bluuebunny/crossref_metadata_2025 huggingface dataset:
Nucleic Acid Amplification Tests for Diagnosis of
Neisseria gonorrhoeae
and
Chlamydia trachomatis
Rectal Infections
Authors: Bachmann Laura H. , Johnson Robert E. , Cheng Hong , Markowitz Lauri , Papp John R. , Palella Frank J. , Hook Edward W.
Published: March 2010

It is uncertain which methods for the diagnosis of rectal gonococcal and chlamydial infection are optimal. This study evaluated the performance of culture and nucleic acid amplification tests (NAATs) for rectal chlamydial and gonococcal diagnosis. From July 2003 until February 2007, 441 rectal test sets were collected from individuals attending a sexually transmitted disease clinic and three HIV clinics who gave a history of anal intercourse or were women at high risk for
Neisseria gonorrhoeae
or
Chlamydia trachomatis
infections. Rectal swab specimens were tested using culture and commercial NAATs employing transcription-mediated amplification (TMA), strand displacement amplification (SDA), and PCR amplification. Test performance was evaluated using a rotating standard by which patients were classified as infected if either two or three comparator tests were positive. Test sensitivities for the detection of
N. gonorrhoeae
ranged from 66.7% to 71.9% for culture to 100% for TMA. Specificities were 99.7% to 100% for culture and greater than 95.5% for all three NAATs. Test sensitivities for
C. trachomatis
ranged from 36.1% to 45.7% for culture and among NAATS from 91.4% to 95.8% for PCR to 100% for TMA. Specificities of the NAATs ranged from 95.6% to 98.5% (two-of-three standard) and from 88.8% to 91.8% (three-of-three standard). Over 60% and 80% of gonococcal and chlamydial infections, respectively, among men who have sex with men and over 20% of chlamydial infections in women would have been missed if the rectal site had not been tested. Currently available NAATs are more sensitive for the detection of chlamydial and gonococcal infection at the rectal site than is culture.
Identification of
81
LGxGxxIxW
89
and
171
EDRW
174
Domains from Human Immunodeficiency Virus Type 1 Vif That Regulate APOBEC3G and APOBEC3F Neutralizing Activity
Authors: Dang Ying , Davis Roderick W. , York Ian A. , Zheng Yong-Hui
Published: March 2010

The human cytidine deaminases APOBEC3G (A3G) and APOBEC3F (A3F) potently restrict human immunodeficiency virus type 1 (HIV-1) replication, but they are neutralized by the viral protein Vif. Vif bridges A3G and A3F with a Cullin 5 (Cul5)-based E3 ubiquitin ligase and mediates their proteasomal degradation. This mechanism has been extensively studied, and several Vif domains have been identified that are critical for A3G and A3F neutralization. Here, we identified two additional domains. Via sequence analysis of more than 2,000 different HIV-1 Vif proteins, we identified two highly conserved amino acid sequences,
81
LGxGxSIEW
89
and
171
EDRWN
175
. Within the
81
LGxGxSIEW
89
sequence, residues L81, G82, G84, and, to a lesser extent, I87 and W89 play very critical roles in A3G/A3F neutralization. In particular, residues L81 and G82 determine Vif binding to A3F, residue G84 determines Vif binding to both A3G and A3F, and residues
86
SIEW
89
affect Vif binding to A3F, A3G, and Cul5. Accordingly, this
81
LGxGxSIEW
89
sequence was designated the
81
LGxGxxIxW
89
domain. Within the
171
EDRWN
175
sequence, all residues except N175 are almost equally important for regulation of A3F neutralization, and consistently, they determine Vif binding only to A3F. Accordingly, this domain was designated
171
EDRW
174
. The LGxGxxIxW domain is also partially conserved in simian immunodeficiency virus Vif from rhesus macaques (SIVmac239) and has a similar activity. Thus,
81
LGxGxxIxW
89
and
171
EDRW
174
are two novel functional domains that are very critical for Vif function. They could become new targets for inhibition of Vif activity during HIV replication.
Inhibition of Xenotropic Murine Leukemia Virus-Related Virus by APOBEC3 Proteins and Antiviral Drugs
Authors: Paprotka Tobias , Venkatachari Narasimhan J. , Chaipan Chawaree , Burdick Ryan , Delviks-Frankenberry Krista A. , Hu Wei-Shau , Pathak Vinay K.
Published: March 2010

Xenotropic murine leukemia virus-related virus (XMRV), a gammaretrovirus, has been isolated from human prostate cancer tissue and from activated CD4
+
T cells and B cells of patients with chronic fatigue syndrome, suggesting an association between XMRV infection and these two diseases. Since APOBEC3G (A3G) and APOBEC3F (A3F), which are potent inhibitors of murine leukemia virus and Vif-deficient human immunodeficiency virus type 1 (HIV-1), are expressed in human CD4
+
T cells and B cells, we sought to determine how XMRV evades suppression of replication by APOBEC3 proteins. We found that expression of A3G, A3F, or murine A3 in virus-producing cells resulted in their virion incorporation, inhibition of XMRV replication, and G-to-A hypermutation of the viral DNA with all three APOBEC3 proteins. Quantitation of A3G and A3F mRNAs indicated that, compared to the human T-cell lines CEM and H9, prostate cell lines LNCaP and DU145 exhibited 50% lower A3F mRNA levels, whereas A3G expression in 22Rv1, LNCaP, and DU145 cells was nearly undetectable. XMRV proviral genomes in LNCaP and DU145 cells were hypermutated at low frequency with mutation patterns consistent with A3F activity. XMRV proviral genomes were extensively hypermutated upon replication in A3G/A3F-positive T cells (CEM and H9), but not in A3G/A3F-negative cells (CEM-SS). We also observed that XMRV replication was susceptible to the nucleoside reverse transcriptase (RT) inhibitors zidovudine (AZT) and tenofovir and the integrase inhibitor raltegravir. In summary, the establishment of XMRV infection in patients may be dependent on infection of A3G/A3F-deficient cells, and cells expressing low levels of A3G/A3F, such as prostate cancer cells, may be ideal producers of infectious XMRV. Furthermore, the anti-HIV-1 drugs AZT, tenofovir, and raltegravir may be useful for treatment of XMRV infection.
High-Resolution Cryo-Electron Microscopy Structures of Murine Norovirus 1 and Rabbit Hemorrhagic Disease Virus Reveal Marked Flexibility in the Receptor Binding Domains
Authors: Katpally Umesh , Voss Neil R. , Cavazza Tommaso , Taube Stefan , Rubin John R. , Young Vivienne L. , Stuckey Jeanne , Ward Vernon K. , Virgin Herbert W. , Wobus Christiane E. , Smith Thomas J.
Published: March 2010

Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to ∼8-Å resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions.
“Resistance” to PSC-RANTES Revisited: Two Mutations in Human Immunodeficiency Virus Type 1 HIV-1
SF162
or Simian-Human Immunodeficiency Virus SHIV
SF162-p3
Do Not Confer Resistance
Authors: Nedellec Rebecca , Coetzer Mia , Lederman Michael M. , Offord Robin E. , Hartley Oliver , Mosier Donald E.
Published: March 2010

Resistance of human immunodeficiency virus type 1 (HIV-1) to small-molecule CCR5 inhibitors is well demonstrated, but resistance to macromolecular CCR5 inhibitors (e.g., PSC-RANTES) that act by both CCR5 internalization and receptor blockade had not been reported until recently (3). The report of a single simian-human immunodeficiency virus SHIV
SF162-p3
variant with one V3 and one gp41 sequence change in gp160 that conferred both altered replicative fitness and resistance to PSC-RANTES was therefore surprising. We introduced the same two mutations into both the parental HIV-1
SF162
and the macaque-adapted SHIV
SF162-p3
and found minor differences in entry fitness but no changes in sensitivity to inhibition by either PSC-RANTES or the small-molecule allosteric inhibitor TAK-779. We attribute the earlier finding to confounding fitness effects with inhibitor sensitivity.
Role of Annexin A2 in the Production of Infectious Hepatitis C Virus Particles
Authors: Backes Perdita , Quinkert Doris , Reiss Simon , Binder Marco , Zayas Margarita , Rescher Ursula , Gerke Volker , Bartenschlager Ralf , Lohmann Volker
Published: March 2010

Hepatitis C virus (HCV) is an important human pathogen affecting 170 million chronically infected individuals. In search for cellular proteins involved in HCV replication, we have developed a purification strategy for viral replication complexes and identified annexin A2 (ANXA2) as an associated host factor. ANXA2 colocalized with viral nonstructural proteins in cells harboring genotype 1 or 2 replicons as well as in infected cells. In contrast, we found no obvious colocalization of ANXA2 with replication sites of other positive-strand RNA viruses. The silencing of ANXA2 expression showed no effect on viral RNA replication but resulted in a significant reduction of extra- and intracellular virus titers. Therefore, it seems likely that ANXA2 plays a role in HCV assembly rather than in genome replication or virion release. Colocalization studies with individually expressed HCV nonstructural proteins indicated that NS5A specifically recruits ANXA2, probably by an indirect mechanism. By the deletion of individual NS5A subdomains, we identified domain III (DIII) as being responsible for ANXA2 recruitment. These data identify ANXA2 as a novel host factor contributing, with NS5A, to the formation of infectious HCV particles.
DifferentIn VivoEffects of HIV-1 Immunodominant Epitope-Specific Cytotoxic T Lymphocytes on Selection of Escape Mutant Viruses
Authors: Koizumi Hirokazu , Hashimoto Masao , Fujiwara Mamoru , Murakoshi Hayato , Chikata Takayuki , Borghan Mohamed Ali , Hachiya Atsuko , Kawashima Yuka , Takata Hiroshi , Ueno Takamasa , Oka Shinichi , Takiguchi Masafumi
Published: March 2010

HIV-1 escape mutants are well known to be selected by immune pressure via HIV-1-specific cytotoxic T lymphocytes (CTLs) and neutralizing antibodies. The ability of the CTLs to suppress HIV-1 replication is assumed to be associated with the selection of escape mutants from the CTLs. Therefore, we first investigated the correlation between the ability of HLA-A*1101-restricted CTLs recognizing immunodominant epitopesin vitroand the selection of escape mutants. The result showed that there was no correlation between the ability of these CTLs to suppress HIV-1 replicationin vitroand the appearance of escape mutants. The CTLs that had a strong ability to suppress HIV-1 replicationin vitrobut failed to select escape mutants expressed a higher level of PD-1in vivo, whereas those that had a strong ability to suppress HIV-1 replicationin vitroand selected escape mutants expressed a low level of PD-1.Ex vivoanalysis of these CTLs revealed that the latter CTLs had a significantly stronger ability to recognize the epitope than the former ones. These results suggest that escape mutations are selected by HIV-1-specific CTLs that have a stronger ability to recognize HIV-1in vivobut notin vitro.
Critical consolute point in hard-sphere binary mixtures: Effect of the value of the eighth and higher virial coefficients on its location
Authors: López De Haro Mariano , Malijevský Anatol , Labík Stanislav
Published: March 2010

Various truncations for the virial series of a binary fluid mixture of additive hard spheres are used to analyze the location of the critical consolute point of this system for different size asymmetries. The effect of uncertainties in the values of the eighth virial coefficients on the resulting critical constants is assessed. It is also shown that a replacement of the exact virial coefficients in lieu of the corresponding coefficients in the virial expansion of the analytical Boublík–Mansoori–Carnahan–Starling–Leland equation of state, which still leads to an analytical equation of state, may lead to a critical consolute point in the system.
How factual do we want the facts? Criteria for a critical appraisal of empirical research for use in ethics
Authors: Strech Daniel
Published: March 2010

Most contributions to the current debate about the consideration and application of empirical information in ethics scholarship deal with epistemological issues such as the role and the meaning of empirical research in ethical reasoning. Despite the increased publication of empirical data in ethics literature we still lack systematic analyses and conceptual frameworks that would help us to understand the rarely discussed methodological and practical problems in appraising empirical research. This paper demonstrates the need for critical appraisal and its crucial methodological role in the application of empirical information in ethical reasoning. Furthermore, it systematically examines the criteria and the appropriate appraisal of empirical research and the associated challenges by highlighting current problems in empirical ethics literature. These problems reveal the following challenges for a critical and responsible consideration of empirical information in ethical reasoning: (i) training in the basic skills of locating and communicating empirical data from the relevant studies; (ii) training in basic knowledge of how to critically appraise empirical (qualitative and quantitative) research and its results; (iii) determination of quality standards for empirical ethics research; (iv) adequate reporting of the methodology and results of empirical ethics research in scientific journals.
A pilot study evaluating an intervention designed to raise awareness of clinical trials among potential participants in the developing world
Authors: Dhai Ames , Etheredge Harriet , Cleaton-Jones Peter
Published: March 2010

Background

This pilot study evaluated the speaking book ‘What it means to be part of a clinical trial’. The book aims at empowering populations with information on their rights and responsibilities when enrolled in clinical research. Wide publication of the book—at significant cost—is anticipated. It is important that the book is evaluated within the communities for whom it is intended, and the necessary changes (if any) are made, before translation and large-scale publication takes place.

Objective

The objective of the study was to measure the efficacy and ease of use of the book.

Methods

Participants were recruited from a catering company. Participants were questioned on their knowledge of clinical trials and were then given the book. Instructions for use of the book were given to one group (‘experimental’ group). The other group (‘control’ group) was not given any instructions. A week later, the investigators returned, repeated the knowledge questions and asked ‘ease of use’ questions.

Results

A two-way repeated measure of covariants showed a statistically significant positive increase in knowledge of clinical trials among the intervention group (p=0.02). Results for the control group displayed trends that were not statistically significant. Percentage analysis of ‘ease of use’ questions proved that the book is easy to use, although some changes would be beneficial.

Conclusion

This study revealed that the speaking book is easy to use. It significantly increased knowledge of clinical trials among the study sample if instructions on use of the book were provided.
Do strong value-based attitudes influence estimations of future events?: Table 1
Authors: Juth Niklas , Lynöe Niels
Published: March 2010

The purpose of the present study was to examine whether or not strong values might influence physicians' estimations of future events. In an empirical study about physicians' attitudes towards physician assisted suicide (PAS) we asked about the physicians' main reasons for being pro, doubtful or contra PAS and also asked them to estimate what would happen with patients' trust if PAS were to be legally accepted in Swedish society. Finally we asked the physicians about their own trust in healthcare in the event of PAS being legally accepted.

We found that in contrast to those who were pro PAS and doubtful, the group who were against PAS did not discriminate between their own opinion and their estimation of what they thought might happen with patients' trust in the future.

Against the backdrop of the present study, we present a hypothesis maintaining that feeling strongly against controversial medical procedures is associated with being inclined to let one's own beliefs influence our capacity to interpret and estimate empirical results. We think this hypothesis merits closer examination.
The use of methylphenidate among students: the future of enhancement?
Authors: Outram Simon M
Published: March 2010

During the past few years considerable debate has arisen within academic journals with respect to the use of smart drugs or cognitive enhancement pharmaceuticals. The following paper seeks to examine the foundations of this cognitive enhancement debate using the example of methylphenidate use among college students. The argument taken is that much of the enhancement debate rests upon inflated assumptions about the ability of such drugs to enhance and over-estimations of either the size of the current market for such drugs or the rise in popularity as drugs for enhancing cognitive abilities. This article provides an overview of the empirical evidence that methylphenidate has the ability to significantly improve cognitive abilities in healthy individuals, and examines whether the presumed uptake of the drug is either as socially significant as implied or growing to the extent that it requires urgent regulatory attention. In addition, it reviews the evidence of side-effects for the use of methylphenidate which may be an influential factor in whether an individual decides to use such drugs. The primary conclusions are that neither drug efficacy, nor the benefit-to-risk balance, nor indicators of current or growing demand provide sufficient evidence that methylphenidate is a suitable example of a cognitive enhancer with mass appeal. In light of these empirically based conclusions, the article discusses why methylphenidate might have become seen as a smart drug or cognitive enhancer.
Deciding against disability: does the use of reproductive genetic technologies express disvalue for people with disabilities?
Authors: Malek Janet
Published: March 2010

This paper focuses on one objection to the use of reproductive genetic technologies (RGTs): the argument known as the expressivist objection. According to this argument, the choice to use reproductive genetic technologies to prevent the birth of individuals with disabilities is an expression of disvalue for existing people with disability. Many have been persuaded by this impassioned perspective. This paper shows that this argument is misguided and so does not constitute a sound objection to the use of RGTs to prevent disability in future children. It first identifies some responses to the objection that may be sound but not completely convincing to proponents of the expressivist position. It then describes a thought experiment designed to demonstrate more clearly that choosing to use RGTs to prevent disability in future children does not convey a negative message about people who have disabilities. After describing a decision that clearly does not send such a message, the paper walks through a series of cases and shows how, despite differences that might seem to be morally relevant, each is morally equivalent to the previous one with respect to the extent that it expresses disvalue for such individuals.
ON GROUPS OF TYPE $\mathcal{L}^{-1}$
Authors: JO JANG HYUN
Published: March 2010

We show that every finite group G has a set of cohomological elements satisfying ceratin algebraic property [Formula: see text] which can be regarded as a generalized notion of an algebraic counterpart to the topological phenomenon of free actions on finite dimensional homotopy spheres. We extend this result to a certain class of groups which contains groups of finite virtual cohomological dimension.
SECOND-ORDER QUASILINEAR PDEs AND CONFORMAL STRUCTURES IN PROJECTIVE SPACE
Authors: BUROVSKIY P. A. , FERAPONTOV E. V. , TSAREV S. P.
Published: March 2010

We investigate second-order quasilinear equations of the form fijuxixj = 0, where u is a function of n independent variables x1, …, xn, and the coefficients fij depend on the first-order derivatives p1 = ux1, …, pn = uxn only. We demonstrate that the natural equivalence group of the problem is isomorphic to SL(n + 1, R), which acts by projective transformations on the space Pn with coordinates p1, …, pn. The coefficient matrix fij defines on Pn a conformal structure fij(p)dpidpj. The necessary and sufficient conditions for the integrability of such equations by the method of hydrodynamic reductions are derived, implying that the moduli space of integrable equations is 20-dimensional. Any equation satisfying the integrability conditions is necessarily conservative, and possesses a dispersionless Lax pair. The integrability conditions imply that the conformal structure fij(p) dpidpj is conformally flat, and possesses infinitely many three-conjugate null coordinate systems parametrized by three arbitrary functions of one variable. Integrable equations provide examples of such conformal structures parametrized by elementary functions, elliptic functions and modular forms.
FREQUENCY SYNCHRONIZATION IN NETWORKS OF COUPLED OSCILLATORS, A MONOTONE DYNAMICAL SYSTEMS APPROACH
Authors: QIN WEN-XIN
Published: March 2010

We propose a new approach to investigate the frequency synchronization in networks of coupled oscillators. By making use of the theory of monotone dynamical systems, we show that frequency synchronization occurs in networks of coupled oscillators, provided the coupling scheme is symmetric, connected, and strongly cooperative. Our criterion is independent of the system size, the coupling strength and the details of the connections, and applies also to nonlinear coupling schemes.
HOPF BIFURCATIONS FOR NEAR-HAMILTONIAN SYSTEMS
Authors: HAN MAOAN , YANG JUNMIN , YU PEI
Published: March 2010

In this paper, we consider bifurcation of limit cycles in near-Hamiltonian systems. A new method is developed to study the analytical property of the Melnikov function near the origin for such systems. Based on the new method, a computationally efficient algorithm is established to systematically compute the coefficients of Melnikov function. Moreover, we consider the case that the Hamiltonian function of the system depends on parameters, in addition to the coefficients involved in perturbations, which generates more limit cycles in the neighborhood of the origin. The results are applied to a quadratic system with cubic perturbations to show that the system can have five limit cycles in the vicinity of the origin.
AN EFFICIENT AND ACCURATE METHOD FOR THE ESTIMATION OF ENTROPY AND OTHER DYNAMICAL INVARIANTS FOR PIECEWISE AFFINE CHAOTIC MAPS
Authors: ADDABBO TOMMASO , FORT ADA , PAPINI DUCCIO , ROCCHI SANTINA , VIGNOLI VALERIO
Published: March 2010

In this paper, we discuss an efficient iterative method for the estimation of the chief dynamical invariants of chaotic systems based on stochastically stable piecewise affine maps (e.g. the invariant measure, the Lyapunov exponent as well as the Kolmogorov–Sinai entropy). The proposed method represents an alternative to the Monte-Carlo methods and to other methods based on the discretization of the Frobenius–Perron operator, such as the well known Ulam's method. The proposed estimation method converges not slower than exponentially and it requires a computation complexity that grows linearly with the iterations. Referring to the theory developed by C. Liverani, we discuss a theoretical tool for calculating a conservative estimation of the convergence rate of the proposed method. The proposed approach can be used to efficiently estimate any order statistics of a symbolic source based on a piecewise affine mixing map.
EVALUATION OF MUTUAL INFORMATION ESTIMATORS FOR TIME SERIES
Authors: PAPANA ANGELIKI , KUGIUMTZIS DIMITRIS
Published: March 2010

We study some of the most commonly used mutual information estimators, based on histograms of fixed or adaptive bin size, k-nearest neighbors and kernels and focus on optimal selection of their free parameters. We examine the consistency of the estimators (convergence to a stable value with the increase of time series length) and the degree of deviation among the estimators. The optimization of parameters is assessed by quantifying the deviation of the estimated mutual information from its true or asymptotic value as a function of the free parameter. Moreover, some commonly used criteria for parameter selection are evaluated for each estimator. The comparative study is based on Monte Carlo simulations on time series from several linear and nonlinear systems of different lengths and noise levels. The results show that the k-nearest neighbor is the most stable and less affected by the method-specific parameter. A data adaptive criterion for optimal binning is suggested for linear systems but it is found to be rather conservative for nonlinear systems. It turns out that the binning and kernel estimators give the least deviation in identifying the lag of the first minimum of mutual information from nonlinear systems, and are stable in the presence of noise.
SELF-ORGANIZATION IN NONADDITIVE SYSTEMS WITH EXTERNAL NOISE
Authors: BAGCI G. BARIS , TIRNAKLI UGUR
Published: March 2010

A nonadditive generalization of Klimontovich's S-theorem [Bagci, 2008] has recently been obtained by employing Tsallis entropy. This general version allows one to study physical systems whose stationary distributions are of the inverse power law in contrast to the original S-theorem, which only allows exponential stationary distributions. The nonadditive S-theorem has been applied to the modified Van der Pol oscillator with inverse power law stationary distribution. By using nonadditive S-theorem, it is shown that the entropy decreases as the system is driven out of equilibrium, indicating self-organization in the system. The allowed values of the nonadditivity index q are found to be confined to the regime (0.5,1].
STABILITY OF MULTICLUSTER SYNCHRONIZATION
Authors: AMRITKAR R. E. , RANGARAJAN GOVINDAN
Published: March 2010

A system of many coupled oscillators on a network can show multicluster synchronization. We obtain existence conditions and stability bounds for such a multicluster synchronization. When the oscillators are identical, we obtain the interesting result that network structure alone can cause multicluster synchronization to emerge even when all the other parameters are the same. We also study occurrence of multicluster synchronization when two different types of oscillators are coupled.
DESIGN AND IMPLEMENTATION OF MULTI-WING BUTTERFLY CHAOTIC ATTRACTORS VIA LORENZ-TYPE SYSTEMS
Authors: YU SIMIN , TANG WALLACE K. S. , LÜ JINHU , CHEN GUANRONG
Published: March 2010

Lorenz system, as the first classical chaotic system, has been intensively investigated over the last four decades. Based on the sawtooth wave function, this paper initiates a novel approach for generating multi-wing butterfly chaotic attractors from the generalized first and second kinds of Lorenz-type systems. Compared with the traditional ring-shaped multi-scroll Lorenz chaotic attractors, the proposed multi-wing butterfly chaotic attractors are much easier to be designed and implemented by analog circuits. The dynamical behaviors of these multi-wing butterfly chaotic systems are further studied. Theoretical analysis shows that every index-2 saddle-focus equilibrium corresponds to a unique wing in the butterfly attractors. Finally, a module-based unified circuit diagram is constructed for realizing various multi-wing butterfly attractors. It should be especially pointed out that this is the first time in the literature that a maximal 10-wing butterfly chaotic attractor is experimentally verified by analog circuits.
AN IMPROVED LOWER BOUND ON THE NUMBER OF LIMIT CYCLES BIFURCATING FROM A QUINTIC HAMILTONIAN PLANAR VECTOR FIELD UNDER QUINTIC PERTURBATION
Authors: JOHNSON TOMAS , TUCKER WARWICK
Published: March 2010

The limit cycle bifurcation of a Z2equivariant quintic planar Hamiltonian vector field under Z2equivariant quintic perturbation is studied. We prove that the given system can have at least 27 limit cycles. This is an improved lower bound on the possible number of limit cycles that can bifurcate from a quintic planar Hamiltonian system under quintic perturbation.
CHAOS IN A THREE-DIMENSIONAL CANCER MODEL
Authors: ITIK MEHMET , BANKS STEPHEN P.
Published: March 2010

In this study, we develop a new dynamical model of cancer growth, which includes the interactions between tumour cells, healthy tissue cells, and activated immune system cells, clearly leading to chaotic behavior. We explain the biological relevance of our model and the ways in which it differs from the existing ones. We perform equilibria analysis, indicate the conditions where chaotic dynamics can be observed, and show rigorously the existence of chaos by calculating the Lyapunov exponents and the Lyapunov dimension of the system. Moreover, we demonstrate that Shilnikov's theorem is valid in the parameter range of interest.
GENERATING 3-SCROLL ATTRACTORS FROM ONE CHUA CIRCUIT
Authors: ELHADJ ZERAOULIA , SPROTT J. C.
Published: March 2010

This paper reports the finding of a 3-scroll chaotic attractor with only three equilibria obtained via direct modification of Chua's circuit. In addition, it is shown numerically that the new system can also generate one-scroll and two-scroll chaotic attractors.
ON THE LOCAL STOCHASTIC STABILITY OF NONLINEAR COMPLEX NETWORKS
Authors: HUANG ZHI-LONG , YAN ZHOU , JIN XIAO-LING , CHEN GUANRONG
Published: March 2010

The local stochastic stability of nonlinear complex networks is studied, subject to stochastic perturbations to the coupling strengths and stochastic parametric excitations to the nodes. The complex network is first linearized at its trivial solution and then the linearized network is reduced to N independent subsystems by using a suitable linear transformation, where N is the size of the network. The largest Lyapunov exponent for each subsystem is then calculated and all the approximate analytical solutions are evaluated for some specific cases. It is found that the largest Lyapunov exponent among all subsystems is the one associated with the subsystem that has the largest or the smallest eigenvalue of the configuration matrix of the network. Finally, an example is given to demonstrate the validity and accuracy of the theoretical analysis.
FLUCTUATION ANALYSIS OF MONTHLY RAINFALL TIME SERIES
Authors: PIERINI JORGE O. , TELESCA LUCIANO
Published: March 2010

The monthly rainfall time series, spanning more than a century, recorded in several sites in the middle Argentina were analyzed. The power spetral density (PSD) method reveals the presence of annual and semi-annual cyclic fluctuations. The detrended fluctuation analysis (DFA) performed on the residual times series (after removing the periodicities) shows a scaling behavior, characterized by DFA scaling exponents ranging between 0.54 and 0.58. These findings could contribute to a better understanding of rainfall dynamics.
THE IONIZATION ENERGIES AND SIMULATED PHOTOELECTRON SPECTRA OF HPCN AND HNCP
Authors: BETTERTON SHARON A. , BERKA ADRIENNE S. , FLEMING PATRICK E.
Published: March 2010

The structures, vibrational frequencies and adiabatic ionization energies of HPCN and HNCP are calculated at several levels of theory. The adiabatic ionization energy of HPCN is found to be 10.16 eV at the G3 level of theory. The singlet state of HPCN+[Formula: see text] is found to be approximately 1.3 eV below the lowest energy triplet state (ã3A ″). Both states have a bent equilibrium molecular geometry. The adiabatic ionization energy for HNCP is calculated to be 8.30 eV at the G3 level of theory. In contrast to HPCN+, the triplet state [Formula: see text] of HNCP+is lower in energy than that of the singlet state (ã1A ′) by approximately 1 eV. Also, the triplet state of HNCP+is linear in contrast to that of HPCN+due to the larger interaction between neighboring 2p orbitals on the central atoms in HNCP+relative to the interaction between the 3p and 2p orbitals on the central atoms in HPCN+. Simulated photoelectron spectra (PES) are presented for the transitions producing both the singlet and triplet ion states of both isomers. As predicted by the dramatic geometry change in the case of [Formula: see text], there is a long progression in the bending mode of the cation in the simulated PES.
MOLECULAR DYNAMIC SIMULATION OF CARBOXYETHYL CHITOSAN: EFFECT OF TEMPERATURE, SALT CONCENTRATION AND pH
Authors: YIN QIANG , ZHOU GE , LIU YAN-YAN , YIN QIN-JIAN , LUO JIAN-HUI , JIANG BO
Published: March 2010

The effect of temperatures and NaCl concentrations on the structures of polyampholyte(carboxyethyl chitosan) under different pH conditions were investigated using molecular dynamics simulations. The radius of gyration (ROG) of the backbone Cαof carboxyethyl chitosan was analyzed and the accessible surface areas (ASA) of entire polyampholytes were estimated. The variation of the ROG and the ASA of polyampholyte with temperatures and different NaCl concentrations under different pH conditions are discussed. The present simulation makes it possible to understand the structures of polyampholyte in aqueous solutions at the molecular level.
QUANTUM-CHEMICAL PREDICTION OF FORMATION ENTHALPY OF CYCLOALKANE
Authors: HONG XIN , SHI JING
Published: March 2010

Based on the s-homodesmotic model and the seven different density functional theory (DFT) methods, we calculate standard formation enthalpy of cycloalkane of up to 10 carbons. Among the 21 different combinations, the scheme using MPWB1K method and working reactions when s = 2 achieves the experimental accuracy with RMSD of 8.49 kJ/mol. Also, credibility of this scheme is proved by discussion on influence from different aspects.
BONDING FEATURES AND REACTION MECHANISM OF THE OXIDATION OF 2-PROPANOL BY A Cp*Ir AMIDO COMPLEX
Authors: LIU LINGJUN , BI SIWEI , SUN MIN , YUAN XIANGAI , LI PING
Published: March 2010

The mechanistic study on the oxidation of 2-propanol by the model complex CpIr [κ2-(N,C)-( NHCMe2–2-C6H4)] (R) is performed using density functional theory (DFT) calculations. It is found that the rate-determining step is the hydrogen migration from 2-propanol to R via a six-membered transition state. The reaction is calculated to be favorable thermodynamically. To further understand the reaction mechanism, some bonding features are discussed, such as the correlation of the geometry of R and the Ir–N π bond involved, the transformation of the nitrogen hybridization, the variation of Ir–N bond distance, and so on.
THERMOCHEMISTRY OF ORGANIC, HETEROORGANIC, AND INORGANIC MOLECULES AND THEIR FRAGMENTS: "QUANTUM-CHEMICAL CALCULATIONS OF THERMOCHEMICAL PARAMETERS: MOLECULES AND THEIR FRAGMENTS"
Authors: GOLOVIN A. V. , PONOMAREV D. A. , TAKHISTOV V. V.
Published: March 2010

Analysis of theoretical enthalpies of formation for about 300 molecules and their fragments (free radicals, biradicals, and ions) was performed to show that the results of semiempirical, DFT, and ab initio methods must be taken with great caution. A brief review of the authors' alternative empirical methodologies for calculation of enthalpies of formation for molecules (enthalpic shift procedure) and free radicals (enthalpies of isodesmic reactions) is given.
ABEEMσπ FLUCTUATING CHARGE FORCE FIELD APPLIED TO ALANINE DIPEPTIDE AND ALANINE DIPEPTIDE–WATER SYSTEMS
Authors: LIU CUI , ZHAO DONG-XIA , YANG ZHONG-ZHI
Published: March 2010

Atom-bond electronegativity equalization method at σπ level fused into molecular mechanics (ABEEMσπ/MM) divides the bond regions into σ and π bond regions on the basis of previous ABEEM/MM. It may suitably reflect intramolecular and intermolecular interaction and polarization. The fitting function k H-bond in the hydrogen bond (HB) interaction region increases the capability of ABEEMσπ/MM to simulate the hydration. Hydration of alanine dipeptide (AD) in aqueous solution is determined by the intramolecular and intermolecular HBs and the competition among the molecular packing effects. The acceptor molecule in HB complex contains at least one pair of lone pair electrons, sometimes contains π bonds, whose orientations directly effect the orientation of HBs. Therefore, ABEEMσπ/MM has obviously predominance to discuss the AD and AD–water systems, which contain many lone pair electrons, π bonds, and abundant HB nets. Properties of six AD conformers, clusters AD +( H2O )1–4 obtained from ABEEMσπ/MM agree well with the results of experiments, ab initio and other force fields. Structural and dynamical properties of the hydration water molecules have just embodied that the ABEEMσπ/MM gives correct hydration description relative to other force fields.
INTERACTION OF BRIDGED PIPERAZINE DERIVATIVES WITH THE μ-OPIOID RECEPTOR — A THEORETICAL MODEL
Authors: MICOVIC VUK , JURANIC IVAN
Published: March 2010

The flexible molecular docking was used to study interactions between a series of 3,6-diazabicyclo[3.1.1]heptanes, 9,10-diazatricyclo[4.2.1.1]decanes, and 2,7-diazatricyclo [4.4.0.0]decanes N-substituted by propanoyl and by arylalkenyl groups, and a model of the μ-opioid receptor. It has been found that the optimal position and orientation of the compounds in the ligand–receptor complex resemble that of fentanyl analogs described earlier.1This model explains stereochemical effects on binding of the two series of 3,6-diazabicyclo[3.1.1]heptanes, suggesting that the steric interaction of the bridge methylenic group plays the major role in modulating μ-receptor affinity of those molecules. Ab initio B3LYP method was used to determine electrostatic potentials of different bridged piperazine derivatives, and to estimate electrostatic contribution to the ligand–receptor complex stability.
A survey and analysis of electronic business document standards
Authors: Kabak Yildiray , Dogac Asuman
Published: March 2010

No document standard is sufficient for all purposes because the requirements significantly differ among businesses, industries, and geopolitical regions. On the other hand, the ultimate aim of business document interoperability is to exchange business data among partners without any prior agreements related to the document syntax and semantics. Therefore, an important characteristic of a document standard is its ability to adapt to different contexts, its extensibility, and its customization. The UN/CEFACT Core Component Technical Specification (CCTS) is an important landmark in this direction.

In this article, we present a survey and an analysis of some of the prominent UN/CEFACT CCTS-based electronic document standards. We describe their document design principles and discuss how they handle customization and extensibility. We address their industry relevance and the recent efforts for their harmonization and convergence. We conclude by mentioning some emerging efforts for the semantic interoperability of different document standards.
Eigenvalue bounds, spectral partitioning, and metrical deformations via flows
Authors: Biswal Punyashloka , Lee James R. , Rao Satish
Published: March 2010

We present a new method for upper bounding the second eigenvalue of the Laplacian of graphs. Our approach uses multi-commodity flows to deform the geometry of the graph; we embed the resulting metric into Euclidean space to recover a bound on the Rayleigh quotient. Using this, we show that every
n
-vertex graph of genus
g
and maximum degree
D
satisfies λ
2
(
G
)=
O
((
g
+1)
3
D
/
n
). This recovers the
O
(
D
/
n
) bound of Spielman and Teng for planar graphs, and compares to Kelner's bound of
O
((
g
+1)poly(
D
)/
n
), but our proof does not make use of conformal mappings or circle packings. We are thus able to extend this to resolve positively a conjecture of Spielman and Teng, by proving that λ
2
(
G
) =
O
(
D
h
6
log
h
/
n
) whenever
G
is
K

h

-minor free. This shows, in particular, that spectral partitioning can be used to recover
O
(√
n
)-sized separators in bounded degree graphs that exclude a fixed minor. We extend this further by obtaining nearly optimal bounds on λ
2
for graphs that exclude small-depth minors in the sense of Plotkin, Rao, and Smith. Consequently, we show that spectral algorithms find separators of sublinear size in a general class of geometric graphs.

Moreover, while the standard “sweep” algorithm applied to the second eigenvector may fail to find good quotient cuts in graphs of unbounded degree, our approach produces a vector that works for
arbitrary
graphs. This yields an alternate proof of the well-known nonplanar separator theorem of Alon, Seymour, and Thomas that states that every excluded-minor family of graphs has
O
(√
n
)-node balanced separators.
Amplifying lower bounds by means of self-reducibility
Authors: Allender Eric , Koucký Michal
Published: March 2010

We observe that many important computational problems in NC
1
share a simple self-reducibility property. We then show that, for any problem
A
having this self-reducibility property,
A
has polynomial-size TC
0
circuits if and only if it has TC
0
circuits of size
n
1+ϵ
for every ϵ> 0 (counting the number of wires in a circuit as the size of the circuit). As an example of what this observation yields, consider the Boolean Formula Evaluation problem (BFE), which is complete for NC
1
and has the self-reducibility property. It follows from a lower bound of Impagliazzo, Paturi, and Saks, that BFE requires depth
d
TC
0
circuits of size
n

1+ϵ

d

. If one were able to improve this lower bound to show that there is some constant ϵ> 0 (independent of the depth
d
) such that every TC
0
circuit family recognizing BFE has size at least
n
1+ϵ
, then it would follow that TC
0
≠ NC
1
. We show that proving lower bounds of the form
n
1+ϵ
is not ruled out by the Natural Proof framework of Razborov and Rudich and hence there is currently no known barrier for separating classes such as ACC
0
, TC
0
and NC
1
via existing “natural” approaches to proving circuit lower bounds.

We also show that problems with small uniform constant-depth circuits have algorithms that simultaneously have small space and time bounds. We then make use of known time-space tradeoff lower bounds to show that SAT requires uniform depth
d
TC
0
and AC
0
[6] circuits of size
n

1+
c

for some constant
c
depending on
d
.
Geometric suffix tree
Authors: Shibuya Tetsuo
Published: March 2010

Protein structure analysis is one of the most important research issues in the post-genomic era, and faster and more accurate index data structures for such 3-D structures are highly desired for research on proteins. This article proposes a new data structure for indexing protein 3-D structures. For strings, there are many efficient indexing structures such as suffix trees, but it has been considered very difficult to design such sophisticated data structures against 3-D structures like proteins. Our index structure is based on the suffix tree and is called the geometric suffix tree. By using the geometric suffix tree for a set of protein structures, we can exactly search for all of their substructures whose RMSDs (root mean square deviations) or URMSDs (unit-vector root mean square deviations) to a given query 3-D structure are not larger than a given bound. Though there are
O
(
N
2
) substructures in a structure of size
N
, our data structure requires only
O
(
N
) space for indexing all the substructures. We propose an
O
(
N
2
) construction algorithm for it, while a naive algorithm would require
O
(
N
3
) time to construct it. Moreover we propose an efficient search algorithm. Experiments show that we can search for similar structures much faster than previous algorithms if the RMSD threshold is not larger than 1Å. The experiments also show that the construction time of the geometric suffix tree is practically almost linear to the size of the database, when applied to a protein structure database.
A dynamic data structure for 3-D convex hulls and 2-D nearest neighbor queries
Authors: Chan Timothy M.
Published: March 2010

We present a fully dynamic randomized data structure that can answer queries about the convex hull of a set of
n
points in three dimensions, where insertions take
O
(log
3
n
) expected amortized time, deletions take
O
(log
6
n
) expected amortized time, and extreme-point queries take
O
(log
2
n
) worst-case time. This is the first method that guarantees polylogarithmic update and query cost for arbitrary sequences of insertions and deletions, and improves the previous
O
(
n
ϵ
)-time method by Agarwal and Matoušek a decade ago. As a consequence, we obtain similar results for nearest neighbor queries in two dimensions and improved results for numerous fundamental geometric problems (such as levels in three dimensions and dynamic Euclidean minimum spanning trees in the plane).
Improved bounds and new techniques for Davenport--Schinzel sequences and their generalizations
Authors: Nivasch Gabriel
Published: March 2010

We present several new results regarding λ

s

(
n
), the maximum length of a Davenport--Schinzel sequence of order
s
on
n
distinct symbols.

First, we prove that λ

s

(
n
) ≤
n
· 2

(1/
t
!)α(
n
)
t
+
O
(α(
n
)

t
-1

)

for
s
≥ 4 even, and λ
s
(
n
) ≤
n
· 2

(1/t!)α(
n
)
t
log
2
α(
n
) +
O
(α(
n
)
t
)

for
s
≥ 3 odd, where
t
= ⌊(
s
-2)/2⌋, and α(
n
) denotes the inverse Ackermann function. The previous upper bounds, by Agarwal et al. [1989], had a leading coefficient of 1 instead of 1/
t
! in the exponent. The bounds for even
s
are now tight up to lower-order terms in the exponent. These new bounds result from a small improvement on the technique of Agarwal et al.

More importantly, we also present a new technique for deriving upper bounds for λ

s

(
n
). This new technique is very similar to the one we applied to the problem of stabbing interval chains [Alon et al. 2008]. With this new technique we: (1) re-derive the upper bound of λ
3
(
n
) ≤ 2
n
α(
n
) +
O
(
n
√α(
n
)) (first shown by Klazar [1999]); (2) re-derive our own new upper bounds for general
s
and (3) obtain improved upper bounds for the generalized Davenport--Schinzel sequences considered by Adamec et al. [1992].

Regarding lower bounds, we show that λ
3
(
n
) ≥ 2
n
α(
n
) -
O
(
n
) (the previous lower bound (Sharir and Agarwal, 1995) had a coefficient of 1/2), so the coefficient 2 is tight. We also present a simpler variant of the construction of Agarwal et al. [1989] that achieves the known lower bounds of λ

s

(
n
) ≥
n
· 2

(1/
t
!) α(
n
)

t

-
O
(α(
n
)

t
-1

)

for
s
≥ 4 even.
Transitive closure logic, nested tree walking automata, and XPath
Authors: Cate Balder Ten , Segoufin Luc
Published: March 2010

We study FO(MTC), first-order logic with monadic transitive closure, a logical formalism in between FO and MSO on trees. We characterize the expressive power of FO(MTC) in terms of nested tree-walking automata. Using the latter, we show that FO(MTC) is strictly less expressive than MSO, solving an open problem. We also present a temporal logic on trees that is expressively complete for FO(MTC), in the form of an extension of the XML document navigation language XPath with two operators: the Kleene star for taking the transitive closure of path expressions, and a subtree relativisation operator, allowing one to restrict attention to a specific subtree while evaluating a subexpression. We show that the expressive power of this XPath dialect equals that of FO(MTC) for Boolean, unary and binary queries. We also investigate the complexity of the automata model as well as the XPath dialect. We show that query evaluation be done in polynomial time (combined complexity), but that emptiness (or, satisfiability) is 2ExpTime-complete.