bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Establishment and Antigen Dependence of Simian Immunodeficiency Virus-Specific CD8+T-Cell Defects
Authors: Mueller Yvonne M. , Petrovas Constantinos , Do Duc H. , Altork Susan R. , Fischer-Smith Tracy , Rappaport Jay , Altman John D. , Lewis Mark G. , Katsikis Peter D. 
Published: August 2007

ABSTRACTDifferentiation and survival defects of human immunodeficiency virus (HIV)-specific CD8+T cells may contribute to the failure of HIV-specific CD8+T cells to control HIV replication. It is not known, however, whether simian immunodeficiency virus (SIV)-infected rhesus macaques show comparable defects in these virus-specific CD8+T cells or when such defects are established during infection. Peripheral blood cells from acutely and chronically infected rhesus macaques were stained ex vivo for memory subpopulations and examined by in vitro assays for apoptosis sensitivity. We show here that SIV-specific CD8+T cells from chronically SIV infected rhesus macaques show defects comparable to those observed in HIV infection, namely, a skewed CD45RA−CD62L−effector memory phenotype, reduced Bcl-2 levels, and increased levels of spontaneous and CD95-induced apoptosis of SIV-specific CD8+T cells. Longitudinal studies showed that the survival defects and phenotype are established early in the first few weeks of SIV infection. Most importantly, they appear to be antigen driven, since most probably the loss of epitope recognition due to viral escape results in the reversal of the phenotype and reduced apoptosis sensitivity, something we observed also for animals treated with antiretroviral therapy. These findings further support the use of SIV-infected rhesus macaques to investigate the phenotypic changes and apoptotic defects of HIV-specific CD8+T cells and indicate that such defects of HIV-specific CD8+T cells are the result of chronic antigen stimulation.
c-Myc and Sp1 Contribute to Proviral Latency by Recruiting Histone Deacetylase 1 to the Human Immunodeficiency Virus Type 1 Promoter
Authors: Jiang Guochun , Espeseth Amy , Hazuda Daria J. , Margolis David M. 
Published: August 2007

ABSTRACT

Histone deacetylase (HDAC) inhibitors such as valproic acid (VPA) induce the expression of quiescent proviral human immunodeficiency virus type 1 (HIV-1) and may deplete proviral infection in vivo. To uncover novel molecular mechanisms that maintain HIV latency, we sought cellular mRNAs whose expression was diminished in resting CD4
+
T cells of HIV-1-infected patients exposed to VPA. c-Myc was prominent among genes markedly downregulated upon exposure to VPA. c-Myc expression repressed HIV-1 expression in chronically infected cell lines. Chromatin immunoprecipitation (ChIP) assays revealed that c-Myc and HDAC1 are coordinately resident at the HIV-1 long terminal repeat (LTR) promoter and absent from the promoter after VPA treatment in concert with histone acetylation, RNA polymerase II recruitment, and LTR expression. Sequential ChIP assays demonstrated that c-Myc, Sp1, and HDAC1 coexist in the same DNA-protein complex at the HIV promoter. Short hairpin RNA inhibition of c-Myc reduces both c-Myc and HDAC1 occupancy, blocks c-Myc repression of Tat activation, and increases LTR expression. These results expand the understanding of mechanisms that recruit HDAC and maintain the latency of HIV-1, suggesting novel therapeutic approaches against latent proviral HIV infection.
Complexes between Herpes Simplex Virus Glycoproteins gD, gB, and gH Detected in Cells by Complementation of Split Enhanced Green Fluorescent Protein
Authors: Avitabile Elisa , Forghieri Cristina , Campadelli-Fiume Gabriella 
Published: August 2007

ABSTRACT

The interactions between herpes simplex virus gD and its nectin1 receptor or between gD, gB, and gH were analyzed by complementation of the N and C portions of split enhanced green fluorescent protein (EGFP) fused to the glycoproteins. The gD
N
-Nect
C
complex was readily detected; the gD
N
-gC
C
complex was undetectable, highlighting the specificity of the assay. Split EGFP complementation was detected between proteins designated gD
N
+gH
C
, gD
N
+gB
C
, and gH
N
+gB
C
+wtgD (gB was deleted of endocytosis motifs), both in cells transfected with two-tree glycoproteins and in syncytia. The in situ assay provides evidence that gD interacts with gH and gB independently of each other and supports a model whereby gH and gB in complex exert their activities to gD.
Effects of size, shape, and edge on vegetation in remnants of the upland boreal mixed-wood forest in agro-environments of Alberta, Canada
Authors: Gignac L. Dennis , Dale Mark R.T. 
Published: July 2007

Forty-one remnants of the aspen-dominated upland forest in three subregions of the dry boreal mixed-wood in Alberta were studied to determine effects of fragment size and shape on native and alien plant species richness and abundance in agro-environments. The percent cover of all vascular plant species was visually estimated in 5 m diameter circular plots along transects that covered the length and the width of each fragment. A subset of 12 of the largest fragments (>900 m2) that had distinct interiors (portions of the fragment >15 m from any edge) was used to measure edge effects on the vegetation. Regression analyses revealed significant positive relationships between species richness and area regardless of the subregion. Species richness stabilized in fragments that were larger than 11 ha. Edges did not affect shrub species richness and only affected herbaceous species richness on west- and south-facing aspects. Shrub abundance decreased and herb abundance increased up to 20 m from the edges regardless of orientation. Edges did not support a different suite of species than interiors, although several species occurred more frequently in the interior than along the edges. Alien species richness and abundance reached their highest values between 5 and 15 m from the edge, and some of those species could be found up to 40 m from the edge. Although larger fragments generally supported more alien species than smaller fragments, the smallest fragments had the greatest number of species per metre squared. Results from this study indicated that it would be preferable to conserve larger woodlots rather then several smaller woodlots on the landscape.
Photoperiod, light quality, and irradiance effects on flowering in the alpine and prairie ecotypes of Stellaria longipes
Authors: Kurepin Leonid V. , Walton Linda J. , Reid David M. , Chinnappa C.C. , Pharis Richard P. 
Published: August 2007

Plants growing in vegetative shade are subjected to reductions in both red to far-red (R/FR) light ratio and in irradiance levels of photosynthetically active radiation (PAR). In this report we have attempted to uncouple the reduced R/FR ratio- and low PAR-mediated effects of shade on flowering in the ramets of Stellaria longipes Goldie s.l. (Caryophyllaceae) ecotypes collected from alpine “sun” and lower elevation prairie “shade” habitats. Both ecotypes were also tested for their flowering response (defined as the number of open flowers per ramet) to daylength. The alpine ecotype plants can best be classified as day-neutral, whereas prairie ecotype plants require long-days (LD). Under a low PAR of 115 μmol m–2·s–1 given under LD conditions at a reduced (0.7) R/FR ratio, alpine ecotype plants flowered significantly later relative to plants grown under the low PAR at a normal (1.22) R/FR ratio. In contrast, plants of the prairie ecotype flowered earlier under the reduced R/FR ratio combined with the same low PAR. Flower number per ramet differed significantly between the two ecotypes, with alpine ecotype plants developing fewer flowers under a low PAR (109 μmol m–2·s–1 irradiance) relative to a high PAR of 611 μmol m–2·s–1 (both given at a normal R/FR ratio). The prairie ecotype plants responded differently and had similar flower numbers under both low and high PARs at the normal (1.22) R/FR ratio. However, growing the prairie ecotype plants under a reduced R/FR ratio at a low PAR showed a significant increase in number of flowers. In contrast, plants grown under high (2.7) and normal (1.9) R/FR ratios combined with low PAR produced many more flowers than the alpine ecotype. Thus, the two components of shade, reduced R/FR ratio and low PAR can cause distinctly different flowering responses in sun and shade plants of S. longipes.
Calculation of the propagation amplitude in the case of a Coulomb interaction via time-independent mean-field theory
Authors: Yekken R , Mekideche F 
Published: July 2007

The exact study of many-body microscopic systems is impossible when the number of particles is large (N ≥ 3). Approximate methods are then used. The time-independent mean-field (TIMF) approximation has been proposed for the description of collisions in many-body systems. Collision amplitudes are derived by the use of a variational principle and the choice of trial functions as products of single-particle orbitals. Resulting mean-field equations with a nonvanishing right-hand side turn out to be a generalization of the traditional Hartree or Hatree–Fock type equations. These TIMF equations are successfully solved numerically for the case of short-range forces. In this paper, we test the validity of this theory for the Coulomb interaction between two particles, that is, a long-range interaction. A numerical comparison between the exact and the mean-field solutions is conducted PACS Nos.: 31.15.Ne, 31.15.Pf, 21.45.+v,25.10.-i
QCD corrections to heavy quark decays
Authors: Blokland I 
Published: July 2007

The calculation of QCD corrections to heavy quark decay rates has progressed steadily in recent years. With the help of specialized techniques, symbolic computation, and a growing base of experience, a wide variety of special cases have been evaluated. These results have been applied to decays such as t → bW, b → s γ, b → u[Formula: see text]ν, and b → c[Formula: see text]ν. PACS Nos.: 12.38.Bx, 13.30.Ce
Multisoliton configurations in Skyrme-like models
Authors: Longpré J -P , Marleau L 
Published: July 2007

We explore the higher topological charge sector for generalized SU(2) Skyrme models in search of the static-field configuration with the lowest energy that would better reproduce what is expected for nuclei. Indeed the Skyrme model leads, for example, to toroidal, tetrahedral, and cubic symmetries for B = 2, 3, and 4 configurations, respectively, whereas nucleons in nuclei are presumably preserving their individuality. It turns out that the symmetries of the soliton solutions for the extended Skyrme models presented in this work are the same as for the Skyrme model at least for topological charges B < 5, which suggest that the Skyrme model has to be modified significantly to preserve the individual nature of the nucleons in nuclei. PACS Nos.: 12.39.Dc, 10.11.Lm
Bose-Einstein condensates and thermal field theory
Authors: Kovalchuk E , Kobes R 
Published: July 2007

We consider a homogeneous nonideal Bose gas in equilibrium at nonzero temperature below the critical temperature Tc in the framework of thermal field theory. Quantum corrections up to second order are calculated, which are shown to be crucial in obtaining the correct behavior in thermodynamic quantities such as the specific heat. PACS Nos.: 67.40.–w, 11.10.Wx
Effective Hamiltonian theory and its applications in quantum information
Authors: James D F , Jerke J 
Published: July 2007

This paper presents a useful compact formula for deriving an effective Hamiltonian describing the time-averaged dynamics of detuned quantum systems. The formalism also works for ensemble-averaged dynamics of stochastic systems. To illustrate the technique, we give examples involving Raman processes, Bloch-Siegert shifts, and quantum logic gates. PACS Nos: 03.65.–w
Semiclassical position and momentum information entropy for sech2 and a family of rational potentials
Authors: Coffey M W 
Published: July 2007

The classical and semiclassical position and momentum information entropies for the reflectionless sech2 potential and a family of rational potentials are obtained explicitly. The sum of these entropies is of interest for the entropic uncertainty principle that is stronger than the Heisenberg uncertainty relation. The analytic results relate the classical period of the motion, total energy, position and momentum entropy, and dependence upon the principal quantum number n. The logarithmic energy dependence of the entropies is presented. The potentials considered include as special cases the attractive delta function and square well. PACS Nos.: 03.67–a, 03.65.Sq, 03.65.Ge, 03.65.–w
Problems with complex actions
Authors: Alexanian G , MacKenzie R , Paranjape M B , Ruel Jonathan 
Published: July 2007

We consider Euclidean functional integrals involving actions that are not exclusively real. This situation arises, for example, when there are t-odd terms in the the Minkowski action. Writing the action in terms of only real fields (which is always possible), such terms appear as explicitly imaginary terms in the Euclidean action. The usual quanization procedure that involves finding the critical points of the action and then quantizing the spectrum of fluctuations about these critical points fails. In the case of complex actions, there do not exist, in general, any critical points of the action on the space of real fields, the critical points are in general complex. The proper definition of the function integral then requires the analytic continuation of the functional integration into the space of complex fields so as to pass through the complex critical points according to the method of steepest descent. We show a simple example where this procedure can be carried out explicitly. The procedure of finding the critical points of the real part of the action and quantizing the corresponding fluctuations, treating the (exponential of the) complex part of the action as a bounded integrable function is shown to fail in our explicit example, at least perturbatively. PACS Nos.: 11.10.–z, 03.70.+k
Simplifying calculations in real time finite temperature field theory
Authors: Fugleberg T , Carrington M E 
Published: July 2007

In this paper, we discuss a Mathematica program that we have written that calculates the integrand for amplitudes in the closed-time-path formulation of real-time finite-temperature field theory. The program is designed to be used by someone with no previous experience with Mathematica. It performs contractions over tensor indices that appear in real-time finite-temperature field theory and gives the result in the 1-2, Keldysh or R/A basis. As an illustration of this program, we discuss the calculation of all 3-point ward identities in finite-temperature quantum electrodynamics with full vertices. PACS Nos.: 11.10.Wx,11.15.-q
Probing new CP-odd thresholds with electric dipole moments
Authors: Ritz A 
Published: July 2007

We dicuss the utility of precision probes for flavour-diagonal CP-violation, namely, searches for electric dipole moments of nucleons, atoms, and molecules, in looking for new physics thresholds that manifest themselves primarily through higher dimensional operators. After reviewing the status of the electric dipole moment (EDM) constraints, we consider first the sensitivity to a generic class of dimension-five operators generated at a supersymmetric threshold, through their contribution to CP- and flavour-violating observables. Such thresholds can be probed by EDMs up to a scale of order 108 GeV depending on the flavour structure. We then turn to consider the possibility that electroweak baryogenesis is made feasible by the introduction of dimension-six operators at a TeV-scale threshold. The EDM costraints on dimension-six couplings of the Higgs to the fermions currently still allow a reasonable window in parameter space for these models, but the next generation of experiments should provide a conclusive test. PACS Nos.: 11.30.Er, 12.60.Fr, 12.60.Jv
Limitations to photosynthetic carbon gain in timberline Abies lasiocarpa seedlings during prolonged drought
Authors: Johnson Daniel M. , Smith William K. 
Published: July 2007

Photosynthesis, water status, and associated physiological parameters were measured in chronically drought-stressed seedlings (5 years of below-average precipitation, 107 cm net deficit) of Abies lasiocarpa (Hook.) Nutt. above (treeline ecotone site, TS) and below (forest site, FS) a Rocky Mountain timberline. In contrast to normal seasonal patterns reported for timberline conifer trees, xylem water potentials were exceptionally low in early summer and remained low for the rest of the summer. Although photosynthesis was not significantly different between the two sites, early season photosynthesis was greater than late-season photosynthesis, especially at FS. Mean daily values of leaf conductance to water vapor (gwv) and transpiration (E) were also low at the beginning of summer (gwv from 0.01 mol·m–2·s–1 to 0.13 mol·m–2·s–1 and E from 0.4 μmol·m–2·s–1 to 2.9 μmol·m–2·s–1) and continued to decrease through summer (an approximate 10-fold decrease in gwv and a 2-fold to 3-fold decrease in E), which resulted in increasing water-use efficiency as summer progressed. Although the slope of instantaneous photosynthesis – intercellular CO2 concentration curves was reduced (lower carboxylation efficiency) from July to September, the relative stomatal limitation to carbon gain was less than 50% over the entire measurement period. Mean daily intercellular CO2 concentrations decreased from near ambient levels (approximately 350–360 ppm) to 290 ppm over the course of summer. Overall, nonstomatal limitations appeared to have the largest impact on photosynthetic carbon gain, although seasonal decreases in leaf conductance and a corresponding depletion of intercellular CO2 indicated that there were also significant stomatal limitations to carbon gain that resulted in a continued regulation of greater water use efficiency.
Forest dynamics following spruce budworm outbreaks in the northern and southern mixedwoods of central Quebec
Authors: Bouchard Mathieu , Kneeshaw Daniel , Messier Christian 
Published: July 2007

The effects of 20th century spruce budworm ( Choristoneura fumiferana (Clem.)) outbreaks on forest dynamics was examined in the southern and northern parts of the mixedwood forest zone in central Quebec, Canada. In each region, three study areas were placed in unmanaged stands that had not burned for more than 200 years. Disturbance impacts and forest succession were evaluated using aerial photographs and dendrochronology. Spruce budworm outbreaks occurred around 1910, 1950, and 1980 in both regions. The 1910 outbreak seemed to have limited impact in both regions, and the 1950 outbreak caused heavy mortality in conifer stands (mostly of balsam fir, Abies balsamea (L.) Mill.) in the southern region. The 1980 outbreak caused major mortality in the northern region, but had little impact in the southern region. Successive spruce budworm outbreaks led to a massive invasion by hardwood species in the last century in the southern region but not in the northern region. The reason for such contrasting dynamics between regions is unknown, but we hypothesize that differences in disturbance intensities, influenced by climate, played a major role. Results from this study emphasize that generalizations about the effect of spruce budworm outbreaks on forest dynamics cannot be derived from observations made during a single outbreak or at a single location.
Riparian forest harvesting and its influence on benthic communities of small streams of sub-boreal British Columbia
Authors: Melody K. Jill , Richardson John S. 
Published: July 2007

Forest harvesting in riparian areas can alter the leaf-litter inputs, shading, and stability of small streams, and many of the details of these impacts are known for coastal streams of the Pacific Northwest. However, little is known about how small streams in the drier, continental areas of western North America respond to logging. We conducted a study of paired stream reaches (comparing one recently harvested (≤3 years) reach and two upstream, forested reaches in each of five streams) in which periphyton, detritus, macroinvertebrate abundance and biomass, and physical features were measured in summer and autumn. In general, recently harvested stream sections tended to be wider and contained more riffle areas than the upstream forested sections. The amounts of leaf litter and algae varied among streams and were not consistently greater or lesser in the forested sections than in the harvested sections. Though the variation in amounts within streams was mainly seasonal, amounts differed more among streams than between pairs of harvested and forested reaches. The communities of benthic invertebrates differed significantly between forested and harvested reaches, but often in opposite directions between streams. The magnitude and direction of differences observed between treatments, streams, or seasons were associated with the specific stream and the method of riparian harvesting used.
The Admonition to Assemble Together in Didache 16.2 Reappraised
Authors: Khomych Taras 
Published: July 2007

AbstractThis contribution focuses on the analysis of a largely neglected passage of the Didache 16.2. After a short overview of some approaches to its interpretation, it attempts to shed some more light on the understanding of this section, adapting Milavec's recent theory about the unity of the Didache and progression of thought within it, while modifying his interpretation of this specific passage. Based on the analysis of the passage and its context, this study concludes that Did. 16.2 gives an admonition to the local community to assemble together in unity. This interpretation is further supported by the analysis of the implied military imagery of Did. 16 and correspondences between the passage in question and references to the eucharist in Did. 9-10 and 14. At the same time, this paper points out that Did. 16.2 is distinct from the other eucharistic passages of the Didache as it contains a reminder of community's responsibility in view of the coming end and presents the local liturgical congregation as an image of the final gathering of the Church in the eschaton.
"Judaizing" Christian Interpretations of the Prophets As Seen by Saint Jerome
Authors: Graves Michael 
Published: July 2007

AbstractAmong the many differing interpretations reported by St. Jerome is the set ascribed to "our Judaizers," who are in reality Christian interpreters with whom Jerome disagrees. In his own exegesis of the prophets, Jerome accepts both the literal/historical meaning of the "Hebrews" (Jews) as it relates to Israel's past (Old Testament history), and the spiritual/allegorical meaning of the church as it relates to the present or future. The interpretations that Jerome regards as "Judaizing" are almost all attempts to assign a literal meaning to the future. It is this combination (literal and future) that Jerome rejects as "Judaizing."
Demons and Divine Illumination: A Consideration of Eight Prayers by Gregory of Nazianzus
Authors: Kalleres Dayna 
Published: July 2007

AbstractThis article considers eight prayers by Gregory of Nazianzus (Patrologia Graeca 37.1397-1406) that are singular in their anti-demonic tone and apotropaic formulae. Reading these texts in light of Gregory's Orations 20, 27, and 38-40 elucidates the Cappadocian's connection between baptism and the acquisition of divine knowledge; thus, we can acquire a rare view into the practical aspects of Gregory's endeavors with theoria in his post-baptismal life. Finally, these prayers bring into sharp relief the consequential materiality of the devil and demons in Gregory of Nazianzus' epistemology, theology, and asceticism. In so doing, this essay seeks to turn attention to the vibrant demonologies cultivated and constructed by elite, educated Christians in the late antique cities of the Greek East.