bluuebunny/crossref_metadata_2025_split huggingface dataset:
An international risk prediction algorithm for the onset of generalized anxiety and panic syndromes in general practice attendees: predictA
Authors: King M. , Bottomley C. , Bellón-Saameño J. A. , Torres-Gonzalez F. , Švab I. , Rifel J. , Maaroos H.-I. , Aluoja A. , Geerlings M. I. , Xavier M. , Carraça I. , Vicente B. , Saldivia S. , Nazareth I. 
Published: January 2011

BackgroundThere are no risk models for the prediction of anxiety that may help in prevention. We aimed to develop a risk algorithm for the onset of generalized anxiety and panic syndromes.MethodFamily practice attendees were recruited between April 2003 and February 2005 and followed over 24 months in the UK, Spain, Portugal and Slovenia (Europe4 countries) and over 6 months in The Netherlands, Estonia and Chile. Our main outcome was generalized anxiety and panic syndromes as measured by the Patient Health Questionnaire. We entered 38 variables into a risk model using stepwise logistic regression in Europe4 data, corrected for over-fitting and tested it in The Netherlands, Estonia and Chile.ResultsThere were 4905 attendees in Europe4, 1094 in Estonia, 1221 in The Netherlands and 2825 in Chile. In the algorithm four variables were fixed characteristics (sex, age, lifetime depression screen, family history of psychological difficulties); three current status (Short Form 12 physical health subscale and mental health subscale scores, and unsupported difficulties in paid and/or unpaid work); one concerned country; and one time of follow-up. The overall C-index in Europe4 was 0.752 [95% confidence interval (CI) 0.724–0.780]. The effect size for difference in predicted log odds between developing and not developing anxiety was 0.972 (95% CI 0.837–1.107). The validation of predictA resulted in C-indices of 0.731 (95% CI 0.654–0.809) in Estonia, 0.811 (95% CI 0.736–0.886) in The Netherlands and 0.707 (95% CI 0.671–0.742) in Chile.ConclusionsPredictA accurately predicts the risk of anxiety syndromes. The algorithm is strikingly similar to the predictD algorithm for major depression, suggesting considerable overlap in the concepts of anxiety and depression.
A high repetitive rate intense electron beam accelerator based on high coupling Tesla transformer
Authors: Peng Jian-Chang , Liu Guo-Zhi , Song Xiao-Xin , Su Jian-Cang 
Published: January 2011

AbstractTesla transformers are widely used in short pulse, repetition pulsed power generators. In this paper, a high repetitive rate intense electron beam accelerator (IEBA) based on high coupling (~1) Tesla transformer, which consists of a primary charging system, coaxial pulse forming line (PFL) charged by Tesla transformer and gas spark switch is described, especially stressed on the high coupling Tesla transformer. By introducing magnetic core to enhance the coupling factor between the primary and secondary windings, the transformer is capable of producing high voltage pulse up to 1.4 MV in approximately 45 µs. A coaxial pulse forming line is closely attached to the transformer that the outer and inner magnetic cores are parts of the PFL's outer and inner conductors respectively. In addition, the parameters of the Tesla transformer and PFL are calculated, including the dimension of the PFL and Tesla transformer. Some experiment results showed that the IEBA is capable of producing electron beams of 300–700 kV/7–13 kA at repetitive rate 100 Hz, with the pulse width 35 ns. The maximal energy efficiency of the Tesla transformer is 83%.
Factors related toCampylobacterspp. carriage in client-owned dogs visiting veterinary clinics in a region of Ontario, Canada
Authors: LEONARD E. K. , PEARL D. L. , JANECKO N. , WEESE J. S. , REID-SMITH R. J. , PEREGRINE A. S. , FINLEY R. L. 
Published: January 2011

SUMMARYFrom July 2008 until May 2009, 240 client-owned pet dogs from seven veterinary clinics in the Region of Waterloo, Ontario, Canada participated in a study to determine pet-related management factors that may be associated with the presence ofCampylobacterspp. in dogs. The prevalence ofCampylobacterspp. carriage in our study population of pet dogs was 22%, with 19% of the dogs positive forC. upsaliensis, and 3% positive forC. jejuni. A significant risk factor from multivariable logistic regression models for bothCampylobacterspp. andC. upsaliensiscarriage was having homemade cooked food as the dog's diet or added to its diet, and a significant sparing factor for both models was treatment with antibiotics in the previous month. Increasing age of the dog decreased the odds ofCampylobacterspp. andC. upsaliensiscarriage. Based on the high prevalence ofCampylobacter, and specificallyC. upsaliensis, further research concerning pet dogs as a risk factor for campylobacteriosis in humans is warranted.
Reliability and validity of a fruit and vegetable self-efficacy instrument for secondary-school students in the Netherlands
Authors: Bannink Rienke , van der Bijl Jaap J 
Published: January 2011

AbstractObjectiveTo develop a ‘fruit self-efficacy’ (FSE) instrument and a ‘vegetable self-efficacy’ (VSE) instrument for secondary-school students in the Netherlands and to test the reliability and validity of these instruments.DesignMethodological research.SettingSeven secondary schools in the Netherlands.SubjectsStudents (11–19 years of age) completed the two instruments in the classroom (n466). Out of the original subject group, 106 students completed the instruments a second time.ResultsThe relevance of the twenty-two items of the two developed instruments was evaluated on two occasions by four experts. This procedure resulted in seventeen items for both instruments. Further analysis was carried out on the basis of the secondary-school students’ answers. Factor analysis identified two unidimensional instruments. Cronbach'sαwas 0·94 for the FSE instrument and 0·95 for the VSE instrument. The intra-class correlation coefficient between the test and the retest for both instruments varied between 0·33 and 0·84 (P< 0·05), depending on how the tests were taken (during class or on the student's own initiative), and the order in which the tests were completed (started or finished with a different instrument used for similar research). The correlation between FSE and fruit consumption was 0·41 (P< 0·01) and between VSE and vegetable consumption was 0·32 (P< 0·01).ConclusionsThe two instruments are sufficiently reliable and valid to assess the FSE and VSE of secondary-school students in the Netherlands. Further research, in which the predominant ethnic minorities in the Netherlands are sufficiently represented, is required to confirm this conclusion.
OPTIMAL PROPORTIONAL REINSURANCE UNDER TWO CRITERIA: MAXIMIZING THE EXPECTED UTILITY AND MINIMIZING THE VALUE AT RISK
Authors: LIANG ZHIBIN , GUO JUNYI 
Published: January 2011

AbstractWe consider the optimal proportional reinsurance from an insurer’s point of view to maximize the expected utility and minimize the value at risk. Under the general premium principle, we prove the existence and uniqueness of the optimal strategies and Pareto optimal solution, and give the relationship between the optimal strategies. Furthermore, we study the optimization problem with the variance premium principle. When the total claim sizes are normally distributed, explicit expressions for the optimal strategies and Pareto optimal solution are obtained. Finally, some numerical examples are presented to show the impact of the major model parameters on the optimal results.
Assessment of the dosimetric consequences of prostate movement through rectal distension for patients receiving 3DCRT
Authors: Redding D.J. , Bragg C.M. 
Published: January 2011

AbstractPurpose: To investigate the dosimetric consequences of rectal distension at the time of the planning computed tomography (CT) scan and any resultant prostate movement on the planned dose delivery for patients receiving three-dimensional conformal radiotherapy (3DCRT) to the prostate.Methods and materials: 25 prostate cancer patients whose planning CT scan demonstrated a full rectum were rescanned after following a laxative protocol. Rectal dimensions on the two scans and 3DCRT treatment plans produced on each plan were compared. The dosimetric implications of changes in rectal size on the treatment plans and the delivered dose were determined. Statistical significance was evaluated with the Wilcoxon signed ranks test.Results: Significant differences in rectal size were found between the initial CT scan and the rescan. The corresponding median change in prostate position was 4.7 mm. The use of planning scans with a full rectum, that is unrepresentative of the rectum, during treatment causes significant reductions in planning target volume (PTV) minimum dose (median reduction 33.7%) and coverage by the 95% isodose (median reduction 3.7% of the PTV).Conclusion: Rectal distension on the initial planning scan can lead to significant PTV underdosage. Patients presenting with large initial rectal fillings must be rescanned in order to avoid a systematic underdosing of the PTV.
Smoothing dispersed counts with applications to mortality data
Authors: Djeundje V. A. B. , Currie I. D. 
Published: January 2011

AbstractMortality data are often classified by age at death and year of death. This classification results in a heterogeneous risk set and this can cause problems for the estimation and forecasting of mortality. In the modelling of such data, we replace the classical assumption that the numbers of claims follow the Poisson distribution with the weaker assumption that the numbers of claims have a variance proportional to the mean. The constant of proportionality is known as the dispersion parameter and it enables us to allow for heterogeneity; in the case of insurance data the dispersion parameter also allows for the presence of duplicates in a portfolio. We use both the quasi-likelihood and the extended quasi-likelihood to estimate models for the smoothing and forecasting of mortality tables jointly with smooth estimates of the dispersion parameters. We present three main applications of our method: first, we show how taking account of dispersion reduces the volatility of a forecast of a mortality table; second, we smooth mortality data by amounts, ie, when deaths are amounts claimed and exposed-to-risk are sums assured; third, we present a joint model for mortality by lives and by amounts with the property that forecasts by lives and by amounts are consistent. Our methods are illustrated with data from the Continuous Mortality Investigation.
Yet More on a Stochastic Economic Model: Part 1: Updating and Refitting, 1995 to 2009
Authors: Wilkie A. D. , Şahin Şule , Cairns A. J. G. , Kleinow Torsten 
Published: January 2011

AbstractIn this paper we review the Wilkie asset model for a variety of UK economic indices, including the Retail Prices Index, both without and with an ARCH model, the wages index, share dividend yields, share dividends and share prices, long term bond yields, short term bond yields and index-linked bond yields, in each case by updating the parameters to June 2009. We discuss how the model has performed from 1994 to 2009 and estimate the values of the parameters and their confidence intervals over various sub-periods to study their stability. Our analysis shows that the residuals of many of the series are much fatter-tailed than in a normal distribution. We observe also that besides the stochastic uncertainty built into the model by the random innovations there is also parameter uncertainty arising from the estimated values of the parameters.
Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)
Authors: Yakimov Michail M , Cono Violetta La , Smedile Francesco , DeLuca Thomas H , Juárez Silvia , Ciordia Sergio , Fernández Marisol , Albar Juan Pablo , Ferrer Manuel , Golyshin Peter N , Giuliano Laura 
Published: January 2011

Abstract
Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and urease were identified and their affiliation demonstrated the presence of ‘deep-sea’ clades distinct from ‘shallow’ representatives. Measured deep-sea dark CO2 fixation estimates were comparable to the median value of photosynthetic biomass production calculated for this area of Tyrrhenian Sea, pointing to the significance of this process in the C cycle of aphotic marine ecosystems. To elucidate the pivotal organisms in this process, we targeted known marine crenarchaeal autotrophy-related genes, coding for acetyl-CoA carboxylase (accA) and 4-hydroxybutyryl-CoA dehydratase (4-hbd). As in case of nirK and ureC, these genes are grouped with deep-sea sequences being distantly related to those retrieved from the epipelagic zone. To pair the molecular data with specific functional attributes we performed [14C]HCO3 incorporation experiments followed by analyses of radiolabeled proteins using shotgun proteomics approach. More than 100 oligopeptides were attributed to 40 marine crenarchaeal-specific proteins that are involved in 10 different metabolic processes, including autotrophy. Obtained results provided a clear proof of chemolithoautotrophic physiology of bathypelagic crenarchaeota and indicated that this numerically predominant group of microorganisms facilitate a hitherto unrecognized sink for inorganic C of a global importance.
CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments
Authors: Yamada Lixy , Nomura Mamoru , Ogasawara Michio , Yaguchi Junko , Takahashi Hiroki , Konno Alu , Nakajima Ayako , Yasunori Sasakura , Yoshizawa Akiyasu , Endo Toshinori , Taniguchi Hisaaki , Ueno Keisuke , Yamasaki Chisato , Yonezawa Kouki , Sera Miho , Mineta Katsuhiko , Imanishi Tadashi , Inaba Kazuo , Hotta Kohji , Nakachi Mia , Satou Yutaka 
Published: January 2011

AbstractCIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics.
Development and comparison of ECC-rtPCR with in vivo method to determine the viability and infectivity of Giardial cysts
Authors: Ijaz M. Khalid , Alum Absar , Sbai Basel , Asaad Hamas , Rubino Joseph 
Published: January 2011

AbstractGlobally, Giardia is one of the major cause of diarrheal illnesses and rapid diagnostic methods differentiating infectious cysts are critical for developing intervention strategies through contaminated surfaces, food and water. This is currently hampered by lack of an in vitro model. We evaluated mRNA expression in trophozoites and their attachment to a CaCo2 (C2bb) cell monolayer and changes in trans-cellular resistance as an indicator of Giardia viability and infectivity. Heat shock mRNA in Giardia cysts and variant specific protein (VSP) mRNA in trophozoites were quantified by RT-PCR. When compared with neonatal mice infectivity, the attachment of trophozoites to cell monolayers, expression of VSP, and changes in the trans-cellular resistance, the infectivity directly correlated with infectivity in neonatal mice. This study highlights the use of a molecular method combined with electrophysiological analysis of cell culture (ECC-rtPCR) post-trophozoite’s attachment for assessing viability and infectivity of environmental isolates of Giardial cysts.
Prediction of a hexagonal SiO
2
phase affecting stabilities of MgSiO
3
and CaSiO
3
at multimegabar pressures
Authors: Tsuchiya Taku , Tsuchiya Jun 
Published: January 2011

Ultrahigh-pressure phase relationship of SiO
2
silica in multimegabar pressure condition is still quite unclear. Here, we report a theoretical prediction on a previously uncharacterized stable structure of silica with an unexpected hexagonal Fe
2
P-type form. This phase, more stable than the cotunnite-type structure, a previously postulated postpyrite phase, was discovered to stabilize at 640 GPa through a careful structure search by means of ab initio density functional computations over various structure models. This is the first evidential result of the pressure-induced phase transition to the Fe
2
P-type structure among all dioxide compounds. The crystal structure consists of closely packed, fairly regular SiO
9
tricapped trigonal prisms with a significantly compact lattice. Additional investigation further elucidates large effects of this phase change in SiO
2
on the stability of MgSiO
3
and CaSiO
3
at multimegabar pressures. A postperovskite phase of MgSiO
3
breaks down at 1.04 TPa along an assumed adiabat of super-Earths and yields Fe
2
P-type SiO
2
and CsCl (B2)-type MgO. CaSiO
3
perovskite, on the other hand, directly dissociates into SiO
2
and metallic CaO, skipping a postperovskite polymorph. Predicted ultrahigh-pressure and temperature phase diagrams of SiO
2
, MgSiO
3
, and CaSiO
3
indicate that the Fe
2
P-type SiO
2
could be one of the dominant components in the deep mantles of terrestrial exoplanets and the cores of gas giants.
Therapeutic enzyme deimmunization by combinatorial T-cell epitope removal using neutral drift
Authors: Cantor Jason R. , Yoo Tae Hyeon , Dixit Aakanksha , Iverson Brent L. , Forsthuber Thomas G. , Georgiou George 
Published: January 2011

A number of heterologous enzymes have been investigated for cancer treatment and other therapeutic applications; however, immunogenicity issues have limited their clinical utility. Here, a new approach has been created for heterologous enzyme deimmunization whereby combinatorial saturation mutagenesis is coupled with a screening strategy that capitalizes on the evolutionary biology concept of neutral drift, and combined with iterative computational prediction of T-cell epitopes to achieve extensive reengineering of a protein sequence for reduced MHC-II binding propensity without affecting catalytic and pharmacological properties.Escherichia coliL-asparaginase II (EcAII), the only nonhuman enzyme approved for repeated administration, is critical in treatment of childhood acute lymphoblastic leukemia (ALL), but elicits adverse antibody responses in a significant fraction of patients. The neutral drift screening of combinatorial saturation mutagenesis libraries at a total of 12 positions was used to isolate an EcAII variant containing eight amino acid substitutions within computationally predicted T-cell epitopes—of which four were nonconservative—while still exhibitingkcat/KM = 106 M-1 s-1for L-Asn hydrolysis. Further, immunization of HLA-transgenic mice expressing the ALL-associated DRB1*0401 allele with the engineered variant resulted in significantly reduced T-cell responses and a 10-fold reduction in anti-EcAII IgG titers relative to the existing therapeutic. This significant reduction in the immunogenicity of EcAII may be clinically relevant for ALL treatment and illustrates the potential of employing neutral drift screens to achieve large jumps in sequence space as may be required for the deimmunization of heterologous proteins.
Model selection in Bayesian segmentation of multiple DNA alignments
Authors: Oldmeadow Christopher , Keith Jonathan M. 
Published: January 2011

AbstractMotivation: The analysis of multiple sequence alignments is allowing researchers to glean valuable insights into evolution, as well as identify genomic regions that may be functional, or discover novel classes of functional elements. Understanding the distribution of conservation levels that constitutes the evolutionary landscape is crucial to distinguishing functional regions from non-functional. Recent evidence suggests that a binary classification of evolutionary rates is inappropriate for this purpose and finds only highly conserved functional elements. Given that the distribution of evolutionary rates is multi-modal, determining the number of modes is of paramount concern. Through simulation, we evaluate the performance of a number of information criterion approaches derived from MCMC simulations in determining the dimension of a model.Results: We utilize a deviance information criterion (DIC) approximation that is more robust than the approximations from other information criteria, and show our information criteria approximations do not produce superfluous modes when estimating conservation distributions under a variety of circumstances. We analyse the distribution of conservation for a multiple alignment comprising four primate species and mouse, and repeat this on two additional multiple alignments of similar species. We find evidence of six distinct classes of evolutionary rates that appear to be robust to the species used.Availability: Source code and data are available at http://dl.dropbox.com/u/477240/changept.zipContact: jonathan.keith@monash.edu; christopher.oldmeadow@newcastle.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
MBRole: enrichment analysis of metabolomic data
Authors: Chagoyen Monica , Pazos Florencio 
Published: January 2011

AbstractSummary: While many tools exist for performing enrichment analysis of transcriptomic and proteomic data in order to interpret them in biological terms, almost no equivalent tools exist for metabolomic data. We present Metabolite Biological Role (MBRole), a web server for carrying out over-representation analysis of biological and chemical annotations in arbitrary sets of metabolites (small chemical compounds) coming from metabolomic data of any organism or sample.Availability and Implementation: The web server is freely available at http://csbg.cnb.csic.es/mbrole. It was tested in the main web browsers.Contact: monica.chagoyen@cnb.csic.es
flowPhyto: enabling automated analysis of microscopic algae from continuous flow cytometric data
Authors: Ribalet Francois , Schruth David M. , Armbrust E. Virginia 
Published: January 2011

AbstractMotivation: Flow cytometry is a widely used technique among biologists to study the abundances of populations of microscopic algae living in aquatic environments. A new generation of high-frequency flow cytometers collects up to several hundred samples per day and can run continuously for several weeks. Automated computational methods are needed to analyze the different phytoplankton populations present in each sample. Software packages in the programming environment R provide powerful tools for conducting such analyses.Results: We introduce flowPhyto, an R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.Availability: Freely accessible at http://www.bioconductor.orgContact: armbrust@u.washington.edu