bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics and electric currents of morningside Sun‐aligned auroral arcs
Authors: Kozlovsky Alexander , Aikio Anita , Turunen Tauno , Nilsson Hans , Sergienko Tima , Safargaleev Vladimir , Kauristie Kirsti
Published: June 2007

On 13 December 2004, morningside Sun‐aligned auroral arcs were observed at about 8 MLT over Svalbard (around 75 MLAT) during about 1.5 hours after the IMF Bz component had turned to strongly northward (+10 nT). The arcs appeared periodically (6.7 min) and moved poleward at a velocity of about 700 m/s. The arcs occurred during substorm recovery and appeared to develop from the area of enhanced luminosity seen in the western (nightside) horizon toward east. The electric fields and currents associated with the arcs have been calculated from the EISCAT Svalbard radar observations. The arcs were associated with periodic spatial structures of 270 km in latitudinal width. Each of the 270‐km wide structure consists of four specific FAC regions: the upward FAC region 75‐km wide containing the optical arc, the return downward FAC region 100‐km wide poleward of the arc; and a secondary weaker arc equatorward of the main arc with a pair of FACs similar to the main arc, but narrower in width. The interchange instability with the ionospheric feedback is suggested as a suitable generation mechanism for such kind arcs.
Effects of rainfall on mass transfer across the air‐water interface
Authors: Takagaki Naohisa , Komori Satoru
Published: June 2007

The effects of rainfall on mass transfer across the air‐water interface and turbulent structure were investigated through laboratory experiments in a turbulent open‐channel flow. The air‐water CO2transfer coefficient due to raindrops impinging on the air‐water surface and turbulence quantities in an open‐channel flow were measured. The results show that rainfall enhances turbulent mixing near the free surface on the liquid side, and the enhancement results in increase of CO2transfer across the air‐water interface. The mass transfer coefficient on the liquid side is well correlated with the mean vertical momentum flux of rainfall (MF), but it is not well correlated with the mean kinetic energy flux of raindrops impinging on the unit area of the air‐water interface (KEF), as has been proposed in previous studies. The maximum value of the mass transfer coefficient obtained in the present rain experiments corresponds to that observed in oceans with high wind speeds. This suggests that it is of great importance to consider the effects of rainfall in precisely estimating the local air‐sea CO2exchange rate.
Aerosol source plume physical characteristics from space‐based multiangle imaging
Authors: Kahn Ralph A. , Li W.‐H. , Moroney Catherine , Diner David J. , Martonchik John V. , Fishbein Evan
Published: June 2007

Models that assess aerosol effects on regional air quality and global climate parameterize aerosol sources in terms of amount, type, and injection height. The multiangle imaging spectroradiometer (MISR) aboard NASA’s Terra satellite retrieves total column aerosol optical thickness (AOT), and aerosol type over cloud‐free land and water. A stereo‐matching algorithm automatically retrieves reflecting‐layer altitude wherever clouds or aerosol plumes have discernable spatial contrast, with about 500‐m accuracy, at 1.1‐km horizontal resolution. Near‐source biomass burning smoke, volcanic effluent, and desert dust plumes are observed routinely, providing information about aerosol amount, particle type, and injection height useful for modeling applications. Compared to background aerosols, the plumes sampled have higher AOT, contain particles having expected differences in Angstrom exponent, size, single‐scattering albedo, and for volcanic plume and dust cloud cases, particle shape. As basic thermodynamics predicts, thin aerosol plumes lifted only by regional winds or less intense heat sources are confined to the boundary layer. However, when sources have sufficient buoyancy, the representative plumes studied tend to concentrate within discrete, high‐elevation layers of local stability; the aerosol is not uniformly distributed up to a peak altitude, as is sometimes assumed in modeling. MISR‐derived plume heights, along with meteorological profile data from other sources, make it possible to relate radiant energy flux observed by the moderate resolution imaging spectroradiometer (MODIS), also aboard the Terra spacecraft, to convective heat flux that plays a major role in buoyant plume dynamics. A MISR climatology of plume behavior based on these results is being developed.
Permafrost in steep bedrock slopes and its temperature‐related destabilization following climate change
Authors: Gruber S. , Haeberli W.
Published: June 2007

Permafrost in steep bedrock is abundant in many cold‐mountain areas, and its degradation can cause slope instability that is unexpected and unprecedented in location, magnitude, frequency, and timing. These phenomena bear consequences for the understanding of landscape evolution, natural hazards, and the safe and sustainable operation of high‐mountain infrastructure. Permafrost in steep bedrock is an emerging field of research. Knowledge of rock temperatures, ice content, mechanisms of degradation, and the processes that link warming and destabilization is often fragmental. In this article we provide a review and discussion of existing literature and pinpoint important questions. Ice‐filled joints are common in bedrock permafrost and possibly actively widened by ice segregation. Broad evidence of destabilization by warming permafrost exists despite problems of attributing individual events to this phenomenon with certainty. Convex topography such as ridges, spurs, and peaks is often subject to faster and deeper thaw than other areas. Permafrost degradation in steep bedrock can be strongly affected by percolating water in fractures. This degradation by advection is difficult to predict and can lead to quick and deep development of thaw corridors along fractures in permafrost and potentially destabilize much greater volumes of rock than conduction would. Although most research on steep bedrock permafrost originates from the Alps, it will likely gain importance in other geographic regions with mountain permafrost.
Analytical behavior of two-dimensional incompressible flow in porous media
Authors: Córdoba Diego , Gancedo Francisco , Orive Rafael
Published: June 2007

In this paper we study the analytic structure of a two-dimensional mass balance equation of an incompressible fluid in a porous medium given by Darcy’s law. We obtain local existence and uniqueness by the particle-trajectory method and we present different global existence criterions. These analytical results with numerical simulations are used to indicate nonformation of singularities. Moreover, blow-up results are shown in a class of solutions with infinite energy.
Accurate evaluation of nonlinear absorption coefficients in InAs, InSb, and HgCdTe alloys
Authors: Krishnamurthy Srinivasan , Yu Zhi Gang , Gonzalez Leonel P. , Guha Shekhar
Published: June 2007

We present a full band structure calculation of temperature- and wavelength-dependent two-photon absorption (TPA) coefficients and free carrier absorption (FCA) cross sections in InAs, InSb, and Hg1−xCdxTe alloys. The wavelength dependence of the TPA coefficients agrees well with a widely used analytical expression. However, the magnitudes of the TPA coefficients obtained here are smaller by a factor of 1.2–2.5 than the analytical values. In addition, the TPA coefficient is found to depend sensitively on the photoexcited carrier density in small gap materials. The FCA is found to arise predominantly from hole absorption. The FCA cross section is found to be independent of the carrier density, but is strongly dependent on the temperature. The calculated TPA, FCA coefficients, and lifetimes are fitted to closed-form expressions and are used in solving the rate equations to obtain the transmitted pump and probe intensities as functions of incident intensity and sample thickness. The calculated pump transmission and time-dependent probe transmission in InAs agree very well with the measured values.
Influence of surface roughness on quartz crystal microbalance measurements in liquids
Authors: Rechendorff K. , Hovgaard M. B. , Foss M. , Besenbacher F.
Published: June 2007

The influence of nanometer scale surface roughness on the frequency and dissipation responses of a quartz crystal microbalance operating in a liquid environment has been investigated by exposing quartz crystals, with a rough tantalum coating, to water solutions with varying concentrations of sucrose. A clear correlation between the measured surface roughness and the frequency shift is observed, while the shift in the dissipation factor is nearly unaffected by an increase in surface roughness. The experimental results are compared to published theoretical models for the frequency shift and shift in dissipation factor which incorporate roughness effects. For a high surface roughness the data cannot be satisfactorily explained by a model where the only effect of roughness is rigidly coupled liquid. A more advanced model, taking pressure gradients into account, provides a better description of the data.
Synthesis of homogeneous anisotropic divergence-free turbulent fields with prescribed second-order statistics by vortex dipoles
Authors: Kornev Nikolai , Hassel Egon
Published: June 2007

This Communication presents a mathematical procedure for generation of turbulent velocity fields with prescribed shell-summed energy spectra. The velocity field is represented as the sum of velocities induced by a set of randomly distributed vortex dipoles (vortons). Closed-form analytical solutions are found for the inner structure of the vortons from the condition that the shell-summed energy spectrum of the synthesizing field is equal to the prescribed one. The proposed procedure is applied to turbulent fields with the spectrum of the decaying turbulence and the typical velocity energy spectrum of homogeneous turbulence. The solution for decaying turbulence is the exact analytical solution of the Navier-Stokes equation for the turbulent field in the final stage of the decay.
In situ study of aggregation of soot particles in an acetylene flame by small-angle x-ray scattering
Authors: Sztucki M. , Narayanan T. , Beaucage G.
Published: June 2007

The nucleation and growth of soot particles in an acetylene flame were investigated by synchrotron small-angle x-ray scattering. The scattered intensity spanning over a wide scattering vector (q) range, 10−3nm−1⩽q⩽0.5nm−1, was analyzed using the unified scattering function involving up to three structural levels corresponding to primary particles, aggregates, and agglomerates. The primary particles have a compact morphology with a terminal radius of gyration (Rg) of about 27nm and their growth dynamics is consistent with the nucleation and growth process. The evolution of aggregate Rg reveals a diffusion limited growth mechanism resulting in a fractal dimension (df)≈2 and Rg∼250nm. Although the production of soot dramatically increases with the flow rate, the aggregation dynamics, terminal Rg, and df remain nearly the same. The flow rate used in this study extended to the regime of aerogelation of soot but the aggregation dynamics is found to be similar to the nongelling case.
Ferromagnetic resonance in evaporated Co∕Si(100) and Co∕glass thin films
Authors: Kharmouche A. , Ben Youssef J. , Layadi A. , Chérif S.-M.
Published: June 2007

Ferromagnetic resonance, at different frequencies (6–12GHz), has been used to investigate the magnetic properties of a series of Co thin films evaporated onto Si (100) and glass substrates. The Co thickness tCo ranges from 50to195nm. The thinner films are characterized by a single magnetic region; as the film grows, a second magnetic region appears and becomes even more important than the first one as tCo is increased further. The first region, presumably located at the substrate-film interface, is characterized by a magnetocrystalline anisotropy constant Ku(1) between (3.05and4.31)×106erg∕cm3. The constant Ku(2) of the second region, located next to the surface, is practically the same for all thick samples (about 2.5×106erg∕cm3), i.e., Ku(2) is independent of the substrate and of the Co thickness. Moreover, Ku(2) is always lower than Ku(1). The linewidth ΔH(1) of the peak associated with the interfacial region is larger than ΔH(2) of the surface region, indicating that the surface region is magnetically more homogeneous (probably less anisotropy axis dispersion) than the interfacial region. Moreover, a sequence of spin wave resonance (SWR) modes is observed when H is applied perpendicular to the film plane. These SWR modes follow, mainly, the low resonant field indicating a pinning of the interfacial layer. It was found that the linewidth of the nth mode ΔHn varies as ΔHn=n2(ΔH′)+ΔH″; this type of linewidth variation suggests that the spin waves are associated with dynamic pinning.
Unusual room temperature ductility of a Zr-based bulk metallic glass containing nanoparticles
Authors: Qiang J. B. , Zhang W. , Xie G. Q. , Inoue A.
Published: June 2007

Highly ductile Zr65Al7.5Cu27.5 bulk metallic glass (BMG) containing nanometer scaled fcc phase was obtained by copper mold casting. Room temperature compression tests revealed superior mechanical properties of the alloy: yielding stress of 1670MPa, Young’s modulus of 90GPa, elastic strain of 2%, and especially a remarkable plasticity of over 50%. The marginal BMG is a useful model system to examine the nanocrystal coalescence model and the shear-transformation-zone model proposed for large scale plastic deformations of metallic glasses.
Solution deposited liquid crystalline semiconductors on a photoalignment layer for organic thin-film transistors
Authors: Fujiwara Takenori , Locklin Jason , Bao Zhenan
Published: June 2007

Highly ordered liquid crystalline semiconductors on a light induced alignment layer results in an anisotropic electrical characteristic and an enhanced mobility of solution processed thin-film transistors. In the case of poly-9,9′-dioctyl-fluorene-co-bithiophene, a mobility as high as 0.02cm2V−1s−1 has been achieved by aligning a polymer chain parallel to the charge transport direction. Using an oligomeric semiconductor, 5,5′-bis(4-octyloxyphenyl)bithiophene, an enhanced mobility of 0.05cm2V−1s−1 was obtained by the alignment of the π-π intermolecular packing direction parallel to the charge transport direction.
Effects of the surface roughness of plastic-compatible inorganic dielectrics on polymeric thin film transistors
Authors: Chabinyc Michael L. , Lujan Rene , Endicott Fred , Toney Michael F. , McCulloch Iain , Heeney Martin
Published: June 2007

The effects of the roughness of the gate dielectric on the performance of thin film transistors (TFTs) fabricated with poly(2,5-bis(3-hexadecylthiophen-2-yl)thieno[3,2-b] thiophene) (PBTTT-C16) were examined. The field effect mobility of coplanar TFTs made with PBTTT-C16 and plasma-enhanced chemical vapor deposited SiO2∕SiNx dielectrics decreased nearly exponentially with surface roughness. Films of PBTTT-C16 have similar crystalline structure on smooth and rough surfaces, but the domain size decreases with increasing roughness. Surface roughness was found to have less of an impact on field effect mobility than the chemical treatment of the dielectric.
Automated reverse engineering of nonlinear dynamical systems
Authors: Bongard Josh , Lipson Hod
Published: June 2007

Complex nonlinear dynamics arise in many fields of science and engineering, but uncovering the underlying differential equations directly from observations poses a challenging task. The ability to symbolically model complex networked systems is key to understanding them, an open problem in many disciplines. Here we introduce for the first time a method that can automatically generate symbolic equations for a nonlinear coupled dynamical system directly from time series data. This method is applicable to any system that can be described using sets of ordinary nonlinear differential equations, and assumes that the (possibly noisy) time series of all variables are observable. Previous automated symbolic modeling approaches of coupled physical systems produced linear models or required a nonlinear model to be provided manually. The advance presented here is made possible by allowing the method to model each (possibly coupled) variable separately, intelligently perturbing and destabilizing the system to extract its less observable characteristics, and automatically simplifying the equations during modeling. We demonstrate this method on four simulated and two real systems spanning mechanics, ecology, and systems biology. Unlike numerical models, symbolic models have explanatory value, suggesting that automated “reverse engineering” approaches for model-free symbolic nonlinear system identification may play an increasing role in our ability to understand progressively more complex systems in the future.
Evolution of robustness in the signaling network of
Pristionchus
vulva development
Authors: Zauner Hans , Sommer Ralf J.
Published: June 2007

Robustness to environmental or genetic perturbation, like any other trait, is affected by evolutionary change. However, direct studies on the interplay of robustness and evolvability are limited and require experimental microevolutionary studies of developmental processes. One system in which such microevolutionary studies can be performed is vulva development in the nematode
Pristionchus pacificus
. Three vulval precursor cells respond to redundant cell–cell interactions, including signals from the gonad and the epidermal cell P8.p. Interestingly,
P. pacificus
P8.p is involved in cell fate specification of the future vulva cells by lateral inhibition but is incompetent to respond to the inductive signal from the gonad itself. These functional properties of P8.p are unknown from other nematodes, such as
Caenorhabditis elegans
. We began an experimental and genetic analysis of the microevolution of P8.p function. We show that vulva misspecification events differ between
Pristionchus
strains and species. Similarly, lateral inhibition and developmental competence of P8.p evolved within the genus
Pristionchus
and between natural isolates of
P. pacificus
. Surprisingly, in some recombinant inbred lines of two distinct
P. pacificus
isolates, P8.p gained competence to form vulva tissue, a trait that was never observed in
P. pacificus
isolates. Our results suggest differences in developmental stability between natural isolates, and we hypothesize that the remarkable evolvability of redundant cell–cell interactions allows for adaptive evolution of robustness to developmental noise.
Ventrolateral prefrontal cortex and tactile memory disambiguation in the human brain
Authors: Kostopoulos Penelope , Albanese Marie-Claire , Petrides Michael
Published: June 2007

Tactile sensory information is first channeled from the primary somatosensory cortex on the postcentral gyrus to the parietal opercular region (i.e., the secondary somatosensory cortex) and the rostral inferior parietal lobule and, from there, to the prefrontal cortex, with which bidirectional connections exist. Although we know that tactile memory signals can be found in the prefrontal cortex, the contribution of the different prefrontal areas to tactile memory remains unclear. The present functional MRI study shows that a specific part of the prefrontal cortex in the human brain, namely the midventrolateral prefrontal region (cytoarchitectonic areas 47/12 and 45), is involved in active controlled retrieval processing necessary for the disambiguation of vibrotactile information in short-term memory. Furthermore, we demonstrate that this particular part of the prefrontal cortex interacts functionally with the secondary somatosensory areas in the parietal operculum and the rostral inferior parietal lobule during controlled processing for the retrieval of specific tactile information.
Transient 2D IR spectroscopy of ubiquitin unfolding dynamics
Authors: Chung Hoi Sung , Ganim Ziad , Jones Kevin C. , Tokmakoff Andrei
Published: June 2007

Transient two-dimensional infrared (2D IR) spectroscopy is used as a probe of protein unfolding dynamics in a direct comparison of fast unfolding experiments with molecular dynamics simulations. In the experiments, the unfolding of ubiquitin is initiated by a laser temperature jump, and protein structural evolution from nanoseconds to milliseconds is probed using amide I 2D IR spectroscopy. The temperature jump prepares a subensemble near the unfolding transition state, leading to quasi-barrierless unfolding (the “burst phase”) before the millisecond activated unfolding kinetics. The burst phase unfolding of ubiquitin is characterized by a loss of the coupling between vibrations of the β-sheet, a process that manifests itself in the 2D IR spectrum as a frequency blue-shift and intensity decrease of the diagonal and cross-peaks of the sheet's two IR active modes. As the sheet unfolds, increased fluctuations and solvent exposure of the β-sheet amide groups are also characterized by increases in homogeneous linewidth. Experimental spectra are compared with 2D IR spectra calculated from the time-evolving structures in a molecular dynamics simulation of ubiquitin unfolding. Unfolding is described as a sequential unfolding of strands in ubiquitin's β-sheet, using two collective coordinates of the sheet: (
i
) the native interstrand contacts between adjacent β-strands I and II and (
ii
) the remaining β-strand contacts within the sheet. The methods used illustrate the general principles by which 2D IR spectroscopy can be used for detailed dynamical comparisons of experiment and simulation.
Six closely related YbT
2
Zn
20
(T = Fe, Co, Ru, Rh, Os, Ir) heavy fermion compounds with large local moment degeneracy
Authors: Torikachvili M. S. , Jia S. , Mun E. D. , Hannahs S. T. , Black R. C. , Neils W. K. , Martien Dinesh , Bud'ko S. L. , Canfield P. C.
Published: June 2007

Heavy fermion compounds represent one of the most strongly correlated forms of electronic matter and give rise to low temperature states that range from small moment ordering to exotic superconductivity, both of which are often in close proximity to quantum critical points. These strong electronic correlations are associated with the transfer of entropy from the local moment degrees of freedom to the conduction electrons, and, as such, are intimately related to the low temperature degeneracy of the (originally) moment bearing ion. Here we report the discovery of six closely related Yb-based heavy fermion compounds, YbT
2
Zn
20
, that are members of the larger family of dilute rare earth bearing compounds: RT
2
Zn
20
(T = Fe, Co, Ru, Rh, Os, Ir). This discovery doubles the total number of Yb-based heavy fermion materials. Given these compounds' dilute nature, systematic changes in T only weakly perturb the Yb site and allow for insight into the effects of degeneracy on the thermodynamic and transport properties of these model correlated electron systems.
Molecular sabotage of plant defense by aphid saliva
Authors: Will Torsten , Tjallingii W. Fred , Thönnessen Alexandra , van Bel Aart J. E.
Published: June 2007

Aphids, which constitute one of the most important groups of agricultural pests, ingest nutrients from sieve tubes, the photoassimilate transport conduits in plants. Aphids are able to successfully puncture sieve tubes with their piercing mouthparts (stylets) and ingest phloem sap without eliciting the sieve tubes' normal occlusion response to injury. Occlusion mechanisms are calcium-triggered and may be prevented by chemical constituents in aphid saliva injected into sieve tubes before and during feeding. We recorded aphid feeding behavior with the electrical penetration graph (EPG) technique and then experimentally induced sieve tube plugging. Initiation of sieve tube occlusion caused a change in aphid behavior from phloem sap ingestion to secretion of watery saliva. Direct proof of “unplugging” properties of aphid saliva was provided by the effect of aphid saliva on forisomes. Forisomes are proteinaceous inclusions in sieve tubes of legumes that show calcium-regulated changes in conformation between a contracted state (below calcium threshold) that does not occlude the sieve tubes and a dispersed state (above calcium threshold) that occludes the sieve tubes. We demonstratedin vitrothat aphid saliva induces dispersed forisomes to revert back to the nonplugging contracted state. Labeling Western-blotted saliva proteins with45Ca2+or ruthenium red inferred the presence of calcium-binding domains. These results demonstrate that aphid saliva has the ability to prevent sieve tube plugging by molecular interactions between salivary proteins and calcium. This provides aphids with access to a continuous flow of phloem sap and is a critical adaptation instrumental in the evolutionary success of aphids.
Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome
Authors: Korbel Jan O. , Urban Alexander Eckehart , Grubert Fabian , Du Jiang , Royce Thomas E. , Starr Peter , Zhong Guoneng , Emanuel Beverly S. , Weissman Sherman M. , Snyder Michael , Gerstein Mark B.
Published: June 2007

Copy-number variants (CNVs) are an abundant form of genetic variation in humans. However, approaches for determining exact CNV breakpoint sequences (physical deletion or duplication boundaries) across individuals, crucial for associating genotype to phenotype, have been lacking so far, and the vast majority of CNVs have been reported with approximate genomic coordinates only. Here, we report an approach, calledBreakPtr, for fine-mapping CNVs (available fromhttp://breakptr.gersteinlab.org). We statistically integrate both sequence characteristics and data from high-resolution comparative genome hybridization experiments in a discrete-valued, bivariate hidden Markov model. Incorporation of nucleotide-sequence information allows us to take into account the fact that recently duplicated sequences (e.g., segmental duplications) often coincide with breakpoints. In anticipation of an upcoming increase in CNV data, we developed an iterative, “active” approach to initially scoring with a preliminary model, performing targeted validations, retraining the model, and then rescoring, and a flexible parameterization system that intuitively collapses from a full model of 2,503 parameters to a core one of only 10. Using our approach, we accurately mapped >400 breakpoints on chromosome 22 and a region of chromosome 11, refining the boundaries of many previously approximately mapped CNVs. Four predicted breakpoints flanked known disease-associated deletions. We validated an additional four predicted CNV breakpoints by sequencing. Overall, our results suggest a predictive resolution of ≈300bp. This level of resolution enables more precise correlations between CNVs and across individuals than previously possible, allowing the study of CNV population frequencies. Further, it enabled us to demonstrate a clear Mendelian pattern of inheritance for one of the CNVs.
Riboswitching on RNA virus replication
Authors: Wang Sheng , White K. Andrew
Published: June 2007

Positive-strand RNA viruses direct different virus-specific processes during their infection of host cells. Fundamental events such as viral RNA genome replication are controlled by viral regulatory RNA elements (REs). Here, we have investigated the possibility of specifically modulating the action of a viral RE using RNA aptamer technology. Through rational design, a tombusvirus RE, which has the structure of a perfect RNA stem loop in the plus-strand RNA genome, was replaced with a theophylline-binding RNA aptamer sequence, an imperfect stem loop. The aptamer–RE hybrid was designed so that, upon binding theophylline, it would become more stable and structurally mimic the functional RE (i.e., represent a ligand-inducible RE riboswitch). Initial experiments were conducted with a small noncoding virus genome-derived RNA replicon, and the results showed that replication was inducible, up to ≈10-fold, in a theophylline-specific and dose-dependent manner. A similar level of theophylline-dependent induction was also observed when a full-length viral genome containing an RE riboswitch was tested. Analysis of this engineered viral genome revealed that this RE, located in the 5′ untranslated region, specifically mediates efficient accumulation of plus-strands of the virus genome. Therefore, in addition to allowing for modulation of virus reproduction, the RE riboswitch system also provided insight into RE function. The ability to chemically induce a viral process via modulation of virus genome structure could be useful for basic and applied aspects of research.
dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
Authors: Bae Seung-Hee , Tang Haixu , Wu Jing , Xie Jun , Kim Sun
Published: June 2007

Motivation: Transcription factor binding sites (TFBSs) are typically short in length, thus search with a profile model from known TFBSs produces many false positives. When combined with additional information, gene expression data in this article, sensitivity and specificity of TFBS search can be improved significantly.

Results: By modifying our previous REFINEMENT approach, we developed dPattern that searches for occurrences of TFBSs in the promotor regions of up/down regulated or random genes.

Availability:  http://platcom.org/projects/dpattern

Contact:  sun.kim@acm.org or sunkim2@indiana.edu
The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins
Authors: Salwinski Lukasz , Eisenberg David
Published: June 2007

Summary: The MiSink Plugin converts Cytoscape, an open-source bioinformatics platform for network visualization, to a graphical interface for the database of interacting proteins (DIP: http://dip.doe-mbi.ucla.edu). Seamless integration is possible by providing bi-directional communication between Cytoscape and any Web site supplying data in XML or tab-delimited format.

Availability: MiSink is freely available for download at http://dip.doe-mbi.ucla.edu/Software.cgi

Contact:  lukasz@mbi.ucla.edu
Co-circulation of multiple rubella virus strains in Belarus forming novel genetic groups within clade 1
Authors: Hübschen Judith M. , Yermalovich Marina , Semeiko Galina , Samoilovich Elena , Blatun Elena , De Landtsheer Sébastien , Muller Claude P.
Published: June 2007

Although the WHO recommends a comprehensive genetic characterization, little is known about circulating strains and genotypes of rubella virus (RUBV) for many European countries. Studies investigating the genetic diversity of a sizeable number of strains from a certain location are rare. This study presents the first molecular characterization of isolates from Belarus. Throat swab and urine samples were collected between 2004 and 2005 from patients presenting in two infectious disease hospitals and three outpatient clinics in and around Minsk. In total, 14 isolates were obtained from this clinical material. Phylogenetic analysis of the E1 gene sequence of these isolates showed that three distinct groups of RUBV strains co-circulated. One group of isolates was assigned to genotype 1E, whereas the other two did not group with any of the recognized genotypes but grouped with a strain belonging to the provisional genotype 1g. Detailed analysis showed that the group comprising 1g strains also contained sequences formerly attributed to genotype 1B and could be divided into four subgroups, one of which might represent a putative novel provisional genotype of clade 1. These findings show that three distinct strains with limited variability are present in Belarus, suggesting independent introductory events. As there currently seem to be misattributions of strains to genotypes and unclear phylogenetic relationships, criteria for genotyping of RUBV should be clarified further.
Induction of nitric oxide synthase by rotavirus enterotoxin NSP4: implication for rotavirus pathogenicity
Authors: Borghan Mohamed A. , Mori Yoshio , El-Mahmoudy Abu-Baker , Ito Naoto , Sugiyama Makoto , Takewaki Tadashi , Minamoto Nobuyuki
Published: June 2007

Rotavirus non-structural protein (NSP) 4 can induce aqueous secretion in the gastrointestinal tract of neonatal mice through activation of an age- and Ca2+-dependent plasma membrane anion permeability. Accumulating evidence suggests that nitric oxide (NO) plays a role in the modulation of aqueous secretion and the barrier function of intestinal cells. This study investigated transcriptional changes in inducible NO synthase (iNOS), an enzyme responsible for NO production, after rotavirus infection in mice and after treatment of intestinal cells with NSP4. Diarrhoea was observed in 5-day-old CD-1 mice from days 1 to 3 after inoculation with 107focus-forming units of different rotavirus strains. Ileal iNOS mRNA expression was induced as early as 6 h post-inoculation, before the onset of clinical diarrhoea in infected mice, and was upregulated during the course of rotavirus-induced diarrhoea.Ex vivotreatment of ilea excised from CD-1 suckling mice with NSP4 resulted in upregulation of ileal iNOS mRNA expression within 4 h. Furthermore, NSP4 was able to induce iNOS expression and NO production in murine peritoneal macrophages and RAW264.7 cells. The specificity of NSP4 inducibility was confirmed by the inhibitory effect of anti-NSP4 serum. Using a series of truncated NSP4s, the domain responsible for iNOS induction in macrophages was mapped to the reported enterotoxin domain, aa 109–135. Thus, rotavirus infection induces ileal iNOS expressionin vivoand rotavirus NSP4 also induces iNOS expression in the ileum and macrophages. Together, these findings suggest that NO plays a role in rotavirus-induced diarrhoea.
Universal and mutation-resistant anti-enteroviral activity: potency of small interfering RNA complementary to the conserved cis-acting replication element within the enterovirus coding region
Authors: Lee Hui Sun , Ahn Jeonghyun , Jee Youngmee , Seo Il Sun , Jeon Eun Jung , Jeon Eun-Seok , Joo Chul Hyun , Kim Yoo Kyum , Lee Heuiran
Published: June 2007

The promising potential of RNA interference-based antiviral therapies has been well established. However, the antiviral efficacy is largely limited by genomic diversity and genetic instability of various viruses, including human enterovirus B (HEB). In this work, the first evidence supporting the anti-HEB activity of the small interfering RNA (siRNA) targeting the highly conserved cis-acting replication element (CRE) within virus coding region 2C is presented. HeLa cells pre-treated with siRNA complementary to the conserved sequence of the loop region of CRE(2C) were effectively rescued from the cytopathic effects of HEBs. Downregulation of virus replication and attenuation of cytotoxicity were consistently observed in various reference strains and clinical isolates. Cells treated with this siRNA were resistant to the emergence of viable escape mutants and showed sustained antiviral ability. Collectively, the data suggest that the siRNA based on the disordered structure within the highly conserved cis-acting coding region has potential as a universal, persistent anti-HEB agent. The same strategy can be successfully applied to the development of siRNA with consistent antiviral effects in other virus groups possessing similar RNA elements.
Genomic sequence of a clonal isolate of the vaccinia virus Lister strain employed for smallpox vaccination in France and its comparison to other orthopoxviruses
Authors: Garcel Aude , Crance Jean-Marc , Drillien Robert , Garin Daniel , Favier Anne-Laure
Published: June 2007

Since 1980 there has been global eradication of smallpox due to the success of the vaccination programme using vaccinia virus (VACV). During the eradication period, distinct VACV strains circulated, the Lister strain being the most commonly employed in Europe. Analysis of the safety of smallpox vaccines has suggested that they display significant heterogeneity. To gain a more detailed understanding of the diversity of VACV strains it is important to determine their genomic sequences. Although the sequences of three isolates of the Japanese Lister original strain (VACV-LO) are available, no analysis of the relationship of any Lister sequence compared to other VACV genomes has been reported. Here, we describe the sequence of a representative clonal isolate of the Lister vaccine (VACV-List) used to inoculate the French population. The coding capacity of VACV-List was compared to other VACV strains. The 201 open reading frames (ORFs) were annotated in the VACV-List genome based on protein size, genomic localization and prior characterization of many ORFs. Eleven ORFs were recognized as pseudogenes as they were truncated or fragmented counterparts of larger ORFs in other orthopoxviruses (OPVs). The VACV-List genome also contains several ORFs that have not been annotated in other VACVs but were found in other OPVs. VACV-List and VACV-LO displayed a high level of nucleotide sequence similarity. Compared to the Copenhagen strain of VACV, the VACV-List sequence diverged in three main regions, one of them corresponding to a substitution in VACV-List with coxpox virus GRI-90 strain ORFs, suggestive of prior genetic exchanges. These studies highlight the heterogeneity between VACV strains and provide a basis to better understand differences in safety and efficacy of smallpox vaccines.
Epstein–Barr virus induces a distinct form of DNA-bound STAT1 compared with that found in interferon-stimulated B lymphocytes
Authors: McLaren James , Rowe Martin , Brennan Paul
Published: June 2007

Since ‘constitutive activation’ of STAT1 was first described in Epstein–Barr virus (EBV)-immortalized lymphoblastoid cell lines (LCLs), there has been controversy regarding the molecular identity of the STAT1 DNA-binding complex found in these cells. The post-translational modifications of STAT1 in LCLs have been analysed and an LMP1-induced STAT1 DNA-binding complex, different from that generated by alpha interferon (IFN) stimulation and not involving tyrosine phosphorylation, is demonstrated. STAT1 is serine-phosphorylated downstream of PI3K and MEK in LCLs and this modification restricts IFN-stimulated STAT1–DNA binding. These data suggest that EBV induces a distinct form of DNA-bound STAT1 in virus-infected cells.
Activity of the LMP1 gene promoter in Epstein–Barr virus-transformed cell lines is modulated by sequence variations in the promoter-proximal CRE site
Authors: Jansson Ann , Johansson Pegah , Li Susann , Rymo Lars
Published: June 2007

The Epstein–Barr virus (EBV)-encoded tumour-associated latent membrane protein 1 (LMP1) gene expression is transactivated by EBV nuclear antigen 2 (EBNA2) in human B cells. We have previously identified a cyclic AMP-responsive element (CRE) in the B95-8 LMP1 promoter that is essential for transcription activation. Sequencing of LMP1 promoter in the P3HR1-derived EREB2.5 cell line revealed 25 single base pair substitutions in comparison to the B95-8 virus, one of them localized in the CRE element. Sequence variations in this element have been identified in several EBV isolates of both African and Asian origins. The effect of the P3HR1 CRE site variation on binding of factors to the LMP1 promoter sequence (LRS) and promoter activation was investigated with electrophoretic mobility-shift assays and reporter gene transfection assays. ATF1 and CREB1 transcription factors bound with reduced efficiency to the P3HR1 variant and below the detection level to the other tested variants. Accordingly, reporter plasmids carrying the P3HR1 CRE sequence in a B95-8 LRS context displayed 50 % lower activity in all tested cell lines. The impaired ability to activate transcription caused by the C to A substitution in CRE was not apparent when the mutated site was placed in a P3HR1 LRS context and the reporter transfected into Jijoye cells, most likely as a consequence of the other base pair substitutions in P3HR1 LRS. Overall, our results suggest that the mutations in the LRS CRE site have been conserved to adjust LMP1 expression to levels that favour cell survival in certain cellular and environmental contexts.
Genomic regions of tomato leaf curl virus DNA satellite required for replication and for satellite-mediated delivery of heterologous DNAs
Authors: Li Dongmei , Behjatnia S. A. Akbar , Dry Ian B. , Randles John W. , Eini Omid , Rezaian M. Ali
Published: June 2007

Tomato leaf curl virus (TLCV) satellite DNA (sat-DNA) is a 682 nt, circular, single-stranded molecule that lacks an open reading frame (ORF) or an apparent promoter. It contains binding motifs for the TLCV replication-associated protein, but these are dispensable for replication. To identify the regions of the sat-DNA critical for replication, the entire sequence was scanned by deletion/replacement mutagenesis. Transient assays usingNicotiana benthamianarevealed that sequences within nt 296–35 (through nt 682) are essential for replication. Sequence deletions and replacements between nt 35 and 296 were tolerated but with a significant loss of infectivity, indicating that genome size strongly influences replication efficiency. Within the permissible region, inserts of 100–700 nt were retained in transient assays although with a slight reduction in replication. In addition, sat-DNA constructs containing short non-viral DNAs replicated and spread in tobacco plants, indicating their potential as gene-delivery vectors.
Dissociated roles for the lateral and medial septum in elemental and contextual fear conditioning
Authors: Calandreau Ludovic , Jaffard Robert , Desmedt Aline
Published: June 2007

Extensive evidence indicates that the septum plays a predominant role in fear learning, yet the direction of this control is still a matter of debate. Increasing data suggest that the medial (MS) and lateral septum (LS) would be differentially required in fear conditioning depending on whether a discrete conditional stimulus (CS) predicts, or not, the occurrence of an aversive unconditional stimulus (US). Here, using a tone CS-US pairing (predictive discrete CS, context in background) or unpairing (context in foreground) conditioning procedure, we show, in mice, that pretraining inactivation of the LS totally disrupted tone fear conditioning, which, otherwise, was spared by inactivation of the MS. Inactivating the LS also reduced foreground contextual fear conditioning, while sparing the higher level of conditioned freezing to the foreground (CS-US unpairing) than to the background context (CS-US pairing). In contrast, inactivation of the MS totally abolished this training-dependent level of contextual freezing. Interestingly, inactivation of the MS enhanced background contextual conditioning under the pairing condition, whereas it reduced foreground contextual conditioning under the unpairing condition. Hence, the present findings reveal a functional dissociation between the LS and the MS in Pavlovian fear conditioning depending on the predictive value of the discrete CS. While the requirement of the LS is crucial for the appropriate processing of the tone CS-US association, the MS is crucial for an appropriate processing of contextual cues as foreground or background information.
Hypertension in the Elderly
Authors: Webb‐Peploe Katharine M. , MacGregor Graham A.
Published: June 2007

Hypertension as a risk factor for cardiac and cerebrovascular morbidity and mortality poses a major health problem for our increasingly elderly population. Recent trials have shown large reductions in stroke, heart failure, and coronary artery disease when elderly hypertensive patients are treated. These benefits are also seen in elderly patients with isolated systolic hypertension. The elderly patient with hypertension should be investigated and managed in a similar manner to their younger counterpart. Nonpharmacological measures, such as dietary salt and calorie restriction, regular exercise, cessation of smoking, and reduction of excess alcohol intake, should be recommended. If these are insufficient, pharmacological treatment should be tailored to the individual patient. Diuretics have been shown to improve outcome measures in the elderly. Other antihypertensive drugs may be added or substituted depending on the patient's blood pressure response to therapy and their comorbid conditions. If all elderly hypertensive patients were treated, a major reduction in cardiovascular and cerebrovascular mortality and morbidity would result. Consideration also needs to be given to nonpharmacological treatment, particularly salt restriction in older subjects where blood pressure is at the upper limit of normal, as this would also result in a major reduction in cardiovascular morbidity and mortality.
Results of Stent Supported Percutaneous Transluminal Coronary Angioplasty in Octogenarians With Coronary Artery Disease
Authors: Hussain K. M.A. , Sankari A.H. , Jain A. , Bargout R. , Chandra H. , Denes P.
Published: June 2007

Between January 1995 and July 1998, percutaneous transluminal coronary angioplasty was performed on 27 lesions in 24 octogenarians. Half of the patients were African American. Women comprised 67% of the study group. Patients with unstable angina and myocardial infarction constituted 54% of the cohort. Two‐thirds of the patients (83%) had single vessel disease with predominant class A and B lesion complexity of the angioplasty site. Acute success rate was 92%. Stents were successfully placed in 11 subjects (46%). None had acute myocardial infarction, emergency coronary artery bypass surgery, or stroke as a complication of the procedure. One patient presenting with acute myocardial infarction complicated by cardiogenic shock, died. Significant bleeding complications requiring blood transfusions occurred in 17% of patients. Of the patients, 23 (96%) were discharged in a clinically stable condition. Follow up during a two year period was completed in 21 patients (88%). One patient died of cancer. Four subjects (19%) underwent repeat percutaneous transluminal coronary angioplasty. One other patient had recurrent chest pain requiring multiple hospitalizations. The remaining 16 patients (76%) remained free of recurrence of angina. We concluded that percutaneous transluminal coronary angioplasty with stent placement can be performed in octogenarians with a high rate of clinical and angiographic success with an acceptable range of morbidity and mortality, and favorable long term (two year) outcome.
Normal Age‐Related Changes in the Heart: Relevance to Echocardiography in the Elderly
Authors: Kitzman Dalane W.
Published: June 2007

Age‐appropriate normal reference standards are important for the accurate diagnosis of cardiac disease in the elderly. However, it can be difficult to definitively prove that frequently observed changes are due to primary, biologic aging. A gender differential is frequently observed in normative studies of cardiovascular aging. There are mild age‐related increases in left ventricular mass and wall thickness, and a slight decrease in left ventricular internal diastolic and systolic dimensions, particularly in women. The left atrium and aortic root show significant age‐related dilation in both genders. The valve leaflets thicken, and there is an age‐related increase in physiologic valvular regurgitation. Increased epicardial fat widens the echolucent pericardial stripe, both anterior and posterior, particularly in women. The atrial septum thickens and becomes stiffer. Patent foramen ovale is less prevalent with advancing age but, when present, tends to be larger. There are important alterations in left ventricular diastolic filling, with decreased early and increased atrial filling velocity and mildly prolonged early deceleration and isovolumic relaxation time. These changes in diastolic function are relatively uniform and independent of other age‐related changes. There are no significant aging changes in resting left ventricular systolic function. These normal age‐related changes decrease cardiovascular reserve and lower the threshold for expression of cardiovascular disease among older persons. An important finding is that echocardiographic image quality is more frequently poor in older patients. Age, gender, and body size should be taken into account when interpreting echocardiographic findings.