bluuebunny/crossref_metadata_2025 huggingface dataset:
Periodic orbits, localization in normal mode space, and the Fermi–Pasta–Ulam problem
Authors: Flach S. , Ivanchenko M. V. , Kanakov O. I. , Mishagin K. G.
Published: March 2008

The Fermi–Pasta–Ulam problem was one of the first computational experiments. It has stirred the physics community since, and resisted a simple solution for half a century. The combination of straightforward simulations, efficient computational schemes for finding periodic orbits, and analytical estimates allows us to achieve significant progress. Recent results on q-breathers, which are time-periodic solutions that are localized in the space of normal modes of a lattice and maximize the energy at a certain mode number, are discussed, together with their relation to the Fermi–Pasta–Ulam problem. The localization properties of a q-breather are characterized by intensive parameters, that is, energy densities and wave numbers. By using scaling arguments, q-breather solutions are constructed in systems of arbitrarily large size. Frequency resonances in certain regions of wave number space lead to the complete delocalization of q-breathers. The relation of these features to the Fermi–Pasta–Ulam problem are discussed.
Simple models of complex chaotic systems
Authors: Sprott J. C.
Published: March 2008

Many phenomena in the real world are inherently complex and involve many dynamical variables interacting nonlinearly through feedback loops and exhibiting chaos, self-organization, and pattern formation. It is useful to ask if there are generic features of such systems, and if so, how simple can such systems be and still display these features. This paper describes several such systems that are accessible to undergraduates and might serve as useful examples of complexity.
Invitation to embarrassingly parallel computing
Authors: Breen Barbara J. , Weidert Christine E. , Lindner John F. , Walker Lisa May , Kelly Kasey , Heidtmann Evan
Published: March 2008

A surprising number of physical systems problems are well suited to “embarrassingly parallel" computations which do not require complicated algorithms or specialized hardware. As faculty and students at small institutions, we are readily incorporating parallel computing in diverse levels of our curricula and are embracing the opportunity to utilize high performance computing to do cutting edge research. We describe three typical examples: spatiotemporal patterns of one-way coupled oscillators, ray-tracing in curved spacetime, and solar escape as a three-body problem.
Symbolic manipulators affect mathematical mindsets
Authors: Bing Thomas J. , Redish Edward F.
Published: March 2008

The use of symbolic calculators such as MATHEMATICA is becoming more commonplace among upper level physics students. The presence of such powerful calculators can couple strongly to the type of mathematical reasoning students employ. These tools do not merely offer students a convenient way to perform the calculations they would have otherwise done by hand. We present examples from the work of upper level physics majors where MATHEMATICA plays an active role in focusing and sustaining their thoughts around calculation. These students still engage in powerful mathematical reasoning while they calculate, but struggle because of the narrowed breadth of their thinking. We model MATHEMATICA’S influence as an integral part of the constant feedback that occurs in how students frame, and hence focus, their work.
Computational physics in the introductory calculus-based course
Authors: Chabay Ruth , Sherwood Bruce
Published: March 2008

The integration of computation into the introductory calculus-based physics course can potentially provide significant support for the development of conceptual understanding. Computation can support three-dimensional visualizations of abstract quantities, offer opportunities to construct symbolic rather than numeric solutions to problems, and provide experience with the use of vectors as coordinate-free entities. Computation can also allow students to explore models in a way not possible using the analytical tools available to first-year students. We describe how we have incorporated computer programming into an introductory calculus-based course taken by science and engineering students.
Electrodynamics on a grid: The finite-difference time-domain method applied to optics and cloaking
Authors: Sipos M. , Thompson B. G.
Published: March 2008

Maxwell’s curl equations lead to energy transport via electric and magnetic fields because spatial variations of one field lead to a temporal change in the other. The finite-difference time-domain (FDTD) method of calculating electromagnetic fields takes advantage of this interplay of the fields by using a suitable grid and time stepping method. The method is simple and instructive for understanding the genesis of electromagnetic transport phenomena. Reflection, refraction, interference, and diffraction result directly from the linked first-order derivatives of the fields. Extension of the method to include permittivity and permeability tensors with extreme values of these properties allows a wave to be bent around a central region thus cloaking (rendering invisible) any object inside.
Integrating computation into the undergraduate curriculum: A vision and guidelines for future developments
Authors: Chonacky Norman , Winch David
Published: March 2008

There is substantial evidence of a need to make computation an integral part of the undergraduate physics curriculum. This need is consistent with data from surveys in both the academy and the workplace, and has been reinforced by two years of exploratory efforts by a group of physics faculty for whom computation is a special interest. We have examined past and current efforts at reform and a variety of strategic, organizational, and institutional issues involved in any attempt to broadly transform existing practice. We propose a set of guidelines for development based on this past work and discuss our vision of computationally integrated physics.
Interactive learning tutorials on quantum mechanics
Authors: Singh Chandralekha
Published: March 2008

We discuss the development and evaluation of quantum interactive learning tutorials (QuILTs), which are suitable for undergraduate courses in quantum mechanics. QuILTs are based on the investigation of student difficulties in learning quantum physics. They exploit computer-based visualization tools and help students build links between the formal and conceptual aspects of quantum physics without compromising the technical content. They can be used both as supplements to lectures or as self-study tools.
A project-oriented course in computational physics: Algorithms, parallel computing, and graphics
Authors: Rebbi C.
Published: March 2008

I describe an undergraduate course in computational physics in which by focusing on a limited number of physics projects, the students are gradually introduced to numerical algorithms, parallel computing, graphics rendering, and visualization.
Teaching statistical physics by thinking about models and algorithms
Authors: Tobochnik Jan , Gould Harvey
Published: March 2008

We discuss several ways of illustrating fundamental concepts in statistical and thermal physics by considering various models and algorithms. We emphasize the importance of replacing students’ incomplete mental images by models that are physically accurate. In some cases it is sufficient to discuss the results of an algorithm or the behavior of a model rather than having students write a program.
Computation in classical mechanics
Authors: Timberlake Todd , Hasbun Javier E.
Published: March 2008

One way to introduce computation into the physics curriculum is to include it in a standard upper-level physics course. A course in intermediate classical mechanics is well-suited for this purpose. We discuss our approach and examples of student projects on solving differential equations and Liouville’s theorem, projectile motion on a rotating Earth, motion of a charged particle in electric and magnetic fields, and approximate analytical and numerical solutions for a classical model of a molecule. The projects introduce students to these physics topics and develop the students’ computational skills.
Comparing the influence of physical and virtual manipulatives in the context of the Physics by Inquiry curriculum: The case of undergraduate students’ conceptual understanding of heat and temperature
Authors: Zacharia Zacharias C. , Constantinou Constantinos P.
Published: March 2008

We compare the effect of experimenting with physical or virtual manipulatives on undergraduate students’ conceptual understanding of heat and temperature. A pre–post comparison study design was used to replicate all aspects of a guided inquiry classroom except the mode in which students performed their experiments. This study is the first on physical and virtual manipulative experimentation in physics in which the curriculum, method of instruction, and resource capabilities were explicitly controlled. The participants were 68 undergraduates in an introductory course and were randomly assigned to an experimental or a control group. Conceptual tests were administered to both groups to assess students’ understanding before, during, and after instruction. The result indicates that both modes of experimentation are equally effective in enhancing students’ conceptual understanding. This result is discussed in the context of an ongoing debate on the relative importance of virtual and real laboratory work in physics education.
The Chlorine Isotope Composition of Earth's Mantle
Authors: Bonifacie M. , Jendrzejewski N. , Agrinier P. , Humler E. , Coleman M. , Javoy M.
Published: March 2008

Chlorine stable isotope compositions (δ
37
Cl) of 22 mid-ocean ridge basalts (MORBs) correlate with Cl content. The high-δ
37
Cl, Cl-rich basalts are highly contaminated by Cl-rich materials (seawater, brines, or altered rocks). The low-δ
37
Cl, Cl-poor basalts approach the composition of uncontaminated, mantle-derived magmas. Thus, most or all oceanic lavas are contaminated to some extent during their emplacement. MORB-source mantle has δ
37
Cl ≤ –1.6 per mil (‰), which is significantly lower than that of surface reservoirs (∼ 0‰). This isotopic difference between the surface and deep Earth results from net Cl isotopic fractionation (associated with removal of Cl from the mantle and its return by subduction over Earth history) and/or the addition (to external reservoirs) of a late volatile supply that is
37
Cl-enriched.
Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics
Authors: Bashor Caleb J. , Helman Noah C. , Yan Shude , Lim Wendell A.
Published: March 2008

Scaffold proteins link signaling molecules into linear pathways by physically assembling them into complexes. Scaffolds may also have a higher-order role as signal-processing hubs, serving as the target of feedback loops that optimize signaling amplitude and timing. We demonstrate that the Ste5 scaffold protein can be used as a platform to systematically reshape output of the yeast mating MAP kinase pathway. We constructed synthetic positive- and negative-feedback loops by dynamically regulating recruitment of pathway modulators to an artificial binding site on Ste5. These engineered circuits yielded diverse behaviors: ultrasensitive dose response, accelerated or delayed response times, and tunable adaptation. Protein scaffolds provide a flexible platform for reprogramming cellular responses and could be exploited to engineer cells with novel therapeutic and biotechnological functions.
Amyloid Fibrils of the HET-s(218–289) Prion Form a β Solenoid with a Triangular Hydrophobic Core
Authors: Wasmer Christian , Lange Adam , Van Melckebeke Hélène , Siemer Ansgar B. , Riek Roland , Meier Beat H.
Published: March 2008

Prion and nonprion forms of proteins are believed to differ solely in their three-dimensional structure, which is therefore of paramount importance for the prion function. However, no atomic-resolution structure of the fibrillar state that is likely infectious has been reported to date. We present a structural model based on solid-state nuclear magnetic resonance restraints for amyloid fibrils from the prion-forming domain (residues 218 to 289) of the HET-s protein from the filamentous fungus
Podospora anserina
. On the basis of 134 intra- and intermolecular experimental distance restraints, we find that HET-s(218–289) forms a left-handed β solenoid, with each molecule forming two helical windings, a compact hydrophobic core, at least 23 hydrogen bonds, three salt bridges, and two asparagine ladders. The structure is likely to have broad implications for understanding the infectious amyloid state.
Superconductivity in Hydrogen Dominant Materials: Silane
Authors: Eremets M. I. , Trojan I. A. , Medvedev S. A. , Tse J. S. , Yao Y.
Published: March 2008

The metallization of hydrogen directly would require pressure in excess of 400 gigapascals (GPa), out of the reach of present experimental techniques. The dense group IVa hydrides attract considerable attention because hydrogen in these compounds is chemically precompressed and a metallic state is expected to be achievable at experimentally accessible pressures. We report the transformation of insulating molecular silane to a metal at 50 GPa, becoming superconducting at a transition temperature of
T

c

= 17 kelvin at 96 and 120 GPa. The metallic phase has a hexagonal close-packed structure with a high density of atomic hydrogen, creating a three-dimensional conducting network. These experimental findings support the idea of modeling metallic hydrogen with hydrogen-rich alloy.
Direct Visualization of Horizontal Gene Transfer
Authors: Babić Ana , Lindner Ariel B. , Vulić Marin , Stewart Eric J. , Radman Miroslav
Published: March 2008

Conjugation allows bacteria to acquire genes for antibiotic resistance, novel virulence attributes, and alternative metabolic pathways. Using a fluorescent protein fusion, SeqA-YFP, we have visualized this process in real time and in single cells of
Escherichia coli
. We found that the F pilus mediates DNA transfer at considerable cell-to-cell distances. Integration of transferred DNA by recombination occurred in up to 96% of recipients; in the remaining cells, the transferred DNA was fully degraded by the RecBCD helicase/nuclease. The acquired integrated DNA was tracked through successive replication rounds and was found to occasionally split and segregate with different chromosomes, leading to the inheritance of different gene clusters within the cell lineage. The incidence of DNA splitting corresponds to about one crossover per cell generation.
Enzyme-Linked Immunosorbent Assays Using Novel Japanese Encephalitis Virus Antigen Improve the Accuracy of Clinical Diagnosis of Flavivirus Infections
Authors: Chiou Shyan-Song , Crill Wayne D. , Chen Li-Kuang , Chang Gwong-Jen J.
Published: March 2008

The cross-reactive antibodies induced by flavivirus infections confound serodiagnosis and pathogenesis, especially in secondary infections caused by antigenically closely related yet distinct flaviviruses. The envelope (E) glycoprotein fusion peptide contains immunodominant cross-reactive determinants. Using a recombinant Japanese encephalitis virus (JEV) premembrane and E expression plasmid producing JEV virus-like particles (VLPs), dramatic reductions in cross-reactivity were produced by the G106K-L107D (KD) double-mutant VLP against a panel of flavivirus murine monoclonal antibodies. Human serum panels from patients with recent flavivirus infections were analyzed to compare the accuracy of JEV wild-type (WT) and KD VLPs as serodiagnostic antigens in enzyme-linked immunosorbent assays. Statistical analysis demonstrated significant differences in assay performances for accurate determination of current JEV infections between WT and KD antigens by detecting immunoglobulin M antibodies at a serum dilution of 1:4,000 (likelihood ratios = 2.74 [WT] and 22 [KD]). The application and continued development of cross-reactivity-reduced antigens should improve both flavivirus infection serodiagnosis and estimates of disease burden.
Prevention of Assay Interference in Infectious-Disease Serology Tests Done on the Liaison Platform
Authors: Berth Mario , Bosmans Eugene
Published: March 2008

Immunoassay interference causing unexpected reactive results in magnetic-microparticle-based assays was detected. A systematic evaluation of Liaison Epstein-Barr virus immunoglobulin M showed that 5% of the positive results (0.4% of tested samples) could be explained by such interference. Adding chemical blocking reagents (polyvinylpyrrolidone and polyvinyl alcohol) to the assay buffers partially prevented this phenomenon.
Thoracic Vertebral Actinomycosis:Actinomyces israeliiandFusobacterium nucleatum
Authors: Honda Hitoshi , Bankowski Matthew J. , Kajioka Eric H. N. , Chokrungvaranon Nalurporn , Kim Wesley , Gallacher Scott T.
Published: March 2008

Actinomycesspp. are considered rare pathogens in today's medicine, especially with thoracic vertebral involvement. Classic actinomycosis (50%) presents as an oral-cervicofacial (“lumpy jaw”) infection. This report describes a case of spinal cord compression caused byActinomyces israeliiwith the coisolation ofFusobacterium nucleatum. There are limited numbers of similar cases.
Variable Patterns of Programmed Death-1 Expression on Fully Functional Memory T Cells after Spontaneous Resolution of Hepatitis C Virus Infection
Authors: Bowen David G. , Shoukry Naglaa H. , Grakoui Arash , Fuller Michael J. , Cawthon Andrew G. , Dong Christine , Hasselschwert Dana L. , Brasky Kathleen M. , Freeman Gordon J. , Seth Nilufer P. , Wucherpfennig Kai W. , Houghton Michael , Walker Christopher M.
Published: March 2008

The inhibitory receptor programmed death-1 (PD-1) is present on CD8
+
T cells in chronic hepatitis C virus (HCV), but expression patterns in spontaneously resolving infections are incompletely characterized. Here we report that PD-1 was usually absent on memory CD8
+
T cells from chimpanzees with resolved infections, but sustained low-level expression was sometimes observed in the absence of apparent virus replication. PD-1-positive memory T cells expanded and displayed antiviral activity upon reinfection with HCV, indicating conserved function. This animal model should facilitate studies of whether PD-1 differentially influences effector and memory T-cell function in resolved versus persistent human infections.
Domain within Herpes Simplex Virus 1 Scaffold Proteins Required for Interaction with Portal Protein in Infected Cells and Incorporation of the Portal Vertex into Capsids
Authors: Yang Kui , Baines Joel D.
Published: March 2008

The portal vertex of herpesvirus capsids serves as the conduit through which DNA is inserted during the assembly process. In herpes simplex virus (HSV), the portal is composed of 12 copies of the U
L
6 gene product, pU
L
6. Previous results identified a domain in the major capsid scaffold protein, ICP35, required for interaction with pU
L
6 and its incorporation into capsids formed in vitro (G. P. Singer et al., J. Virol. 74:6838-6848, 2005). In the current studies, pU
L
6 and scaffold proteins were found to coimmunoprecipitate from lysates of both HSV-infected cells and mammalian cells expressing scaffold proteins and pU
L
6. The coimmunoprecipitation of pU
L
6 and scaffold proteins was precluded upon deletion of codons 143 to 151 within U
L
26.5, encoding ICP35. While wild-type scaffold proteins colocalized with pU
L
6 when transiently coexpressed as viewed by indirect immunofluorescence, deletion of U
L
26.5 codons 143 to 151 precluded this colocalization. A recombinant herpes simplex virus, vJB11, was generated that lacked U
L
26.5 codons 143 to 151. A virus derived from this mutant but bearing a restored U
L
26.5 was also generated. vJB11 was unable to cleave or package viral DNA, whereas the restored virus packaged DNA normally. vJB11 produced ample numbers of B capsids in infected cells, but these lacked normal levels of pU
L
6. The deletion in U
L
26.5 also rendered pU
L
6 resistant to detergent extraction from vJB11-infected cells. These data indicate that, as was observed in vitro, amino acids 143 to 151 of ICP35 are critical for (i) interaction between scaffold proteins and pU
L
6 and (ii) incorporation of the HSV portal into capsids.
Identification and In Vitro Expansion of Functional Antigen-Specific CD25
+
FoxP3
+
Regulatory T Cells in Hepatitis C Virus Infection
Authors: Ebinuma Hirotoshi , Nakamoto Nobuhiro , Li Yun , Price David A. , Gostick Emma , Levine Bruce L. , Tobias J. , Kwok William W. , Chang Kyong-Mi
Published: March 2008

CD4
+
CD25
+
regulatory T cells (CD25
+
Tregs) play a key role in immune regulation. Since hepatitis C virus (HCV) persists with increased circulating CD4
+
CD25
+
T cells and virus-specific effector T-cell dysfunction, we asked if CD4
+
CD25
+
T cells in HCV-infected individuals are similar to natural Tregs in uninfected individuals and if they include HCV-specific Tregs using the specific Treg marker FoxP3 at the single-cell level. We report that HCV-infected patients display increased circulating FoxP3
+
Tregs that are phenotypically and functionally indistinguishable from FoxP3
+
Tregs in uninfected subjects. Furthermore, HCV-specific FoxP3
+
Tregs were detected in HCV-seropositive persons with antigen-specific expansion, major histocompatibility complex class II/peptide tetramer binding affinity, and preferential suppression of HCV-specific CD8 T cells. Transforming growth factor β contributed to antigen-specific Treg expansion in vitro, suggesting that it may contribute to antigen-specific Treg expansion in vivo. Interestingly, FoxP3 expression was also detected in influenza virus-specific CD4 T cells. In conclusion, functionally active and virus-specific FoxP3
+
Tregs are induced in HCV infection, thus providing targeted immune regulation in vivo. Detection of FoxP3 expression in non-HCV-specific CD4 T cells suggests that immune regulation through antigen-specific Treg induction extends beyond HCV.
Human Herpesvirus 8 Infects and Replicates in Primary Cultures of Activated B Lymphocytes through DC-SIGN
Authors: Rappocciolo Giovanna , Hensler Heather R. , Jais Mariel , Reinhart Todd A. , Pegu Amarendra , Jenkins Frank J. , Rinaldo Charles R.
Published: March 2008

Human herpesvirus 8 (HHV-8) is the etiological agent of Kaposi's sarcoma, primary effusion lymphoma, and some forms of multicentric Castleman's disease. Although latent HHV-8 DNA can be detected in B cells from persons with these cancers, there is little information on the replication of HHV-8 in B cells. Indeed, B cells are relatively resistant to HHV-8 infection in vitro. We have recently shown that DC-SIGN, a C-type lectin first identified on dendritic cells (DC), is an entry receptor for HHV-8 on DC and macrophages. We have also demonstrated previously that B lymphocytes from peripheral blood and tonsils express DC-SIGN and that this expression increases after B-cell activation. Here we show that activated blood and tonsillar B cells can be productively infected with HHV-8, as measured by an increase in viral DNA, the expression of viral lytic and latency proteins, and the production of infectious virus. The infection of B cells with HHV-8 was blocked by the pretreatment of the cells with antibody specific for DC-SIGN or with mannan but not antibody specific for xCT, a cystine/glutamate exchange transporter that has been implicated in HHV-8 fusion to cells. The infection of B cells with HHV-8 resulted in increased expression of DC-SIGN and a decrease in the expression of CD20 and major histocompatibility complex class I. HHV-8 could also infect and replicate in B-cell lines transduced to express full-length DC-SIGN but not in B-cell lines transduced to express DC-SIGN lacking the transmembrane domain, demonstrating that the entry of HHV-8 into B cells is related to DC-SIGN-mediated endocytosis. The role of endocytosis in viral entry into activated B cells was confirmed by blocking HHV-8 infection with endocytic pathway inhibitors. Thus, the expression of DC-SIGN is essential for productive HHV-8 infection of and replication in B cells.
CD81 and Claudin 1 Coreceptor Association: Role in Hepatitis C Virus Entry
Authors: Harris Helen J. , Farquhar Michelle J. , Mee Christopher J. , Davis Christopher , Reynolds Gary M. , Jennings Adam , Hu Ke , Yuan Fei , Deng HongKui , Hubscher Stefan G. , Han Jang H. , Balfe Peter , McKeating Jane A.
Published: March 2008

Hepatitis C virus (HCV) is an enveloped positive-stranded RNA hepatotropic virus. HCV pseudoparticles infect liver-derived cells, supporting a model in which liver-specific molecules define HCV internalization. Three host cell molecules have been reported to be important entry factors or receptors for HCV internalization: scavenger receptor BI, the tetraspanin CD81, and the tight junction protein claudin-1 (CLDN1). None of the receptors are uniquely expressed within the liver, leading us to hypothesize that their organization within hepatocytes may explain receptor activity. Since CD81 and CLDN1 act as coreceptors during late stages in the entry process, we investigated their association in a variety of cell lines and human liver tissue. Imaging techniques that take advantage of fluorescence resonance energy transfer (FRET) to study protein-protein interactions have been developed.Aequorea coerulescensgreen fluorescent protein- andDiscosomasp. red-monomer fluorescent protein-tagged forms of CD81 and CLDN1 colocalized, and FRET occurred between the tagged coreceptors at comparable frequencies in permissive and nonpermissive cells, consistent with the formation of coreceptor complexes. FRET occurred between antibodies specific for CD81 and CLDN1 bound to human liver tissue, suggesting the presence of coreceptor complexes in liver tissue. HCV infection and treatment of Huh-7.5 cells with recombinant HCV E1-E2 glycoproteins and anti-CD81 monoclonal antibody modulated homotypic (CD81-CD81) and heterotypic (CD81-CLDN1) coreceptor protein association(s) at specific cellular locations, suggesting distinct roles in the viral entry process.
VISUALIZATION OF CHAOTIC DYNAMICAL SYSTEMS BASED ON MANDELBROT SET METHODOLOGY
Authors: CHENG JIN , TAN JIANRONG , GAN CHUNBIAO
Published: March 2008

Although there are lots of methods to analyze chaotic systems, they tend to be of local nature and reveal only limited information about a certain group of control parameters. This paper explores a visualization technique on the basis of Mandelbrot set (M-set) methodology to give an overall view of a chaotic system's dynamical performance in the parameter space. Firstly, the Lyapunov spectra with regard to different points in the parameter space are calculated, according to which the color of these points is defined. Then points in the given parameter space are mapped to the computer screen and a colorful image named Lyapunov distribution map (LDM) is generated, which conveys a wealth of information about a system's dynamic behavior across variations in its control parameters. The results of visualizing two typical chaotic systems proved the feasibility and validity of this technique. The study suggests that desired dynamical performance of a system can be conveniently achieved by selecting a point from some color region in its LDM and adjusting the control parameters according to the point value. Furthermore, there is no need for any prior knowledge of the system under evaluation and the complicated mathematical analysis before the formulation of appropriate rules for a new system can also be avoided since uniform rules are employed in the classification of parameter points for any system and the LDM is generated via the same algorithm.
RESEARCH FRACTAL STRUCTURES OF GENERALIZED M-J SETS USING THREE ALGORITHMS
Authors: WANG XING-YUAN , GU LI-NA
Published: March 2008

Extreme modulus escaping time algorithm, decomposition algorithm and fisheye algorithm are analyzed in this thesis, and we construct a series of generalized Mandelbrot-Julia (M-J) sets using these three algorithms. By studying the structural character of generalized M-J sets, we find: (1) extreme modulus escaping time algorithm and decomposition algorithm are simple modifications of classic escaping time algorithm, they can both construct the structure of non-boundary areas of generalized M-J sets; (2) non-boundary areas of generalized M-J sets have fractal characters; (3) generalized M-J sets have symmetry, and the process of evolvement depends on range of phase angle; (4) we can observe not only the whole structure of generalized Mandelbrot sets but also the details of some parts by using fisheye algorithm.
MEASURING THE TEMPERATURE OF TEXTS
Authors: MIYAZIMA SASUKE , YAMAMOTO KEIZO
Published: March 2008

An innovative method for measuring the temperature of texts is introduced by measuring deviation from a standard Maxwell-Boltzmann (M–B) distribution for a corpus of English words. The temperature of English texts for junior and senior high schools in Japan and grades one through 12 in the US are measured and found to be between 148 K and 87 K, when the temperature of ANC (American National Corpus) is assumed to be 100 K as a standard. The temperature of several books by famous authors (Einstein, Darwin, etc.) is also analyzed. The present technique also can be applied to many other topics. Application to mortality rate distribution in Japan is discussed as an example.
FRACTIONAL ANALYSIS OF WAVE PACKET PROPAGATION AND SOME ASPECTS OF VSL WITH GUP
Authors: MEHDIPOUR S. HAMID , NOZARI KOUROSH , SADATIAN S. DAVOOD
Published: March 2008

In this paper, we consider the problem of wave packet broadening in the framework of the Generalized Uncertainty Principle (GUP) of quantum gravity. Then we find a fractal Klein-Gordon equation to further analyze the wave packet broadening in a foamy spacetime. We derive a Modified Dispersion Relation (MDR) in the context of GUP which shows an extra broadening due to gravitational induced uncertainty. As a result of these dispersion relations, a generalized Klein-Gordon equation can be obtained. We solve this generalized equation under certain conditions to find both analytical and numerical results. We show that GUP can lead to a variation of the fundamental constants such as speed of light. With this novel properties, we find a time-dependent equation of state for perfect fluid in de Sitter universe and we interpret its physical implications.
A FRACTAL ANALYSIS OF SUBCOOLED NUCLEATE POOL BOILING
Authors: XIAO BOQI , WANG ZONGCHI , YU BOMING
Published: March 2008

A fractal model for the subcooled nucleate pool boiling heat transfer is proposed in this paper. The analytical expressions for the subcooled nucleate pool boiling heat transfer are derived based on the fractal distribution of nucleation sites on boiling surfaces. The proposed fractal model for the subcooled nucleate pool boiling heat transfer is found to be a function of wall superheat, liquid subcooling, fractal dimension, the minimum and maximum active cavity size, the contact angle and physical properties of fluid. No additional/new empirical constant is introduced, and the proposed model contains less empirical constants than the conventional models. The model predictions are compared with the existing experimental data, and fair agreement between the model predictions and experimental data is found for different liquid subcoolings.
Vestibular System: The Many Facets of a Multimodal Sense
Authors: Angelaki Dora E. , Cullen Kathleen E.
Published: March 2008

Elegant sensory structures in the inner ear have evolved to measure head motion. These vestibular receptors consist of highly conserved semicircular canals and otolith organs. Unlike other senses, vestibular information in the central nervous system becomes immediately multisensory and multimodal. There is no overt, readily recognizable conscious sensation from these organs, yet vestibular signals contribute to a surprising range of brain functions, from the most automatic reflexes to spatial perception and motor coordination. Critical to these diverse, multimodal functions are multiple computationally intriguing levels of processing. For example, the need for multisensory integration necessitates vestibular representations in multiple reference frames. Proprioceptive-vestibular interactions, coupled with corollary discharge of a motor plan, allow the brain to distinguish actively generated from passive head movements. Finally, nonlinear interactions between otolith and canal signals allow the vestibular system to function as an inertial sensor and contribute critically to both navigation and spatial orientation.
Peripheral ghrelin treatment stabilizes body weights of senescent male Brown Norway rats at baseline and after surgery
Authors: Yukawa Michi , Weigle David S. , Davis Charles D. , Marck Brett T. , Wolden-Hanson Tami
Published: March 2008

Unintentional weight loss may occur spontaneously in older humans and animals. Further weight losses after surgery or illness in the older patients result in increased morbidity, mortality, and hospital readmission rate. A growing body of work has shown increased appetite and weight gain in response to administration of ghrelin, the “hunger hormone.” We conducted two studies in senescent male Brown Norway rats to assess the ability of peripheral administration of ghrelin to increase body weight and food intake. One study assessed the effect of 2 wk of daily subcutaneous ghrelin administration (1 mg·kg−1·day−1) to senescent rats in a baseline condition; a second study used the same administration protocol in an interventional experiment with aged rats subjected to a surgery with 10–15% blood loss as a model of elective surgery. In both studies, animals receiving ghrelin maintained their body weights, whereas control animals lost weight. Body weight stability was achieved in ghrelin-treated animals despite a lack of increase in daily or cumulative food intake in both experiments. Hormone and proinflammatory cytokine levels were measured before surgery and after 14 days of treatment. Ghrelin treatment appeared to blunt declining ghrelin levels and also to blunt cytokine increases seen in the surgical control group. The ability of peripheral ghrelin treatment to maintain body weights of senescent rats without concomitant increases in food intake may be due to its known ability to decrease sympathetic activity and metabolic rate, perhaps by limiting cytokine-driven inflammation.
Association of overactive bladder and stress urinary incontinence in rats with pudendal nerve ligation injury
Authors: Furuta Akira , Kita Masafumi , Suzuki Yasuyuki , Egawa Shin , Chancellor Michael B. , de Groat William C. , Yoshimura Naoki
Published: March 2008

Approximately one-third of patients with stress urinary incontinence (SUI) also suffer from urgency incontinence, which is one of the major symptoms of overactive bladder (OAB) syndrome. Pudendal nerve injury has been recognized as a possible cause for both SUI and OAB. Therefore, we investigated the effects of pudendal nerve ligation (PNL) on bladder function and urinary continence in female Sprague-Dawley rats. Conscious cystometry with or without capsaicin pretreatment (125 mg/kg sc), leak point pressures (LPPs), contractile responses of bladder muscle strips to carbachol or phenylephrine, and levels of nerve growth factor (NGF) protein and mRNA in the bladder were compared in sham and PNL rats 4 wk after the injury. Urinary frequency detected by a reduction in intercontraction intervals and voided volume was observed in PNL rats compared with sham rats, but it was not seen in PNL rats with capsaicin pretreatment that desensitizes C-fiber-afferent pathways. LPPs in PNL rats were significantly decreased compared with sham rats. The contractile responses of detrusor muscle strips to phenylephrine, but not to carbachol, were significantly increased in PNL rats. The levels of NGF protein and mRNA in the bladder of PNL rats were significantly increased compared with sham rats. These results suggest that pudendal nerve neuropathy induced by PNL may be one of the potential risk factors for OAB, as well as SUI. Somato-visceral cross sensitization between somatic (pudendal) and visceral (bladder) sensory pathways that increases NGF expression and α1-adrenoceptor-mediated contractility in the bladder may be involved in this pathophysiological mechanism.
Angiotensin II increases the expression of the transcription factor ETS-1 in mesangial cells
Authors: Pearse Damien D. , Tian Run-Xia , Nigro Jessica , Iorgulescu Julian B. , Puzis Leopold , Jaimes Edgar A.
Published: March 2008

Maladaptive activation of the renin-angiotensin system (RAS) has been shown to play a critical role in the pathogenesis of chronic kidney disease. Reactive oxygen species (ROS) are critical signals for many of the nonhemodynamic effects of angiotensin II (ANG II). We have demonstrated that ANG II increases mesangial and cortical cyclooxygenase-2 (COX-2) expression and activity via NADPH oxidase-derived ROS. The transcription factor ETS-1 (E26 transformation-specific sequence) has been identified as a critical regulator of growth-related responses and inflammation. The present studies were designed to determine: 1) whether ANG II induces ETS-1 expression in vitro in cultured rat mesangial cells and in vivo in rats infused with ANG II; and 2) whether ROS and COX-2 are mediators of ETS-1 induction in response to ANG II. Mesangial cells stimulated with ANG II (10−7M) exhibited a significant increase in ETS-1 expression that was prevented by the angiotensin type 1 receptor blocker candesartan. NADPH oxidase inhibition with dyphenilene iodinium or apocynin also prevented ETS-1 induction, establishing the role of ROS as mediators of ETS-1 expression in response to ANG II. COX-2 inhibition prevented ETS-1 expression in response to ANG II, suggesting that COX-2 is required for ETS-1 induction. By utilizing short interfering RNAs against ETS-1, we have also determined that ETS-1 is required to induce the production of fibronectin in response to ANG II. Furthermore, rats infused with ANG II manifested increased glomerular expression of ETS-1. These studies unveil novel pathways that may play an important role in the pathogenesis of renal injury when RAS is activated.
How Do Brain Areas Communicate During the Processing of Noxious Stimuli? An Analysis of Laser-Evoked Event-Related Potentials Using the Granger Causality Index
Authors: Weiss Thomas , Hesse Wolfram , Ungureanu Mihaela , Hecht Holger , Leistritz Lutz , Witte Herbert , Miltner Wolfgang H. R.
Published: March 2008

Several imaging techniques have identified different brain areas involved in the processing of noxious stimulation and thus in the constitution of pain. However, only little is known how these brain areas communicate with one another after activation by stimulus processing and which areas directionally affect or modulate the activity of succeeding areas. One measure for the analysis of such interactions is represented by the Granger Causality Index (GCI). In applying time-varying bivariate and partial variants of this concept (tvGCI), the aim of the present study was to investigate the interaction of neural activities between a set of scalp electrodes that best represent the brain electrical neural activity of major cortical areas involved in the processing of noxious laser-heat stimuli and their variation in time. Bivariate and partial tvGCIs were calculated within four different intervals of laser-evoked event-related potentials (LEPs) including a baseline period prior to stimulus application and three intervals immediately following stimulus application, i.e., between 170 and 200 ms (at the N2 component), between 260 and 320 ms (P2 component), and between 320 and 400 ms (P3 component of LEPs). Results show some similarities, but also some striking differences between bivariate and partial tvGCIs. These differences might be explained by the nature of bivariate and partial tvGCIs. However, both tvGCI approaches revealed a directed interaction between medial and lateral electrodes of the centroparietal region. This result was interpreted as a directed interaction between the anterior cingulate cortex and the secondary somatosensory cortex and the insula, structures that are significantly involved in the constitution of pain.
Human Updating of Visual Motion Direction During Head Rotations
Authors: Ruiz-Ruiz Mario , Martinez-Trujillo Julio C.
Published: March 2008

Previous studies have demonstrated that human subjects update the location of visual targets for saccades after head and body movements and in the absence of visual feedback. This phenomenon is known as spatial updating. Here we investigated whether a similar mechanism exists for the perception of motion direction. We recorded eye positions in three dimensions and behavioral responses in seven subjects during a motion task in two different conditions: when the subject's head remained stationary and when subjects rotated their heads around an anteroposterior axis (head tilt). We demonstrated that after head-tilt subjects updated the direction of saccades made in the perceived stimulus direction (direction of motion updating), the amount of updating varied across subjects and stimulus directions, the amount of motion direction updating was highly correlated with the amount of spatial updating during a memory-guided saccade task, subjects updated the stimulus direction during a two-alternative forced-choice direction discrimination task in the absence of saccadic eye movements (perceptual updating), perceptual updating was more accurate than motion direction updating involving saccades, and subjects updated motion direction similarly during active and passive head rotation. These results demonstrate the existence of an updating mechanism for the perception of motion direction in the human brain that operates during active and passive head rotations and that resembles the one of spatial updating. Such a mechanism operates during different tasks involving different motor and perceptual skills (saccade and motion direction discrimination) with different degrees of accuracy.
Biophysical Properties of Human Nav1.7 Splice Variants and Their Regulation by Protein Kinase A
Authors: Chatelier Aurélien , Dahllund Leif , Eriksson Anders , Krupp Johannes , Chahine Mohamed
Published: March 2008

The sodium channel Nav1.7 is preferentially expressed in nociceptive neurons and is believed to play a crucial role in pain sensation. Four alternative splice variants are expressed in human dorsal root ganglion neurons, two of which differ in exon 5 by two amino acids in the S3 segment of domain I (exons 5A and 5N). Two others differ in exon 11 by the presence (11L) or absence (11S) of an 11 amino acid sequence in the loop between domains I and II, an important region for PKA regulation. In the present study, we used the whole cell configuration of the patch-clamp technique to investigate the biophysical properties and 8-bromo-cyclic adenosine monophosphate (8Br-cAMP) modulation of these splice variants expressed in tsA201 cells in the presence of the β1-subunit. The alternative splicing of Nav1.7 had no effect on most of the biophysical properties of this channel, including activation, inactivation, and recovery from inactivation. However, development of inactivation experiments revealed that the isoform containing exon 5A had slower kinetics of inactivation for negative potentials than that of the variant containing exon 5N. This difference was associated with higher ramp current amplitudes for isoforms containing exon 5A. Moreover, 8Br-cAMP–mediated phosphorylation induced a negative shift of the activation curve of variants containing exon 11S, whereas inactivation properties were unchanged. Isoforms with exon 11L were not modulated by 8Br-cAMP–induced phosphorylation. We conclude that alternative splicing of human Nav1.7 can specifically modulate the biophysical properties and cAMP-mediated regulation of this channel. Changing the proportions of these variants may thus influence neuronal excitability and pain sensation.
Baseline Cortical Excitability Determines Whether TMS Disrupts or Facilitates Behavior
Authors: Silvanto Juha , Cattaneo Zaira , Battelli Lorella , Pascual-Leone Alvaro
Published: March 2008

Transcranial magnetic stimulation (TMS) is increasingly used to modify brain activity noninvasively and to study brain-behavior relations. However, results can be variable and the conditions that affect the functional efficacy of TMS remain unclear. Here we show that on-line TMS can either facilitate or suppress perceptual functions depending on the baseline level of activity of the targeted brain region. When TMS was applied over the motion selective region V5/MT during a simple motion-detection task, subjects’ motion-detection ability was impaired. Similarly, suppression of V5/MT activity using off-line 1 Hz repetitive TMS (rTMS) disrupted performance in a subsequent motion-detection task. However, paradoxically, on-line V5/MT TMS had a facilitatory effect on motion detection if V5/MT had been suppressed by off-line 1-Hz rTMS prior to the motion-detection task. These results demonstrate that TMS can have an unexpected facilitatory effect on behavior when the targeted neural population is in a suppressed state. Our findings provide further evidence for the view that the effects of TMS are modulated by the initial activation state of the targeted neural population.
The Protein Phosphatase Activity of PTEN Regulates Src Family Kinases and Controls Glioma Migration
Authors: Dey Nandini , Crosswell Hal E. , De Pradip , Parsons Ramon , Peng Qiong , Su Jing Dong , Durden Donald L.
Published: March 2008

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is mutated or lost in 60% to 70% of advanced gliomas and is associated with malignant phenotypic changes such as migration, which contribute to the morbidity and mortality of this disease. Most of the tumor suppressor function of PTEN has been attributed to its ability to dephosphorylate the second messenger, phosphatidylinositol 3,4,5-triphosphate, resulting in the biological control of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway. Despite recent work suggesting that the protein phosphatase activity of PTEN controls glioma cell migration, the mechanisms by which this occurs are unclear. Herein, we show using glioma cell lines (U87MG and U373MG) stably transfected with wild-type PTEN or catalytically altered mutants of PTEN that PTEN controls integrin-directed migration in a lipid phosphatase, PI3K/AKT–independent manner. Confirming this observation, we show that the stable overexpression of COOH-terminal Src kinase, the physiologic negative regulator of SRC family kinases (SFK), or treatment with the SFK inhibitor PP1 abrogates glioma migration. The results provide direct evidence that the downstream effect of the protein phosphatase activity of PTEN is to suppress SFK and FYN, and to regulate RAC-GTPase activity after αv integrin stimulation. Furthermore, studying vitronectin-directed migration using (a) Fyn small interfering RNA and (b) astrocytes from Fyn heterozygous (+/−) mice, Pten heterozygous (+/−) mice, Pten and Fyn double heterozygous (+/−) mice, or Fyn knockout (−/−) mice confirmed a role of FYN in αv integrin–mediated haptotaxis in glial cells. Our combined results provide direct biochemical and genetic evidence that PTEN's protein phosphatase activity controls FYN kinase function in glioma cells and regulates migration in a PI3K/AKT–independent manner. [Cancer Res 2008;68(6):1862–71]