bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct versus resonances mediated F+OH collisions on a new A″3 potential energy surface
Authors: Gómez-Carrasco Susana , González-Sánchez Lola , Aguado Alfredo , Roncero Octavio , Alvariño José M. , Hernández M. Luz , Paniagua Miguel
Published: August 2004

A theoretical study of the F(2P)+OH(2Π)→HF(1Σ+)+O(3P) reactive collisions is carried out on a new global potential energy surface (PES) of the ground A″3 adiabatic electronic state. The ab initio calculations are based on multireference configuration interaction calculations, using the aug-cc-pVTZ extended basis sets of Dunning et al. A functional representation of the PES shows no nominal barrier to reaction, contrary to previous results by others. Wave packet and quasiclassical trajectory calculations have been performed for this PES to study the F+OH(v=0,j) reactive collision. The comparison was performed at fixed and constant values of the total angular momentum from 0 to 110 and relative translational energy up to 0.8 eV. The reaction presents a dynamical barrier, essentially due to the zero-point energy for the bending vibration near the saddle point. This determines two different reaction mechanisms. At energies higher than ≈0.125 eV the reaction is direct, while below that value it is indirect and mediated by heavy-light-heavy resonances. Such resonances, also found in the simulations of the photodetachment spectrum of the triatomic anion, manifest themselves in the quasiclassical simulations, too, where they are associated to periodic orbits.
A guiding-center Fokker–Planck collision operator for nonuniform magnetic fields
Authors: Brizard Alain J.
Published: August 2004

A formulation for collisional kinetic theory is presented based on the use of Lie-transform methods to eliminate fast orbital time scales from a general bilinear collision operator. As an application of this formalism, a general guiding-center bilinear Fokker–Planck (FP) collision operator is derived following the elimination of the fast gyromotion time scale of a charged particle moving in a nonuniform magnetic field. It is expected that classical transport processes in a strongly magnetized nonuniform plasma can, thus, be described in terms of this reduced guiding-center FP kinetic theory. The present paper introduces the reduced-collision formalism only, while its applications are left to future work.
A theory of polymer solutions without the mean-field approximation in Flory-Huggins theory
Authors: Qiao Baofu , Zhao Delu
Published: August 2004

The concept of the volume fraction at chain end is proposed, which is the conditional probability for a site having been occupied, knowing that an adjacent site is occupied by polymer end. The overall entropy of polymer/solvent system is separated into two fundamentally different parts, i.e., the translational entropy and the conformational entropy. Based on these a theory of polymer solutions is established. When a mean-field approximation is introduced, Flory-Huggins (FH) theory is recovered. The FH interaction parameters and spinodal curves of the polystyrene/cyclohexane system are calculated and compared with the experimental data. The good prediction of them two is achieved.
Modeling of intramolecular reactions of polymers: An efficient method based on Brownian dynamics simulations
Authors: Klenin Konstantin V. , Langowski Jörg
Published: August 2004

By the traditional approach to the Brownian dynamics simulations of intrachain reactions of polymers, the initial chain conformation is sampled from the equilibrium distribution. A dynamic trajectory is carried out until a “collision” of the reactive groups takes place, i.e., the distance between their centers becomes less that a certain reaction radius. The average length of the trajectory is equal to the mean time τF of a diffusion-controlled reaction. In this work we propose another computational scheme. The trajectory begins at the instant of collision and is carried out until the chain is relaxed. The length of the trajectory has the order of the relaxation time τrel of the distance between the reactive groups. For polymer systems with τrel≪τF, this scheme allows the computation of τF with considerable gain in computational time. Using the present approach, we calculated the mean time of DNA cyclization for the molecule length in the range from 50 to 500 nm.
Soft effective interactions between weakly charged polyelectrolyte chains
Authors: Konieczny M. , Likos C. N. , Löwen H.
Published: August 2004

We apply extensive molecular dynamics simulations and analytical considerations in order to study the conformations and the effective interactions between weakly charged, flexible polyelectrolyte chains in salt-free conditions. We focus on charging fractions lying below 20%, for which case there is no Manning condensation of counterions and the latter can be thus partitioned in two states: those that are trapped within the region of the flexible chain and the ones that are free in the solution. We examine the partition of counterions in these two states, the chain sizes and the monomer distributions for various chain lengths, finding that the monomer density follows a Gaussian shape. We calculate the effective interaction between the centers of mass of two interacting chains, under the assumption that the chains can be modeled as two overlapping Gaussian charge profiles. The analytical calculations are compared with measurements from molecular dynamics simulations. Good quantitative agreement is found for charging fractions below 10%, where the chains assume coil-like configurations, whereas deviations develop for charge fraction of 20%, in which case a conformational transition of the chain towards a rodlike configuration starts to take place.
A molecular dynamics simulation study of the α-relaxation in a 1,4-polybutadiene melt as probed by the coherent dynamic structure factor
Authors: Smith Grant D. , Bedrov Dmitry , Paul Wolfgang
Published: August 2004

The dynamic coherent structure factor Scoh(q,t) for a 1,4-polybutadiene (PBD) melt has been investigated using atomistic molecular dynamics simulations. The relaxation of Scoh(q,t) at q=1.44 Å−1 and q=2.72 Å−1, corresponding to the first and second peaks in the static structure factor for PBD, was studied in detail over a wide range of temperature. It was found that time-temperature superposition holds for the α-relaxation for both q values over a wide temperature range and that the α-relaxation can be well described by a stretched (Kohlrauch-William-Watts) exponential with temperature independent but q dependent amplitude and stretching exponent. The α-relaxation times for both q values were found to exhibit the same non-Arrhenius temperature dependence, indicating that the same physical processes are responsible for relaxation on both length scales. The α-relaxation time was found to depend strongly upon the dynamical range of data utilized in determining the relaxation time, accounting for qualitative discrepancies between α-relaxation times reported here and those extracted for PBD from experimentally measured Scoh(q,t).
Selective bonding of pyrazine to silicon(100)-2×1 surfaces: The role of nitrogen atoms
Authors: Huang Hai Gou , Huang Jing Yan , Ning Yue Sheng , Xu Guo Qin
Published: August 2004

The covalent binding of pyrazine on Si(100) have been investigated using high-resolution electron energy loss spectroscopy (HREELS) and x-ray photoelectron spectroscopy. Experimental results clearly suggest that the attachment occurs exclusively through the bonding of the two para-nitrogen atoms with the surface without the involvement of the carbon atoms, as evidenced from the retention of the (sp2) C-H stretching mode in HREELS and a significant down shift of 1.6 eV in the binding energy of N 1s. The binding mechanism for pyrazine on Si(100) demonstrates that reaction channels for heteroatomic aromatic molecules are strongly dependent on the electronic properties of the constituent atoms.
Methyl rotational tunneling dynamics of p-xylene confined in a crystalline zeolite host
Authors: Nair Sankar , Dimeo Robert M. , Neumann Dan A. , Horsewill Anthony J. , Tsapatsis Michael
Published: August 2004

The methyl rotational tunneling spectrum of p-xylene confined in nanoporous zeolite crystals has been measured by inelastic neutron scattering (INS) and proton nuclear magnetic resonance (NMR), and analyzed to extract the rotational potential energy surfaces characteristic of the methyl groups in the host-guest complex. The number and relative intensities of the tunneling peaks observed by INS indicate the presence of methyl-methyl coupling interactions in addition to the methyl-zeolite interactions. The INS tunneling spectra from the crystals (space group P212121 with four crystallographically inequivalent methyl rotors) are quantitatively interpreted as a combination of transitions involving two coupled methyl rotors as well as a transition involving single-particle tunneling of a third inequivalent rotor, in a manner consistent with the observed tunneling energies and relative intensities. Together, the crystal structure and the absence of additional peaks in the INS spectra suggest that the tunneling of the fourth inequivalent rotor is strongly hindered and inaccessible to INS measurements. This is verified by proton NMR measurements of the spin-lattice relaxation time which reveal the tunneling characteristics of the fourth inequivalent rotor.
Two-dimensional radio-frequency sheath dynamics over a nonflat electrode with perpendicular magnetic field
Authors: Hou Lu-Jing , Wang You-Nian , Mišković Z. L.
Published: August 2004

A self-consistent fluid model is developed to simulate the radio-frequency (rf) plasma sheath dynamics over a nonflat electrode, with a magnetic field applied perpendicular to it. The model consists of the two-dimensional (2D) time-dependent fluid equations, coupled with the Poisson equation, and it uses an equivalent-circuit model to self-consistently determine the relationship between the instantaneous voltage at the rf-biased electrode and the sheath thickness. In addition to the usual plasma molding effects, different properties of the azimuthal ion flow associated with the E×B drift are observed and studied under varying discharge pressures and the magnetic field intensities. It is found that the azimuthal flow exhibits rather nonuniform distribution with a peak around the edge of a hole in the electrode. In addition, when the discharge pressure increases, the velocity of the azimuthal ion flow, as well as the velocities of ion flow in all other directions, are found to decrease, whereas the sheath edge is found to move closer to the electrode. While the variation of the magnetic field is found to have no significant effect on the sheath structure, the azimuthal ion flow velocity is found to increase in proportion to the magnetic field.
Study of hard x-ray emission from intense femtosecond Ti:sapphire laser–solid target interactions
Authors: Chen L. M. , Forget P. , Fourmaux S. , Kieffer J. C. , Krol A. , Chamberlain C. C. , Hou B. X. , Nees J. , Mourou G.
Published: August 2004

Interaction of intense Ti:sapphire laser with solid targets has been studied experimentally by measuring hard x-ray and hot electron generation. Hard x-ray (8–100 keV) emission spectrum and Kα x-ray conversion efficiency (ηK) from plasma have been studied as a function of laser intensity (1017–1019  W/cm2), pulse duration (70–400)fs, and laser pulse fluence. For intensity I>1×1017 W/cm2, the Ag ηK increases to reach a maximum value of 2×10−5 at an intensity I=4×1018 W/cm2. Hot electron temperature (KTh) and ηK scaling laws have been studied as a function of the laser parameters. A stronger dependence of KTh and ηK as a function of the laser fluence than on pulse duration or laser intensity has been observed. The contribution of another nonlinear mechanism, besides resonance absorption, to hard x-ray enhancement has been demonstrated via hot electron angular distribution and particle-in-cell simulations.
Dual control cell reaction ensemble molecular dynamics: A method for simulations of reactions and adsorption in porous materials
Authors: Lı́sal Martin , Brennan John K. , Smith William R. , Siperstein Flor R.
Published: August 2004

We present a simulation tool to study fluid mixtures that are simultaneously chemically reacting and adsorbing in a porous material. The method is a combination of the reaction ensemble Monte Carlo method and the dual control volume grand canonical molecular dynamics technique. The method, termed the dual control cell reaction ensemble molecular dynamics method, allows for the calculation of both equilibrium and nonequilibrium transport properties in porous materials such as diffusion coefficients, permeability, and mass flux. Control cells, which are in direct physical contact with the porous solid, are used to maintain the desired reaction and flow conditions for the system. The simulation setup closely mimics an actual experimental system in which the thermodynamic and flow parameters are precisely controlled. We present an application of the method to the dry reforming of methane reaction within a nanoscale reactor model in the presence of a semipermeable membrane that was modeled as a porous material similar to silicalite. We studied the effects of the membrane structure and porosity on the reaction species permeability by considering three different membrane models. We also studied the effects of an imposed pressure gradient across the membrane on the mass flux of the reaction species. Conversion of syngas (H2/CO) increased significantly in all the nanoscale membrane reactor models considered. A brief discussion of further potential applications is also presented.
Micellization behavior of star-block copolymers in a selective solvent: A Brownian dynamics simulation approach
Authors: Huh June , Kim Kwang Hee , Ahn Cheol-Hee , Jo Won Ho
Published: August 2004

Micellization behavior of (AB)n type star-block copolymer in a selective solvent for its outer block is investigated by using a Brownian dynamics simulation. Micellar properties are compared in terms of the arm number (n) of star-block copolymer. It is observed that the critical micelle concentration (cmc) shows a minimum when the cmc is plotted against the arm number. The star-block copolymer with longer soluble block shows the cmc minimum at smaller arm number than that with shorter soluble block. Although the star-block copolymer with multiple arms forms more compact core as compared to diblock copolymer, the average aggregation number is inversely proportional to the arm number (∼1/n), which implies that the micelle size is invariant with the arm number. Theoretical predictions based on a simple mean field theory agree qualitatively well with the simulation results.
Accurate intermolecular ground state potential of the Ne-HCl van der Waals complex
Authors: Cagide Fajı́n José Luis , López Cacheiro Javier , Fernández Berta
Published: August 2004

From an accurate ground state intermolecular potential energy surface we evaluate the rovibrational spectrum of the Ne-HCl van der Waals complex. The intermolecular potential is obtained by fitting a considerable number of interaction energies obtained at the coupled cluster singles and doubles including connected triple excitations level and with the augmented correlation consistent polarized valence quintuple zeta basis set extended with a set of 3s3p2d1f1g midbond functions. This basis set is selected after a systematic basis set study carried out at geometries close to those of the three main surface stationary points. The surface is characterized by two linear minima, i.e. Ne-ClH and Ne-HCl, with distances from the Ne atom to the HCl center of mass of 3.398 and 3.833 Å, respectively; and binding energies of −65.10 and −66.85 cm−1, respectively. These results agree well with the experimental data available in contrast to previous theoretical results. The rovibrational spectra calculated for the different isotopic species are also compared to the experiments.
Ionization waves: Hopf–Hopf bifurcations and nonlinear wave-wave interactions
Authors: Bruhn B.
Published: August 2004

The nonlinear dynamics within the transition region between p and s waves is studied for a neon glow discharge. Starting from a Hopf–Hopf bifurcation, the normal form constants are determined and their dependence upon the plasma parameters is discussed. The coexisting state of both waves is a stable two torus in the limit of a large external resistance. Taking into account the extension of the plasma by using a coupled set of complex Ginzburg–Landau equations, the two torus becomes unstable for a system length greater than the typical wavelength of ionization waves. Any initial condition decays and as a rule, the asymptotic states are pure regular s waves or Benjamin–Feir unstable pure p waves. Intermittency is found for selected values of the control parameters. This coexisting regime represents a state of strong nonlinear wave-wave interaction that can only be described by the coupled system.
Susceptibility to astrocytoma in mice mutant for
Nf1
and
Trp53
is linked to chromosome 11 and subject to epigenetic effects
Authors: Reilly Karlyne M. , Tuskan Robert G. , Christy Emily , Loisel Dagan A. , Ledger Jeremy , Bronson Roderick T. , Smith C. Dahlem , Tsang Shirley , Munroe David J. , Jacks Tyler
Published: August 2004

Astrocytoma is the most common malignant brain tumor in humans. Loss of the p53 signaling pathway and up-regulation of the ras signaling pathway are common during tumor progression. We have shown previously that mice mutant for
Trp53
and
Nf1
develop astrocytoma, progressing to glioblastoma, on a C57BL/6J strain background. In contrast, here we present data that mice mutant for
Trp53
and
Nf1
on a 129S4/SvJae background are highly resistant to developing astrocytoma. Through analysis of F
1
progeny, we demonstrate that susceptibility to astrocytoma is linked to chromosome 11, and that the modifier gene(s) responsible for differences in susceptibility is closely linked to
Nf1
and
Trp53
. Furthermore, this modifier of astrocytoma susceptibility is itself epigenetically modified. These data demonstrate that epigenetic effects can have a strong effect on whether cancer develops in the context of mutant ras signaling and mutant p53, and that this mouse model of astrocytoma can be used to identify modifier phenotypes with complex inheritance patterns that would be unidentifiable in humans. Because analysis of gene function in the mouse is often performed on a mixed C57BL/6,129 strain background, these data also provide a powerful example of the potential of these strains to mask interesting gene functions.
Coherent vibrational climbing in carboxyhemoglobin
Authors: Ventalon Cathie , Fraser James M. , Vos Marten H. , Alexandrou Antigoni , Martin Jean-Louis , Joffre Manuel
Published: August 2004

We demonstrate vibrational climbing in the CO stretch of carboxyhemoglobin pumped by midinfrared chirped ultrashort pulses. By use of spectrally resolved pump-probe measurements, we directly observed the induced absorption lines caused by excited vibrational populations up to
v
= 6. In some cases, we also observed stimulated emission, providing direct evidence of vibrational population inversion. This study provides important spectroscopic parameters on the CO stretch in the strong-field regime, such as transition frequencies and dephasing times up to the
v
= 6to
v
= 7 vibrational transition. We measured equally spaced vibrational transitions, in agreement with the energy levels of a Morse potential up to
v
= 6. It is interesting that the integral of the differential absorption spectra was observed to deviate far from zero, in contrast to what one would expect from a simple one-dimensional Morse model assuming a linear dependence of dipole moment with bond length.
Chimerism and tolerance in transplantation
Authors: Starzl Thomas E.
Published: August 2004

Studies in experimental models (1953–1956) demonstrated that acquired donor-specific allotolerance in immunologically immature or irradiated animals is strongly associated with donor leukocyte chimerism. Bone marrow transplantation in immune-deficient or cytoablated human recipients was a logical extension (1968). In contrast, clinical (1959) and then experimental organ transplantation was systematically accomplished in the apparent absence of leukocyte chimerism. Consequently, it was assumed for many years that success with organ and bone marrow transplantation involved fundamentally different mechanisms. With the discovery in 1992 of small numbers of donor leukocytes in the tissues or blood of long-surviving organ recipients (microchimerism), we concluded that organ engraftment was a form of leukocyte chimerism-dependent partial tolerance. In this initially controversial paradigm, alloengraftment after both kinds of transplantation is the product of a double immune reaction in which responses, each to the other, of coexisting donor and recipient immune systems results in variable reciprocal clonal exhaustion, followed by peripheral clonal deletion. It was proposed with Rolf Zinkernagel that the individual alloresponses are the equivalent of the MHC-restricted T cell recognition of, and host response to, intracellular parasites and that the mechanisms of immune responsiveness, or nonresponsiveness, are governed by the migration and localization of the respective antigens. Elucidation of the mechanisms of nonresponsiveness (clonal exhaustion-deletion and immune ignorance) and their regulation removed much of the historical mystique of transplantation. The insight was then applied to improve the timing and dosage of immunosuppression of current human transplant recipients.
Polymorphisms of cardiac presynaptic α
2C
adrenergic receptors: Diverse intragenic variability with haplotype-specific functional effects
Authors: Small Kersten M. , Mialet-Perez Jeanne , Seman Carrie A. , Theiss Cheryl T. , Brown Kari M. , Liggett Stephen B.
Published: August 2004

The presynaptic α
2C
adrenergic receptors (AR) act to inhibit norepinephrine release in cardiac and other presynaptic nerves. We have recently shown that a genetic variant in the α
2C
AR coding region (Del322-325), which renders the receptor partially uncoupled from G
i
, is a risk factor for heart failure. However, variability of heart failure phenotypes and a dominance of Del322-325 in those of African descent led us to hypothesize that other regions of this gene have functional polymorphisms. In a multiethnic population, we found 20 polymorphisms within 4,625 bp of contiguous sequence of this intronless gene encompassing the promoter, 5′ UTR, coding, and 3′ UTR. These polymorphisms occur in 24 distinct haplotypes with complex organizations, including multiple 5′-upstream polymorphisms in regions known to direct expression, a 3′ UTR substitution polymorphism within an insertion/deletion sequence, and the radical coding polymorphism that deletes four amino acids. Relatively low linkage disequilibrium between many polymorphisms, few cosmopolitan haplotypes, prevalent ethnic-specific haplotypes, and substantial genetic divergence among haplotypes was noted. The dysfunctional Del322-325 allele was partitioned into multiple haplotypes, with frequencies of 48% to 2%. The functional implications of the haplotypes were ascertained by whole-gene transfections of human neuronal cells, where haplotype was significantly related (
P
< 0.001) to expression levels of receptor transcript and protein. Expression varied by as much as ≈50% by haplotype, and such studies enabled haplotype clustering by phenotypic, rather than genotypic, similarities. Thus, depending on phenotype, expression-specific haplotypes may amplify, attenuate, or dominate the cardiomyopathic effect attributed to the α
2C
Del322-325 marker.
Mechanosensory function of microvilli of the kidney proximal tubule
Authors: Du Zhaopeng , Duan Yi , Yan QingShang , Weinstein Alan M. , Weinbaum Sheldon , Wang Tong
Published: August 2004

Normal variations in glomerular filtration induce proportional changes in proximal tubule Na
+
reabsorption. This “glomerulotubular balance” derives from flow dependence of Na
+
uptake across luminal cell membranes; however, the underlying physical mechanism is unknown. Our hypothesis is that flow-dependent reabsorption is an autoregulatory mechanism that is independent of neural and hormonal systems. It is signaled by the hydrodynamic torque (bending moment) on epithelial microvilli. Such signals need to be transmitted to the terminal web to modulate Na
+
-H
+
-exchange activity. To investigate this hypothesis, we examined Na
+
transport and tubular diameter in response to different flow rates during the microperfusion of isolated S
2
proximal tubules from mouse kidneys. The data were analyzed by using a mathematical model to estimate the microvillous torque as function of flow. In this model, increases in luminal diameter have the effect of blunting the impact of flow velocity on microvillous shear stress and, thus, microvillous torque. We found that variations in microvillous torque produce nearly identical fractional changes in Na
+
reabsorption. Furthermore, the flow-dependent Na
+
transport is increased by increasing luminal fluid viscosity, diminished in Na
+
-H
+
exchanger isoform 3 knockout mice, and abolished by nontoxic disruption of the actin cytoskeleton. These data support our hypothesis that the “brush-border” microvilli serve a mechanosensory function in which fluid dynamic torque is transmitted to the actin cytoskeleton and modulates Na
+
absorption in kidney proximal tubules.
Kidney Slices of Human and Rat to Characterize Cisplatin-Induced Injury on Cellular Pathways and Morphology
Authors: Vickers Alison E.M. , Rose Kristine , Fisher Robyn , Saulnier Muriel , Sahota Pritam , Bentley Philip
Published: August 2004

Kidney slices represent an in vitro model that has the cellular complexity of in vivo tissue to provide insights into mechanisms of organ injury, as shown in this study with the model nephrotoxicant cisplatin. Cell pathways altered by cisplatin exposure are assessed by gene expression analysis, cell function, and morphology in human and rat kidney slices in comparison to rat kidney from an in vivo study. The acute nephrosis of the tubular epithelium induced by cisplatin in vivo was reproduced in both human and rat kidney slices, while the glomerulus appeared resistant even at high concentrations. Kidney gene expression changes of in vivo and in vitro samples were indicative of transcription, DNA damage, cell cycle, proliferation, and apoptosis that are in agreement with the mechanism of cisplatin causing DNA damage, growth arrest, and apoptosis; while genes indicative of protein damage, the disruption of transport and calcium homeostasis, cellular metabolism, and oxidative stress are pathways linked with cisplatin binding to various cellular proteins and macromolecules. Both concentration and time-dependent gene expression changes evident in the in vitro model preceded a change in tissue morphology. Functional assays confirming cell dysfunction and increased apoptosis revealed the rat kidney to be more sensitive to the effects of cisplatin than human kidney as demonstrated by significant decreases in slice ATP and GSH levels, significant increases in caspase 9 and 3 activity, p53 protein levels, and increased DNA laddering. The regional markers of proximal and distal tubular injury, alpha- and pi-glutathione S-transferases, were shown for the human kidney slices to be significantly increased by cisplatin. In this study, cisplatin-induced nephrotoxicity was demonstrated morphologically in rat and human kidney slices, and the associated gene expression and functional changes characterized the cellular pathways involved.
Calcium‐Independent Release of Endothelial Nitric Oxide in the Arteriolar Network: Onset During Rapid Juvenile Growth
Authors: NURKIEWICZ TIMOTHY R. , BOEGEHOLD MATTHEW A.
Published: August 2004

Objective: In young rats, skeletal muscle arterioles respond to acetylcholine, which elicits Ca2+‐dependent endothelial nitric oxide (NO) release, but not to shear stress, which does not require increased intracellular Ca2+ for endothelial NO release. The aim of this study was to determine if, in general, signaling pathways for endothelial NO release that differ in their reliance on Ca2+ may be developing at different times during normal arteriolar network growth in skeletal muscle.

Methods: Arteriolar responses to intraluminal infusion of the Ca2+ ionophore A23187, and the Ca2+‐independent agonists vascular endothelial growth factor (VEGF) and simvastatin, were studied before and during NO synthase (NOS) inhibition with NG‐monomethyl‐L‐arginine (L‐NMMA) in the exteriorized spinotrapezius muscle of weanling (age 4–5 wks) and juvenile (7–8 wks) rats.

Results: There were no age‐dependent differences in arteriolar responses to A23187 applied over a concentration range that dilated arterioles from 9 ± 2 to 74 ± 8% of maximum, and L‐NMMA attenuated these responses by the same amount in both age groups. In juveniles, arterioles dilated up to 39± 5% of maximum in response to VEGF, and up to 83 ± 6% of maximum in response to simvastatin, with L‐NMMA greatly reducing the responses to both agonists. In contrast, arterioles in weanlings did not dilate in response to either agonist.

Conclusions: These findings suggest that some Ca2+‐independent signaling pathways for endothelial NO release may not initially be operational in the arteriolar network, but quickly become established during juvenile growth. This is consistent with the idea that microvascular control mechanisms are not fixed at birth, but rather undergo progressive changes in concert with microvascular network growth and changes in tissue metabolic requirements.
Effects of Arg‐Gly‐Asp Sequence Peptide and Hyperosmolarity on the Permeability of Interstitial Matrix and Fenestrated Endothelium in Joints
Authors: POLI A. , MASON R. M. , LEVICK J. R.
Published: August 2004

Objectives: The aims were to assess the contribution of arg‐gly‐asp (RGD) mediated cell integrin–matrix bonds to interstitial hydraulic resistance and to fenestrated endothelial permeability in joints. Joint fluid is generated by filtration from fenestrated capillaries and drains through a fibronectin‐rich synovial intercellular matrix. The role of parenchymal cell–matrix bonding in determining tissue hydraulic resistance is unknown.

Methods: The knee cavity of anesthetized rabbits was infused with saline or the competitive hexapeptide blocker GRGDTP, with or without added osmotic stress (600 mosm saline). Intra‐articular pressure Pj, net trans‐synovial drainage rate s, and the permeation of Evans blue‐labeled albumin (EVA) from plasma into the joint cavity were measured.

Results: GRGDTP increased the hydraulic conductance of the synovial drainage pathway, ds/dPj, by 71% (p = .02, paired t test, n = 6 animals). Synovial plasma EVA clearance (control 7.1 ± 0.8 μL h−1, mean ± SEM, n = 15) was unaffected by GRGDTP (7.0 ± 2.3 μL h−1, n = 6) or hyperosmolarity (4.9 ± 1.5 μL h−1, n = 8) but was increased by GRGDTP and hyperosmolarity together (15.9 ± 4.8 μL h−1, n = 5) (p = .01, ANOVA). Changes in dPj/dt evoked by GRGDTP plus hyperosmolarity, but neither alone, demonstrated increased microvascular filtration into the joint cavity (p < .001, ANOVA), as did changes in fluid absorption from the infusion system at fixed Pj.

Conclusions: RGD‐mediated bonds between the parenchymal cells and interstitial polymers reduce the interstitial hydraulic conductance by 42%. This helps to retain the lubricating fluid inside a joint cavity. RGD‐mediated bonds also support the macromolecular barrier function of fenestrated endothelium, but in vivo this is evident only in stressed endothelium (cf. in vitro).
Regulation of T‐Lymphocyte Trafficking by ICAM‐1, MAdCAM‐1, and CCR7 in Microcirculation of Appendicular and Intestinal Lymphoid Tissues
Authors: NAGAMATSU HIDEYASU , TSUZUKI YOSHIKAZU , MATSUZAKI KOJI , MIYAZAKI JUNICHI , OKADA YOSHIKIYO , HOKARI RYOTA , KAWAGUCHI ATSUSHI , NAGAO SHIGEAKI , ITOH KAZURO , MIURA SOICHIRO
Published: August 2004

Objective: Although the appendix is recognized as an inductive site of intestinal inflammation, lymphocyte migration to lymphoid tissues of the appendix has not been characterized. The authors investigated if there are specific features in T‐lymphocyte adhesion to microvessels of the appendix compared to mouse Peyer's patches (PPs).

Methods: T‐lymphocyte interaction with postcapillary venules (PCVs) of lymph follicles of the appendix and PPs was observed using an intravital microscope. Antibodies against ICAM‐1, MAdCAM‐1, or anti‐L‐selectin were administered prior to lymphocyte administration, and in some experiments CCR7 on T‐lymphocytes was desensitized by excess CCL21.

Results: The number of adhered T‐lymphocytes reached the maximum value earlier in PCVs of PPs than in those of the appendix. T‐lymphocyte adherence was significantly inhibited by anti‐MAdCAM‐1 at either the appendix or PPs, but adherence in the appendix was also significantly inhibited by anti‐ICAM‐1, suggesting a dependency on ICAM‐1 in the appendix. Histologically, there was a significant ICAM‐1 expression in the appendix. Desensitization of CCR7 suppressed T‐cell adhesion in PCVs of the appendix and PPs to the same extent.

Conclusion: ICAM‐1 appeared to be more important in T‐lymphocyte sticking in PCVs of the appendix compared with intestinal PPs, while MAdCAM‐1 and CCR7 were shown to play important roles in T‐lymphocyte adherence in all sites.
Expression of Inducible Nitric Oxide Synthase in Cultured Smooth Muscle Cells from Rat Mesenteric Lymphatic Vessels
Authors: ROBERTSON DEBORAH A. F. , HUGHES GWEN A. , LYLES GEOFFREY A.
Published: August 2004

Objective: The objective was to devise a method for establishing cultures of rat mesenteric lymphatic vessel smooth muscle cells (LSMC) and to investigate if inducible nitric oxide synthase (iNOS) expression could be activated in LSMC treated with bacterial lipopolysaccharide (LPS).

Methods: LSMC were successfully grown from explanted rat lymphatic microvessels and maintained by subculture. Treatment of LSMC for 24 h with LPS (1–100 μg/mL) activated iNOS protein induction, associated with (1) assay of increased nitrite concentrations in the medium representing cellular nitric oxide synthesis, and (2) demonstration of iNOS in cell extracts by Western blotting.

Results: The protein synthesis inhibitor cycloheximide (10 μM) blocked both LPS‐induced nitrite formation and iNOS protein expression in LSMC. 1400 W (1 μM), a selective iNOS inhibitor, prevented LPS‐induced nitrite formation but not iNOS expression. As well as induction of iNOS by LPS, “constitutive” iNOS was present in some cultures, producing nitrite in amounts that were also subsequently reduced after cell treatment with 1400 W.

Conclusion: Rat mesenteric LSMC produce nitrite and express iNOS in response to bacterial LPS. Cultured LSMC may provide a useful model for studying mechanisms of iNOS induction in relation to possible influences of iNOS upon lymphatic vessel function.
Ca2+ Flux Through Voltage‐Gated Channels with Flow Cessation in Pulmonary Microvascular Endothelial Cells
Authors: WEI ZHIHUA , MANEVICH YEFIM , AL‐MEHDI ABU B. , CHATTERJEE SHAMPA , FISHER ARON B.
Published: August 2004

Objective: To investigate the role of voltage‐gated Ca2+ channels in Ca2+ influx with flow cessation in flow‐adapted rat pulmonary microvascular endothelial cells.

Methods: Cells were evaluated for mRNA and protein levels for major components of the voltage‐gated Ca2+ channels. Ca2+ influx with flow cessation and cell membrane potential were measured in real time with fluorescent dyes. Mibefradil and nifedipine were used as inhibitors of Ca2+ channel activity.

Results: Voltage‐gated Ca2+ channel protein and mRNA for the T‐type channel were expressed at a relatively low level in endothelial cells cultured under static conditions and expression was induced significantly during flow adaptation. Flow‐adapted but not control cells showed Ca2+ influx during flow cessation that was blocked by mibefradil but not by nifedipine. Ca2+ influx also was blocked by cromakalim, a KATP channel agonist. Cell membrane depolarization with flow cessation was unaffected by mibefradil.

Conclusions: Rat pulmonary microvascular endothelial cells express T‐type voltage‐gated Ca2+ channels that are induced during adaptation to flow and are responsible for Ca2+ influx that occurs as a result of flow cessation‐mediated membrane depolarization.
Supervised identification of allergen-representative peptides forin silicodetection of potentially allergenic proteins
Authors: Björklund Åsa K. , Soeria-Atmadja Daniel , Zorzet Anna , Hammerling Ulf , Gustafsson Mats G.
Published: August 2004

Motivation: Identification of potentially allergenic proteins is needed for the safety assessment of genetically modified foods, certain pharmaceuticals and various other products on the consumer market. Current methods in bioinformatic allergology exploit common features among allergens for the detection of amino acid sequences of potentially allergenic proteins. Features for identification still unexplored include the motifs occurring commonly in allergens, but rarely in ordinary proteins. In this paper, we present an algorithm for the identification of such motifs with the purpose of biocomputational detection of amino acid sequences of potential allergens.

Results: Identification of allergen-representative peptides (ARPs) with low or no occurrence in proteins lacking allergenic properties is the essential component of our new method, designated DASARP (Detection based on Automated Selection of Allergen-Representative Peptide). This approach consistently outperforms the criterion based on identical peptide match for predicting allergenicity recommended by ILSI/IFBC and FAO/WHO and shows results comparable to the alignment-based criterion as outlined by FAO/WHO.

Availability: The detection software and the ARP set needed for the analysis of a query protein reported here are properties of the Swedish National Food Agency and are available upon request. The protein sequence sets used in this work are publicly available on http://www.slv.se/templatesSLV/SLV_Page____9343.asp. Allergenicity assessment for specific protein sequences of interest is also possible via ulfh@slv.se

Contact:  ulfh@slv.se
Simulating genetic networks made easy: network construction with simple building blocks
Authors: Vercruysse Steven , Kuiper Martin
Published: August 2004

Summary: We present SIM-plex, a genetic network simulator with a very intuitive interface in which a user can easily specify interactions as simple ‘if-then’ statements. The simulator is based on the mathematical model of Piecewise Linear Differential Equations (PLDEs). With PLDEs, genetic interactions are approximated as acting in a switch-like manner.

Availability: The Java program, examples and a tutorial are available at http://www.psb.ugent.be/cbd/

Contact:  {stcru,makui}@psb.ugent.be
Similarity of position frequency matrices for transcription factor binding sites
Authors: Schones Dustin E. , Sumazin Pavel , Zhang Michael Q.
Published: August 2004

Motivation: Transcription-factor binding sites (TFBS) in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices (PFM). The ability to compare PFMs representing binding sites is especially important for de novo sequence motif discovery, where it is desirable to compare putative matrices to one another and to known matrices.

Results: We describe a PFM similarity quantification method based on product multinomial distributions, demonstrate its ability to identify PFM similarity and show that it has a better false positive to false negative ratio compared to existing methods.

We grouped TFBS frequency matrices from two libraries into matrix families and identified the matrices that are common and unique to these libraries. We identified similarities and differences between the skeletal-muscle-specific and non-muscle-specific frequency matrices for the binding sites of Mef-2, Myf, Sp-1, SRF and TEF of Wasserman and Fickett. We further identified known frequency matrices and matrix families that were strongly similar to the matrices given by Wasserman and Fickett. We provide methodology and tools to compare and query libraries of frequency matrices for TFBSs.

Availability: Software is available to use over the Web at http://rulai.cshl.edu/MatCompare

Contact:  dschones@cshl.edu

Supplementary information: Database and clustering statistics, matrix families and representatives are available at http://rulai.cshl.edu/MatCompare/Supplementary
MCQTL: multi-allelic QTL mapping in multi-cross design
Authors: Jourjon Marie-Françoise , Jasson Sylvain , Marcel Jacques , Ngom Baba , Mangin Brigitte
Published: August 2004

Summary: The aim of the MCQTL software package is to perform QTL mapping in multi-cross designs. It allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all of them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families.

The implemented model is a linear regression model. A composite interval mapping and an iterative QTL mapping are implemented to deal with multiple QTL models. Marker cofactor selections by forward or backward stepwise methods are implemented as well as computation of threshold test value by permutation.

Availability: The program is available on request after signing a licence agreement; free of charge for academic and non-profit organizations at http://www.genoplante.org(Bioinformatics products).

Contact:  contactbioinf@genoplante.com
Predicting protein–protein interactions using signature products
Authors: Martin Shawn , Roe Diana , Faulon Jean-Loup
Published: August 2004

Motivation: Proteome-wide prediction of protein–protein interaction is a difficult and important problem in biology. Although there have been recent advances in both experimental and computational methods for predicting protein–protein interactions, we are only beginning to see a confluence of these techniques. In this paper, we describe a very general, high-throughput method for predicting protein–protein interactions. Our method combines a sequence-based description of proteins with experimental information that can be gathered from any type of protein–protein interaction screen. The method uses a novel description of interacting proteins by extending the signature descriptor, which has demonstrated success in predicting peptide/protein binding interactions for individual proteins. This descriptor is extended to protein pairs by taking signature products. The signature product is implemented within a support vector machine classifier as a kernel function.

Results: We have applied our method to publicly available yeast, Helicobacter pylori, human and mouse datasets. We used the yeast and H.pylori datasets to verify the predictive ability of our method, achieving from 70 to 80% accuracy rates using 10-fold cross-validation. We used the human and mouse datasets to demonstrate that our method is capable of cross-species prediction. Finally, we reused the yeast dataset to explore the ability of our algorithm to predict domains.

Contact:  smartin@sandia.gov.
Diagnosis Murder: The Death of State Death Taxes
Authors: Conway Karen Smith , Rork Jonathan C.
Published: August 2004

Since 1976, more than 30 states have eliminated their “death” taxes and many others have reduced them. This unexplored case of interstate tax competition presents a unique opportunity to develop a new, more satisfying definition of competitor based on historical elderly migration patterns. Using data from 1967 onward, we outline the recent history of state death tax competitio n and present a spatial econometric analysis. Interstate tax competition is evident and grows stronger when using migration‐based definitions of competitors. The article concludes with still more evidence of interstate tax competition—the recent movement by states to effectively revive their death taxes.
Labor Market Search and Optimal Retirement Policy
Authors: Bhattacharya Joydeep , Mulligan Casey B. , Reed Robert R.
Published: August 2004

A popular and long‐standing view is that social security is a means for young, unemployed people to “purchase” jobs from older workers. Can social security, by encouraging retirement and hence creating job vacancies for the young, improve the allocation of workers to jobs? Maybe, according to a standard model of labor market search, but public retirement programs currently pay the elderly substantially more than their jobs are worth. An important effect is that retirement reduces the value of other vacant jobs. Our results imply that recent reforms aimed at reducing retirement incentives are likely to improve labor market efficiency.
Mutual Raiding of Production and the Emergence of Exchange
Authors: Hausken Kjell
Published: August 2004

Joint exchange and raiding can emerge in a world of mutual raiding when the appropriated production is less valuable to the appropriator than to the defender and the defense is not too inferior to attack. The amounts of resources allocated to production and raiding and the amounts of goods exchanged reciprocally are determined endogenously. The model reduces to pure exchange and pure raiding as special cases. Pure exchange emerges when the usability of appropriation is sufficiently low. Pure raiding emerges if the defense is sufficiently inferior to attack. The results of the model are intermediate between the results of the two extreme cases.
Growth with Endogenous Risk of Biological Invasion
Authors: Barbier Edward B. , Shogren Jason F.
Published: August 2004

We model biological invasions as an unintended by‐product of capital accumulation. We distinguish three spillover effects: (1) a negative production externality, (2) a negative or positive consumption externality and (3) an increase in the risk of future welfare loss. We also consider the implications when households self‐protect by allocating income to reduce the potential damages from a biological invasion. An optimal output tax for production externalities is straightforward and can be augmented in the case of negative or positive spillover effects on consumer welfare. Policies to correct the effect of invasions on endogenous risk are more difficult to design.
Life Expectancy, Schooling Time, Retirement, and Growth
Authors: Echevarría Cruz A.
Published: August 2004

I analyze how changes in life expectancy affect retirement age, education time, and growth rates of economies. I set up a continuous time, overlapping generations model of endogenous growth with externalities in human capital production. I find that increases in life expectancy give rise to first, higher retirement ages and second, higher education spans. A threshold level for life expectancy exists such that per capita growth rates follow an inverted U pattern.
Government Debt and Excess Sensitivity of Private Consumption: Estimates from OECD Countries
Authors: Pozzi Lorenzo , Heylen Freddy , Dossche Maarten
Published: August 2004

This article investigates the role of government debt in the degree of excess sensitivity of private consumption to current disposable income. Because this type of excess sensitivity is generally attributed to liquidity constraints, this amounts to a test of the impact of government debt on the amount of credit extended to individuals. Controlling for financial liberalization we find that, for a panel of OECD countries in the 1990s, a high government debt leads to more excess sensitivity. This result supports the idea that a high government debt induces lenders to tighten credit conditions. Our findings survive several robustness checks.