bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Cryo-Electron Microscopy Structure of Feline Calicivirus Bound to Junctional Adhesion Molecule A at 9-Angstrom Resolution Reveals Receptor-Induced Flexibility and Two Distinct Conformational Changes in the Capsid Protein VP1
Authors: Bhella David , Goodfellow Ian G. 
Published: August 2011

ABSTRACT

Caliciviridae
are small icosahedral positive-sense RNA-containing viruses and include the human noroviruses, a leading cause of infectious acute gastroenteritis and feline calicivirus (FCV), which causes respiratory illness and stomatitis in cats. FCV attachment and entry is mediated by feline junctional adhesion molecule A (fJAM-A), which binds to the outer face of the capsomere, inducing a conformational change in the capsid that may be important for viral uncoating. Here we present the results of our structural investigation of the virus-receptor interaction and ensuing conformational changes. Cryo-electron microscopy and three-dimensional image reconstruction were used to solve the structure of the virus decorated with a soluble fragment of the receptor at subnanometer resolution. In initial reconstructions, the P domains of the capsid protein VP1 and fJAM-A were poorly resolved. Sorting experiments led to improved reconstructions of the FCV–fJAM-A complex both before and after the induced conformational change, as well as in three transition states. These data showed that the P domain becomes flexible following fJAM-A binding, leading to a loss of icosahedral symmetry. Furthermore, two distinct conformational changes were seen; an anticlockwise rotation of up to 15° of the P domain was observed in the AB dimers, while tilting of the P domain away from the icosahedral 2-fold axis was seen in the CC dimers. A list of putative contact residues was calculated by fitting high-resolution coordinates for fJAM-A and VP1 to the reconstructed density maps, highlighting regions in both virus and receptor important for virus attachment and entry.
Prevalence of owner‐reported behaviours in dogs separated from the litter at two different ages
Authors: Pierantoni L. , Albertini M. , Pirrone F. 
Published: August 2011

The present study examined the prevalence of behaviours in dogs separated from the litter for adoption at different ages. Seventy adult dogs separated from their dam and littermates and adopted between the ages of 30 and 40 days were compared with 70 adult dogs that had been taken from the litter for adoption at two months. Owners were asked to complete a questionnaire eliciting information on whether their dog exhibited potentially problematic behaviours when in its usual environment. Binary logistic regression analysis was performed to investigate whether the age at which the dog was separated from the litter might predispose it to developing undesirable behaviours. The odds of displaying destructiveness, excessive barking, fearfulness on walks, reactivity to noises, toy possessiveness, food possessiveness and attention‐seeking were significantly greater for the dogs that had been removed from the litter earlier during the socialisation period. In addition, dogs purchased from a pet shop at 30 to 40 days of age were reported to exhibit some of the listed behaviours with a significantly higher frequency than dogs purchased from a pet shop at two months. No significant differences were observed with dogs obtained from other types of sources. The dogs in the youngest age group (18 to 36 months) had a higher probability of displaying destructiveness and tail chasing. These findings indicate that, compared with dogs that remained with their social group for 60 days, dogs that had been separated from the litter earlier were more likely to exhibit potentially problematic behaviours, especially if they came from a pet shop.
Menstrual cycle and oral contraceptives’ effects on growth hormone response to sprinting
Authors: Sunderland Caroline , Tunaley Victoria , Horner Fleur , Harmer Daniel , Stokes Keith A. 
Published: August 2011

The present study examined the impact of the menstrual cycle and oral contraceptive (OC) use on the growth hormone response to nonmotorized treadmill sprinting. Nine monophasic OC users (21.5 ± 4.7 years old), and 8 normally menstruating women (NM; 21.4 ± 2.9 years old) participated in the study. Each participant completed 2 main trials, each consisting of an all-out 30-s treadmill sprint. The NM group performed one trial in the midfollicular phase (NM follicular) and one in the midluteal phase (NM luteal); the OC group’s trials occurred one week into the start of the pill-taking cycle and once during the week in which pills were not taken.Venous blood samples were analyzed for growth hormone, pH, lactate, glucose, and progesterone concentrations. Peak and mean power output did not differ between the groups or with menstrual phase, or between the OC-free and OC trials. Integrated growth hormone was greater in the OC group than in the NM group (p = 0.04) with no phase difference (p = 0.80, mean (SD); NM follicular: 421 (335) and NM luteal: 345 (304) vs. OC free: 737 (471) and OC: 758 (389) µg·L–1·90 min–1). Blood lactate was higher in the OC group than in the NM group (p = 0.007) and, conversely, pH was lower in the OC group (p = 0.01). These results demonstrate that OC users who take high-androgenicity pills have a higher growth hormone response to sprint running than do normally menstruating women.
Consumer perceptions of trans fats in 2009 show awareness of negative effects but limited concern regarding use in snack foods
Authors: Nasser Roseann , Cook Stephanie , Bashutski Megan , Hill Karen , Norton Darci , Coleman Jean , Walker Sharon , Charlebois Sylvain 
Published: August 2011

The purpose of this study was to determine consumers’ perceptions of industrially produced trans fats. A cross-sectional study was conducted in Regina at 3 different grocery store chains located in 3 different regions. A 21-item survey was administered in English by 3 research assistants at the grocery stores over a 5-day period. Of 498 potential respondents who were approached, 211 completed the survey, for a 42% response rate. The majority of respondents were female and over 61 years of age. When respondents were asked if they looked for information on food packages while grocery shopping, none of the respondents indicated that they looked for trans fat on the food label. Ninety-six percent of respondents identified that trans fat is found in processed foods, whereas 42% of respondents incorrectly identified trans fat as being found in nonhydrogenated margarines. More female respondents self-reported that they had made dietary changes to decrease trans fat intake as compared with male respondents (p < 0.05). Those participants who made dietary changes to decrease trans fat intake had higher mean knowledge scores than did those who did not make changes (p < 0.043). Sixty-three percent of respondents indicated that they would not make dietary changes to their snack food selections even if their selections contained trans fat. Consumers know a little about trans fats and consider them to be a concern. However, consumers are reluctant to make dietary changes to limit these fats in their snack food selections.
Age at onset as a determinant of presenting phenotype and initial relapse recovery in multiple sclerosis
Authors: Cossburn M , Ingram G , Hirst C , Ben-Shlomo Y , Pickersgill TP , Robertson NP 
Published: August 2011

Background: Age at onset modifies prognosis in multiple sclerosis (MS) and may also exert an effect on the characteristics of disease ignition. Understanding how age influences presentation informs disease management and may allow differentiation of distinct clinical sub-groups. Objectives: To determine the nature of age-specific presentations of relapsing–remitting MS (RRMS) with respect to onset symptoms, gender ratios and index event outcomes. Methods: In a prospective, population-based sample of 1424 patients in South-East Wales we examined associations between age at onset, clinical features and outcome of the onset event, making specific comparisons between paediatric, adolescent and late-onset MS. Results: Age at onset varied significantly between sexes (Male 31.2, Female 29.3, p = 0.002), 0.7% had paediatric onset, 2.7% adolescent onset and 2.8% late-onset MS (>50 years). Optic neuritis was common in younger patients and declined after age 30. Lower limb motor, facial sensory, sexual and sphincteric symptoms rose with age independent of sex and disease course. F:M ratios were highest <16 years of age and declined with increasing age, with a male excess in those over 50. Probability of complete recovery from index event declined with age from 87.4% in the youngest group to 68% in the eldest ( p = 0.009). Conclusions: Age at disease onset in RRMS exerts a significant effect on gender ratios and presenting phenotype, and allows identification of specific clinical sub-groups. In addition, ability to recover from initial relapse declines with age, suggesting accumulation of disability in MS is an age-dependent response to relapse.
Angiopoietin-2 promotes myeloid cell infiltration in a β2-integrin–dependent manner
Authors: Scholz Alexander , Lang Victoria , Henschler Reinhard , Czabanka Marcus , Vajkoczy Peter , Chavakis Emmanouil , Drynski Janina , Harter Patrick N. , Mittelbronn Michel , Dumont Daniel J. , Plate Karl H. , Reiss Yvonne 
Published: August 2011

Abstract
In human inflammatory diseases, we identified endothelial angiopoietin-2 (Ang-2) expression to be strongly associated with inflammations mediated by myeloid cells but not lymphocytes. To identify the underlying mechanism, we made use of a transgenic mouse model with inducible endothelial cell-specific expression of Ang-2. In this model, in the absence of inflammatory stimuli, long-term expression of Ang-2 led to a time-dependent accumulation of myeloid cells in numerous organs, suggesting that Ang-2 is sufficient to recruit myeloid cells. In models of acute inflammation, such as delayed-type hypersensitivity and peritonitis, Ang-2 transgenic animals showed an increased responsiveness. Intravital fluorescence video microscopy revealed augmented cell adhesion as an underlying event. Consequently, we demonstrated that Ang-2 is able to induce strong monocyte adhesion under shear in vitro, which could be blocked by antibodies to β2-integrin. Taken together, our results describe Ang-2 as a novel, endothelial-derived regulator of myeloid cell infiltration that modulates β2-integrin–mediated adhesion in a paracrine manner.
Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment
Authors: Naznin Farhana , Sarker Ruhul , Essam Daryl 
Published: August 2011

Abstract

Background
Many Bioinformatics studies begin with a multiple sequence alignment as the foundation for their research. This is because multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence structure relationships.

Results
In this paper, we have proposed a Vertical Decomposition with Genetic Algorithm (VDGA) for Multiple Sequence Alignment (MSA). In VDGA, we divide the sequences vertically into two or more subsequences, and then solve them individually using a guide tree approach. Finally, we combine all the subsequences to generate a new multiple sequence alignment. This technique is applied on the solutions of the initial generation and of each child generation within VDGA. We have used two mechanisms to generate an initial population in this research: the first mechanism is to generate guide trees with randomly selected sequences and the second is shuffling the sequences inside such trees. Two different genetic operators have been implemented with VDGA. To test the performance of our algorithm, we have compared it with existing well-known methods, namely PRRP, CLUSTALX, DIALIGN, HMMT, SB_PIMA, ML_PIMA, MULTALIGN, and PILEUP8, and also other methods, based on Genetic Algorithms (GA), such as SAGA, MSA-GA and RBT-GA, by solving a number of benchmark datasets from BAliBase 2.0.

Conclusions
The experimental results showed that the VDGA with three vertical divisions was the most successful variant for most of the test cases in comparison to other divisions considered with VDGA. The experimental results also confirmed that VDGA outperformed the other methods considered in this research.
Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing
Authors: Wong Melissa ML , Cannon Charles H , Wickneswari Ratnam 
Published: August 2011

Abstract

Background

Acacia auriculiformis × Acacia mangium hybrids are commercially important trees for the timber and pulp industry in Southeast Asia. Increasing pulp yield while reducing pulping costs are major objectives of tree breeding programs. The general monolignol biosynthesis and secondary cell wall formation pathways are well-characterized but genes in these pathways are poorly characterized in Acacia hybrids. RNA-seq on short-read platforms is a rapid approach for obtaining comprehensive transcriptomic data and to discover informative sequence variants.

Results
We sequenced transcriptomes of A. auriculiformis and A. mangium from non-normalized cDNA libraries synthesized from pooled young stem and inner bark tissues using paired-end libraries and a single lane of an Illumina GAII machine. De novo assembly produced a total of 42,217 and 35,759 contigs with an average length of 496 bp and 498 bp for A. auriculiformis and A. mangium respectively. The assemblies of A. auriculiformis and A. mangium had a total length of 21,022,649 bp and 17,838,260 bp, respectively, with the largest contig 15,262 bp long. We detected all ten monolignol biosynthetic genes using Blastx and further analysis revealed 18 lignin isoforms for each species. We also identified five contigs homologous to R2R3-MYB proteins in other plant species that are involved in transcriptional regulation of secondary cell wall formation and lignin deposition. We searched the contigs against public microRNA database and predicted the stem-loop structures of six highly conserved microRNA families (miR319, miR396, miR160, miR172, miR162 and miR168) and one legume-specific family (miR2086). Three microRNA target genes were predicted to be involved in wood formation and flavonoid biosynthesis. By using the assemblies as a reference, we discovered 16,648 and 9,335 high quality putative Single Nucleotide Polymorphisms (SNPs) in the transcriptomes of A. auriculiformis and A. mangium, respectively, thus yielding useful markers for population genetics studies and marker-assisted selection.

Conclusion
We have produced the first comprehensive transcriptome-wide analysis in A. auriculiformis and A. mangium using de novo assembly techniques. Our high quality and comprehensive assemblies allowed the identification of many genes in the lignin biosynthesis and secondary cell wall formation in Acacia hybrids. Our results demonstrated that Next Generation Sequencing is a cost-effective method for gene discovery, identification of regulatory sequences, and informative markers in a non-model plant.
Molecular targeting of prostate cancer cells by a triple drug combination down-regulates integrin driven adhesion processes, delays cell cycle progression and interferes with the cdk-cyclin axis
Authors: Wedel Steffen , Hudak Lukasz , Seibel Jens-Michael , Makarević Jasmina , Juengel Eva , Tsaur Igor , Waaga-Gasser Ana , Haferkamp Axel , Blaheta Roman A 
Published: August 2011

AbstractBackgroundSingle drug use has not achieved satisfactory results in the treatment of prostate cancer, despite application of increasingly widespread targeted therapeutics. In the present study, the combined impact of the mammalian target of rapamycin (mTOR)-inhibitor RAD001, the dual EGFr and VGEFr tyrosine kinase inhibitor AEE788 and the histone deacetylase (HDAC)-inhibitor valproic acid (VPA) on prostate cancer growth and adhesion in vitro was investigated.MethodsPC-3, DU-145 and LNCaP cells were treated with RAD001, AEE788 or VPA or with a RAD-AEE-VPA combination. Tumor cell growth, cell cycle progression and cell cycle regulating proteins were then investigated by MTT-assay, flow cytometry and western blotting, respectively. Furthermore, tumor cell adhesion to vascular endothelium or to immobilized extracellular matrix proteins as well as migratory properties of the cells was evaluated, and integrin α and β subtypes were analyzed. Finally, effects of drug treatment on cell signaling pathways were determined.ResultsAll drugs, separately applied, reduced tumor cell adhesion, migration and growth. A much stronger anti-cancer effect was evoked by the triple drug combination. Particularly, cdk1, 2 and 4 and cyclin B were reduced, whereas p27 was elevated. In addition, simultaneous application of RAD001, AEE788 and VPA altered the membranous, cytoplasmic and gene expression pattern of various integrin α and β subtypes, reduced integrin-linked kinase (ILK) and deactivated focal adhesion kinase (FAK). Signaling analysis revealed that EGFr and the downstream target Akt, as well as p70S6k was distinctly modified in the presence of the drug combination.ConclusionsSimultaneous targeting of several key proteins in prostate cancer cells provides an advantage over targeting a single pathway. Since strong anti-tumor properties became evident with respect to cell growth and adhesion dynamics, the triple drug combination might provide progress in the treatment of advanced prostate cancer.
Evaluation of the impact of the voucher and accreditation approach on improving reproductive behaviors and status in Cambodia
Authors: Bellows Benjamin , Warren Charlotte , Vonthanak Saphonn , Chhorvann Chhea , Sokhom Hean , Men Chean , Bajracharya Ashish , Rob Ubaidur , Rathavy Tung 
Published: August 2011

Abstract

Background
Cost of delivering reproductive health services to low income populations will always require total or partial subsidization by government and/or development partners. Broadly termed "demand-side financing" or "output-based aid", these strategies include a range of interventions that channel government or donor subsidies to the user rather than the service provider. Initial pilot assessments of reproductive health voucher programs suggest that they can increase access, reduce inequities, and enhance program efficiency and service quality. However, there is a paucity of evidence describing how these programs function in different settings for various reproductive health services.

Methods/Design
Population Council, funded by the Bill and Melinda Gates Foundation, intends to generate evidence around the "voucher and accreditation" approaches to improving the reproductive health of low-income women in Cambodia. The study comprises of four populations: facilities, providers, women of reproductive age using facilities, and women and men who have been pregnant and/or used family planning within the previous 12 months. The study will be carried out in a sample of 20 health facilities that are accredited to provide maternal and newborn health and family planning services to women holding vouchers from operational districts in three provinces: Kampong Thom, Kampot and Prey Veng and a matched sample of non-accredited facilities in three other provinces. Health facility assessments will be conducted at baseline and endline to track temporal changes in quality-of-care, client out-of-pocket costs, and utilization. Facility inventories, structured observations, and client exit interviews will be used to collect comparable data across facilities. Health providers will also be interviewed and observed providing care. A population survey of about 3000 respondents will also be conducted in areas where vouchers are distributed and similar non-voucher locations.

Discussion
A quasi-experimental study will investigate the impact of the voucher approach on improving reproductive health behaviors, reproductive health status and reducing inequities at the population level and assess effects on access, equity and quality of care at the facility level. If the voucher scheme in Cambodia is found effective, it may help other countries adopt this approach for improving utilization and access to reproductive health and family planning services.
Socio-demographic, psychosocial and home-environmental attributes associated with adults' domestic screen time
Authors: Van Dyck Delfien , Cardon Greet , Deforche Benedicte , Owen Neville , De Cocker Katrien , Wijndaele Katrien , De Bourdeaudhuij Ilse 
Published: August 2011

Abstract

Background
Sedentary behaviors (involving prolonged sitting time) are associated with deleterious health consequences, independent of (lack of) physical activity. To inform interventions, correlates of prevalent sedentary behaviors need to be identified. We examined associations of socio-demographic, home-environmental and psychosocial factors with adults' TV viewing time and leisure-time Internet use; and whether psychosocial and environmental correlates differed according to gender, age and educational attainment.

Methods
This cross-sectional study was conducted in Ghent, Belgium, between March and May 2010. Respondents to a mail-out survey (n = 419; 20-65 years; mean age 48.5 [12.1] years; 47.3% men) completed a questionnaire on sedentary behaviors and their potential socio-demographic, psychosocial and home environmental correlates. Statistical analyses were performed using multiple linear regression models.

Results
The independent variables explained 31% of the variance in TV viewing time and 38% of the variance in leisure-time Internet use. Higher education, greater perceived pros of and confidence about reducing TV time were negatively associated with TV viewing time; older age, higher body mass index, larger TV set size and greater perceived cons of reducing TV time showed positive associations. Perceived pros of and confidence about reducing Internet use were negatively associated with leisure-time Internet use; higher education, number of computers in the home, positive family social norms about Internet use and perceived cons of reducing Internet use showed positive associations. None of the socio-demographic factors moderated these associations.

Conclusions
Educational level, age, self-efficacy and pros/cons were the most important correlates identified in this study. If further cross-sectional and longitudinal research can confirm these findings, tailored interventions focusing on both psychosocial and environmental factors in specific population subgroups might be most effective to reduce domestic screen time.
Renal cell carcinoma with a tumor thrombus in the ureter: a case report
Authors: Fujita Osamu , Wada Koichiro , Yamasaki Tomoya , Manabe Daisuke , Takeda Katsuji , Nakamura Satoko 
Published: August 2011

Abstract

Background
Renal cell carcinoma (RCCs) is the most common malignancy of the kidney. When RCC progresses, it is known to form tumor thrombus in the renal vein and/or inferior vena cava. However, RCC does not normally form tumor thrombus in the ureter or renal pelvis.

Case presentation
A 43-year-old man presented to our department for the treatment of a renal tumor with asymptomatic gross hematuria. In a dynamic CT study, contrast enhancement revealed a tumor suspected to be RCC, but atypical finding as a tumor thrombus that filled the renal pelvis and the whole ureter was also observed. Nephroureterectomy was performed, and the tumor was diagnosed histopathologically as RCC.

Conclusion
We report here a very rare case of RCC with a tumor thrombus in the whole ureter.