bluuebunny/crossref_metadata_2025 huggingface dataset:
Orthographic Processing in Baboons (
Papio papio
)
Authors: Grainger Jonathan , Dufau Stéphane , Montant Marie , Ziegler Johannes C. , Fagot Joël
Published: April 2012

Monkey See, Monkey Read

An orthographic object such as a set of letters, and the ability to recognize such sets as words, is a key component of reading. The ability to develop these skills has often been attributed to the prior acquisition of a complex language. For example, we learn how letters sound and thus recognize when a particular letter makes up part of a word. However, orthographic processing is also a visual process, because we learn to recognize words as discrete objects, and the ability to read may thus be related to an ability to recognize and classify objects.

Grainger
et al.

(p.
245
; see the Perspective by

Platt and Adams

) tested orthographic skills in baboons. Captive, but freely ranging, baboons were trained to distinguish real English words from combinations of similar letters that are not words, and they were able to distinguish real words with remarkable accuracy. Thus, a basic ability to recognize words as objects does not require complex linguistic understanding.
The Strangest Terrestrial Planet
Authors: McKinnon William B.
Published: April 2012

NASA's MESSENGER mission previously revealed that Mercury has a volcanic crust; now it finds evidence for an inner “anticrust.”
Sleep Study Suggests Triggers for Diabetes and Obesity
Authors: Leslie Mitch
Published: April 2012

According to the longest sleep-limitation study to date, published this week in
Science Translational Medicine
, many people are on sleep and work schedules that prime them for diabetes and obesity.
Peptide Microarray Analysis ofIn Silico-Predicted Epitopes for Serological Diagnosis of Toxoplasma gondii Infection in Humans
Authors: Maksimov Pavlo , Zerweck Johannes , Maksimov Aline , Hotop Andrea , Groß Uwe , Pleyer Uwe , Spekker Katrin , Däubener Walter , Werdermann Sandra , Niederstrasser Olaf , Petri Eckhardt , Mertens Marc , Ulrich Rainer G. , Conraths Franz J. , Schares Gereon
Published: April 2012

Toxoplasma gondiiinfections occur worldwide in humans and animals. In immunocompromised or prenatally infected humans,T. gondiican cause severe clinical symptoms. The identification of specific epitopes onT. gondiiantigens is essential for the improvement and standardization of the serological diagnosis of toxoplasmosis. We selected 20 peptides mimicking linear epitopes on GRA1, GRA2, GRA4, and MIC3 antigenicT. gondiiproteinsin silicousing the software ABCpred. A further 18 peptides representing previously published epitopes derived from GRA1, SAG1, NTPase1, and NTPase2 antigens were added to the panel. A peptide microarray assay was established to prove the diagnostic performance of the selected peptides with human serum samples. Seropositive human serum samples (n= 184) were collected from patients presenting with acute toxoplasmosis (n= 21), latentT. gondiiinfection (n= 53), and inactive ocular toxoplasmosis (n= 10) and from seropositive forest workers (n= 100). To adjust the cutoff values for each peptide, sera from seronegative forest workers (n= 75) and patients (n= 65) were used. Univariate logistic regression suggested the significant diagnostic potential of eight novel and two previously published peptides. A test based on these peptides had an overall diagnostic sensitivity of 69% (100% in ocular toxoplasmosis patients, 86% in acutely infected patients, 81% in latently infected patients, and 57% in seropositive forest workers). The analysis of seronegative sera performed with these peptides revealed a diagnostic specificity of 84%. The results of our study suggest that the use of a bioinformatic approach for epitope prediction in combination with peptide microarray testing is a powerful method for the selection ofT. gondiiepitopes as candidate antigens for serological diagnosis.
Macrolide Resistance Determination and Molecular Typing of Mycoplasma pneumoniae in Respiratory Specimens Collected between 1997 and 2008 in The Netherlands
Authors: Spuesens Emiel B. M. , Meijer Adam , Bierschenk Damien , Hoogenboezem Theo , Donker Gé A. , Hartwig Nico G. , Koopmans Marion P. G. , Vink Cornelis , van Rossum Annemarie M. C.
Published: April 2012

An important role in the treatment regimens for
Mycoplasma pneumoniae
infections is played by macrolide (ML) antibiotics. In the past few years, however, a steady increase has been detected in the worldwide prevalence of ML-resistant (ML
r
)
M. pneumoniae
strains. It is obvious that this increase necessitates a continuous monitoring of ML
r
and, when detected, modification of antibiotic treatment modalities. Previously, we developed a pyrosequencing-based assay system for the genetic determination of ML
r
as well as molecular typing of
M. pneumoniae
. In this study, the sensitivity of this system was improved by the inclusion of a nested-PCR protocol. The modified system was applied to 114
M. pneumoniae
-positive specimens that were obtained from a collection of 4,390 samples from patients with acute respiratory tract infections. These samples were collected between 1997 and 2008 in The Netherlands. The pyrosequencing system produced reliable data in 86% of the specimens that contained >500
M. pneumoniae
genome copies/ml of patient sample. Each of these samples contained DNA of the ML-sensitive genotype. While 43% of the samples were found to harbor the
M. pneumoniae
subtype 1 genotype, 57% contained the subtype 2 genotype. We conclude that the pyrosequencing-based assay system is a useful tool for ML
r
determination and molecular typing of
M. pneumoniae
in patient samples. ML
r
-associated
M. pneumoniae
genotypes, however, were not found in the current study population.
Fatal Case of Brucellosis Misdiagnosed in Early Stages of Brucella suis Infection in a 46-Year-Old Patient with Marfan Syndrome
Authors: Carrington M. , Choe U. , Ubillos S. , Stanek D. , Campbell M. , Wansbrough L. , Lee P. , Churchwell G. , Rosas K. , Zaki S. R. , Drew C. , Paddock C. D. , DeLeon-Carnes M. , Guerra M. , Hoffmaster A. R. , Tiller R. V. , De B. K.
Published: April 2012

We report a fatal case of
Brucella suis
endocarditis initially misdiagnosed by automated identification systems as
Ochrobactrum anthropi
infection in a patient with a history of Marfan syndrome and recreational feral swine hunting. This report emphasizes the need to consider brucellosis as a part of the differential diagnosis of acute febrile illness, particularly in patients with known risk of exposure.
Genetic Diversity of Streptococcus equi subsp. zooepidemicus and Doxycycline Resistance in Kennelled Dogs
Authors: Chalker Victoria J. , Waller Andrew , Webb Katy , Spearing Emma , Crosse Patricia , Brownlie Joe , Erles Kerstin
Published: April 2012

The genetic diversity and antibiotic resistance profiles of 38Streptococcus equisubsp.zooepidemicusisolates were determined from a kennelled canine population during two outbreaks of hemorrhagic pneumonia (1999 to 2002 and 2007 to 2010). Analysis of theszpgene hypervariable region and the 16S-23S rRNA intergenic spacer region and multilocus sequence typing (MLST) indicated a predominanttetO-positive, doxycycline-resistant ST-10 strain during 1999 to 2002 and a predominanttetM-positive doxycycline-resistant ST-62 strain during 2007 to 2010.
Structural Basis for RNA Binding and Homo-Oligomer Formation by Influenza B Virus Nucleoprotein
Authors: Ng Andy Ka-Leung , Lam Mandy Ka-Han , Zhang Hongmin , Liu Jinhuan , Au Shannon Wing-Ngor , Chan Paul Kay-Sheung , Wang Jiahuai , Shaw Pang-Chui
Published: April 2012

Influenza virus nucleoprotein (NP) is the major component of the viral ribonucleoprotein complex, which is crucial for the transcription and replication of the viral genome. We have determined the crystal structure of influenza B virus NP to a resolution of 3.2 Å. Influenza B NP contains a head, a body domain, and a tail loop. The electropositive groove between the head and body domains of influenza B NP is crucial for RNA binding. This groove also contains an extended flexible charged loop (amino acids [aa] 125 to 149), and two lysine clusters at the first half of this loop were shown to be crucial for binding RNA. Influenza B virus NP forms a crystallographic homotetramer by inserting the tail loop into the body domain of the neighboring NP molecule. A deeply buried salt bridge between R472 and E395 and a hydrophobic cluster at F468 are the major driving forces for the insertion. The analysis of the influenza B virus NP structure and function and comparisons with influenza A virus NP provide insights into the mechanisms of action and underpin efforts to design inhibitors for this class of proteins.
A Novel Variant Marking HLA-DP Expression Levels Predicts Recovery from Hepatitis B Virus Infection
Authors: Thomas Rasmi , Thio Chloe L. , Apps Richard , Qi Ying , Gao Xiaojiang , Marti Darlene , Stein Judy L. , Soderberg Kelly A. , Moody M. Anthony , Goedert James J. , Kirk Gregory D. , Hoots W. Keith , Wolinsky Steven , Carrington Mary
Published: April 2012

Variants near theHLA-DPgene show the strongest genome-wide association with chronic hepatitis B virus (HBV) infection and HBV recovery/persistence in Asians. To test the effect of the HLA-DP region on outcomes to HBV infection, we sequenced the polymorphicHLA-DPB1andDPA1coding exons and the corresponding 3′ untranslated regions (3′UTRs) in 662 individuals of European-American and African-American ancestry. The genome-wide association study (GWAS) variant (rs9277535;550A/G) in the 3′UTR of theHLA-DPB1gene that associated most significantly with chronic hepatitis B and outcomes to HBV infection in Asians had a marginal effect on HBV recovery in our European- and African-American samples (odds ratio [OR] = 0.39,P= 0.01, combined ethnic groups). However, we identified a novel variant in theHLA-DPB13′UTR region,496A/G(rs9277534), which associated very significantly with HBV recovery in both European and African-American populations (OR = 0.37,P= 0.0001, combined ethnic groups). The496A/Gvariant distinguishes the most protectiveHLA-DPB1allele (DPB1*04:01) from the most susceptible (DPB1*01:01), whereas550A/Gdoes not.496A/Ghas a stronger effect than any individualHLA-DPB1orDPA1allele and any otherHLAalleles that showed an association with HBV recovery in our European-American cohort. The496GGgenotype, which confers recessive susceptibility to HBV persistence, also associates in a recessive manner with significantly higher levels of HLA-DP surface protein and transcript level expression in healthy donors, suggesting that differences in expression of HLA-DP may increase the risk of persistent HBV infection.
Distinct Effects of Two HIV-1 Capsid Assembly Inhibitor Families That Bind the Same Site within the N-Terminal Domain of the Viral CA Protein
Authors: Lemke Christopher T. , Titolo Steve , von Schwedler Uta , Goudreau Nathalie , Mercier Jean-François , Wardrop Elizabeth , Faucher Anne-Marie , Coulombe René , Banik Soma S. R. , Fader Lee , Gagnon Alexandre , Kawai Stephen H. , Rancourt Jean , Tremblay Martin , Yoakim Christiane , Simoneau Bruno , Archambault Jacques , Sundquist Wesley I. , Mason Stephen W.
Published: April 2012

The emergence of resistance to existing classes of antiretroviral drugs necessitates finding new HIV-1 targets for drug discovery. The viral capsid (CA) protein represents one such potential new target. CA is sufficient to form mature HIV-1 capsids
in vitro
, and extensive structure-function and mutational analyses of CA have shown that the proper assembly, morphology, and stability of the mature capsid core are essential for the infectivity of HIV-1 virions. Here we describe the development of an
in vitro
capsid assembly assay based on the association of CA-NC subunits on immobilized oligonucleotides. This assay was used to screen a compound library, yielding several different families of compounds that inhibited capsid assembly. Optimization of two chemical series, termed the benzodiazepines (BD) and the benzimidazoles (BM), resulted in compounds with potent antiviral activity against wild-type and drug-resistant HIV-1. Nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic analyses showed that both series of inhibitors bound to the N-terminal domain of CA. These inhibitors induce the formation of a pocket that overlaps with the binding site for the previously reported CAP inhibitors but is expanded significantly by these new, more potent CA inhibitors. Virus release and electron microscopic (EM) studies showed that the BD compounds prevented virion release, whereas the BM compounds inhibited the formation of the mature capsid. Passage of virus in the presence of the inhibitors selected for resistance mutations that mapped to highly conserved residues surrounding the inhibitor binding pocket, but also to the C-terminal domain of CA. The resistance mutations selected by the two series differed, consistent with differences in their interactions within the pocket, and most also impaired virus replicative capacity. Resistance mutations had two modes of action, either directly impacting inhibitor binding affinity or apparently increasing the overall stability of the viral capsid without affecting inhibitor binding. These studies demonstrate that CA is a viable antiviral target and demonstrate that inhibitors that bind within the same site on CA can have distinct binding modes and mechanisms of action.
CD4+CD25+Regulatory T Cells Impair HIV-1-Specific CD4 T Cell Responses by Upregulating Interleukin-10 Production in Monocytes
Authors: Kwon Douglas S. , Angin Mathieu , Hongo Tomoyuki , Law Kenneth M. , Johnson Jessica , Porichis Filippos , Hart Meghan G. , Pavlik David F. , Tighe Daniel P. , Kavanagh Daniel G. , Streeck Hendrik , Addo Marylyn M. , Kaufmann Daniel E.
Published: April 2012

T cell dysfunction in the presence of ongoing antigen exposure is a cardinal feature of chronic viral infections with persistent high viremia, including HIV-1. Although interleukin-10 (IL-10) has been implicated as an important mediator of this T cell dysfunction, the regulation of IL-10 production in chronic HIV-1 infection remains poorly understood. We demonstrated that IL-10 is elevated in the plasma of individuals with chronic HIV-1 infection and that blockade of IL-10 signaling results in a restoration of HIV-1-specific CD4 T cell proliferation, gamma interferon (IFN-γ) secretion, and, to a lesser extent, IL-2 production. Whereas IL-10 blockade leads to restoration of IFN-γ secretion by HIV-1-specific CD4 T cells in all categories of subjects investigated, significant enhancement of IL-2 production and improved proliferation of CD4 T helper cells are restricted to viremic individuals. In peripheral blood mononuclear cells (PBMCs), this IL-10 is produced primarily by CD14+monocytes, but its production is tightly controlled by regulatory T cells (Tregs), which produce little IL-10 directly. When Tregs are depleted from PBMCs of viremic individuals, the effect of the IL-10 signaling blockade is abolished and IL-10 production by monocytes decreases, while the production of proinflammatory cytokines, such as tumor necrosis factor alpha (TNF-α), increases. The regulation of IL-10 by Tregs appears to be mediated primarily by contact or paracrine-dependent mechanisms which involve IL-27. This work describes a novel mechanism by which regulatory T cells control IL-10 production and contribute to dysfunctional HIV-1-specific CD4 T cell help in chronic HIV-1 infection and provides a unique mechanistic insight into the role of regulatory T cells in immune exhaustion.
A Triclade DNA Vaccine Designed on the Basis of a Comprehensive Serologic Study Elicits Neutralizing Antibody Responses against All Clades and Subclades of Highly Pathogenic Avian Influenza H5N1 Viruses
Authors: Zhou Fan , Wang Guiqin , Buchy Philippe , Cai Zhipeng , Chen Honglin , Chen Zhiwei , Cheng Genhong , Wan Xiu-Feng , Deubel Vincent , Zhou Paul
Published: April 2012

Because of their rapid evolution, genetic diversity, broad host range, ongoing circulation in birds, and potential human-to-human transmission, H5N1 influenza viruses remain a major global health concern. Their high degree of genetic diversity also poses enormous burdens and uncertainties in developing effective vaccines. To overcome this, we took a new approach, i.e., the development of immunogens based on a comprehensive serologic study. We constructed DNA plasmids encoding codon-optimized hemagglutinin (HA) from 17 representative strains covering all reported clades and subclades of highly pathogenic avian influenza H5N1 viruses. Using DNA plasmids, we generated the corresponding H5N1 pseudotypes and immune sera. We performed an across-the-board pseudotype-based neutralization assay and determined antigenic clusters by cartography. We then designed a triclade DNA vaccine and evaluated its immunogenicity and protection in mice. We report here that (sub)clades 0, 1, 3, 4, 5, 6, 7.1, and 9 were grouped into antigenic cluster 1, (sub)clades 2.1.3.2, 2.3.4, 2.4, 2.5, and 8 were grouped into another antigenic cluster, with subclade 2.2.1 loosely connected to it, and each of subclades 2.3.2.1 and 7.2 was by itself. Importantly, the triclade DNA vaccine encoding HAs of (sub)clades 0, 2.3.2.1, and 7.2 elicited broadly neutralizing antibody responses against all H5 clades and subclades and protected mice against high-lethal-dose heterologous H5N1 challenge. Thus, we conclude that broadly neutralizing antibodies against all H5 clades and subclades can indeed be elicited with immunogens on the basis of a comprehensive serologic study. Further evaluation and optimization of such an approach in ferrets and in humans is warranted.
Uncommon Pathways of Immune Escape Attenuate HIV-1 Integrase Replication Capacity
Authors: Brockman Mark A. , Chopera Denis R. , Olvera Alex , Brumme Chanson J. , Sela Jennifer , Markle Tristan J. , Martin Eric , Carlson Jonathan M. , Le Anh Q. , McGovern Rachel , Cheung Peter K. , Kelleher Anthony D. , Jessen Heiko , Markowitz Martin , Rosenberg Eric , Frahm Nicole , Sanchez Jorge , Mallal Simon , John Mina , Harrigan P. Richard , Heckerman David , Brander Christian , Walker Bruce D. , Brumme Zabrina L.
Published: April 2012

An attenuation of the HIV-1 replication capacity (RC) has been observed for immune-mediated escape mutations in Gag restricted by protective HLA alleles. However, the extent to which escape mutations affect other viral proteins during natural infection is not well understood. We generated recombinant viruses encoding plasma HIV-1 RNA integrase sequences from antiretroviral-naïve individuals with early (
n
= 88) and chronic (
n
= 304) infections and measured the
in vitro
RC of each. In contrast to data from previous studies of Gag, we observed little evidence that host HLA allele expression was associated with integrase RC. A modest negative correlation was observed between the number of HLA-B-associated integrase polymorphisms and RC in chronic infection (
R
= −0.2;
P
= 0.003); however, this effect was not driven by mutations restricted by protective HLA alleles. Notably, the integrase variants S119R, G163E, and I220L, which represent uncommon polymorphisms associated with HLA-C*05, -A*33, and -B*52, respectively, correlated with lower RC (all
q
< 0.2). We identified a novel C*05-restricted epitope (HTDNGSNF
114–121
) that likely contributes to the selection of the S119R variant, the polymorphism most significantly associated with lower RC in patient sequences. An NL4-3 mutant encoding the S119R polymorphism displayed a ∼35%-reduced function that was rescued by a single compensatory mutation of A91E. Together, these data indicate that substantial HLA-driven attenuation of integrase is not a general phenomenon during HIV-1 adaptation to host immunity. However, uncommon polymorphisms selected by HLA alleles that are not conventionally regarded to be protective may be associated with impaired protein function. Vulnerable epitopes in integrase might therefore be considered for future vaccine strategies.
A Single Amino Acid at the Hemagglutinin Cleavage Site Contributes to the Pathogenicity and Neurovirulence of H5N1 Influenza Virus in Mice
Authors: Zhang Yi , Sun Yipeng , Sun Honglei , Pu Juan , Bi Yuhai , Shi Yi , Lu Xishan , Li Jing , Zhu Qingyu , Gao George F. , Yang Hanchun , Liu Jinhua
Published: April 2012

H5 influenza viruses containing a motif of multiple basic amino acids at the hemagglutinin (HA) cleavage site (HACS) are highly pathogenic in chicken but display different virulence phenotypes in mammals. Previous studies have shown that multiple basic amino acids of H5N1 influenza virus are a prerequisite for lethality in mice. However, it remains unclear which specific residue at the cleavage site affects the pathogenicity of H5N1 in mammals. A comprehensive genetic analysis of the H5N1 HACS showed that residues at P6 (position 325, by H3 numbering) were the most polymorphic, including serine (S), arginine (R), deletion (*), glycine (G), and isoleucine (I). To determine whether a single residue at P6 could affect virulence, we introduced different mutations at P6 of an avirulent clade 7 H5N1 strain, rg325G, by reverse genetics. Among the recombinant viruses, the rg325S virus showed the highest cleavage efficiency
in vitro
. All these viruses were highly pathogenic in chicken but exhibited different virulences in mice. The rg325S virus exhibited the highest pathogenicity in terms of unrestricted organ tropism and neurovirulence. Remarkably, the HA-325S substitution dramatically increased the pathogenicity of H5N1 viruses of other clades, including clades 2.2, 2.3.2, and 2.3.4, indicating that this residue impacts genetically divergent H5N1 viruses. An analysis of predicted structures containing these mutations showed that the cleavage site loop with 325S was the most exposed, which might be responsible for the efficient cleavage and high virulence. Our results demonstrate that an amino acid substitution at the P6 cleavage site alone could modulate the virulence of H5N1 in mice.
Structural Insight into the Unique Properties of Adeno-Associated Virus Serotype 9
Authors: DiMattia Michael A. , Nam Hyun-Joo , Van Vliet Kim , Mitchell Matthew , Bennett Antonette , Gurda Brittney L. , McKenna Robert , Olson Norman H. , Sinkovits Robert S. , Potter Mark , Byrne Barry J. , Aslanidi George , Zolotukhin Sergei , Muzyczka Nicholas , Baker Timothy S. , Agbandje-McKenna Mavis
Published: April 2012

Adeno-associated virus serotype 9 (AAV9) has enhanced capsid-associated tropism for cardiac muscle and the ability to cross the blood-brain barrier compared to other AAV serotypes. To help identify the structural features facilitating these properties, we have used cryo-electron microscopy (cryo-EM) and three-dimensional image reconstruction (cryo-reconstruction) and X-ray crystallography to determine the structure of the AAV9 capsid at 9.7- and 2.8-Å resolutions, respectively. The AAV9 capsid exhibits the surface topology conserved in all AAVs: depressions at each icosahedral two-fold symmetry axis and surrounding each five-fold axis, three separate protrusions surrounding each three-fold axis, and a channel at each five-fold axis. The AAV9 viral protein (VP) has a conserved core structure, consisting of an eight-stranded, β-barrel motif and the αA helix, which are present in all parvovirus structures. The AAV9 VP differs in nine variable surface regions (VR-I to -IX) compared to AAV4, but at only three (VR-I, VR-II, and VR-IV) compared to AAV2 and AAV8. VR-I differences modify the raised region of the capsid surface between the two-fold and five-fold depressions. The VR-IV difference produces smaller three-fold protrusions in AAV9 that are less “pointed” than AAV2 and AAV8. Significantly, residues in the AAV9 VRs have been identified as important determinants of cellular tropism and transduction and dictate its antigenic diversity from AAV2. Hence, the AAV9 VRs likely confer the unique infection phenotypes of this serotype.
Endovascular recanalization for chronic symptomatic middle cerebral artery total occlusion
Authors: Ma Ning , Mo Da-Peng , Gao Feng , Miao Zhong-Rong
Published: April 2012

The optimal treatment of chronic middle cerebral artery (MCA) occlusion is unclear. Angioplasty and stenting may be an alternative treatment for patients with recurrent ischemic symptoms despite medical therapy. Two patients with chronic right MCA occlusion successfully treated with stenting are reported, together with their long term follow-up to illustrate the feasibility of endovascular recanalization. One patient remained asymptomatic at the 29-month follow-up. Another patient developed symptomatic in-stent restenosis at 12 months which resolved after repeat angioplasty. Further larger scale pilot studies are needed to determine the efficacy and long term outcome of this treatment.
Le fondu de Lyman
Authors: Poquérusse Alain
Published: April 2012

Simulant par dynamique moléculaire une assemblée d’ions hydrogénoïdes, on étudie comment leur voisinage perturbe la série de Lyman et son prolongement continu de recombinaison, avec en appui la solution exacte à deux noyaux. Tant que deux raies au moins sont distinctes, le fondu enchaîné vers le continu demeure très lisse.
VISCOUS FRW MODELS WITH PARTICLE CREATION IN EARLY UNIVERSE
Authors: SINGH C. P.
Published: April 2012

We discuss the dynamical effects of bulk viscosity and particle creation on the early evolution of the Friedmann–Robertson–Walker model in the framework of open thermodynamical systems. We consider bulk viscosity and particle creation as separate irreversible processes. Exact solutions of the Einstein field equations are obtained by using the "gamma-law" equation of state p = (γ-1)ρ, where the adiabatic parameter γ varies with scale factor of the metric. We consider the cosmological model to study the early phases of the evolution of the universe as it goes from an inflationary phase to a radiation-dominated era in the presence of bulk viscosity and particle creation. Analytical solutions are obtained for particle number density and entropy for all models. It is found that, by choosing appropriate functions for particle creation rate and bulk viscous coefficient, the models exhibit singular and non-singular beginnings.
LIGHT SCALAR DECAY IN A DIQUARK CHIRAL EFFECTIVE THEORY
Authors: HONG DEOG KI , SONG CHAEJUN
Published: April 2012

We calculate the decay rate of light scalar mesons, using a diquark chiral effective theory, recently proposed to describe exotic hadrons. In the effective theory the light scalar mesons are postulated to be bound states of diquark and antidiquark. We find our results are in good agreement with experimental data. The axial couplings of diquarks with pions and kaons are found to be quite small and the perturbation is reliable. It shows that the diquark picture captures the correct physics of light scalar mesons.
ANCHORING OF TWISTED CHIRAL NEMATIC LIQUID CRYSTALS ON A THIN POLYMERIC FILM
Authors: ZHOU XUAN , ZHANG ZHIDONG , ZHANG YANJUN , XUAN LI
Published: April 2012

A generalized form of anisotropic surface energy for the description of twisted chiral nematic samples with side-chain polymeric layers is proposed, and the anchoring properties of such samples are analyzed, using the equivalent anchoring energy method proposed by Alexe-Ionescu et al. Our results give a more general expression for the equivalent anchoring energy, the new variables included in the expression are determined by the anchoring of the side chains and by the sterical interaction of the side chains with the nematic liquid crystals (NLCs). In addition, the coupling of the polymer side chains with the surface, reduces the equivalent anchoring energy as well as the threshold field.
QUASI TWO-DIMENSIONAL ANALYSIS OF THE SURFACE POTENTIAL FOR POLY-Si THIN FILM TRANSISTORS BASED ON THE CHANNEL POTENTIAL
Authors: ZHU ZHEN , CHU JUNHAO
Published: April 2012

A quasi two-dimensional analysis of the surface potential for polycrystalline silicon thin film transistors based on the channel potential is developed. Since the drain bias is taken into account, the surface potential model is proposed to approach the surface potential in the two-dimensional device although this model is developed by solving the one-dimensional Poisson's equation. This model is derived under the relative high gate and low drain biases while devices are operated in the strong inversion region. It is obtained by introducing the channel potential expression containing the drain bias and the normalized channel distance. And this channel-potential-based surface potential model is verified by the two-dimensional-device simulator in various gate voltages, various drain voltages and various channel lengths. This model well characterizes the surface potential distribution along the device's channel in the strong inversion region under the relative high gate and low drain biases.
STRUCTURE AND CONDUCTIVITY FLUCTUATIONS OF THE Y3Ba5Cu8O18 SUPERCONDUCTOR
Authors: LANDÍNEZ TÉLLEZ D. A. , CABRERA BÁEZ M. , ROA-ROJAS J.
Published: April 2012

Synthesis of the Y 3 Ba 5 Cu 8 O 18 superconducting material by the standard solid state reaction is reported. DC resistivity measurements reveal a bulk Tc = 97.86 K, which was determined by the criterion of the maximum in the numerical temperature derivative of electrical resistivity. Structure characterization was performed by means of the X-ray diffraction (XRD) technique. A Rietveld refinement of XRD patterns shows that the material crystallizes in an orthorhombic structure, space group Pmm2 with cell parameters a = 3.9211(3) Å, b = 3.8514(1) Å and c = 31.0170(0) Å. In order to study the pairing mechanism close to Tc, conductivity fluctuation analysis was performed by the method of logarithmic temperature derivative of the conductivity excess. Close and above Tc, the conductivity fluctuation analysis revealed the occurrence of two fluctuation regimes characterized by the critical exponents λ 3D = 0.48 and λ 2D = 0.97. These regions were interpreted as corresponding to 3D and 2D Gaussian regimes, respectively. By the utilization of the Ginzburg–Landau theory, we experimentally determined the Ginzburg number. Our results are in agreement with that reported on YBa 2 Cu 3 O 7-δ, but an enhancement of the Gaussian fluctuation regimes was experimentally detected. The correlations of the critical exponents with the dimensionality of the fluctuation system for each Gaussian regime were performed by using the Aslamazov–Larkin theory. Closer to Tc, a genuinely critical regime was identified. Scaling of our results permits to establish that the dynamical of fluctuation system has the universality class described by the 3D-XY model. Below Tc, it is observed that for several values of transport current density, this material evidences a paracoherent regime followed by a coherent transition, which occurs in the regime of the zero resistance state.
ENHANCED TRANSMISSION OF PLASMONIC WAVEPLATES WITH A PERIODIC ARRAY OF NANORECTANGLES
Authors: LI HENGYI , LUO XIANGANG , GUO ZHEN , WEN KUNHUA , YAN LIANSAN
Published: April 2012

Plasmonic waveplates with enhanced transmission can be achieved in the proposed structure with a periodic array of nanorectangles. Based on the model of nanoslits, both the transverse electric (TE) and transverse magnetic (TM) waves can be transmitted through the nanorectangles, enhancing the transmission of the incident polarized light. Simulation results show that the transmission ratio and phase shift of TE and TM waves can be manipulated by the nanorectangles structures, enabling plasmonic waveplates with enhanced transmission.
GUIDING PROBABILISTIC SEARCH OF THE PROTEIN CONFORMATIONAL SPACE WITH STRUCTURAL PROFILES
Authors: OLSON BRIAN , MOLLOY KEVIN , HENDI S. FARID , SHEHU AMARDA
Published: April 2012

The roughness of the protein energy surface poses a significant challenge to search algorithms that seek to obtain a structural characterization of the native state. Recent research seeks to bias search toward near-native conformations through one-dimensional structural profiles of the protein native state. Here we investigate the effectiveness of such profiles in a structure prediction setting for proteins of various sizes and folds. We pursue two directions. We first investigate the contribution of structural profiles in comparison to or in conjunction with physics-based energy functions in providing an effective energy bias. We conduct this investigation in the context of Metropolis Monte Carlo with fragment-based assembly. Second, we explore the effectiveness of structural profiles in providing projection coordinates through which to organize the conformational space. We do so in the context of a robotics-inspired search framework proposed in our lab that employs projections of the conformational space to guide search. Our findings indicate that structural profiles are most effective in obtaining physically realistic near-native conformations when employed in conjunction with physics-based energy functions. Our findings also show that these profiles are very effective when employed instead as projection coordinates to guide probabilistic search toward undersampled regions of the conformational space.
FOUR-VECTOR VERSUS FOUR-SCALAR REPRESENTATION OF THE DIRAC WAVE FUNCTION
Authors: ARMINJON MAYEUL , REIFLER FRANK
Published: April 2012

In a Minkowski spacetime, one may transform the Dirac wave function under the spin group, as one transforms coordinates under the Poincaré group. This is not an option in a curved spacetime. Therefore, in the equation proposed independently by Fock and Weyl, the four complex components of the Dirac wave function transform as scalars under a general coordinate transformation. Recent work has shown that a covariant complex four-vector representation is also possible. Using notions of vector bundle theory, we describe these two representations in a unified framework. We prove theorems that relate together the different representations and the different choices of connections within each representation. As a result, either of the two representations can account for a variety of inequivalent, linear, covariant Dirac equations in a curved spacetime that reduce to the original Dirac equation in a Minkowski spacetime. In particular, we show that the standard Dirac equation in a curved spacetime, with any choice of the tetrad field, is equivalent to a particular realization of the covariant Dirac equation for a complex four-vector wave function.
MULTITIME BOUSSINESQ SOLITONS
Authors: MATEI LAURA GABRIELA , UDRIŞTE CONSTANTIN , GHIU CRISTIAN
Published: April 2012

The paper is devoted to the achievements of two complementary multitime missions — to state a multitime Boussinesq PDE, as geometrical prolongation of the classical one, and to obtain its multitime soliton solutions. The advantages of geometrical ingredients capable to create this significant multitime PDE are clearly shown together with problems that were or should be overcome in the similar problems. The main goal of both missions is the investigation of multitemporal Boussinesq waves. Stressing the importance of the geometry on the multitime evolution phenomena, we add original results on multitime Boussinesq solitons and on Riccati ODEs of superior order.
VHE GAMMA-RAY INDUCED PAIR CASCADES IN BLAZARS AND RADIO GALAXIES
Authors: BÖTTCHER MARKUS , ROUSTAZADEH PARISA
Published: April 2012

Recent discoveries by VERITAS, H.E.S.S., and MAGIC indicate that very-high-energy (VHE) gamma-rays may be produced in all types of blazars, including radio-loud quasars. In the dense nuclear radiation fields (BLR, dust torus IR) in these objects, VHE gamma-rays may be efficiently absorbed and initiate Compton-supported pair cascades. We have developed a Monte-Carlo code following the full 3-dimensional development of pair cascades in AGN environments. We have shown that even very weak magnetic fields may lead to efficient quasi-isotropization of the cascade emission, escaping predominantly in MeV – GeV gamma-rays. We propose this as a potential contributor to the Fermi gamma-ray flux from several radio galaxies, and present model fits to the Fermi-detected radio galaxies NGC 1275 and Cen A.
GAMMA RAYS FROM RADIO GALAXIES: FERMI/LAT OBSERVATIONS
Authors:   On behalf of the Fermi-LAT collaboration, GRANDI PAOLA
Published: April 2012

We review the high energy properties of Misaligned AGNs associated with γ-ray sources detected by Fermi in 24 months of survey. Most of them are nearby emission low power radio galaxies (i.e FRIs) which probably have structured jets. On the contrary, high power radio sources (i.e FRIIs) with GeV emission are rare. The small number of FRIIs does not seem to be related to their higher redshifts. Assuming proportionality between the radio core flux and the γ-ray flux, several of them are expected to be bright enough to be detected above 100 MeV in spite of their distance. We suggest that beaming/jet structural differences are responsible for the detection rate discrepancy observed between FRIs and FRIIs.
VERITAS OBSERVATIONS OF RELATIVISTIC JETS
Authors: MUKHERJEE RESHMI
Published: April 2012

VERITAS is an array of four imaging atmospheric Cherenkov telescopes located in southern Arizona, and is now starting its fifth year of observations of the northern Sky at energies > 100 GeV. Observations of astrophysical objects in the TeV band are sensitive probes of highly energetic processes occurring in these sources. The majority of the active galaxies detected at TeV energies are blazars, sources where we view the jet nearly along its axis. TeV and multiwavelength observations of blazars help us to better understand the mechanisms of ultrarelativistic jet production by supermassive black holes, and constrain models of particle acceleration in blazar jets. Galactic sources at TeV energies include supernova remnants, pulsar wind nebulae, and binary systems, and TeV emission is a key diagnostic of highly energetic particles in these objects. This report presents recent results from VERITAS on Galactic and extragalactic sources.
NON-THERMAL EMISSION FROM GALACTIC JETS
Authors: BOSCH-RAMON VALENTÍ
Published: April 2012

Jets are ubiquitous in the Universe. They are collimated outflows whose origin is associated to an accretion disc and a central object, and can be very powerful non-thermal emitters. Jets form in active galactic nuclei, gamma-ray bursts, microquasars, and young stellar objects. Galactic jets emitting non-thermal emission are typically associated to microquasars, although the jets of massive young stellar objects are also non-thermal sources. The production of non-thermal radiation, in particular radio synchrotron emission, is a clear indication that particle acceleration is taking place in the source, which hints to the generation of photons even at high energies. In this work, we will discuss the emitting sites in, or related to, microquasar jets, and briefly comment on the possibility of high-energy emission in jets from young stellar objects.
STRUCTURE AND EMISSION OF COMPACT BLAZAR JETS
Authors: MARSCHER ALAN P.
Published: April 2012

Relativistic jets in blazars on parsec scales can now be explored with direct imaging at radio wavelengths as well as observations of time variability of flux and linear polarization at various wavebands. The results thus far suggest that the millimeter-wave "core" is usually a standing, conical shock and that the jet plasma is turbulent. Disturbances and turbulent plasma crossing the standing shock can explain much of the observed variability, as well as the appearance of bright knots moving down the jet at superluminal apparent speeds. The core, located parsecs downstream of the central engine, appears to be the site of many of the outbursts observed at optical, X-ray, and γ-ray energies. Rotations in the optical polarization position angle prior to the passage of a knot through the millimeter-wave core provide evidence for helical magnetic fields that accelerate and collimate the jet before turbulence tangles the fields.
THE 2010 M 87 VHE FLARE AND ITS ORIGIN: THE MULTI-WAVELENGTH PICTURE
Authors:   for the H.E.S.S., MAGIC, VERITAS and FERMI-LAT COLLABORATIONS and THE M 87 MWL MONITORING TEAMS, RAUE M. , STAWARZ L. , MAZIN D. , COLIN P. , HUI C. M. , BEILICKE M. , MCCONVILLE W. , GIROLETTI M. , HARRIS D. E. , STEELE I. A. , WALKER R.C.
Published: April 2012

The giant radio galaxy M 87, with its proximity (16 Mpc) and its very massive black hole ((3-6) × 109 M⊙), provides a unique laboratory to investigate very high energy (E>100 GeV; VHE) gamma-ray emission from active galactic nuclei and, thereby, probe particle acceleration to relativistic energies near supermassive black holes (SMBH) and in relativistic jets. M 87 has been established as a VHE γ-ray emitter since 2005. The VHE γ-ray emission displays strong variability on timescales as short as a day. In 2008, a rise in the 43 GHz Very Long Baseline Array (VLBA) radio emission of the innermost region (core; extension of < 100 R s ; Schwarzschild radii) was found to coincide with a flaring activity at VHE. This had been interpreted as a strong indication that the VHE emission is produced in the direct vicinity of the SMBH. In 2010 a flare at VHE was again detected triggering further multi-wavelength (MWL) observations with the VLBA, Chandra, and other instruments. At the same time, M 87 was also observed with the Fermi-LAT telescope at MeV/GeV energies, the European VLBI Network (EVN), and the Liverpool Telescope (LT). Here, preliminary results from the 2010 campaign will be reported.
LARGE-SCALE EMISSION IN FRI JETS
Authors: BORDAS POL , BOSCH-RAMON VALENTÍ , PERUCHO MANEL
Published: April 2012

The termination structures of the jets of Fanaroff & Riley (FR) galaxies are observed to produce extended non-thermal emission in a wide frequency range. The study of these structures can provide valuable insights on the conditions for particle acceleration and radiation at the shock fronts. We have studied the thermal and non-thermal emission that can be expected from the jet termination regions of Fanaroff & Riley type I sources. The broadband emssion from these galaxies has been recently extended to include the high-energy gamma-ray domain, owing to the Fermi detection of Cen A lobes. Exploring the physics behind the jet/medium interactions in FRI can provide valuable insights on the conditions for particle acceleration and radiation in the jet termination shocks. Making use of the results of a fully relativistic numerical simulation code of the evolution of a FRI jet we model the expected radiative output and predict spectra and lightcurves of both thermal and non-thermal emission at different source ages.
HIGH-ENERGY EMISSION FROM GAMMA-RAY BURSTS
Authors: DAIGNE FREDERIC
Published: April 2012

The theoretical consequences of the recent observations of gamma-ray bursts at high-energy by Fermi are discussed, with a focus on the internal-external shock model.
GRB PROMPT EMISSION: TURBULENCE, MAGNETIC FIELD AND JITTER RADIATION
Authors: MAO JIRONG
Published: April 2012

The jitter radiation, which is the emission of relativistic electrons in the random and small-scale magnetic field, is utilized to investigate the high-energy emission of gamma-ray bursts. We produce the random and small-scale magnetic field using turbulent scenario. The electrons can be accelerated by stochastic acceleration. We also estimate the acceleration and cooling timescales, aiming to identify the validation of jitter regime under the GRB fireball framework. The possible maximum energy of electrons in our case is estimated as well.
OBSERVATIONS OF PARTICLE ACCELERATION IN THE BLAST WAVES OF GAMMA-RAY BURSTS
Authors: CURRAN PETER A.
Published: April 2012

The electron energy distribution index, p, is a fundamental parameter of the process by which electrons at shock fronts are accelerated to relativistic speeds and by which they radiate, via synchrotron emission. This acceleration process is applicable to a myriad of astronomical jet sources such as AGN, X-ray binaries and gamma-ray bursts (GRBs), as well as to particle acceleration in the solar wind and supernovae, and the acceleration of cosmic rays. The accurate measurement of the distribution of p is of fundamental importance to differentiate between the possible theories of electron acceleration at any relativistic shock front; there is division as to whether p has a universal value or whether it has a distribution, and if so, what that distribution is.

Here one such source of synchrotron emission is examined: the blast waves of GRB afterglows observed by the Swift satellite. Within the framework of the GRB blast wave model, the constraints placed on the distribution of p by the observed X-ray spectral and temporal indices are examined and the distribution parametrized. The results show that the observed distribution of spectral indices is inconsistent with an underlying distribution of p composed of a single discrete value but consistent with a Gaussian distribution centred at p = 2.4 and having a width of 0.6. This finding disagrees with theoretical work that argues for a single, universal value of p, but also demonstrates that the width of the distribution is not as wide as has been suggested by some authors.
LARGE-SCALE MAGNETIC FIELD IN ACCRETION DISKS AND RELATIVISTIC POYNTING-FLUX JETS
Authors: LOVELACE R. V. E. , BISNOVATYI-KOGAN G. S.
Published: April 2012

In earlier works we pointed out that the disk's surface layers are non-turbulent and thus highly conducting (or non-diffusive) because of hydrodynamic and/or magnetorotational (MRI) instabilities are suppressed high in the disk where the magnetic and radiation pressures are larger than the plasma thermal pressure. We have derived equations for the vertical profiles of stationary accretion flows (with radial and azimuthal components), and the profiles of the large-scale, magnetic field taking into account the turbulent viscosity and diffusivity and the fact that the turbulence vanishes at the surface of the disk. Our recent analysis in Ref. 1 shows that the inward or outward advection of the large-scale magnetic field depends on the ratio [Formula: see text] of the accretion power going into magnetic disk winds to the viscous power dissipation and the plasma-β which is the ratio of the midplane plasma pressure to the magnetic pressure.

Recent radio emission, polarization, and Faraday rotation maps of the radio jet of the galaxy 3C303 have been obtained in Ref. 2 and show that one component of this jet has a galactic-scale electric current of ~ 3 × 1018 A flowing along the jet axis. We show that this current can be used to calculate the electromagnetic energy flow in this magnetically dominated jet.
PROBING HELICAL MAGNETIC FIELDS IN AGN BY ROTATION MEASURE GRADIENTS STUDIES
Authors: ALGABA JUAN C.
Published: April 2012

One of the tools that can provide evidence about the existence of helical magnetic fields in AGN is the observation of rotation measure gradients across the jet. Such observations have been previously made successfully, proving that such gradients are far from being rare, but common and typically persistent over several years, although some of them may show a reversal in the direction along the jet. Further studies of rotation measure gradients can help us in our understanding of the magnetic field properties and structure in the base of the jets. We studied Very Long Baseline Array (VLBA) polarimetric observations of 8 sources consistent of some quasars and BL Lacs at 12, 15, 22, 24 and 43 GHz and we find that all but two sources show indications of rotation measure gradients, either parallel or perpendicular to the jet. We interpret gradients perpendicular to the jet as indications of the change of the line of sight of the magnetic field due to its helicity, and gradients parallel to the jet as the decrease of magnetic field strength and/or electron density as we move along the jet. When comparing our results with the literature, we find temptative evidence of a rotation measure gradient flip, which can be explained as a change of the pitch angle or jet bending.