1,081 research outputs found

    Classification of protein interaction sentences via gaussian processes

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    The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

    The profile of cardiac cytochrome c oxidase (COX) expression in an accelerated cardiac-hypertrophy model

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    The contribution of the mitochondrial components, the main source of energy for the cardiac hypertrophic growth induced by pressure overload, is not well understood. In the present study, complete coarctation of abdominal aorta was used to induce the rapid development of cardiac hypertrophy in rats. One to two days after surgery, we observed significantly higher blood pressure and cardiac hypertrophy, which remained constantly high afterwards. We found an early increased level of cytochrome c oxidase ( COX) mRNA determined by in-situ hybridization and dot blotting assays in the hypertrophied hearts, and a drop to the baseline 20 days after surgery. Similarly, mitochondrial COX protein level and enzyme activity increased and, however, dropped even lower than baseline 20 days following surgery. In addition, in natural hypertension- induced hypertrophic hearts in genetically hypertensive rats, the COX protein was significantly lower than in normotensive rats. Taken together, the lower efficiency of mitochondrial activity in the enlarged hearts of long-term complete coarcted rats or genetically hypertensive rats could be, at least partially, the cause of hypertensive cardiac disease. Additionally, the rapid complete coarctation-induced cardiac hypertrophy was accompanied by a disproportionate COX activity increase, which was suggested to maintain the cardiac energy-producing capacity in overloaded hearts

    Understorey plant community and light availability in conifer plantations and natural hardwood forests in Taiwan

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    Questions: What are the effects of replacing mixed species natural forests with Cryptomeria japonica plantations on understorey plant functional and species diversity? What is the role of the understorey light environment in determining understorey diversity and community in the two types of forest? Location: Subtropical northeast Taiwan. Methods: We examined light environments using hemispherical photography, and diversity and composition of understorey plants of a 35‐yr C. japonica plantation and an adjacent natural hardwood forest. Results: Understorey plant species richness was similar in the two forests, but the communities were different; only 18 of the 91 recorded understorey plant species occurred in both forests. Relative abundance of plants among different functional groups differed between the two forests. Relative numbers of shade‐tolerant and shade‐intolerant seedling individuals were also different between the two forest types with only one shade‐intolerant seedling in the plantation compared to 23 seedlings belonging to two species in the natural forest. In the natural forest 11 species of tree seedling were found, while in the plantation only five were found, and the seedling density was only one third of that in the natural forest. Across plots in both forests, understorey plant richness and diversity were negatively correlated with direct sunlight but not indirect sunlight, possibly because direct light plays a more important role in understorey plant growth. Conclusions: We report lower species and functional diversity and higher light availability in a natural hardwood forest than an adjacent 30‐yr C. japonica plantation, possibly due to the increased dominance of shade‐intolerant species associated with higher light availability. To maintain plant diversity, management efforts must be made to prevent localized losses of shade‐adapted understorey plants

    Characterization of 13 multi-drug resistant Salmonella serovars from different broiler chickens associated with those of human isolates

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    <p>Abstract</p> <p>Background</p> <p><it>Salmonella </it>are frequently isolated from chickens and their products. Prevalent serogroups and serovars of <it>Salmonella </it>as well as their genotypes and antibiograms were determined for cloacal samples from 1595 chickens. To understand the possible serovar and H antigens for transmission between chicken and human, serovars and their H antigens of 164 chicken and 5314 human isolates were compared.</p> <p>Results</p> <p>Prevalence of <it>Salmonella </it>differed among chicken lines and ages. Chicken and human isolates belonged mainly to serogroup B, C1, C2-C3, D, and E. 13 serovars and 66 serovars were identified for chicken and human isolates respectively. The common serovars for chicken and human isolates were <it>S</it>. Typhimurium, <it>S</it>. Enteritidis, <it>S</it>. Albany, <it>S</it>. Derby, and <it>S</it>. Anatum and shared common H1 antigens "g complex; i; e,h; and z4,z24" and H2 antigens "1 complex and -". In human isolates, H1 antigen "i" and H2 antigen "-" were common in all serogroups. In chicken, antimicrobial susceptibility differed among serogroups, serovars and three counties. All isolates were susceptible to cefazolin and ceftriaxone, but highly resistant to ampicillin, chloramphenicol, flumequine, streptomycin, sulfamethoxazole-trimethoprim, and tetracycline. Except those isolates of serogroup C1 of Chick group and serogroup G, all isolates were multi-drug resistance. Only <it>S</it>. Kubacha, <it>S</it>. Typhimurium, <it>S</it>. Grampian, and <it>S</it>. Mons were resistant to ciprofloxacin and/or enrofloxacin.</p> <p>Conclusion</p> <p>In chicken, prevalent serogroups and serovars were associated with chicken ages, lines and regions; and flouroquinolone-resistant and MDR isolates emerged. H1 antigens "g complex and i" and H2 antigens "1 complex and -" might be important for transmission of <it>Salmonella </it>between chicken and human.</p

    Theory-based behavioral change interventions to improve periodontal health

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    Periodontal disease is a significant global health burden affecting half of the world's population. Given that plaque and inflammation control are essential to the attainment of periodontal health, recent trends in preventive dentistry have focused on the use of behavioral models to understand patient psychology and promote self-care and treatment compliance. In addition to their uses in classifying, explaining and predicting oral hygiene practices, behavioral models have been adopted in the design of oral hygiene interventions from individual to population levels. Despite the growing focus on behavioral modification in dentistry, the currently available evidence in the field of periodontology is scarce, and interventions have primarily measured changes in patient beliefs or performance in oral hygiene behaviors. Few studies have measured their impact on clinical outcomes, such as plaque levels, gingival bleeding and periodontal pocket reduction, which serve as indicators of the patient's disease status and quality of oral self-care. The present narrative review aims to summarize selected literature on the use of behavioral models to improve periodontal outcomes. A search was performed on existing behavioral models used to guide dental interventions to identify their use in interventions measuring periodontal parameters. The main models were identified and subsequently grouped by their underlying theoretical area of focus: patient beliefs (health belief model and cognitive behavioral principles); stages of readiness to change (precaution adoption process model and transtheoretical model); planning behavioral change (health action process approach model, theory of planned behavior and client self-care commitment model); and self-monitoring (self-regulation theory). Key constructs of each model and the findings of associated interventions were described. The COM-B model, a newer behavioral change system that has been increasingly used to guide interventions and policy changes, is discussed with reference to its use in oral health settings. Within the limitations of the available evidence, interventions addressing patient beliefs, motivation, intention and self-regulation could lead to improved outcomes in periodontal health. Direct comparisons between interventions could not be made due to differences in protocol design, research populations and follow-up periods. The conclusions of this review assist clinicians with implementing psychological interventions for oral hygiene promotion and highlight the need for additional studies on the clinical effects of behavioral model-based interventions

    Cardiomyoblast apoptosis induced by insulin-like growth factor (IGF)-I resistance is IGF-II dependent and synergistically enhanced by angiotensin II

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    Objective: This study explores the synergistic effect of cardiomyoblast apoptosis induced by angiotensin II (Ang II) and Insulin-like growth factor (IGF)-I resistance, and elucidates the role of IGF-II via IGF-II receptor (R) and calcineurin pathways in apoptosis induced by Ang II and IGF-I resistance. Methods: Apoptosis of cultured cardiomyoblast H9c2 cells was assessed by DNA fragmentation on agarose gel electrophoresis, nuclear condensation stained with DAPI, and Western blot analysis of pro-apoptotic Bad and cytochrome c in various combinations of control, Ang II, antisense IGF (I or II), IGF (I or II) antibody, IGF (I or II) receptor (R) antibody, or calcineurin inhibitor (Cyclosporine A, (CsA)). Results: We found the following: (I) The combination of Ang II and IGF-I deficiencies had a synergistic effect on apoptosis, confirmed by DNA fragmentation, nuclei condensation, and increases in such proapoptotic proteins as Bad, cytochrome c, caspase 9, and caspase 3 in H9c2 cells. (2) IGF-II and IGF-IIR protein products were increased by antisense IGF-I and IGF-I resistance, but these IGF-II protein products were not affected by sense IGF-I and non-specific antibody IgG in H9c2 cells. (3) The alteration of Bad protein level and the release of cytochrome c, both induced by treatments containing combinations of Ang II and antisense IGF-I, IGF-I antibody or IGF-IR antibody, were inhibited by IGF-II antibody. (4) DNA fragmentation, Bad, and cytochrome c which was induced by treatments combining IGF-IR antibody with Ang II or combining IGF-IR antibody with IGF-II were remarkably attenuated by CsA. Conclusion: IGF-I deficiency and/or IGF-IR resistance induced apoptosis in cardiomyoblast cells. The apoptosis, which might have been caused by the upregulation of IGF-II and IGF-IIR genes possibly activated the downstream calcineurin pathway, was synergistically augmented by Ang II

    Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don) Endl

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    Background: Restoration of rooting competence is important for rejuvenation in Sequoia sempervirens (D. Don) Endl and is achieved by repeatedly grafting Sequoia shoots after 16 and 30 years of cultivation in vitro. Results: Mass spectrometry-based proteomic analysis revealed three proteins that differentially accumulated in different rejuvenation stages, including oxygen-evolving enhancer protein 2 (OEE2), glycine-rich RNA-binding protein (RNP), and a thaumatin-like protein. OEE2 was found to be phosphorylated and a phosphopeptide (YEDNFDGNSNVSVMVpTPpTDK) was identified. Specifically, the protein levels of OEE2 increased as a result of grafting and displayed a higher abundance in plants during the juvenile and rejuvenated stages. Additionally, SsOEE2 displayed the highest expression levels in Sequoia shoots during the juvenile stage and less expression during the adult stage. The expression levels also steadily increased during grafting. Conclusion: Our results indicate a positive correlation between the gene and protein expression patterns of SsOEE2 and the rejuvenation process, suggesting that this gene is involved in the rejuvenation of Sequoia sempervirens
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