bluuebunny/crossref_metadata_2025_split huggingface dataset:
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
Authors: Li Yun , Willer Cristen J. , Ding Jun , Scheet Paul , Abecasis Gonçalo R. 
Published: November 2010

AbstractGenome‐wide association studies (GWAS) can identify common alleles that contribute to complex disease susceptibility. Despite the large number of SNPs assessed in each study, the effects of most common SNPs must be evaluated indirectly using either genotyped markers or haplotypes thereof as proxies. We have previously implemented a computationally efficient Markov Chain framework for genotype imputation and haplotyping in the freely available MaCH software package. The approach describes sampled chromosomes as mosaics of each other and uses available genotype and shotgun sequence data to estimate unobserved genotypes and haplotypes, together with useful measures of the quality of these estimates. Our approach is already widely used to facilitate comparison of results across studies as well as meta‐analyses of GWAS. Here, we use simulations and experimental genotypes to evaluate its accuracy and utility, considering choices of genotyping panels, reference panel configurations, and designs where genotyping is replaced with shotgun sequencing. Importantly, we show that genotype imputation not only facilitates cross study analyses but also increases power of genetic association studies. We show that genotype imputation of common variants using HapMap haplotypes as a reference is very accurate using either genome‐wide SNP data or smaller amounts of data typical in fine‐mapping studies. Furthermore, we show the approach is applicable in a variety of populations. Finally, we illustrate how association analyses of unobserved variants will benefit from ongoing advances such as larger HapMap reference panels and whole genome shotgun sequencing technologies.Genet. Epidemiol. 34: 816‐834, 2010. © 2010 Wiley‐Liss, Inc.
Three‐dimensional modeling of problems in poro‐elasticity via a mixed least‐squares method using linear tetrahedral elements
Authors: Tchonkova Maria , Peters John , Sture Stein 
Published: November 2010

AbstractIn a previous publication we developed a new mixed least‐squares method for poro‐elasticity. The approximate solution was obtained via a minimization of a least‐squares functional, based upon the equations of equilibrium, the equations of continuity and weak forms of the constitutive relationships for elasticity and Darcy flow. The formulation involved four independent types of variables: displacements, stresses, pore pressures and velocities. All of them were approximated by linear continuous triangles. Encouraged by the computational results, obtained from the two‐dimensional implementation of the method, we extended our formulation to three dimensions. In this paper we present numerical examples for the performance of continuous linear tetrahedra within the context of the mixed least‐squares method. The initial results suggest that the method works well in the nearly and entirely incompressible limits for elasticity. For poro‐elasticity, the obtained pore pressures are stable without exhibiting the oscillations, which are observed when the standard Galerkin formulation is used. Copyright © 2010 John Wiley & Sons, Ltd.
Rhabdoid tumors of the liver: Rare, aggressive, and poorly responsive to standard cytotoxic chemotherapy
Authors: Trobaugh‐Lotrario Angela D. , Finegold Milton J. , Feusner James H. 
Published: November 2010

AbstractBackgroundRhabdoid tumors of the liver are rare tumors that are difficult to cure. We compiled all the cases previously reported in the literature to review clinical data, treatments, and outcomes.ProcedurePatients were identified by literature review using PubMed.ResultsThirty‐four patients were identified. The median age at presentation was 8 months. All patients with reported AFP results exhibited normal or minimally increased serum AFP levels. All 10 tumors with reported INI1 immunohistochemistry results were reported as negative. Twenty‐one patients presented with metastatic disease at diagnosis. Thirty patients died of disease or treatment complications. Most deaths occurred within 12 months after diagnosis. Five patients survived at the time of the reports with one patient alive with disease. One patient relapsed and subsequently died after the report was published. Of the four patients alive without disease, all were treated with chemotherapy, and at least three had surgery or transplantation. Two patients received radiation therapy but did not survive.ConclusionsRhabdoid tumors of the liver are aggressive, rare tumors of the infant liver that are often associated with metastases at the time of diagnosis. Mortality is high and often occurs soon after diagnosis. Treatment with aggressive chemotherapy in combination (especially an alkylating agents doxorubicin) with complete resection may lead to improved outcomes. Therapy targeted to the INI1 mutation of these tumors is currently being investigated and may offer greater hope of cure. Pediatr Blood Cancer 2011; 57: 423–428. © 2010 Wiley‐Liss, Inc.
Chlamydia pneumoniae infection‐related hemophagocytic lymphohistiocytosis and acute encephalitis and poliomyelitis‐like flaccid paralysis
Authors: Yagi Kanae , Kano Gen , Shibata Mayumi , Sakamoto Izumi , Matsui Hirofumi , Imashuku Shinsaku 
Published: November 2010

AbstractA 3‐year‐old male presented with Chlamydia pneumoniae infection‐related hemophagocytic lymphohistiocytosis (HLH). The patient developed an episode of HLH with severe skin eruption following C. pneumoniae pneumonia. Symptoms responded to steroid/cyclosporine A therapy, but the patient slowly lost consciousness and developed systemic flaccid paralysis. He was diagnosed with encephalitis/myelitis by brain and spinal MRI. Neurological symptoms and signs gradually resolved. We thought that the immune response to C. pneumoniae infection triggered the development of HLH, associated with unusual neurological complications. This report describes a novel case of C. pneumoniae‐associated HLH and with poliomyelitis like flaccid paralysis. Pediatr Blood Cancer 2011;56:853–855. © 2010 Wiley‐Liss, Inc.
New amoxicillin–poly(lactic acid)‐based conjugates: synthesis and in vitro release of amoxicillin
Authors: Den Berghe Hélène Van , Garric Xavier , Vert Michel , Coudane Jean 
Published: November 2010

AbstractLong‐term antibiotic treatments are required to cure many diseases. Coupling a bioactive compound to a biocompatible polymer offers, in general, many advantages such as better stabilization of drug and controlled release. The work reported deals with the synthesis of new conjugates based on amoxicillin and oligomers of biocompatible and biodegradable poly(lactic acid), as well as release studies of amoxicillin. These new conjugates were obtained via a Curtius rearrangement or acyl chloride activation, leading to substituted urea or amide bonds between amoxicillin and polymer, respectively. Structures of the conjugates were assessed using Fourier transform infrared and 1H NMR spectroscopy, double‐detection size exclusion chromatography and electrospray ionization mass spectrometry. In vitro release profiles of amoxicillin in phosphate buffered saline were determined using high‐performance liquid chromatography, and the release rates of amoxicillin from the two conjugates were compared. Copyright © 2010 Society of Chemical Industry
Highly Insensitive/Reactive Thermite Prepared from Cr2O3 Nanoparticles
Authors: Gibot Pierre , Comet Marc , Eichhorn Alfred , Schnell Fabien , Muller Olivier , Ciszek Fabrice , Boehrer Yannick , Spitzer Denis 
Published: November 2010

AbstractThermites prepared from nanoparticles are currently the subject of growing interest due to their increased performances compared to classical micrometer‐sized thermites. Here, we studied the combustion behavior of energetic composite composed of Al and chromium (III) oxide (Cr2O3) as function of the oxide particle size. Homogeneous composites were prepared by mixing Al nanoparticles (Φ≈50 nm) with Cr2O3 micro‐ and nanoparticles (Φ≈20 nm), respectively, in hexane solution. The dried Cr2O3/Al composite powders were ignited by using a CO2 laser beam. The use of nanosized Cr2O3 particles incontestably improves the energetic performances of the Al/Cr2O3 thermite since the ignition delay time was shortened by a factor 3.5 (16±2 vs 54±4 ms) and the combustion rate (340±10 mm s−1) was significantly accelerated in contrast to those reported until now. Interestingly, the sensitivity to friction of the Al‐based thermites formulated from Cr2O3 is two orders of magnitude lower than the thermite prepared from other metal oxide nanoparticles (MnO2, WO3). Finally, our study shows that the decrease of Cr2O3 particle size has an interesting and beneficial effect on the energetic properties of Cr2O3/Al thermites and appears as an alternative to tune the properties of these energetic materials.
Fabrication and charge‐transfer characteristics of CdS QDs sensitized vertically grown flower‐like ZnO solar cells with CdSe cosensitizers
Authors: Sudhagar P. , Chandramohan S. , Kumar R. Saravana , Sathyamoorthy R. , Hong Chang‐Hee , Kang Yong Soo 
Published: November 2010

AbstractThis paper proposes the concept of using bisensitizers (CdS and CdSe) to improve the light‐harvesting capabilities and charge transfer in ZnO photoelectrodes. The novel flower‐like ZnO nanoarrays were grown by chemical bath deposition and they are sensitized with CdS quantum dots (QDs) and a CdSe overlayer. We observed a strong quenching of band‐edge emission following the growth of QDs on ZnO, which is evidence for the occurrence of charge transfer between the QDs and the ZnO. A possible charge‐transfer mechanism is proposed and discussed on the basis of energy‐band alignment. Bisensitized ZnO electrodes resulted in a higher photoconversion efficiency (η = 1.08%) than that of single CdS QD‐sensitized solar cells (η = 0.52%). The high photocurrent and improved power conversion are attributed to more charge‐carrier generation facilitated by an extended spectral response and charge injection between the QDs and TiO2. magnified image
Schematic representation of CdS and CdSe bisensitized flower‐like ZnO solar cell structure investigated in this study.
Synthesis, characterization, and optical properties of Mg‐doped zinc oxide single‐crystal microprisms
Authors: Li Junlin , Zhuang Huizhao , Wang Jie , Xu Peng 
Published: November 2010

AbstractNovel zinc oxide (ZnO) microprisms doped with Mg have been synthesized on Mg (NO3)2‐coated Si (111) substrates successfully by a thermal chemical vapor deposition method. The as‐prepared Mg‐doped zinc oxide single‐crystal microprisms were characterized with X‐ray diffraction (XRD), scanning electron microscopy (SEM), high‐resolution transmission electron microscopy (HRTEM), and photoluminescence (PL). The results show that the microstructures consist of hexagonal pyramids tips and hexagonal prisms. The whole structure is a perfect single crystal and has preferred growth along the [0001] direction. PL reveals ultraviolet (UV) emission at 388 nm and a strong green light emission peak at 500 nm. Mg‐doped microprisms will provide an improvement for novel electronic and optical devices. In addition, the growth mechanism of the special Mg‐doped ZnO microstructure is proposed based on a solid–vapor approach.
Trajectory optimization of a mining dragline using the method of Lagrange multipliers
Authors: McInnes C. H. , Meehan P. A. 
Published: November 2010

AbstractThe nonlinear coupled dynamic behaviour of a mining dragline is optimized to increase productivity and reduce metal fatigue on the boom. Draglines are very large crane‐like robots used in open cut mining, primarily for the removal of overburden that covers a coal seam. The dynamic behaviour of the machine is a key determinant of productivity and fatigue‐based maintenance. The Newton–Lagrange method is applied to a field‐validated model to optimize slew torque under nonlinear constraints. Two scenarios are analysed: the minimization of cycle time with a time penalty for duty (estimated fatigue damage) and fixed rope lengths, and the minimization of duty under a fixed cycle time and measured rope lengths. The results from the second scenario compare favourably with earlier efforts to optimize slew torque using intuitive manual techniques. In particular, the numerical optimization procedure achieved a 50–60% reduction in duty, improving upon manual optimization results by 10–30%. Techniques are presented for solving convergence issues related to the high degree of nonlinearity of the model and constraints, actuator limitations and noise introduced by measured data. Copyright © 2010 John Wiley & Sons, Ltd.
Close target reconnaissance with guaranteed collision avoidance
Authors: Shames Iman , Fidan Barış , Anderson Brian D. O. 
Published: November 2010

AbstractThis manuscript considers the problem of close target reconnaissance by a group of autonomous agents. The overall close target reconnaissance (CTR) involves subtasks of avoiding inter‐agent collisions, reaching a close vicinity of a specific target position, and forming an equilateral polygon formation around the target. The agents performing the task fly at a constant speed to mimic the velocity behavior of small fixed‐wing unmanned aerial vehicles (UAV). A decentralized control scheme is developed for this overall task and the finite‐time convergence of the system under the proposed control law is established. Furthermore, it is guaranteed that no collision occurs among the agent. The relevant analysis and simulation test results are provided. Copyright © 2010 John Wiley & Sons, Ltd.
Behaviour of two small pelagic and demersal fish species in diverse hydraulic environments
Authors: Kilsby Nadine N. , Walker Keith F. 
Published: November 2010

ABSTRACTIncreased hydraulic diversity could be a means to promote fish diversity in rivers, but little is known of the behaviour of fish in hydraulic environments. This study concerns the behaviour of two species of small native Australian freshwater fish in variable hydraulic environments and ecological habit, with regard for (a) whether the apparent differences in swimming ability are reflected in the behaviour of the species and (b) the influence of changing hydraulic conditions on their patterns of use. An artificial channel was constructed with three levels of discharge, and fish were allowed to swim freely for 3 h without human interference. Their movements and habitat choices reflected their swimming ability and ecological habit, in that the stronger swimming, pelagic common galaxias (Galaxias maculatus) spent most time cruising in the open channel, preferring the turbulent inflow, and the demersal flat‐headed gudgeon (Philypnodon grandiceps) remained in the shelter of boulders. In effect, the galaxias changed their behaviour with changes in hydraulic conditions, while the gudgeons continued to use their preferred habitat. This study, therefore, provides support for the use of hydraulic diversity as a tool to foster fish diversity. Copyright © 2010 John Wiley & Sons, Ltd.
Dependent random choice
Authors: Fox Jacob , Sudakov Benny 
Published: November 2010

AbstractWe describe a simple and yet surprisingly powerful probabilistic technique which shows how to find in a dense graph a large subset of vertices in which all (or almost all) small subsets have many common neighbors. Recently this technique has had several striking applications to Extremal Graph Theory, Ramsey Theory, Additive Combinatorics, and Combinatorial Geometry. In this survey we discuss some of them. © 2010 Wiley Periodicals, Inc. Random Struct. Alg., 2011
Extensions of net reclassification improvement calculations to measure usefulness of new biomarkers
Authors: Pencina Michael J. , D'Agostino Ralph B. , Steyerberg Ewout W. 
Published: November 2010

AbstractAppropriate quantification of added usefulness offered by new markers included in risk prediction algorithms is a problem of active research and debate. Standard methods, including statistical significance and c statistic are useful but not sufficient. Net reclassification improvement (NRI) offers a simple intuitive way of quantifying improvement offered by new markers and has been gaining popularity among researchers. However, several aspects of the NRI have not been studied in sufficient detail.In this paper we propose a prospective formulation for the NRI which offers immediate application to survival and competing risk data as well as allows for easy weighting with observed or perceived costs. We address the issue of the number and choice of categories and their impact on NRI. We contrast category‐based NRI with one which is category‐free and conclude that NRIs cannot be compared across studies unless they are defined in the same manner. We discuss the impact of differing event rates when models are applied to different samples or definitions of events and durations of follow‐up vary between studies. We also show how NRI can be applied to case–control data. The concepts presented in the paper are illustrated in a Framingham Heart Study example.In conclusion, NRI can be readily calculated for survival, competing risk, and case–control data, is more objective and comparable across studies using the category‐free version, and can include relative costs for classifications. We recommend that researchers clearly define and justify the choices they make when choosing NRI for their application. Copyright © 2010 John Wiley & Sons, Ltd.
Analysis of multilevel grouped survival data with time‐varying regression coefficients
Authors: Wong May C. M. , Lam K. F. , Lo Edward C. M. 
Published: November 2010

AbstractCorrelated or multilevel grouped survival data are common in medical and dental research. Two common approaches to analyze such data are the marginal and the random‐effects approaches. Models and methods in the literature generally assume that the treatment effect is constant over time. A researcher may be interested in studying whether the treatment effects in a clinical trial vary over time, say fade out gradually. This is of particular clinical value when studying the long‐term effect of a treatment. This paper proposed to extend the random effects grouped proportional hazards models by incorporating the possibly time‐varying covariate effects into the model in terms of a state‐space formulation. The proposed model is very flexible and the estimation can be performed using the MCMC approach with non‐informative priors in the Bayesian framework. The method is applied to a data set from a prospective clinical trial investigating the effectiveness of silver diamine fluoride (SDF) and sodium fluoride (NaF) varnish in arresting active dentin caries in the Chinese preschool children. It is shown that the treatment groups with caries removal prior to the topical fluoride applications are most effective in shortening the arrest times in the first 6‐month interval, but their effects fade out rapidly since then. The effects of treatment groups without caries removal prior to topical fluoride application drop at a very slow rate and can be considered as more or less constant over time. The applications of SDF solution is found to be more effective than the applications of NaF vanish. Copyright © 2010 John Wiley & Sons, Ltd.
Joint modeling of survival time and longitudinal data with subject‐specific changepoints in the covariates
Authors: Tapsoba Jean de Dieu , Lee Shen‐Ming , Wang C. Y. 
Published: November 2010

AbstractJoint models are frequently used in survival analysis to assess the relationship between time‐to‐event data and time‐dependent covariates, which are measured longitudinally but often with errors. Routinely, a linear mixed‐effects model is used to describe the longitudinal data process, while the survival times are assumed to follow the proportional hazards model. However, in some practical situations, individual covariate profiles may contain changepoints. In this article, we assume a two‐phase polynomial random effects with subject‐specific changepoint model for the longitudinal data process and the proportional hazards model for the survival times. Our main interest is in the estimation of the parameter in the hazards model. We incorporate a smooth transition function into the changepoint model for the longitudinal data and develop the corrected score and conditional score estimators, which do not require any assumption regarding the underlying distribution of the random effects or that of the changepoints. The estimators are shown to be asymptotically equivalent and their finite‐sample performance is examined via simulations. The methods are applied to AIDS clinical trial data. Copyright © 2010 John Wiley & Sons, Ltd.
Comparison of the morphological, crystalline, and thermal properties of different crystalline types of starches after acid hydrolysis
Authors: Xia Li , Wenyuan Gao , Juan Wang , Qianqian Jiang , Luqi Huang 
Published: November 2010

AbstractA‐type maize starch, B‐type Fritillaria ussurensis, and C‐type Rhizoma dioscorea starches were hydrolyzed (32 days) with 2.2 N HCl. Regardless of the crystallinity level, starch with predominant B‐crystalline type was less susceptible to acid degradation than A‐type and C‐type starches, and initial rates of hydrolysis in B‐type was lower than others. The SEM and XRD results revealed that different types of starch displayed different hydrolysis mechanisms. The acid corrosion started from the exterior surface of A‐type and B‐type starches followed by the core of granules. However, the hydrogen ions primarily attacked the interior of the C‐type R. dioscorea starch granules and then the exterior. FT‐IR results confirmed that the amorphous regions in the starch granules were hydrolysed first. After 8–32 days of hydrolysis, the acid‐modified C‐type starch showed typical A‐type characteristics upon analysis of the XRD pattern. The average particle size of hydrolytic starch decreased with increasing hydrolysis time. The thermal results revealed that the hydrolytic starch showed lower ΔH than the native starch, while displaying higher peak width (Tc − To) value.
Riluzole pharmacokinetics in young patients with spinal muscular atrophy
Authors: Abbara Chadi , Estournet Brigitte , Lacomblez Lucette , Lelièvre Benedicte , Ouslimani Amal , Lehmann Blandine , Viollet Louis , Barois Annie , Diquet Bertrand 
Published: November 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• Spinal muscular atrophy (SMA) is a neuromuscular disorder of childhood.• Riluzole is an anti‐excitatory agent recommended for the treatment of amyotrophic lateral sclerosis (ALS).• Riluzole pharmacokinetics are well documented in patients with ALS.WHAT THIS STUDY ADDS• Riluzole pharmacokinetics have never documented in patients with SMA.• This study showed that the administration of 50 mg riluzole once a day to patients with SMA leads to total riluzole daily exposure comparable with that obtained after the administration of 50 mg twice a day in healthy volunteers or ALS patients.AIMSThe objective of the present study was to assess the pharmacokinetics of riluzole in patients with spinal muscular atrophy (SMA).METHODSFourteen patients were enrolled in an open‐label, nonrandomized and repeat‐dose pharmacokinetic study. All participants were assigned to receive 50 mg riluzole orally for 5 days. Riluzole plasma concentrations were determined from samples obtained at day 5.RESULTSThe pharmacokinetic analysis demonstrated that a dose of 50 mg once a day was sufficient to obtain a daily total exposure [AUC(0,24 h) = 2257 ng ml−1 h] which was comparable with results obtained in adult healthy volunteers or ALS patients in whom a dose of 50 mg twice a day is recommended. The pharmacokinetic simulation demonstrated that the administration of 50 mg twice a day could result in higher concentrations, hence reduced safety margin.CONCLUSIONThe dose of 50 mg once a day was chosen for the clinical trial evaluating the efficacy of riluzole in SMA patients.