bluuebunny/crossref_metadata_2025 huggingface dataset:
The limiting behavior of the thermal conductivity of nanoparticles and nanofluids
Authors: Teja Amyn S. , Beck Michael P. , Yuan Yanhui , Warrier Pramod
Published: June 2010

We present experimental evidence of negative thermal conductivity enhancement in nanofluids consisting of 2 nm titania nanoparticles dispersed in 50% (w/w) water+ethylene glycol. This behavior is unlike that of other nanofluids, which have been shown to exhibit positive thermal conductivity enhancements. Our results for titania nanofluids suggest that the thermal conductivity of 2 nm titania nanoparticles is smaller than the thermal conductivity of the base fluid at the same temperature, indicating a dramatic decrease in the thermal conductivity of titania particles as the particle size becomes of the same order as the phonon mean free path. Although such a decrease has been predicted for semiconductor nanoparticles by theory and simulation, experimental evidence has hitherto been lacking. Our results provide indirect experimental evidence for this decrease in metal oxide particles, and validate our previous work on alumina nanofluids that showed an exponential decrease in the thermal conductivity of alumina particles with decreasing particle size, from a limiting value for large (micron-sized) particles.
BRST detour quantization: Generating gauge theories from constraints
Authors: Cherney D. , Latini E. , Waldron A.
Published: June 2010

We present the Becchi–Rouet–Stora–Tyutin (BRST) cohomologies of a class of constraint (super) Lie algebras as detour complexes. By interpreting the components of detour complexes as gauge invariances, Bianchi identities, and equations of motion, we obtain a large class of new gauge theories. The pivotal new machinery is a treatment of the ghost Hilbert space designed to manifest the detour structure. Along with general results, we give details for three of these theories which correspond to gauge invariant spinning particle models of totally symmetric, antisymmetric, and Kähler antisymmetric forms. In particular, we give details of our recent announcement of a (p,q)-form Kähler electromagnetism. We also discuss how our results generalize to other special geometries.
Exchange bias in a single phase ferrimagnet
Authors: West K. G. , Nam D. N. H. , Lu J. W. , Bassim N. D. , Picard Y. N. , Stroud R. M. , Wolf S. A.
Published: June 2010

We report on peculiar magnetic hysteresis behavior of Ru0.25Cr0.75O2 thin films. We describe three unusual magnetic phenomena inherent to this material; (i) intrinsic positive exchange bias in a single phase epitaxial thin film ferrimagnet with the absence of a clear and distinct magnetic-magnetic interface, (ii) field modulation of the shifted M(H) loop along the field axis direction, and (iii) inverted hysteresis loops in which the overall area of the loop is nearly zero over the entire field cycle. These results can be understood within the context of a very unusual interface of the epitaxial film with the TiO2 (001) substrate.
Two-component magnetic structure of iron oxide nanoparticles mineralized in Listeria innocua protein cages
Authors: Usselman Robert J. , Klem Michael T. , Russek Stephen E. , Young Mark , Douglas Trevor , Goldfarb Ron B.
Published: June 2010

Magnetometry was used to determine the magnetic properties of maghemite (γ-Fe2O3) nanoparticles formed within Listeria innocua protein cage. The electron magnetic resonance spectrum shows the presence of at least two magnetization components. The magnetization curves are explained by a sum of two Langevin functions in which each filled protein cage contains both a large magnetic iron oxide core plus an amorphous surface consisting of small noncoupled iron oxide spin clusters. This model qualitatively explains the observed decrease in the temperature dependent saturation moment and removes an unrealistic temperature dependent increase in the particle moment often observed in nanoparticle magnetization measurements.
Electron transport and charge induction in cadmium zinc telluride detectors with space charge build up under intense x-ray irradiation
Authors: Bale Derek S. , Szeles Csaba
Published: June 2010

Under intense x-ray irradiation, wide band gap semiconductor radiation detectors fabricated from crystals with low hole transport properties develop a steady-state space charge distribution that results from a dynamic equilibrium between charge carrier dynamics and the incident photon field. At a high enough x-ray flux, this space charge can collapse the electric field within the detector, resulting in the paralyzation of photon counting (i.e., high-flux polarization). However, well before polarization causes a catastrophic device failure, there can be enough space charge present to significantly modify the electric field. A modified field affects the electron transport and, therefore, signal generation within the sensor, which can ultimately degrade the performance of high-rate photon counting electronics. In this study, we analytically solve the fundamental equation of charge conservation to derive the modified electron transport in the presence of an exponential space charge distribution that results from the incident x-rays. We use these space-time solutions to calculate and study the time dependence of the resulting charge-induced signals. The predicted induced signals are compared throughout with numerical solutions of the full charge transport equation. In addition, we present analogous closed-form signals for a uniform distribution relevant to a broader class of γ-ray applications. Finally, we use these solutions to derive a two-parameter family of modified Hecht curves that naturally predict a voltage offset that appears due to the space charge.
Scaling laws of resistive magnetohydrodynamic reconnection in the high-Lundquist-number, plasmoid-unstable regime
Authors: Huang Yi-Min , Bhattacharjee A.
Published: June 2010

The Sweet–Parker layer in a system that exceeds a critical value of the Lundquist number (S) is unstable to the plasmoid instability. In this paper, a numerical scaling study has been done with an island coalescing system driven by a low level of random noise. In the early stage, a primary Sweet–Parker layer forms between the two coalescing islands. The primary Sweet–Parker layer breaks into multiple plasmoids and even thinner current sheets through multiple levels of cascading if the Lundquist number is greater than a critical value Sc≃4×104. As a result of the plasmoid instability, the system realizes a fast nonlinear reconnection rate that is nearly independent of S, and is only weakly dependent on the level of noise. The number of plasmoids in the linear regime is found to scales as S3/8, as predicted by an earlier asymptotic analysis [N. F. Loureiro et al., Phys. Plasmas 14, 100703 (2007)]. In the nonlinear regime, the number of plasmoids follows a steeper scaling, and is proportional to S. The thickness and length of current sheets are found to scale as S−1, and the local current densities of current sheets scale as S−1. Heuristic arguments are given in support of theses scaling relations.
Zn/Cu-vegetative batteries, bioelectrical characterizations, and primary cost analyses
Authors: Golberg Alex , Rabinowitch Haim D. , Rubinsky Boris
Published: June 2010

Developing a cheap, sustainable, and simple to use low power electrical energy source will substantially improve the life quality of 1.6×109 people, comprising 32% of the developing non-Organization for Economic Co-Operation and Development populations currently lacking access to electrical infrastructure (World Energy Outlook, 2006, http://www.worldenergyoutlook.org/2006.asp, 10 September 2009). Such a source will provide important needs as lighting, telecommunication, and information transfer. Our previous studies on Zn/Cu electrolysis in animal tissues revealed a new fundamental bioelectrical property: the galvanic apparent internal impedance (GAII) [A. Golberg, H. D. Rabinowitch, and B. Rubinsky, Biochem. Biophys. Res. Commun. 389, 168 (2009)], with potential use for tissue typing. We now report on new fundamental studies on GAII in vegetative matter and on a simple way for significant performance improvement of Zn/Cu-vegetative battery. We show that boiled or irreversible electroporated potato tissues with disrupted cell membranes generate electric power up to tenfold higher than equal galvanic cell made of untreated potato. The study brought about basic engineering data that make possible a systematic design of a Zn/Cu-potato electrolytic battery. The ability to produce and utilize low power electricity was demonstrated by the construction of a light-emitting diode based system powered by potato cells. Primary cost analyses showed that treated Zn/Cu-potato battery generates portable energy at ∼9 USD/kW h, which is 50-fold cheaper than the currently available 1.5 V AA alkaline cell (retail) or D cells (∼49–84 USD/kW h). Admittedly very simple, the treated potato or similarly treated other plant tissues could provide an immediate, environmental friendly, and inexpensive solution to many of the low power energy needs in areas of the world lacking access to electrical infrastructure.
Investigation of mixed spinel structure of nanostructured nickel ferrite
Authors: Jacob John , Khadar M. Abdul
Published: June 2010

Single crystalline nickel ferrite (NiFe2O4) which has an inverse spinel structure is reported to exhibit a mixed spinel structure when its grain size is reduced to nanometer range. It is known that structural transformations in the nanosize regime are not akin to those of bulk crystals. Additionally, magnetic properties like superparamagnetism and contribution to it by surface layers are critically influenced by the synthesis route of the samples. In this article, we present an investigation on the structural transformation of nanostructured NiFe2O4 using x-ray diffraction (XRD), Mössbauer and magnetization measurements, and Fourier transform infrared (FTIR) and micro-Raman spectroscopy. Nanostructured NiFe2O4 samples were synthesized by a coprecipitation technique followed by thermal processing. Four samples having average grain sizes 13, 20, 26, and 51 nm were synthesized. XRD results confirmed the samples to be nanostructured NiFe2O4 and gave evidence for the mixed spinel structure of the samples of lower grain sizes. Mössbauer study of the smallest and largest grain-sized samples revealed surface spin canting and change in coordination of the iron ions at tetrahedral and octahedral sites with reduction in grain size. The spin canting angle and the coordination factor were determined from the Mössbauer spectra. Vibrating sample magnetometer measurements gave a lower value of magnetization for the samples of lowest grain size and this observation could be explained on the basis of a structural transformation of the sample from inverse to mixed spinel. FTIR and micro-Raman spectroscopic studies also yielded convincing evidence for a transformation of the structure. The results of the present study lead to the inference that the properties of nanosized NiFe2O4 particle emerged from a transformation of their structure from inverse spinel structure to mixed spinel.
Car–Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate
Authors: Pirc Gordana , Stare Jernej , Mavri Janez
Published: June 2010

We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car–Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrödinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm−1 and a half width of about 700 cm−1, which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm−1, respectively. The hydrogen probability densities obtained by solving the vibrational Schrödinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.
Energy band structure calculations based on screened Hartree–Fock exchange method: Si, AlP, AlAs, GaP, and GaAs
Authors: Shimazaki Tomomi , Asai Yoshihiro
Published: June 2010

The screening effect on the Hartree–Fock (HF) exchange term plays a key role in the investigation of solid-state materials by first-principles electronic structure calculations. We recently proposed a novel screened HF exchange potential, in which the inverse of the dielectric constant represents the fraction of the HF exchange term incorporated into the potential. We demonstrated that this approach can be used to reproduce the energy band structure of diamond well [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009)]. In the present paper, we report that the screened HF exchange method is applicable to other semiconductors such as silicon, AlP, AlAs, GaP, and GaAs.
A kinetic simulation study of the mechanisms of aluminum induced layer exchange process
Authors: Sarikov Andrey , Schneider Jens , Berghold Juliane , Muske Martin , Sieber Ina , Gall Stefan , Fuhs Walther
Published: June 2010

The aluminum induced layer exchange (ALILE) process allows the formation of thin polycrystalline Si (poly-Si) layers of large grain size on foreign substrates such as glass at low process temperatures. This paper is devoted to a computer simulation study of the kinetics of the ALILE process taking into account the mechanisms of its separate stages: Si diffusion in the AlOx membrane, nucleation and growth of grains, and the formation of preferential (100) orientation. The characteristics of the ALILE process are explained based on the evolution of the Si concentration within the Al layer. In particular it is demonstrated that the characteristic suppression of nucleation after short annealing times results from a decrease in the Si concentration in the Al layer due to the growth of existing grains. A number of important parameters of ALILE process are estimated comparing the results of simulation to the experimental data.
Enhancing magnetorheology with nonmagnetizable particles
Authors: Ulicny John C. , Snavely Keith S. , Golden Mark A. , Klingenberg Daniel J.
Published: June 2010

Experimental results illustrate an enhancement in the field-induced yield stress of magnetorheological (MR) fluids caused by the presence of nonmagnetizable particles. Particle-level simulations in three dimensions show similar behavior. However, the enhancement does not appear in simulations in which the spheres are confined to a monolayer. A mechanistic explanation of these observations is currently lacking. Nonetheless, the ability to enhance the MR response by replacing magnetizable particles with nonmagnetizable particles offers several advantages for applications.
Adsorption of small aromatic molecules on the (111) surfaces of noble metals: A density functional theory study with semiempirical corrections for dispersion effects
Authors: Tonigold Katrin , Groß Axel
Published: June 2010

The adsorption of benzene, thiophene, and pyridine on the (111) surface of gold and copper have been studied using density functional theory (DFT). Adsorption geometries and energies as well as the nature of bonding have been analyzed and compared to experimental results. Dispersion effects between neighboring molecules and between molecules and the surface have been taken into account via a semiempirical C6R−6 approach. The C6 coefficients for metal atoms have been deduced using both atomic properties and a hybrid QM:QM approach. Whereas the pure DFT calculations underestimate the adsorption energies significantly, a good agreement with experimental results is obtained using the DFT-D method based on the QM:QM hybrid approach.
Electronic transport properties in a bimolecular device modulated with different side groups
Authors: Fan Zhi-Qiang , Chen Ke-Qiu , Wan Qing , Zhang Yan
Published: June 2010

By using nonequilibrium Green’s functions in combination with the density-functional theory, we investigate the electronic transport properties in a bimolecular device, which is substituted by two amino groups or two nitro groups. The results show that the side groups can modulate the transport properties by their substituted position. The current of the system substituted by two amino groups on the same side is bigger than that on the different side. Contrarily, the current of the system substituted by two nitro groups on the same side is smaller than that on the different side. More importantly, the negative differential resistance (NDR) behavior can be observed only when the system substituted by two amino groups on the same side. The mechanisms are proposed for the effect of the side groups and NDR behavior.
Asymmetrical giant magnetoimpedance in exchange-biased NiFe
Authors: García C. , Florez J. M. , Vargas P. , Ross C. A.
Published: June 2010

Linear asymmetrical magnetoimpedance (MI) has been obtained in thin multilayer strips of exchange-coupled FeNi(5 nm)/IrMn(15 nm)/FeNi(40 nm)/Cu(100 nm)/FeNi(40 nm)/IrMn(15 nm)/FeNi(5 nm), in which the MI response is enhanced by including a Cu layer between the two 40 nm NiFe layers. The antiferromagnetic layer creates an exchange bias that shifts both the hysteresis loop and the MI response. The asymmetrical MI peak positions are shifted to higher magnetic field as the probe frequency increases. Linear MI behavior can be tuned around zero external field without the need for external biasing fields or additional coils, by changing the frequency. The impedance of a planar magnetic conductor was modeled based on a modified Stoner–Wohlfarth energy density.
Electrode oxygen-affinity influence on voltage nonlinearities in high-k metal-insulator-metal capacitors
Authors: Vallée C. , Gonon P. , Jorel C. , El Kamel F.
Published: June 2010

This work highlights the influence of the oxygen affinity of the metal electrodes used in high-k metal-insulator-metal capacitors. Several metallic electrodes are tested in order to investigate the role of the metal work function, and the role of the electrode oxygen-affinity in nonlinear behavior of HfO2 and BaTiO3 capacitors. It is shown that the magnitude of the quadratic coefficient of nonlinearity is better explained by the electrode oxygen-affinity rather than by its work function. It is thought that electrode oxidation increases the number of oxygen vacancies at the electrode/dielectric interface, and so increases the magnitude of nonlinearity.
Memory mechanisms of vertical organic memory transistors
Authors: Yu Li-Zhen , Chen Hung-Chun , Lee Ching-Ting
Published: June 2010

Three-terminal vertical organic memory transistors were fabricated to investigate the memory mechanisms and the relation between memory behavior and applied electrical field. The 9,10-di(2-naphthyl)anthracene was used as the active channel layer for the organic memory transistors. In both the ON and OFF state of the organic memory transistors, the drain-source currents (IDS) were modulated by applying various gate-source voltages (VGS). The switching drain-source voltage (VDS) decreased with an increase in applied VGS voltages. The ON/OFF IDS current ratio of the organic memory transistors could be modulated up to the maximum value of 2.02×105 by applying VGS voltage bias.
Near-field light detection by conservative and dissipative force modulation methods using a piezoelectric cantilever
Authors: Satoh Nobuo , Fukuma Takeshi , Kobayashi Kei , Watanabe Shunji , Fujii Toru , Matsushige Kazumi , Yamada Hirofumi
Published: June 2010

We demonstrated near-field light detection by dynamic force microscope using a self-sensing piezoelectric cantilever having a lead zirconate titanate thin film layer. The cantilever tip was brought close to a glass plate with a patterned chromium film on a right angle prism. The backside of the prism was irradiated by an intensity modulated laser light to create an evanescent field at the glass surface. We obtained near-field optical images of the patterned glass by detecting the frequency shift modulation or the amplitude modulation induced by the near-field light while the tip-sample distance was regulated by the frequency modulation method in ambient condition.
Thermodynamics of Enzyme-Catalyzed Reactions: Part 5. Isomerases and Ligases
Authors: Goldberg Robert N. , Tewari Yadu B.
Published: June 2010

Equilibrium constants and enthalpy changes for reactions catalyzed by the isomerase and ligase classes of enzymes have been compiled. For each reaction the following information is given: the reference for the data; the reaction studied; the name of the enzyme used and its Enzyme Commission number; the method of measurement; the conditions of measurement (temperature, pH, ionic strength, and the buffer(s) and cofactor(s) used); the data and an evaluation of it; and, sometimes, commentary on the data and on any corrections which have been applied to it or any calculations for which the data have been used. The data from 176 references have been examined and evaluated. Chemical Abstract Service registry numbers are given for the substances involved in these various reactions. There is a cross reference between the substances and the Enzyme Commission numbers of the enzymes used to catalyze the reactions in which the substances participate.
High Merino weaner survival rates are a function of weaning weight and positive post-weaning growth rates
Authors: Hatcher S. , Eppleston J. , Thornberry K. J. , Watt B.
Published: June 2010

Survival and subsequent productivity of Merino ewe weaners (weaned in 2006 and 2007, respectively) on commercial properties in the New South Wales Central Tablelands were monitored through routine liveweight measurement until weaning of their own progeny from their maiden joining. Growth rates were calculated from the regular liveweight measurements with survival determined by the continuing presence of an individual animal at subsequent measurements. This study demonstrates that high weaner survival rates are a function of both weaning weight and post-weaning growth rates. Importantly, it indicates that low post-weaning growth rates can negate the survival benefit conferred by a high weaning weight such that weaners who were unable to sustain positive post-weaning growth rates were at high risk of death. Furthermore, classification of weaners into liveweight profile groups based on their weaning weight and post-weaning growth rates identified another group of weaners that are also at high risk of death. These weaners (14% of the mob) had above average weaning weights but low post-weaning growth rates and a mortality rate nearly 1.5 times that of the lightest cohort of weaners. High weaner survival rates about the 95% industry benchmark are possible if weaners show positive growth rates post weaning. Weaning weight continues to have a residual influence on the subsequent productivity of ewe weaners until they wean their first lambs. Maiden ewes that were heavier at weaning tend to have higher scanning percentages and are more likely to successfully rear their progeny to marking than their lighter weight counterparts. This finding should be taken into account when economic analyses of the benefits of alternative management strategies to promote weaner survival are undertaken.
Eastern grey kangaroo (Macropus giganteus) myofibres. 1. A simplified classification method using two commercially available antibodies
Authors: Spiegel N. B. , Johns W. H. , Sinclair S. D. , Wynn P. C. , Thompson J. M. , Greenwood P. L.
Published: June 2010

Skeletal muscles from eastern grey kangaroos (Macropus giganteus) were assessed for myofibre contractile and metabolic characteristics using immunocytochemical and histological staining of serial sections. Myofibre classification using monoclonal antibodies that typically bind to mammalian slow (clone WB-MHC), fast (clone MY-32) and Types 1, 2X and 2B (clone S5 8H2) myosin heavy chains was validated using acid- and alkali-preincubated myofibrillar ATPase, NADH and α-glycerophosphate dehydrogenase stains. Myofibres were classified as Type 1 (slow oxidative), Type 2A (fast oxidative-glycolytic), Type 2X/2B (fast glycolytic) or intermediate or transitional myofibre Types 2C (Type 1–Type 2A intermediate) and 2AX/B (Type 2A–Type 2X/2B intermediate). The Type 2 (fast) antibody (clone MY-32) used in the present study did not bind to a subset of fast myofibres in any of the eight kangaroo muscles investigated. These myofibres were identified as Type 2A using clone S5 8H2 and on the basis of the histochemical staining profile. Hence, a simplified immunostaining system using only clones WB-MHC (anti-Type 1) and MY-32 (anti-Type 2X/2B) allowed five myofibre types to be identified based on the staining pattern and intensity of staining for the two antibodies. It is concluded that the myofibres of muscles from kangaroos can be quickly classified into five types using two commercially available antibodies. This method is directly applicable for routine investigations into the myofibre properties of commercially important muscles from the kangaroo musculature and, when combined with enzymatic assays for oxidative and glycolytic activity, will allow for a better understanding of factors influencing the quality of meat from kangaroos.
Factors affecting the response of Bali cattle (Bos sondaicus) calves to supplementation prior to weaning
Authors: Jelantik I. G. N , Mullik M. L. , Leo-Penu C. , Copland R.
Published: June 2010

Some factors that contribute to variation in the responses of Bali cattle calves to dry season supplementation before weaning were examined on-farm in 10 villages located in three districts in East Nusa Tenggara Province, Indonesia from June to December 2008. The altitudes of the three districts were 0–100, 400 and 800 m above sea level. A total of 199 Bali (Banteng, Bos sondaicus) calves were offered a concentrate supplement from 1 month after birth (or June for calves born before May) at a level of 2% liveweight. The supplement consisted of grass hay and concentrate (rice bran, corn meal, leucaena leaf and fish meal) containing 18.6% crude protein. The supplement was offered to calves in the morning while confined to calf pens when the dams were released for grazing. Calves were reunited with the cows during the night. The effects of districts, herd size and month of birth on mortality rate, liveweight gain (LWG) and growth in supplemented calves were examined. Mortality rate averaged 1.0% and was not affected by month of birth, herd size or districts. The month of calving varied from March to September, but was mostly concentrated during June and July (55%). Month of birth did not significantly affect (P > 0.05) LWG of the calves, but the heart girth of calves born early (May) did increase at a slower rate (P < 0.05) than calves born late (August) (10 mm/day versus 27 mm/day). LWG of supplemented calves was faster (P < 0.05) in herds of 10 or less cow-calf pairs (220 g/day) than in herds of more than 10 cow-calf pairs (160 g/day). Altitude affected LWG (P < 0.05) of supplemented calves; gains were 170, 210 and 280 g/day for the three districts with altitudes of 1–100, 400 and 800 m, respectively. Implications of the factors affecting response to supplementation are discussed.
From third plural to passive
Authors: Siewierska Anna
Published: June 2010

This paper explores the development of third person plural impersonal constructions into passive ones with the aim of determining the conditions most conducive to the emergence of a canonical passive, i.e. one which is both promotional (with an overt lexical subject) and agentive (with an overt agent). On the basis of cross-linguistic data it is argued that the required conditions are, on the one hand, the existence of a morphological alignment which does not distinguish between the O of a transitive clause and the S of a passive one and, on the other hand, the availability of highly grammaticalized third person plural impersonals, i.e. ones which can be used in episodic contexts and with different types of agents, among them individual and specific ones. The documented rarity of promotional passives originating from third person plural impersonal constructions is attributed to the rarity of the coincidence of the above two sets of independent factors.
Functional Cross-Talk between Rab14 and Rab4 through a Dual Effector, RUFY1/Rabip4
Authors: Yamamoto Hideaki , Koga Hiroshi , Katoh Yohei , Takahashi Senye , Nakayama Kazuhisa , Shin Hye-Won
Published: June 2010

The small GTPase Rab14 localizes to early endosomes and the trans-Golgi network, but its cellular functions on endosomes and its functional relationship with other endosomal Rab proteins are poorly understood. Here, we report that Rab14 binds in a GTP-dependent manner to RUFY1/Rabip4, which had been originally identified as a Rab4 effector. Rab14 colocalizes well with Rab4 on peripheral endosomes. Depletion of Rab14, but not Rab4, causes dissociation of RUFY1 from endosomal membranes. Coexpression of RUFY1 with either Rab14 or Rab4 induces clustering and enlargement of endosomes, whereas a RUFY1 mutant lacking the Rab4-binding region does not induce a significant morphological change in the endosomal structures even when coexpressed with Rab14 or Rab4. These findings suggest that Rab14 and Rab4 act sequentially, together with RUFY1; Rab14 is required for recruitment of RUFY1 onto endosomal membranes, and subsequent RUFY1 interaction with Rab4 may allow endosomal tethering and fusion. Depletion of Rab14 or RUFY1, as well as Rab4, inhibits efficient recycling of endocytosed transferrin, suggesting that Rab14 and Rab4 regulate endosomal functions through cooperative interactions with their dual effector, RUFY1.
SPEX2: automated concise extraction of spatial gene expression patterns from Fly embryo ISH images
Authors: Puniyani Kriti , Faloutsos Christos , Xing Eric P.
Published: June 2010

Motivation: Microarray profiling of mRNA abundance is often ill suited for temporal–spatial analysis of gene expressions in multicellular organisms such as Drosophila. Recent progress in image-based genome-scale profiling of whole-body mRNA patterns via in situ hybridization (ISH) calls for development of accurate and automatic image analysis systems to facilitate efficient mining of complex temporal–spatial mRNA patterns, which will be essential for functional genomics and network inference in higher organisms.

Results: We present SPEX2, an automatic system for embryonic ISH image processing, which can extract, transform, compare, classify and cluster spatial gene expression patterns in Drosophila embryos. Our pipeline for gene expression pattern extraction outputs the precise spatial locations and strengths of the gene expression. We performed experiments on the largest publicly available collection of Drosophila ISH images, and show that our method achieves excellent performance in automatic image annotation, and also finds clusters that are significantly enriched, both for gene ontology functional annotations, and for annotation terms from a controlled vocabulary used by human curators to describe these images.

Availability: Software will be available at http://www.sailing.cs.cmu.edu/

Contact:  epxing@cs.cmu.edu

Supplementary information:  Supplementary data are avilable at Bioinformatics online.
Multivariate multi-way analysis of multi-source data
Authors: Huopaniemi Ilkka , Suvitaival Tommi , Nikkilä Janne , Orešič Matej , Kaski Samuel
Published: June 2010

Motivation: Analysis of variance (ANOVA)-type methods are the default tool for the analysis of data with multiple covariates. These tools have been generalized to the multivariate analysis of high-throughput biological datasets, where the main challenge is the problem of small sample size and high dimensionality. However, the existing multi-way analysis methods are not designed for the currently increasingly important experiments where data is obtained from multiple sources. Common examples of such settings include integrated analysis of metabolic and gene expression profiles, or metabolic profiles from several tissues in our case, in a controlled multi-way experimental setup where disease status, medical treatment, gender and time-series are usual covariates.

Results: We extend the applicability area of multivariate, multi-way ANOVA-type methods to multi-source cases by introducing a novel Bayesian model. The method is capable of finding covariate-related dependencies between the sources. It assumes the measurements consist of groups of similarly behaving variables, and estimates the multivariate covariate effects and their interaction effects for the discovered groups of variables. In particular, the method partitions the effects to those shared between the sources and to source-specific ones. The method is specifically designed for datasets with small sample sizes and high dimensionality.

We apply the method to a lipidomics dataset from a lung cancer study with two-way experimental setup, where measurements from several tissues with mostly distinct lipids have been taken. The method is also directly applicable to gene expression and proteomics.

Availability: An R-implementation is available at http://www.cis.hut.fi/projects/mi/software/multiWayCCA/

Contact:  ilkka.huopaniemi@tkk.fi; samuel.kaski@tkk.fi
Reconstruction of the neuromuscular junction connectome
Authors: Srinivasan Ranga , Li Qing , Zhou Xiaobo , Lu Ju , Lichtman Jeff , Wong Stephen T.C.
Published: June 2010

Motivation: Unraveling the structure and behavior of the brain and central nervous system (CNS) has always been a major goal of neuroscience. Understanding the wiring diagrams of the neuromuscular junction connectomes (full connectivity of nervous system neuronal components) is a starting point for this, as it helps in the study of the organizational and developmental properties of the mammalian CNS. The phenomenon of synapse elimination during developmental stages of the neuronal circuitry is such an example. Due to the organizational specificity of the axons in the connectomes, it becomes important to label and extract individual axons for morphological analysis. Features such as axonal trajectories, their branching patterns, geometric information, the spatial relations of groups of axons, etc. are of great interests for neurobiologists in the study of wiring diagrams. However, due to the complexity of spatial structure of the axons, automatically tracking and reconstructing them from microscopy images in 3D is an unresolved problem. In this article, AxonTracker-3D, an interactive 3D axon tracking and labeling tool is built to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. The ease of use along with accuracy of results makes AxonTracker-3D an attractive tool to obtain valuable quantitative information from axon datasets.

Availability: The software is freely available for download at http://www.cbi-tmhs.org/AxonTracker/

Contact:  stwong@tmhs.org
VARiD: A variation detection framework for color-space and letter-space platforms
Authors: Dalca Adrian V. , Rumble Stephen M. , Levy Samuel , Brudno Michael
Published: June 2010

Motivation: High-throughput sequencing (HTS) technologies are transforming the study of genomic variation. The various HTS technologies have different sequencing biases and error rates, and while most HTS technologies sequence the residues of the genome directly, generating base calls for each position, the Applied Biosystem's SOLiD platform generates dibase-coded (color space) sequences. While combining data from the various platforms should increase the accuracy of variation detection, to date there are only a few tools that can identify variants from color space data, and none that can analyze color space and regular (letter space) data together.

Results: We present VARiD—a probabilistic method for variation detection from both letter- and color-space reads simultaneously. VARiD is based on a hidden Markov model and uses the forward-backward algorithm to accurately identify heterozygous, homozygous and tri-allelic SNPs, as well as micro-indels. Our analysis shows that VARiD performs better than the AB SOLiD toolset at detecting variants from color-space data alone, and improves the calls dramatically when letter- and color-space reads are combined.

Availability: The toolset is freely available at http://compbio.cs.utoronto.ca/varid

Contact:  varid@cs.toronto.edu
TEAM: efficient two-locus epistasis tests in human genome-wide association study
Authors: Zhang Xiang , Huang Shunping , Zou Fei , Wang Wei
Published: June 2010

As a promising tool for identifying genetic markers underlying phenotypic differences, genome-wide association study (GWAS) has been extensively investigated in recent years. In GWAS, detecting epistasis (or gene–gene interaction) is preferable over single locus study since many diseases are known to be complex traits. A brute force search is infeasible for epistasis detection in the genome-wide scale because of the intensive computational burden. Existing epistasis detection algorithms are designed for dataset consisting of homozygous markers and small sample size. In human study, however, the genotype may be heterozygous, and number of individuals can be up to thousands. Thus, existing methods are not readily applicable to human datasets. In this article, we propose an efficient algorithm, TEAM, which significantly speeds up epistasis detection for human GWAS. Our algorithm is exhaustive, i.e. it does not ignore any epistatic interaction. Utilizing the minimum spanning tree structure, the algorithm incrementally updates the contingency tables for epistatic tests without scanning all individuals. Our algorithm has broader applicability and is more efficient than existing methods for large sample study. It supports any statistical test that is based on contingency tables, and enables both family-wise error rate and false discovery rate controlling. Extensive experiments show that our algorithm only needs to examine a small portion of the individuals to update the contingency tables, and it achieves at least an order of magnitude speed up over the brute force approach.

Contact:  xiang@cs.unc.edu
SuperTriplets: a triplet-based supertree approach to phylogenomics
Authors: Ranwez Vincent , Criscuolo Alexis , Douzery Emmanuel J.P.
Published: June 2010

Motivation: Phylogenetic tree-building methods use molecular data to represent the evolutionary history of genes and taxa. A recurrent problem is to reconcile the various phylogenies built from different genomic sequences into a single one. This task is generally conducted by a two-step approach whereby a binary representation of the initial trees is first inferred and then a maximum parsimony (MP) analysis is performed on it. This binary representation uses a decomposition of all source trees that is usually based on clades, but that can also be based on triplets or quartets. The relative performances of these representations have been discussed but are difficult to assess since both are limited to relatively small datasets.

Results: This article focuses on the triplet-based representation of source trees. We first recall how, using this representation, the parsimony analysis is related to the median tree notion. We then introduce SuperTriplets, a new algorithm that is specially designed to optimize this alternative formulation of the MP criterion. The method avoids several practical limitations of the triplet-based binary matrix representation, making it useful to deal with large datasets. When the correct resolution of every triplet appears more often than the incorrect ones in source trees, SuperTriplets warrants to reconstruct the correct phylogeny. Both simulations and a case study on mammalian phylogenomics confirm the advantages of this approach. In both cases, SuperTriplets tends to propose less resolved but more reliable supertrees than those inferred using Matrix Representation with Parsimony.

Availability: Online and JAVA standalone versions of SuperTriplets are available at http://www.supertriplets.univ-montp2.fr/

Contact:  vincent.ranwez@univ-montp2.fr
Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
Authors: Richards Adam J. , Muller Brian , Shotwell Matthew , Cowart L. Ashley , Rohrer Bäerbel , Lu Xinghua
Published: June 2010

Motivation: The results of initial analyses for many high-throughput technologies commonly take the form of gene or protein sets, and one of the ensuing tasks is to evaluate the functional coherence of these sets. The study of gene set function most commonly makes use of controlled vocabulary in the form of ontology annotations. For a given gene set, the statistical significance of observing these annotations or ‘enrichment’ may be tested using a number of methods. Instead of testing for significance of individual terms, this study is concerned with the task of assessing the global functional coherence of gene sets, for which novel metrics and statistical methods have been devised.

Results: The metrics of this study are based on the topological properties of graphs comprised of genes and their Gene Ontology annotations. A novel aspect of these methods is that both the enrichment of annotations and the relationships among annotations are considered when determining the significance of functional coherence. We applied our methods to perform analyses on an existing database and on microarray experimental results. Here, we demonstrated that our approach is highly discriminative in terms of differentiating coherent gene sets from random ones and that it provides biologically sensible evaluations in microarray analysis. We further used examples to show the utility of graph visualization as a tool for studying the functional coherence of gene sets.

Availability: The implementation is provided as a freely accessible web application at: http://projects.dbbe.musc.edu/gosteiner. Additionally, the source code written in the Python programming language, is available under the General Public License of the Free Software Foundation.

Contact:  lux@musc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Robust unmixing of tumor states in array comparative genomic hybridization data
Authors: Tolliver David , Tsourakakis Charalampos , Subramanian Ayshwarya , Shackney Stanley , Schwartz Russell
Published: June 2010

Motivation: Tumorigenesis is an evolutionary process by which tumor cells acquire sequences of mutations leading to increased growth, invasiveness and eventually metastasis. It is hoped that by identifying the common patterns of mutations underlying major cancer sub-types, we can better understand the molecular basis of tumor development and identify new diagnostics and therapeutic targets. This goal has motivated several attempts to apply evolutionary tree reconstruction methods to assays of tumor state. Inference of tumor evolution is in principle aided by the fact that tumors are heterogeneous, retaining remnant populations of different stages along their development along with contaminating healthy cell populations. In practice, though, this heterogeneity complicates interpretation of tumor data because distinct cell types are conflated by common methods for assaying the tumor state. We previously proposed a method to computationally infer cell populations from measures of tumor-wide gene expression through a geometric interpretation of mixture type separation, but this approach deals poorly with noisy and outlier data.

Results: In the present work, we propose a new method to perform tumor mixture separation efficiently and robustly to an experimental error. The method builds on the prior geometric approach but uses a novel objective function allowing for robust fits that greatly reduces the sensitivity to noise and outliers. We further develop an efficient gradient optimization method to optimize this ‘soft geometric unmixing’ objective for measurements of tumor DNA copy numbers assessed by array comparative genomic hybridization (aCGH) data. We show, on a combination of semi-synthetic and real data, that the method yields fast and accurate separation of tumor states.

Conclusions: We have shown a novel objective function and optimization method for the robust separation of tumor sub-types from aCGH data and have shown that the method provides fast, accurate reconstruction of tumor states from mixed samples. Better solutions to this problem can be expected to improve our ability to accurately identify genetic abnormalities in primary tumor samples and to infer patterns of tumor evolution.

Contact:  tolliver@cs.cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Optimal algorithms for haplotype assembly from whole-genome sequence data
Authors: He Dan , Choi Arthur , Pipatsrisawat Knot , Darwiche Adnan , Eskin Eleazar
Published: June 2010

Motivation: Haplotype inference is an important step for many types of analyses of genetic variation in the human genome. Traditional approaches for obtaining haplotypes involve collecting genotype information from a population of individuals and then applying a haplotype inference algorithm. The development of high-throughput sequencing technologies allows for an alternative strategy to obtain haplotypes by combining sequence fragments. The problem of ‘haplotype assembly’ is the problem of assembling the two haplotypes for a chromosome given the collection of such fragments, or reads, and their locations in the haplotypes, which are pre-determined by mapping the reads to a reference genome. Errors in reads significantly increase the difficulty of the problem and it has been shown that the problem is NP-hard even for reads of length 2. Existing greedy and stochastic algorithms are not guaranteed to find the optimal solutions for the haplotype assembly problem.

Results: In this article, we proposed a dynamic programming algorithm that is able to assemble the haplotypes optimally with time complexity O(m × 2k × n), where m is the number of reads, k is the length of the longest read and n is the total number of SNPs in the haplotypes. We also reduce the haplotype assembly problem into the maximum satisfiability problem that can often be solved optimally even when k is large. Taking advantage of the efficiency of our algorithm, we perform simulation experiments demonstrating that the assembly of haplotypes using reads of length typical of the current sequencing technologies is not practical. However, we demonstrate that the combination of this approach and the traditional haplotype phasing approaches allow us to practically construct haplotypes containing both common and rare variants.

Contact:  danhe@cs.ucla.edu