bluuebunny/crossref_metadata_2025 huggingface dataset:
Migration properties of non‐volcanic tremor in Shikoku, southwest Japan
Authors: Obara Kazushige , Matsuzawa Takanori , Tanaka Sachiko , Kimura Takeshi , Maeda Takuto
Published: May 2011

Based on the precise locations of deep non‐volcanic tremor in southwest Japan, which show a depth‐dependent behavior, we clarified characteristic properties of tremor migration. Major tremor swarms are mainly initiated at deep levels of the tremor zone, corresponding to areas of frequent minor tremor, and migrate up‐dip along the subduction interface. In central and eastern Shikoku, tremor occurs in two clusters, separated by a small gap, with the timing of tremor activity in the clusters differing by 1 or 2 days. The time evolution of tremor activity in western Shikoku reveals that the migration front of tremor propagates continuously and radially, even in the case of a tremor gap. These findings indicate that the rupture front of slow slip events propagates continuously and radially from the deep levels through the area without tremor activity. The occurrence of tremor may depend on the existence of inhomogeneous patches upon the plate interface.
Pollution from China increases cloud droplet number, suppresses rain over the East China Sea
Authors: Bennartz Ralf , Fan Jiwen , Rausch John , Leung L. Ruby , Heidinger Andrew K.
Published: May 2011

Rapid economic growth over the last 30 years in China has led to a significant increase in aerosol loading, which is mainly due to the increased emissions of its precursors such as SO2 and NOx. Here we show that these changes significantly affect wintertime clouds and precipitation over the East China Sea downwind of major emission sources. Satellite observations show an increase of cloud droplet number concentration from less than 200 cm−3 in the 1980s to more than 300 cm−3 in 2005. In the same time period, precipitation frequency reported by voluntary ship observers was reduced from more than 30% to less than 20% of the time. A back trajectory analysis showed the pollution in the investigation area to originate from the Shanghai‐Nanjing and Jinan industrial areas. A model sensitivity study was performed, isolating the effects of changes in emissions of the aerosol precursors SO2 and NOx on clouds and precipitation using a state‐of‐the‐art mesocale model including chemistry and aerosol indirect effects. Similar changes in cloud droplet number concentration over the East China Sea were obtained when the current industrial emissions in China were reduced to the 1980s levels. Simulated changes in precipitation were somewhat smaller than the observed changes but still significant.
Learning Features of Simple and Complex Cells: A Generative Approach via Multiplicative Interactions
Authors: Huang Wentao , Ji Zhengping , Kenyon Garrett
Published: May 2011

We develop a hierarchical generative model to learn features of simple and complex cells in the primary visual cortex via multiplicative interactions and address the problem of learning invariant visual representation from natural image sequences. Generally, the overall objective of a generative sparse coding model (Olshausen and Field, Nature, 1996) is to reconstruct the input *x* via a linear combination of feature bases *A = [A~1~,A~2~,...,A~M~]*, such that *x = As*, where s is the latent representation with a sparse constraint.In the proposed model, we added another hidden layer with complex cells to modulate the latent representation *s*, such that *s* is generated via an element-wise product of bottom-up representation *y = A^T^x* and top-down representation *z = Bc*, i.e., *s = y.*z* . Here *c* represents the top layer with complex cells, and *B* is the feature matrix connecting from the simple cell layer to the complex cell layer. Similar to the well known bilinear models (Tenenbaum and Freeman, Neural Computation, 2000) for invariant representation, the complex cell layer here represents the content variables and the simple cell layer represents the style variables. However, instead of using three-order tensor weight parameters as in the bilinear models, our model provides a factorized approach by the product of two two-order tensor weight parameters *A* and *B*, and thus makes learning simpler and more efficient. Moreover, while bilinear models dealt with two latent variables, our model contains only one latent variable *c* for invariant representation.The penalties of sparseness and slowness priors are integrated into this model as well. In addition, non-negativity constraints of the latent variable c and weight matrices *A* and *B* are enforced to fit the known neurophysiology better. We utilize the gradient descent algorithm to train our model from natural image sequences. A dictionary of Gabor-like orientation selective features is developed in the simple cell layer, where topography of receptive fields is automatically generated. In this way, similar simple cell receptive fields are pooled together to produce locally-invariant representation in complex cells.
Influences of film microstructure and defects on magnetization reversal in bit patterned Co/Pt multilayer thin film media
Authors: Guo Vickie W. , Lee Hwan-Soo , Zhu Jian-Gang
Published: May 2011

Quasisingle crystalline and polycrystalline Co/Pt multilayered films were prepared via sputtering technique. The polycrystalline Co/Pt multilayers exhibited an appreciable number of planar defects such as twin boundaries and stacking faults whereas few defects were present for the quasisingle crystalline films. The polycrystalline films had smoother surface, and as patterned into arrays of small islands, a smaller critical size for single domain was unexpectedly observed. The corresponding magnetic domain images revealed that nucleation interestingly occurred at any locations of a patterned element, which was attributed to the observed defects. Moreover, micromagnetic modeling was utilized to further quantitatively study influences of an anisotropically soft region (which can represent existing defects) in the patterned element on nucleation field in terms of exchange coupling strength.
Systematic method of generating new integrable systems via inverse Miura maps
Authors: Tsuchida Takayuki
Published: May 2011

We provide a new natural interpretation of the Lax representation for an integrable system; that is, the spectral problem is the linearized form of a Miura transformation between the original system and a modified version of it. On the basis of this interpretation, we formulate a systematic method of identifying modified integrable systems that can be mapped to a given integrable system by Miura transformations. Thus, this method can be used to generate new integrable systems from known systems through inverse Miura maps; it can be applied to both continuous and discrete systems in 1 + 1 dimensions as well as in 2 + 1 dimensions. The effectiveness of the method is illustrated using examples such as the nonlinear Schrödinger (NLS) system, the Zakharov–Ito system (two-component KdV), the three-wave interaction system, the Yajima–Oikawa system, the Ablowitz–Ladik lattice (integrable space-discrete NLS), and two (2 + 1)-dimensional NLS systems.
Domain wall and microwave assisted switching in an exchange spring bilayer
Authors: Fal T. J. , Livesey K. L. , Camley R. E.
Published: May 2011

We explore the response of a magnetic bilayer to a driving microwave field using micromagnetic simulations. The bilayer consists of 8 nm of a material with a high uniaxial anisotropy and 56 nm of a material with a lower uniaxial anisotropy. The width and length of the structure is 100 × 100 square microns. A small applied field, opposite to the magnetization, switches most of the lower anisotropy material but not the higher anisotropy material, forming a domain wall between the two materials. We evaluate the frequencies of the magnetic eigenmodes for the entire system using Fourier analysis and then drive the structure with an oscillating magnetic field at each of the eigenfrequencies. When the oscillating microwave field is added, the static switching field required to align both layers is decreased compared to the undriven case. With a driving field strength of 120 Oe the switching field is reduced by about 40%, from 1.12 kOe for the undriven case to 0.55 Oe for the driven case.
Two-dimensional Vlasov simulation of electron plasma wave trapping, wavefront bowing, self-focusing, and sideloss
Authors: Banks J. W. , Berger R. L. , Brunner S. , Cohen B. I. , Hittinger J. A. F.
Published: May 2011

Two-dimensional Vlasov simulations of nonlinear electron plasma waves are presented, in which the interplay of linear and nonlinear kinetic effects is evident. The plasma wave is created with an external traveling wave potential with a transverse envelope of width Δy such that thermal electrons transit the wave in a “sideloss” time, tsl~Δy/ve. Here, ve is the electron thermal velocity. The quasisteady distribution of trapped electrons and its self-consistent plasma wave are studied after the external field is turned off. In cases of particular interest, the bounce frequency, ωbe=keϕ/me, satisfies the trapping condition ωbetsl>2π such that the wave frequency is nonlinearly downshifted by an amount proportional to the number of trapped electrons. Here, k is the wavenumber of the plasma wave and ϕ is its electric potential. For sufficiently short times, the magnitude of the negative frequency shift is a local function of ϕ. Because the trapping frequency shift is negative, the phase of the wave on axis lags the off-axis phase if the trapping nonlinearity dominates linear wave diffraction. In this case, the phasefronts are curved in a focusing sense. In the opposite limit, the phasefronts are curved in a defocusing sense. Analysis and simulations in which the wave amplitude and transverse width are varied establish criteria for the development of each type of wavefront. The damping and trapped-electron-induced focusing of the finite-amplitude electron plasma wave are also simulated. The damping rate of the field energy of the wave is found to be about the sideloss rate, νe~tsl-1. For large wave amplitudes or widths Δy, a trapping-induced self-focusing of the wave is demonstrated.
Barrier height of Pt–InxGa1−xN (≤x≤0.5) nanowire Schottky diodes
Authors: Guo Wei , Banerjee Animesh , Zhang Meng , Bhattacharya Pallab
Published: May 2011

The barrier height of Schottky diodes made on InxGa1−xN nanowires have been determined from capacitance-voltage measurements. The nanowires were grown undoped on n-type (001) silicon substrates by plasma-assisted molecular beam epitaxy. The length, diameter and density of the nanowires are ∼1 μm, 20 nm, and 1×1011 cm−2. The Schottky contact was made on the top surface of the nanowires with Pt after planarizing with parylene. The measured barrier height ΦB varies from 1.4 eV (GaN) to 0.44 eV (In0.5Ga0.5N) and agrees well with the ideal barrier heights in the Schottky limit.
Whispering gallery mode enhanced luminescence from an individual ZnO micro- and nanoscaled optical resonator
Authors: Yang Y. H. , Dong J. W. , Wang N. W. , Yang G. W.
Published: May 2011

A whispering gallery mode optical resonator has been achieved using individual ZnO micro- and nanocolumns. Monochromatic cathodoluminescence images of the ZnO micro- and nanocolumns show that enhanced luminescence intensity is located across the profile of the micro- and nanocolumns, and is mainly attributed to the whispering gallery mode (WGM) enhanced emission. The individual hexagonal ZnO micro- and nanocolumns are regarded as an optical resonator structure. Theoretical calculations and computer simulations based on the finite-difference time-domain suggest that the WGMs are generated in the ZnO micro- and nanocolumns, and these results agree closely with the experimental results.
Metal-semiconductor transition in NiFe2O4 nanoparticles due to reverse cationic distribution by impedance spectroscopy
Authors: Younas M. , Nadeem M. , Atif M. , Grossinger R.
Published: May 2011

We have investigated the magnetic and electrical response of the sol-gel synthesized NiFe2O4 nanoparticles. Changes in the impedance plane plots with temperature have been discussed and correlated to the microstructure of the material. Thermally activated hopping carriers between Fe3+-Fe2+ and Ni2+-Ni3+ ions have been determined for a decrease in the resistance of the sample and a change in the conduction mechanism around 318 K. The mixed spinel structure and broken exchange bonds due to small size effects are due to the canted spin structure at the surface of the nanoparticles. The magnetization is found to be influenced by the surface spin canting and anisotropy. We have established the semiconducting to metallic transition (SMT) temperature to be around 358 K in terms of localized and delocalized eg electrons along with a transition from less conductive [Fe3+–O2−–Fe3+] and [Ni2+–O2−–Ni2+] linkage to more conductive [Fe3+–Fe2+] and [Ni2+–Ni3+] linkage at the octahedral B site. A decrease in the dielectric constant with temperature has been discussed in terms of the depletion of space charge layers due to the repulsion of delocalized eg electrons from the grain boundary planes. The anomalies in tangent loss and conductivity data around 358 K are discussed in the context of the SMT.
State resolved vibrational relaxation modeling for strongly nonequilibrium flows
Authors: Boyd Iain D. , Josyula Eswar
Published: May 2011

Vibrational relaxation is an important physical process in hypersonic flows. Activation of the vibrational mode affects the fundamental thermodynamic properties and finite rate relaxation can reduce the degree of dissociation of a gas. Low fidelity models of vibrational activation employ a relaxation time to capture the process at a macroscopic level. High fidelity, state-resolved models have been developed for use in continuum gas dynamics simulations based on computational fluid dynamics (CFD). By comparison, such models are not as common for use with the direct simulation Monte Carlo (DSMC) method. In this study, a high fidelity, state-resolved vibrational relaxation model is developed for the DSMC technique. The model is based on the forced harmonic oscillator approach in which multi-quantum transitions may become dominant at high temperature. Results obtained for integrated rate coefficients from the DSMC model are consistent with the corresponding CFD model. Comparison of relaxation results obtained with the high-fidelity DSMC model shows significantly less excitation of upper vibrational levels in comparison to the standard, lower fidelity DSMC vibrational relaxation model. Application of the new DSMC model to a Mach 7 normal shock wave in carbon monoxide provides better agreement with experimental measurements than the standard DSMC relaxation model.
Reversible phase changes in Ge–Au nanoparticles
Authors: Guzman J. , Boswell-Koller C. N. , Beeman J. W. , Bustillo K. C. , Conry T. , Dubón O. D. , Hansen W. L. , Levander A. X. , Liao C. Y. , Lieten R. R. , Sawyer C. A. , Sherburne M. P. , Shin S. J. , Stone P. R. , Watanabe M. , Yu K. M. , Ager J. W. , Chrzan D. C. , Haller E. E.
Published: May 2011

We demonstrate a reversible phase transition in nanoparticles composed of a binary eutectic alloy, Ge–Au. The structure, 9 nm diameter nanoparticles embedded in silica, can be switched from bilobe to mixed using a 30 ns ultraviolet laser pulse. The structure can be switched back to bilobe by heating at 80 °C. The bilobe/mixed switching can be performed on the same sample at least ten times. Synchrotron X-ray diffraction studies reveal that the bilobe structure contains crystalline Ge and Au while the mixed structure consists of crystalline Ge and β Ge–Au.
Testing the parametric two-electron reduced-density-matrix method with improved functionals: Application to the conversion of hydrogen peroxide to oxywater
Authors: Schwerdtfeger Christine A. , DePrince A. Eugene , Mazziotti David A.
Published: May 2011

Parametrization of the two-electron reduced density matrix (2-RDM) has recently enabled the direct calculation of electronic energies and 2-RDMs at the computational cost of configuration interaction with single and double excitations. While the original Kollmar energy functional yields energies slightly better than those from coupled cluster with single-double excitations, a general family of energy functionals has recently been developed whose energies approach those from coupled cluster with triple excitations [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)]. In this paper we test the parametric 2-RDM method with one of these improved functionals through its application to the conversion of hydrogen peroxide to oxywater. Previous work has predicted the barrier from oxywater to hydrogen peroxide with zero-point energy correction to be 3.3-to-3.9 kcal/mol from coupled cluster with perturbative triple excitations [CCSD(T)] and -2.3 kcal/mol from complete active-space second-order perturbation theory (CASPT2) in augmented polarized triple-zeta basis sets. Using a larger basis set than previously employed for this reaction—an augmented polarized quadruple-zeta basis set (aug-cc-pVQZ)—with extrapolation to the complete basis-set limit, we examined the barrier with two parametric 2-RDM methods and three coupled cluster methods. In the basis-set limit the M parametric 2-RDM method predicts an activation energy of 2.1 kcal/mol while the CCSD(T) barrier becomes 4.2 kcal/mol. The dissociation energy of hydrogen peroxide to hydroxyl radicals is also compared to the activation energy for oxywater formation. We report energies, optimal geometries, dipole moments, and natural occupation numbers. Computed 2-RDMs nearly satisfy necessary N-representability conditions.
Surface chemical reaction of laser ablated aluminum sample for detonation initiation
Authors: Kim Chang-hwan , Yoh Jack J.
Published: May 2011

We explore the evolution of metal plasma generated by high laser irradiances and its effect on the surrounding air by using shadowgraph images after laser pulse termination; hence the formation of laser supported detonation and combustion processes has been investigated. The essence of the paper is in observing initiation of chemical reaction between ablated aluminum plasma and oxygen from air by inducing high power laser pulse (>1000 mJ/pulse) and conduct a quantitative comparison of chemically reactive laser initiated waves with the classical detonation of exploding aluminum (dust) cloud in air. Findings in this work may lead to a new method of initiating detonation from metal sample in its bulk form without the need of mixing nano-particles with oxygen for initiation.
The intermolecular structure of phosphoric acid–N,N-dimethylformamide mixtures as studied by computer simulation
Authors: Fedorova Irina V. , Kiselev Michael G. , Safonova Lyubov P.
Published: May 2011

The computer simulation of H3PO4–N,N-dimethylformamide (DMF) mixtures over the whole concentration range using molecular dynamic (MD) methods has been carried out. The preferential orientations of the nearest neighbors of H3PO4 and DMF molecules were obtained using the ranked radial distribution functions technique. On the basis of MD results, the parameters of hydrogen bonds between molecules in mixture were calculated. The changes of the intermolecular structure of mixture as a function of acid composition over the whole concentration range were analyzed and reported. Analysis of O···H distance distributions and angles between O−H (H3PO4) and C=O (DMF) or P=O (H3PO4) vector distributions showed that O(DMF) and O(H3PO4) may each have two hydrogen bonds.
U(N) coherent states for loop quantum gravity
Authors: Freidel Laurent , Livine Etera R.
Published: May 2011

We investigate the geometry of the space of N-valent SU(2) intertwiners. We propose a new set of holomorphic operators acting on this space and a new set of coherent states which are covariant under U(N) transformations. These states are labeled by elements of the Grassmannian GrN, 2, they possess a direct geometrical interpretation in terms of framed polyhedra and are shown to be related to the well-known coherent intertwiners.
Far field subwavelength focusing using optical eigenmodes
Authors: Baumgartl Jörg , Kosmeier Sebastian , Mazilu Michael , Rogers Edward T. F. , Zheludev Nikolay I. , Dholakia Kishan
Published: May 2011

We report the focusing of light to generate a subdiffractive, subwavelength focal spot of full width half maximum 222 nm at an operating wavelength of 633 nm using an optical eigenmode approach. Crucially, the spot is created in the focal plane of a microscope objective thus yielding a practical working distance for applications. The optical eigenmode approach is implemented using an optimal superposition of Bessel beams on a spatial light modulator. The effects of partial coherence are also discussed. This far field method is a key advance toward the generation of subdiffractive optical features for imaging and lithographic purposes.
Mass spectrometric study on inactivation mechanism of spore-forming bacteria by low-pressure surface-wave excited oxygen plasma
Authors: Zhao Ying , Ogino Akihisa , Nagatsu Masaaki
Published: May 2011

In this letter, the etching phenomena of the spore-forming bacteria by oxygen plasma were investigated by using quadrupole mass spectrometry. The etching by-products of H2O and CO2 were obviously detected during the oxygen plasma irradiation by the multiple ion detection measurement. Inactivation of roughly 106 spores population was achieved under almost the same reduced spore shapes for three different incident microwave powers. It is considered from the present results that the oxygen radical etching could cause damage to the germinant receptors located in the inner membrane inevitable for germination of spores, without any damage of the DNA in the cores.
Frequency modulation of spin torque oscillator pairs
Authors: Pogoryelov Ye. , Muduli P. K. , Bonetti S. , Iacocca E. , Mancoff Fred , Åkerman Johan
Published: May 2011

The current controlled modulation of nanocontact based spin torque oscillator (STO) pairs is studied in both the synchronized and nonsynchronized states. The synchronized state shows a well behaved modulation and demonstrates robust mutual locking even under strong modulation. The power distribution of the modulation sidebands can be quantitatively described by assuming a single oscillator model. However, in the nonsynchronized state, the modulation sidebands are not well described by the model, indicating interactions between the two individual nanocontact STOs. These findings are promising for potential applications requiring the modulation of large synchronized STO arrays.
Negative thermal expansion in ZnF2
Authors: Chatterji Tapan , Zbiri Mohamed , Hansen Thomas C.
Published: May 2011

We have investigated temperature dependence of the lattice parameters and the unit cell volume of ZnF2 by neutron diffraction and have discovered negative thermal expansion (NTE) at low temperature. To understand why this simple compound exhibits NTE we performed first principle calculations. These calculations reproduce qualitatively the experimental temperature dependence of volume.
Micronutrient fractionation and plant availability in bauxite-processing residue sand
Authors: Thiyagarajan Chitdeshwari , Phillips I. R. , Dell B. , Bell Richard W.
Published: May 2011

Bauxite-processing residue must be disposed of in specifically designed facilities for long-term management. Consideration of alkalinity, salinity, sodium content, and poor nutritional status is essential for successful rehabilitation of residue disposal areas (RDA). The aim of this study was to examine the availability and distribution of the micronutrients, B, Cu, Fe, Mn, and Zn, in (i) fresh bauxite-processing residue sand (particle size >150 μm) with and without gypsum amendment, and (ii) aged residue sand from a 4-year-old rehabilitated RDA that had received past gypsum and fertiliser addition. Samples of fresh residue sand from India and Australia exhibited high alkalinity, high salinity, and sodicity. Gypsum addition significantly lowered pH, soluble Na, and alkalinity. Aged residue sand had low levels of all micronutrients, with low extractability for Zn and Mn followed by B, Cu, and Fe. Fractionation showed that 30–78% of Zn and Mn and 40–60% of B existed in non-available (residual) forms. The next most dominant fractions were the Fe and Mn oxide-bound and carbonate-bound fractions. Plant-available fractions (i.e. exchangeable and organically bound) contributed <1% of the total concentration. Total concentration was found to be a reliable indicator for Zn, Cu, and B extractability but not for DTPA-extractable forms of Fe and Mn. Leaf analysis of vegetation grown on aged residue sand indicated deficiencies of Mn and B. Results demonstrated that bauxite-processing residue sand contained very low levels of B, Mn, and Zn and these concentrations may be limiting to plant growth. Distribution of micronutrients among chemical pools was significantly influenced by pH, organic carbon, exchangeable Na, and alkalinity of residue. Nutrient management strategies that account for the characteristics of residue sand need to be developed for residue rehabilitation. Importantly, strategies to limit the conversion of nutrients to non-available forms are required to minimise micronutrient disorders.
Emergence of segregation in evolving social networks
Authors: Henry Adam Douglas , Prałat Paweł , Zhang Cun-Quan
Published: May 2011

In many social networks, there is a high correlation between the similarity of actors and the existence of relationships between them. This paper introduces a model of network evolution where actors are assumed to have a small aversion from being connected to others who are dissimilar to themselves, and yet no actor strictly prefers a segregated network. This model is motivated by Schelling’s [Schelling TC (1969) Models of segregation.
Am Econ Rev
59:488–493] classic model of residential segregation, and we show that Schelling’s results also apply to the structure of networks; namely, segregated networks always emerge regardless of the level of aversion. In addition, we prove analytically that attribute similarity among connected network actors always reaches a stationary distribution, and this distribution is independent of network topology and the level of aversion bias. This research provides a basis for more complex models of social interaction that are driven in part by the underlying attributes of network actors and helps advance our understanding of why dysfunctional social network structures may emerge.
Quiver varieties and path realizations arising from adjoint crystals of type 𝐴_{𝑛}⁽¹⁾
Authors: Kang Seok-Jin , Park Euiyong
Published: May 2011

Let

B
(

Λ
0

)

B(\Lambda _0)

be the level 1 highest weight crystal of the quantum affine algebra

U
q

(

A
n

(
1
)

)

U_q(A_n^{(1)})

. We construct an explicit crystal isomorphism between the geometric realization

B

(

Λ
0

)

\mathbb {B}(\Lambda _0)

of

B
(

Λ
0

)

B(\Lambda _0)

via quiver varieties and the path realization

P

ad

(

Λ
0

)

{\mathcal P}^{\textrm {ad}}(\Lambda _0)

of

B
(

Λ
0

)

B(\Lambda _0)

arising from the adjoint crystal

B

ad

B^{\textrm {ad}}

.
Release mode of large and small dense-core vesicles specified by different synaptotagmin isoforms in PC12 cells
Authors: Zhang Zhen , Wu Yao , Wang Zhao , Dunning F. Mark , Rehfuss Jonathan , Ramanan Deepshika , Chapman Edwin R. , Jackson Meyer B.
Published: May 2011

Many cells release multiple substances in different proportions according to the specific character of a stimulus. PC12 cells, a model neuroendocrine cell line, express multiple isoforms of the exocytotic Ca2+sensor synaptotagmin. We show that these isoforms sort to populations of dense-core vesicles that differ in size. These synaptotagmins differ in their Ca2+sensitivities, their preference for full fusion or kiss-and-run, and their sensitivity to inhibition by synaptotagmin IV. In PC12 cells, vesicles that harbor these different synaptotagmin isoforms can be preferentially triggered to fuse by different forms of stimulation. The mode of fusion is specified by the synaptotagmin isoform activated, and because kiss-and-run exocytosis can filter small molecules through a size-limiting fusion pore, the activation of isoforms that favor kiss-and-run will select smaller molecules over larger molecules packaged in the same vesicle. Thus synaptotagmin isoforms can provide multiple levels of control in the release of different molecules from the same cell.
GEST: a gene expression search tool based on a novel Bayesian
similarity metric
Authors: Hunter Lawrence , Taylor Ronald C. , Leach Sonia M. , Simon Richard
Published: May 2011

Gene expression array technology has made possible the assay of expression levels of tens of thousands of genes at a time; large databases of such measurements are currently under construction. One important use of such databases is the ability to search for experiments that have similar gene expression levels as a query, potentially identifying previously unsuspected relationships among cellular states. Such searches depend crucially on the metric used to assess the similarity between pairs of experiments. The complex joint distribution of gene expression levels, particularly their correlational structure and non-normality, make simple similarity metrics such as Euclidean distance or correlational similarity scores suboptimal for use in this application. We present a similarity metric for gene expression array experiments that takes into account the complex joint distribution of expression values. We provide a computationally tractable approximation to this measure, and have implemented a database search tool based on it. We discuss implementation issues and efficiency, and we compare our new metric to other standard metrics.

Contact: larry.hunter@uchsc.edu
Design of a compartmentalized shotgun assembler for the human

genome
Authors: Huson Daniel H. , Reinert Knut , Kravitz Saul A. , Remington Karin A. , Delcher Art L. , Dew Ian M. , Flanigan Mike , Halpern Aaron L. , Lai Zhongwu , Mobarry Clark M. , Sutton Granger G. , Myers Eugene W.
Published: May 2011

Two different strategies for determining the human genome are currently being pursued: one is the “clone-by-clone” approach, employed by the publicly funded project, and the other is the “whole genome shotgun assembler” approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called compartmentalized shotgun assembly, makes use of preliminary data produced by both approaches. In this paper we describe the design, implementation and operation of the “compartmentalized shotgun assembler”.

Contact: Knut.Reinert@celera.com
Designing fast converging phylogenetic methods
Authors: Nakhleh Luay , Roshan Usman , St. John Katherine , Sun Jerry , Warnow Tandy
Published: May 2011

Absolute fast converging phylogenetic reconstruction methods are provably guaranteed to recover the true tree with high probability from sequences that grow only polynomially in the number of leaves, once the edge lengths are bounded arbitrarily from above and below. Only a few methods have been determined to be absolute fast converging; these have all been developed in just the last few years, and most are polynomial time. In this paper, we compare pre-existing fast converging methods as well as some new polynomial time methods that we have developed. Our study, based upon simulating evolution under a wide range of model conditions, establishes that our new methods outperform both neighbor joining and the previous fast converging methods, returning very accurate large trees, when these other methods do poorly.

Contact: usman@cs.utexas.edu
An algorithm for finding signals of unknown length in DNA
sequences
Authors: Pavesi Giulio , Mauri Giancarlo , Pesole Graziano
Published: May 2011

Pattern discovery in unaligned DNA sequences is a challenging problem in both computer science and molecular biology. Several different methods and techniques have been proposed so far, but in most of the cases signals in DNA sequences are very complicated and avoid detection. Exact exhaustive methods can solve the problem only for short signals with a limited number of mutations. In this work, we extend exhaustive enumeration also to longer patterns. More in detail, the basic version of algorithm presented in this paper, given as input a set of sequences and an error ratio ε < 1, finds all patterns that occur in at least q sequences of the set with at most εm mutations, where m is the length of the pattern. The only restriction is imposed on the location of mutations along the signal. That is, a valid occurrence of a pattern can present at most ⌈εi⌉ mismatches in the first i nucleotides, and so on. However, we show how the algorithm can be used also when no assumption can be made on the position of mutations. In this case, it is also possible to have an estimate of the probability of finding a signal according to the signal length, the error ratio, and the input parameters. Finally, we discuss some significance measures that can be used to sort the patterns output by the algorithm.

Contact: pavesi@disco.unimib.it
Inferring subnetworks from perturbed expression profiles
Authors: Pe’er Dana , Regev Aviv , Elidan Gal , Friedman Nir
Published: May 2011

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways.

Contact: danab@cs.huji.ac.il
An insight into domain combinations
Authors: Apic Gordana , Gough Julian , Teichmann Sarah A.
Published: May 2011

Domains are the building blocks of all globular proteins, and are units of compact three-dimensional structure as well as evolutionary units. There is a limited repertoire of domain families, so that these domain families are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products. The processes that produce new genes are duplication and recombination as well as gene fusion and fission. We attempt to gain an overview of these processes by studying the structural domains in the proteins of seven genomes from the three kingdoms of life: Eubacteria, Archaea and Eukaryota. We use here the domain and superfamily definitions in Structural Classification of Proteins Database (SCOP) in order to map pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 624 out of the 764 superfamilies in SCOP in these genomes, and the 624 families occur in 585 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour. This type of pattern can be described by a scale-free network. Finally, we study domain repeats and we compare the set of the domain combinations in the genomes to those in PDB, and discuss the implications for structural genomics.

Contact: apic@mrc-lmb.cam.ac.uk
The metric space of proteins—comparative study of clustering algorithms
Authors: Sasson Ori , Linial Nathan , Linial Michal
Published: May 2011

Motivation: A large fraction of biological research concentrates on individual proteins and on small families of proteins. One of the current major challenges in bioinformatics is to extend our knowledge to very large sets of proteins. Several major projects have tackled this problem. Such undertakings usually start with a process that clusters all known proteins or large subsets of this space. Some work in this area is carried out automatically, while other attempts incorporate expert advice and annotation.

Results: We propose a novel technique that automatically clusters protein sequences. We consider all proteins in SWISSPROT, and carry out an all-against-all BLAST similarity test among them. With this similarity measure in hand we proceed to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. Here we compare the clusters that result from alternative merging rules, and validate the results against InterPro.

Our preliminary results show that clusters that are consistent with several rather than a single merging rule tend to comply with InterPro annotation. This is an affirmation of the view that the protein space consists of families that differ markedly in their evolutionary conservation.

Availability: The outcome of these investigations can be viewed in an interactive Web site at http://www.protonet.cs.huji.ac.il

Supplementary information: Biological examples for comparing the performance of the different algorithms used for classification are presented in http://www.protonet.cs.huji.ac.il/examples.html

Contact: ori@cs.huji.ac.il

Keywords: protein families; protein classification; sequence alignment; clustering.
Evaluating machine learning approaches for aiding probe
selection for gene-expression arrays
Authors: Tobler J. B. , Molla M.N. , Nuwaysir E.F. , Green R.D. , Shavlik J.W.
Published: May 2011

Motivation: Microarrays are a fast and cost-effective method of performing thousands of DNA hybridization experiments simultaneously. DNA probes are typically used to measure the expression level of specific genes. Because probes greatly vary in the quality of their hybridizations, choosing good probes is a difficult task. If one could accurately choose probes that are likely to hybridize well, then fewer probes would be needed to represent each gene in a gene-expression microarray, and, hence, more genes could be placed on an array of a given physical size. Our goal is to empirically evaluate how successfully three standard machine-learning algorithms—naïve Bayes, decision trees, and artificial neural networks—can be applied to the task of predicting good probes. Fortunately it is relatively easy to get training examples for such a learning task: place various probes on a gene chip, add a sample where the corresponding genes are highly expressed, and then record how well each probe measures the presence of its corresponding gene. With such training examples, it is possible that an accurate predictor of probe quality can be learned.

Results: Two of the learning algorithms we investigate—naïve Bayes and neural networks—learn to predict probe quality surprisingly well. For example, in the top ten predicted probes for a given gene not used for training, on average about five rank in the top 2.5% of that gene's hundreds of possible probes. Decision-tree induction and the simple approach of using predicted melting temperature to rank probes perform significantly worse than these two algorithms. The features we use to represent probes are very easily computed and the time taken to score each candidate probe after training is minor. Training the naïve Bayes algorithm takes very little time, and while it takes over 10 times as long to train a neural network, that time is still not very substantial (on the order of a few hours on a desktop workstation). We also report the information contained in the features we use to describe the probes. We find the fraction of cytosine in the probe to be the most informative feature. We also find, not surprisingly, that the nucleotides in the middle of the probes sequence are more informative than those at the ends of the sequence.

Contact: molla@cs.wisc.edu

Keywords: microarrays; probe selection; artificial neural networks; decision trees; naïve Bayes.

*To whom correspondence should be addressed.
Multiple genome rearrangement: a general approach via the evolutionary genome graph
Authors: Korkin Dmitry , Goldfarb Lev
Published: May 2011

Motivation: In spite of a well-known fact that genome rearrangements are supposed to be viewed in the light of the evolutionary relationships within and between the species involved, no formal underlying framework based on the evolutionary considerations for treating the questions arising in the area has been proposed. If such an underlying framework is provided, all the basic questions in the area can be posed in a biologically more appropriate and useful form: e.g., the similarity between two genomes can then be computed via the nearest ancestor, rather than ‘directly’, ignoring the evolutionary connections.

Results: We outline an evolution-based general framework for answering questions related to the multiple genome rearrangement. In the proposed model, the evolutionary genome graph (EG-graph) encapsulates an evolutionary history of a genome family. For a set of all EG-graphs, we introduce a family of similarity measures, each defined via a fixed set of genome transformations. Given a set of genomes and restricting ourselves to the transpositions, an algorithm for constructing an EG-graph is presented. We also present the experimental results in the form of an EG-graph for a set of concrete genomes (for several species). This EG-graph turns out to be very close to the corresponding known phylogenetic tree.

Contact: dkorkin@unb.ca

Keywords: genome rearrangement; evolutionary model; gene transformations; longest common subsequence; ETS framework.

*To whom correspondence should be addressed.
Mining viral protease data to extract cleavage knowledge
Authors: Narayanan Ajit , Wu Xikun , Yang Z. Rong
Published: May 2011

Motivation: The motivation is to identify, through machine learning techniques, specific patterns in HIV and HCV viral polyprotein amino acid residues where viral protease cleaves the polyprotein as it leaves the ribosome. An understanding of viral protease specificity may help the development of future anti-viral drugs involving protease inhibitors by identifying specific features of protease activity for further experimental investigation. While viral sequence information is growing at a fast rate, there is still comparatively little understanding of how viral polyproteins are cut into their functional unit lengths. The aim of the work reported here is to investigate whether it is possible to generalise from known cleavage sites to unknown cleavage sites for two specific viruses—HIV and HCV. An understanding of proteolytic activity for specific viruses will contribute to our understanding of viral protease function in general, thereby leading to a greater understanding of protease families and their substrate characteristics.

Results: Our results show that artificial neural networks and symbolic learning techniques (See5) capture some fundamental and new substrate attributes, but neural networks outperform their symbolic counterpart.

Availability: Publicly available software was used (Stuttgart Neural Network Simulator—http://www-ra.informatik.uni-tuebingen.de/SNNS/ and See5—http://www.rulequest.com. The datasets used (HIV, HCV) for See5 are available at: http://www.dcs.ex.ac.uk/~anarayan/bioinf/ismbdatasets/

Keywords: protase cleavage; protease inhibitors; machine learning; neural networks; decision trees.

Contact: a.narayanan@ex.ac.uk; wuxikun@yahoo.com; z.r.yang@ex.ac.uk
Support vector regression applied to the determination of
the developmental age of a Drosophila embryo from its
segmentation gene expression patterns
Authors: Myasnikova E. , Samsonova A. , Samsonova M. , Reinitz J.
Published: May 2011

Motivation: In this paper we address the problem of the determination of developmental age of an embryo from its segmentation gene expression patterns in Drosophila.

Results: By applying support vector regression we have developed a fast method for automated staging of an embryo on the basis of its gene expression pattern. Support vector regression is a statistical method for creating regression functions of arbitrary type from a set of training data. The training set is composed of embryos for which the precise developmental age was determined by measuring the degree of membrane invagination. Testing the quality of regression on the training set showed good prediction accuracy. The optimal regression function was then used for the prediction of the gene expression based age of embryos in which the precise age has not been measured by membrane morphology. Moreover, we show that the same accuracy of prediction can be achieved when the dimensionality of the feature vector was reduced by applying factor analysis. The data reduction allowed us to avoid over-fitting and to increase the efficiency of the algorithm.

Availability: This software may be obtained from the authors.

Contact: samson@fn.csa.ru

Keywords: gene expression patterns; development; embryo staging; support vector regression; segmentation genes; Drosophila.

*To whom correspondence should be addressed.
Estonian Genome Project—before the take-off and
take-off
Authors: Metspalu Andres
Published: May 2011

I will give an overview of the preparations of the EGP including all aspects of the project and current satus of the pilot phase, describe the informatics part of the project together with other aspects (legal, ethical, logistics, financial etc.) and where we stand in terms of population genetics and genotyping technology in order to start using the sample collection for case—control studies for revealing the genetic component of the common diseases.
Proteome analysis based on motif statistics
Authors: Nicodème P. , Doerks T. , Vingron M.
Published: May 2011

Motivation: Even for the amino acid motifs collected in the Prosite database there may be chance occurences as opposed to those occurences where the motif is involved in fold or function of a protein. With recent mathematical advances in assessing the significance of observing such a motif a particular number of times, we can now study the over- or under-representation of particular motifs in a complete genome and attempt to make functional deductions.

Results: We demonstrate that statistical over- or under-representation of motifs in complete proteomes may be an indicator of whether, in that organism, we are looking at chance occurrences of the motif or whether the occurrences are sufficiently numerous to suggest a systematic, and thus functionally important occurrence. This has important implications on databank annotations.

Availability: The complete dataset comprising the plotted statistics of 266 Prosite motifs on 42 proteomes is available at http://algo.inria.fr/nicodeme/proteomes/proteocomp.html. The software used to compute this data has been described by Nicodème (2000, 2001). They are available either by web access as mentioned in these articles or by direct request from Pierre Nicodème.

Contact: nicodeme@genopole.cnrs.fr
Correlating gene promoters and expression in gene disruption experiments
Authors: Palin Kimmo , Ukkonen Esko , Brazma Alvis , Vilo Jaak
Published: May 2011

Motivation: Finding putative transcription factor binding sites in the upstream sequences of similarly expressed genes has recently become a subject of intensive studies. In this paper we investigate how much gene expression regulation can be attributed to the presence of various binding sites in the gene promoters by correlating the binding sites and the changes in gene expression resulting from gene disruptions (e.g. knockouts).

Results: We have developed a data analysis method for comparing mRNA measurements of gene disruption experiments with information about gene promoters. The method was applied to a well–known dataset to uncover correlations between known transcription factor binding site motifs in the upstream regions of all S. cerevisiae genes and the gene expression changes in various gene disruption experiments. The possible explanations of the correlations were categorized and analyzed using e.g. expression cascades. Several correlations turned out to be consistent with existing biological knowledge while some new ones suggest themselves for further study.

Availability: The resulting tables are available at http://www.cs.helsinki.fi/u/kpalin/CorrDisrupt/.

Contact: kimmo.palin@cs.helsinki.fi