of this study was to determine the effects of physical and chemical restraint on hematologic and biochemical analytes in captive brown brocket deer (Mazama gouazoubira).Methods: Six adult deer were physically restrained and randomly anesthetized in a crossover design using 3 protocols (P). In P1, anesthesia was induced directly with isoflurane using a face mask and was maintained with isoflurane delivered by endotracheal tube. In P2, oral premedication with midazolam was followed 1 hour later by induction and maintenance of anesthesia with isoflurane, as in P1. In P3, intravenous anesthesia with a combination of ketamine, xylazine, and atropine was followed by anesthesia with isoflurane, as in P1. Blood was collected immediately after physical restraint (T0) and during anesthesia at 20‐minute intervals (T15, T35, and T55). Hematologic and biochemical constituents were determined using manual methods or automated analyzers, with cortisol measured by enzyme immunoassay.Results: During physical restraint, following food and water restriction, significant hemoconcentration, increased WBC count, and lower cortisol concentration were observed compared with results at T15, T35, and T55. During anesthesia, lymphocyte count was lower in P2 than P1, urea concentration was decreased at T15 using P2, and plasma glucose concentration was increased after T0 (P<.01). Among the anesthetic protocols, there was a trend for decreased cortisol concentration using P2.Conclusions: Physical restraint and anesthesia affect some blood constituents in captive brown brocket deer, and midazolam premedication may modify the intensity of the stress response.
In vitro study of biofilm formation and effectiveness of antimicrobial treatment on various dental material surfaces
Authors: Li L. , Finnegan M.B. , Özkan S. , Kim Y. , Lillehoj P.B. , Ho C.‐M. , Lux R. , Mito R. , Loewy Z. , Shi W. 
Published: October 2010

SummaryElevated proportions of Candida albicans in biofilms formed on dentures are associated with stomatitis whereas Streptococcus mutans accumulation on restorative materials can cause secondary caries. Candida albicans, S. mutans, saliva‐derived and C. albicans/saliva‐derived mixed biofilms were grown on different materials including acrylic denture, porcelain, hydroxyapatite (HA), and polystyrene. The resulting biomass was analysed by three‐dimensional image quantification and assessment of colony‐forming units. The efficacy of biofilm treatment with a dissolved denture cleansing tablet (Polident®) was also evaluated by colony counting. Biofilms formed on HA exhibited the most striking differences in biomass accumulation: biofilms comprising salivary bacteria accrued the highest total biomass whereas C. albicans biofilm formation was greatly reduced on the HA surface compared with other materials, including the acrylic denture surface. These results substantiate clinical findings that acrylic dentures can comprise a reservoir for C. albicans, which renders patients more susceptible to C. albicans infections and stomatitis. Additionally, treatment efficacy of the same type of biofilms varied significantly depending on the surface. Although single‐species biofilms formed on polystyrene surfaces exhibited the highest susceptibility to the treatment, the most surviving cells were recovered from HA surfaces for all types of biofilms tested. This study demonstrates that the nature of a surface influences biofilm characteristics including biomass accumulation and susceptibility to antimicrobial treatments. Such treatments should therefore be evaluated on the surfaces colonized by the target pathogen(s).
Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing
Authors: Xie G. , Chain P.S.G. , Lo C.‐C. , Liu K.‐L. , Gans J. , Merritt J. , Qi F. 
Published: October 2010

SummaryHuman dental plaque is a complex microbial community containing an estimated 700 to 19,000 species/phylotypes. Despite numerous studies analysing species richness in healthy and diseased human subjects, the true genomic composition of the human dental plaque microbiota remains unknown. Here we report a metagenomic analysis of a healthy human plaque sample using a combination of second‐generation sequencing platforms. A total of 860 million base pairs of non‐human sequences were generated. Various analysis tools revealed the presence of 12 well‐characterized phyla, members of the TM‐7 and BRC1 clade, and sequences that could not be classified. Both pathogens and opportunistic pathogens were identified, supporting the ecological plaque hypothesis for oral diseases. Mapping the metagenomic reads to sequenced reference genomes demonstrated that 4% of the reads could be assigned to the sequenced species. Preliminary annotation identified genes belonging to all known functional categories. Interestingly, although 73% of the total assembled contig sequences were predicted to code for proteins, only 51% of them could be assigned a functional role. Furthermore, ∼ 2.8% of the total predicted genes coded for proteins involved in resistance to antibiotics and toxic compounds, suggesting that the oral cavity is an important reservoir for antimicrobial resistance.
Deletion of competence‐induced genes over‐expressed in biofilms caused transformation deficiencies in Streptococcus mutans
Authors: Eaton R.E. , Jacques N.A. 
Published: October 2010

SummaryPrevious studies identified nine genes with increased expression in Streptococcus mutans biofilms of which six possessed putative ComX promoter sequences and were homologous to competence‐induced genes in Streptococcus pneumoniae, Streptococcus gordonii and Bacillus subtilis. As competence increases in biofilms, a study was undertaken into the roles that these biofilm‐induced genes might play in transformation. Only five of the nine gene deletions had a significant effect on transformation efficiency. Deletion of the genes for recombinase A, recA, DNA processing protein, dprA and single‐stranded DNA‐binding protein, ssbA, produced results comparable with those from other bacteria, supporting the contention that these proteins have similar functions in S. mutans competence. The uncharacterized genes SMU.769 and SMU.836 produced results in variance to deletion mutants of putative homologues in S. pneumoniae. Deletion of SMU.769 reduced chromosomal transformation 2.3‐fold. SMU.769 belongs to a family of conserved genes induced by the competence‐stimulating peptide and which have no established function. In contrast, deletion of SMU.836 reduced transformation of both plasmid and chromosomal DNA to <3%. Homology searches suggested that Smu.836 belongs to a family of competence‐induced peptidoglycan hydrolases with a conserved enzyme domain and a species‐variable cell‐binding domain for which the best characterized member is the choline‐binding protein D, CbpD, of S. pneumoniae.
Activity of antimicrobial peptide mimetics in the oral cavity: I. Activity against biofilms of Candida albicans
Authors: Hua J. , Yamarthy R. , Felsenstein S. , Scott R.W. , Markowitz K. , Diamond G. 
Published: October 2010

SummaryNaturally occurring antimicrobial peptides hold promise as therapeutic agents against oral pathogens such as Candida albicans but numerous difficulties have slowed their development. Synthetic, non‐peptidic analogs that mimic the properties of these peptides have many advantages and exhibit potent, selective antimicrobial activity. Several series of mimetics (with molecular weight < 1000) were developed and screened against oral Candida strains as a proof‐of‐principle for their antifungal properties. One phenylalkyne and several arylamide compounds with reduced mammalian cytotoxicities were found to be active against C. albicans. These compounds demonstrated rapid fungicidal activity in liquid culture even in the presence of saliva, and demonstrated synergy with standard antifungal agents. When assayed against biofilms grown on denture acrylic, the compounds exhibited potent fungicidal activity as measured by metabolic and fluorescent viability assays. Repeated passages in sub‐minimum inhibitory concentration levels did not lead to resistant Candida, in contrast to fluconazole. Our results demonstrate the proof‐of principle for the use of these compounds as anti‐Candida agents, and their further testing is warranted as novel anti‐Candida therapies.
Activity of antimicrobial peptide mimetics in the oral cavity: II. Activity against periopathogenic biofilms and anti‐inflammatory activity
Authors: Hua J. , Scott R.W. , Diamond G. 
Published: October 2010

SummaryWhereas periodontal disease is ultimately of bacterial etiology, from multispecies biofilms of gram‐negative anaerobic microorganisms, much of the deleterious effects are caused by the resultant epithelial inflammatory response. Hence, development of a treatment that combines anti‐biofilm antibiotic activity with anti‐inflammatory activity would be of great utility. Antimicrobial peptides (AMPs) such as defensins are naturally occurring peptides that exhibit broad‐spectrum activity as well as a variety of immunomodulatory activities. Furthermore, bacteria do not readily develop resistance to these agents. However, clinical studies have suggested that they do not represent optimal candidates for exogenous therapeutic agents. Small‐molecule mimetics of these AMPs exhibit similar activities to the parent peptides, in addition to having low toxicity, high stability and low cost. To determine whether AMP mimetics have the potential for treatment of periodontal disease, we examined the activity of one mimetic, mPE, against biofilm cultures of Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis. Metabolic assays as well as culture and biomass measurement assays demonstrated that mPE exhibits potent activity against biofilm cultures of both species. Furthermore, as little as 2 μg ml−1 mPE was sufficient to inhibit interleukin‐1β‐induced secretion of interleukin‐8 in both gingival epithelial cells and THP‐1 cells. This anti‐inflammatory activity is associated with a reduction in activation of nuclear factor‐κB, suggesting that mPE can act both as an anti‐biofilm agent in an anaerobic environment and as an anti‐inflammatory agent in infected tissues.
Detection of clonality in follicular lymphoma using formalin-fixed, paraffin-embedded tissue samples and BIOMED-2 immunoglobulin primers
Authors: Berget Ellen , Helgeland Lars , Molven Anders , Vintermyr Olav Karsten 
Published: October 2010

AimsThe BIOMED-2 multiplex PCR protocol is a commonly used procedure for assessing B cell clonality in lymphoma diagnostics. Follicular lymphoma poses a special challenge for PCR-based analyses because of high prevalence of somatic hypermutations in the rearranged immunoglobulin (IG) domains. This study aimed to evaluate the BIOMED-2 protocol performance in detection of B cell clonality in follicular lymphoma using formalin-fixed, paraffin-embedded (FFPE) tissue.MethodsFFPE samples from 118 patients diagnosed with follicular lymphoma in the period 1998–2008 were used in the study. Clonality of IG heavy (IGH) and light chains (IGK,IGL) was assessed using a PCR procedure that was optimised for FFPE tissue.ResultsThe highest clonal detection rates were 67.8% with theIGHVн-FR2-Jн assay and 66.1% with theIGKVκ-Jκ assay. Clonality was detected in 94.9% of all FFPE follicular lymphoma samples when all assays were combined. FFPE samples stored for 1–5 years did not perform significantly differently from those stored for 6–11 years. Interobserver agreement of clonality was tested for all analyses. The lowest score (Cohen'sκvalue = 0.56) was observed for theIGKVκ-Jκ clonality assay.ConclusionsAn improved PCR protocol for detection of clonality in FFPE samples using BIOMED-2 IG primers is presented. For best performance, a combination ofIGHandIGKanalyses is recommended.
Sensitive multiplex detection of KRAS codons 12 and 13 mutations in paraffin-embedded tissue specimens
Authors: Laosinchai-Wolf Walairat , Ye Fei , Tran Vu , Yang Zhe , White Roxanna , Bloom Kenneth , Choppa Paul , Labourier Emmanuel 
Published: October 2010

BackgroundColorectal cancer patients harbouring KRAS mutations in codon 12 or 13 do not benefit from current anti-epidermal growth factor receptor (EGFR) monoclonal antibody therapies. Efficient and robust methods are therefore required for routine clinical testing of KRAS mutation status.AimsTo evaluate a novel multiplex assay for the rapid detection of common KRAS mutations in formalin-fixed paraffin-embedded (FFPE) tissues.MethodsGenomic DNA was amplified by multiplex PCR using primers targeting the KRAS codon 12/13 region and an internal control gene. PCR products were hybridised on a liquid bead array containing target-specific probes and detected by particle flow cytometry.ResultsAnalytical performance assessed with plasmid DNA and genomic DNA extracted from cell lines or model FFPE cell line dilutions showed specific detection of seven distinct KRAS mutations with a limit of detection equivalent to 1% tumour. The assay was evaluated at two independent sites with a total of 140 clinical specimens. At site 1, about 45% of the specimens from a set of 86 archived FFPE blocks with unknown KRAS mutation status were found positive for a KRAS mutation. At site 2, each of the seven mutations was detected in at least five independent specimens from a selected set of 54 residual genomic DNAs previously tested with an ARMS/Scorpion laboratory-developed test.ConclusionsThis novel single-well assay is a sensitive tool compatible with the clinical laboratory workflow for the rapid assessment of KRAS mutations in solid tumour specimens. Its performance and multiplex format warrant the development of broader panels including other relevant mutations in the EGFR pathway.
Comparative use of CO2laser, diode laser and monopolar electrocautery for resection of the soft palate in dogs with brachycephalic airway obstructive syndrome
Authors: Dunié‐Mérigot A. , Bouvy B. , Poncet C. 
Published: October 2010

Clinical results, complications and the outcome of using either a carbon dioxide (CO2) laser, diode laser or electrocautery (ELEC) for resection of the soft palate with an extended palatoplasty technique in brachycephalic dogs with upper airway obstructive syndrome were compared. Dogs were randomly allocated into three groups (n=20 in each group): ELEC, diode and CO2groups. The palatoplasty was made at the rostral aspect of the tonsils. A respiratory clinical score, ranging from 0 (normal) to 4 (cyanosis), was attributed to each dog before surgery and at 0 hours, 24 hours, two weeks and six months after surgery. A favourable outcome was defined as a one point or greater decrease in score 24 hours after surgery. The proportion of dogs with a favourable outcome was significantly higher in the CO2(n=15) and ELEC groups (n=15) in comparison with the diode group (n=7) (OR=5.6, 95 per cent confidence interval 1.4 to 21.9). Surgical time was significantly shorter (P<0.001; mean [sd] 510 [178] seconds), and bleeding was less common (P<0.001; 30 per cent of cases) in the CO2group. Complications were most frequent with the diode group (two cases of death and two cases of tracheostomy). The final outcome for all groups (n=57) was considered excellent in 79 per cent of cases and was considered good in 21 per cent.
Mycobacterium bovis genotypes in Northern Ireland: herd‐level surveillance (2003 to 2008)
Authors: Skuce R. A. , Mallon T. R. , McCormick C. M. , McBride S. H. , Clarke G. , Thompson A. , Couzens C. , Gordon A. W. , McDowell S. W. J. 
Published: October 2010

Surveillance genotyping (variable number tandem repeat profiling and spoligotyping) of Mycobacterium bovis isolates from culture‐confirmed bovine tuberculosis (TB)‐affected herds in Northern Ireland is presented for the years 2003 to 2008 inclusive. A total of 175 M bovis genotypes were identified in 8630 isolates from 6609 herds. On average, 73 genotypes were identified each year, with 29 genotypes present in all six years. Highly significant differences (P<0.0001) were observed between the relative frequency of some genotypes in the years 2003 to 2008. The spatial distribution of M bovis genotypes was not random (P<0.0001). Significant geographical localisation of M bovis genotypes was evident, suggesting that sources tended to be local. Despite regions being dominated by geographically localised genotypes, substantial and exploitable local diversity was still evident. Genotypes were also translocated significant distances from their normal geographical location.
Artificial neural network application for the prediction of ground surface movements induced by shield tunnelling
Authors: Boubou Rim , Emeriault Fabrice , Kastner Richard 
Published: October 2010

This paper presents a methodology to correlate ground surface movements and tunnel boring machine (TBM) operation parameters. Two approaches are proposed and evaluated based on a case study of a shallow tunnel in a dense urban area. The first approach is based on a least square approximation and the second one uses an artificial neural network model. Data analysed were selected from the excavation of the subway line B tunnel in Toulouse, France, which was performed mainly by a shield TBM. Ground movements measured on the 4.7 km long contract 2 are reproduced with reasonable agreement by each of the two approaches. The amount of data (in particular for TBM operation parameters), the rather small amplitude of measured movements (a few millimetres), and the accuracy of these measurements (designed for routine construction management) make it necessary to create a pre-processing technique for the data, and a step-by-step improvement of approaches used. An elimination procedure is proposed to identify the most influential operation parameters and a sensitivity analysis shows their respective effect on ground movements.
Highly Purified Eicosapentaenoic Acid as Free Fatty Acids Strongly Suppresses Polyps in ApcMin/+ Mice
Authors: Fini Lucia , Piazzi Giulia , Ceccarelli Claudio , Daoud Yahya , Belluzzi Andrea , Munarini Alessandra , Graziani Giulia , Fogliano Vincenzo , Selgrad Michael , Garcia Melissa , Gasbarrini Antonio , Genta Robert M. , Boland C. Richard , Ricciardiello Luigi 
Published: October 2010

Abstract
Purpose: Although cyclooxygenase (COX)-2 inhibitors could represent the most effective chemopreventive tool against colorectal cancer (CRC), their use in clinical practice is hampered by cardiovascular side effects. Consumption of ω-3-polyunsaturated fatty acids (ω-3-PUFAs) is associated with a reduced risk of CRC. Therefore, in this study, we assessed the efficacy of a novel 99% pure preparation of ω-3-PUFA eicosapentaenoic acid as free fatty acids (EPA-FFA) on polyps in ApcMin/+ mice.
Experimental design: ApcMin/+ and corresponding wild-type mice were fed control diet (Ctrl) or diets containing either EPA-FFA 2.5% or 5%, for 12 weeks while monitoring food intake and body weight.
Results: We found that both EPA-FFA diets protected from the cachexia observed among ApcMin/+ animals fed Ctrl diet (P &lt; 0.0054), without toxic effect, in conjunction with a significant decrease in lipid peroxidation in the treated arms. Moreover, both EPA-FFA diets dramatically suppressed polyp number (by 71.5% and 78.6%, respectively; P &lt; 0.0001) and load (by 82.5% and 93.4%, respectively; P &lt; 0.0001) in both small intestine and colon. In addition, polyps less than 1 mm in size were predominantly found in the EPA-FFA 5% arm whereas those 1 to 3 mm in size were more frequent in the Ctrl arm (P &lt; 0.0001). Interestingly, in the EPA-FFA groups, mucosal arachidonic acid was replaced by EPA (P &lt; 0.0001), leading to a significant reduction in COX-2 expression and β-catenin nuclear translocation. Moreover, in the EPA-FFA arms, we found a significant decrease in proliferation throughout the intestine together with an increase in apoptosis.
Conclusions: Our data make 99% pure EPA-FFA an excellent candidate for CRC chemoprevention. Clin Cancer Res; 16(23); 5703–11. ©2010 AACR.
Bevacizumab plus Fotemustine as First-line Treatment in Metastatic Melanoma Patients: Clinical Activity and Modulation of Angiogenesis and Lymphangiogenesis Factors
Authors: Del Vecchio Michele , Mortarini Roberta , Canova Stefania , Di Guardo Lorenza , Pimpinelli Nicola , Sertoli Mario R. , Bedognetti Davide , Queirolo Paola , Morosini Paola , Perrone Tania , Bajetta Emilio , Anichini Andrea 
Published: October 2010

AbstractPurpose: To assess the clinical and biological activity of the association of bevacizumab and fotemustine as first-line treatment in advanced melanoma patients.Experimental Design: Previously untreated, metastatic melanoma patients (n = 20) received bevacizumab (at 15 mg/kg every 3 weeks) and fotemustine (100 mg/m2 by intravenous administration on days 1, 8, and 15, repeated after 4 weeks) in a multicenter, single-arm, open-label, phase II study. Primary endpoint was the best overall response rate; other endpoints were toxicity, time to progression (TTP), and overall survival (OS). Serum cytokines, angiogenesis, and lymphangiogenesis factors were monitored by multiplex arrays and by in vitro angiogenesis assays. Effects of fotemustine on melanoma cells, in vitro, on vascular endothelial growth factor (VEGF)-C release and apoptosis were assessed by ELISA and flow cytometry, respectively.Results: One complete response, 2 partial responses (PR), and 10 patients with stable disease were observed. TTP and OS were 8.3 and 20.5 months, respectively. Fourteen patients experienced adverse events of toxicity grade 3–4. Serum VEGF-A levels in evaluated patients (n = 15) and overall serum proangiogenic activity were significantly inhibited. A significant reduction in VEGF-C levels was found in several post-versus pretherapy serum samples. In vitro, fotemustine inhibited VEGF-C release by melanoma cells without inducing significant cell death. Serum levels of interleukin (IL)-10 and IL-12p70 showed the highest levels in sera of PR patients, compared with patients with stable or progressive disease whereas IL-23 showed the opposite pattern.Conclusions: The combination of bevacizumab plus fotemustine has clinical activity in advanced melanoma and promotes systemic modulation of angiogenesis and lymphangiogenesis factors. Clin Cancer Res; 16(23); 5862–72. ©2010 AACR.