bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating atom‐based and residue‐based scoring functions for protein–protein docking
Authors: Vreven Thom , Hwang Howook , Weng Zhiping 
Published: July 2011

AbstractMost scoring functions for protein–protein docking algorithms are either atom‐based or residue‐based, with the former being able to produce higher quality structures and latter more tolerant to conformational changes upon binding. Earlier, we developed the ZRANK algorithm for reranking docking predictions, with a scoring function that contained only atom‐based terms. Here we combine ZRANK's atom‐based potentials with five residue‐based potentials published by other labs, as well as an atom‐based potential IFACE that we published after ZRANK. We simultaneously optimized the weights for selected combinations of terms in the scoring function, using decoys generated with the protein–protein docking algorithm ZDOCK. We performed rigorous cross validation of the combinations using 96 test cases from a docking benchmark. Judged by the integrative success rate of making 1000 predictions per complex, addition of IFACE and the best residue‐based pair potential reduced the number of cases without a correct prediction by 38 and 27% relative to ZDOCK and ZRANK, respectively. Thus combination of residue‐based and atom‐based potentials into a scoring function can improve performance for protein–protein docking. The resulting scoring function is called IRAD (integration of residue‐ and atom‐based potentials for docking) and is available at http://zlab.umassmed.edu.
High power lithium ion battery materials by computational design
Authors: Adams Stefan , Rao R. Prasada 
Published: July 2011

AbstractEmpirical bond length–bond valence (BV) relations provide insight into the link between structure of and ion transport in solid electrolytes and mixed conductors. Building on our earlier systematic adjustment of BV parameters to the bond softness, here we discuss how the squared BV mismatch is linked to the absolute energy scale and used as a general Morse‐type interaction potential for analyzing low‐energy ion migration paths in ion conducting solids or mixed conductors by either an energy landscape approach or molecular dynamics (MD) simulations. For a wide range of lithium oxides we could thus model ion transport revealing significant differences to an earlier geometric approach. This novel BV‐based force‐field has then been applied to investigate a range of mixed conductors, focusing on cathode materials for lithium ion battery (LIB) applications to promote a systematic design of LIB cathodes that combine high energy density with high power density. To demonstrate the versatility of the new BV‐based force field it is applied in exploring various strategies to enhance the power performance of safe low cost LIB materials including LiFePO4, LiVPO4F, LiFeSO4F, etc.
Magnetoelectric properties of lead‐free Li0.06K0.47Na0.47NbO3CoFe2O4 nanocomposite films fabricated by a one‐step chemical process
Authors: Cheng T. D. , Wang G. Y. , Wang Y. , Tang X. G. , Chan H. L. W. 
Published: July 2011

AbstractLead‐free composite thin films composed of Li0.06K0.47Na0.47NbO3 and CoFe2O4 were prepared using a one‐step chemical method. By analysis using X‐ray diffraction, thermogravimetry (TG), and differential scanning calorimetry, it was found that the Li0.06K0.47Na0.47NbO3 and CoFe2O4 phases were crystallized at different stages of the thermal treatment, which resulted in the formation of a composite structure. The phase segregation was confirmed by observations on scanning electron microscopy and magnetic force microscopy. By electrical and magnetic measurements it was found that the composite showed a coupled magnetoelectric behavior at room temperature with a magnetoelectric coefficient of ∼185 mV/cm · Oe.
Doping and grain size effects on pyroelectric properties of Ba0.7Sr0.3TiO3 for uncooled infrared bolometer
Authors: Zhang Guangzu , Jiang Shenglin , Zeng Yike , Zhang Yangyang , Zhang Qingfeng , Yu Yan , Wang Jing 
Published: July 2011

AbstractBa0.7Sr0.3TiO3 (BST) ceramics with different dopants and various grain sizes were fabricated by the solid‐state reaction process, and the doping and grain size effects on dielectric and dc bias field‐induced pyroelectric properties were systemically investigated. When acceptors were added, the dielectric loss of the BST was decreased effectively, whereas the pyroelectric coefficient was decreased for the broadening of dielectric constant peaks. With the increase of the content of acceptors and the adding of donors simultaneously, the decrease of pyroelectric coefficient caused by the doping effect could be weakened. The dielectric and dc bias field‐induced pyroelectric properties were also affected by the grain size effects dramatically. In this paper, the best pyroelectric coefficient of 105 × 10−8 C/cm2 °C and figure‐of‐merit of 22 × 10−5 Pa−0.5 could be obtained when the grain size was 1 µm. The systemic investigation of doping and grain size effects would contribute to the development of high pyroelectric properties of BST for uncooled infrared detector.
First‐principles study of the reconstruction and hydroxylation of the polar NiO(111) surface
Authors: Ebensperger Christina , Meyer Bernd 
Published: July 2011

AbstractDensity‐functional theory (DFT) calculations have been combined with a thermodynamic formalism to determine a phase diagram of lowest‐energy structures and compositions of the polar NiO(111) surface in equilibirum with oxygen, hydrogen, and water reservoirs at finite temperatures and pressures. Consistent with experiment we find that for a wide range of oxygen and hydrogen chemical potentials the surface is fully hydroxylated and shows a (1 × 1) periodicity. At higher temperatures and H‐poor conditions water can be removed from the surface and the two (2 × 2) octopolar reconstructions become the thermodynamically most stable configurations. Other structures, which have been proposed on the basis of experimental data after high‐temperature annealing, have to be considered to be kinetically limited metastable phases. In O‐poor conditions no reduced surface structures are found to be thermodynamically stable. However, in O‐rich environments and at low hydrogen chemical potential the surface can be oxidized by a partial removal of hydrogen or incorporation of additional oxygen. The structural motifs are closely related to the cadmium iodide structure of Ni(OH)2 and NiO2.
How much of the placebo ‘effect’ is really statistical regression?
Authors: McDonald Clement J. , Mazzuca Steven A. , McCabe George P. 
Published: July 2011

AbstractStatistical regression to the mean predicts that patients selected for abnormalcy will, on the average, tend to improve. We argue that most improvements attributed to the placebo effect are actually instances of statistical regression. First, whereas older clinical trials susceptible to regression resulted in a marked improvement in placebo‐treated patients, in a modern series of clinical trials whose design tended to protect against regression, we found no significant improvement (median change 0·3 per cent, p > 0·05) in placebo‐treated patients. Secondly, regression can yield sizeable improvements, even among biochemical tests. Among a series of 15 biochemical tests, theoretical estimates of the improvement due to regression by selection of patients as high abnormals (i.e. 3 standard deviations above the mean) ranged from 2·5 per cent for serum sodium to 26 per cent for serum lactate dehydrogenase (median 10 per cent); empirical estimates ranged from 3·8 per cent for serum chloride to 37·3 per cent for serum phosphorus (median 9·5 per cent). Thus, we urge caution in interpreting patient improvements as causal effects of our actions and should avoid the conceit of assuming that our personal presence has strong healing powers.
Measuring and analysing quality of life in cancer clinical trials: A review
Authors: Fayers P. M. , Jones D. R. 
Published: July 2011

AbstractAfter brief consideration of the definition of the term ‘quality of life’, methods previously adopted and problems encountered in assessing and evaluating quality of life in clinical studies of cancer are reviewed. Desirable properties of any such assessment methods and approaches to the analysis of quality of life data are discussed.Illustrations are provided by reference to the methods of assessment of quality of life incorporated in two recently‐initiated studies of cancer treatment.
Validity and power investigation of a test for serial correlation in univariate repeated measures analysis
Authors: Hearne Erwin M. , Clark Gary M. 
Published: July 2011

AbstractA common design in biostatistics and psychometrics is the repeated measures design. A popular example is a clinical trial with one grouping factor, e.g. treatment or drug, and one repeated measures factor, e.g. time or visit. For selected ‘real world’ parameter sets, we performed a validity and power study on a test for serial correlation in repeated measures analysis and also conducted a similar study of a test for sphericity. Simulation showed that the serial correlation test identified the serial correlation structure, whereas the sphericity test, for some parameter sets, failed to detect this non‐spherical pattern as often as 85 per cent of the time.
Pax7 Expressing Cells Contribute to Dermal Wound Repair, Regulating Scar Size through a β-Catenin Mediated Process
Authors: Amini-Nik Saeid , Glancy Dylan , Boimer Corey , Whetstone Heather , Keller Charles , Alman Benjamin A. 
Published: July 2011

Abstract
During skin wound healing, fibroblast-like cells reconstitute the dermal compartment of the repaired skin filling the wound gap. A subset of these cells are transcriptionally active for β-catenin/T-cell factor (TCF) signaling during the proliferative phase of the repair process, and β-catenin levels control the size of the scar that ultimately forms by regulating the number of dermal fibroblasts. Here, we performed cell lineage studies to reveal a source of the dermal cells in which β-catenin signaling is activated during wound repair. Using a reporter mouse, we found that cells in the early wound in which TCF-dependent transcription is activated express genes involved in muscle development. Using mice in which cells express Pax7 (muscle progenitors) or Mck (differentiated myocytes) are permanently labeled, we showed that one quarter of dermal cells in the healing wound are Pax7 expressing progeny, but none are Mck progeny. Removing one allele of β-catenin in Pax7 expressing progeny resulted in a significantly smaller scar size with fewer Pax7 expressing progeny cell contributing to wound repair. During wound healing, β-catenin activation causes muscle satellite cells to adopt a fibrotic phenotype and this is a source of dermal cells in the repair process.
Trans‐18:1 and CLA Isomers in Rumen and Duodenal Digesta of Bulls Fed n‐3 and n‐6 PUFA‐Based Diets
Authors: Shen Xiangzhen , Dannenberger Dirk , Nuernberg Karin , Nuernberg Gerd , Zhao Ruqian 
Published: July 2011

AbstractThe aim of the study was to investigate the effect of n‐6 PUFA (maize silage/grass silage, soybean meal and soybean oil, control) and n‐3 PUFA (grass silage, rapeseed cake and rapeseed oil, experiment) based diets on the occurrence of rumen‐ and duodenal digesta trans‐C18:1 and CLA isomers of German Simmental bulls. The results based on rumen and duodenal digesta samples immediately taken from the bulls just after slaughter. The diet affected the occurrence of individual trans‐C18:1 and CLA isomers in the rumen and duodenal digesta in different ways. The isomer trans‐11,cis‐13 CLA was detected as the most abundant isomer in the rumen of n‐3 PUFA based diet fed bulls compared to n‐6 PUFA based diet fed bulls. The trans‐7,cis‐9 CLA isomer was not detected in the rumen samples of bulls fed both diets, however abundant trans‐7,cis‐9 CLA was identified and quantified in the duodenum digesta. Both the concentration of the sum of trans‐18:1 fatty acids and individual isomers in the rumen were not affected by the diet, except trans‐16‐18:1. The concentration of trans‐16‐18:1 was significantly decreased in the rumen of n‐3 PUFA supplemented‐fed bulls compared to n‐6 PUFA supplemented‐fed bulls.
Transmission dynamics of primary pneumonic plague in the USA
Authors: HINCKLEY A. F. , BIGGERSTAFF B. J. , GRIFFITH K. S. , MEAD P. S. 
Published: July 2011

SUMMARYPlague is thought to have killed millions during three catastrophic pandemics. Primary pneumonic plague, the most severe form of the disease, is transmissible from person-to-person and has the potential for propagating epidemics. Efforts to quantify its transmission potential have relied on published data from large outbreaks, an approach that artificially inflates the basic reproductive number (R0) and skews the distribution of individual infectiousness. Using data for all primary pneumonic plague cases reported in the USA from 1900 to 2009, we determined that the majority of cases will fail to transmit, even in the absence of antimicrobial treatment or prophylaxis. Nevertheless, potential for sustained outbreaks still exists due to superspreading events. These findings challenge current concepts regarding primary pneumonic plague transmission.
Early development ofBrycon orthotaenia(Pisces: Characidae)
Authors: Gomes Rafael Zeferino , Sato Yoshimi , Rizzo Elizete , Bazzoli Nilo 
Published: July 2011

SummaryBrycon orthotaeniais an important fish for commercial and sport fishing and may reach 7 kg in body weight; it is endangered in some regions of Brazil's São Francisco River Basin. Breeders were subjected to spawning induction to analyse the early development; oocytes and semen were obtained by manual extrusion and fertilization was carried out using the dry method. After fertilization, eggs were kept in incubators at 24°C. Egg samples were collected every 10 min until hatching in order to monitor embryonic development and were analysed and photographed. Larvae samples were collected daily until the seventh day to analyse the larvae development; larvae were fixed in Bouin's fluid and subjected to routine histological and histochemical techniques for glycoprotein and glyco-conjugated detection. Oocyte extrusion occurred 6 h after the second hormone dose at 26°C. The recently extruded oocytes were spherical, dark green and non-adhesive, with a diameter of 1479.67 ± 53.18 and 3094.60 ± 80.34 μm after hydration. The blastopore closure occurred within 7 h 30 min of fertilization and the fertilization rate was 50.0 ± 5.5 % at 24°C. Embryonic development was completed within 21 h 30 min of fertilization. Complete yolk sac resorption and mouth opening occurred on the third day after hatching, at which time an adhesive organ with mucosubstances was observed. On the third day, an olfactory chamber with cilia and intense cannibalism amongst the larvae was observed. The complete differentiation of the digestive system occurred on the fifth day and the nervous and sensorial systems differentiation occurred on the sixth to seventh days.
Predictors of nutrition label viewing during food purchase decision making: an eye tracking investigation
Authors: Graham Dan J , Jeffery Robert W 
Published: July 2011

AbstractObjectiveNutrition label use could help consumers eat healthfully. Despite consumers reporting label use, diets are not very healthful and obesity rates continue to rise. The present study investigated whether self-reported label use matches objectively measured label viewing by monitoring the gaze of individuals viewing labels.DesignThe present study monitored adults viewing sixty-four food items on a computer equipped with an eye-tracking camera as they made simulated food purchasing decisions. ANOVA and t tests were used to compare label viewing across various subgroups (e.g. normal weight v. overweight v. obese; married v. unmarried) and also across various types of foods (e.g. snacks v. fruits and vegetables).SettingParticipants came to the University of Minnesota's Epidemiology Clinical Research Center in spring 2010.SubjectsThe 203 participants were ⩾18 years old and capable of reading English words on a computer 76 cm (30 in) away.ResultsParticipants looked longer at labels for ‘meal’ items like pizza, soup and yoghurt compared with fruits and vegetables, snack items like crackers and nuts, and dessert items like ice cream and cookies. Participants spent longer looking at labels for foods they decided to purchase compared with foods they decided not to purchase. There were few between-group differences in nutrition label viewing across sex, race, age, BMI, marital status, income or educational attainment.ConclusionsNutrition label viewing is related to food purchasing, and labels are viewed more when a food's healthfulness is ambiguous. Objectively measuring nutrition label viewing provides new insight into label use by various sociodemographic groups.
What is the real cost of our food? Implications for the environment, society and public health nutrition
Authors: O'Kane Gabrielle 
Published: July 2011

AbstractThe current, globalised food system supplies ‘cheap’ food to a large proportion of the world's population, but with significant social, environmental and health costs that are poorly understood. The present paper examines the nature and extent of these costs for both rural and urban communities, by illustrating the financial pressures on food producers and manufacturers to produce cheap food, the disconnection people experience with how and where their food is produced, and the rise in obesity levels that plague the globe. The paper then proposes that community food systems may play an important role in mitigating the adverse environmental, economic and social effects of the dominant food system, by the use of more sustainable food production methods, the development of local economies and enabling closer connections between farmers and consumers. There are many opportunities for public health nutritionists to contribute to the local food system literature to ascertain whether these systems improve inequities, provide better access to healthy food and help stem the tide of rising global obesity levels. Public health nutritionists can play a key role in supporting people to become food citizens and to advocate for democratic and sustainable food systems.
Complex traits analysis of chicken growth using targeted genetical genomics
Authors: Cabrera C. P. , Dunn I. C. , Fell M. , Wilson P. W. , Burt D. W. , Waddington D. , Talbot R. , Hocking P. M. , Law A. , Knott S. , Haley C. S. , de Koning D. J. 
Published: July 2011

SummaryDissecting the genetic control of complex trait variation remains very challenging, despite many advances in technology. The aim of this study was to use a major growth quantitative trait locus (QTL) in chickens mapped to chromosome 4 as a model for a targeted approach to dissect the QTL. We applied a variant of the genetical genomics approach to investigate genome‐wide gene expression differences between two contrasting genotypes of a marked QTL. This targeted approach allows the direct quantification of the link between the genotypes and the genetic responses, thus narrowing the QTL‐phenotype gap using fewer samples (i.e. microarrays) compared with the genome‐wide genetical genomics studies. Four differentially expressed genes were localized under the region of the QTL. One of these genes is a potential positional candidate gene (AADAT) that affects lysine and tryptophan metabolism and has alternative splicing variants between the two genotypes. In addition, the lysine and glycolysis metabolism pathways were significantly enriched for differentially expressed genes across the genome. The targeted approach provided a complementary route to fine mapping of QTL by characterizing the local and the global downstream effects of the QTL and thus generating further hypotheses about the action of that QTL.
Managing multiple myeloma: the emerging role of novel therapies and adapting combination treatment for higher risk settings
Authors: Richardson Paul G. , Laubach Jacob , Mitsiades Constantine S. , Schlossman Robert , Hideshima Teru , Redman Katherine , Chauhan Dharminder , Ghobrial Irene M. , Munshi Nikhil , Anderson Kenneth C. 
Published: July 2011

SummaryNovel therapies have transformed the treatment paradigm for multiple myeloma with significant improvements in survival now seen in both younger and older patients. Nonetheless, the disease is heterogeneous and high‐risk patients in particular continue to have poor outcome. Moreover, the disease remains incurable. Efforts to refine risk stratification and disease characteristics continue with the use of cytogenetics, enhanced imaging techniques and other new technologies, such as genomics. The integration of novel therapies into induction therapy, consolidation and maintenance continues to evolve, and the appropriate use of combination strategies including proteasome inhibition and immunomodulatory treatment is emerging as a platform with application across the disease spectrum. Despite these advances, resistance to novel agents occurs and so the identification of new targets and the recognition of clonal heterogeneity are especially important as improvements to current treatment strategies are developed, with the goal of further improving patient outcome.
A follow‐up evaluation of the impact of the Chief Nursing Officer’s review of mental health nursing in Mental Health Trusts and Universities in England: comparisons of two e‐surveys
Authors: Baker John , Swarbrick Caroline , Campbell Malcolm , Playle John , Lovell Karina 
Published: July 2011

baker j., swarbrick c., campbell m., playle j. & lovell k. (2012) A follow‐up evaluation of the impact of the Chief Nursing Officer’s review of mental health nursing in Mental Health Trusts and Universities in England: comparisons of two e‐surveys. Journal of Advanced Nursing68(3), 625–635.AbstractAims.  This article is a report of a study that aimed to establish a national picture of the implementation of Review recommendations over time in both Mental Health Trusts and Higher Education Institutions (Universities) in England.Background.  The 2006 Review of Mental Health Nursing in England by the Chief Nursing Officer made 17 key recommendations for Mental Health Trusts and Universities to improve mental health nursing. This article outlines key findings from a national survey of National Health Service Trusts and Universities in England with regard to prioritization and progress on implementation of these recommendations.Methods.  An e‐survey was carried out in 2008‐2009 based on the Chief Nursing Officer review recommendations and guidance. Participants included all Trusts which delivered mental health services (n = 68) and Universities which delivered pre‐registration mental health nursing education (n = 50) in England.Results.  There appears to be some evidence that the Chief Nursing Officer review of Mental Health Nursing in England continues to be implemented in both Mental Health Trusts and Universities. There is variety in levels of implementation, but Mental Health Trusts and Universities broadly agree on priority areas.Conclusions.  The Chief Nursing Officer review has been influential in focusing the care and education of mental health nurses and services in England. There appears to be a range of barriers and facilitators which aid the implementation of healthcare policy. More attention is required from researchers to enhance and evaluate the impact of policy implementation on the quality of care provided.