bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of phonons on the ac conductance of molecular junctions
Authors: Ueda Akiko , Entin-Wohlman Ora , Aharony Amnon 
Published: March 2011

AbstractWe theoretically examine the effect of a single phonon mode on the structure of the frequency dependence of the ac conductance of molecular junctions, in the linear response regime. The conductance is enhanced (suppressed) by the electron-phonon interaction when the chemical potential is below (above) the energy of the electronic state on the molecule.PACS numbers: 71.38.-k, 73.21.La, 73.23.-b
Ordered GeSi nanorings grown on patterned Si (001) substrates
Authors: Ma Yingjie , Cui Jian , Fan Yongliang , Zhong Zhenyang , Jiang Zuimin 
Published: March 2011

AbstractAn easy approach to fabricate ordered pattern using nanosphere lithography and reactive iron etching technology was demonstrated. Long-range ordered GeSi nanorings with 430 nm period were grown on patterned Si (001) substrates by molecular beam epitaxy. The size and shape of rings were closely associated with the size of capped GeSi quantum dots and the Si capping processes. Statistical analysis on the lateral size distribution shows that the high growth temperature and the long-term annealing can improve the uniformity of nanorings.PACS code1·PACS code2·moreMathematics Subject Classification (2000) MSC code1·MSC code2·more
Mixed convective boundary layer flow over a vertical wedge embedded in a porous medium saturated with a nanofluid: Natural Convection Dominated Regime
Authors: Gorla Rama Subba Reddy , Chamkha Ali Jawad , Rashad Ahmed Mohamed 
Published: March 2011

AbstractA boundary layer analysis is presented for the mixed convection past a vertical wedge in a porous medium saturated with a nano fluid. The governing partial differential equations are transformed into a set of non-similar equations and solved numerically by an efficient, implicit, iterative, finite-difference method. A parametric study illustrating the influence of various physical parameters is performed. Numerical results for the velocity, temperature, and nanoparticles volume fraction profiles, as well as the friction factor, surface heat and mass transfer rates have been presented for parametric variations of the buoyancy ratio parameter Nr, Brownian motion parameter Nb, thermophoresis parameter Nt, and Lewis number Le. The dependency of the friction factor, surface heat transfer rate (Nusselt number), and mass transfer rate (Sherwood number) on these parameters has been discussed.
Intracerebral infection with dengue-3 virus induces meningoencephalitis and behavioral changes that precede lethality in mice
Authors: Amaral Debora CG , Rachid Milene A , Vilela Marcia C , Campos Roberta DL , Ferreira Gustavo P , Rodrigues David H , Lacerda-Queiroz Norinne , Miranda Aline S , Costa Vivian V , Campos Marco A , Kroon Erna G , Teixeira Mauro M , Teixeira Antonio L 
Published: March 2011

Abstract

Background
Dengue, one of the most important arboviral diseases of humans, may cause severe systemic disease. Although dengue virus (DENV) has been considered to be a non-neurotropic virus, dengue infection has been associated recently with a series of neurological syndromes, including encephalitis. In this work, we evaluated behavioral changes and inflammatory parameters in C57BL/6 mice infected with non-adapted dengue virus 3 (DENV-3) genotype I.

Methods
C57BL/6 mice received 4 × 103 PFU of DENV-3 by an intracranial route. We evaluated the trafficking of leukocytes in brain microvasculature using intravital microscopy, and evaluated chemokine and cytokine profiling by an ELISA test at 3 and 6 days post infection (p.i.). Furthermore, we determined myeloperoxidase activity and immune cell populations, and also performed histopathological analysis and immunostaining for the virus in brain tissue.

Results
All animals developed signs of encephalitis and died by day 8 p.i. Motor behavior and muscle tone and strength parameters declined at day 7 p.i. We observed increased leukocyte rolling and adhesion in brain microvasculature of infected mice at days 3 and 6 p.i. The infection was followed by significant increases in IFN-γ, TNF-α, CCL2, CCL5, CXCL1, and CXCL2. Histological analysis showed evidence of meningoencephalitis and reactive gliosis. Increased numbers of neutrophils, CD4+ and CD8+ T cells were detected in brain of infected animals, notably at day 6 p.i. Cells immunoreactive for anti-NS-3 were visualized throughout the brain.

Conclusion
Intracerebral infection with non-adapted DENV-3 induces encephalitis and behavioral changes that precede lethality in mice.
Clustering based on adherence data
Authors: Kiwuwa-Muyingo Sylvia , Oja Hannu , Walker Sarah A , Ilmonen Pauliina , Levin Jonathan , Todd Jim 
Published: March 2011

AbstractAdherence to a medical treatment means the extent to which a patient follows the instructions or recommendations by health professionals. There are direct and indirect ways to measure adherence which have been used for clinical management and research. Typically adherence measures are monitored over a long follow-up or treatment period, and some measurements may be missing due to death or other reasons. A natural question then is how to describe adherence behavior over the whole period in a simple way. In the literature, measurements over a period are usually combined just by using averages like percentages of compliant days or percentages of doses taken. In the paper we adapt an approach where patient adherence measures are seen as a stochastic process. Repeated measures are then analyzed as a Markov chain with finite number of states rather than as independent and identically distributed observations, and the transition probabilities between the states are assumed to fully describe the behavior of a patient. The patients can then be clustered or classified using their estimated transition probabilities. These natural clusters can be used to describe the adherence of the patients, to find predictors for adherence, and to predict the future events. The new approach is illustrated and shown to be useful with a simple analysis of a data set from the DART (Development of AntiRetroviral Therapy in Africa) trial in Uganda and Zimbabwe.
Comparison of the efficacy of tenofovir and adefovir in the treatment of chronic hepatitis B: A Systematic Review
Authors: Zhao Shu-Shan , Tang Lan-Hua , Dai Xia-Hong , Wang Wei , Zhou Rong-Rong , Chen Li-Zhang , Fan Xue-Gong 
Published: March 2011

AbstractChronic viral hepatitis B remains a global public health concern. Currently, several drugs, such as tenofovir and adefovir, are recommended for treatment of patients with chronic hepatitis B. tenofovir is a nucleoside analog with selective activity against hepatitis b virus and has been shown to be more potent in vitro than adefovir. But the results of trials comparing tenofovir and adefovir in the treatment of chronic hepatitis B were inconsistent. However, there was no systematic review on the comparison of the efficacy of tenofovir and adefovir in the treatment of chronic hepatitis B. To evaluate the comparison of the efficacy of tenofovir and adefovir in the treatment of chronic hepatitis B we conducted a systematic review and meta-analysis of clinical trials. We searched PUBMED, Web of Science, EMBASE, CNKI, VIP database, WANFANG database, the Cochrane Central Register of Controlled Trials and the Cochrane Database of Systematic Review. Finally six studies were left for analysis which involved 910 patients in total, of whom 576 were included in tenofovir groups and 334 were included in adefovir groups. At the end of 48-week treatment, tenofovir was superior to adefovir at the HBV-DNA suppression in patients[RR = 2.59; 95%CI(1.01-6.67), P = 0.05]. While there was no significant difference in the ALT normalization[RR = 1.15; 95%CI(0.96-1.37), P = 0.14], HBeAg seroconversion[RR = 1.32; 95%CI(1.00-1.75), P = 0.05] and HBsAg loss rate[RR = 1.19; 95%CI(0.74-1.91), P = 0.48]. More high-quality, well-designed, randomized controlled, multi-center trails are clearly needed to guide evolving standards of care for chronic hepatitis B.
Anthocyanidins-enriched bilberry extracts inhibit 3T3-L1 adipocyte differentiation via the insulin pathway
Authors: Suzuki Rieko , Tanaka Masami , Takanashi Masakatsu , Hussain Aashiq , Yuan Bo , Toyoda Hiroo , Kuroda Masahiko 
Published: March 2011

Abstract

Background
Obesity and metabolic syndrome are important public concerns, and there is increasing demand for effective therapeutic strategies. Flavonoids are expected to improve the risk factors associated with metabolic syndrome. Anthocyanidins are a kind of flavonoids; well known for their anti-oxidative, anti-inflammatory and anti-tumor properties. However, their effects on adipocytes and molecular systems are not well defined. In this study, we examined the effects of anthocyanidins-enriched bilberry extracts on adipocyte differentiation.

Methods
Utilizing 3T3-L1 cell line, we investigated that bilberry extracts and anthocyanidins induced inhibition of lipid accumulation during adipogenesis. To identify what is the most important bilberry mediated-effect, we analyzed the expressions of key transcriptional factors associated with adipocyte differentiation by Real Time (RT)-PCR. From the results of RT-PCR, we hypothesized that bilberry extracts and anthocyanidins blocks insulin signal, we determined the phosphorylation of tyrosine residues of insulin receptor substrate 1 (IRS1) protein by western blotting analysis. In addition, we compared the whole-genome expression profiles of early stage of adipocyte differentiation under four different growth conditions (DMSO, bilberry, two anthocyanidins) by microarray analyses and Gene Set Enrichment Analysis (GSEA).

Results
Exposure to bilberry extracts and anthocyanidins during adipocyte differentiation inhibited 3T3-L1 differentiation. During this period, bilberry extracts and anthocyanidin significantly decreased a key adipocyte differentiation-associated marker, peroxisome proliferator-activated receptor- γ (Ppar γ ) and sterol regulatory element-binding protein 1c (Srebp1c). Western blotting analysis showed that bilberry extracts and anthocyanidin decreased the phosphorylation of tyrosine residues of IRS1. In addition, microarray experiments and GSEA data revealed significantly altered expression of the known genes of the insulin pathway in cells treated with bilberry extracts or anthocyanidins in the early differentiation stages.

Conclusions
Our data demonstrate that anthocyanidin enriched bilberry extracts strongly inhibit the adipocyte differentiation via the insulin pathway. Furthermore, bilberry extracts might be used as a potential complementary treatment for the obese patients with metabolic syndrome.
Validation of a single biopsy approach and bolus protein feeding to determine myofibrillar protein synthesis in stable isotope tracer studies in humans
Authors: Burd Nicholas A , West Daniel WD , Rerecich Tracy , Prior Todd , Baker Steven K , Phillips Stuart M 
Published: March 2011

Abstract

Background
Minimizing the number of muscle biopsies has important methodological implications and minimizes subject discomfort during a stable isotope amino acid infusion. We aimed to determine the reliability of obtaining a single muscle biopsy for the calculation of muscle protein fractional synthetic rate (FSR) as well as the amount of incorporation time necessary to obtain that biopsy after initiating a stable isotope infusion (Study 1). The calculation of muscle protein FSR requires tracer steady-state during the stable isotope infusion. Therefore, a second aim was to examine if steady-state conditions are compromised in the precursor pools (plasma free or muscle intracellular [IC]) after ingestion of a tracer enriched protein drink and after resistance exercise (Study 2).

Methods
Sixteen men (23 ± 3 years; BMI = 23.8 ± 2.2 kg/m2, means ± SD) were randomized to perform Study 1 or Study 2 (n = 8, per study). Subjects received a primed, constant infusion of L-[ring-13C6]phenylalanine coupled with muscle biopsies of the vastus lateralis to measure rates of myofibrillar protein synthesis (MPS). Subjects in Study 2 were fed 25 g of whey protein immediately after an acute bout of unilateral resistance exercise.

Results
There was no difference (P = 0.3) in rates of MPS determined using the steady-state precursor-product equation and determination of tracer incorporation between sequential biopsies 150 min apart or using plasma protein as the baseline enrichment, provided the infusion length was sufficient (230 ± 0.3 min). We also found that adding a modest amount of tracer (4% enriched), calculated based on the measured phenylalanine content of the protein (3.5%) in the drink, did not compromise steady-state conditions (slope of the enrichment curve not different from zero) in the plasma free or, more importantly, the IC pool (both P > 0.05).

Conclusions
These data demonstrate that the single biopsy approach yields comparable rates of muscle protein synthesis, provided a longer incorporation time is utilized, to that seen with a traditional two biopsy approach. In addition, we demonstrate that enriching protein-containing drinks with tracer does not disturb isotopic steady-state and thus both are reliable techniques to determine rates of MPS in humans.
Initiation of health-behaviour change among employees participating in a web-based health risk assessment with tailored feedback
Authors: Colkesen Ersen B , Niessen Maurice AJ , Peek Niels , Vosbergen Sandra , Kraaijenhagen Roderik A , van Kalken Coenraad K , Tijssen Jan GP , Peters Ron JG 
Published: March 2011

Abstract

Background
Primary prevention programs at the worksite can improve employee health and reduce the burden of cardiovascular disease. Programs that include a web-based health risk assessment (HRA) with tailored feedback hold the advantage of simultaneously increasing awareness of risk and enhancing initiation of health-behaviour change. In this study we evaluated initial health-behaviour change among employees who voluntarily participated in such a HRA program.

Methods
We conducted a questionnaire survey among 2289 employees who voluntarily participated in a HRA program at seven Dutch worksites between 2007 and 2009. The HRA included a web-based questionnaire, biometric measurements, laboratory evaluation, and tailored feedback. The survey questionnaire assessed initial self-reported health-behaviour change and satisfaction with the web-based HRA, and was e-mailed four weeks after employees completed the HRA.

Results
Response was received from 638 (28%) employees. Of all, 86% rated the program as positive, 74% recommended it to others, and 58% reported to have initiated overall health-behaviour change. Compared with employees at low CVD risk, those at high risk more often reported to have increased physical activity (OR 3.36, 95% CI 1.52-7.45). Obese employees more frequently reported to have increased physical activity (OR 3.35, 95% CI 1.72-6.54) and improved diet (OR 3.38, 95% CI 1.50-7.60). Being satisfied with the HRA program in general was associated with more frequent self-reported initiation of overall health-behaviour change (OR 2.77, 95% CI 1.73-4.44), increased physical activity (OR 1.89, 95% CI 1.06-3.39), and improved diet (OR 2.89, 95% CI 1.61-5.17).

Conclusions
More than half of the employees who voluntarily participated in a web-based HRA with tailored feedback, reported to have initiated health-behaviour change. Self-reported initiation of health-behaviour change was more frequent among those at high CVD risk and BMI levels. In general employees reported to be satisfied with the HRA, which was also positively associated with initiation of health-behaviour change. These findings indicate that among voluntary participating employees a web-based HRA with tailored feedback may motivate those in greatest need of health-behaviour change and may be a valuable component of workplace health promotion programs.
Ethnobotanical study of indigenous knowledge on medicinal plant use by traditional healers in Oshikoto region, Namibia
Authors: Cheikhyoussef Ahmad , Shapi Martin , Matengu Kenneth , Mu Ashekele Hina 
Published: March 2011

Abstract
Background
The objective of this study was to establish a regional profile of the indigenous knowledge system (IKS) for medicinal plant use and cultural practices associated with the healing process of these plants by traditional healers in the Oshikoto region, Namibia.

Methods
An ethnobotanical survey was undertaken to collect information from traditional healers during September and October 2008. Data was collected through the use of questionnaires and personal interviews during field trips in the ten constituencies of the Oshikoto region. A total of 47 respondents were interviewed with most of them aged 66 and above.

Results
The traditional healers in Oshikoto region use 61 medicinal plant species that belong to 25 families for the treatment of various diseases and disorders with the highest number of species being used for mental diseases followed by skin infection and external injuries. Trees (28 species) were found to be the most used plants followed by herbs (15 species), shrubs (10 species) and climbers (4 species). The average of the informant consensus factor (FIC) value for all ailment categories was 0.75. High FIC values were obtained for Pergularia daemia, and Tragia okanyua, which were reported to treat weakness and dizziness problems, snake bite, swelling and cardiovascular problems indicating that these species traditionally used to treat these ailments are worth examining for bioactive compounds.

Conclusions
The traditional healers in Oshikoto possess rich ethno-pharmacological knowledge. This study allows for identifying many high value medicinal plant species, indicating high potential for economic development through sustainable collection of these medicinal plants.
Mosquito salivary gland protein preservation in the field for immunological and biochemical analysis
Authors: Fontaine A , Pascual A , Diouf I , Bakkali N , Bourdon S , Fusai T , Rogier C , Almeras L 
Published: March 2011

AbstractMosquito salivary proteins are involved in several biological processes that facilitate their blood feeding and have also been reported to elicit an IgG response in vertebrates. A growing number of studies have focused on this immunological response for its potential use as a biological marker of exposure to arthropod bites. As mosquito saliva collection is extremely laborious and inefficient, most research groups prefer to work on mosquito salivary glands (SGs). Thus, SG protein integrity is a critical factor in obtaining meaningful data from immunological and biochemical analysis. Current methodologies rely on an immediate freezing of SGs after their collection. However, the maintenance of samples in a frozen environment can be hard to achieve in field conditions. In this study, SG proteins from two mosquito species (Aedes aegyptiandAnopheles gambiae s.s.) stored in different media for 5 days at either +4°C or room temperature (RT) were evaluated at the quantitative (i.e., ELISA) and qualitative (i.e., SDS-PAGE and immunoblotting) levels. Our results indicated that PBS medium supplemented with an anti-protease cocktail seems to be the best buffer to preserve SG antigens for 5 days at +4°C for ELISA analysis. Conversely, cell-lysis buffer (Urea-Thiourea-CHAPS-Tris) was best at preventing protein degradation both at +4°C and RT for further qualitative analysis. These convenient storage methods provide an alternative to freezing and are expected to be applicable to other biological samples collected in the field.
Mining semantic networks of bioinformatics e-resources from the literature
Authors: Afzal Hammad , Eales James , Stevens Robert , Nenadic Goran 
Published: March 2011

Abstract

Background
There have been a number of recent efforts (e.g. BioCatalogue, BioMoby) to systematically catalogue bioinformatics tools, services and datasets. These efforts rely on manual curation, making it difficult to cope with the huge influx of various electronic resources that have been provided by the bioinformatics community. We present a text mining approach that utilises the literature to automatically extract descriptions and semantically profile bioinformatics resources to make them available for resource discovery and exploration through semantic networks that contain related resources.

Results
The method identifies the mentions of resources in the literature and assigns a set of co-occurring terminological entities (descriptors) to represent them. We have processed 2,691 full-text bioinformatics articles and extracted profiles of 12,452 resources containing associated descriptors with binary and tf*idf weights. Since such representations are typically sparse (on average 13.77 features per resource), we used lexical kernel metrics to identify semantically related resources via descriptor smoothing. Resources are then clustered or linked into semantic networks, providing the users (bioinformaticians, curators and service/tool crawlers) with a possibility to explore algorithms, tools, services and datasets based on their relatedness. Manual exploration of links between a set of 18 well-known bioinformatics resources suggests that the method was able to identify and group semantically related entities.

Conclusions
The results have shown that the method can reconstruct interesting functional links between resources (e.g. linking data types and algorithms), in particular when tf*idf-like weights are used for profiling. This demonstrates the potential of combining literature mining and simple lexical kernel methods to model relatedness between resource descriptors in particular when there are few features, thus potentially improving the resource description, discovery and exploration process. The resource profiles are available at http://gnode1.mib.man.ac.uk/bioinf/semnets.html
The Role of XPG in Processing (CAG)n/(CTG)n DNA Hairpins
Authors: Hou Caixia , Zhang Tianyi , Tian Lei , Huang Jian , Gu Liya , Li Guo-Min 
Published: March 2011

Abstract

Background
During DNA replication or repair, disease-associated (CAG)n/(CTG)n expansion can result from formation of hairpin structures in the repeat tract of the newly synthesized or nicked DNA strand. Recent studies identified a nick-directed (CAG)n/(CTG)n hairpin repair (HPR) system that removes (CAG)n/(CTG)n hairpins from human cells via endonucleolytic incisions. Because the process is highly similar to the mechanism by which XPG and XPF endonucleases remove bulky DNA lesions during nucleotide excision repair, we assessed the potential role of XPG in conducting (CAG)n/(CTG)n HPR.

Results
To determine if the XPG endonuclease is involved in (CAG)n/(CTG)n hairpin removal, two XPG-deficient cell lines (GM16024 and AG08802) were examined for their ability to process (CAG)n/(CTG)n hairpins in vitro. We demonstrated that the GM16024 cell line processes all hairpin substrates as efficiently as HeLa cells, and that the AG08802 cell line is partially defective in HPR. Analysis of repair intermediates revealed that nuclear extracts from both XPG-deficient lines remove CAG/CTG hairpins via incisions, but the incision products are distinct from those generated in HeLa extracts. We also show that purified recombinant XPG protein greatly stimulates HPR in XPG-deficient extracts by promoting an incision 5' to the hairpin.

Conclusions
Our results strongly suggest that 1) human cells possess multiple pathways to remove (CAG)n/(CTG)n hairpins located in newly synthesized (or nicked) DNA strand; and 2) XPG, although not essential for (CAG)n/(CTG)n hairpin removal, stimulates HPR by facilitating a 5' incision to the hairpin. This study reveals a novel role for XPG in genome-maintenance and implicates XPG in diseases caused by trinucleotide repeat expansion.