bluuebunny/crossref_metadata_2025 huggingface dataset:
Computation vs. cloning: evaluation of two methods for haplotype determination
Authors: HARRIGAN RYAN J. , MAZZA MAUREEN E. , SORENSON MICHAEL D.
Published: August 2009

Nuclear sequence data, often from multiple loci, are increasingly being employed in analyses of population structure and history, yet there has been relatively little evaluation of methods for accurately and efficiently separating the alleles or haplotypes in heterozygous individuals. We compared the performance of a computational method of haplotype reconstruction and standard cloning methods using a highly variable intron (ornithine decarboxylase, intron 6) in three closely related species of dabbling ducks (genus Anas). Cloned sequences from 32 individuals were compared to results obtained from phase 2.1.1 . phase correctly identified haplotypes in 28 of 30 heterozygous individuals when the underlying model assumed no recombination. Haplotypes of the remaining two individuals were also inferred correctly except for unique polymorphisms, the phase of which was appropriately indicated as uncertain (phase probability = 0.5). For a larger set of 232 individuals, results were essentially identical regardless of the recombination model used and haplotypes for all 30 of the tested heterozygotes were correctly inferred, with the exception of uncertain phase for unique polymorphisms in one individual. In contrast, initial sequences of one clone per sample yielded accurate haplotype determination in only 26 of 30 individuals; polymerase chain reaction (PCR)/cloning errors resulting from misincorporation of individual nucleotides could be recognized and avoided by comparison to direct sequences, but errors due to PCR recombination resulted in incorrect haplotype reconstruction in four individuals. The accuracy of haplotypes reconstructed by phase, even when dealing with a relatively small number of samples and numerous variable sites, suggests broad utility of computational approaches for reducing the cost and improving the efficiency of data collection from nuclear sequence loci.
Development of microsatellite markers for the wood cricket, Nemobius sylvestris (Orthoptera: Gryllidae)
Authors: VANHALA TYTTI , COTTRELL JOAN
Published: August 2009

Thirty‐four novel microsatellite markers developed for wood cricket (Nemobius sylvestris) were tested and optimized. Twenty‐five microsatellite loci were polymorphic, exhibiting between two and nine alleles. Observed heterozygosities ranged from 0.038 to 0.925. The microsatellites were also tested in a species belonging to another genus of the Gryllidae family (Gryllus bimaculatus). Two markers produced clear banding patterns with the expected product size. These markers will be used to study the effects of forest fragmentation on genetic connectivity using wood cricket as a model species.
Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi
Authors: ANDERSON SHARON J. , STONE CHRISTINE L. , POSADA‐BUITRAGO MARTHA LUCIA , BOORE JEFFREY L. , NEELAM BEENA A. , STEPHENS ROBERT M. , LUSTER DOUGLAS G. , FREDERICK REID D. , PEDLEY KERRY F.
Published: August 2009

Twenty‐four simple sequence repeat markers were developed for Phakopsora pachyrhizi, a fungal pathogen of soybean (Glycine max) and other legumes. All 24 of the loci were evaluated on 28 isolates of P. pachyrhizi. Twenty‐one loci were polymorphic, with allelic diversity ranging from two to eight alleles, and null alleles were observed for eight of the 24 loci. A preliminary screen with the closely related species, P. meibomiae, indicated that these primer pairs are specific to P. pachyrhizi.
Microsatellite loci for two East African tree species, Leptonychia usambarensis (Sterculiaceae) and Sorindeia madagascariensis (Anacardiaceae)
Authors: CORDEIRO N. J. , FELDHEIM K. A. , IKEJIMBA E. , NDANGALASI H. J.
Published: August 2009

We isolated 20 trinucleotide microsatellites from two African tree species: Sorindeia madagascariensis (nine microsatellites) and Leptonychia usambarensis (11 microsatellites). Number of alleles ranged from three to seven in Sorindeia and two to 10 in Leptonychia. Observed heterozygosity ranged from 0.025 to 0.829 for Sorindeia and from 0.226 to 0.933 for Leptonychia. Two loci from each species departed from Hardy–Weinberg equilibrium. These microsatellite markers will be used to study how forest fragmentation affects pollination and seed dispersal processes of these tree species.
Development of simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon)
Authors: WHANKAEW SUKHUMAN , TANGPHATSORNRUANG SITHICHOKE , TRIWITAYAKORN KANOKPORN
Published: August 2009

In this study, we describe the development of expressed sequence tag–simple sequence repeat markers from expressed sequence tags of the black tiger shrimp (Penaeus monodon) deposited in public sequence databases. A total of 46 primer pairs were designed and screened on 26 individuals of P. monodon from a natural population. Of these, 16 primer pairs showed polymorphic profiles with between two and five alleles per locus. The average unbiased and direct count heterozygosities were 0.4662 and 0.3516, respectively. Cross‐amplification was tested with five individuals of Penaeus vannamei and polymorphic products were detected at five loci.
Species identification of aphids (Insecta: Hemiptera: Aphididae) through DNA barcodes
Authors: FOOTTIT R. G. , MAW H. E. L. , VON DOHLEN C. D. , HEBERT P. D. N.
Published: August 2009

A 658‐bp fragment of mitochondrial DNA from the 5′ region of the mitochondrial cytochrome c oxidase 1 (COI) gene has been adopted as the standard DNA barcode region for animal life. In this study, we test its effectiveness in the discrimination of over 300 species of aphids from more than 130 genera. Most (96%) species were well differentiated, and sequence variation within species was low, averaging just 0.2%. Despite the complex life cycles and parthenogenetic reproduction of aphids, DNA barcodes are an effective tool for identification.
Eleven polymorphic microsatellite markers forOedaleus decorus(Orthoptera, Acrididae), an endangered grasshopper in Central Europe
Authors: BERTHIER K. , LOISEAU A. , STREIFF R. , ARLETTAZ R.
Published: August 2009

We isolated and characterized 11 microsatellite loci in the grasshopperOedaleus decorus(Orthoptera: Acrididae), an endangered species in Central Europe. Polymorphism was studied from two populations, one out of two populations known from Switzerland (n = 20 individuals) and one site from south of France (n = 20). The number of alleles and the expected heterozygosity ranged from five to 12 and from 0.559 to 0.898, respectively, in the Swiss population, and from 14 to 23 and from 0.895 to 0.974, respectively, in the French population. These microsatellite markers are suitable for further conservation genetic studies ofO. decorus.
Non‐invasive genetic identification of small mammal species using real‐time polymerase chain reaction
Authors: MORAN S. , TURNER P. D. , O’REILLY C.
Published: August 2009

DNA identification of non‐invasive samples is a potentially useful tool for monitoring small mammal species. Here we describe a novel method for identifying five small mammal species: wood mouse, bank vole, common shrew, pygmy shrew and water shrew. Species‐specific real‐time polymerase chain reaction primers were designed to amplify fragments of the mitochondrial cytochrome b gene from hair and scat samples. We also amplified nuclear DNA from scats, demonstrating their potential as a source of DNA for population genetic studies.
Development of 11 polymorphic microsatellite loci in the small abalone (Haliotis diversicolor Reeve)
Authors: REN PENG , WANG ZHIYONG , YAO CUILUAN , LIU YING , KE CAIHUAN
Published: August 2009

Eleven polymorphic microsatellite loci for Haliotis diversicolor were isolated and characterized from (CT)n‐ and (AC)n‐enriched library. They were tested in 24 individuals from a natural population. All of them were polymorphic, with the number of alleles varying between three and 10. The observed heterozygosities and expected heterozygosities ranged from 0.083 to 0.913 and from 0.159 to 0.856, respectively. The 11 isolated microsatellite loci, except SA‐JMU6 and SA‐JMU12, followed Hardy–Weinberg expectations. Seven sets of primers also amplify in closely related species, H. ovina and H. asinine. These 11 polymorphic microsatellites will be useful for analysing the population structure and genetic diversity in H. diversicolor.
DNA barcoding discriminates echinoderm species
Authors: WARD ROBERT D. , HOLMES BRONWYN H. , O’HARA TIM D.
Published: August 2009

DNA barcode sequences (a 657‐bp segment of the mtDNA cytochrome oxidase I gene, COI) were collected from 191 species (503 specimens) of Echinodermata. All five classes were represented: Ophiuroidea, Asteroidea, Echinoidea, Holothuroidea and Crinoidea. About 30% of sequences were collected specifically for this study, the remainder came from GenBank. Fifty‐one species were represented by multiple samples, with a mean intraspecific divergence of 0.62%. Several possible instances of cryptic speciation were noted. Thirty‐two genera were represented by multiple species, with a mean congeneric divergence of 15.33%. One hundred and eighty‐seven of the 191 species (97.9%) could be distinguished by their COI barcodes. Those that could not were from the echinoid genusAmblypneustes. Neighbour‐joining trees of COI sequences generally showed low bootstrap support for anything other than shallow splits, although with very rare exceptions, members of the same class clustered together. Two ophiuran species, in both nucleotide and amino acid neighbour‐joining trees, grouped loosely as sister taxa to Crinoidea rather than Ophiuroidea; sequences of these two species appear to have evolved very quickly. Results suggest that DNA barcoding is likely to be an effective, accurate and useful method of species diagnosis for all five classes of Echinodermata.
Characterization of polymorphic microsatellite DNA markers in Banksia nivea, formerly Dryandra nivea
Authors: MILLAR M. A. , BYRNE M.
Published: August 2009

A genomic library was constructed and 10 novel polymorphic microsatellite markers were developed for Banksia nivea subsp. uliginosa, a woody shrub endemic to the southwest of Western Australia. Polymorphism was investigated for these markers in 30 individuals from one population located in restricted habitat at the base of the Whicher Range east of Busselton. Expected heterozygosity ranged from 0.124 to 0.898 and averaged 0.570. Observed heterozygosity ranged from 0.133 to 0.933 and averaged 0.544. The number of alleles per locus ranged from 2.0 to 16.0 and averaged 7.3. These markers also produced amplification products in three other Banksia species and will be used to assay genetic diversity in these species.
Development and characterization of novel, polymorphic microsatellite markers for oat crown rust, Puccinia coronata
Authors: DAMBROSKI HATTIE R , CARSON MARTIN L
Published: August 2009

We report the development of 37 novel and polymorphic microsatellite markers for oat crown rust, Puccinia coronata f.sp. avenae. The allelic diversity ranged from two to 16 alleles per locus. Observed heterozygosity ranged from 0.000 to 0.971, and expected heterozygosity from 0.057 to 0.848. Thirteen of the loci were not in Hardy‐Weinberg equilibrium, due to either the presence of null alleles, small sample size, or the effects of population subdivision (Wahlund's effect). All 37 primer pairs were tested with P. graminis and P. triticina showing that they are specific to P. coronata.
Isolation and characterization of microsatellite marker loci in the greylag goose (Anser anser)
Authors: WEIß B. M. , POGGEMANN K. , OLEK K. , FOERSTER K. , HIRSCHENHAUSER K.
Published: August 2009

Ten novel polymorphic microsatellite loci were isolated and characterized from the greylag goose, Anser anser, a long‐term monogamous and biparental bird. Additionally, five new primers pairs were designed based on previously published microsatellite locus sequences from closely related species. Multiplex polymerase chain reactions conditions were optimized for all 15 primer pairs. The number of alleles ranged from two to 12 per locus with an observed heterozygosity ranging from 0.07 to 0.85. This marker set will be used to determine rates and origins of extra‐pair and parasitic young in a population of individually banded greylag geese with known life histories.
Improving the reliability of molecular sexing of birds using a W‐specific marker
Authors: SHIZUKA DAIZABURO , LYON BRUCE E.
Published: August 2009

Molecular techniques for identifying sex of birds utilize length differences between CHD‐Z and CHD‐W introns, but in some cases these methods can lead to sexing errors. Here we show that an additional W‐specific primer can be used in conjunction with a pre‐existing sexing primer pair to dramatically improve the reliability of molecular sexing methods. We illustrate the approach with American coots (Fulica americana), a species with CHD‐Z polymorphism that could not be accurately sexed using traditional methods. We developed a reverse primer GWR2 designed to sit within the intron of the W chromosome and amplify a distinctively small DNA fragment that serves as a W‐specific marker. Analysis of known‐sex individuals indicates that this W‐specific primer provides an efficient and reliable protocol to identify the sex of F. americana. The development of such sex‐specific primers will likely increase the reliability of molecular sexing methods in other birds as well. Comparisons between CHD‐Z alleles of coots and common moorhens (Gallinula chloropus) revealed that CHD‐Z polymorphism evolved separately in these two closely related species. We discuss the implications of repeated evolution of CHD‐Z polymorphisms among birds.
Eight variable microsatellite loci for a Neotropical tree, Jacaranda copaia (Aubl.) D.Don (Bignoniaceae)
Authors: VINSON C. C. , SAMPAIO I. , CIAMPI A. Y
Published: August 2009

The Dendrogene Project (Genetic Conservation within Managed Forests in Amazonia) aims to understand the genetic and ecological processes that underpin tree species survival and in particular their response to forest management regimes. As part of the project, we developed eight microsatellite markers for Jacaranda copaia to be used for genetic structure, gene flow and reproductive biology studies. Polymorphism was evaluated using 96 adult trees from the Tapajos National Forest in the Eastern Brazilian Amazon. An average of 22 alleles per locus were detected, with expected heterozygosity ranging from 0.731 to 0.94.
The influence of family groups on inferences made with the program Structure
Authors: ANDERSON E. C. , DUNHAM K. K.
Published: August 2009

Unsupervised clustering algorithms, like the program Structure, are increasingly used to infer the presence of population structure from a sample of genotyped individuals. We evaluate the extent to which the presence of related individuals can lead such algorithms to the false inference that there is population structure. First, we demonstrate this problem using a real data set from a rainbow trout (Oncorhynchus mykiss) population. Then we perform an extensive series of simulations involving the program Structure. Our simulations encompass both a simple scenario with fixed numbers of full‐ and half‐siblings in the sample, and a more complicated scenario in which we investigate 360 combinations of population divergence, fraction of population sampled, variance in family size, mating system and number of loci. We find that the inclusion of family members in a sample may produce very strong evidence of population structure, even when population structure is absent. This problem becomes more pronounced when more loci are genotyped, and it is particularly likely in studies of monogamous species, especially if variance in family size is high and a large fraction of a small population has been sampled. Researchers working in such situations should test observed clusters for the presence of family members to distinguish family‐induced structure from real population structure. Additionally, this work shows that Structure's ability to estimate the number of subpopulations may be influenced by a number of factors, and therefore should be interpreted guardedly.
STORM: software for testing hypotheses of relatedness and mating patterns
Authors: FRASIER TIMOTHY R.
Published: August 2009

Storm is a software package that allows users to test a variety of hypotheses regarding patterns of relatedness and patterns of mate choice and/or mate compatibility within a population. These functions are based on four main calculations that can be conducted either independently or in the hypothesis‐testing framework: internal relatedness; homozygosity by loci; pairwise relatedness; and a new metric called allele inheritance, which calculates the proportion of loci at which an offspring inherits a paternal allele different from that inherited from its mother. STORM allows users to test four hypotheses based on these calculations and Monte Carlo simulations: (i) are individuals within observed associations or groupings more/less related than expected; (ii) do observed offspring have more/less genetic variability (based on internal relatedness or homozygosity by loci) than expected from the gene pool; (iii) are observed mating pairs more/less related than expected if mating is random with respect to relatedness; and (iv) do observed offspring inherit paternal alleles different from those inherited from the mother more/less often than expected based on Mendelian inheritance.
Prevalence and genetic diversity of pathogenic populations of Vibrio parahaemolyticus in coastal waters of Galicia, Spain
Authors: Rodriguez‐Castro Alba , Ansede‐Bermejo Juan , Blanco‐Abad Veronica , Varela‐Pet Jose , Garcia‐Martin Oscar , Martinez‐Urtaza Jaime
Published: August 2009

The natural reservoirs and biological characteristics of pathogenic populations of Vibrio parahaemolyticus in marine habitats remain unclear due to difficulties in obtaining pathogenic strains from the environment. The distribution and characteristics of pathogenic V. parahaemolyticus were investigated over 1 year in three coastal environments in Galicia (Spain), including areas of the major international ports in the region. Vibrio parahaemolyticus was present in 35.3% of the samples analysed, and 535 strains were isolated over the period of study. Virulence genes were detected in 94 strains with diverse genetic traits: 66 trh+/tdh−, 24 trh−/tdh+ and 4 trh+/tdh+. Different spatial and seasonal patterns were observed in relation to genetic traits. The trh+/tdh− strains were detected exclusively in northern areas and prevailed in the autumn, when seawater is warmer and less saline, whereas the trh−/tdh+ strains were found in all three areas throughout winter and spring. Characterization of potentially pathogenic strains from the environment revealed an unexpectedly diverse array of serotypes and pulsed‐field gel electrophoresis (PFGE) profiles (pulsotypes) that were unrelated to clinical strains of V. parahaemolyticus that are prevalent in Spain. The results of the current study provide a novel view of V. parahaemolyticus in Europe, in which diverse pathogenic groups are constitutive components of the environmental populations in coastal habitats.
Functional genomics to identify therapeutic prophylactic targets
Authors: Frank Christian G. , Bengoechea José A
Published: August 2009

Infectious diseases are a leading cause of global human mortality. The use of antimicrobials remains the most common strategy for treatment. However, the isolation of pathogens resistant to virtually all antimicrobials makes it urgent to develop effective therapeutics based on new targets. Here we review a new drug discovery paradigm focusing on identifying and targeting host factors important for infection as well as pathogen determinants involved in disease progression. We summarize innovative strategies which by combining bioinformatics with transcriptomics and chemical genetics have already identified host factors essential for pathogen entry, survival and replication. We describe how the discovery of RNA interference which allows loss‐of‐function studies has facilitated functional genomic studies in human cells. It is expected that these studies will identify targets to be used as host‐directed drug therapy which, together with antimicrobials targeting microbial virulence factors, will efficiently eliminate the invading pathogen.
Stability Analysis of LTI Systems With Three Independent Delays—A Computationally Efficient Procedure
Authors: Sipahi Rifat , Fazelinia Hassan , Olgac Nejat
Published: August 2009

A practical numerical procedure is introduced for determining the stability robustness map of a general class of higher order linear time invariant systems with three independent delays, against uncertainties in the delays. The procedure is based on an efficient and exhaustive frequency-sweeping technique within a single loop. This operation results in determination of the complete description of the kernel and the offspring hypersurfaces, which constitute exhaustively the potential stability switching loci in the space of the delays. The new numerical procedure corresponds to the first step in the overarching framework, called the cluster treatment of characteristic roots. The results of this treatment can also be represented in another domain (called the spectral delay space) within a finite dimensional cube called the building block, which is much simpler to view and analyze. The paper also offers several case studies to demonstrate the practicality of the new numerical methodology.
Minimum Tracking Error Control of Flexible Ball Screw Drives Using a Discrete-Time Sliding Mode Controller
Authors: Okwudire Chinedum , Altintas Yusuf
Published: August 2009

This paper presents modeling, identification, and discrete-time sliding mode control of ball screw drives with structural flexibility. The mechanical system of the drive is modeled by a two degree-of-freedom system dominated by the coupled longitudinal and torsional dynamics of the drive assembly whose parameters are identified. A mode-compensating disturbance adaptive discrete-time sliding mode controller is then designed to actively suppress the vibrations of the drive. However, it is shown theoretically that, without using minimum tracking error filters, the tracking errors of the drive do not go to zero when sliding mode is reached. Therefore, a method for designing stable and robust minimum tracking error filters, irrespective of the identified open-loop behavior of the drive is proposed. The identification and control of flexible ball screw drives are experimentally tested, and the tracking accuracy of the drives is shown to improve considerably as a result of the designed minimum tracking error filters.
Synthesis and Control of Flexible Systems With Component-Level Uncertainties
Authors: Maghami Peiman G. , Lim Kyong B.
Published: August 2009

An efficient and computationally robust method for synthesis of component dynamics is developed. The method defines the interface forces/moments as feasible vectors in transformed coordinates to ensure that connectivity requirements of the combined structure are met. The synthesized system is then defined in a transformed set of feasible coordinates. The simplicity of form is exploited to effectively deal with modeling parametric and nonparametric uncertainties at the substructure level. Uncertainty models of reasonable size and complexity are synthesized for the combined structure from those in the substructure models. In particular, we address frequency and damping uncertainties at the component level. The approach first considers the robustness of synthesized flexible systems. It is then extended to deal with nonsynthesized dynamic models with component-level uncertainties by projecting uncertainties to the system level. A numerical example is given to demonstrate the feasibility of the proposed approach.
Differential Transformation and Its Application to Nonlinear Optimal Control
Authors: Hwang Inseok , Li Jinhua , Du Dzung
Published: August 2009

A novel numerical method based on the differential transformation is proposed for solving nonlinear optimal control problems in this paper. The differential transformation is a linear operator that transforms a function from the original time and/or space domain into another domain in order to simplify the differential calculations. The optimality conditions for the optimal control problems can be represented by algebraic and differential equations. Using the differential transformation, these algebraic and differential equations with their boundary conditions are first converted into a system of nonlinear algebraic equations. Then the numerical optimal solutions are obtained in the form of finite-term Taylor series by solving the system of nonlinear algebraic equations. The differential transformation algorithm is similar to the spectral element methods in that the computational region splits into several subregions but it uses polynomials of high degrees by keeping a small number of subregions. The differential transformation algorithm could solve the finite- (or infinite-) time horizon optimal control problems formulated as either the algebraic and ordinary differential equations using Pontryagin’s minimum principle or the Hamilton–Jacobi–Bellman partial differential equation using dynamic programming in one unified framework. In addition, the differential transformation algorithm can efficiently solve optimal control problems with the piecewise continuous dynamics and/or nonsmooth control. The performance is demonstrated through illustrative examples.
Active Control of Rotor Vibrations by Two Feedforward Control Algorithms
Authors: Tammi Kari
Published: August 2009

Resonance vibrations (critical speeds) play a significant role in rotor vibration control. Active vibration control methods for rotors are studied to develop solutions to enhance machines’ dynamic behavior, durability, and operating range. This paper reports rotor vibration attenuation with a supplementary electromagnetic actuator located outside the rotor bearing span. Feedback and feedforward control system design are shown, and comparative experiments on two active vibration control methods for mass unbalance compensation are reported. The methods compared are adaptive FIR filter with the least mean squares (LMS) algorithm and convergent control (CC) method with a frequency-domain adaptation algorithm. The methods were experimentally validated on the rotor test rig (rotor weight 2.7 kg, length 560 mm, and first critical speed about 50 Hz). The feedback system provided wideband damping in the sub- and supercritical regions. The feedforward systems attenuated vibratory responses at the speed of rotation and its harmonic. The attenuation achieved was about 20 dB depending on the rotor speed. Also, discrete-time CC algorithm is shown to have a feedback equivalent circuit. The significance of feedback control lies in making the system phase-characteristics sufficiently smooth for feedforward control methods. Then, feedforward algorithms provided a good vibration damping performance over the operating range. CC was found to be a more effective and simpler algorithm for the purpose than the adaptive FIR filter with the LMS algorithm. The equivalent feedback circuit derived for CC, and systems similar to CC, facilitates their stability and robustness analysis.
Experimental Characterization and Static Modeling of McKibben Actuators
Authors: Kothera Curt S. , Jangid Mamta , Sirohi Jayant , Wereley Norman M.
Published: August 2009

McKibben actuators are pneumatic actuators with very high force to weight ratios. Their ability to match the behavior of biological muscles better than any other actuators has motivated much research into the characterization and modeling of these actuators. The purpose of this paper is to experimentally characterize the behavior of McKibben artificial muscles with basic geometric parameters, and present a model that is able to predict the static behavior accurately in terms of blocked force and free displacement. A series of experiments aimed at understanding the static behavior of the actuators was conducted. The results for three different lengths (4 in., 6 in., and 8 in.), three diameters (1/8 in., 1/4 in., and 3/8 in.), and one wall thickness (1/16 in.) at pressures ranging from 10 psi to 60 psi illustrate the key design trends seen in McKibben actuator geometry. While existing models predict this static behavior, there are varying degrees of accuarcy, which motivates the present study. Using knowledge gained from the experimental study, improvements for the two modeling approaches were explored, including effects from elastic energy storage, noncylindrical shape, and variable thickness. To increase model accuracy, another set of experiments was used to characterize the elasticity of the rubber tubes and fibers of the braid. Comparisons of the measured data to the improved model indicate that the ability to accurately predict the static behavior of McKibben actuators has increased.
Piezohydraulic Actuator Development for Microjet Flow Control
Authors: Oates William S. , Liu Fei
Published: August 2009

This paper describes the development of a piezohydraulic actuator for broadband microjet flow control applications. The actuator utilizes a lead zirconate titanate (PZT) stack actuator and a hydraulic amplification design to achieve relatively large displacements in a compact actuator to control flow through a microjet orifice. Displacement amplification of 81 times the stack actuator displacement was achieved using a new dual-diaphragm design. The nonlinear and hysteretic field-coupled material behavior, structural dynamics, and fluid dynamics of the actuator are modeled using a system dynamic model and compared with experimental results. The nonlinear and hysteretic piezohydraulic actuator characteristics are shown to be strongly dependent on the nonlinear deformation of the rubber diaphragm and minor loop hysteresis of the PZT stack actuator. The modeling technique provides a design tool for broadband performance predictions and system optimization to facilitate implementation of the actuator in a flow environment.
Design of Shape Memory Alloy Actuators for Morphing Laminar Wing With Flexible Extrados
Authors: Georges Thomas , Brailovski Vladimir , Morellon Emeric , Coutu Daniel , Terriault Patrick
Published: August 2009

An active structure of a morphing wing designed for subsonic cruise flight conditions is composed of three principal subsystems: (1) flexible extrados, (2) rigid intrados, and (3) an actuator group located inside the wing box. The four-ply laminated composite flexible extrados is powered by two individually controlled shape memory alloy (SMA) actuators. Fulfilling the requirements imposed by the morphing wing application to the force-displacement characteristics of the actuators, a novel design methodology to determine the geometry of the SMA active elements and their adequate assembly conditions is presented. This methodology uses the results of the constrained recovery testing of the selected SMA. Using a prototype of the morphing laminar wing powered by SMA actuators, the design approach proposed in this study is experimentally validated.
Energy Harvesting Utilizing Single Crystal PMN-PT Material and Application to a Self-Powered Accelerometer
Authors: Song H. J. , Choi Y. T. , Wang G. , Wereley N. M.
Published: August 2009

This study investigates the performance of an energy harvester (EH) utilizing a single crystal lead magnesium niobate-lead titanate (PMN-PT) material via analysis and experiment. The EH, intended to convert mechanical energy at a harmonic frequency such as from a fixed revolutions per minute (RPM) rotating machine, was composed of a cantilever beam having a single crystal PMN-PT patch, a tip mass, a rectifier, and an electric load. The fundamental frequency of the EH was finely adjusted via moving a tip mass spanwise. The analysis was used to select an optimal EH configuration based on a weight constraint (less than 200 g) and a narrow band frequency range (nominally 60 Hz). The analysis and performance were validated experimentally for different excitation levels. The harvested dc power was measured for low acceleration levels of 0.05–0.2 g (where 1 g=9.81 m/s2) typical of rotating machinery. The maximum dc power generated was 19 mW for an excitation of 0.2 g. The measured power density (i.e., maximum dc power over total device volume) and measured specific power (i.e., maximum dc power over total device mass) of the energy harvester were 0.73 mW/cc and 0.096 mW/g, respectively. The EH developed in this study was compared with other configurations and types via metrics of mean square acceleration weighted power (MSAP) and MSAP density. Charging performance of the single crystal PMN-PT based EH was evaluated by recharging a battery. In addition, the effect of the capacitance of the rectifier circuit on charging time was also investigated. Finally, the EH was also used to drive an accelerometer using only energy that was harvested from ambient vibration. The accelerometer was continuously and successfully operated when the persistent excitation level exceeded 0.1 g.
Multi-Objective Optimization of Piezoelectric Actuator Placement for Shape Control of Plates Using Genetic Algorithms
Authors: Kudikala Rajesh , Kalyanmoy Deb , Bhattacharya Bishakh
Published: August 2009

Shape control of adaptive structures using piezoelectric actuators has found a wide range of applications in recent years. In this paper, the problem of finding optimal distribution of piezoelectric actuators and corresponding actuation voltages for static shape control of a plate is formulated as a multi-objective optimization problem. The two conflicting objectives considered are minimization of input control energy and minimization of mean square deviation between the desired and actuated shapes with constraints on the maximum number of actuators and maximum induced stresses. A shear lag model of the smart plate structure is created, and the optimization problem is solved using an evolutionary multi-objective optimization algorithm: nondominated sorting genetic algorithm-II. Pareto-optimal solutions are obtained for different case studies. Further, the obtained solutions are verified by comparing them with the single-objective optimization solutions. Attainment surface based performance evaluation of the proposed optimization algorithm has been carried out.
Design of a Bone Transport Device Using Smart Material Actuators
Authors: Luo Yuehao , Hutapea Parsaoran
Published: August 2009

The ultimate goal of our research is to develop a wireless, remotely activated, and implantable bone transport (lengthening) device. Our device is subcutaneously mounted on the periosteal surface of the tibia. Smart materials such as temperature-driven nitinol and magnetostrictive terfenol-D were investigated to be used as actuators to provide the required forces for the bone transport process. It was found that an actuator based on terfenol-D with a magnetic field applied transversely (along the material’s magnetic moment) was the more appropriate technology. Design concepts and proof-of-concept work of both smart material technologies are presented.
Sensing Behavior of Magnetorheological Elastomers
Authors: Wang Xiaojie , Gordaninejad Faramarz , Calgar Mert , Liu Yanming , Sutrisno Joko , Fuchs Alan
Published: August 2009

A magnetorheological elastomer (MRE) is comprised of ferromagnetic particles aligned in a polymer medium by exposure to a magnetic field. The structures of the magnetic particles within elastomers are very sensitive to the external stimulus of either mechanical force or magnetic field, which result in multiresponse behaviors in a MRE. In this study, the sensing properties of MREs are investigated through experimentally characterizing the electrical properties of MRE materials and their interfaces with external stimulus (magnetic field or stress/strain). A phenomenological model is proposed to understand the impedance response of MREs under mechanical loads and magnetic fields. Results show that MRE samples exhibit significant changes in measured values of impedance and resistance in response to compressive deformation, as well as the applied magnetic field.
Stress Relief in Contact-Aided Compliant Cellular Mechanisms
Authors: Mehta Vipul , Frecker Mary , Lesieutre George A.
Published: August 2009

Compliant cellular structures with an internal contact mechanism are described in this paper. Contact during deformation reduces failure-causing bending stresses through stress relief, thereby enabling such cellular structures to be stretched more than the corresponding structures without contact. Finite element analysis (FEA) is carried out to simulate the structure. An analytical model is developed to get results quicker than FEA and to develop insight into the mechanics of the deformation process. The error in prediction of the maximum stretching capacity using the analytical model is less than 7% when compared with finite element simulations. Several materials are investigated for such structures. Although the allowable strain of all these materials is small, the overall strain of the contact-aided cellular structures is at least an order of magnitude greater than that of the constitutive material. The contact mechanism and the induced stress relief increase the stretching capacity of the contact-aided cellular structures by as much as 100%. Experiments are conducted to validate the models, and good agreement is found. A high-strain morphing aircraft skin is examined as an application of these mechanisms. The results indicate that the proposed skin structure not only increases the morphing capacity but also decreases the structural mass by 13% as compared with a cellular skin without contact.
Authors' Response
Authors: Ludwigsen Dan , Svinarich Kathryn
Published: August 2009

We are grateful for the feedback we've received from Gabriel Kessler regarding our example of using dimensionless plots. Kessler captures the spirit of this technique with his suggestions for a modified analysis with the parameter F/(m2g). We also agree that the analysis should yield a coefficient of kinetic friction that is less than the coefficient of static friction for the maximum force of static friction. However, what we attributed to experimental error associated with numerical differentiation was more likely an oversight in the analysis. Private communication with Donald Fahnline helped us identify this mistake.
Equinox Disparity
Authors: Mallinckrodt A. John
Published: August 2009

Paul Hewitt's April Figuring Physics column (pp. 198, 214) asks the reader to determine what accounts for the seven- day difference between the 179 days from the autumnal to vernal equinox and the 186 days from the vernal to autumnal equinox. His answer—Earth moves faster during the shorter period—is the only one of the offered choices that conceivably could account for the difference. Alas, it doesn't because it implicitly and incorrectly assumes that the distances traveled during the two periods are the same.
Physics for the Non-Scientist: A Middle Way
Authors: Sobel Michael
Published: August 2009

Recently a comedian in a comedy club in New York asked me if I was a professor. I said, “Yes, a professor of physics.” “Physics!” he said. “I was in a bookstore and saw a book, Physics for Dummies. I opened it and it said, ‘You'd better cheat.’” Physics has that reputation, as all of us in the field know, and yet I'm not sure if we have grappled with the reason why.
Motors and Bulbs in Series
Authors: Whitaker Robert J.
Published: August 2009

One of Paul Hewitt's “Figuring Physics” that appeared in this journal dealt with the heating of a motor. This phenomenon can be demonstrated with a miniature motor and a bulb as part of a series of activities with “batteries and bulbs.” Students examine the effect on the brightness of a single bulb when a second, identical bulb is placed in series with it (Fig. 1). The second bulb is then replaced with the motor (Fig. 2). When the motor is running, the first bulb is dimmer than it was in series with the other bulb. However, if the shaft of the motor is held so it cannot move (like Hewitt's saw motor), the bulb is noticeably brighter. If one uses the brightness of the bulb as a qualitative measure of current, then there is clearly more current when the motor is not moving. This provides an opportunity to introduce some very interesting physics.
Objects in Telescope Are Farther Than They Appear
Authors: Graney Christopher M.
Published: August 2009

The wave nature of light is not part of students' common experiences, so often physics teachers and textbooks will add a historical anecdote about how scientists, too, were tricked by light. A common one is how, in the early 19th century, Poisson declared that since Fresnel's ideas on the wave nature of light implied that the shadow cast by a disk would contain a bright spot at its center, Fresnel's ideas were obviously flawed. The spot was later detected, proving Fresnel right! But recent studies of Galileo's work have brought to light a story about diffraction that may displace Poisson's spot as the favored historical anecdote, for it seems that diffraction tricked Galileo, too. Diffraction of light caused Galileo to mismeasure the distances to the stars.
Another Way of Tracking Moving Objects Using Short Video Clips
Authors: Vera Francisco , Romanque Cristian
Published: August 2009

Physics teachers have long employed video clips to study moving objects in their classrooms and instructional labs. A number of approaches exist, both free and commercial, for tracking the coordinates of a point using video. The main characteristics of the method described in this paper are: it is simple to use; coordinates can be tracked using any standard Internet navigator; it can be used with examples available on our webserver or with a modified example in the user's own computer; the web pages with new sequences of images are easy to upload to a web server; it is possible to track and analyze any complex one- or two-dimensional motion of objects; and the code is open source. The setup is very simple, intuitive, and can easily be scaled up.
Half and Rough
Authors: Korsunsky Boris
Published: August 2009

A small block slides down a slanted board when released. The upper half of the board is smooth and the lower is rough, so that the acceleration of the block on the smooth half is three times greater than it is on the rough half. The block reaches the bottom of the board in time t1. The board is then flipped so that the upper half is rough and the lower part is smooth, and the block is released from the top again. This time, the block reaches the bottom of the board in time t2. In both cases, the board makes the same angle with the horizontal. Find the ratio t1/t2.
Bigger Is Bigger
Authors: Riendeau Diane
Published: August 2009

When you really want to get a point across to your students, you set up explorations or experiments, and do demonstrations. Sometimes I find myself thinking, “If I only had….” This month's videos add “wow” factor to the experiences you provide for your students in the classroom!

Thanks to Jaime Stasiorowski (Deerfield High School), Tony Zito (Dutchess Community College), and Bob Beichner (NC State) and Chris Chiaverina for their contributions to this month's column.
Three Physics and Astronomy blogs
Authors: Hubbard Richard
Published: August 2009

— Cocktail Party Physics is an irreverent, humorous blog dealing with physics from the point of view of someone who isn't a professional physicist, but who is interested in the subject. Multiple bloggers add interesting, differing viewpoints on current events from a physics standpoint. http://twisted-physics.typepad.com/cocktail_party_physics/— Astronomycast http://www.astronomycast.com/ is a website and podcast created by Dr. Pamela Gay from the University of Southern Illinois and Frasier Cain, publisher of Universe Today. The podcasts include weekly discussion topics, and mostly weekly “question shows” where listeners are invited to send Dr. Gay her questions, which she will answer in the podcast. Dr. Gay also has her own blog, Star Stryder at http://www.starstryder.com/, blogging the life of an astronomer.
The LivePhoto Physics videos and video analysis site
Authors: Abbott David
Published: August 2009

The LivePhoto site is similar to an archive of short films for video analysis. Some videos have Flash tools for analyzing the video embedded in the movie. Most of the videos address mechanics topics with titles like Rolling Pencil (check this one out for pedagogy and content knowledge—nicely done!), Juggler, Yo-yo, Puck and Bar (this one is an inelastic collision with rotation), but there are a few titles in other areas (E&M, waves, thermo, etc.).
Evaluation of the eclipse electron Monte Carlo dose calculation for small fields
Authors: Xu Zhigang , Walsh Sarah E. , Telivala Tejas P. , Meek Allen G. , Yang Guozhen
Published: August 2009

Varian Medical Systems (Palo Alto, CA) has implemented the Monte Carlo electron dose calculation algorithm (eMC) in the Eclipse treatment planning system. Previous algorithms for electron treatment planning were limited in their calculation ability for small field depth doses and monitor units. An old rule of thumb to approximate the limiting cutout size for an electron field was determined by the lateral scatter equilibrium and approximated by E (MeV)/2.5 in centimeters of water. In this study, we compared eMC calculations and measurements of depth doses, isodose distributions, and monitor units for several different energy and small field cutout size combinations at different SSDs. Measurements were made using EBT film (International Specialty Products, Wayne, NJ) and a PinPoint ion chamber (PTW‐New York Corp., Hicksville, NY). Our results indicate that the eMC algorithm can accurately predict depth doses, isodose distributions, and monitor units (within 2.5%) for field sizes as small as 3.0 cm diameter for energies in the 6 to 20 MeV range at 100 cm SSD. Therefore, the previous energy dependent rule of thumb does not apply to the Eclipse electron Monte Carlo code. However, at extended SSDs (105–110 cm), the results show good agreement (within 4%) only for higher energies (12, 16, and 20 MeV) for a field size of 3 cm.

PACS number: 87.53.Hv