bluuebunny/crossref_metadata_2025 huggingface dataset:
A Conserved N-Terminal Domain Mediates Required DNA Replication Activities and Phosphorylation of the Transcriptional Activator IE1 of Autographa californica Multicapsid Nucleopolyhedrovirus
Authors: Taggart David J. , Mitchell Jonathan K. , Friesen Paul D.
Published: April 2012

IE1 is the principal transcriptional regulator of the baculoviruses. Like multifunctional transcription factors of other large DNA viruses, IE1 is an essential, site-specific DNA-binding phosphoprotein that activates virus gene expression and promotes genome replication. To define the poorly understood mechanisms by which IE1 achieves its diverse functions, we identified IE1 domains that contribute to productive infection of
Autographa californica
multicapsid nucleopolyhedrovirus (AcMNPV), the baculovirus prototype. Site-directed mutagenesis revealed that the N-terminal 23 residues of IE1 are required for origin-specific DNA replication and AcMNPV propagation, but not for DNA-binding-dependent transcriptional activation. Within this defined replication domain, we identified an invariant TPXR/H motif that resembles a consensus cyclin-dependent kinase phosphorylation site. Amino acid substitutions of potential phosphorylation sites within or near this motif caused loss of IE1-mediated DNA replication activity. Remarkably, substitution of the single threonine (residue 15) within the TPXR/H motif caused complete loss of AcMNPV multiplication. The replication domain was required for IE1 phosphorylation. It was also sufficient for conferring phosphorylation of a heterologous protein. Importantly, IE1 hyperphosphorylation coincided exclusively with AcMNPV DNA replication. The temporal regulation of IE1 phosphorylation and the essential nature of the TPXR/H motif suggest that phosphorylation critically alters and possibly activates DNA replication activity of IE1 during infection. The striking conservation of the TPXR/H motif among IE1 proteins further suggests that this molecular switch may be a common mechanism by which the alphabaculoviruses coordinate DNA replication and gene expression by using a single regulator.
Temperature-Dependent Survival of Turnip Crinkle Virus-Infected Arabidopsis Plants Relies on an RNA Silencing-Based Defense That Requires DCL2, AGO2, and HEN1
Authors: Zhang Xiuchun , Zhang Xiaofeng , Singh Jasleen , Li Dawei , Qu Feng
Published: April 2012

While RNA silencing is a potent antiviral defense in plants, well-adapted plant viruses are known to encode suppressors of RNA silencing (VSR) that can neutralize the effectiveness of RNA silencing. As a result, most plant genes involved in antiviral silencing were identified by using debilitated viruses lacking silencing suppression capabilities. Therefore, it remains to be resolved whether RNA silencing plays a significant part in defending plants against wild-type viruses. We report here that, at a higher plant growth temperature (26°C) that permits rigorous replication of
Turnip crinkle virus
(TCV) in
Arabidopsis
, plants containing loss-of-function mutations within the
Dicer-like 2
(
DCL2
),
Argonaute 2
(
AGO2
), and
HEN1
RNA methyltransferase genes died of TCV infection, whereas the wild-type Col-0 plants survived to produce viable seeds. To account for the critical role of DCL2 in ensuring the survival of wild-type plants, we established that higher temperature upregulates the activity of DCL2 to produce viral 22-nucleotide (nt) small interfering RNAs (vsRNAs). We further demonstrated that DCL2-produced 22-nt vsRNAs were fully capable of silencing target genes, but that this activity was suppressed by the TCV VSR. Finally, we provide additional evidence supporting the notion that TCV VSR suppresses RNA silencing through directly interacting with AGO2. Together, these results have revealed a specialized RNA silencing pathway involving DCL2, AGO2, and HEN1 that provides the host plants with a competitive edge against adapted viruses under environmental conditions that facilitates robust virus reproduction.
Frequent and Strong Antibody-Mediated Natural Killer Cell Activation in Response to HIV-1 Env in Individuals with Chronic HIV-1 Infection
Authors: Thobakgale Christina F. , Fadda Lena , Lane Kimberly , Toth Ildiko , Pereyra Florencia , Bazner Suzane , Ndung'u Thumbi , Walker Bruce D. , Rosenberg Eric S. , Alter Galit , Carrington Mary , Allen Todd M. , Altfeld Marcus
Published: April 2012

Natural killer (NK) cells play a critical role in the control of HIV-1 infection, and NK cells that respond to HIV-1 peptides have been recently described. However, the mechanisms by which NK cells recognize HIV-1 antigens are not fully understood. We investigated NK cell activation in response to HIV-1 peptides during early and chronic HIV-1 clade B infection using a whole-blood assay and multiparameter flow cytometry. Antibody-mediated NK cell activation in response to HIV-1 peptides was not detected in HIV-1-uninfected individuals. In contrast, 79% of individuals with chronic infection and 22% of individuals with early infection had detectable gamma interferon (IFN-γ) NK cell responses to HIV-1 antigens (
P
< 0.00001). IFN-γ- and tumor necrosis factor alpha (TNF-α)-producing NK cells most frequently targeted Env gp120 (median of 4% and range of 0 to 31% of all NK cells). NK cells rarely targeted other HIV-1 proteins such as Gag, Pol, and Nef. Antibody-mediated NK cell responses to peptides mapped predominantly to Env protein, required the presence of plasma or plasma IgG, and resulted in lower CD16 expression on NK cells, suggesting an antibody-mediated activation of NK cells. Further studies are needed to assess the consequences of these antibody-mediated NK cell responses for HIV-1 disease progression and vaccine-induced protection from infection.
Coordinate Regulation of DNA Damage and Type I Interferon Responses Imposes an Antiviral State That Attenuates Mouse Gammaherpesvirus Type 68 Replication in Primary Macrophages
Authors: Mboko Wadzanai P. , Mounce Bryan C. , Wood Brittani M. , Kulinski Joseph M. , Corbett John A. , Tarakanova Vera L.
Published: April 2012

DNA damage response (DDR) is a sophisticated cellular network that detects and repairs DNA breaks. Viruses are known to activate the DDR and usurp certain DDR components to facilitate replication. Intriguingly, viruses also inhibit several DDR proteins, suggesting that this cellular network has both proviral and antiviral features, with the nature of the latter still poorly understood. In this study we show that irradiation of primary murine macrophages was associated with enhanced expression of several antiviral interferon (IFN)-stimulated genes (ISGs). ISG induction in irradiated macrophages was dependent on type I IFN signaling, a functional DNA damage sensor complex, and ataxia-telangiectasia mutated kinase. Furthermore, IFN regulatory factor 1 was also required for the optimal expression of antiviral ISGs in irradiated macrophages. Importantly, DDR-mediated activation of type I IFN signaling contributed to increased resistance to mouse gammaherpesvirus 68 replication, suggesting that the coordinate regulation of DDR and type I IFN signaling may have evolved as a component of the innate immune response to virus infections.
Oligodendroglioma arising in the glial component of ovarian teratomas: a series of six cases and review of literature
Authors: Ud Din Nasir , Memon Aisha , Aftab Kanwal , Ahmad Zubair , Ahmed Rashida , Hassan Sheema
Published: April 2012

Aims

To report the exceedingly rare occurrence of oligodendroglioma in the glial component of ovarian teratomas.

Methods

Six cases of oligodendrogliomas arising in the glial component of ovarian teratomas were studied and the literature was reviewed. Immunohistochemistry was performed by the Flex technique.

Results

The ages of the patients ranged from 12 to 28 years (mean 21 years). Four tumours were located in the right and one in the left ovary. The size of the ovarian cysts ranged from 7 cm to 29 cm (mean 19.6 cm). Four cases arose in immature and two cases in mature teratomas. In all cases, oligodendroglioma was WHO grade II. On immunohistochemistry, glial fibrillary acidic protein stain was positive in all cases. The Mib 1 (Ki 67) proliferative index was low and the tumour cells were negative for synaptophysin. Follow-up was available in five patients and ranged from 1 to 42 months. Two patients died of disease after 1 and 36 months of diagnosis, respectively. In both these cases oligodendroglioma arose in an immature teratoma. The remaining three patients are alive with a follow-up of 4–42 months.

Conclusions

Oligodendroglioma arising in the glial component of ovarian teratomas is exceedingly rare. Ovarian teratomas should be extensively sampled and carefully evaluated to rule out the possibility of a glial tumour. This is the single and largest series of oligodendrogliomas arising in ovarian teratomas. The prognosis is good for oligodendrogliomas arising in mature teratomas compared with those arising in immature teratomas, although long-term follow-up is needed to determine the exact behaviour.
Impact of integrated cerebrovascular program on outcomes in patients with intracranial aneurysms
Authors: Krishna Vibhor , Walsh Kelsey , Turner Raymond D , Chalela Julio , Turk Aquilla , Patel Sunil J
Published: April 2012

Background

Recent evidence indicates that multidisciplinary care improves patient outcomes in cerebrovascular (CV) disease. A multidisciplinary integrated CV program was recently instituted at a high-volume tertiary referral center, providing the opportunity to evaluate patient outcomes before and after its introduction.

Objective

To evaluate outcomes after treatment of patients with intracranial aneurysm in relation to the introduction of a CV program at our institution.

Methodology

A retrospective chart review was performed on all new patient encounters for a 6-month period each before and immediately after the introduction of the CV program, as well as at a more recent 6-month period to evaluate long-term results. Data were collected on demographic variables, rupture status, medical comorbidities, hospital complications, in-hospital procedures, hospital course and modified Rankin score at discharge and follow up.

Results

The total number of patients treated increased from 55 in the 6-month period before the introduction of the CV program to 112 in the most recent time period (p<0.05). Both the surgical clipping and endovascular coiling procedures increased (p<0.05). A significant increase occurred in patients with multiple comorbidities (30.5% vs 34.7%, p=0.035). The mean length of stay decreased from 12.22±13.26 days before the program to 9.23±12.04 days in the most current data (p<0.05).

Conclusions

Creation of an integrated CV program at a large-volume tertiary referral center resulted in better outcomes for an increased number of more medically complicated patients with intracranial aneurysms. This study provides preliminary data for developing an integrated model of multidisciplinary care for the management of CV disease.
Effects of periparturient events on subsequent culling and fertility in eight UK dairy herds
Authors: Hayes E. P. B. , Christley R. M. , Dobson H.
Published: April 2012

The occurrence of five periparturient events and their effects on subsequent culling and fertility was recorded in eight herds in the UK. Combining data from all 2105 calvings, the proportion affected by assisted calving, dead calf, retained fetal membranes (RFM), milk fever or twins was 5·9, 8·2, 5·3, 5·0 or 3·3 per cent, respectively. Compared with unaffected herdmates, cows with an assisted calving or a dead calf had higher early (but not late) culling rates, (assisted calving: 8·8 per cent being culled before 100 days after calving compared with 5·7 per cent; P = 0·05; dead calf: 12·2 per cent culled compared with 5·3 per cent; P = 0·001). Compared with unaffected animals, cows with milk fever were four times more likely to be culled before 100 days after calving (16·2 per cent compared with 5·3 per cent; P = 0·001), whereas those with RFM were twice as likely to be culled between 100 and 200 days (14·3 per cent compared with 7·6 per cent; P = 0·003), and both groups were twice as likely to not be pregnant by 200 days. Cows with RFM or milk fever also had markedly reduced subsequent fertility: both conditions extended calving to pregnancy intervals (by 20 days; P = 0·001, or by 13 days; P = 0·03, respectively), lowered 100‐day in‐calf rates (by 24·5 per cent; P = 0·001, or by 17·8 per cent; P = 0·008, respectively) and lowered 200‐day in‐calf rates (by 20 per cent; P = 0·001, or by 15 per cent; P = 0·002, respectively). The birth of twins had no effect on subsequent culling or fertility.
Elastic and thermodynamic properties of divalent transition metal carbides MC (M = Ti, Zr, Hf, V, Nb, Ta)
Authors: Srivastava Anurag , Diwan Bhoopendra Dhar
Published: April 2012

We have investigated the elastic and thermodynamic properties of transition metal carbides (TiC, ZrC, HfC, VC, NbC, and TaC) using the three body force potential model and density functional theory based ab initio approach. The computed second-order elastic constants (C11, C12, C44) are in close agreement with the available experimental as well as theoretical results. The other related elastic parameters (B0, B0′, CS, CL, G, ν, E, A, β, ξ, λ, Cauchy pressure (C12 – C44), B0/G, and E/ρ ratio) have also been computed successfully. The calculated Debye temperatures are in reasonably good agreement with the available data.
Collision-induced absorption in the second overtone band of H2
Authors: Abu-Kharma M.
Published: April 2012

The second overtone band of H2–H2 spectra at 77 K were recorded for gas densities between 350 and 1000 amg (1 amg = 44.614 981 mol/m3) with a 2 m stainless steel high-pressure transmission-type absorption cell. The profile analyses of these spectra were carried out using the Birnbaum–Cohen line shape function for the quadrupolar transitions and the Levine–Birnbaum line shape function for the overlap transitions. The observed spectra were modeled with synthetic profiles which are composed of the superposition of an overlap-induced and a quadrupolar-induced profile. The fitting parameters were determined from the analysis. Satisfactory agreement of the measurements with the calculated profiles is observed.
Some characteristics of a double plasma device operated as a triode
Authors: Mishra M.K. , Phukan A.
Published: April 2012

Experimentally it is shown that a triode-like scenario can be achieved in a double plasma device. The source chamber of the device, where plasma is produced by hot filament discharge, is considered to be the cathode, and the target chamber, which is at a positive potential, is considered to be the anode. The separation grid of the device is used as the control grid. The patterns of both anode characteristics and mutual characteristics are found to be similar to that of a triode valve. The estimated values of the parameters are found to depend on the anode current. In the case of anode characteristics, the floating potential in the source chamber is found to increase towards the positive but in mutual characteristics, the floating potential increases towards the negative.
Laboratory measurements of the dielectronic recombination satellite transitions of He-like Fe XXV and H-like Fe XXVI
Authors: Gu M.F. , Beiersdorfer P. , Brown G.V. , Graf A. , Kelley R.L. , Kilbourne C.A. , Porter F.S. , Kahn S.M.
Published: April 2012

We present laboratory spectra of dielectronic recombination (DR) satellite transitions attached to the He-like and H-like iron resonance lines obtained with the NASA Goddard Space Flight Center X-ray calorimeter and produced by a thermal plasma simulation technique on the EBIT-I electron beam ion trap at the Lawrence Livermore National Laboratory. We demonstrate that the calorimeter has sufficient spectral resolution in the 6–9 keV range to provide reliable measurements not only of standard DR satellite to resonance line intensities but also of DR satellite to DR satellite ratios that can be used to diagnose nonthermal electron distributions. Electron temperatures derived from the measured line intensities are consistent with the temperature of the simulated plasma. Temperature measurements based on DR satellite transitions have significant advantages over those based on collisional ionization equilibrium or continuum shape. Thus, successful demonstration of this method with the X-ray calorimeter is an important step for its application in X-ray astronomy.
Variable G correction for dark energy model in higher dimensional cosmology
Authors: Chakraborty Shuvendu , Debnath Ujjal , Jamil Mubasher
Published: April 2012

In this work, we have considered N( = 4 + d)-dimensional Einstein field equations in which 4-dimensional space–time is described by a Friedmann–Robertson–Walker metric and that of the extra d-dimensions by an euclidean metric. We have calculated the corrections to statefinder parameters due to variable gravitational constant G in higher dimensional cosmology. We have considered two special cases: whether dark energy and dark matter interact or not. In a universe where the gravitational constant is dynamic, the variable G-correction to statefinder parameters is inevitable. The statefinder parameters are also obtained for generalized Chaplygin gas in the effect of the variation of G correction.
Power law singularities in n-vector models
Authors: Kaupužs J.
Published: April 2012

Power law singularities and critical exponents in n-vector models are considered within a theoretical approach called GFD (grouping of Feynman diagrams) theory. It is discussed how possible values of the critical exponents can be related to specific n-vector models in this approach. A good agreement with the estimates of the perturbative renormalization group (RG) theory can be obtained. Predictions for corrections to scaling of the perturbative RG and GFD approaches are different. A nonperturbative proof is provided, supporting corrections to scaling of the GFD theory. Highly accurate experimental data very close to the λ-transition point in liquid helium, as well as the Goldstone mode singularities in n-vector spin models, evaluated from Monte Carlo simulation results, are discussed with an aim to test the theoretical predictions. Our analysis shows that in both cases the data can be well interpreted within GFD theory.
Induced energy polarization of the vacuum as the source of the baryonic Tully–Fisher relationship and the Pioneer anomaly
Authors: Penner A. Raymond
Published: April 2012

A theory where the gravitational field of a mass induces a gravitational field contribution from the cosmos is presented. In this theory, entities of both net positive and net negative energy come into existence throughout the cosmos with a maximum lifetime in accordance with Heisenberg’s uncertainty principle. A model of the resulting contribution that these entities make to the gravitational field is provided and is shown to lead to both the baryonic Tully–Fisher relationship and the Pioneer anomaly.
One-dimensional point interaction with Griffiths’ boundary conditions
Authors: Coutinho F.A.B. , Nogami Y. , Toyama F.M.
Published: April 2012

Griffiths proposed a pair of boundary conditions that define a point interaction in one dimensional quantum mechanics. The conditions involve the nth derivative of the wave function where n is a non-negative integer. We re-examine the interaction so defined and explicitly confirm that it is self-adjoint for any even value of n and for n = 1. The interaction is not self-adjoint for odd n > 1. We then propose a similar but different pair of boundary conditions with the nth derivative of the wave function such that the ensuing point interaction is self-adjoint for any value of n.
UPSILON PRODUCTION IN pp COLLISIONS AT LHC
Authors: KISSLINGER LEONARD S.
Published: April 2012

This is a continuation of recent studies of ϒ(nS) production at the LHC in pp collisions. Our previous studies were for 2.76 TeV, while the present predictions are for 7.0 TeV collisions.
INVESTIGATING ELECTRIC FIELD CONTROL OF MAGNETISM WITH NEUTRON SCATTERING, NONLINEAR OPTICS AND SYNCHROTRON X-RAY SPECTROMICROSCOPY
Authors: HOLCOMB M. B. , POLISETTY S. , RODRÍGUEZ A. FRAILE , GOPALAN V. , RAMESH R.
Published: April 2012

This paper discusses recent efforts to control magnetism with electric fields in single and multilayer oxides, which has great potential to improve a variety of technological endeavors, such as magnetic sensing and magnetoelectric (ME) logic. The importance of electrical control of magnetism is followed by a discussion of multiferroics and MEs, which are the leading contenders for this task. The focus of this paper is on complementary methods in understanding the ME coupling, an essential step to electrical control of magnetism. Neutron scattering, nonlinear optics and X-ray spectromicroscopy are addressed in providing key parameters in the study of ME coupling. While primarily direct (single-phase multiferroics) ME materials are used as examples, the techniques discussed are also valuable to the study of indirect (e.g., multilayers and pillars) magnetoelectrics. We conclude with a summary of the field and future directions.
GINZBURG–LANDAU LIKE THEORY OF HIGH TEMPERATURE SUPERCONDUCTIVITY IN THE CUPRATES: EMERGENT d-WAVE ORDER
Authors: RAMAKRISHNAN T. V.
Published: April 2012

High temperature superconductivity in the cuprates remains one of the most widely investigated, constantly surprising and poorly understood phenomena in physics. Here, we describe briefly a new phenomenological theory inspired by the celebrated description of superconductivity due to Ginzburg and Landau and believed to describe its essence. This posits a free energy functional for the superconductor in terms of a complex order parameter characterizing it. We propose that there is, for superconducting cuprates, a similar functional of the complex, in plane, nearest neighbor spin singlet bond (or Cooper) pair amplitude ψij. Further, we suggest that a crucial part of it is a (short range) positive interaction between nearest neighbor bond pairs, of strength J′. Such an interaction leads to nonzero long wavelength phase stiffness or superconductive long range order, with the observed d-wave symmetry, below a temperature Tc~z J′ where z is the number of nearest neighbors; d-wave superconductivity is thus an emergent, collective consequence. Using the functional, we calculate a large range of properties, e.g., the pseudogap transition temperature T* as a function of hole doping x, the transition curve Tc(x), the superfluid stiffness ρs(x, T), the specific heat (without and with a magnetic field) due to the fluctuating pair degrees of freedom and the zero temperature vortex structure. We find remarkable agreement with experiment. We also calculate the self-energy of electrons hopping on the square cuprate lattice and coupled to electrons of nearly opposite momenta via inevitable long wavelength Cooper pair fluctuations formed of these electrons. The ensuing results for electron spectral density are successfully compared with recent experimental results for angle resolved photo emission spectroscopy (ARPES), and comprehensively explain strange features such as temperature dependent Fermi arcs above Tc and the "bending" of the superconducting gap below Tc.
THE PRINCIPLE OF LOCAL ROTATIONAL INVARIANCE AND THE COEXISTENCE OF MAGNETISM, CHARGE AND SUPERCONDUCTIVITY
Authors: DORIA MAURO M. , VARGAS-PAREDES ALFREDO A. , HELAYËL-NETO JOSÉ A.
Published: April 2012

We propose a macroscopic description of the superconducting state in presence of an applied external magnetic field in terms of first order differential equations. They describe a corrugated two-component order parameter intertwined with a spin-charged background, caused by spin correlations and charged dislocations. The first order differential equations are a consequence of a Weitzenböck–Liechnorowitz identity which renders a SUL(2) ⊗ UL(1) invariant ground state, based on (L) local rotational and electromagnetic gauge symmetry. The proposal is based on a long ago developed formalism by Élie Cartan to investigate curved spaces, viewed as a collection of small Euclidean granules that are translated and rotated with respect to each other. Élie Cartan's formalism unveils the principle of local rotational invariance as a gauge symmetry because the global SU(2) invariance of the order parameter is turned local by the interlacement of spin and charge to pairing.
PHYSICAL MEANING OF THE PARAMETERS IN THE TWO-PARAMETER (κ, ζ) GENERALIZED STATISTICS
Authors: GUO LINA
Published: April 2012

The physical meaning of the parameters (κ, ζ), emerging in the statistical theory [G. Kaniadakis, Eur. Phys. J. B70 (2009) 3; D. P. Mittal, Metrika22 (1975) 35; B. D. Sharma and I. J. Taneja, Metrika22 (1975) 205] considered by Kaniadakis, is explained by considering the (κ, ζ)-kinetics of a particle system, in presence of an external force field F. By using the method [J. L. Du, Phys. Lett. A329 (2004) 262] developed by Du, we show: First, the external force field necessarily induces in the system a temperature gradient ∇T. Second, the parameters (κ, ζ) are univocally related to the magnitude and the angular separation of the vectors F and ∇T. The achievements of the present paper have a general validity, holding independently on the particular approximation used to describe the collision term, in the equation governing the system evolution (i.e. Boltzmann or Fokker–Planck kinetics).
ELECTRON IMPACT DISSOCIATIVE IONIZATION OF NITROSYL CHLORIDE
Authors: WANG PENGQIAN
Published: April 2012

Electron impact dissociative ionization of nitrosyl chloride ( ClNO ) has been studied at the electron beam energy of 200 eV. The dissociation channels of up to triply ionized ClNO are investigated by two- and three-dimensional covariance mapping methods. The absolute cross-sections for the different dissociation channels are measured. No stable ClNO + or ClNO 2+ ions are observed in the mass spectrum. The most possible pathway for the dissociation of ClNO + is ClNO + → NO + + Cl . The total double ionization cross-section of ClNO is found to be 6.3% compared to the total single ionization cross-section. The main ion-pair dissociation channels for ClNO 2+ are ClNO 2+ → N + + O ++ Cl and ClNO 2+ → NO + + Cl +. The ClNO trications dissociate into either an ion pair or an ion triple, with comparable probabilities.
COMMENTS ON THE ELASTIC PROPERTIES IN SOLID SOLUTIONS OF SILVER HALIDES
Authors: SKORDAS EFTHIMIOS S.
Published: April 2012

Recently first principles microscopic calculations, using the generalized gradient approximation, appeared for the solid mixed system AgCl x Br 1-x at various compositions. Here, we suggest a model that can estimate the compressibility of the mixed crystals in terms of the compressibilities of the end members alone. This model makes use of a single parameter, i.e. the compressibility of a defect volume, when considering the volume variation produced by the addition of a "foreign molecule" to a host crystal as a defect volume.
GRAVITATIONAL COLLAPSE AND BLACK HOLE THERMODYNAMICS IN BRANEWORLD SCENARIO
Authors: MAIER R. , SOARES I. DAMIÃO
Published: April 2012

We examine the dynamics of the gravitational collapse in a 4-dim Lorentzian brane embedded in a 5-dim bulk with an extra timelike dimension. By considering the collapse of pure dust on the brane we derive a bouncing FLRW interior solution and match it with a corrected Schwarzschild exterior geometry. In the physical domain considered for the parameters of the solution, the analytical extension is built, exhibiting an exterior event horizon and a Cauchy horizon, analogous to the Reissner–Nordstrom solution. For such an exterior geometry we examine the effects of the bulk-brane corrections in the Hawking radiation. In this scenario the model extends Bekenstein's black hole geometrical thermodynamics for quasi-extremal configurations, with an extra work term in the laws associated with variations of the brane tension. We also propose a simple statistical mechanics model for the entropy of the bouncing collapsed matter by quantizing its fluctuations and constructing the associated partition function. This entropy differs from the geometrical entropy by an additive constant proportional to the area of the extremal black hole and satisfies an analogous first law of thermodynamics. A possible connection between both entropies is discussed.
RECURSIVE PROTEIN MODELING: A DIVIDE AND CONQUER STRATEGY FOR PROTEIN STRUCTURE PREDICTION AND ITS CASE STUDY IN CASP9
Authors: CHENG JIANLIN , EICKHOLT JESSE , WANG ZHENG , DENG XIN
Published: April 2012

After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of structural modeling, two types of modeling techniques — template-based modeling and template-free modeling — have been developed. Template-based modeling can often generate a moderate- to high-resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling, such as fragment-based assembly, may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e. certain) and template-free (i.e. uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can significantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction.
P.R.E.S.S. — AN R-PACKAGE FOR EXPLORING RESIDUAL-LEVEL PROTEIN STRUCTURAL STATISTICS
Authors: HUANG YUANYUAN , BONETT STEPHEN , KLOCZKOWSKI ANDRZEJ , JERNIGAN ROBERT , WU ZHIJUN
Published: April 2012

P.R.E.S.S. is an R-package developed to allow researchers to get access to and manipulate a large set of statistical data on protein residue-level structural properties such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles. A large set of high-resolution protein structures is downloaded and surveyed. Their residue-level structural properties are calculated and documented. The statistical distributions and correlations of these properties can be queried and displayed. Tools are also provided for modeling and analyzing a given structure in terms of its residue-level structural properties. In particular, new tools for computing residue-level statistical potentials and displaying residue-level Ramachandran-like plots are developed for structural analysis and refinement. P.R.E.S.S. has been released in R as an open source software package, with a user-friendly GUI, accessible and executable by a public user in any R environment. P.R.E.S.S. can also be downloaded directly at http://www.math.iastate.edu/press/ .
SPECIAL PROJECTIVE ALGEBRA OF RANDERS METRICS OF CONSTANT S-CURVATURE
Authors: RAFIE-RAD M.
Published: April 2012

The collection of all projective vector fields on a Finsler space (M, F) is a finite-dimensional Lie algebra with respect to the usual Lie bracket, called the projective algebra. A specific Lie sub-algebra of projective algebra of Randers spaces (called the special projective algebra) of non-zero constant S-curvature is studied and it is proved that its dimension is at most [Formula: see text]. Moreover, a local characterization of Randers spaces whose special projective algebra has maximum dimension is established. The results uncover somehow the complexity of projective Finsler geometry versus Riemannian geometry.
4D-POLYTOPES AND THEIR DUAL POLYTOPES OF THE COXETER GROUP W(A4) REPRESENTED BY QUATERNIONS
Authors: KOCA MEHMET , KOCA NAZIFE OZDES , AL-AJMI MUDHAHIR
Published: April 2012

Four-dimensional A4 polytopes and their dual polytopes have been constructed as the orbits of the Coxeter–Weyl group W(A4) where the group elements and the vertices of the polytopes are represented by quaternions. Projection of an arbitrary W(A4) orbit into three dimensions is made using the subgroup W(A3). A generalization of the Catalan solids for 3D-polyhedra has been developed and dual polytopes of the uniform A4 polytopes have been constructed.
JETTED ACTIVE GALACTIC NUCLEI
Authors: GHISELLINI GABRIELE
Published: April 2012

Most of the electromagnetic output of blazars (BL Lac objects and Flat Spectrum Radio Quasars) comes out in the γ–ray band, making the Large Area Telescope [0.1–100 GeV] onboard the Fermi satellite and the Cherenkov telescopes crucial for gather crucial data and thus to understand their physics. These data are complemented by the observations of the Swift satellite in the X–ray and optical–UV bands, and by ground based optical and radio telescopes. This rich coverage of the spectrum allows a robust modelling, from which important trends start to emerge. In powerful sources we see the contribution of the accretion disk that, once modeled, give us the black hole mass and the accretion rate. Even when not directly visible, the disk luminosity can be derived through the broad emission lines. Therefore we start to know the jet power, the disk luminosity, and the black hole mass, 3 crucial ingredients if we want to draw a general scenario. At the start, jets are believed to be magnetically dominated. And yet, on the scale where they emit most of their luminosity, their power is already in the form of kinetic energy of particles. Relativistic jets are formed for a very broad range of the disk luminosity, from close to Eddington down to at least 10-4Eddington. Their power correlates with the accretion rate, and can be even more powerful than the accretion disk luminosity.
MAGIC RESULTS ON BINARY SYSTEMS
Authors:   on behalf of the Magic Collaboration, ZANIN ROBERTA , BLANCH OSCAR , CORTINA JUAN , JOGLER TOBIAS , MUNAR-ADROVER PERE , PAREDES JOSEP M. , RIBÓ MARC , ZABALZA VÍCTOR , BORDAS POL
Published: April 2012

Three X-ray binary systems have been unambiguously detected at TeV energies: LS 5039, LS I +61° +303, PSR B1259-63. Additionally, the TeV source HESS J0632+057 has been found to be a new binary system. The recent detection of the microquasar Cygnus X-3, between 100 MeV and few GeV, confirms that also this sub-class of accreting binaries displaying radio relativistic jets provides interesting candidates for very-high-energy (VHE) gamma-ray observations. The MAGIC telescopes made a significant effort to search for signals from X-ray binaries. This article will present the new results on LS I 61° +303, which show a reduction in the VHE γ-ray flux in the periodic outburst phase with respect to previous campaigns. MAGIC observed also HESS J0632 +057 in 2010 and 2011, covering an X-ray outburst reported by Swift in February 2011. These observations show significant activity in VHE gamma-rays temporally coincident with the X-ray outburst. In addition, this article will review MAGIC results on the microquasars Cygnus X-3, Cygnus X-1, and Scorpius X-1 which report constraining flux upper limits in different X-ray spectral states and as well as during flux enhancements at high energies.
ON THE NATURE OF THE X-RAY CORONA OF BLACK HOLE BINARIES
Authors: MALZAC JULIEN
Published: April 2012

We discuss the nature of the X-ray emitting plasma of black hole binaries. It is well known that the temperature and optical depth of the Comptonising electrons of the X-ray corona of black hole binaries can be measured using spectroscopy in the 1 keV-1 MeV energy band. We emphasize recent developments in the modeling of high energy radiation processes which allow us to constrain other important physical parameters of the corona, such as the strength of magnetic field, or the temperature of the ions. The results appear to challenge current accretion models. In particular, standard advection dominated accretion flow do not match the observed properties of bright hard state X-ray binaries such as Cygnus X-1 or GX 339-4. On the other hand, we find that all the data would be consistent with a multi-zone magnetically dominated hot accretion flow model. We also emphasize that besides the usual spectral state transitions observed at luminosities above a few percent of Eddington, there is observational evidence for at least two additional, more subtle, radiative transitions occuring at lower luminosities.
THE RELATIVISTIC WIND IN PWNe
Authors: BUCCIANTINI NICCOLÒ
Published: April 2012

Pulsar Wind Nebulae (PWNe) are bubbles of relativistic plasma that form when the relativistic pulsar wind is confined by the SNR or the ISM. They have a broad band spectrum extending from from Radio to γ-rays, via synchrotron and Inverse Compton emission, and their study can provide important clues on the otherwise unobservable properties of the cold pulsar wind. The richness of emission features, revealed by recent observations, has driven a renewed interest in the theoretical modeling of these objects. In recent years an MHD paradigm has emerged. which has proved successful in explaining the richness of emission features observed in the X-ray band, and that has contributed to settle many old issues. PWNe are perhaps the best systems where relativistic dynamics can be investigated with high accuracy, given their proximity and the fact that they are persistent sources, and understanding their behavior is an essential step for the field of high energy astrophysics in general. I present here the current status of MHD models: what are the key ingredients, their successes, and open questions.
POWERFUL RELATIVISTIC JETS IN SPIRAL GALAXIES
Authors: FOSCHINI LUIGI
Published: April 2012

The discovery of high-energy (E > 100 MeV) γ rays from Narrow-Line Seyfert 1 Galaxies (γ-NLS1s) has confirmed the presence of powerful relativistic jets in this class of active galactic nuclei (AGN). Although the jet emission is similar to that of blazars and radio galaxies, γ-NLS1s have some striking differences: relatively small masses (106-8 M⊙), high accretion rates (0.1-1 times the Eddington limit) and are generally hosted by spiral galaxies. It is now possible to study a rather unexplored range of mass and accretion rates of AGN with relativistic jets. Specifically, in this work I present some results obtained by comparing a sample of blazars and γ-NLS1s with another sample of Galactic binaries with relativistic jets (stellar mass black holes and neutron stars).
RESULTS FROM MAGIC OBSERVATIONS OF EXTRAGALACTIC RELATIVISTIC SOURCES
Authors:   on behalf of the MAGIC Collaboration, DE ALMEIDA ULISSES BARRES
Published: April 2012

The Major Atmospheric Gamma-ray Imaging Cherenkov (MAGIC) experiment is an array of two 17-meter telescopes located in the Canary Island of La Palma that observes the very-high energy (VHE) gamma-ray sky in stereoscopic mode since 2009. MAGIC is distinguished by its low-energy threshold of approximately 50 GeV, which grants the system a unique potential in the study of distant extragalactic sources whose gamma-ray emission is significantly attenuated due to absorption by the extragalactic background light (EBL). The observation of non-thermal gamma rays in the GeV-TeV range from extragalactic sources is a characteristic signature of their relativistic nature and therefore fundamentally important for our understanding of the physics of these objects. Since the beginning of its stereo operation, MAGIC has observed a large number of active galactic nuclei (AGN) of different classes, including several blazars and distant quasars. In this paper we will review some of the most important results of these observations.
POLARIZATION IN VERY EARLY GAMMA-RAY BURST AFTERGLOW
Authors: KOBAYASHI SHIHO
Published: April 2012

Polarization offers the capacity to diagnose the structure of the magnetic fields in the GRB ejecta which could provide a clue to pin down the jet acceleration process. The recent early-time polarization detection at about 10% level opens the exciting possibility of measuring the time-resolved evolution of polarization degree and angle of early optical afterglow.
SIMULATION OF RELATIVISTIC JETS AND ASSOCIATED SELF-CONSISTENT RADIATION
Authors: NISHIKAWA K.-I. , NIEMIEC J. , ZHANG B. , MEDVEDEV M. , HARDEE P. , MIZUNO Y. , NORDLUND Å. , FREDERIKSEN J. , SOL H. , POHL M. , HARTMANN D. H. , FISHMAN G. J.
Published: April 2012

Plasma instabilities are responsible not only for the onset and mediation of collisionless shocks but also for the associated acceleration of particles. We have investigated particle acceleration and shock structure associated with an unmagnetized relativistic electron-positron jet propagating into an unmagnetized electron-positron plasma. Cold jet electrons are thermalized and slowed while the ambient electrons are swept up to create a partially developed hydrodynamic-like shock structure. In the leading shock, electron density increases by a factor of about 3.5 in the simulation frame. Strong electromagnetic fields are generated in the trailing shock and provide an emission site. These magnetic fields contribute to the electrons transverse deflection and, more generally, relativistic acceleration behind the shock. We have calculated, self-consistently, the radiation from electrons accelerated in the turbulent magnetic fields. We found that the synthetic spectra depend on the Lorentz factor of the jet, its thermal temperature and strength of the generated magnetic fields. The properties of the radiation may be important for understanding the complex time evolution and/or spectral structure in gamma-ray bursts, relativistic jets in general, and supernova remnants.
LOCATION OF THE γ-RAY FLARING EMISSION IN THE PARSEC-SCALE JET OF THE BL LAC OBJECT AO 0235+164
Authors: AGUDO IVÁN , MARSCHER A. P. , JORSTAD S. G. , LARIONOV V. M. , GÓMEZ J. L. , LÄHTEENMÄKI A. , SMITH P. S. , NILSSON K. , READHEAD A. C. S. , ALLER M. F. , HEIDT J. , GURWELL M. , THUM C. , WEHRLE A. E. , KURTANIDZE O. M.
Published: April 2012

We locate the γ-ray and lower frequency emission in flares of the BL Lac object AO 0235+164 at ≳12 pc in the jet of the source from the central engine. We employ time-dependent multi-spectral-range flux and linear polarization monitoring observations, as well as ultra-high resolution (~0.15 milliarcsecond) imaging of the jet structure at λ = 7 mm . The time coincidence in the end of 2008 of the propagation of the brightest superluminal feature detected in AO 0235+164 (Qs) with an extreme multi-spectral-range (γ-ray to radio) outburst, and an extremely high optical and 7 mm (for Qs) polarization degree provides strong evidence supporting that all these events are related. This is confirmed at high significance by probability arguments and Monte-Carlo simulations. These simulations show the unambiguous correlation of the γ-ray flaring state in the end of 2008 with those in the optical, millimeter, and radio regime, as well as the connection of a prominent X-ray flare in October 2008, and of a series of optical linear polarization peaks, with the set of events in the end of 2008. The observations are interpreted as the propagation of an extended moving perturbation through a re-collimation structure at the end of the jet's acceleration and collimation zone.
FORMATION AND DESTRUCTION OF JETS IN X-RAY BINARIES
Authors: CONTOPOULOS IOANNIS , KYLAFIS NIKOLAOS D. , KAZANAS DEMOSTHENES , CHRISTODOULOU DIMITRIS M.
Published: April 2012

Neutron-star and black hole X-ray binaries (XRBs) exhibit radio jets, whose properties depend on the X-ray spectral state and history of the source. There is general agreement about the type of the accretion disk around the compact object in the various spectral states. What is missing is a physical explanation for the appearance, disappearance, and re-appearance of jets. We will demonstrate that by invoking a simple physical mechanism proposed more than ten years ago, the so-called Poynting-Robertson Cosmic Battery (PRCB), we can explain in a natural way the disk–jet connection in XRBs.
HADRONIC MODELING OF AGN VARIABILITY
Authors: SPANIER FELIX , WEIDINGER MATTHIAS
Published: April 2012

The ongoing search for extragalactic gamma-ray sources reveals more and more blazars not classified as high-peaked BL Lac objects. These sources may not be understood in the context of purely leptonic emission models. In the present paper we study lepto-hadronic emission models, especially their time variation patterns. Since a number of non-linear processes are involved, timing relations are far more complex than in purely leptonic models and might eventually be used to discriminate different emission scenarios. First complete time dependent applications to 3C279 and 3C454.3 are presented.
AN EXPERIMENT TO LOCATE THE SITE IN M87 OF TeV FLARING
Authors: HARRIS D. E. , BEILICKE M. , CHEUNG C. C. , COLIN P. , HORNS D. , LEBOHEC S. , MASSARO F. , MAZIN D. , MUKHERJEE R. , RAUE M. , STAWARZ L. , WAGNER R. , WAGNER S.
Published: April 2012

We describe a Chandra ToO project designed to isolate the site of TeV flaring in the radio galaxy M87. To date, we have triggered the Chandra observations only once (2010 April) and by the time of our first observation, the TeV flare had ended. However, we found that the X-ray intensity of the unresolved nucleus was at an elevated level at the time of our first of 9 observations. Of the ~70 observations we have made of the M87 jet covering 9 years, the nucleus was measured at > 1 keV/s only 3 times. Two of these occasions can be associated with TeV flaring, and at the time of the third event, there were no TeV monitoring activities. We discuss the implications of these data.
EFFICIENCY OF INTERNAL SHOCKS IN MAGNETIZED RELATIVISTIC JETS
Authors: MIMICA PETAR , ALOY MIGUEL ANGEL
Published: April 2012

We study the dynamic and radiative efficiency of conversion of kinetic-to-thermal/magnetic energy by internal shocks in relativistic magnetized outflows. A parameter study of a large number of collisions of cylindrical shells is performed. We explore how, while keeping the total flow luminosity constant, the variable fluid magnetization influences the efficiency and find that the interaction of shells in a mildly magnetized jet yields higher dynamic, but lower radiative efficiency than in a non-magnetized flow. A multi-wavelength radiative signature of different shell magnetizations is computed assuming that relativistic particles are accelerated at internal shocks.
VLBA ASTROMETRY OF LS 5039 AND PSR J1825-1446: WHICH SOURCE IS RELATED TO SNR G016.8-01.1?
Authors: MOLDÓN J. , RIBÓ M. , PAREDES J. M. , BRISKEN W. , KRAMER M. , LYNE A. G. , STAPPERS B. W.
Published: April 2012

The supernova remnant SNR G016.8-01.1 is close to the gamma-ray binary system LS 5039, one of the five gamma-ray binaries currently known. LS 5039 appears to have been born in the SNR G016.8-01.1 just ~ 105 yr ago, as indicated by its proper motion. This association would provide direct implications on the nature and properties of the unknown compact object in the binary system. However, there is another source close to SNR G016.8-01.1 that could have been born during the SN explosion: the pulsar PSR J1825-1446, for which the proper motion is unknown. We are measuring the proper motion of both sources by means of VLBI radio observations in order to constrain their origin. Here we present the first results of a VLBA campaign on PSR J1825-1446 to measure its proper motion. We discuss the possible kinematical age of this pulsar, and the possible association of LS 5039 and PSR J1825-1446 with the supernova remnant.