bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of a mycoplasma isolated from infectious bovine keratoconjunctivitis: M. bovoculi sp. nov.
Authors: Langford E. V. , Leach R. H.
Published: February 2010

Two strains representative of numerous mycoplasmas isolated from the eyes of cattle with infectious bovine keratoconjunctivitis (IBK) have been characterized. On the basis of their cultural, morphological, biological, and serological properties, these and other antigenically similar strains have been classified as belonging to a new species of Mycoplasmatales for which the name Mycoplasma bovoculi has been proposed. A taxonomic description of the new species is provided. The potential significance of M. bovoculi in the etiology of IBK is currently being investigated.
Estimating the density of individual bacterial populations introduced into natural ecosystems
Authors: Danso S. K. A. , Habte M. , Alexander M.
Published: February 2010

The abundance of individual strains of Xanthomonas, Erwinia, and Rhizobium added to soil was determined by a method that allows for the enumeration of surviving cells of the introduced population in the presence of many other soil microorganisms. The method should be useful for measuring numbers of other bacteria in heterogeneous communities.
Relationship between the biosynthesis of virus-like particles and mycophenolic acid in Penicillium stoloniferum and Penicillium brevi-compactum
Authors: Detroy R. W. , Freer S. N. , Fennell D. I.
Published: February 2010

Several strains of Penicillium stoloniferum and P. brevi-compactum containing no virus-like particles (VLP) synthesize mycophenolic acid (MA), an antiviral metabolite; one strain of P. stoloniferum producing more than 600 μg VLP/g dry weight mycelia synthesized no detectable MA. However, one strain of P. brevi-compactum produced 5 μg VLP/g dry weight plus MA. Preliminary data suggest that MA may act as an antivirus in controlling fungal virus infection or its replication, or both.
Synthesis of enterotoxin B by Staphylococcus aureus strain S6 after recovery from heat injury
Authors: Collins-Thompson D. L. , Hurst A. , Kruse H.
Published: February 2010

After sublethal heat treatment of Staphylococcus aureus S6 at 52C for 15 min in either 0.1 M sodium phosphate (Na cells) or 0.1 M potassium phosphate (K cells), more than 99% of the cells were unable to grow on a medium containing 7.5% NaCl. When placed in H and K medium the survivors recovered their salt tolerance and grew after a lag of 3 h (Na cells) or 5 h (K cells). In the absence of glucose, the total amount of enterotoxin B synthesized by the Na and K cells was similar to the control cells. Addition of 0.1% glucose to the medium increased the total amount of toxin formed by Na, K, and control cells.
Studies on possible routes of ammonium assimilation in soybean root nodule bacteroids
Authors: Dunn Stanley D. , Klucas Robert V.
Published: February 2010

Glutamine amide–2-oxoglutarate aminotransferase NAD+ oxidoreductase (GOGAT), glutamine synthetase (GS), glutamate dehydrogenase (GD), and alanine dehydrogenase (AD) were studied in soybean root nodules. GS, GOGAT, and AD were present in bacteroids at levels that could account for ammonium assimilation, but GD activity was quite low. The total activities of GS and GD were higher in the cytosol than in the bacteroids by factors of 20 and 7, respectively, whereas GOGAT was not detected in the cytosol. GS (transferase activity) was inhibited by alanine, CTP, glycine, and tryptophan at 5 mM but was relatively unaffected by asparagine, aspartic acid, CMP, glucosamine, and histidine at 5 mM. GOGAT activity was unaffected by ATP, ADP, 8-hydroxyquinoline, and 1,10-phenanthroline but was inhibited by EDTA, citrate, and parachloromercuribenzoate. GOGAT activity (reductive amination) was also inhibited 97% by preincubation with 10−4 M azaserine for 30 min but GD activity was inhibited only 13%. The apparent Km values for NH4+ by AD was 7.4 × 10−3 M and by GD was 7.3 × 10−2 M while for glutamine by GOGAT it was 9.3 × 10−5 M. Activities and kinetic properties for these enzymes may suggest potential routes of nitrogen assimilation in vivo.
The ultrastructure of Geotrichum candidum hyphae
Authors: Steele S. D. , Fraser T. W.
Published: February 2010

Complete septa divide the hyphae of Geotrichum candidum into many compartments or cells. Two cell types are readily recognizable, (i) the apical cell, delimited by one septum and the surrounding cell wall, and (ii) the sub- or non-apical cell, delimited by two septa and the surrounding cell wall. Vacuolation of the apical cells is slight compared with that of subapical cells. Apical cells contain many vesicles, some of which are elongated and branched, possibly forming an interconnecting tubular network; other vesicles were observed distributed about the apical zone or aggregated to form an apical body (the Spitzenkörper). Vesicles are also evident in subapical cells, but only in association with developing septa. Golgi bodies were not observed in any cells, their function in vesicle production possibly being taken by a modification of part of the endoplasmic reticulum. Both cell types contained mitochondria with contrasting electron-staining properties. Some stages of mitosis were observed. The nucleus appears to retain its envelope throughout division and exhibits intranuclear microtubules attached to spindle plaques. Septa were formed by a centripetal deposition of wall material, plasmodesmata developing during this process. Another deposition of wall material occurs after the centripetal deposition thus allowing a secondary thickening of the septum to take place.
Influence of phenethyl alcohol and other organic solvents on cellulase production
Authors: Stranks D. W.
Published: February 2010

Phenethyl alcohol and some other specific solvents enhanced the production of cellulase by several fungi when added to culture growth media in minimal amounts. This solvent effect is considered to be cytoplasmic membrane-oriented. Cellulase synthesis possibly occurs in the same region of the cell.
EFFICIENT TESTING OF FORECASTS
Authors: CHANG CHING-LUEH , LYUU YUH-DAUH
Published: February 2010

Each day a weather forecaster predicts a probability for each type of weather for the next day. After n days, all the predicted probabilities and the real weather data are sent to a test which decides whether to accept the forecaster as having prior knowledge about the distribution of nature. Consider tests that accept with high probability forecasters who know the distribution of nature. Sandroni shows that any such test can be passed with high probability by a forecaster who has no prior knowledge about the distribution of nature, provided that the duration n is revealed to the forecaster in advance [14]. However, Fortnow and Vohra show that Sandroni's result requires forecasters with high computational complexity [6]. Consider the family [Formula: see text] of forecasters who select a deterministic Turing-machine forecaster according to an arbitrary distribution and then use that machine for all future forecasts. We show that Sandroni's result requires forecasters even more powerful than those in [Formula: see text]. We also show that Sandroni's result does not apply when the duration n is not revealed to the forecaster in advance.
CONSTRUCTING MULTIPLE INDEPENDENT SPANNING TREES ON RECURSIVE CIRCULANT GRAPHS G(2m, 2)
Authors: YANG JINN-SHYONG , CHANG JOU-MING , TANG SHYUE-MING , WANG YUE-LI
Published: February 2010

A recursive circulant graph G(N,d) has N = cdm vertices labeled from 0 to N - 1, where d ⩾ 2, m ⩾ 1, and 1 ⩽ c < d, and two vertices x,y ∈ G(N,d) are adjacent if and only if there is an integer k with 0 ⩽ k ⩽ ⌈ log d N⌉ - 1 such that x ± dk ≡ y ( mod N). With the aid of recursive structure, such class of graphs has many attractive features and was considered as a topology of interconnection networks for computing systems. The design of multiple independent spanning trees (ISTs) has many applications in network communication. For instance, it is useful for fault-tolerant broadcasting and secure message distribution. In the previous work of Yang et al. (2009), we provided a constructing scheme to build k ISTs on G(cdm,d) with d ⩾ 3, where k is the connectivity of G(cdm,d). However, the proposed constructing rules cannot be applied to the case of d = 2. For the integrity of solving the IST problem on recursive circulant graphs, this paper deals with the case of G(2m,2) using a set of different constructing rules. Especially, we show that the heights of ISTs for G(2m,2) are lower than the known optimal construction of hypercubes with the same number of vertices.
SELF HEALING COMPOSITE FOR AIRCRAFT'S STRUCTURAL APPLICATION
Authors: TEOH S.H. , CHIA H.Y. , LEE M.S. , NASYITAH A.J.N. , LUQMAN H.B.S.M. , NURHIDAYAH S. , TAN WILLY. C.K.
Published: February 2010

When one cuts himself, it is amazing to watch how quickly the body acts to mend the wound. Immediately, the body works to pull the skin around the cut back together. The concept of repair by bleeding of enclosed functional agents serves as the biomimetic inspiration of synthetic self repair systems. Such synthetic self repair systems are based on advancement in polymeric materials; the process of human thrombosis is the inspiration for the application of self healing fibres within the composite materials. Results based on flexural 3 point bend test on the prepared samples have shown that the doubled layer healed hollow fibre laminate subjected to a healing regime of 3 weeks has a healed strength increase of 27% compared to the damaged baseline laminate. These results gave us confidence that there is a great potential to adopt such self healing mechanism on actual composite parts like in aircraft's composite structures.
EFFECTS OF PLASTIC ANISOTROPY AND HARDENING ON INDENTATION MODULUS OF THIN FILMS
Authors: KALKHORAN SALMON M. , CHOLLACOOP NUWONG , GOULDSTONE ANDREW
Published: February 2010

In this study we have modeled the Berkovich indentation response of elastic-plastic thin films on elastic-plastic substrates, the modulus of film and substrate being equivalent, using FEM. The stimulus for this investigation was experimental indentation data of rapidly quenched nickel thin films on stainless steel substrates, for which depth-dependent, significantly low (>50% decrease) moduli were extracted via the Oliver-Pharr method. This was notable because both film and substrate had the same elastic modulus. Previous studies showed that differences in plastic behavior could elicit such a modulus drop, for extremely hard films on substrates. In this study, we performed further FEM models to explore the modulus decrease, using aspects of continuum plastic behavior that could be hypothesized from microstructural observations. Specifically, we used plastic anisotropy and significant delayed hardening that would be expected from the nano-scale, highly columnar grain structure as input, and results showed a significant modulus decrease for reasonable values of hardness.
SURPRISING SIMPLICITY OF $\mathcal{N}=8$ SUPERGRAVITY
Authors: BJERRUM-BOHR N. E. J. , VANHOVE PIERRE
Published: February 2010

Gravity amplitudes are, via the Kawai–Lewellen–Tye relations intimately linked to products of Yang–Mills amplitudes. Explicitly, this shows up in computations of [Formula: see text] supergravity where the perturbative expansion and ultraviolet behavior of this theory is akin to [Formula: see text] super-Yang–Mills at least through three loops. Full persistence to all loop orders would be truly remarkable and imply finiteness of [Formula: see text] supergravity in four dimensions.
HORIZONS IN MATTER: BLACK HOLE HAIR VERSUS NULL BIG BANG
Authors: BRONNIKOV K. A. , ZASLAVSKII OLEG B.
Published: February 2010

It is shown that only particular kinds of matter (in terms of the "radial" pressure-to-density ratio w) can coexist with Killing horizons in black hole or cosmological space–times. Thus, for arbitrary (not necessarily spherically symmetric) static black holes, admissible are vacuum matter (w = −1, i.e. the cosmological constant or its generalization with the same value of w) and matter with certain values of w between 0 and −1, in particular a gas of disordered cosmic strings (w = −1/3). If the cosmological evolution starts from a horizon (the so-called null big bang scenarios), this horizon can coexist with vacuum matter and certain kinds of phantom matter with w ≤ −3. It is concluded that normal matter in such scenarios is entirely created from vacuum.
SIMPLE OBSERVATIONS CONCERNING BLACK HOLES AND PROBABILITY
Authors: HEGYI SÁNDOR
Published: February 2010

What is common to a black hole and a bell-shaped curve? The question does not seem to make much sense but it is argued that black holes and the limit distributions of probability theory share several properties when their entropy and information content are compared. In particular, the no-hair theorem, the entropy maximization and holographic bound, and the quantization of entropy of black holes have their respective analogs for stable limit distributions. This observation suggests that the central limit theorem can play a fundamental role in black hole statistical mechanics and in a possibly emergent nature of gravity.
THE BIG BANG AS THE ULTIMATE TRAFFIC JAM
Authors: JEJJALA VISHNU , KAVIC MICHAEL , MINIC DJORDJE , TZE CHIA-HSIUNG
Published: February 2010

We present a novel solution to the nature and formation of the initial state of the Universe. It derives from the physics of a generally covariant extension of matrix theory. We focus on the dynamical state space of this background-independent quantum theory of gravity and matter — an infinite-dimensional, complex, nonlinear Grassmannian. When this space is endowed with a Fubini–Study-like metric, the associated geodesic distance between any two of its points is zero. This striking mathematical result translates into a physical description of a hot, zero-entropy Big Bang. The latter is then seen as a far-from-equilibrium, large-fluctuation-driven, metastable ordered transition — a "freezing by heating" jamming transition. Moreover, the subsequent unjamming transition could provide a mechanism for inflation while rejamming may model a Big Crunch, the final state of gravitational collapse.
HOW FAST CAN A BLACK HOLE RELEASE ITS INFORMATION?
Authors: MATHUR SAMIR D.
Published: February 2010

When a shell collapses through its horizon, semiclassical physics suggests that information cannot escape from this horizon. One might hope that nonperturbative quantum gravity effects will change this situation and avoid the information paradox. We note that string theory has provided a set of states over which the wave function of the shell can spread, and that the number of these states is large enough that such a spreading would significantly modify the classically expected evolution. In this article we perform a simple estimate of the spreading time, showing that it is much shorter than the Hawking evaporation time for the hole. Thus information can emerge from the hole through the relaxation of the shell state into a linear combination of fuzzballs.
MODIFYING GRAVITY IN THE INFRARED BY IMPOSING AN "ULTRASTRONG" EQUIVALENCE PRINCIPLE
Authors: PIAZZA FEDERICO
Published: February 2010

The equivalence principle suggests considering gravity as an infrared phenomenon, whose effects are visible only outside Einstein's free-falling elevator. By curving space–time, general relativity leaves the smallest systems free of classical gravitational effects. However, according to the standard semiclassical treatment, indirect effects of gravity can be experienced inside the elevator through the well-known mechanism of quantum particle production. Here we try a different path than the one historically followed: rather than imposing field quantization on top of a curved manifold, we attempt to upgrade the equivalence principle and extend it to the quantum phenomena. Therefore, we consider, and try to realize in a theoretical framework, a stronger version of the equivalence principle, in which all the effects of gravity are definitely banned from the elevator and confined to the infrared. For this purpose, we introduce infrared modified commutation relations for the global field operators (Fourier modes) that allow us to reabsorb the time-dependent quadratic divergence of the vacuum expectation value of the stress–energy tensor. The proposed modification is effective on length scales comparable to the inverse curvature and, therefore, does not add any dimensional parameter to the theory.
CURVATURE, PHASE SPACE, HOLOGRAPHY AND BLACK HOLE ENTROPY
Authors: SIVARAM C. , ARUN KENATH
Published: February 2010

This paper discusses the thermodynamics of a black hole with respect to Hawking radiation and the entropy. We look at a unified picture of black hole entropy and curvature and how this can lead to the usual black hole luminosity due to Hawking radiation. It is also shown how the volume inside the horizon, apart from the surface area (hologram!), can play a role in understanding the Hawking flux. In addition, holography implies a phase space associated with the interior volume and this happens to be just a quantum of phase space, filled with just one photon. The generalized uncertainty principle can be incorporated in this analysis. These results hold for all black hole masses in any dimension.
THE GRAVITATIONAL ORIGIN OF THE DISTINCTION BETWEEN SPACE AND TIME
Authors: YAHALOM ASHER
Published: February 2010

To the ordinary human it is obvious that there is a clear distinction between the spatial dimensions, in which one can go either way, and the temporal dimension, in which one seems only to move forward. But the uniqueness of time is also rooted in the standard presentation of general relativity, in which the metric of space–time is locally Lorentzian, i.e. ημν = diag (1, -1, -1, -1). This is presented as an independent axiom of the theory, which cannot be deduced. In this essay I will claim otherwise. I will show that the existence of time should not be enforced on the gravitational theory of general relativity but rather should be deduced from it. The method of choice is linear stability analysis of flat space–times.
INSTABILITY OF THE BLACK HOLE HORIZON WITH RESPECT TO ELECTROMAGNETIC EXCITATIONS
Authors: BURINSKII ALEXANDER
Published: February 2010

Analyzing exact solutions to the Einstein–Maxwell equations in the Kerr–Schild formalism, we show that the black hole horizon is unstable with respect to electromagnetic excitations. Contrary to perturbative smooth harmonic solutions, the exact solutions for electromagnetic excitations on the Kerr background are accompanied by singular beams which have very strong back-reaction to the metric and break the horizon, forming the holes which allow radiation to escape from the interior of the black hole. As a result, even the weak vacuum fluctuations break the horizon topologically, covering it by a set of fluctuating microholes. We conclude with a series of nontrivial consequences, one of which is that there is no information loss inside of the black hole.
ON VACUUM DENSITY, THE INITIAL SINGULARITY AND DARK ENERGY
Authors: CARNEIRO SAULO , TAVAKOL REZA
Published: February 2010

Standard cosmology poses a number of important questions. Apart from its singular origin, it possesses early and late accelerating phases required to account for observations. The vacuum energy has been considered as a possible way to resolve some of these questions. The vacuum energy density induced by free fields in an early de Sitter phase has earlier been estimated to be proportional to H4, while more recently it has been suggested that the QCD condensate induces a term proportional to H at late times. These results have been employed in models which are nonsingular and inflationary at early times and accelerating at late times. Here we cast these models in terms of scalar fields and study the corresponding spectrum of primordial perturbations. At early times the spectrum is found to be not scale-invariant, thus implying that slow roll inflation is still required after the phase transition induced by the vacuum. At late times the corresponding scalar field potential is harmonic, with a mass of the order of the Hubble scale — a result that may be understood in the light of the holographic conjecture.
GRAVITATION, THERMODYNAMICS, AND THE BOUND ON VISCOSITY
Authors: HOD SHAHAR
Published: February 2010

The anti-de Sitter/conformal field theory (AdS/CFT) correspondence implies that small perturbations of a black hole correspond to small deviations from thermodynamic equilibrium in a dual field theory. For gauge theories with an Einstein gravity dual, the AdS/CFT correspondence predicts a universal value for the ratio of the shear viscosity to the entropy density, η/s = 1/4π. It was conjectured recently that all fluids conform to the lower bound: η/s ≥ 1/4π. This conjectured bound has been the focus of much recent attention. However, despite the flurry of research in this field we still lack a proof for the general validity of the bound. In this essay we show that this mysterious bound is actually a direct outcome of the interplay between gravity, quantum theory, and thermodynamics.
INFLATION, QUANTUM FIELDS, AND CMB ANISOTROPIES
Authors: AGULLÓ IVÁN , NAVARRO-SALAS JOSÉ , OLMO GONZALO J. , PARKER LEONARD
Published: February 2010

Inflationary cosmology has proven to be the most successful at predicting the properties of the anisotropies observed in the cosmic microwave background (CMB). In this essay we show that quantum field renormalization significantly influences the generation of primordial perturbations and hence the expected measurable imprint of cosmological inflation on the CMB. However, the new predictions remain in agreement with observation, and in fact favor the simplest forms of inflation. In the near future, observations of the influence of gravitational waves from the early universe on the CMB will test our new predictions.
SIGNATURES OF AN EMERGENT GRAVITY FROM BLACK HOLE ENTROPY
Authors: VAZ CENALO
Published: February 2010

The existence of a thermodynamic description of horizons indicates that space–time has a microstructure. While the "fundamental" degrees of freedom remain elusive, quantizing Einstein's gravity provides some clues about their properties. A quantum AdS black hole possesses an equispaced mass spectrum, independent of Newton's constant, G, when its horizon radius is large compared to the AdS length. Moreover, the black hole's thermodynamics in this limit is inextricably connected with its thermodynamics in the opposite (Schwarzschild) limit by a duality of the Bose partition function. G, absent in the mass spectrum, re-emerges in the thermodynamic description through the Schwarzschild limit, which should be viewed as a natural "ground state." It seems that the Hawking–Page phase transition separates fundamental, "particle-like" degrees of freedom from effective, "geometric" ones.
ON THE GLOBAL EXISTENCE OF TIME
Authors: MINGUZZI E.
Published: February 2010

The global existence of time is often taken for granted but should instead be considered for investigation. Using the tools of global Lorentzian geometry the author shows that, under physically reasonable conditions, the impossibility of finding a global time implies the singularity of space–time.
SPECTRAL SENSITIVITY DESIGN FOR OPTICAL SENSORS
Authors: HEIDARY KAVEH , CAULFIELD H. JOHN
Published: February 2010

Artificial Color is the use of technology to emulate the basic means by which animals acquire and use spectral information. It begins with sensing of the scene using multiple broad and overlapping spectral sensitivity functions analogous with cone cells in the human visual system. In this paper we develop an algorithm to obtain a set of near-optimal application-specific spectral sensitivity functions for Artificial Color systems. The user-designed sensitivity functions result in concurrent good intra-class packing and interclass integrity in the color space for reflectance classes with known statistics. This method leads to improved color discrimination and results in more robust spectral classifiers.
DETECTION OF BLOOD VESSELS IN RETINAL IMAGES
Authors: JLASSI HEJER , HAMROUNI KAMEL
Published: February 2010

This paper presents a method to segment blood vessels in retinal images. It is based on mathematical morphology and the anisotropic diffusion and is composed of four steps: image processing by using linear filter and morphological ones, details extraction by using top-hat transform, morphological reconstruction of vascular tree and post processing steps using anisotropic diffusion. Our method is tested on red-free retinal images, taken from two public database. Our results on both public databases were comparable in performance with other authors. The method achieves a good result by mean of the "receiver operating characteristic curve" (ROC). The results show that our method is significantly better than other rule-based methods.
ON THE EVALUATION OF PROGRESSIVE POINT-SAMPLED GEOMETRY
Authors: LIU YONG-JIN
Published: February 2010

Nowadays, point set surfaces have attracted much research attention due to the widespread laser range scanners. In this paper we evaluate several well known methods in terms of progressive point-sampled geometry. The selection of these methods is based on a classification of different surface representations. To serve as a common basis for comparison, a general progressive framework is adopted. The comparison has been done with both data from graphics and CAD models. In addition to surface reconstruction quality and time and space efficiency, several other properties inherent in point sampled geometry, such as sharp feature preservation and data density uniformness, are also considered in the evaluation of progressive geometry.
A NEW PLOT/CHARACTER-BASED INTERACTIVE SYSTEM FOR STORY-BASED VIRTUAL REALITY APPLICATIONS
Authors: ABD EL-SATTAR HUSSEIN KARAM HUSSEIN
Published: February 2010

Building interactive storytelling systems has been a growing topic of research over the past decade. Prior research has identified key problems, such as the trade-off between interactivity and storytelling, the duality between character and plot, narrative causality, the problem of narrative control, the relations between story generation and presentation, and the tools that artists can use to create interactive story worlds. Due to the tradeoff between narrative progression and user interaction, striking a balance between the two is a big challenge. Therefore, there is a need to develop an integrated framework to achieve the balance between conveying a story and enhancing the modeling of character behaviors. This paper attempts to address these problems, in particular, the relations between character and plot by modeling not only the story plot but also the character behavior in a unified smart user-friendly graphical user interface (GUI) platform called Bcreative. The idea is derived from the study of linear logic, Petri nets (PN) and cinematography in interactive storytelling. The system structure is composed of two engines: a story engine and a character engine. The story engine models the story plot based on linear logic and the PN as an operational model, while the character engine enhances the modeling of character behavior based on filmmaking theory. This paper discusses the development process of our proposed system, illustrating the design and implementation in detail. Comparisons with existing techniques are included, and the advantages of our proposed system over existing ones are examined. Evaluation and practical performance results are also demonstrated.
QUANTUM CALCULATION OF PROTEIN SOLVATION AND PROTEIN–LIGAND BINDING FREE ENERGY FOR HIV-1 PROTEASE/WATER COMPLEX
Authors: TONG YAN , MEI YE , ZHANG JOHN Z. H. , DUAN LI L. , ZHANG QING-GANG
Published: February 2010

HIV-1 protease (PR) is a primary target for anti-HIV therapeutics. A well conserved water molecule, denoted as W301, is found in almost all the crystallographic structures of PR/inhibitor complexes and it plays an important role in PR/inhibitor binding. As the PR/inhibitor interaction depends on the ionization state of the cleavage site which contains an aspartyl dyad (Asp25/Asp25′), the determination of the protonation states of aspartyl dyad in PR may be essential for drug design. In this study, a linear scaling quantum mechanical method, molecular fragmentation with conjugate caps (MFCC), is used for interaction study of PR/ABT-538 and W301 at four different monoprotonation states of the Asp25/Asp25′. Combined method of MFCC and conductor-like polarizable continuum model (CPCM) is applied in binding affinity calculation for four minimum energy structures which are extracted from four different molecular dynamics trajectories corresponding to four different monoprotonation states of Asp25/Asp25′. Our result is in good agreement with previous result obtained by FEP/TI method, showing that the conserved W301 contributes significantly to the binding free energy of PR/ABT-538 complex and different protonation states of Asp25/Asp25′ have significant impact on the binding free energy contribution from W301.
EFFECT OF ENVIRONMENT ON SUPEREXCHANGE ELECTRON TRANSFER IN A MULTIPLE BRIDGED DONOR–ACCEPTOR SYSTEM
Authors: CHU XIUMEI , ZHAO YI
Published: February 2010

Electron transfer dynamics in donor–bridge–acceptor (DBA) systems under dissipative environment is investigated by using the quasi-adiabatic propagator path integral approach. The dephasing and relaxation rates are extracted from the Fourier transform of the time-dependent population difference of the donor and the acceptor states. Comparing the rates obtained from the DBA and the effective two state systems, respectively, we reveal the validity of the superexchange mechanism. It is found that the coupling of the environment to the bridges does not affect the superexchange rates for the bridges having high enough electronic energies, and the superexchange mechanism still works quite well even though the population on the bridges is over than 0.2 in a tested system.
MOLECULAR DYNAMICS SIMULATION OF POINT MUTATIONS OF ARG 221 IN THE ACTIVE SITE OF PROTEIN TYROSINE PHOSPHATASE 1B
Authors: LIU MENGYUAN , XU WEIREN , WANG RUNLING , LIU XUYUAN , LIU PENG , TANG LIDA , CHENG XIANCHAO , ZHOU HUI , HU XIAO , LIU BING
Published: February 2010

Protein tyrosine phosphatase 1B (PTP1B) is one of the important regulators of signal transduction pathways. The present study aims to investigate the effect of Arg 221 on the active site of PTP1B. Six mutants were carried out using Schrödinger Suite 2007 and molecular dynamics simulation was performed by using the Tinker package. Results show that point mutations at position 221 have great influence on shape of active site, backbone movement of active site, and interaction between substrate and PTP1B. R221H and R221K lead to increased total interaction energies. R221G, R221F and R221T cause increase in total interaction energies, but decrease in interaction energies between pTyr 4 and P loop (catalytic residues). R221E results in both decreased total interaction energies and interaction energies between pTyr 4 and P loop. This indicates that Arg 221 mutated to basic residues can lead to enhanced binding affinity between substrate and protein; when mutated to acidic residues it will decrease binding affinity and catalytic activity; other kinds of mutations result in increased binding affinity but decreased catalytic activity.
EFFECTS OF ROTATIONAL AND VIBRATIONAL EXCITATION ON THE STEREODYNAMICS OF THE O (D-1) + HCl → OH + Cl REACTION
Authors: WEI QIANG , WU VICTOR WEI-KEH , ZHOU BO
Published: February 2010

The stereodynamics of the title reaction on the ground 1 1A′ potential energy surface (PES) has been studied using quasi-classical trajectory (QCT) method. Collision energy of 6.4 kcal/mol is considered, and vector properties including angular momentum alignment distributions and polarization-dependent differential cross-sections (PDDCS) of the product OH are presented. Furthermore, the influence of reagent rotational excitation and vibrational excitation on the product vector properties has also been studied in the present work. The results indicate that the distribution of the P(θr) and P(ϕr) are sensitively affected by the rotational and vibrational excitation. The rotational excitation decreases the degree of alignment and orientation, while vibrational excitation increases the degree of alignment and orientation. The PDDCS (2π/σ)(dσ20/dωt) and (2π/σ)(dσ22+/dωt) are sensitively influenced by rotational and vibrational excitations, while the PDDCS ((2π/σ)(dσ00/dωt)) and (2π/σ)(dσ21-/dωt) are not. The preference of forward scattering has been found from the results of PDDCS ((2π/σ)(dσ00/dωt)), which is in good agreement with the experimental results.
SINGLET METHYLENE AND HALOCARBENES INSERTIONS INTO POLAR N–H BONDS OF AMINES
Authors: RAMASAMI K. , RAMALINGAM M. , VENUVANALINGAM P.
Published: February 2010

The insertion of singlet 1CH2 , 1CHF , and 1CF2 into polar N–H bonds of RNH2 ( R = –CH3, –C2H5, –C3H7 or –CH(CH3)2 ) has been investigated at HF, MP2, and DFT levels using 6-31g (d, p) basis set. The insertions proceed via a two-step mechanism. The potential energy surface exploration identifies an ylide formation followed by the 1,2-proton shift concertedly giving the secondary amine. The barrier height varies with the type of carbene and amine. HOMO of amines and LUMO of carbenes control the initial interactions and it is confirmed by NBO charge analysis.
THEORETICAL STUDY OF ABOVE THRESHOLD DISSOCIATION OF HD+ IN FEMTOSECOND LASER FIELDS
Authors: YUAN KAI-JUN , LIU ZHENG-TANG , YU JIE , CHEN MAO-DU , CONG SHU-LIN
Published: February 2010

The above threshold dissociation (ATD) of the HD+ molecular ion in a linearly polarized femtosecond laser field is theoretically studied using three-dimensional time-dependent quantum wave packet method. Based on the Born–Oppenheimer approximation (BOA), calculations are performed on two electronic states, the ground state 1sσ and the excited state 2pσ. The energy-dependent distributions of the dissociated fragments, resulting from the ATD, are calculated by using an asymptotic-flow expression in the momentum space. The numerical results demonstrate that, in the laser field of wavelength λ = 800 nm and full-width at half-maximum (FWHM) τ = 30 fs , only two-photon dissociation is observable at a weaker pulse peak intensity, 5.0 × 1012 W cm -2, while at an intense intensity, 1.5 × 1015 W cm -2, the dissociated fragments resulting from four-photon absorption dominates over the photodissociation process. These results are consistent with the experimental observation of Orr et al. [Orr PA et al., Phys Rev Lett98:163001, 2007]. The ac Stark-shift caused by intense laser field will change the kinetic energies of the fragments. The ATD phenomena are quantitatively interpreted in terms of the concept of light-induced potential. The molecular rotation and alignment have some effects on the kinetic energy spectrum of the dissociated fragments. The molecular rotation reduces the ac Stark-shift and broadens the peaks of kinetic energy spectra of the dissociated fragments. However, the intense laser field can effectively align the molecule and is helpful to increase the ATD probability. The ATD spectrum is related to the initial quantum numbers J0 and M0 of the molecule. The ATD spectrum of HD+ is calculated at a limited thermal temperature.
ENERGETICS AND STRUCTURAL INSIGHTS OF MOLECULAR CONDUCTORS USING DENSITY FUNCTIONAL THEORY METHODS: 1,3-DITHIOLE-2-THIONE, 1,3-DITHIOLE-2-ONE, 1,3-DIOXOLE-2-ONE, AND 1,3-DIOXOLE-2-THIONE
Authors: PRASAD R. L. , KUSHWAHA A. , PRASAD RAJENDRA , JAISWAL S. , YADAV R. A.
Published: February 2010

Computations were carried out employing the restricted Hartree–Fock (RHF) and density functional theory (DFT) methods to investigate the geometries and energies for the 1,3-dithiole-2-thione (DTT), 1,3-dithiole-2-one (DTO), 1,3-dioxole-2-thione (DOT), and 1,3-dioxole-2-one (DOO) molecules and their radical cations. The geometrical parameters of all the four molecules suggest a finite extent of extended conjugation across the molecules. The radical cations of the DTT and DOT molecules exhibit increased extent of conjugation compared to their neutral analogues. However, on going from the neutral DOO and DTO molecules to their radical cations, the extent of conjugation across the ions decreases and two unsaturated sites become isolated from each other. Requirement of the relaxation energy for the formation of radical cation is much lower for the DTT and DOT molecules compared to that for the DOO and DTO molecules. Smaller relaxation energy requirement favors minimal resistance to charge transport along the molecular stacking. Therefore, it is speculated that the DTT and DOT molecules are better molecular conductors as compared to the DOO and DTO molecules.
SPECTRAL VS. STATISTIC APPROACH OF STRUCTURE–ACTIVITY RELATIONSHIP. APPLICATION ON ECOTOXICITY OF ALIPHATIC AMINES
Authors: PUTZ MIHAI V. , PUTZ ANA-MARIA , LAZEA MARIUS , CHIRIAC ADRIAN
Published: February 2010

In the context of quantitative structure–activity relationship (QSAR) studies the traditional statistical indices, i.e. simple correlation factor, standard error of estimates, as well as t-Student and Fisher's tests are challenged against the algebraic spectral description of the multi-linear models. While the new correlation approach is built on the algebraic (Euclidian) norms and on the associate correlation factor, the validation and predictive features are assured throughout so-called "ergodic" least action principle across the investigated models. The reliability of the present proposed spectral respecting statistical QSAR analysis is evaluated on modeling the aliphatic amines' ecotoxicity by means of hydrophobicity, polarizability, and total energy structural parameters resulting in better prediction of molecular hierarchy of observed bioactivity being susceptible to such general behavior.
QUASICLASSICAL TRAJECTORY STUDY OF THE STEREODYNAMICS FOR THE REACTION D+ + H2 (ν=0, j = 0) → HD + H+
Authors: ZHANG WENQIN , CHEN MAODU
Published: February 2010

The vector correlations between products and reactants for the reactive noncharge transfer ion–molecule collisions D + + H 2 (ν=0, j = 0)→ HD + H + have been determined by means of the quasiclassical trajectory method on the ground state in the KBNN potential energy surface (J Chem Phys116:654, 2002) at collision energies of 0.224, 0.524, 0.824, and 1.024 eV. The calculated differential cross section (DCS) results indicate that the lifetime of the complex [Formula: see text] in the deep well on the ground PES becomes shorter as collision energy increases. The existence of long-lived complex leads to a weak product rotational polarization at a low collision energy of 0.224 eV. However, the product rotational angular momentum j′ aligns and orients preferentially along the positive direction of the y-axis at a high collision energy of 1.024 eV. The distribution of P(θr, ϕr) indicates that the product molecules are preferentially polarized perpendicular to the scattering plane and that the reaction is dominated by an in-plane mechanism.
Carrier Relaxation in InAs/InGaAs Dots-in-a-Well Structures
Authors: Chen Rui , Liu Hui-Yun , Sun Han-Dong
Published: February 2010

We report on the mechanism of electronic structure and different carrier relaxation processes in InAs/In
x
Ga1-x
As dots-in-a-well (DWELL) structure investigated by comprehensive spectroscopic characterization. Selectively excited photoluminescence and photoluminescence excitation analyses reveal that when excited at different photon energies, carriers relax to the ground state of the quantum dots by distinct schemes. Our investigation clearly manifests the roles of longitudinal optical phonons and absorption continuum states played in the carrier relaxation process in DWELL structures.
The Application of SVMs Method on Exchange Rates Fluctuation
Authors: Zhang Zuoquan , Zhao Qin
Published: February 2010

Technical indicators are very important tools in the analysis of securities investment. In this paper, considering several main technical indicators prevailed in China security market, we predict whether the price of a stock rises or falls with the support vector machines (SVMs). We represent the technical indicators of current four days as input vector. If the price of next day rises, we say that the vector belongs to opposite set, if it falls, we say it belongs to negative set. Studying the samples, the SVMs construct a classification model. Then, based on the data of today and three days before, the SVMs give a prediction of tomorrow price. The experiment shows that the predicting accuracy is all greater than 60%.
Size-Dependent Indirect Excitation of Trivalent Er Ions via Si Nanocrystals Embedded in a Silicon-Rich Silicon Oxide Matrix Deposited by ECR-PECVD
Authors: Zatryb G. , Podhorodecki A. , Misiewicz J. , Wojcik J. , Mascher P.
Published: February 2010

Silicon nanocrystals (Si-nc) embedded in a silicon-rich silicon oxide matrix codoped withEr3+ions have been fabricated by electron-cyclotron plasma-enhanced chemical vapor deposition. Indirect excitation of erbium photoluminescence via silicon nanocrystals has been obtained within a broad pump wavelength range. The influence of different nanocrystal sizes on the excitation transfer from the Si-nc toEr3+ions is discussed.
DSC Study of Collagen in Disc Disease
Authors: Skrzyński S. , Sionkowska A. , Marciniak A.
Published: February 2010

Differential scanning calorimetry (DSC) has been used to estimate the effect of disc disease on the collagen helix-coil transition and morphology for tissue extracted from patients during surgical operation. Forty discs were obtained from patients with degenerative disc disease undergoing surgery for low back pain. The patients were in the age between 20 and 70 years old. The specimens were kept wet during DSC experiment. The data allow the comparison between thermal stability of collagen tissue from healthy patients and from patients suffering from disc disease. In the paper the comparison between thermal helix-coil transition for collagen fibers from patients suffering from disc disease and collagen fibers from healthy organisms has been discussed. The heating rate has an influence on the position on denaturation temperatures of collagen in disc tissues. Higher helix-coil transition temperature of collagen in degenerated disc suggests that additional intermolecular cross linking of collagen fibers occurs. Denaturation temperatures of collagen in degenerated male disc possess smaller values than in female ones. Disc disease induces changes in collagen structure and leads to formation of additional crosslinks between collagen fibers.
Impact of Bee Species and Plant Density on Alfalfa Pollination and Potential for Gene Flow
Authors: Brunet Johanne , Stewart Christy M.
Published: February 2010

In outcrossing crops like alfalfa, various bee species can contribute to pollination and gene flow in seed production fields. With the increasing use of transgenic crops, it becomes important to determine the role of these distinct pollinators on alfalfa pollination and gene flow. The current study examines the relative contribution of honeybees, three bumble bee species, and three solitary bee species to pollination and gene flow in alfalfa. Two wild solitary bee species and one wild bumble bee species were best at tripping flowers, while the two managed pollinators commonly used in alfalfa seed production, honeybees and leaf cutting bees, had the lowest tripping rate. Honeybees had the greatest potential for gene flow and risk of transgene escape relative to the other pollinators. For honeybees, gene flow and risk of transgene escape were not affected by plant density although for the three bumble bee species gene flow and risk of transgene escape were the greatest in high-density fields.
Convergence of Inexact Iterative Schemes for Nonexpansive Set-Valued Mappings
Authors: Reich Simeon , Zaslavski AlexanderJ
Published: February 2010

Taking into account possibly inexact data, we study iterative schemes for approximating fixed points and attractors of contractive and nonexpansive set-valued mappings, respectively. More precisely, we are concerned with the existence of convergent trajectories of nonstationary dynamical systems induced by approximations of a given set-valued mapping.
Macrophage Migration Inhibitory Factor: Critical Role in Obesity, Insulin Resistance, and Associated Comorbidities
Authors: Kleemann Robert , Bucala Richard
Published: February 2010

Obesity is associated with insulin resistance, disturbed glucose homeostasis, low grade inflammation, and comorbidities such as type 2 diabetes and cardiovascular disease. The cytokine macrophage migration inhibitory factor (MIF) is an ubiquitously expressed protein that plays a crucial role in many inflammatory and autoimmune disorders. Increasing evidence suggests that MIF also controls metabolic and inflammatory processes underlying the development of metabolic pathologies associated with obesity. This is a comprehensive summary of our current knowledge on the role of MIF in obesity and obesity-associated comorbidities, based on human clinical data as well as animal models of disease.
Trade-Off between Foraging Activity and Infestation by Nest Parasites in the Primitively Eusocial BeeHalictus scabiosae
Authors: Lienhard Andrea , Mirwald Lea , Hötzl Thomas , Kranner Ilse , Kastberger Gerald
Published: February 2010

Diurnal activities ofHalictus scabiosaebees and their nest parasites (major bee-flies, cuckoo wasps, ichneumon wasps,Sphecodesbees, and velvet ants) were investigated at a study site with 159 nests in Eastern Austria. Foraging activity correlated with ambient temperature only before midday and decreased in the afternoon. The activity of nest-infesting parasites increased during the day and correlated with ambient temperature. The match factorfmbetween the ratios of the foraging activities ofH. scabiosaeand the ratios of aspects of morning temperature was assessed on three consecutive days with different weather. The activity patterns of halictine bees and their nest parasites differed: the parasites exhibited only small time windows in which their activities were synchronised with those of their hosts. The bees exhibited an anticyclic behaviour and collected food in times of low parasite pressure and decreased foraging activity when parasite pressure increased.
Systematic Error in Gas Chromatography-Mass Spectrometry–Based Quantification of Hydrolyzed Urinary Steroids
Authors: Moon Ju-Yeon , Ha Young Wan , Moon Myeong Hee , Chung Bong Chul , Choi Man Ho
Published: February 2010

Gas chromatography-mass spectrometry–based metabolite profiling can lead to an understanding of various disease mechanisms as well as to identifying new diagnostic biomarkers by comparing the metabolites related in quantification. However, the unexpected transformation of urinary steroids during enzymatic hydrolysis with Helix pomatia could result in an underestimation or overestimation of their concentrations. A comparison of β-glucurondase extracted from Escherichia coli revealed 18 conversions of 84 steroids tested as an unexpected transformation under hydrolysis with β-glucuronidase/arylsulfatase extracted from Helix pomatia. In addition to the conversion of 3β-hydroxy-5-ene steroids into 3-oxo-4-ene steroids, which has been reported, the transformation of 3β-hydroxy-5α–reduced and 3β-hydroxy-5β–reduced steroids to 3-oxo-5α–reduced and 3-oxo-5β–reduced steroids, respectively, was newly observed. The formation of by-products was in proportion to the concentration of substrates becoming saturated against the enzyme. The substances belonging to these three steroid groups were undetectable at low concentrations, whereas the corresponding by-products were overestimated. These results indicate that the systematic error in the quantification of urinary steroids hydrolyzed with Helix pomatia can lead to a misreading of the clinical implications. All these hydrolysis procedures are suitable for study purposes, and the information can help prevent false evaluations of urinary steroids in clinical studies. Cancer Epidemiol Biomarkers Prev; 19(2); 388–97