bluuebunny/crossref_metadata_2025 huggingface dataset:
Timing of the Components of the HIV Life Cycle in Productively Infected CD4
+
T Cells in a Population of HIV-Infected Individuals
Authors: Murray John M. , Kelleher Anthony D. , Cooper David A.
Published: August 2011

We estimate the time required for HIV to complete separate stages of its infection cycle in productively infected CD4
+
T cells
in vivo
by comparing initial delays after administration of single antiretroviral drugs until HIV RNA reduction in peripheral blood. Data were obtained from monotherapy studies of eight antiretroviral drugs from all currently licensed HIV drug classes: CCR5 blockers (maraviroc), fusion inhibitors (enfuvirtide), nucleoside and nonnucleoside reverse transcriptase inhibitors (abacavir, tenofovir, and rilpivirine), integrase inhibitors (raltegravir), and protease inhibitors (ritonavir and nelfinavir). We find that HIV requires an average of 52 h between export of virions in one generation to export in the next, with most of this (33 h) taken up by reverse transcription. Reverse transcription
in vivo
was three times longer than
in vitro
and began soon after virion fusion, as we determined no difference in mean times for commencement of reverse transcription and virion fusion as calculated by timing of the effects for tenofovir and maraviroc. Approximately 7 h is required between HIV integration and virion production. First-phase HIV RNA decay (half-life of 17 h over all drugs) seemed to slow as the stage being inhibited by the drug was further from viral production. The mean estimated half-life of plasma virions was 5 min, significantly shorter than previous estimates.
Varicella-Zoster Virus Immediate-Early Protein ORF61 Abrogates the IRF3-Mediated Innate Immune Response through Degradation of Activated IRF3
Authors: Zhu Huifang , Zheng Chunfu , Xing Junji , Wang Shuai , Li Shuping , Lin Rongtuan , Mossman Karen L.
Published: August 2011

Varicella-zoster virus (VZV) infection of differentiated cells within the host and establishment of latency likely requires evasion of innate immunity and limits secretion of antiviral cytokines. Here we report that its immediate-early protein ORF61 antagonizes the beta interferon (IFN-β) pathway. VZV infection down-modulated the Sendai virus (SeV)-activated IFN-β pathway, including mRNA of IFN-β and its downstream interferon-stimulated genes (ISGs), ISG54 and ISG56. Through a primary screening of VZV genes, we found that ORF61 inhibited SeV-mediated activation of IFN-β and ISRE (IFN-stimulated response element) promoter activities but only slightly affected NF-κB promoter activity, implying that the IFN-β pathway may be blocked in the IRF3 branch. An indirect immunofluorescence assay demonstrated that ectopic expression of ORF61 abrogated the detection of IRF3 in SeV-infected cells; however, it did not affect endogenous dormant IRF3 in noninfected cells. Additionally, ORF61 was shown to be partially colocalized with activated IRF3 in the nucleus upon treatment with MG132, an inhibitor of proteasomes, and the direct interaction between ORF61 and activated IRF3 was confirmed by a coimmunoprecipitation assay. Furthermore, Western blot analysis demonstrated that activated IRF3 was ubiquitinated in the presence of ORF61, suggesting that ORF61 degraded phosphorylated IRF3 via a ubiquitin-proteasome pathway. Semiquantitative reverse transcription-PCR (RT-PCR) analysis demonstrated that the level of ISG54 and ISG56 mRNAs was also downregulated by ORF61. Taken together, our results convincingly demonstrate that ORF61 down-modulates the IRF3-mediated IFN-β pathway by degradation of activated IRF3 via direct interaction, which may contribute to the pathogenesis of VZV infection.
Nonnucleoside Reverse Transcriptase Inhibitor-Resistant HIV Is Stimulated by Efavirenz during Early Stages of Infection
Authors: Wang Jiong , Zhang Gang , Bambara Robert A. , Li Dongge , Liang Hua , Wu Hulin , Smith Hannah M. , Lowe Nicholas R. , Demeter Lisa M. , Dykes Carrie
Published: August 2011

Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are potent and commonly prescribed antiviral agents used in combination therapy (CART) of human immunodeficiency virus type 1 (HIV-1) infection. The development of drug resistance is a major limitation of CART. Reverse transcriptase (RT) genotypes with the NNRTI resistance mutations K101E+G190S are highly resistant to efavirenz (EFV) and can develop during failure of EFV-containing regimens in patients. We have previously shown that virus with K101E+G190S mutations can replicate more efficiently in the presence of EFV than in its absence. In this study, we evaluated the underlying mechanism for drug-dependent stimulation, using a single-cycle cell culture assay in which EFV was added either during the infection or the virus production step. We determined that EFV stimulates K101E+G190S virus during early infection and does not affect late steps of virus replication, such as increasing the amount of active RT incorporated into virions. Additionally, we showed that another NNRTI, nevirapine (NVP), stimulated K101E+G190S virus replication during the early steps of infection similar to EFV, but that the newest NNRTI, etravirine (ETR), did not. We also showed that EFV stimulates K101E+Y188L and K101E+V106I virus, but not K101E+L100I, K101E+K103N, K101E+Y181C, or K101E+G190A virus, suggesting that the stimulation is mutation specific. Real-time PCR of reverse transcription intermediates showed that although the drug did not stimulate minus-strand transfer, it did stimulate minus-strand strong-stop DNA synthesis. Our results indicate that stimulation most likely occurs through a mechanism whereby NNRTIs stimulate priming or elongation of the tRNA.
Primary Infection by a Human Immunodeficiency Virus with Atypical Coreceptor Tropism
Authors: Jiang Chunlai , Parrish Nicholas F. , Wilen Craig B. , Li Hui , Chen Yue , Pavlicek Jeffrey W. , Berg Anna , Lu Xiaozhi , Song Hongshuo , Tilton John C. , Pfaff Jennifer M. , Henning Elizabeth A. , Decker Julie M. , Moody M. Anthony , Drinker Mark S. , Schutte Robert , Freel Stephanie , Tomaras Georgia D. , Nedellec Rebecca , Mosier Donald E. , Haynes Barton F. , Shaw George M. , Hahn Beatrice H. , Doms Robert W. , Gao Feng
Published: August 2011

The great majority of human immunodeficiency virus type 1 (HIV-1) strains enter CD4
+
target cells by interacting with one of two coreceptors, CCR5 or CXCR4. Here we describe a transmitted/founder (T/F) virus (ZP6248) that was profoundly impaired in its ability to utilize CCR5 and CXCR4 coreceptors on multiple CD4
+
cell lines as well as primary human CD4
+
T cells and macrophages
in vitro
yet replicated to very high titers (>80 million RNA copies/ml) in an acutely infected individual. Interestingly, the envelope (Env) glycoprotein of this clade B virus had a rare GPEK sequence in the crown of its third variable loop (V3) rather than the consensus GPGR sequence. Extensive sequencing of sequential plasma samples showed that the GPEK sequence was present in virtually all Envs, including those from the earliest time points after infection. The molecularly cloned (single) T/F virus was able to replicate, albeit poorly, in cells obtained from
ccr5
Δ32
homozygous donors. The ZP6248 T/F virus could also infect cell lines overexpressing the alternative coreceptors GPR15, APJ, and FPRL-1. A single mutation in the V3 crown sequence (GPEK->GPGK) of ZP6248 restored its infectivity in CCR5
+
cells but reduced its ability to replicate in GPR15
+
cells, indicating that the V3 crown motif played an important role in usage of this alternative coreceptor. These results suggest that the ZP6248 T/F virus established an acute
in vivo
infection by using coreceptor(s) other than CCR5 or CXCR4 or that the CCR5 coreceptor existed in an unusual conformation in this individual.
Alternative Coreceptor Requirements for Efficient CCR5- and CXCR4-Mediated HIV-1 Entry into Macrophages
Authors: Cashin Kieran , Roche Michael , Sterjovski Jasminka , Ellett Anne , Gray Lachlan R. , Cunningham Anthony L. , Ramsland Paul A. , Churchill Melissa J. , Gorry Paul R.
Published: August 2011

Macrophage tropism of human immunodeficiency virus type 1 (HIV-1) is distinct from coreceptor specificity of the viral envelope glycoproteins (Env), but the virus-cell interactions that contribute to efficient HIV-1 entry into macrophages, particularly via CXCR4, are not well understood. Here, we characterized a panel of HIV-1 Envs that use CCR5 (
n
= 14) or CXCR4 (
n
= 6) to enter monocyte-derived macrophages (MDM) with various degrees of efficiency. Our results show that efficient CCR5-mediated MDM entry by Env-pseudotyped reporter viruses is associated with increased tolerance of several mutations within the CCR5 N terminus. In contrast, efficient CXCR4-mediated MDM entry was associated with reduced tolerance of a large deletion within the CXCR4 N terminus. Env sequence analysis and structural modeling identified amino acid variants at positions 261 and 263 within the gp41-interactive region of gp120 and a variant at position 326 within the gp120 V3 loop that were associated with efficient CXCR4-mediated MDM entry. Mutagenesis studies showed that the gp41 interaction domain variants exert a significant but strain-specific influence on CXCR4-mediated MDM entry, suggesting that the structural integrity of the gp120-gp41 interface is important for efficient CXCR4-mediated MDM entry of certain HIV-1 strains. However, the presence of Ile326 in the gp120 V3 loop stem, which we show by molecular modeling is located at the gp120-coreceptor interface and predicted to interact with the CXCR4 N terminus, was found to be critical for efficient CXCR4-mediated MDM entry of divergent CXCR4-using Envs. Together, the results of our study provide novel insights into alternative mechanisms of Env-coreceptor engagement that are associated with efficient CCR5- and CXCR4-mediated HIV-1 entry into macrophages.
Parenchymal hematoma and total lesion volume in combined IV/IA revascularization stroke therapy
Authors: Tao Haiyang , Ramadas Gowri , Carrozzella Janice , Khatri Pooja , Broderick Joseph , Spilker Judith , Tomsick Thomas ,   for the IMS Investigators
Published: August 2011

Background and purpose

A positive correlation between large parenchymal hematoma (PH) volume and large CT lesion volume in subjects treated with intravenous (IV) recombinant tissue plasminogen activator (rtPA) as well as placebo controls was identified in the European Cooperative Acute Stroke Study II (ECASS II). A study was undertaken to examine the relationship between PH volume and total lesion volume (including both cerebral infarction and hemorrhage) in subjects with symptomatic parenchymal hematoma (sPH) treated with combined IV and intra-arterial (IA) rtPA in the Interventional Management of Stroke (IMS) studies.

Methods

Hematoma and lesion volumes were measured planimetrically and by the ABC/2 method in 105 subjects from IMS studies I and II following combined IV and IA rtPA treatment. PH type 1 or 2 was determined by dichotomizing at >30% of lesion volume. Hematoma and lesion volumes for both symptomatic PH1 (sPH1) and PH2 (sPH2) types were compared using both measurement methods. Both sPH types were compared for baseline NIH Stroke Score, baseline Alberta Stroke Program Early CT score and treatment revascularization score based on the planimetric volume method.

Results

The volume of sPH1 and sPH2 did not differ by either method of measurement. Subjects with sPH2 had a lower lesion volume compared with all PH1 (p=0.004) and sPH1 (p=0.02) by both methods. The ABC/2 method overestimated PH volume by 55±33% and lesion volume by 34±22% for sPH compared with the planimetric method.

Conclusions

In IMS I and II, hemorrhages in subjects with sPH2 were similar in volume to those in subjects with sPH1 and were associated with a smaller rather than a larger total lesion volume compared with other PH in the setting of combined IV/IA therapy. The use of PH2 as a sole surrogate for sPH in studies of stroke treatment may underestimate the incidence of clinically significant hemorrhage.
Prevalence of respiratory pathogens in diseased, non‐vaccinated, routinely medicated veal calves
Authors: Pardon B. , De Bleecker K. , Dewulf J. , Callens J. , Boyen F. , Catry B. , Deprez P.
Published: August 2011

The prevalence of respiratory pathogens in diseased veal calves was determined in 24 respiratory disease outbreaks in 15 herds in Belgium. Bacteria were cultured from nasopharyngeal swabs and seroconversion against viruses and Mycoplasma bovis was determined on paired sera. At the individual calf level, Mycoplasma species, Mannheimia haemolytica and Pasteurella multocida, were isolated from 70.5 per cent, 21.5 per cent and 26.0 per cent of swabs, respectively. At the herd level, the presence of M bovis could be confirmed in 84.6 per cent of the herds examined. Seroconversion against bovine viral diarrhoea virus (BVDV) was present in 71.4 per cent of herds, parainfluenzavirus type 3 in 53.3 per cent, bovine respiratory syncytial virus in 40.0 per cent, bovine adenovirus type 3 in 46.7 per cent, bovine coronavirus in 30.0 per cent, and bovine herpesvirus type 1 in 26.7 per cent. At postmortem examination, Mycoplasma species could be cultured from 61.9 per cent of pneumonic lungs (n=21). Sixty per cent of calves tested were positive for BVDV (n=20), and 20.0 per cent were positive for bovine respiratory syncytial virus (n=16).
THE SPIN-TORSION COUPLING AND CAUSALITY FOR THE STANDARD MODEL
Authors: FABBRI LUCA
Published: August 2011

We study the influence of the spin-torsion coupling prescription and we prove the causal propagation for the fields of the standard model.
CLONES OF ALGEBRAS WITH PARALLELOGRAM TERMS
Authors: KEARNES KEITH A. , SZENDREI ÁGNES
Published: August 2011

We describe a manageable set of relations that generates the finitary relational clone of an algebra with a parallelogram term. This result applies to any algebra with a Maltsev term and to any algebra with a near unanimity term. One consequence of the main result is that on any finite set and for any finite k there are only finitely many clones of algebras with a k-ary parallelogram term which generate residually small varieties.
UNREASONABLE LATTICES OF QUASIVARIETIES
Authors: NURAKUNOV A. M.
Published: August 2011

A quasivariety is a universal Horn class of algebraic structures containing the trivial structure. The set [Formula: see text] of all subquasivarieties of a quasivariety [Formula: see text] forms a complete lattice under inclusion. A lattice isomorphic to [Formula: see text] for some quasivariety [Formula: see text] is called a lattice of quasivarieties or a quasivariety lattice. The Birkhoff–Maltsev Problem asks which lattices are isomorphic to lattices of quasivarieties. A lattice L is called unreasonable if the set of all finite sublattices of L is not computable, that is, there is no algorithm for deciding whether a finite lattice is a sublattice of L. The main result of this paper states that for any signature σ containing at least one non-constant operation, there is a quasivariety [Formula: see text] of signature σ such that the quasivariety lattice [Formula: see text] is unreasonable. Moreover, there are uncountable unreasonable lattices of quasivarieties. We also present some corollaries of the main result.
THE LATTICE OF ALTER EGOS
Authors: DAVEY BRIAN A. , PITKETHLY JANE G. , WILLARD ROSS
Published: August 2011

We introduce a new Galois connection for partial operations on a finite set, which induces a natural quasi-order on the collection of all partial algebras on this set. The quasi-order is compatible with the basic concepts of natural duality theory, and we use it to turn the set of all alter egos of a given finite algebra into a doubly algebraic lattice. The Galois connection provides a framework for us to develop further the theory of natural dualities for partial algebras. The development unifies several fundamental concepts from duality theory and reveals a new understanding of full dualities, particularly at the finite level.
EVIDENCE OF VARIATION OF THE ACCRETION FLOW GEOMETRY IN GRS 1915 + 105 FROM IXAE AND RXTE DATA
Authors: PAL PARTHA SARATHI , CHAKRABARTI SANDIP K. , NANDI ANUJ
Published: August 2011

The Galactic microquasar GRS 1915 + 105 exhibits various types of light curves. There is, however, no understanding of when a certain type of light curve will be exhibited and only in a handful of cases, the transitions from one type to another have actually been observed. We study the detailed spectral properties in these cases to show that different classes have different ratio of the power-law photon and the blackbody photon. Since the power-law photons are from the Compton cloud, and the intensity of the power-law photon component depends on the degree of interception of the soft photons by the Compton cloud, we conclude that not only the accretion rate, but the accretion flow geometry must also change during a class transition.
A FUNDAMENTAL EQUATION FOR SUPERMASSIVE BLACK HOLES
Authors: FEOLI ANTONIO , MANCINI LUIGI
Published: August 2011

We developed a theoretical model that is able to give a common origin to the correlations between the mass M• of supermassive black holes and the mass, velocity dispersion, kinetic energy and momentum parameter of the corresponding host galaxies. Our model is essentially based on the transformation of the angular momentum of the interstellar material, which falls into the black hole, into the angular momentum of the radiation emitted in this process. In this framework, we predict the existence of a relation of the form M• ∝ R e σ3, which is confirmed by the experimental data and can be the starting point to understand the other popular scaling laws too.
TRAPPED SURFACES
Authors: SENOVILLA JOSÉ M. M.
Published: August 2011

I review the definition and types of (closed) trapped surfaces. Surprising global properties are shown, such as their "clairvoyance" and the possibility that they enter into flat portions of the spacetime. Several results on the interplay of trapped surfaces with vector fields and with spatial hypersurfaces are presented. Applications to the quasi-local definition of Black Holes are discussed, with particular emphasis set onto marginally trapped tubes, trapping horizons and the boundary of the region with closed trapped surfaces. Finally, the core of a trapped region is introduced, and its importance discussed.
AN INTRODUCTION TO LOCAL BLACK HOLE HORIZONS IN THE 3+1 APPROACH TO GENERAL RELATIVITY
Authors: JARAMILLO JOSÉ LUIS
Published: August 2011

We present an introduction to dynamical trapping horizons as quasi-local models for black hole horizons, from the perspective of an Initial Value Problem approach to the construction of generic black hole spacetimes. We focus on the geometric and structural properties of these horizons aiming, as a main application, at the numerical evolution and analysis of black hole spacetimes in astrophysical scenarios. In this setting, we discuss their dual role as an a priori ingredient in certain formulations of Einstein equations and as an a posteriori tool for the diagnosis of dynamical black hole spacetimes. Complementary to the first-principles discussion of quasi-local horizon physics, we place an emphasis on the rigidity properties of these hypersurfaces and their role as privileged geometric probes into near-horizon strong-field spacetime dynamics.
SIZE DEPENDENT SWITCHING FROM REVERSE SATURABLE TO SATURABLE ABSORPTION IN CARBOXYLATE-MODIFIED MICROSPHERES
Authors: VAISHAKH MANU , MATHEW S. , NAMPOORI V. P. N.
Published: August 2011

The third order nonlinear optical properties of two different sized carboxylate-modified microspheres are investigated at different pump powers. The nonlinear absorption (NLA) is measured at 532 nm using 10 Hz, 7 ns pulses from the second harmonic generated from a Q-switched Nd -YAG laser in an open aperture Z-scan setup. The nonlinear response is size-dependent, and switching from reverse saturable absorption (RSA) to saturable absorption (SA) is observed as the size increases.
CONTROL OF COLLAPSE-REVIVAL PHENOMENON USING A TIME VARYING SQUEEZED FIELD
Authors: PRIYESH K. V. , THAYYULLATHIL RAMESH BABU
Published: August 2011

We have investigated the interaction of two level atom with time varying quadrature squeezed light field. Jaynes-Cummings model is used for solving the atom radiation interaction. Time evolution of the system for different squeezing parameter and phase have been studied. There are no well-defined revivals in population inversion when the squeezed phase is π and the squeezing parameter is greater than 0.5. Using a time varying frequency for the light field, it is found that the randomness of the population inversion and the collapse revival phenomena can be controlled. Frequency modulation of the field can thus be used as a tool for manipulating the squeezed light atom interaction.
NON-LINEAR REFRACTIVE INDEX MEASUREMENT OF (2E)-3-[4-(DIMETHYLAMINO)PHENYL]-1-(2,5-DIMETHYLTHIOPHEN-3-YL)PROP-2-EN-1-ONE AND (2E)-3-(3,4-DIMETHOXYPHENYL)-1-(2,5-DIMETHYLTHIOPHEN-3-YL)PROP-2-EN-1-ONE
Authors: HENARI FRYAD Z. , ASIRI ABDULLAH M.
Published: August 2011

We report results from investigations of the nonlinear refractive index and nonlinear absorption coefficient of (2E)-3-[4-(Dimethylamino)phenyl]-1-(2,5-dimethylthiophen-3-yl)prop-2-en-1-one and (2E)-3-(3,4-Dimethoxyphenyl)-1-(2,5-dimethylthiophen-3-yl) prop-2-en-1-one using Z-scan technique with a continuous wave (cw) laser at wavelengths 488 nm and 514 nm. The nonlinear refractive index and nonlinear absorption coefficient of both samples were evaluated. The origin of the nonlinear effects was discussed. Optical limiting based on light induced nonlinear refractive index variation is demonstrated. The limiting thresholds were estimated for both samples. The results suggested that these materials offer promise as candidates for optical limiting and optical devices in the low power regime.
ALL-OPTICAL SWITCHES BASED ON GaAs/AlGaAs QUANTUM DOTS VERTICAL CAVITY
Authors: ISMAIL F. D. , JOMTARAK R. , TEEKA C. , ALI J. , YUPAPIN P. P.
Published: August 2011

In this paper, an all-optical switch based on self-assembled GaAs/AlAs quantum dots (QDs) within a vertical cavity is designed and proposed. Two essential aspects of this novel device have been investigated, which include the QD/cavity nonlinearity with appropriately designed mirrors and the intersubband carrier dynamics inside QDs. The vertical-reflection-type switches have been investigated with an asymmetric cavity that consists of 12 periods of GaAs/Al0.8Ga0.2As and 25 periods for the front and back mirrors, respectively. The thicknesses of the GaAs and AlGaAs layers are chosen to be 89 and 102 nm, respectively. To give a dot-in-a-well (DWELL) structure, the 65 nm dimension of Si was recommended to deposit within a 20 nm AlAs QW. Results obtained have shown that all-optical switching via the QD excited states has been achieved with a time constant down to 275-fs and over 29.5 nm tunable wavelengths. These results demonstrated that QDs within a vertical cavity have great potential to realize low-power, consumption polarization-insensitive and micrometer-sized switching devices for future optical communication and signal processing systems.
COMPARATIVE STUDIES ON THE THIRD-ORDER NONLINEAR OPTICAL PROPERTIES OF THREE METAL-ORGANIC COMPOUNDS
Authors: ZHANG PENGFEI
Published: August 2011

The third-order optical nonlinearities of three planar transition metal ( Ni, Cu and Pd ) compounds with rigid quadridentate Schiff base derived from S-benzyl dithiocarbazate, were investigated systematically by Z-scan technique with picosecond laser pulses at 1064 nm. The three compounds exhibit both strong two-photon absorption and effective self-focusing performance. Due to the heavy atom effect, the second hyperpolarizability of PdZ molecule (〈γ〉 = 1.2 × 10-29 esu) was found to be the highest compared to that of the other two molecules. The optical limiting properties were also measured, and the results suggest that PdZ may be a promising candidate for the application to optical limiting in the near-infrared region.
BLIND IMAGE RESTORATION WITH MODIFIED CMA
Authors: SU LIYUN , LIU RUIHUA
Published: August 2011

In this paper, a new blind restoration scheme for blurred noisy image is proposed. The blurred noisy image is assumed to be the output of a linear space-invariant (LSI) system with an unknown point spread function (PSF) contaminated by an additive noise. The scheme passes the blurred noisy image through a two-dimensional (2D) finite impulse response filter whose parameters are updated by the modified constant modulus algorithm (CMA) with averaging and variable step size adaptive filter. When convergence occurs, the output of the filter is an estimate of the unobserved true image. Simulation and real blurred noisy image results show that the presented algorithm is effective and robust.
KANNADA ALPHABETS RECOGNITION WITH APPLICATION TO BRAILLE TRANSLATION
Authors: UROLAGIN SIDDHALING , PREMA K. V. , SUBBA REDDY N. V.
Published: August 2011

In this paper, an effort is made to apply optical character recognition (OCR) for Braille translation on Kannada characters. In general, OCR systems for Indian language are more complex due to larger number of vowels, consonants, and conjuncts and Indian languages are inflectional and agglutinative in nature. Specifically, characters of Kannada script have higher similarity in shape and higher variability across fonts, making recognition of characters a difficult task. A decision tree is developed in this research work. The main motivations are that decision trees provide a natural way to incorporate prior knowledge of domain and many Kannada characters have similar looking shapes. The similar looking characters can be grouped and then further partitioned into categories at various levels to effectively create a decision tree. To facilitate this, three modular classifiers are developed based on the nature of Kannada characters. These modular classifiers are employed at nodes of the decision tree. The Braille equivalent of Kannada characters is obtained by translation rules. An overall accuracy of classification and Braille translation of 93.80% is obtained.
ROBUST EXTRACTION OF STATISTICS FROM IMAGES OF MATERIAL FRAGMENTATION
Authors: KAMATH CHANDRIKA , HURRICANE OMAR A.
Published: August 2011

The extraction of statistics of interest in experimental or observational images is often challenging due to the noise in the data and the variation across images in a dataset. For an objective analysis, any algorithms used must be relatively insensitive to the choice of parameters. In addition, to avoid manual analysis, which is tedious and error-prone, these algorithms must also lend themselves to full or partial automation, especially when the number of images is large. In this paper, we describe the use of image analysis techniques to extract various statistics from experimental images resulting from the fragmentation of materials. We show how we can use a sequence of relatively simple algorithms to provide a robust solution for the extraction of statistics on the fragments and the gaps between them.
SPEEDING UP BEST NEIGHBORHOOD MATCHING ALGORITHM FOR HIGH-DEFINITION IMAGE ON GPU PLATFORM
Authors: HE LIQIANG , ZHANG GUANGYONG , ZHANG YANYAN
Published: August 2011

Error concealment restores the visual integrity of image content that has been damaged due to a bad network transmission. Best neighborhood matching (BNM) is an effective image-recovery method that exploits the information redundancy in a block-coded broken image to find similar content that it then uses to repair or conceal errors. On a high-definition image, BNM is traditionally implemented sequentially, which requires a relatively long time and thus is not suitable for real-time or high-volume use. In this paper, we analyze the data access patterns of the BNM algorithm, and exploit a graphics process unit (GPU) platform to speed up the execution through a parallel implementation. We compare and combine several different GPU optimization methods (coalesced global memory access, shared memory, register files, etc.), and propose an improvement to the parallel BNM algorithm. Experimental results show that our approach can speed up BNM 62 times over the sequential approach without any obvious loss of accuracy.
AGENT-BASED SOCIAL PSYCHOLOGY: FROM NEUROCOGNITIVE PROCESSES TO SOCIAL DATA
Authors: CATICHA NESTOR , VICENTE RENATO
Published: August 2011

Moral Foundation Theory states that groups of different observers may rely on partially dissimilar sets of moral foundations, thereby reaching different moral valuations. The use of functional imaging techniques has revealed a spectrum of cognitive styles with respect to the differential handling of novel or corroborating information that is correlated to political affiliation. Here we characterize the collective behavior of an agent-based model whose inter individual interactions due to information exchange in the form of opinions are in qualitative agreement with experimental neuroscience data. The main conclusion derived connects the existence of diversity in the cognitive strategies and statistics of the sets of moral foundations and suggests that this connection arises from interactions between agents. Thus a simple interacting agent model, whose interactions are in accord with empirical data on conformity and learning processes, presents statistical signatures consistent with moral judgment patterns of conservatives and liberals as obtained by survey studies of social psychology.
THE SMALL-WORLD PROPERTY IN NETWORKS GROWING BY ACTIVE EDGES
Authors: GIABBANELLI PHILIPPE J.
Published: August 2011

In the last three years, we have witnessed an increasing number of complex network models based on a 'fractal' approach, in which parts of the network are repeatedly replaced by a given pattern. Our focus is on models that can be defined by repeatedly adding a pattern network to selected edges, called active edges. We prove that when a pattern network has at least two active edges, then the resulting network has an average distance at most logarithmic in the number of nodes. This suggests that real-world networks based on a similar growth mechanism are likely to have small average distance. We provide an estimate of the clustering coefficient and verify its accuracy using simulations. Using numerous examples of simple patterns, our simulations show various ways to generate small-world networks. Finally, we discuss extensions to our framework encompassing probabilistic patterns and active subnetworks.
ANT COLONY OPTIMIZATION WITH A NEW RANDOM WALK MODEL FOR COMMUNITY DETECTION IN COMPLEX NETWORKS
Authors: JIN DI , LIU DAYOU , YANG BO , LIU JIE , HE DONGXIAO
Published: August 2011

Detecting communities from complex networks has recently triggered great interest. Aiming at this problem, a new ant colony optimization strategy building on the Markov random walks theory, which is named as MACO, is proposed in this paper. The framework of ant colony optimization is taken as the basic framework in this algorithm. In each iteration, a Markov random walk model is employed as heuristic rule; all of the ants' local solutions are aggregated to a global one through an idea of clustering ensemble, which then will be used to update a pheromone matrix. The strategy relies on the progressive strengthening of within-community links and the weakening of between-community links. Gradually this converges to a solution where the underlying community structure of the complex network will become clearly visible. The proposed MACO has been evaluated both on synthetic benchmarks and on some real-world networks, and compared with some present competing algorithms. Experimental result has shown that MACO is highly effective for discovering communities.
ACCELERATED INNOVATION AND INCREASED SPATIAL DIVERSITY OF US POPULAR CULTURE
Authors: BENTLEY R. ALEXANDER , ORMEROD PAUL
Published: August 2011

We observe a marked increase in the spatial homogeneity of the popularity of first names across the United States in recent decades. We explain this by calibrating a modified standard model of neutral cultural evolution to the record of first name popularities for the United States as a whole since 1900 and across the individual states over the last 50 years. We obtain estimates of both the temporal and spatial diversity of the speed of cultural evolution during the 20th century and early 21st century. We find that the speed of innovation of popular baby names accelerated substantially since the end of the 20th century. We suggest that the increased inventiveness has driven a drift process that increased the geographic diversity across the United States.
THE SPATIAL AND TEMPORAL DIFFUSION OF STYLISTIC INNOVATIONS IN MATERIAL CULTURE
Authors: SCHOLNICK JONATHAN B.
Published: August 2011

Many explanations for the sigmoid or S-shaped curves that characterize the diffusion of innovations through time have been proposed. Recent studies demonstrate that social learning mechanisms, including conformist strategies, and heterogeneous adoption thresholds related to economic inequality and the decreasing cost of goods can generate these S-shaped cumulative frequency curves. The present study of a regional material culture sequence expands our inquiry concerning the underlying social forces that structure diffusion through both space and time. Using historic New England gravestones and their associated documents, this study considers both cultural transmission between stone carvers and consumer choices. Social learning among consumers can generate both wave-like diffusion patterns through space and lead to the persistence of cultural variants in certain locales.
LOCAL EXTINCTIONS, CONNECTEDNESS, AND CULTURAL EVOLUTION IN STRUCTURED POPULATIONS
Authors: PREMO L. S.
Published: August 2011

Population geneticists have shown that the effects of local extinction and recolonization on selectively neutral genetic diversity are sensitive to the number of individuals that migrate between groups. Here, we employ a spatially explicit metapopulation model to investigate the extent to which the effects of local extinction on selectively neutral cultural diversity and change are sensitive to intergroup cultural transmission — the rate at which cultural variants are transmitted between groups. Our results show that the level of intergroup cultural transmission as well as the topology of the social network that mediates cultural transmission between groups influence the way in which local extinctions affect total diversity, group differentiation, and the rate at which copy errors accumulate in structured populations. The results are discussed in the context of the archaeological record of Middle and Upper Paleolithic societies.
MODELING BOUNDARIES BETWEEN CONVERGING FRONTS IN PREHISTORY
Authors: SILVA FABIO , STEELE JAMES
Published: August 2011

We introduce a modeling framework that can be applied to cases of multiple converging fronts during episodes of population expansion and innovation diffusion, referring to two prehistoric case studies known archaeologically (the spread of pottery-making in Europe, and the spread of farming in southern Africa). We model front propagation using Fast Marching methods, drawing on the analogy with crystallization processes to build compoundly-weighted Voronoi diagrams of a spatially partitioned surface in which the zones of influence of each competing spreading process are determined by their respective front initiation times and propagation rates. We analyze the phase space for the general two-source case, and illustrate the potential of this approach by modeling the evolving interface for the archaeological case studies.
THE CULTURAL EVOLUTION OF ADAPTIVE-TRAIT DIVERSITY WHEN RESOURCES ARE UNCERTAIN AND FINITE
Authors: LAKE MARK W. , CREMA ENRICO R.
Published: August 2011

In this paper, we seek to build on existing mathematical studies of cultural change by exploring how the diversity of adaptive cultural traits evolves by innovation and cultural transmission when the payoff from adopting traits is both uncertain and frequency dependent. The model is particularly aimed at understanding the evolution of subsistence trait diversity, since the payoff from exploiting particular resources is often variable and subject to diminishing returns as a result of overexploitation. We find that traits that exploit the same shared resource evolve most quickly when intermediate rates of cultural transmission promote fluctuation in trait diversity. Higher rates of cultural transmission, which promote predominantly low diversity, and lower rates, which promote predominantly high diversity, both retard the adoption of traits offering higher payoff. We also find that the distribution of traits that exploit independent resources can evolve towards the theoretical Ideal Free Distribution so long as the rate of cultural transmission is low. Increasing the rate of cultural transmission reduces trait diversity, so that a more limited number of "niches" are occupied at any given time.
Enhancement of Photoluminescence by Photonic Crystal Scattering and Nanocrystalline Surface Scattering From Y2O3:Tb3+ Film Phosphors
Authors: Rok Oh Jeong , Kyu Park Byung , Kwang Lee Young , Huh Young-Duk , Rag Do Young
Published: August 2011

Thin film phosphors (TFPs) are generally less efficient than powder phosphors because a large fraction of the light generated within the film is lost by the wave-guiding effect. This study examined the effects of the grain size of sol-gel derived nanocrystalline Y2O3:Tb3+ TFPs on the extraction efficiency of emission light and the absorption of UV excitation light caused by Bragg scattering from an over-coated two-dimensional (2D) polystyrene (PS) photonic crystal layer (PCL). The total scattering enhancement of the integrated photoluminescence (PL) efficiency from the 20 mol % Li-doped TFP modified with the 580 nm 2D PS was 9.3 times higher than that of pure flat Y2O3:Tb3+. This was attributed to a combination of increased emission in the anomalous surface scattering enhancement of nanocrystalline films, and both emission and excitation in the Bragg scattering enhancement of 2D PCLs.
Enterohemorrhagic Escherichia coli infection stimulates Shiga toxin 1 macropinocytosis and transcytosis across intestinal epithelial cells
Authors: Lukyanenko Valeriy , Malyukova Irina , Hubbard Ann , Delannoy Michael , Boedeker Edgar , Zhu Chengru , Cebotaru Liudmila , Kovbasnjuk Olga
Published: August 2011

Gastrointestinal infection with Shiga toxins producing enterohemorrhagic Escherichia coli causes the spectrum of gastrointestinal and systemic complications, including hemorrhagic colitis and hemolytic uremic syndrome, which is fatal in ∼10% of patients. However, the molecular mechanisms of Stx endocytosis by enterocytes and the toxins cross the intestinal epithelium are largely uncharacterized. We have studied Shiga toxin 1 entry into enterohemorrhagic E. coli-infected intestinal epithelial cells and found that bacteria stimulate Shiga toxin 1 macropinocytosis through actin remodeling. This enterohemorrhagic E. coli-caused macropinocytosis occurs through a nonmuscle myosin II and cell division control 42 (Cdc42)-dependent mechanism. Macropinocytosis of Shiga toxin 1 is followed by its transcytosis to the basolateral environment, a step that is necessary for its systemic spread. Inhibition of Shiga toxin 1 macropinocytosis significantly decreases toxin uptake by intestinal epithelial cells and in this way provides an attractive, antibiotic-independent strategy for prevention of the harmful consequences of enterohemorrhagic E. coli infection.
Lysophosphatidic acid 5 receptor induces activation of Na+/H+ exchanger 3 via apical epidermal growth factor receptor in intestinal epithelial cells
Authors: Yoo Byong Kwon , He Peijian , Lee Sei-Jung , Yun C. Chris
Published: August 2011

Na+ absorption is a vital process present in all living organisms. We have reported previously that lysophosphatidic acid (LPA) acutely stimulates Na+ and fluid absorption in human intestinal epithelial cells and mouse intestine by stimulation of Na+/H+ exchanger 3 (NHE3) via LPA5 receptor. In the current study, we investigated the mechanism of NHE3 activation by LPA5 in Caco-2bbe cells. LPA5-dependent activation of NHE3 was blocked by mitogen-activated protein kinase kinase (MEK) inhibitor PD98059 and U0126, but not by phosphatidylinositol 3-kinase inhibitor LY294002 or phospholipase C-β inhibitor U73122. We found that LPA5 transactivated the epidermal growth factor receptor (EGFR) and that inhibition of EGFR blocked LPA5-dependent activation of NHE3, suggesting an obligatory role of EGFR in the NHE3 regulation. Confocal immunofluorescence and surface biotinylation analyses showed that LPA5 was located mostly in the apical membrane. EGFR, on the other hand, showed higher expression in the basolateral membrane. However, inhibition of apical EGFR, but not basolateral EGFR, abrogated LPA-induced regulation of MEK and NHE3, indicating that LPA5 selectively activates apical EGFR. Furthermore, transactivation of EGFR independently activated the MEK-ERK pathway and proline-rich tyrosine kinase 2 (Pyk2). Similarly to MEK inhibition, knockdown of Pyk2 blocked activation of NHE3 by LPA. Furthermore, we showed that RhoA and Rho-associated kinase (ROCK) are involved in activation of Pyk2. Interestingly, LPA5 did not directly activate RhoA but was required for transactivation of EGFR. Together, these results unveil a pivotal role of apical EGFR in NHE3 regulation by LPA and show that the RhoA-ROCK-Pyk2 and MEK-ERK pathways converge onto NHE3.
Physiological and histological changes in skeletal muscle following in vivo gene transfer by electroporation
Authors: Roche Joseph A. , Ford-Speelman Diana L. , Ru Lisa W. , Densmore Allison L. , Roche Renuka , Reed Patrick W. , Bloch Robert J.
Published: August 2011

Electroporation (EP) is used to transfect skeletal muscle fibers in vivo, but its effects on the structure and function of skeletal muscle tissue have not yet been documented in detail. We studied the changes in contractile function and histology after EP and the influence of the individual steps involved to determine the mechanism of recovery, the extent of myofiber damage, and the efficiency of expression of a green fluorescent protein (GFP) transgene in the tibialis anterior (TA) muscle of adult male C57Bl/6J mice. Immediately after EP, contractile torque decreased by ∼80% from pre-EP levels. Within 3 h, torque recovered to ∼50% but stayed low until day 3. Functional recovery progressed slowly and was complete at day 28. In muscles that were depleted of satellite cells by X-irradiation, torque remained low after day 3, suggesting that myogenesis is necessary for complete recovery. In unirradiated muscle, myogenic activity after EP was confirmed by an increase in fibers with central nuclei or developmental myosin. Damage after EP was confirmed by the presence of necrotic myofibers infiltrated by CD68+ macrophages, which persisted in electroporated muscle for 42 days. Expression of GFP was detected at day 3 after EP and peaked on day 7, with ∼25% of fibers transfected. The number of fibers expressing green fluorescent protein (GFP), the distribution of GFP+ fibers, and the intensity of fluorescence in GFP+ fibers were highly variable. After intramuscular injection alone, or application of the electroporating current without injection, torque decreased by ∼20% and ∼70%, respectively, but secondary damage at D3 and later was minimal. We conclude that EP of murine TA muscles produces variable and modest levels of transgene expression, causes myofiber damage due to the interaction of intramuscular injection with the permeabilizing current, and that full recovery requires myogenesis.
NF-κB plays an important role in indoxyl sulfate-induced cellular senescence, fibrotic gene expression, and inhibition of proliferation in proximal tubular cells
Authors: Shimizu Hidehisa , Bolati Dilinaer , Adijiang Ayinuer , Muteliefu Gulinuer , Enomoto Atsushi , Nishijima Fuyuhiko , Dateki Minori , Niwa Toshimitsu
Published: August 2011

We previously demonstrated that indoxyl sulfate induces senescence and dysfunction of proximal tubular cells by activating p53 expression. However, little is known about the role of nuclear factor (NF)-κB in these processes. The present study examines whether activation (phosphorylation) of NF-κB by indoxyl sulfate promotes senescence and dysfunction in human proximal tubular cells (HK-2 cells). Indoxyl sulfate induced phosphorylation of NF-κB p65 on Ser-276, which was suppressed by N-acetylcysteine, an antioxidant. Furthermore, indoxyl sulfate induced NF-κB p65 expression. Inhibitors of NF-κB (pyrrolidine dithiocarbamate and isohelenin) and NF-κB p65 small interfering RNA (siRNA) suppressed indoxyl sulfate-induced senescence-associated β-galactosidase activity and expression of p53, transforming growth factor (TGF)-β1, and α-smoothe muscle actin (SMA). The induction of p53 expression and p53 promoter activity by indoxyl sulfate were inhibited by pifithrin-α, p-nitro, an inhibitor of p53, whereas p53-transfected cells showed enhanced p53 promoter activity. NF-κB inhibitors suppressed indoxyl sulfate-induced p21 expression, whereas NF-κB p65 siRNA enhanced its expression. NF-κB inhibitors partially alleviated indoxyl sulfate-induced inhibition of cellular proliferation. NF-κB p65 siRNA-transfected cells showed less proliferation in the presence of indoxyl sulfate than control cells. Phosphorylated NF-κB p65 was expressed and colocalized with p53, p21, β-galactosidase, TGF-β1, and α-SMA in the kidneys of chronic renal failure (CRF) rats. AST-120, which reduces serum indoxyl sulfate level, suppressed their expression in the CRF rat kidneys. Taken together, NF-κB plays an important role in indoxyl sulfate-induced cellular senescence, fibrotic gene expression, and inhibition of proliferation in proximal tubular cells. More notably, indoxyl sulfate accelerates proximal tubular cell senescence with progression of CRF through reactive oxygen species-NF-κB-p53 pathway.
Caveolin-2 is a negative regulator of anti-proliferative function and signaling of transforming growth factor-β in endothelial cells
Authors: Xie Leike , Vo-Ransdell Chi , Abel Britain , Willoughby Cara , Jang Sungchan , Sowa Grzegorz
Published: August 2011

Using a combination of wild-type (WT) and caveolin-2 (Cav-2) knockout along with retroviral reexpression approaches, we provide the evidence for the negative role of Cav-2 in regulating anti-proliferative function and signaling of transforming growth factor β (TGF-β) in endothelial cells (ECs). Although, TGF-β had a modest inhibitory effect on WT ECs, it profoundly inhibited proliferation of Cav-2 knockout ECs. To confirm the specificity of the observed difference in response to TGF-β, we have stably reexpressed Cav-2 in Cav-2 knockout ECs using a retroviral approach. Similar to WT ECs, the anti-proliferative effect of TGF-β was dramatically reduced in the Cav-2 reexpressing ECs. The reduced anti-proliferative effect of TGF-β in Cav-2-positive cells was evidenced by three independent proliferation assays: 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), cell count, and bromodeoxyuridine incorporation and correlated with a loss of TGF-β-mediated upregulation of cell cycle inhibitor p27 and subsequent reduction of the levels of hyperphosphorylated (inactive) form of the retinoblastoma protein in Cav-2 reexpressing ECs. Mechanistically, Cav-2 inhibits anti-proliferative action of TGF-β by suppressing Alk5-Smad2/3 pathway manifested by reduced magnitude and length of TGF-β-induced Smad2/3 phosphorylation as well as activation of activin receptor-like kinase-5 (Alk5)-Smad2/3 target genes plasminogen activator inhibitor-1 and collagen type I in Cav-2-positive ECs. Expression of Cav-2 does not appear to significantly change targeting of TGF-β receptors I and Smad2/3 to caveolar and lipid raft microdomains as determined by sucrose fractionation gradient. Overall, the negative regulation of TGF-β signaling and function by Cav-2 is independent of Cav-1 expression levels and is not because of changing targeting of Cav-1 protein to plasma membrane lipid raft/caveolar domains.