bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence-Divergent Chordopoxvirus Homologs of the O3 Protein Maintain Functional Interactions with Components of the Vaccinia Virus Entry-Fusion Complex
Authors: Satheshkumar P. S. , Moss Bernard 
Published: November 2011

ABSTRACT

Composed of 35 amino acids, O3 is the smallest characterized protein encoded by vaccinia virus (VACV) and is an integral component of the entry-fusion complex (EFC). O3 is conserved with 100% identity in all orthopoxviruses except for monkeypox viruses, whose O3 homologs have 2 to 3 amino acid substitutions. Since O3 is part of the EFC, high conservation could suggest an immutable requirement for interaction with multiple proteins. Chordopoxviruses of other genera also encode small proteins with a characteristic predicted N-terminal α-helical hydrophobic domain followed by basic amino acids and proline in the same relative genome location as that of VACV O3. However, the statistical significance of their similarity to VACV O3 is low due to the large contribution of the transmembrane domain, their small size, and their sequence diversity. Nevertheless,
trans
-complementation experiments demonstrated the ability of a representative O3-like protein from each chordopoxvirus genus to rescue the infectivity of a VACV mutant that was unable to express endogenous O3. Moreover, recombinant viruses expressing O3 homologs in place of O3 replicated and formed plaques as well or nearly as well as wild-type VACV. The O3 homologs expressed by the recombinant VACVs were incorporated into the membranes of mature virions and, with one exception, remained stably associated with the detergent-extracted and affinity-purified EFC. The ability of the sequence-divergent O3 homologs to coordinate function with VACV entry proteins suggests the conservation of structural motifs. Analysis of chimeras formed by swapping domains of O3 with those of other proteins indicated that the N-terminal transmembrane segment was responsible for EFC interactions and for the complementation of infectivity.
Origin and Evolution of the Unique Hepatitis C Virus Circulating Recombinant Form 2k/1b
Authors: Raghwani Jayna , Thomas Xiomara V. , Koekkoek Sylvie M. , Schinkel Janke , Molenkamp Richard , van de Laar Thijs J. , Takebe Yutaka , Tanaka Yasuhito , Mizokami Masashi , Rambaut Andrew , Pybus Oliver G. 
Published: November 2011

ABSTRACT
Since its initial identification in St. Petersburg, Russia, the recombinant hepatitis C virus (HCV) 2k/1b has been isolated from several countries throughout Eurasia. The 2k/1b strain is the only recombinant HCV to have spread widely, raising questions about the epidemiological background in which it first appeared. In order to further understand the circumstances by which HCV recombinants might be formed and spread, we estimated the date of the recombination event that generated the 2k/1b strain using a Bayesian phylogenetic approach. Our study incorporates newly isolated 2k/1b strains from Amsterdam, The Netherlands, and has employed a hierarchical Bayesian framework to combine information from different genomic regions. We estimate that 2k/1b originated sometime between 1923 and 1956, substantially before the first detection of the strain in 1999. The timescale and the geographic spread of 2k/1b suggest that it originated in the former Soviet Union at about the time that the world's first centralized national blood transfusion and storage service was being established. We also reconstructed the epidemic history of 2k/1b using coalescent theory-based methods, matching patterns previously reported for other epidemic HCV subtypes. This study demonstrates the practicality of jointly estimating dates of recombination from flanking regions of the breakpoint and further illustrates that rare genetic-exchange events can be particularly informative about the underlying epidemiological processes.
Establishment of a Novel Permissive Cell Line for the Propagation of Hepatitis C Virus by Expression of MicroRNA miR122
Authors: Kambara Hiroto , Fukuhara Takasuke , Shiokawa Mai , Ono Chikako , Ohara Yuri , Kamitani Wataru , Matsuura Yoshiharu 
Published: November 2011

ABSTRACTThe robust cell culture systems for hepatitis C virus (HCV) are limited to those using cell culture-adapted clones (HCV in cell culture [HCVcc]) and cells derived from the human hepatoma cell line Huh7. However, accumulating data suggest that host factors, including innate immunity and gene polymorphisms, contribute to the variation in host response to HCV infection. Therefore, the existingin vitrosystems for HCV propagation are not sufficient to elucidate the life cycle of HCV. A liver-specific microRNA, miR122, has been shown to participate in the efficient replication of HCV. In this study, we examined the possibility of establishing a new permissive cell line for HCV propagation by the expression of miR122. A high level of miR122 was expressed by a lentiviral vector placed into human liver cell lines at a level comparable to the endogenous level in Huh7 cells. Among the cell lines that we examined, Hep3B cells stably expressing miR122 (Hep3B/miR122) exhibited a significant enhancement of HCVcc propagation. Surprisingly, the levels of production of infectious particles in Hep3B/miR122 cells upon infection with HCVcc were comparable to those in Huh7 cells. Furthermore, a line of “cured” cells, established by elimination of HCV RNA from the Hep3B/miR122 replicon cells, exhibited an enhanced expression of miR122 and a continuous increase of infectious titers of HCVcc in every passage. The establishment of the new permissive cell line for HCVcc will have significant implications not only for basic HCV research but also for the development of new therapeutics.
Genome-Wide Association Study of Vascular Dementia
Authors: Schrijvers Elisabeth M.C. , Schürmann Britta , Koudstaal Peter J. , van den Bussche Hendrik , Van Duijn Cornelia M. , Hentschel Frank , Heun Reinhard , Hofman Albert , Jessen Frank , Kölsch Heike , Kornhuber Johannes , Peters Oliver , Rivadeneira Fernando , Rüther Eckart , Uitterlinden André G. , Riedel-Heller Steffi , Dichgans Martin , Wiltfang Jens , Maier Wolfgang , Breteler Monique M.B. , Ikram M. Arfan 
Published: November 2011

Background and Purpose—
Most studies investigating the genetics of dementia have focused on Alzheimer disease, but little is known about the genetics of vascular dementia. The aim of our study was to identify new loci associated with vascular dementia.

Methods—
We performed a genome-wide association study in the Rotterdam Study, a large prospective population-based cohort study in the Netherlands. We sought to replicate genome-wide significant loci in 2 independent replication samples.

Results—

In the discovery analysis of 5700 dementia-free individuals, 67 patients developed incident vascular dementia over a mean follow-up time of 9.3±3.2 years. We showed genome-wide significance for rs12007229, which is located on the X chromosome near the androgen receptor gene (OR, 3.7; 95% CI, 2.3–5.8, per copy of the minor allele;
P
=1.3×10
−8
). This association was further confirmed in 2 independent populations (probability value of combined replication samples=0.024).

Conclusions—
Our study shows a novel genetic locus for vascular dementia on the X chromosome. Further replication of this finding is required.
Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01
Authors: Gounder Kamini , Brzuszkiewicz Elzbieta , Liesegang Heiko , Wollherr Antje , Daniel Rolf , Gottschalk Gerhard , Reva Oleg , Kumwenda Benjamin , Srivastava Malay , Bricio Carlos , Berenguer José , van Heerden Esta , Litthauer Derek 
Published: November 2011

Abstract

Background
Many strains of Thermus have been isolated from hot environments around the world. Thermus scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different Thermus thermophilus strains have been completed. This paper represents the completed genome from a second Thermus species - T. scotoductus.

Results
The genome of Thermus scotoductus SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the Thermus thermophilus genomes. The T. thermophilus megaplasmid genes are part of the T. scotoductus chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of T. scotoductus and T. thermophilus. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from Meiothermus ruber. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of Thermus scotoductus was confirmed experimentally as expected as most of the proteins of the natural transformation system of Thermus thermophilus are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle.

Conclusions
The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.
Small- bowel mucosal changes and antibody responses after low- and moderate-dose gluten challenge in celiac disease
Authors: Lähdeaho Marja-Leena , Mäki Markku , Laurila Kaija , Huhtala Heini , Kaukinen Katri 
Published: November 2011

Abstract

Background
Due to the restrictive nature of a gluten-free diet, celiac patients are looking for alternative therapies. While drug-development programs include gluten challenges, knowledge regarding the duration of gluten challenge and gluten dosage is insufficient.
We challenged adult celiac patients with gluten with a view to assessing the amount needed to cause some small-bowel mucosal deterioration.

Methods
Twenty-five celiac disease adults were challenged with low (1-3 g) or moderate (3-5g) doses of gluten daily for 12 weeks. Symptoms, small-bowel morphology, densities of CD3+ intraepithelial lymphocytes (IELs) and celiac serology were determined.

Results
Both moderate and low amounts of gluten induced small-bowel morphological damage in 67% of celiac patients. Moderate gluten doses also triggered mucosal inflammation and more gastrointestinal symptoms leading to premature withdrawals in seven cases. In 22% of those who developed significant small- intestinal damage, symptoms remained absent. Celiac antibodies seroconverted in 43% of the patients.

Conclusions
Low amounts of gluten can also cause significant mucosal deterioration in the majority of the patients. As there are always some celiac disease patients who will not respond within these conditions, sample sizes must be sufficiently large to attain to statistical power in analysis.
What do parents think about parental participation in school-based interventions on energy balance-related behaviours? a qualitative study in 4 countries
Authors: Van Lippevelde Wendy , Verloigne Maïté , De Bourdeaudhuij Ilse , Bjelland Mona , Lien Nanna , Fernández-Alvira Juan M , Moreno Luis A , Kovacs Eva , Brug Johannes , Maes Lea 
Published: November 2011

Abstract

Background
Overweight and obesity in youth has increased dramatically. Therefore, overweight prevention initiatives should start early in life and target modifiable energy balance-related behaviours. Parental participation is often advocated as important for school-based interventions, however, getting parents involved in school-based interventions appears to be challenging based on earlier intervention experiences. The purpose of this study was to get insight into the determinants of and perspectives on parental participation in school-interventions on energy balance-related behaviours (physical activity, healthy eating, sedentary behaviours) in parents of ten- to twelve-year olds in order to develop an effective parental module for school-based interventions concerning energy balance-related behaviours.

Methods
Four countries (Belgium, Hungary, Norway and Spain) conducted the focus group research based on a standardised protocol and a semi-structured questioning route. A variation in parental socio-economic status (SES) and parental school involvement was taken into account when recruiting the parents. The audio taped interviews were transcribed, and a qualitative content analysis of the transcripts was conducted in each country.

Results
Seventeen focus group interviews were conducted with a total of 92 parents (12 men, 80 women). Physical activity was considered to be a joint responsibility of school and parents, nutrition as parent's responsibility but supported by the school, and prevention of sedentary behaviours as parent's sole responsibility. Parents proposed interactive and practical activities together with their child as the best way to involve them such as cooking, food tasting, nutrition workshops, walking or cycling tours, sport initiations together with their child. Activities should be cheap, on a convenient moment, focused on their children and not on themselves, not tutoring, not theoretical, and school-or home-based.

Conclusions
Parents want to be involved in activities related to energy balance-related behaviours if this implies 'doing things together' with their child at school or at home.
Maternal educational level, parental preventive behavior, risk behavior, social support and medical care consumption in 8-month-old children in Malmö, Sweden
Authors: Mangrio Elisabeth , Hansen Kristina , Lindström Martin , Köhler Marie , Rosvall Maria 
Published: November 2011

Abstract

Background
The social environment in which children grow up is closely associated with their health. The aim of this study was to investigate the relationship between maternal educational level, parental preventive behavior, parental risk behavior, social support, and use of medical care in small children in Malmö, Sweden. We also wanted to investigate whether potential differences in child medical care consumption could be explained by differences in parental behavior and social support.

Methods
This study was population-based and cross-sectional. The study population was 8 month-old children in Malmö, visiting the Child Health Care centers during 2003-2007 for their 8-months check-up, and whose parents answered a self-administered questionnaire (n = 9,289 children).

Results
Exclusive breast feeding ≥4 months was more common among mothers with higher educational level. Smoking during pregnancy was five times more common among less-educated mothers. Presence of secondhand tobacco smoke during the first four weeks of life was also much more common among children with less-educated mothers. Less-educated mothers more often experienced low emotional support and low practical support than mothers with higher levels of education (>12 years of education). Increased exposure to unfavorable parental behavioral factors (maternal smoking during pregnancy, secondhand tobacco smoke and exclusive breastfeeding <4 months) was associated with increased odds of in-hospital care and having sought care from a doctor during the last 8 months. The odds were doubled when exposed to all three risk factors. Furthermore, children of less-educated mothers had increased odds of in-hospital care (OR = 1.34 (95% CI: 1.08, 1.66)) and having sought care from a doctor during the last 8 months (OR = 1.28 (95% CI: 1.09, 1.50)), which were reduced and turned statistically non-significant after adjustment for unfavorable parental behavioral factors.

Conclusion
Children of less-educated mothers were exposed to more health risks, fewer health-promoting factors, worse social support, and had higher medical care consumption than children with higher educated mothers. After adjustment for parental behavioral factors the excess odds of doctor's visits and in-hospital care among children with less-educated mothers were reduced. Improving children's health calls for policies targeting parents' health-related behaviors and social support.
Necessary conditions for thermal rectification and negative differential thermal conductance in graphene nanoribbons
Authors: Wang Yan , Ruan Xiulin 
Published: November 2011

ABSTRACTWe have studied negative differential thermal conductance (NDTC) and thermal rectification (TR) in graphene nanoribbons (GNRs) using nonequilibrium molecular dynamics simulations. Strong ballistic transport regime and sufficient temperature gradient are found to be necessary conditions for the onset of both NDTC and TR in GNRs, while the latter also requires asymmetry in structure. Preferred direction of heat transport is also discussed for TR.
ChemInform Abstract: Ordered Large‐Pore Mesoporous Li4Ti5O12 Spinel Thin Film Electrodes with Nanocrystalline Framework for High Rate Rechargeable Lithium Batteries: Relationships Among Charge Storage, Electrical Conductivity, and Nanoscale Structure.
Authors: Haetge Jan , Hartmann Pascal , Brezesinski Kirstin , Janek Juergen , Brezesinski Torsten 
Published: November 2011

AbstractThe title thin film electrodes with both a well‐defined mesoporous morphology and a nanocrystalline framework are synthesized by a polymer‐directed sol—gel route from a mixture of Ti(OBu)4, EtOH, AcOH, LiOAc, 2‐methoxyethanol, and a poly(ethylene‐co‐butylene)‐block‐poly(ethylene oxide) diblock copolymer as the structure‐directing agent (dip‐coating on polar substrates, 300 °C, 12 h).
Influence of weft‐knitted tubular fabric on radial mechanical property of coaxial three‐layer small‐diameter vascular graft
Authors: Yang Hongjun , Zhu Guocheng , Zhang Zhen , Wang Zhenzhen , Fang Jian , Xu Weilin 
Published: November 2011

AbstractThe goal of this study was to evaluate the radial mechanical property of the small‐diameter polyurethane vascular grafts reinforced by weft‐knitted tubular polyester/spandex fabrics. The polyester/spandex tubular fabrics with different blend ratios were prepared on a weft‐knitting machine to reinforce small‐diameter polyurethane vascular grafts. Phase separation technique was employed to produce coaxial three‐layer small‐diameter polyurethane vascular grafts at room temperature. Morphology of the polyurethane vascular grafts was examined by scanning electron microscope (SEM), and micropores were observed on both inner and cross section surfaces. Radial tensile property and compliance of small‐diameter polyurethane vascular grafts with and without reinforcement by polyester/spandex tubular fabrics were characterized. The effect of polyester/spandex tubular fabric on the mechanical property of polyurethane vascular grafts was studied. The results indicated that the radial tensile strength of the vascular graft was improved by the tubular fabric, and that the influence of tubular fabric on compliance was small compared to that of wall thickness. It was notable that the wall thickness of the vascular grafts was a major factor in controlling the compliance in the radial direction. Therefore, a coaxial three‐layer small‐diameter polyurethane vascular graft with excellent compliance and tensile strength could be obtained by controlling the wall thickness and using polyester/spandex fabric as reinforcement. © 2011 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 100B: 342–349, 2012.
Simple models for InGaN alloys
Authors: Elfituri Fathi , Hourahine Ben 
Published: November 2011

AbstractThe properties of InGaN alloys are important for many applications in optoelectronics, since their fundamental gap spans the visible range. Calculating properties, particularly for InN, is theoretically challenging, especially to obtain accurate values for the band gap. We have developed a semi‐empirical parametrisation of (In,Ga) N using the density functional based tight binding method (DFTB), where the band gaps of InN and GaN have been empirically corrected to experiment. We demonstrate the performance of this method by calculating a range of properties for the two materials, including elastic constants and carrier effective masses. There are several methods to model alloys of these material, one of the simplest being the virtual crystal approximation, which we apply to derive electronic properties over the whole composition range for InGaN.
Estimating surface long‐wave radiative fluxes at global scale
Authors: Nussbaumer Eric A. , Pinker Rachel T. 
Published: November 2011

AbstractA new approach for calculating downwelling surface long‐wave radiation (DSLW) under all sky conditions is presented. The DSLW model (DSLW/UMD) is driven with a synthesis of the latest 1° resolution Moderate‐resolution Imaging Spectroradiometer (MODIS) level‐3 cloud parameters and information from the European Centre for Medium‐Range Weather Forecasts (ECMWF) ERA‐Interim model. The DSLW/UMD's clear‐sky contribution is based on the Rapid Radiative Transfer Model (RRTM) and is globally applicable, while a statistical cloud structure model and parametrization determine the cloud contribution to DSLW. Daily averaged estimates of DSLW for 2003–2007 along with four commonly used methods based on radiative transfer (RT) theory are compared against ground measurements from the Baseline Surface Radiation Network (BSRN). It is shown that for all four years, the proposed approach performs as well as or better than the available RT‐based models when evaluated against BSRN measurements. Correlation coefficients, absolute value of bias (W m−2), and RMSE (W m−2) are 0.973 to 0.974, −0.07 to 1.9, and 16.82 to 17.35, respectively. When stratified into Tropical, Midlatitude, and Polar latitudinal belts, largest discrepancies against ground observations are found at high latitudes. Copyright © 2011 Royal Meteorological Society
Robotic‐assisted laparoscopic stage II restorative proctectomy for toxic ulcerative colitis
Authors: McLemore Elisabeth C. , Cullen John , Horgan Santiago , Talamini Mark A. , Ramamoorthy Sonia 
Published: November 2011

AbstractBackgroundThere is a paucity of literature reporting minimally invasive proctectomy for ulcerative colitis (UC). We report a novel application of a robotic system to perform restorative proctectomy in patients with toxic UC.MethodsRetrospective review, case series report.ResultsRobotic‐assisted laparoscopic proctectomy with ileal J‐pouch anal anastomosis was performed in three patients with toxic UC. All patients previously underwent urgent laparoscopic total abdominal colectomy. One female and two male patients were aged 39, 24 and 43, respectively. The procedures were performed safely with minimal complications. The robotic proctectomy operative time was reduced from 134 to 106 min. None of the patients have experienced fecal incontinence, nocturnal seepage or sexual dysfunction.ConclusionsThis is a case series report of a robotic‐assisted laparoscopic proctectomy with restorative ileal J‐pouch in patients with toxic UC. This technique has been previously described for use in patients with medically refractory UC and neoplasia associated with chronic UC. This series exemplifies an ideal application of a robotic system with improved visibility, rotation and ergonomics. Copyright © 2011 John Wiley & Sons, Ltd.