bluuebunny/crossref_metadata_2025 huggingface dataset:
The HELP inequality for lim-p Hamiltonian systems
Authors: Brown B. M. , Marletta M.
Published: July 2007

In a recent paper, Brown, Evans and Marletta extended the HardyEverittLittlewoodPolya inequality from 2nth-order formally self-adjoint ordinary differential equations to a wide class of linear Hamiltonian systems in 2n variables. The paper considered only problems on semi-infinite intervals [a, ∞) with a limit-point type singularity at infinity. In this paper we extend the theory to cover all types of endpoint ( lim-p for n ≤ p ≤ 2n ).
Generalized scalar curvature type equations on compact Riemannian manifolds
Authors: Druet Olivier
Published: July 2007

The paper is concerned with nonlinear equations of critical Sobolev growth involving the p-Laplace operator. These equations generalize the more classical scalar curvature equation.
The initial value problem for the non-homogeneous Navier—Stokes equations with general slip boundary condition
Authors: Itoh S. , Tani A.
Published: July 2007

The initial-boundary value problem for the non-homogeneous Navier-Stokes equations including the slipping on the solid boundary is considered. The unique solvability is established locally in time for the three-dimensional problem and globally in time for the two-dimensional problem without so-called smallness restrictions.
Timoshenko's beam equation as limit of a nonlinear one-dimensional von Kármán system
Authors: Menzala G. Perla , Zuazua E.
Published: July 2007

We consider a dynamical one-dimensional nonlinear von Kármán model depending on one parameter ε > 0 and study its weak limit as ε → 0. We analyse various boundary conditions and prove that the nature of the limit system is very sensitive to them. We prove that, depending on the type of boundary condition we consider, the nonlinearity of Timoshenko's model may vanish.
Weakly invariant regions for reaction—diffusion systems and applications
Authors: Zheng Si Ning
Published: July 2007

The important theory of invariant regions in reaction-diffusion equations has only restricted applications because of its strict requirements on both the reaction terms and the regions. The concept of weakly invariant regions was introduced by us to admit wider reaction-diffusion systems. In this paper we first extend the L∞ estimate technique of semilinear parabolic equations of Rothe to the more general case with convection terms, and then propose more precise criteria for the bounded weakly invariant regions. We illustrate, by three model examples, that they are very convenient for establishing the global existence of solutions for reaction-diffusion systems, especially those from ecology and chemical processes.
Regularity and propagation of moments in some nonlinear Vlasov systems
Authors: Gasser I. , Jabin P.-E. , Perthame B.
Published: July 2007

We introduce a new variant to prove the regularity of solutions to transport equations of the Vlasov type. Our approach is mainly based on the proof of propagation of velocity moments, as in a previous paper by Lions and Perthame. We combine it with moment lemmas which assert that, locally in space, velocity moments can be gained from the kinetic equation itself. We apply our theory to two cases. First, to the Vlasov–Poisson system, and we solve a long-standing conjecture, namely the propagation of any moment larger than two. Next, to the Vlasov–Stokes system, where we prove the same result for fairly singular kernels.
Dynamics of the diffusive Nicholson's blowflies equation with distributed delay
Authors: Gourley S. A. , Ruan S.
Published: July 2007

In this paper we study the diffusive Nicholson's blowflies equation. Generalizing previous works, we model the generation delay by using an integral convolution over all past times and results are obtained for general delay kernels as far as possible. The linearized stability of the non-zero uniform steady state is studied in detail, mainly by using the principle of the argument. Global stability both of this state and of the zero state are studied by using energy methods and by employing a comparison principle for delay equations. Finally, we consider what bifurcations are possible from the non-zero uniform state in the case when it is unstable.
Existence of topological multivortex solutions in the self-dual gauge theories
Authors: Han Jongmin
Published: July 2007

This paper is concerned with the existence of topological multivortex solutions in (2 + 1) self-dual gauge theories such as the classical abelian Higgs model or the Chern–Simons Higgs gauge theories. A general form of topological multivortex equations is presented with the inclusion of antivortices. Two kinds of solutions are considered; topological vortex solutions and topological vortex–antivortex solutions. We construct these solutions by super and subsolution methods, and derive the exponential decay of solutions at infinity and the quantized integral formula. As an application, we prove the existence of a topological multivortex solutions in a generalized Chern–Simons Higgs theory.
Uniqueness of positive radial solutions of a semilinear Dirichlet problem in an annulus
Authors: Yadava S. L.
Published: July 2007

We establish the uniqueness of positive radial solutions of −Δu = up − u in B(R1, R2), u = 0 on ∂B(R1, R2), where B(R1, R2) is an annulus and 0 < R1 < R2 ≤ ∞, in the following cases.

(a) n ∈ {3, 4} and 1 < p ≤ n/(n − 2).

(b) n ∈ {5, 6, 7, 8} and 1 < p ≤ p0(n) for some p0(n) < n/(n − 2).

Earlier to this result, the uniqueness has been obtained by Coffman for n = 3 and 1 < p ≤ 3 and by Yadava for p ≥ (n + 2)/(n − 2) and n ≥ 3.
Global BV solutions and relaxation limit for a system of conservation laws
Authors: Amadori Debora , Guerra Graziano
Published: July 2007

We consider the Cauchy problem for the (strictly hyperbolic, genuinely nonlinear) system of conservation laws with relaxation

Assume there exists an equilibrium curve A(u), such that r(u,A(u)) = 0. Under some assumptions on σ and r, we prove the existence of global (in time) solutions of bounded variation, uε, υε, for ε > 0 fixed.

As ε → 0, we prove the convergence of a subsequence of uε, υε to some u, υ that satisfy the equilibrium equations
Very singular solutions to a nonlinear parabolic equation with absorption. I. Existence
Authors: Benachour Said , Laurençot Philippe
Published: July 2007

We prove the existence of a very singular solution to

when 1 < p < (N + 2)/(N + 1).
A spatial dynamics approach to three-dimensional gravity-capillary steady water waves
Authors: Groves M. D. , Mielke A.
Published: July 2007

This paper contains a rigorous existence theory for three-dimensional steady gravity-capillary finite-depth water waves which are uniformly translating in one horizontal spatial direction x and periodic in the transverse direction z. Physically motivated arguments are used to find a formulation of the problem as an infinite-dimensional Hamiltonian system in which x is the time-like variable, and a centre-manifold reduction technique is applied to demonstrate that the problem is locally equivalent to a finite-dimensional Hamiltonian system. General statements concerning the existence of waves which are periodic or quasiperiodic in x (and periodic in z) are made by applying standard tools in Hamiltonian-systems theory to the reduced equations.

A critical curve in Bond number–Froude number parameter space is identified which is associated with bifurcations of generalized solitary waves. These waves are three dimensional but decay to two-dimensional periodic waves (small-amplitude Stokes waves) far upstream and downstream. Their existence as solutions of the water-wave problem confirms previous predictions made on the basis of model equations.
A general blow-up result on nonlinear boundary-value problems on exterior domains
Authors: Zhang Qi S.
Published: July 2007

In the first part, we study several exterior boundary-value problems covering three types of semilinear equations: elliptic, parabolic and hyperbolic. By a unified approach, we show that these problems share a common critical behaviour. In the second part we prove a blow-up result for an inhomogeneous porous medium equation with the critical exponent, which was left open in a previous paper.
A study of the total lightning activity in two hailstorms
Authors: Montanyà Joan , Soula Serge , Pineda Nicolau
Published: July 2007

Two thunderstorms which developed in the northeastern region of Spain on 17 August 2004 are analyzed. According to radar and ground observations, one of these storms produced large hail (larger than 19 mm) and therefore could be severe. Both thunderstorms exhibited strong vertical developments with cloud tops reaching 17.5 and 14 km for the severe and the nonsevere ones, respectively. The total lightning activity was monitored, thanks to the Spanish magnetic‐direction‐finding and time‐of‐arrival (MDF/TOA) network and thanks to a regional very‐high‐frequency (VHF) interferometer network. Both storms presented low cloud‐to‐ground (CG) flash rates (lower than 2 min−1) during their mature phase, while the intracloud (IC) flash rate reached 92 min−1 for the severe one. The IC/CG flash ratio was very high for both storms: 35 and 60 in average value for the severe and the nonsevere ones, respectively. The lightning characteristics exhibited low values in terms of peak current and multiplicity for negative CG (−CG) flashes and in terms of VHF source number per flash for IC flashes. The average multiplicity of the −CG flashes was 1.74 and 1.17 for the severe and the nonsevere storms, respectively, and their average peak current was −11.7 and −10.65 kA, respectively. When the presence of hail is suspected from high radar reflectivity values in both cells, the flash rates tended to substantially decrease. The severe storm produced positive CG (+CG) flashes during 1 hour, and at that moment, the multiplicity and peak currents of −CG flashes were very low. Lightning activity for both storms ended with a substantial increase of the −CG flash rate. The elevated charge hypothesis is consistent with the observations, especially if we consider two aspects of this hypothesis, the one about charge separation, which could be limited by the strong updrafts, and the one about the lightning initiation, which could be favored by low pressures at high altitude.
Simulations of the redistribution of formaldehyde, formic acid, and peroxides in the 10 July 1996 Stratospheric‐Tropospheric Experiment: Radiation, Aerosols, and Ozone deep convection storm
Authors: Barth M. C. , Kim S.‐W. , Skamarock W. C. , Stuart A. L. , Pickering K. E. , Ott L. E.
Published: July 2007

By using a three‐dimensional convective cloud model to simulate the 10 July 1996, Stratospheric‐Tropospheric Experiment: Radiation, Aerosols, and Ozone‐Deep Convection experiment storm, we investigate the fate of formaldehyde (CH2O), formic acid (HCOOH), hydrogen peroxide (H2O2), and methyl hydrogen peroxide (CH3OOH) in an isolated thunderstorm. CH2O, H2O2, and CH3OOH are important HOx radical and ozone (O3) precursors in the upper troposphere. Thus, determining their source strength to the upper troposphere is important for estimating O3 production. The model simulates O3‐NOx‐CH4 chemistry (no nonmethane hydrocarbon chemistry) which is affected by the cloud microphysics and production of NOx by lightning. The retention of the soluble species within ice, snow, and hail during drop freezing results in less transport of the species to the upper troposphere than when the species is degassed during drop‐freezing processes. Aqueous‐phase chemistry is found to be inadequate in producing sufficient quantities of HCOOH so that HCOOH could serve as a reliable indicator of cloud‐processed air. The production of nitrogen oxides by lightning has little to no effect on convective outflow mixing ratios of CH2O, H2O2, and CH3OOH within 100 km of the convective cores. Thus, it is unlikely that lightning affects concentrations of HOx precursors near active convection. Scavenging of CH2O and H2O2 significantly affects their concentrations in the convective outflow, although H2O2 mixing ratios were still similar to CH3OOH indicating that both peroxides can contribute equally to O3 production downwind of convection.
Self‐organization of shallow basins in tidal flats and salt marshes
Authors: Defina A. , Carniello L. , Fagherazzi S. , D'Alpaos L.
Published: July 2007

Shallow tidal basins such as the Venice Lagoon, Italy, are often characterized by extensive tidal flats and salt marshes that lie within specific ranges of elevation. Tidal flats lie just below the mean sea level, approximately between −0.6 and −2.0 meters above the mean sea level (m a.m.s.l.), whereas salt marshes lie at an average elevation higher than mean sea level (i.e., between +0.1 and +0.5 m a.m.s.l.). Only a small fraction of the tidal basin area has elevations between −0.6 and +0.1 m a.m.s.l. This occurrence suggests that the morphodynamic processes responsible for sediment deposition and erosion produce either tidal flats or salt marshes but no landforms located in the above intermediate range of elevations. A conceptual model describing this evolutionary trend has recently been proposed. The model assumes that the bimodal distribution of bottom elevations stems from the characteristics of wave induced sediment resuspension and demonstrates that areas at intermediate elevations are inherently unstable and tend to become either tidal flats or salt marshes. In this work, the conceptual model is validated through comparison with numerical results obtained with a two‐dimensional wind wave‐tidal model applied to the Lagoon of Venice, Italy. Both the present and the 1901 bathymetries of the Venice Lagoon are used in the simulations and the obtained numerical results confirm the validity of the conceptual model. A new framework that explains the long‐term evolution of shallow tidal basins based on the results presented herein is finally proposed and discussed.
Ionospheric Doppler and echo phase measured by the Wuhan Ionospheric Oblique Backscattering Sounding System
Authors: Chen Gang , Zhao Zhengyu , Zhang Yuannong
Published: July 2007

Wuhan Ionospheric Oblique Backscattering Sounding System (WIOBSS) is a high‐frequency (HF) sky wave over‐the‐horizon radar developed for ionospheric research and HF channel management. This radar, located in Wuhan (30.35°N, 114.33°E) has been under construction by the Ionosphere Lab of Wuhan University since 2002. WIOBSS uses long coded pulses and pulse compression to achieve good sensitivity and measures the bitemporal ionospheric response, channel scattering function, and phase of echoes simultaneously and then displays the processed data as ionograms and Dopplionograms in real time. Bitemporal ionospheric response is a matrix composed of the ionospheric transmission function with delay and time variables, while the scattering function shows the spectrum of the received signals as a function of the delay and Doppler coordinates, and is obtained by the Fourier Transform of the bitemporal ionospheric response over the time variable. The application of pulse compression and coherent integration allows WIOBSS to measure ionospheric Doppler with high resolution and very low power. A method is developed to get phase data directly from the bitemporal ionospheric response. The measured phase is strung in a series and then divided into linear and nonlinear components. The angular frequency of the linear component is in direct proportion to ionospheric Doppler velocity while the fluctuation of the nonlinear component includes the information of Doppler velocity spread. The phase method based on pulse impression is able to obtain the statistic Doppler information from weak backscattered echoes in short detection time.
Modeling suspended sediment discharge from the Waipaoa River system, New Zealand: The last 3000 years
Authors: Kettner A. J. , Gomez B. , Syvitski J. P. M.
Published: July 2007

HydroTrend, a hydrologic‐transport model, is used to simulate the water and suspended sediment discharge of the Waipaoa River system over the last 3 Kyr, a time period in which a well‐documented sequence of natural events and anthropogenic activities that profoundly impacted drainage basin processes occurred. Comparisons between observed and simulated data show that the model output replicates the frequency and distribution of flow events and the suspended sediment concentration‐discharge relationship, and the long‐term trends in suspended sediment discharge are consistent with the sediment record preserved on the middle shelf. Water discharge tracks precipitation, and average annual discharge may have been up to 20% higher and 6% lower at different times in the past. Suspended sediment discharge changed from 2.3 ± 4.5 to 14.9 ± 8.7 Mt yr−1 during the Anthropocene, increasing by 140% after Polynesian arrival, by 350% after European colonization, and by 660% after the catchment headwaters were deforested.
Effect of soil stratification on the development and migration of headcuts in upland concentrated flows
Authors: Gordon Lee M. , Bennett Sean J. , Wells Robert R. , Alonso Carlos V.
Published: July 2007

Experiments were conducted to examine the effect of vertical stratification in soil erodibility on the development and migration of steady state headcut scour holes in upland concentrated flows typical of agricultural fields. Packed soil beds with a preformed step were subjected to identical simulated rainstorms and clear‐water overland flow rates, which resulted in predictable, actively migrating headcut scour holes with nearly identical characteristics. When an erosion‐resistant layer was incorporated into the packed soil bed at a depth that exceeded this expected plunge pool scour depth, the erosion and hydraulic processes of the migrating headcuts remained unchanged. When the erosion‐resistant layer was placed so as to intersect this potential headcut scour depth, the erosivity of the reattached wall jet was unable to erode this layer, and the depth of scour, the nappe entry angle, and sediment efflux all were reduced inversely proportional to the relative depth of the resistant layer. These data were successfully predicted using modified jet impingement theory for headcut scour holes and demonstrate further the effects of soil management and tillage practices on total soil losses from agricultural fields.
A new dynamical mechanism for major climate shifts
Authors: Tsonis Anastasios A. , Swanson Kyle , Kravtsov Sergey
Published: July 2007

We construct a network of observed climate indices in the period 1900–2000 and investigate their collective behavior. The results indicate that this network synchronized several times in this period. We find that in those cases where the synchronous state was followed by a steady increase in the coupling strength between the indices, the synchronous state was destroyed, after which a new climate state emerged. These shifts are associated with significant changes in global temperature trend and in ENSO variability. The latest such event is known as the great climate shift of the 1970s. We also find the evidence for such type of behavior in two climate simulations using a state‐of‐the‐art model. This is the first time that this mechanism, which appears consistent with the theory of synchronized chaos, is discovered in a physical system of the size and complexity of the climate system.
Total Cerebral Blood Flow and Total Brain Perfusion in the General Population: The Rotterdam Scan Study
Authors: Vernooij Meike W , van der Lugt Aad , Ikram Mohammad Arfan , Wielopolski Piotr A , Vrooman Henri A , Hofman Albert , Krestin Gabriel P , Breteler Monique MB
Published: July 2007

Reduced cerebral perfusion may contribute to the development of cerebrovascular and neurodegenerative diseases. Little is known on cerebral perfusion in the general population, as most measurement techniques are too invasive for application in large groups of healthy individuals. Total cerebral blood flow (tCBF) can be noninvasively measured by magnetic resonance imaging (MRI) but is highly correlated with brain volume. We calculated total brain perfusion by dividing tCBF by brain volume, and we investigated determinants of total brain perfusion in comparison with tCBF. Secondly, we studied whether persons with a low tCBF or low total brain perfusion have a larger volume of white matter lesions (WML). This study is based on 892 persons aged 60 to 91 years from the Rotterdam Study, a population-based cohort study. We performed two-dimensional (2D) phase-contrast MRI for tCBF measurement. Brain volume and WML volume were quantitatively assessed. Cardiovascular determinants were assessed by interview and physical examination. We assessed associations between cardiovascular determinants and flow measures with linear regression models, adjusted for age and sex. Associations between tCBF or total brain perfusion and WML volume were assessed using general linear models. We found that determinants of tCBF and total brain perfusion differed largely due to the large influence of brain volume on tCBF values. Persons with low total brain perfusion had a significantly larger WML volume compared with those with high total brain perfusion. Prospective studies are required to unravel whether hypoperfusion contributes to WML formation or that tissue damage, manifested by WML, leads to brain hypoperfusion.
Puerto Rican Mothers' Beliefs and Home Literacy Practices
Authors: Hammer Carol Scheffner , Rodriguez Barbara L. , Lawrence Frank R. , Miccio Adele W.
Published: July 2007

Purpose

The aims of this investigation were to examine the parenting beliefs and literacy practices of mothers of Puerto Rican descent and to determine if relationships existed between the mothers' beliefs and practices.

Method

Eighty-one mothers of bilingual children who attended Head Start programs participated in the project. As part of a larger project, the children were divided into 2 groups depending on the timing of when they were exposed to English. Children who were exposed to Spanish and English from birth were classified as having home English communication (HEC); children who were not expected to communicate in English until age 3 when they entered Head Start were classified as having school English communication (SEC). Trained home visitors used questionnaires to collect information from the mothers on their background, beliefs about parenting and education, and home literacy practices.

Results

The results revealed that Puerto Rican mothers held both traditional and progressive beliefs. Additionally, differences between the mothers of children in the HEC and SEC groups were observed on some of the measures of beliefs and practices. Relationships between beliefs and practices were not observed.

Implications

The findings demonstrated that Puerto Rican mothers integrated aspects of both the Puerto Rican culture and the mainstream culture of the U.S. mainland into their views concering child rearing and education. Implications for practice are discussed.
Bilingual Children’s Language Abilities and Early Reading Outcomes in Head Start and Kindergarten
Authors: Hammer Carol Scheffner , Lawrence Frank R. , Miccio Adele W.
Published: July 2007

Purpose

The purpose of this study was to investigate the relationship between Head Start children’s receptive language development and their kindergarten reading outcomes.

Method

Eighty-eight bilingual children who were eligible to attend Head Start for 2 years participated in the study. Growth curve models were used to examine the relationship between children’s language abilities during 2 years in Head Start and end-of-kindergarten reading outcomes.

Results

The results revealed that children’s English and Spanish receptive language abilities increased during Head Start, and children’s early reading abilities in English were within the typical range of monolingual norms at the end of kindergarten. Children’s early reading abilities in Spanish were nearly 1SDbelow the test mean or lower. The results also showed that children’s growth in their English and Spanish language abilities during Head Start predicted their early reading abilities in English and Spanish.

Implications

The findings imply that preschool programs are needed that target children’sgrowthin language and not their performance measured at a particular point in time. Also, the results demonstrate the importance of early and regular evaluation of bilingual children’s development in both languages in order to monitor children’s growth in their two languages.
The Cross-Linguistic Transfer of Early Literacy Skills: The Role of Initial L1 and L2 Skills and Language of Instruction
Authors: Cárdenas-Hagan Elsa , Carlson Coleen D. , Pollard-Durodola Sharolyn D.
Published: July 2007

Purpose

The purpose of this study was to examine the effects of initial first and second language proficiencies as well as the language of instruction that a student receives on the relationship between native language ability of students who are English language learners (ELLs) and their development of early literacy skills and the second language.

Method

This study investigated the development of early language and literacy skills among Spanish-speaking students in 2 large urban school districts, 1 middle-size urban district, and 1 border district. A total of 1,016 ELLs in kindergarten participated in the study. Students were administered a comprehensive battery of tests in English and Spanish, and classroom observations provided information regarding the Spanish or English language use of the teacher.

Results

Findings from this study suggest that Spanish-speaking students with high Spanish letter name and sound knowledge tend to show high levels of English letter name and sound knowledge. ELLs with low Spanish and English letter name and sound knowledge tend to show high levels of English letter name and sound knowledge when they are instructed in English. Letter name and sound identification skills are fairly highly positively correlated across languages in the beginning of the kindergarten year. In addition, phonological awareness skills appear to be the area with the most significant and direct transfer of knowledge, and language skills do not appear to be a factor in the development of phonological awareness. Finally, the relationship between oral language skills across languages was low, suggesting little relationship between oral language skills across languages at the beginning of the kindergarten year.

Implications for Practice

Results from this study suggest that pedagogical decisions for ELLs should not only consider effective instructional literacy strategies but also acknowledge that the language of instruction for Spanish-speaking ELLs may produce varying results for different students.
Reflections on cavitation nuclei in water
Authors: Mørch K. A.
Published: July 2007

The origin of cavitation bubbles, cavitation nuclei, has been a subject of debate since the early years of cavitation research. This paper presents an analysis of a representative selection of experimental investigations of cavitation inception and the tensile strength of water. At atmospheric pressure, the possibility of stabilization of free gas bubbles by a skin has been documented, but only within a range of bubble sizes that makes them responsible for tensile strengths up to about 1.5bar, and values reaching almost 300bar have been measured. However, cavitation nuclei can also be harbored on the surface of particles and bounding walls. Such nuclei can be related to the full range of tensile strengths measured, when differences of experimental conditions are taken into consideration. The absence or presence of contamination on surfaces, as well as the structure of the surfaces, are central to explaining why the tensile strength of water varies so dramatically between the experiments reported. A model for calculation of the critical pressure of skin-covered free gas bubbles as well as that of interfacial gaseous nuclei covered by a skin is presented. This model is able to bridge the apparently conflicting results of the many scientists, who have been working in the field over the years.
Whistler waves, core ion heating, and nonstationarity in oblique collisionless shocks
Authors: Scholer Manfred , Burgess David
Published: July 2007

One-dimensional full particle simulations of supercritical collisionless shocks with an ion and electron beta of 0.1 (particle to magnetic field pressure) over a wide Alfvén Mach number range and range of shock normal-magnetic field angles between ΘBn=60° and ΘBn=80° are presented. The whistler critical Mach number Mw, below which a linear phase-standing whistler can exist, is proportional to the square root of the ion-to-electron mass ratio and to cosΘBn. In small mass ratio simulations of oblique shocks, Mw can be artificially small and close to the first critical Mach number Mc, above which the process of ion reflection is needed in order to achieve shock dissipation. We use in the simulations the physical ion-to-electron mass ratio so that Mc and Mw are well separated. This also allows excitation of the modified two-stream instability (MTSI) between incoming ions and electrons. We find that in oblique but close to perpendicular (ΘBn⩾80°) shocks, upstream whistler waves do occur, but reformation is due to accumulation of reflected-gyrating ions at the upstream edge of the foot. In less oblique shocks above the whistler critical Mach number, the whistler amplitude in the foot upstream of the ramp grows, leading to vortices of the incoming ions and the reflected ions in velocity phase space, and eventually to phase mixing. The shock re-forms at the upstream edge of the whistler wave train, which is particularly evident in very high Mach number shocks where the scale of the foot is large compared with the whistler wave train. After reformation, the region with phase-mixed incoming and reflected ions constitutes a hot core downstream of the shock ramp. In this whistler induced reformation process, the MTSI results mainly in heating of the incoming ions in the foot.
The octic E8 invariant
Authors: Cederwall Martin , Palmkvist Jakob
Published: July 2007

We give an explicit expression for the primitive E8-invariant tensor with eight symmetric indices. The result is presented in a manifestly spin(16)∕Z2-covariant notation.
Optical properties of MgO–TiO2 amorphous composite films
Authors: Ye C. , Pan S. S. , Teng X. M. , Li G. H.
Published: July 2007

The microstructure and optical properties of MgO–TiO2 composite thin films prepared by radio frequency magnetron sputtering were studied. The composite films have an amorphous structure and the growth rate of the composite film increases with increasing Mg content. The refractive index almost linearly decreases with increasing Mg content in the composite films at wavelength larger than 300nm and can be adjusted in the wide range between the refractive index of TiO2 and that of MgO. The extinction coefficient decreases with Mg content and is nearly zero at visible light region. The optical band gap of the composite films determined from the absorption spectra increases with Mg content, and has a good agreement with that obtained from spectroscopic ellipsometry simulation. A broad photoluminescence band in the visible region was observed in the composite films with high Mg content and was considered resulted from the oxygen vacancies.
Synchrotron radiation study of chloromethane clusters: Effects of polarizability and dipole moment on core level chemical shifts
Authors: Rosso A. , Lindblad A. , Lundwall M. , Rander T. , Svensson S. , Tchaplyguine M. , Öhrwall G. , Björneholm O.
Published: July 2007

Free neutral chloromethane clusters have been produced by adiabatic expansion and investigated by means of photoelectron spectroscopy. By studying the differences between the cluster binding energy shifts at the Cl 2p and C 1s thresholds we have shown that antiparallel packing is the dominant local structure of the clusters. This geometry is induced by the polar character of the constituent molecules, and it accords with the structures of chloromethane solids and dimers. Furthermore, results obtained from the analysis of the outer valence levels of the clusters support the suggested local structure. The roles of the polarizability and of the dipole moment of the constituent molecules in the cluster binding energy shifts are discussed in comparison with a recent investigation of bromomethane clusters.
Crystalline and amorphous structures of Ge–Sb–Te nanoparticles
Authors: Park Gyeong-Su , Kwon Ji-Hwan , Kim Miyoung , Yoon H. R. , Jo W. , Kim T. K. , Zuo Jian-Min , Khang Yoonho
Published: July 2007

We report effects of thermal annealing on the structures of Ge–Sb–Te (GST) nanoparticles synthesized by pulsed laser ablation deposition. The average diameter of the GST nanoparticles is an order of 10nm. The as-prepared sample contains nanocrystals surrounded by an amorphous phase. Further crystallization occurs during annealing. The structures of the nanocrystals and amorphous phase were studied by electron diffraction and radial distribution function analyses. The results show that the nanoparticles annealed at 100°C are crystalline, consisting of a mixture of face centered cubic (fcc) and hexagonal Ge2Sb2Te5 (dominant). In comparison, the nanoparticles annealed at 200°C are mostly fcc. The surrounding amorphous phase has similar atomic arrangements to the previously reported amorphous GST thin films.
Fast dynamics of supercoiled DNA revealed by single-molecule experiments
Authors: Crut Aurélien , Koster Daniel A. , Seidel Ralf , Wiggins Chris H. , Dekker Nynke H.
Published: July 2007

The dynamics of supercoiled DNA play an important role in various cellular processes such as transcription and replication that involve DNA supercoiling. We present experiments that enhance our understanding of these dynamics by measuring the intrinsic response of single DNA molecules to sudden changes in tension or torsion. The observed dynamics can be accurately described by quasistatic models, independent of the degree of supercoiling initially present in the molecules. In particular, the dynamics are not affected by the continuous removal of the plectonemes. These results set an upper bound on the hydrodynamic drag opposing plectoneme removal, and thus provide a quantitative baseline for the dynamics of bare DNA.
Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals
Authors: Piskurek Oliver , Okada Norihiro
Published: July 2007

Poxviruses (Poxviridae) are a family of double-stranded DNA viruses with no RNA stage. Members of the genus
Orthopoxvirus
(OPV) are highly invasive and virulent. It was recently shown that the taterapox virus (TATV) from a West African rodent is the sister of camelpox virus and therefore belongs to the clade closest to the variola virus (VARV), the etiological agent of smallpox. Although these OPVs are among the most dreaded pathogens on Earth, our current knowledge of their genomes, their origins, and their possible hosts is still very limited. Here, we report the horizontal transfer of a retroposon (known only from reptilian genomes) to the TATV genome. After isolating and analyzing different subfamilies of short interspersed elements (SINEs) from lizards and snakes, we identified a highly poisonous snake (
Echis ocellatus
) from West Africa as the closest species from which the SINE sequence discovered in the TATV genome (TATV-SINE) was transferred to the virus. We discovered direct repeats derived from the virus flanking the TATV-SINE, and the absence of any snake-derived DNA flanking the SINE. These data provide strong evidence that the TATV-SINE was actually transferred within the snake to the viral genome by retrotransposition and not by any horizontal transfer at the DNA level. We propose that the snake is another host for TATV, suggesting that VARV-related epidemiologically relevant viruses may have derived from our cold-blooded ancestors and that poxviruses are possible vectors for horizontal transfer of retroposons from reptiles to mammals.
An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization
Authors: Qian Ziliang , Lu Lingyi , Liu XiaoJun , Cai Yu-Dong , Li Yixue
Published: July 2007

Motivation: To understand transcription regulatory mechanisms, it is indispensable to investigate transcription factor (TF) DNA binding preferences. We noted that the generally acknowledged information of functional annotations of TFs as well as that of their target genes should provide useful hints in determining TF DNA binding preferences.

Results: In this contribution, we developed an integrative method based on the Nearest Neighbor Algorithm, to predict DNA binding preferences through integrating both the functional/structural information of TFs and the interaction between TFs and their targets. The accuracy of cross-validation tests on the dataset consisting of 3430 positive samples and 7000 negative samples reaches 87.0 % for 10-fold cross-validation and 87.9 % for jackknife cross-validation test, which is a much better result than that in our previous work. The prediction result indicates that the improved method we developed could be a powerful approach to infer the TF DNA preference in silico.

Contact:  cyd@picb.ac.cn

Supplementary information: Supplementary data are available at Bioinformatics online
A quantitative genotype algorithm reflecting H5N1 Avian influenza niches
Authors: Wan Xiu-Feng , Chen Guorong , Luo Feng , Emch Michael , Donis Ruben
Published: July 2007

Motivation: Computational genotyping analyses are critical for characterizing molecular evolutionary footprints, thus providing important information for designing the strategies of influenza prevention and control. Most of the current methods that are available are based on multiple sequence alignment and phylogenetic tree construction, which are time consuming and limited by the number of taxa. Arbitrarily defining genotypes further complicates the interpretation of genotyping results.

Methods: In this study, we describe a quantitative influenza genotyping algorithm based on the theory of quasispecies. First, the complete composition vector (CCV) was utilized to calculate the pairwise evolutionary distance between genotypes. Next, Hierarchical Bayesian Modeling using the Gibbs Sampling algorithm was applied to identify the segment genotype threshold, which is used to identify influenza segment genotype through a modularity calculation. The viral genotype was defined by combining eight segment genotypes based on the genetic reassortment feature of influenza A viruses.

Results: We applied this method for H5N1 avian influenza viruses and identified 107 niches among 283 viruses with a complete genome set. The diversity of viral genotypes, and their correlation with geographic locations suggests that these viruses form local niches after being introduced to a new ecological environment through poultry trade or bird migration. This novel method allows us to define genotypes in a robust, quantitative as well as hierarchical manner.

Contact:  wanhenry@yahoo.com or fvq7@cdc.gov

Supplementary information: Supplementary data are available at Bioinformatics online.
RefPlus: an R package extending the RMA Algorithm
Authors: Harbron Chris , Chang Kai-Ming , South Marie C.
Published: July 2007

Summary: RMA has become a widely used methodology to pre-process Affymetrix gene expression microarrays. A limitation of RMA is that the calculated probeset intensities change when a set of microarrays is re-pre-processed after the inclusion of additional microarrays into the analysis set. Here we report the availability of the RefPlus package containing functions to perform the Extrapolation Strategy and Extrapolation Averaging algorithms which address these issues.

Availability: The software is implemented in the R language and can be downloaded from the Bioconductor project website (http://www.bioconductor.org).

Contact:  Chris.Harbron@AstraZeneca.Com

Supplementary information: Further details of the workings and evaluation of these functions are given in the documentation available on the Bioconductor website.
Distinct Biphasic mRNA Changes in Response to Asian Soybean Rust Infection
Authors: van de Mortel Martijn , Recknor Justin C. , Graham Michelle A. , Nettleton Dan , Dittman Jaime D. , Nelson Rex T. , Godoy Cláudia V. , Abdelnoor Ricardo V. , Almeida Álvaro M. R. , Baum Thomas J. , Whitham Steven A.
Published: July 2007

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi, is now established in all major soybean-producing countries. Currently, there is little information about the molecular basis of ASR–soybean interactions, which will be needed to assist future efforts to develop effective resistance. Toward this end, abundance changes of soybean mRNAs were measured over a 7-day ASR infection time course in mock-inoculated and infected leaves of a soybean accession (PI230970) carrying the Rpp2 resistance gene and a susceptible genotype (Embrapa-48). The expression profiles of differentially expressed genes (ASR-infected compared with the mock-inoculated control) revealed a biphasic response to ASR in each genotype. Within the first 12 h after inoculation (hai), which corresponds to fungal germination and penetration of the epidermal cells, differential gene expression changes were evident in both genotypes. mRNA expression of these genes mostly returned to levels found in mock-inoculated plants by 24 hai. In the susceptible genotype, gene expression remained unaffected by rust infection until 96 hai, a time period when rapid fungal growth began. In contrast, gene expression in the resistant genotype diverged from the mock-inoculated control earlier, at 72 h, demonstrating that Rpp2-mediated defenses were initiated prior to this time. These data suggest that ASR initially induces a non-specific response that is transient or is suppressed when early steps in colonization are completed in both soybean genotypes. The race-specific resistance phenotype of Rpp2 is manifested in massive gene expression changes after the initial response prior to the onset of rapid fungal growth that occurs in the susceptible genotype.
Role of the Transcriptional Activator XlnR of Fusarium oxysporum in Regulation of Xylanase Genes and Virulence
Authors: Calero-Nieto Fernando , Di Pietro Antonio , Roncero M. Isabel G. , Hera Concepcion
Published: July 2007

Fungal infection of plants involves degradation of the host cell wall through the action of lytic enzymes secreted by the pathogen. The role of these enzymes in virulence is difficult to determine due to their functional redundancy and, therefore, remains controversial. Here, we have studied XlnR, a zinc-finger transcription factor from the vascular wilt pathogen Fusarium oxysporum that is orthologous to the major transcriptional activator of xylanase genes in Aspergillus spp. Transcription of the xlnR gene was activated by inducing carbon sources such as oat spelt xylan (OSX) and repressed by glucose. Targeted knockout of xlnR in F. oxysporum resulted in lack of transcriptional activation of structural xylanase genes, both in culture and during infection of tomato plants, as well as in dramatically reduced extracellular xylanase activity. By contrast, overexpression of xlnR under the control of the Aspergillus nidulans gpdA promoter did not significantly increase xylanase activity, suggesting that XlnR is regulated not only at the transcriptional but also at the post-translational level. The ΔxlnR mutants were still fully virulent on tomato plants. Thus, XlnR, the major transcriptional activator of xylanase genes, is not an essential virulence determinant in F. oxysporum.
A Thioredoxin of Sinorhizobium meliloti CE52G Is Required for Melanin Production and Symbiotic Nitrogen Fixation
Authors: Castro-Sowinski Susana , Matan Ofra , Bonafede Paula , Okon Yaacov
Published: July 2007

A miniTn5-induced mutant of a melanin-producing strain of Sinorhizobium meliloti (CE52G) that does not produce melanin was mapped to a gene identified as a probable thioredoxin gene. It was proved that the thiol-reducing activity of the mutant was affected. Addition to the growth medium of substrates that induce the production of melanin (l-tyrosine, guaiacol, orcinol) increased the thioredoxin-like (trxL) mRNA level in the wild-type strain. The mutant strain was affected in the response to paraquat-induced oxidative stress, symbiotic nitrogen fixation, and both laccase and tyrosinase activities. The importance of thioredoxin in melanin production in bacteria, through the regulation of laccase or tyrosinase activities, or both, by the redox state of structural or catalytic SH groups, is discussed.
Prunus necrotic ringspot virusEarly Invasion and Its Effects on Apricot Pollen Grain Performance
Authors: Amari Khalid , Burgos Lorenzo , Pallas Vicente , Sanchez-Pina María Amelia
Published: July 2007

The route of infection and the pattern of distribution of Prunus necrotic ringspot virus (PNRSV) in apricot pollen were studied. PNRSV was detected both within and on the surface of infected pollen grains. The virus invaded pollen during its early developmental stages, being detected in pollen mother cells. It was distributed uniformly within the cytoplasm of uni- and bicellular pollen grains and infected the generative cell. In mature pollen grains, characterized by their triangular shape, the virus was located mainly at the apertures, suggesting that PNRSV distribution follows the same pattern as the cellular components required for pollen tube germination and cell wall tube synthesis. PNRSV also was localized inside pollen tubes, especially in the growth zone. In vitro experiments demonstrated that infection with PNRSV decreases the germination percentage of pollen grains by more than half and delays the growth of pollen tubes by ≈24 h. However, although PNRSV infection affected apricot pollen grain performance during germination, the presence of the virus did not completely prevent fertilization, because the infected apricot pollen tubes, once germinated, were able to reach the apricot embryo sacs, which, in the climatic conditions of southeastern Spain, mature later than in other climates. Thus, infected pollen still could play an important role in the vertical transmission of PNRSV in apricot.
Population Genetic Structure of Septoria passerinii in Northern Great Plains Barley
Authors: Lee S. H. , Neate S. M.
Published: July 2007

The genetic structure of Septoria passerinii from nine field populations was examined at several scales (within lesions, among lesions in a leaf, among leaves in a field, and among fields in North Dakota and western Minnesota) by using amplified fragment length polymorphism (AFLP) markers. A total of 390 isolates were sampled from seven barley fields located in North Dakota and two barley fields located nearby in western Minnesota in 2003 and 2004. Based on 57 polymorphic AFLP markers, AFLP DNA fingerprints identified 176 different genotypes among 390 (non-clone-corrected) isolates in nine different fields. In two intensively sampled sites, ND16 (Williston, ND) and ND17 (Langdon, ND), only one to four different genotypes were found within a lesion. A higher level of genetic and genotypic diversity was found within a leaf in which six to nine different genotypes were found from lesions on a leaf. The genetic diversity within a leaf was similar to the genetic diversity within a field. The average genetic diversity (H) within a field across all AFLP loci was approximately 0.3, except at site ND12 (Carrington, ND) where it was 0.16. Genotypic diversity was high in all populations, and with the exception of ND15 (Rothsay, MN), very low multilocus linkage disequilibrium values ( rd) were found in all populations. The population differentiation, GST, was relatively high (GST = 0.238) among the nine populations due to the high GST in ND12, ND14 (Twin Valley, MN), and ND15. Population differentiation without those three populations was 0.09. A lack of correlation between geographical distance and genetic distance was found, suggesting the potential for a high level of gene flow between different geographical regions. The population genetic structure described in this study for S. passerinii in North Dakota and western Minnesota is consistent with that of a sexually reproducing fungus.