bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian EM algorithm for scoring polymorphic deletions from SNP data and application to a common CNV on 8q24
Authors: Zöllner Sebastian , Su Gang , Stewart William C. L. , Chen Yi , McInnis Melvin G , Burmeister Margit 
Published: December 2008

AbstractCopy number variations (CNVs) in the human genome provide exciting candidates for functional polymorphisms. Hence, we now assess association between CNV carrier status and diseases status by evaluating the signal intensity of SNP genotyping assays. Here, we present a novel statistical method designed to perform such inference and apply this method to a known CNV in a bipolar disorder linkage region. Using Bayesian computations we calculate the posterior probability for carrier status of a CNV in each individual of a sample by jointly analyzing genotype information and hybridization intensity. We model the signal intensity as a mixture of normal distributions, allowing for locus‐specific and allele‐specific distributions. Using an expectation maximization algorithm we estimate the parameters of these distributions and use these estimates for inferring carrier status of each individual and for the boundaries of the CNV. We applied the method to a sample of 3,512 individuals to a previously described common deletion on 8q24, a region consistently showing linkage to bipolar disorder, and unambiguously inferred 172 heterozygous and 1 homozygous deletion carrier. We observed no significant association between bipolar disorder and carrier status. We carefully assessed the validity of the inferred carrier status and observed no indication of errors. Furthermore, the algorithm precisely identifies the boundaries of the CNV. Finally, we assessed the power of this algorithm to detect shorter CNVs by sub‐sampling from the SNPs covered by this deletion, demonstrating that our EM algorithm produces precise estimates of carrier status.Genet. Epidemiol. 2009. © 2008 Wiley‐Liss, Inc.
Coupling between Marine Plankton and Freshwater Flow in the Plumes off a Small Estuary
Authors: Schlacher Thomas A. , Skillington Anna J. , Connolly Rod M. , Robinson Wayne , Gaston Troy F. 
Published: December 2008

AbstractFreshwater discharge from rivers is a powerful forcing agent in coastal ecosystems. It not only generates strong ecological effects in estuaries, but also drives the dynamics of nearshore marine waters where prominent river plumes form biogeochemical hot spots in coastal seas worldwide. Large plumes from major rivers exert important controls on pelagic processes. The majority of estuaries are smaller, however, and the importance of the smaller plumes they generate is unknown. We measured the degree of coupling between freshwater flow and inshore zooplankton in such a plume from a subtropical estuary on the east coast of Australia. Flow regimes encompassed long periods of low freshwater input, punctuated by pulsed freshets that initiated the formation of buoyant, lower‐salinity plumes in the nearshore marine zone. Plumes stimulated phytoplankton biomass in the receiving waters, and ultimately changes in zooplankton assemblages. Zooplankton responded strongly to river discharge: (1) in the absence of substantial freshwater flows and plumes, zooplankton was broadly similar in density and biomass across the estuarine‐marine gradient; (2) freshets that generated significant plumes strongly modified hydrological conditions and lowered zooplankton in the estuarine and nearshore waters, and (3) after the initial freshet, zooplankton in the residual plume was at a higher density in nearshore than shelf waters. We demonstrate that coupling between riverine and coastal pelagic systems operates in small plumes, but that there is substantial temporal variance linked to fluctuations in freshwater delivery. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Comparative study of biphasic calcium phosphates with different HA/TCP ratios in mandibular bone defects. A long‐term histomorphometric study in minipigs
Authors: Jensen Simon Storgård , Bornstein Michael M. , Dard Michel , Bosshardt Dieter D. , Buser Daniel 
Published: December 2008

AbstractThree biphasic calcium phosphate (BCP) bone substitute materials with hydroxyapatite (HA)/tricalcium phosphate (TCP) ratios of 20/80, 60/40, and 80/20 were compared to coagulum, particulated autogenous bone, and deproteinized bovine bone mineral (DBBM) in membrane‐protected bone defects. The defects were prepared in the mandibles of 24 minipigs that were divided into four groups of six with healing times of 4, 13, 26, and 52 weeks, respectively. The histologic and histomorphometric evaluation focused on differences in amount and pattern of bone formation, filler degradation, and the interface between bone and filler. Collapse of the expanded polytetrafluoroethylene barrier membrane into the coagulum defects underlined the necessity of a filler material to maintain the augmented volume. Quantitatively, BCP 20/80 showed bone formation and degradation of the filler material similar to autografts, whereas BCP 60/40 and BCP 80/20 rather equaled DBBM. Among the three BCP's, the amount of bone formation and degradation of filler material seemed to be inversely proportional to the HA/TCP ratio. The fraction of filler surface covered with bone was highest for autografts at all time points and was higher for DBBM than BCP 80/20 and 60/40 at the early healing phase. TRAP‐positive multinucleated cells were identified on BCP and DBBM surfaces without showing typical signs of resorption lacunae. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
Dynamic in vitro dehydration patterns of unworn and worn silicone hydrogel contact lenses
Authors: González‐Méijome J. M. , López‐Alemany A. , Almeida J. B. , Parafita M. A. 
Published: December 2008

AbstractPurpose: To evaluate the effect of wear on dynamic in vitro dehydration of silicone hydrogel (Si‐Hi) contact lens (CL) using a previously described gravimetric procedure. Methods: Five different silicone hydrogel (Si‐Hi) contact lenses (CL) were evaluated after being worn by patients under daily wear conditions for 15 days to 1 month. Lenses were conditioned and disinfected with a multipurpose solution after each day of wear. Lenses were left to dehydrate in an analytical balance under controlled conditions of temperature and relative humidity and the results compared with data from new lens samples of the same power and material. Several quantitative parameters were obtained and compared between worn and unworn samples. Results: The quantitative parameters derived from the dehydration curves showed statistically significant differences between worn and unworn lenses regarding the initial dehydration rate and ability to maintain their original hydration. Worn lenses showed shorter phase I duration (decreased by 30 to 60% compared to unworn samples), a significantly faster initial dehydration rate (increased by about 1%/minute), and lower water retention index (decreased by 10 to 20%) as derived from the initial cumulative dehydration. All the differences were statistically significant for all lenses (p < 0.05). Conclusion: The initial dehydration rates were significantly increased in all CL after wear. This could be of clinical interest because it represents the average initial dehydration rates during the first moments when the lens is left to dehydrate after a blink. This study suggests that even after the lenses had been equilibrated in saline solution for several days, the materials lose their ability to retain water. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
Crystallinity control of apatite through Ca‐EDTA complexes and porous composites with PLGA
Authors: Mochizuki Chihiro , Sasaki Yuji , Hara Hiroki , Sato Mitsunobu , Hayakawa Tohru , Yang Fei , Hu Xixue , Shen Hong , Wang Shenguo 
Published: December 2008

AbstractApatite compounds with different levels of crystallinity were prepared using Ca‐EDTA complexes. Ca‐deficient hydroxyapatite (CDHA) with low crystallinity was synthesized by ultrasonic stirring of a mixture of Ca‐EDTA complex, phosphoric acid, and ammonium hydroxide in hydrogen peroxide aqueous solution. Mixtures of carbonate hydroxyapatite (HA) and CDHA with higher crystallinity were also prepared from a solution involving the same complex. The porous composites with lower or higher crystallinity apatite with a copolymer of poly(L‐lactide‐co‐glycilide)(70/30) (PLGA(70/30)) were fabricated by a solution‐casting/particles leaching method. The apatites and porous composites were characterized, and it was found that the degradation of composites of apatite with a low level of crystallinity was fastest in phosphate‐bufferd saline (PBS) solution compared with other apatite composites with higher levels of crystallinity; however, the rate was smaller than that of PLGA alone. Plasma treatment influenced the degradation of composites in PBS and apatite precipitation in simulated body fluid (SBF). Hydroxyapatite deposition on the PLGA composite with the low crystallinity occurred six times faster than that on PLGA alone after immersion in SBF. The incorporation of apatite into the PLGA matrix did not cause any adverse effects on cell attachment in an assay employing human gingival fibroblasts. This study suggested that the current apatite and PLGA porous composite will be a promising scaffold material for tissue engineering. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2009
Odontoblasts in the dental pulp immune response
Authors: Farges Jean‐Christophe , Keller Jean‐François , Carrouel Florence , Durand Stephanie H. , Romeas Annick , Bleicher Françoise , Lebecque Serge , Staquet Marie‐Jeanne 
Published: December 2008

AbstractRecent studies have demonstrated that human dental pulp cells sense pathogens and elicit innate and/or adaptive immunity. Particular attention has been paid to odontoblasts that are situated at the pulp–dentin interface and constitute the first line of defense to cariogenic bacteria entering dentin after enamel disruption. In this review, recent in vitro and in vivo data suggesting that odontoblasts initiate immune/inflammatory events within the dental pulp in response to cariogenic bacteria are discussed. These data include sensing of pathogens by Toll‐like receptors (TLRs), production of chemokines upon cell stimulation with microbial by‐products and induction of dendritic cell migration. Additional results presented here reveal that all TLR genes are expressed in the healthy human dental pulp that is thus well equipped to combat pathogens entering the tissue. Seventeen chemokine genes including CXCL12, CCL2, CXCL9, CX3CL1, CCL8, CXCL10, CCL16, CCL5, CXCL2, CCL4, CXCL11 and CCL3, and 9 chemokine receptor genes including CXCR4, CCR1, CCR5, CX3CR1, CCR10 and CXCR3, are also expressed in pulp. TLR2, CCL2 and CXCL1 are upregulated in odontoblasts both under caries lesions and upon stimulation with pathogen by‐products. These molecules thus appear as preferential targets for the design of therapeutic agents able to reduce the immune/inflammatory response to cariogenic bacteria and favor pulp healing. J. Exp. Zool. (Mol. Dev. Evol.) 312B:425–436, 2009. © 2008 Wiley‐Liss, Inc.
Sensitivity analysis of snow patterns in Swiss ski resorts to shifts in temperature, precipitation and humidity under conditions of climate change
Authors: Uhlmann Bastienne , Goyette Stéphane , Beniston Martin 
Published: December 2008

AbstractThe value of snow as a resource has considerably increased in Swiss mountain regions, in particular in the context of winter tourism. In the perspective of a warming climate, it is thus important to quantify the potential changes in snow amount and duration that could have large repercussions on the economy of ski resorts. Because of the fine spatial variability of snow, the use of a Surface Energy Balance Model (SEBM) is adequate to simulate local snow cover evolution. A perturbation method has been developed to generate plausible future meteorological input data required for SEBM simulations in order to assess the changes in snow cover patterns. Current and future snow depths have also been simulated within the ski areas themselves. The results show a large decrease of the snow depths and duration, even at high elevation in a warmer climate and emphasize the sensitivity of snow to topographical characteristics of the resorts. The most vulnerable areas would be the Western regions of Switzerland or the Eastern Prealps whereas the Central Alps or Valais would be less affected. The study highlights the fact that not only the altitude of a domain but also its exposure, localization inland and slope gradients need to be taken into account when evaluating current and future snow depths. This method enables a precise assessment of the snow pattern over a small area. Copyright © 2008 Royal Meteorological Society
An analysis of the seasonal precipitation forecasts in South America using wavelets
Authors: Pezzi Luciano Ponzi , Kayano Mary Toshie 
Published: December 2008

AbstractA post‐processing technique was applied to statistically correct the seasonal rainfall forecasts over South America (SA). The aim of this work was to reduce errors in the seasonal climate simulations obtained from the Centro de Previsão de Tempo e Estudos Climáticos (CPTEC) atmospheric general circulation model (AGCM) which was run with different deep cumulus convection parameterizations. One of the main contributions of this study is the discussion of the super‐ensemble approach to reduce errors in the seasonal rainfall prediction for SA. A novel aspect here is the use of the wavelet technique to compare forecast and observed time series by investigating their time‐frequency structures. This methodology has not yet been applied to super‐ensemble model validations. The statistical algorithm used in the super‐ensemble technique was based on the linear multiple regression method. The time series of the super‐ensemble forecast (FCT), arithmetic averaged forecast (MEM) and individual model forecasts and the observed (OBS) ones for selected areas of SA were compared by calculating the root mean square errors (RMSEs) and by applying the wavelet technique on these time series. In general, for the analysed areas we obtained a super‐ensemble skill superior to that for the MEM. The wavelet analysis proved to be very useful to compare forecast and observed time series. In fact, differences and similarities among the time series such as the dominant scale of variability and the time location of the largest variances in the time series were detected with the wavelet analyses. Copyright © 2008 Royal Meteorological Society
Kinetic study of transesterification of methyl acetate with n‐butanol catalyzed by NKC‐9
Authors: Xu Baoyun , Zhang Weijiang , Zhang Xuemei , Zhou Cuifang 
Published: December 2008

AbstractThe transesterification of methyl acetate and n‐butanol catalyzed by cation‐exchange resin, NKC‐9, was studied in this work to obtain the reaction kinetics. The experiments were carried out in a stirred batch reactor at different temperatures (328.15, 333.15, 338.15, 343.15, 345.15 K) under atmospheric pressure. The effects of temperature, molar ratio of reactants, and catalyst loading on the reaction rate were researched under the condition of eliminating the effect of diffusion. The experimental data were correlated with a kinetic model based on the pseudo‐homogeneous catalysis. The kinetic equation describing the reaction catalyzed by NKC‐9 was developed. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 41: 101–106, 2009
Thermochemistry of chlorine‐containing hydrocarbons related to waste combustion
Authors: Burcat Alexander , Khachatryan Lavrent , Dellinger Barry 
Published: December 2008

AbstractThe thermochemistry of 25 chlorinated compounds potentially involved in chemical reactions related to waste combustion has been calculated using ab initio methods. Some of these species have never been reported in the literature. To check the validity of our calculations, 11 additional brominated analogues were also calculated. The thermochemical properties of these compounds were used in reaction kinetic models designed to estimate the performance of waste incinerators. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 41: 113–122, 2009
Thermodynamics and kinetics of indole oligomerization: Preliminary results in aqueous sulfuric acid
Authors: Quartarone G. , Ronchin L. , Tortato C. , Vavasori A. 
Published: December 2008

AbstractReaction rates and equilibrium constants of indole dimerization and trimerization in aqueous sulfuric acid at 298 K are reported. The equilibrium of oligomerization is attained in about 4–5 h, and formation of oligomers with more than three monomeric unit is not observed. The equilibrium of formation of the indole dimer is influenced by the protonation equilibrium of indole, which means the pKIH values of indole strongly influences equilibria and kinetics of the whole process. In the evaluation of the kinetic constants, the pKIH values of indole have been taken into account; in this way, the kinetic constant of formation of the dimer (kD) results almost four order of magnitude larger than that of the trimer (kT), suggesting a higher electrophilicity of the 3H‐indolium cations with respect to the protonated dimer (which is an aliphatic ammonium salt). Further indole addition to the trimer, which is a protonated 2‐alkyl‐aniline, does not occur, since the anilinium ion is ineffective as an electrophile. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 41: 107–112, 2009
Kinetics and mechanism of the reactions of n‐butanal and n‐pentanal with chlorine atoms
Authors: Singh Sukhdip , Hernandez Samuel , Ibarra Yesenia , Hasson Alam S. 
Published: December 2008

AbstractThe kinetics and mechanism of the reaction of chlorine atoms with n‐butanal and n‐pentanal have been investigated in a 142‐L reaction cell coupled to a Fourier transform infrared (FTIR) spectrometer at 298 ± 2 K and at 800 ± 3 Torr. The rate coefficients for Cl + n‐butanal and Cl + n‐pentanal were measured using the relative rate technique with isopropanol and ethene as the reference compounds. The yield of acyl radicals was determined by measuring yields of acid chloride and carbon monoxide products from the reaction of Cl + aldehyde in the absence of oxygen. The rate coefficients for Cl + n‐butanal and Cl + n‐pentanal are (1.63 ± 0.59) × 10−10 cm3 molecule−1 s− 1 and (2.37 ± 0.82) × 10−10 cm3 molecule−1 s−1, respectively. The yields of acyl radicals from the reactions are 0.66 ± 0.04 for n‐butanal and 0.45 ± 0.04 for n‐pentanal. Under ambient conditions, the acyl radicals generated will react almost exclusively with oxygen. Mechanistic implications of these measurements are discussed. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 41: 133–141, 2009
Parental leave policies and parents' employment and leave‐taking
Authors: Han Wen‐Jui , Ruhm Christopher , Waldfogel Jane 
Published: December 2008

AbstractWe describe trends in maternal employment and leave‐taking after birth of a newborn and analyze the extent to which these behaviors are influenced by parental leave policies. Data are from the June Current Population Survey (CPS) Fertility Supplements, merged with other months of the CPS, and cover the period 1987 to 1994. This time span is one during which parental leave legislation expanded at both the state and federal level. We also provide the first comprehensive examination of employment and leave‐taking by fathers of infants. Our main finding is that leave expansions are associated with increased leave‐taking by both mothers and fathers. The magnitudes of the changes are small in absolute terms but large relative to the baseline for men and much greater for college‐educated or married mothers than for their less‐educated or single counterparts. © 2009 by the Association for Public Policy Analysis and Management
Using private demand studies to calculate socially optimal vaccine subsidies in developing countries
Authors: Cook Joseph , Jeuland Marc , Maskery Brian , Lauria Donald , Sur Dipika , Clemens John , Whittington Dale 
Published: December 2008

AbstractAlthough it is well known that vaccines against many infectious diseases confer positive economic externalities via indirect protection, analysts have typically ignored possible herd protection effects in policy analyses of vaccination programs. Despite a growing literature on the economic theory of vaccine externalities and several innovative mathematical modeling approaches, there have been almost no empirical applications.The first objective of the paper is to develop a transparent, accessible economic framework for assessing the private and social economic benefits of vaccination. We also describe how stated preference studies (for example, contingent valuation and choice modeling) can be useful sources of economic data for this analytic framework. We demonstrate socially optimal policies using a graphical approach, starting with a standard textbook depiction of Pigouvian subsidies applied to herd protection from vaccination programs. We also describe nonstandard depictions that highlight some counterintuitive implications of herd protection that we feel are not commonly understood in the applied policy literature.We illustrate the approach using economic and epidemiological data from two neighborhoods in Kolkata, India. We use recently published epidemiological data on the indirect effects of cholera vaccination in Matlab, Bangladesh (Ali et al., 2005) for fitting a simple mathematical model of how protection changes with vaccine coverage. We use new data on costs and private demand for cholera vaccines in Kolkata, India, and approximate the optimal Pigouvian subsidy. We find that if the optimal subsidy is unknown, selling vaccines at full marginal cost may, under some circumstances, be a preferable second‐best option to providing them for free. © 2009 by the Association for Public Policy Analysis and Management.
The effects of NBPTS‐certified teachers on student achievement
Authors: Harris Douglas N. , Sass Tim R. 
Published: December 2008

AbstractIn this study, we consider the efficacy of a relatively new and widely accepted certification system for teachers established by the National Board for Professional Teaching Standards (NBPTS). We utilize an extensive database covering the universe of teachers and students in Florida for a four‐year span to determine the relationship between NBPTS certification and the impact of teachers on student test scores from both low‐stakes and high‐stakes exams. Contrary to some previous studies, we find evidence that NBPTS certification provides a positive signal of a teacher's contribution to student achievement only in a few isolated cases. However, our results do reinforce evidence from previous research that the process of becoming NBPTS certified does not increase teacher productivity. © 2009 by the Association for Public Policy Analysis and Management.