Coherent QCD phenomena in the Coherent Pion-Nucleon and Pion-Nucleus Production of Two Jets at High Relative Momenta

We use QCD to compute the cross section for coherent production of a di-jet (treated as a $q\bar q$ moving at high relative transverse momentum,$\kappa_t$). In the target rest frame,the space-time evolution of this reaction is dominated by the process in which the high $\kappa_t$ $q\bar q$ component of the pion wave function is formed before reaching the target. It then interacts through two gluon exchange. In the approximation of keeping the leading order in powers of $\alpha_s$ and all orders in $\alpha_{s}\ln(\kappa_{t}^2/k_{0}^2),$ the amplitudes for other processes are shown to be smaller at least by a power of $\alpha_{s}$. The resulting dominant amplitude is proportional to $z(1-z) \kappa_t^{-4}$ ($z$ is the fraction light-cone(+)momentum carried by the quark in the final state) times the skewed gluon distribution of the target. For the pion scattering by a nuclear target, this means that at fixed $x_{N}= 2\kappa_{t}^2/s$ (but $\kappa_{t}^2\to \infty$) the nuclear process in which there is only a single interaction is the most important one to contribute to the reaction. Thus in this limit color transparency phenomena should occur.These findings are in accord with E971 experiment at FNAL. We also re-examine a potentially important nuclear multiple scattering correction which is positive and $\propto A^{1/3}/\kappa_t^4$. The meaning of the signal obtained from the experimental measurement of pion diffraction into two jets is also critically examined and significant corrections are identified.We show also that for values of $\kappa_t$ achieved at fixed target energies, di-jet production by the e.m. field of the nucleus leads to an insignificant correction which gets more important as $\kappa_t$ increases.Comment: 23 pages, 9 figure

Model of multifragmentation, Equation of State and phase transition

We consider a soluble model of multifragmentation which is similar in spirit to many models which have been used to fit intermediate energy heavy ion collision data. We draw a p-V diagram for the model and compare with a p-V diagram obtained from a mean-field theory. We investigate the question of chemical instability in the multifragmentation model. Phase transitions in the model are discussed.Comment: Revtex, 9 pages including 6 figures: some change in the text and Fig.

Color Transparency versus Quantum Coherence in Electroproduction of Vector Mesons off Nuclei

So far no theoretical tool for the comprehensive description of exclusive electroproduction of vector mesons off nuclei at medium energies has been developed. We suggest a light-cone QCD formalism which is valid at any energy and incorporates formation effects (color transparency), the coherence length and the gluon shadowing. At medium energies color transparency (CT) and the onset of coherence length (CL) effects are not easily separated. Indeed, although nuclear transparency measured by the HERMES experiment rises with Q^2, it agrees with predictions of the vector dominance model (VDM) without any CT effects. Our new results and observations are: (i) the good agreement with the VDM found earlier is accidental and related to the specific correlation between Q^2 and CL for HERMES kinematics; (ii) CT effects are much larger than have been estimated earlier within the two channel approximation. They are even stronger at low than at high energies and can be easily identified by HERMES or at JLab; (iii) gluon shadowing which is important at high energies is calculated and included; (iv) our parameter-free calculations explain well available data for variation of nuclear transparency with virtuality and energy of the photon; (v) predictions for electroproduction of \rho and \phi are provided for future measurements at HERMES and JLab.Comment: Latex 57 pages and 17 figure

Task swapping networks in distributed systems

In this paper we propose task swapping networks for task reassignments by using task swappings in distributed systems. Some classes of task reassignments are achieved by using iterative local task swappings between software agents in distributed systems. We use group-theoretic methods to find a minimum-length sequence of adjacent task swappings needed from a source task assignment to a target task assignment in a task swapping network of several well-known topologies.Comment: This is a preprint of a paper whose final and definite form is published in: Int. J. Comput. Math. 90 (2013), 2221-2243 (DOI: 10.1080/00207160.2013.772985

Experimental and Theoretical Challenges in the Search for the Quark Gluon Plasma: The STAR Collaboration's Critical Assessment of the Evidence from RHIC Collisions

We review the most important experimental results from the first three years of nucleus-nucleus collision studies at RHIC, with emphasis on results from the STAR experiment, and we assess their interpretation and comparison to theory. The theory-experiment comparison suggests that central Au+Au collisions at RHIC produce dense, rapidly thermalizing matter characterized by: (1) initial energy densities above the critical values predicted by lattice QCD for establishment of a Quark-Gluon Plasma (QGP); (2) nearly ideal fluid flow, marked by constituent interactions of very short mean free path, established most probably at a stage preceding hadron formation; and (3) opacity to jets. Many of the observations are consistent with models incorporating QGP formation in the early collision stages, and have not found ready explanation in a hadronic framework. However, the measurements themselves do not yet establish unequivocal evidence for a transition to this new form of matter. The theoretical treatment of the collision evolution, despite impressive successes, invokes a suite of distinct models, degrees of freedom and assumptions of as yet unknown quantitative consequence. We pose a set of important open questions, and suggest additional measurements, at least some of which should be addressed in order to establish a compelling basis to conclude definitively that thermalized, deconfined quark-gluon matter has been produced at RHIC.Comment: 101 pages, 37 figures; revised version to Nucl. Phys.

The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha

Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation

Mitochondrial perturbation is a key event in chemical-induced organ toxicities that is incompletely understood. Here, we studied how electron transport chain (ETC) complex I, II, or III (CI, CII and CIII) inhibitors affect mitochondrial functionality, stress response activation, and cell viability using a combination of high-content imaging and TempO-Seq in HepG2 hepatocyte cells. CI and CIII inhibitors perturbed mitochondrial membrane potential (MMP) and mitochondrial and cellular ATP levels in a concentration- and time-dependent fashion and, under conditions preventing a switch to glycolysis attenuated cell viability, whereas CII inhibitors had no effect. TempO-Seq analysis of changes in mRNA expression pointed to a shared cellular response to CI and CIII inhibition. First, to define specific ETC inhibition responses, a gene set responsive toward ETC inhibition (and not to genotoxic, oxidative, or endoplasmic reticulum stress) was identified using targeted TempO-Seq in HepG2. Silencing of one of these genes, NOS3, exacerbated the impact of CI and CIII inhibitors on cell viability, indicating its functional implication in cellular responses to mitochondrial stress. Then by monitoring dynamic responses to ETC inhibition using a HepG2 GFP reporter panel for different classes of stress response pathways and applying pathway and gene network analysis to TempO-Seq data, we looked for downstream cellular events of ETC inhibition and identified the amino acid response (AAR) as being triggered in HepG2 by ETC inhibition. Through in silico approaches we provide evidence indicating that a similar AAR is associated with exposure to mitochondrial toxicants in primary human hepatocytes. Altogether, we (i) unravel quantitative, time- and concentration-resolved cellular responses to mitochondrial perturbation, (ii) identify a gene set associated with adaptation to exposure to active ETC inhibitors, and (iii) show that ER stress and an AAR accompany ETC inhibition in HepG2 and primary hepatocytes.Toxicolog

The Role of Viral Introductions in Sustaining Community-Based HIV Epidemics in Rural Uganda: Evidence from Spatial Clustering, Phylogenetics, and Egocentric Transmission Models

Background:It is often assumed that local sexual networks play a dominant role in HIV spread in sub-Saharan Africa. The aim of this study was to determine the extent to which continued HIV transmission in rural communities-home to two-thirds of the African population-is driven by intra-community sexual networks versus viral introductions from outside of communities.Methods and Findings:We analyzed the spatial dynamics of HIV transmission in rural Rakai District, Uganda, using data from a cohort of 14,594 individuals within 46 communities. We applied spatial clustering statistics, viral phylogenetics, and probabilistic transmission models to quantify the relative contribution of viral introductions into communities versus community- and household-based transmission to HIV incidence. Individuals living in households with HIV-incident (n = 189) or HIV-prevalent (n = 1,597) persons were 3.2 (95% CI: 2.7-3.7) times more likely to be HIV infected themselves compared to the population in general, but spatial clustering outside of households was relatively weak and was confined to distances <500 m. Phylogenetic analyses of gag and env genes suggest that chains of transmission frequently cross community boundaries. A total of 95 phylogenetic clusters were identified, of which 44% (42/95) were two individuals sharing a household. Among the remaining clusters, 72% (38/53) crossed community boundaries. Using the locations of self-reported sexual partners, we estimate that 39% (95% CI: 34%-42%) of new viral transmissions occur within stable household partnerships, and that among those infected by extra-household sexual partners, 62% (95% CI: 55%-70%) are infected by sexual partners from outside their community. These results rely on the representativeness of the sample and the quality of self-reported partnership data and may not reflect HIV transmission patterns outside of Rakai.Conclusions:Our findings suggest that HIV introductions into communities are common and account for a significant proportion of new HIV infections acquired outside of households in rural Uganda, though the extent to which this is true elsewhere in Africa remains unknown. Our results also suggest that HIV prevention efforts should be implemented at spatial scales broader than the community and should target key populations likely responsible for introductions into communities.Please see later in the article for the Editors' Summary

Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites