bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jet launching and field advection in quasi-Keplerian discs
Authors: Ferreira Jonathan , Petrucci Pierre Olivier 
Published: February 2011

AbstractThe fact that self-confined jets are observed around black holes, neutron stars and young forming stars points to a jet launching mechanism independent of the nature of the central object, namely the surrounding accretion disc. The properties of Jet Emitting Discs (JEDs) are briefly reviewed. It is argued that, within an alpha prescription for the turbulence (anomalous viscosity and diffusivity), the steady-state problem has been solved. Conditions for launching jets are very stringent and require a large scale magnetic field Bz close to equipartition with the total (gas and radiation) pressure. The total power feeding the jets decreases with the disc thickness: fat ADAF-like structures with h ~ r cannot drive super-Alfvénic jets. However, there exist also hot, optically thin JED solutions that would be observationally very similar to ADAFs.Finally, it is argued that variations in the large scale magnetic Bz field is the second parameter required to explain hysteresis cycles seen in LMXBs (the first one would be Ṁa).
Transient high-energy flares from accreting black holes
Authors: Vieyro Florencia L. , Romero Gustavo E. 
Published: February 2011

AbstractWe present a model for high-energy flares in accreting black holes based on the injection in a magnetized corona of a non-thermal population of relativistic particles. Coupled transport equations are solved for all species of particles and the electromagnetic and neutrino output is predicted for the case of Galactic black holes.
Isolating the jet in broadband spectra of XBs
Authors: Russell David M. , Lewis Fraser , Maitra Dipankar , Dunn Robert J. H. , Markoff Sera , Jonker Peter G. , Linares Manuel , Tudose Valeriu 
Published: February 2011

AbstractMost accretion-powered relativistic jet sources in our Galaxy are transient X-ray binaries (XBs). Efforts to coordinate multiwavelength observations of these objects have improved dramatically over the last decade. Now the challenge is to interpret broadband spectral energy distributions (SEDs) of XBs that are well sampled in both wavelength and time. Here we focus on the evolution of the jet in their broadband spectra. Some of the most densely sampled broadband SEDs of a neutron star transient (IGR J00291+5934) are used to constrain the optically thick–thin break in the jet spectrum. For the black hole transient XTE J1550-564, infrared – X-ray correlations, evolution of broadband spectra and timing signatures indicate that synchrotron emission from the jet likely dominates the X-ray power law at low luminosities (~(2 × 10−4 − 2 × 10−3) LEdd) during the hard state outburst decline.
Radiative MHD simulations of the jets from RW Aurigae
Authors: Teşileanu Ovidiu , Mignone Andrea , Massaglia Silvano , Stute Matthias 
Published: February 2011

AbstractThe MHD simulations of stellar jets recently included complex models of radiative emission computation, allowing for better predictions in terms of emission line ratios. Employing also Adaptive Mesh Refinement, the large-scale propagation of jets could be followed. The simulation of multiple shockwaves originating in perturbations close to the jet origin and travelling along the jet beam allows for the construction of synthetic emission maps at various wavelengths, to be directly compared to observations. We apply this procedure for the jets originating from RW Aurigae.
Coherent control of the isomerization of retinal in bacteriorhodopsin in the high intensity regime
Authors: Prokhorenko Valentyn I. , Halpin Alexei , Johnson Philip J. M. , Miller R. J. Dwayne , Brown Leonid S. 
Published: February 2011

Coherent control protocols provide a direct experimental determination of the relative importance of quantum interference or phase relationships of coupled states along a selected pathway. These effects are most readily observed in the high intensity regime where the field amplitude is sufficient to overcome decoherence effects. The coherent response of retinal photoisomerization in bacteriorhodopsin to the phase of the photoexcitation pulses was examined at fluences of 1015 – 2.5 × 1016 photons per square centimeter, comparable to or higher than the saturation excitation level of the S0 − S1 retinal electronic transition. At moderate excitation levels of ∼6 × 1015 photons/cm2 (&lt;100 GW/cm2), chirping the excitation pulses increases the all-trans to 13-cis isomerization yield by up to 16% relative to transform limited pulses. The reported results extend previous weak-field studies [Prokhorenko et al., Science 313, 1257 (2006)] and further illustrate that quantum coherence effects persist along the reaction coordinate in strong fields even for systems as complex as biological molecules. However, for higher excitation levels of ∼200 GW/cm2, there is a dramatic change in photophysics that leads to multiphoton generated photoproducts unrelated to the target isomerization reaction channel and drastically changes the observed isomerization kinetics that appears, in particular, as a red shift of the transient spectra. These results explain the apparent contradictions of the work by Florean et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 10896 (2009)] in the high intensity regime. We are able to show that the difference in observations and interpretation is due to artifacts associated with additional multiphoton-induced photoproducts. At the proper monitoring wavelengths, coherent control in the high intensity regime is clearly observable. The present work highlights the importance of conducting coherent control experiments in the low intensity regime to access information on quantum interference effects along specific reaction coordinates.
BiC: a web server for calculating bimodality of coexpression between gene and protein networks
Authors: Linderman George C. , Patel Vishal N. , Chance Mark R. , Bebek Gurkan 
Published: February 2011

Abstract
Summary: Bimodal patterns of expression have recently been shown to be useful not only in prioritizing genes that distinguish phenotypes, but also in prioritizing network models that correlate with proteomic evidence. In particular, subgroups of strongly coexpressed gene pairs result in an increased variance of the correlation distribution. This variance, a measure of association between sets of genes (or proteins), can be summarized as the bimodality of coexpression (BiC). We developed an online tool to calculate the BiC for user-defined gene lists and associated mRNA expression data. BiC is a comprehensive application that provides researchers with the ability to analyze both publicly available and user-collected array data.
Availability: The freely available web service and the documentation can be accessed at http://gurkan.case.edu/software.
Contact: gurkan@case.edu
Conservation of Galápagos land iguanas: genetic monitoring and predictions of a long‐term program on the island of Santa Cruz
Authors: Fabiani A. , Trucchi E. , Rosa S. , Marquez C. , Snell H. L. , Snell H. M. , Tapia Aguilera W. , Gentile G. 
Published: February 2011

AbstractThe distribution of the Galápagos land iguanas Conolophus subcristatus has been strongly affected by human activities in the last century. Previously widespread throughout the whole archipelago, today they inhabit only few islands, with populations often small and isolated. In this study, we analyzed the population genetic structure of land iguanas from Santa Cruz Island to investigate the genetic implications of a semi‐captive conservation program that started in middle 1970s and is still ongoing. Nine microsatellites were used to measure the level of genetic variability and to detect potential evidence of inbreeding and genetic sub‐structure. Furthermore, we used approximate Bayesian computation, together with software packages for coalescent‐based simulations, to test a priori hypotheses in different demographic scenarios. Despite the abrupt reduction in size of the original population, no evidence of inbreeding was found, and the levels of genetic variability were similar to those of undisturbed populations of the archipelago. Nevertheless, the source and the repatriated populations started differentiating (FST=0.016) and genetic sub‐structure was found. Following our results and the simulation of possible future scenarios, we suggest the genetic measures that should be adopted to avoid further genetic variability depletion and preserve this vulnerable endemic species.
Coopetitive Buyer–Supplier Relationship: An Investigation of Bargaining Power, Relational Context, and Investment Strategies
Authors: Nair Anand , Narasimhan Ram , Bendoly Elliot 
Published: February 2011

ABSTRACTThis study proposes an analytical approach combined with a behavioral experiment for a joint examination of the competitive and cooperative (i.e., coopetitive) relationship between a buyer and a supplier. Specifically, the article considers the scenario in which the buyer and the supplier invest in strategic capabilities to increase their relative bargaining power. The article examines how dynamic investments in strategic assets are influenced by the locus of bargaining power and by the underlying context (synergistic vs. adversarial) of the interfirm relationship. The dynamic evolution of bargaining power is also examined. A dynamic game model is considered to examine the evolution of investment strategies in critical resources and to investigate the issues of bargaining power in a buyer–supplier dyad. Equilibrium expressions for the investment strategies of the buyer and the supplier are presented and their implications for buyer–supplier relationships are examined. The behavioral experiment complements the analytical model and examines the correspondence between optimal behavior suggested by the analytical model and the boundedly rational behavior of decision makers in an experimental context. The results from the model and behavioral experiments suggest that the strategies are a function of the risk‐adjusted returns obtained from investments. The experiment shows that, in a synergistic relational context when the buyer maintains bargaining power, the investment shifts of the buyer and the supplier accord well with theoretical predictions. In an adversarial relational context, the results of the experimental study do not correspond well with that predicted by the theoretical model. The implications of the results are discussed and directions for future research are presented.
Effect of Separating Load Eccentricity on the Clamp Load Loss in a Bolted Joint Using a Strain Hardening Model
Authors: Nassar Sayed A. , Ganganala Mohan 
Published: February 2011

Abstract
A nonlinear model is proposed for studying the effect of the eccentricity of applied tensile forces on the clamp load loss in bolted joints that were initially tightened beyond the bolt elastic limit while the joint remained in the elastic range. A closed form solution is obtained for the amount of clamp load loss due to a cyclic separating force. The proposed model takes into account two sources of nonlinearity, namely, the strain hardening behavior of the yielded bolt material as well as the nonlinear deformation behavior of the clamped plates under an external separating load. After the initial tightening of the fastener past its elastic limit, the subsequent application of a tensile separating force on the joint tends to increase the fastener tension in a nonlinear fashion, and, simultaneously, reduce the clamping force in the bolted joint from its initial value. Upon the removal of the cyclic tensile load, the bolted joint system reaches a new equilibrium point between the residual fastener tension and the joint clamping force. At the new equilibrium point, the fastener tension is reduced from its preload due to its plastic elongation; simultaneously, a partial yet permanent loss in the clamp load level takes place. Excessive clamp load loss may lead to joint leakage, fastener loosening, or fatigue failure. For a known amplitude of the external cyclic tensile load, the increase in bolt tension and corresponding reduction in the joint clamp load are highly sensitive to the eccentricity of the tensile load (from the bolt center). Variables studied include the eccentricity value of the separating load, rate of strain hardening of the bolt material, compressive and tensile stiffness of the clamped plates, bolt stiffness, bolt preload, and magnitude of the separating tensile load.
Recurrent Sepsis Caused by Streptococcus pyogenes
Authors: Rasmussen Magnus 
Published: February 2011

ABSTRACT

I report that a 75-year-old man with severe atherosclerosis experienced two episodes of bacteremia with
Streptococcus pyogenes
of type
emm
87. Recurrent sepsis with
S. pyogenes
is extremely rare, and a foot ulcer was the suspected point of entry. The patient did not develop opsonizing antibodies to the isolate.
Multivariate Analyses Revealed Distinctive Features Differentiating Human and Cattle Isolates of Shiga Toxin-Producing Escherichia coli O157 in Japan
Authors: Lee Ken-ichi , French Nigel P. , Hara-Kudo Yukiko , Iyoda Sunao , Kobayashi Hideki , Sugita-Konishi Yoshiko , Tsubone Hirokazu , Kumagai Susumu 
Published: February 2011

ABSTRACTGenotypes of Shiga toxin-producingEscherichia coli(STEC) O157 isolated from humans and cattle were analyzed by uni- and multivariable logistic regression, and population structure methods, to gain insight into transmission and the nature of human infection. Eleven genotyping assays, including PCR typing of five virulence factors (stx1,stx2,stx2c,eae, andehxA) and a lineage-specific polymorphism assay using six markers (LSPA6), were considered in the analyses. The prevalence of thestx1,stx2, andstx2cvirulence factors was significantly different between human and cattle isolates. However, multivariable regression revealed that the presence of only thestx2gene was significantly associated with human isolates after controlling for confounding effects. LSPA6 typing demonstrated an apparent difference in the distribution of LSPA6 lineages between human and cattle isolates and a strong association betweenstxgenotypes and LSPA6 genotypes. Population genetics tools identified three genetically distinct clusters of STEC O157. Each cluster was characterized bystxgenotypes and LSPA6 genotypes. The human isolates typically comprised LSPA6 lineage I withstx1stx2strains and LSPA6 lineage I/II withstx2orstx2stx2cstrains. In contrast, the cattle isolates comprised LSPA6 lineage II strains withstx2corstx2stx2cstrains in addition to the clusters identified for the human isolates. Our analyses provide new evidence that thestx2gene is the most distinctive feature in human isolates compared to cattle isolates in Japan, and only a subset of the genetically diverse population isolated from cattle is involved in human illnesses. Our results may contribute to international comparisons and risk assessments of STEC O157.
Association of Src-Related Kinase Lyn with the Interleukin-2 Receptor and Its Role in Maintaining Constitutive Phosphorylation of JAK/STAT in Human T-Cell Leukemia Virus Type 1-Transformed T Cells
Authors: Shuh Maureen , Morse Barry A. , Heidecker Gisela , Derse David 
Published: February 2011

ABSTRACTHuman T-cell leukemia virus type 1 (HTLV-1) infection and transformation are associated with an incremental switch in the expression of the Src-related protein tyrosine kinases Lck and Lyn. We examined the physical and functional interactions of Lyn with receptors and signal transduction proteins in HTLV-1-infected T cells. Lyn coimmunoprecipitates with the interleukin-2 beta receptor (IL-2Rβ) and JAK3 proteins; however, the association of Lyn with the IL-2Rβ and Lyn kinase activity was independent of IL-2 stimulation. Phosphorylation of Janus kinase 3 (JAK3) and signal transducers and activator of transcription 5 (STAT5) proteins was reduced by treatment of cells with the Src kinase inhibitor PP2 or by ectopic expression of a dominant negative Lyn kinase protein.
N-Terminal Hemagglutinin Tag Renders Lysine-Deficient APOBEC3G Resistant to HIV-1 Vif-Induced Degradation by Reduced Polyubiquitination
Authors: Wang Yudi , Shao Qiujia , Yu Xianghui , Kong Wei , Hildreth James E. K. , Liu Bindong 
Published: February 2011

ABSTRACT
APOBEC3G, a potent HIV-1 host restriction factor, is overcome by HIV-1 viral infectivity factor (Vif), which induces its polyubiquitination and proteasomal degradation. Here we show that lysine-deficient APOBEC3G with an N-terminal hemagglutinin (HA) tag fusion (HA-A3G20K/R) was resistant to HIV-1 Vif-induced proteasomal degradation. HA-A3G20K/R molecules were packaged into wild-type HIV-1 particles, and HA-A3G20K/R drastically decreased wild-type HIV-1 reverse transcription products and infectivity. We also showed that the N terminus of A3G was a target of polyubiquitination induced by HIV-1 Vif. Thus, fusion of the HA tag to the N terminus of A3G20K/R reduced its polyubiquitination, the likely mechanism for the resistance of this protein to HIV-1 Vif-induced proteasomal degradation. Finding such ways to induce resistance of A3G to Vif may provide new approaches to anti-HIV/AIDS therapy.
Uncoupling Uncoating of Herpes Simplex Virus Genomes from Their Nuclear Import and Gene Expression
Authors: Rode Kathrin , Döhner Katinka , Binz Anne , Glass Mandy , Strive Tanja , Bauerfeind Rudolf , Sodeik Beate 
Published: February 2011

ABSTRACT

Incoming capsids of herpes simplex virus type 1 (HSV-1) enter the cytosol by fusion of the viral envelopes with host cell membranes and use microtubules and microtubule motors for transport to the nucleus. Upon docking to the nuclear pores, capsids release their genomes into the nucleoplasm. Progeny genomes are replicated in the nucleoplasm and subsequently packaged into newly assembled capsids. The minor capsid protein pUL25 of alphaherpesviruses is required for capsid stabilization after genome packaging and for nuclear targeting of incoming genomes. Here, we show that HSV-1 pUL25 bound to mature capsids within the nucleus and remained capsid associated during assembly and nuclear targeting. Furthermore, we tested potential interactions between parental pUL25 bound to incoming HSV-1 capsids and host factors by competing for such interactions with an experimental excess of cytosolic pUL25. Overexpression of pUL25, GFPUL25, or UL25GFP prior to infection reduced gene expression of HSV-1. Electron microscopy and
in situ
hybridization studies revealed that an excess of GFPUL25 or UL25GFP prevented efficient nuclear import and/or transcription of parental HSV-1 genomes, but not nuclear targeting of capsids or the uncoating of the incoming genomes at the nuclear pore. Thus, the uncoating of HSV-1 genomes could be uncoupled from their nuclear import and gene expression. Most likely, surplus pUL25 competed with important interactions between the parental capsids, and possibly between authentic capsid-associated pUL25, and cytosolic or nuclear host factors required for functional interaction of the incoming genomes with the nuclear machinery.
Kaposi's Sarcoma-Associated Herpesvirus Viral Interferon Regulatory Factor 3 Inhibits Gamma Interferon and Major Histocompatibility Complex Class II Expression
Authors: Schmidt Katharina , Wies Effi , Neipel Frank 
Published: February 2011

ABSTRACTKaposi's sarcoma-associated herpesvirus (KSHV) carries four genes with homology to human interferon regulatory factors (IRFs). One of these IRFs, the viral interferon regulatory factor 3 (vIRF-3), is expressed in latently infected primary effusion lymphoma (PEL) cells and required for their continuous proliferation. Moreover, vIRF-3 is known to be involved in modulation of the type I interferon (IFN) response. We now show that vIRF-3 also interferes with the type II interferon system and antigen presentation to the adaptive immune system. Starting with an analysis of the transcriptome, we show that vIRF-3 inhibits expression of major histocompatibility complex class II (MHC II) molecules: small interfering RNA (siRNA)-mediated knockdown of vIRF-3 in KSHV-infected PEL cell lines resulted in increased MHC II levels; overexpression of vIRF-3 in KSHV-negative B cells leads to downmodulation of MHC II. This regulation could be traced back to inhibition of class II transactivator (CIITA) transcription by vIRF-3. Reporter assays revealed that the gamma interferon (IFN-γ)-sensitive CIITA promoters PIV and PIII were inhibited by vIRF-3. Consistently, IFN-γ levels increased upon vIRF-3 knockdown in PEL cells. IFN-γ regulation by vIRF-3 was confirmed in reporter assays as well as by upregulation of typical IFN-γ target genes upon knockdown of vIRF-3 in PEL cells. In summary, we conclude that vIRF-3 contributes to the viral immunoevasion by downregulation of IFN-γ and CIITA and thus MHC II expression.
Environmental and Antigen Receptor-Derived Signals Support Sustained Surveillance of the Lungs by Pathogen-Specific Cytotoxic T Lymphocytes
Authors: Lee Young-Tae , Suarez-Ramirez Jenny E. , Wu Tao , Redman Jason M. , Bouchard Keith , Hadley Gregg A. , Cauley Linda S. 
Published: February 2011

ABSTRACTViral infections often gain access to the body of their host by exploiting areas of natural vulnerability, such as the semipermeable surfaces of mucosal tissues which are adapted for adsorption of nutrients and other diffusible molecules. Once the microbes have crossed the epithelial barrier, they can disperse to other tissues where eradication may not be possible. The best opportunity for successful immune intervention is immediately after infection while the pathogen is confined to a localized area of the body. Cytotoxic T lymphocytes (CTL) which reside at the site where the infection begins can make an important contribution to immunity by reducing early dissemination of the infection. Because the lungs provide easy access points for many pathogens to enter the body, they require protection from many complementary mechanisms, including pathogen-specific cytotoxic T cells. In this study we show that an enduring response to pathogen-derived peptide antigens facilitates sustained surveillance of the lungs by pathogen-specific CTL during the recovery from influenza virus infection. Our studies show that these processed peptide antigens reinforce expression of two homing receptors (CD69 and CD103) which help recently activated virus-specific CTL colonize the lungs during a mild inflammatory response. We suggest that this requirement for prolonged antigen presentation to reinforce local CTL responses in the lungs explains why protective cellular immunity quickly declines following influenza virus infection and other viral infections that enter the body via mucosal tissues.