bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Protection against Hepatitis B Virus Conferred byCCR5Δ32: Evidence that CCR5 Contributes to Viral Persistence
Authors: Thio Chloe L. , Astemborski Jacquie , Bashirova Arman , Mosbruger Timothy , Greer Spencer , Witt Mallory D. , Goedert James J. , Hilgartner Margaret , Majeske Audrey , O'Brien Stephen J. , Thomas David L. , Carrington Mary 
Published: December 2006

ABSTRACTRecovery from acute hepatitis B virus (HBV) infection requires a broad, vigorous T-cell response, which is enhanced in mice when chemokine receptor 5 (CCR5) is missing. To test the hypothesis that production of a nonfunctional CCR5 (CCR5Δ32[a functionally null allele containing a 32-bp deletion]) increases the likelihood of recovery from hepatitis B in humans, we studied 526 persons from three cohorts in which one person with HBV persistence was matched to two persons who recovered from an HBV infection. Recovery or persistence was determined prior to availability of lamivudine. We determined genotypes forCCR5Δ32and for polymorphisms in theCCR5promoter and in coding regions of the neighboring genes, chemokine receptor 2 (CCR2) and chemokine receptor-like 2 (CCRL2). Allele and haplotype frequencies were compared among the 190 persons with viral recovery and the 336 with persistence by use of conditional logistic regression.CCR5Δ32reduced the risk of developing a persistent HBV infection by nearly half (odds ratio [OR], 0.53; 95% confidence interval [CI], 0.33 to 0.83;P =0.006). This association was virtually identical in persons with and without a concomitant human immunodeficiency virus infection. Of the nine individuals who were homozygous for the deletion, eight recovered from infection (OR, 0.25; 95% CI, 0.03 to 1.99;P= 0.19). None of the other neighboring polymorphisms examined were associated with HBV outcome. These data demonstrate a protective effect ofCCR5Δ32in recovery from an HBV infection, provide genetic epidemiological evidence for a role of CCR5 in the immune response to HBV, and suggest a potential therapeutic treatment for patients persistently infected with HBV.
The Amino-Conserved Domain of Human Cytomegalovirus UL80a Proteins Is Required for Key Interactions during Early Stages of Capsid Formation and Virus Production
Authors: Loveland Amy N. , Nguyen Nang L. , Brignole Edward J. , Gibson Wade 
Published: December 2006

ABSTRACT
Assembly of many spherical virus capsids is guided by an internal scaffolding protein or group of proteins that are often cleaved and eliminated in connection with maturation and incorporation of the genome. In cytomegalovirus there are at least two proteins that contribute to this scaffolding function; one is the maturational protease precursor (pUL80a), and the other is the assembly protein precursor (pUL80.5) encoded by a shorter genetic element within UL80a. Yeast GAL4 two-hybrid assays established that both proteins contain a carboxyl-conserved domain that is required for their interaction with the major capsid protein (pUL86) and an amino-conserved domain (ACD) that is required for their self-interaction and for their interaction with each other. In the work reported here, we demonstrate that when the ACD is deleted (δACD) or disrupted by a point mutation (L47A), the bacterially expressed mutant protein sediments as a monomer during rate-velocity centrifugation, whereas the wild-type protein sediments mainly as oligomers. We also show that the L47A mutation reduces the production of infectious virus by at least 90%, results in the formation of irregular nuclear capsids, gives rise to tube-like structures in the nucleus that resemble the capsid core in cross-section and contain UL80 proteins, slows nuclear translocation of the major capsid protein, and may slow cleavage by the maturational protease. We provide physical corroboration that mutating the ACD disrupts self-interaction of the UL80 proteins and biological support for the proposal that the ACD has a critical role in capsid assembly and production of infectious virus.
Adenoviruses Use Lactoferrin as a Bridge for CAR-Independent Binding to and Infection of Epithelial Cells
Authors: Johansson Cecilia , Jonsson Mari , Marttila Marko , Persson David , Fan Xiao-Long , Skog Johan , Frängsmyr Lars , Wadell Göran , Arnberg Niklas 
Published: December 2006

ABSTRACTMost adenoviruses bind to the coxsackie- and adenovirus receptor (CAR). Surprisingly, CAR is not expressed apically on polarized cells and is thus not easily available to viruses. Consequently, alternative mechanisms for entry of coxsackievirus and adenovirus into cells have been suggested. We have found that tear fluid promotes adenovirus infection, and we have identified human lactoferrin (HLf) as the tear fluid component responsible for this effect. HLf alone was found to promote binding of adenovirus to epithelial cells in a dose-dependent manner and also infection of epithelial cells by adenovirus. HLf was also found to promote gene delivery from an adenovirus-based vector. The mechanism takes place at the binding stage and functions independently of CAR. Thus, we have identified a novel binding mechanism whereby adenovirus hijacks HLf, a component of the innate immune system, and uses it as a bridge for attachment to host cells.
CELLULAR AUTOMATA OVER SEMI-DIRECT PRODUCT GROUPS: REDUCTION AND INVERTIBILITY RESULTS
Authors: CAPOBIANCO SILVIO 
Published: December 2006

Cellular automata are transformations of configuration spaces over finitely generated groups, such that the next state in a point only depends on the current state of a finite neighborhood of the point itself. Many questions arise about retrieving global properties from such local descriptions, and finding algorithms to perform these tasks. We consider the case when the group is a semi-direct product of two finitely generated groups, and show that a finite factor (whatever it is) can be thought of as part of the alphabet instead of the group, preserving both the dynamics and some "finiteness" properties. We also show that, under reasonable hypotheses, this reduction is computable: this leads to some reduction theorems related to the invertibility problem.
Rain Reevaporation, Boundary Layer–Convection Interactions, and Pacific Rainfall Patterns in an AGCM
Authors: Bacmeister Julio T. , Suarez Max J. , Robertson Franklin R. 
Published: December 2006

Sensitivity experiments with an atmospheric general circulation model (AGCM) show that parameterized rain reevaporation has a large impact on simulated precipitation patterns in the tropical Pacific, especially on the configuration of the model’s intertropical convergence zone (ITCZ). Weak reevaporation leads to the formation of a “double ITCZ” during the northern warm season. The double ITCZ is accompanied by strong correlation between precipitation and high-frequency vertical motion in the planetary boundary layer (PBL). Strong reevaporation leads to a better overall agreement of simulated precipitation with observations. The model’s double ITCZ bias is reduced. At the same time, correlation between high-frequency (periods < 15 days) vertical motion in the PBL and precipitation is reduced. Experiments with modified physics indicate that evaporative cooling by rain near the PBL top weakens the coupling between precipitation-related heating and vertical motion in high-frequency motions. The strength of high-frequency vertical motions in the PBL was also reduced directly through the introduction of a diffusive cumulus momentum transport (DCMT) parameterization. The DCMT had a visible impact on simulated precipitation in the Tropics but did not reduce the model’s double ITCZ bias in all cases. Further analyses of mass and water vapor budgets, as well as vertical motion statistics, in the ITCZ complex, show that time-mean moisture convergence in the southern ITCZ is largely dominated by high-frequency modes, while in the northern ITCZ time-mean moisture convergence contains large contributions from slower modes. This may explain why the simulated southern ITCZ is more susceptible to parameterization changes that alter high-frequency coupling between moist heating and PBL convergence.
In Situ Observations of the Microphysical Properties of Wave, Cirrus, and Anvil Clouds. Part I: Wave Clouds
Authors: Baker Brad A. , Lawson R. Paul 
Published: December 2006

The microphysical properties of wave clouds based on data collected during 17 missions flown by a Learjet research aircraft are presented and discussed. This extensive dataset expands upon previous aircraft studies of wave clouds and introduces some new findings. While most aspects of the observations are consistent with basic cloud physics, some aspects remain difficult to interpret. Most notable among these are ice nucleation and aspects of the dynamical structure of wave clouds. A new hypothesis to explain the ice nucleation behavior is presented. The average and standard deviation of bulk microphysical parameters are presented for various locations within the wave clouds. Using digital imagery from a cloud particle imager (CPI), the shapes of ice particles are studied and crystal habits are classified. For certain categories—rosette shapes, columns, and irregular shapes—power-law parameterizations of particle area from particle length are presented. Polycrystals with rosette shapes dominate the ice mass while small spheroidal and irregularly shaped crystals dominate the ice number concentration. The concept and difficulties of using wave clouds as natural cloud physics laboratories are discussed and evaluated. A study of the riming threshold size of columns is in good agreement with the results of previous studies, showing that column width is the predominate factor in determining riming threshold. The first reported studies of the riming threshold size of rosette shapes and the threshold size for side-plane growth are presented.
In Situ Observations of the Microphysical Properties of Wave, Cirrus, and Anvil Clouds. Part II: Cirrus Clouds
Authors: Lawson R. Paul , Baker Brad , Pilson Bryan , Mo Qixu 
Published: December 2006

A Learjet research aircraft was used to collect microphysical data, including cloud particle imager (CPI) measurements of ice particle size and shape, in 22 midlatitude cirrus clouds. The dataset was collected while the aircraft flew 104 horizontal legs, totaling over 15 000 km in clouds. Cloud temperatures ranged from −28° to −61°C. The measurements show that cirrus particle size distributions are mostly bimodal, displaying a maximum in number concentration, area, and mass near 30 μm and another smaller maximum near 200–300 μm. CPI images show that particles with rosette shapes, which include mixed-habit rosettes and platelike polycrystals, constitute over 50% of the surface area and mass of ice particles >50 μm in cirrus clouds. Approximately 40% of the remaining mass of ice particles >50 μm are found in irregular shapes, with a few percent each in columns and spheroidal shapes. Plates account for <1% of the total mass. Particles <50 μm account for 99% of the total number concentration, 69% of the shortwave extinction, and 40% of the mass in midlatitude cirrus. Plots and average equations for area versus particle size are shown for various particle habits, and can be used in studies involving radiative transfer. The average particle concentration in midlatitude cirrus is on the order of 1 cm−3 with occasional 10-km averages exceeding 5 cm−3. There is a strong similarity of microphysical properties of ice particles between wave clouds and cirrus clouds, suggesting that, like wave clouds, cirrus ice particles first experience conversion to liquid water and/or solution drops before freezing.
A Cascade-Type Global Energy Conversion Diagram Based on Wave–Mean Flow Interactions
Authors: Uno Sachiyo , Iwasaki Toshiki 
Published: December 2006

A cascade-type energy conversion diagram is proposed for the purpose of diagnosing the atmospheric general circulation based on wave–mean flow interactions. Mass-weighted isentropic zonal means facilitate the expression of nongeostrophic wave effects, conservation properties, and lower boundary conditions. To gain physical insights into energetics based on the nonacceleration theorem, the wave energy W is defined as the sum of the eddy available potential energy PE and the eddy kinetic energy KE. The mainstream of the energy cascade is as follows: The diabatic heating produces the zonal mean available potential energy PZ, which is converted into the zonal mean kinetic energy KZ through the mean meridional circulation. The KZ is mainly converted to W through zonal wave–mean flow interactions and the rest is dissipated through friction. Not only the dynamical conversion but also the diabatic heating generates W, which is dissipated through friction. A diagnosis package is designed to analyze actual atmospheric data on the standard pressure surfaces. A validation study of the package is made by using the output from a general circulation model. The scheme accurately expresses tendencies of the zonal mean and eddy available potential energy equations, showing the diagnosis capability. On shorter time scales, PE changes in accordance with KE, good correlation indicating the relevance of the definition of wave energy. A preliminary study is made of the climate in December–February (DJF), and June–August (JJA), using the NCEP–NCAR reanalysis. The dynamical wave energy generation rate C(KZ, W) is about 60% of the conversion rate C(PZ, KZ), which means that KZ is dissipated through friction at a rate of about 40%. In the extratropics, C(KZ, W) is almost equal to C(PZ, KZ), as is expected from quasigeostrophic balance. In the subtropics, however, C(KZ, W) is much smaller than C(PZ, KZ), which suggests the importance of nongeostrophic effects on the energetics. The energetics is substantially different between the two solstices. Both C(PZ, KZ) and C(KZ, W) are about 30% larger in DJF than those in JJA, reflecting differences in wave activity. Stationary waves contribute considerably to energy conversions in the Northern Hemispheric winter, while baroclinic instability waves do more in the Southern Hemispheric winter than in the Northern Hemispheric winter.
Simulation of Inertia–Gravity Waves in a Poleward-Breaking Rossby Wave
Authors: Zülicke Christoph , Peters Dieter 
Published: December 2006

Poleward-breaking Rossby waves often induce an upper-level jet streak over northern Europe. Dominant inertia–gravity wave packets are observed downstream of this jet. The physical processes of their generation and propagation, in such a configuration, are investigated with a mesoscale model. The study is focused on an observational campaign from 17 to 19 December 1999 over northern Germany. Different simulations with the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) have been performed. For a high-resolution process study, three domains were set up that encompass the evolution of Rossby waves and that of inertia–gravity waves. To minimize the impact of model damping, the horizontal and vertical resolution has been adjusted appropriately. With a novel statistical approach, the properties of inertia–gravity wave packets have been estimated. This method uses the horizontal divergence field and takes into account the spatial extension of a wave packet. It avoids the explicit treatment of the background field and works for arbitrary wavelength. Two classes of inertia–gravity waves were found: subsynoptic waves with a horizontal wavelength of about 500 km and mesoscale waves with a horizontal wavelength of about 200 km. The subsynoptic structures were also detected in radiosonde observations during this campaign. The similarity between simulated and observed wavelengths and amplitudes suggests that the simulations can be considered as near realistic. Spontaneous radiation from unbalanced flow is an important process of inertia–gravity wave generation. Synoptic-scale imbalances in the exit region of the upper-tropospheric jet streak were identified with the smoothed cross-stream Lagrangian Rossby number. In a number of simulations with different physics, it was found that the inertia–gravity wave activity was related to the tropospheric jet, orography, and moist convection. The upward propagation of inertia–gravity waves was favored during this event of a poleward-breaking Rossby wave. The presence of the polar vortex induced background winds exceeding the critical line. Consequently, the activity of inertia–gravity waves in the lower stratosphere increased by an order of magnitude during the case study. The successful simulation of the complex processes of generation and propagation showed the important role of poleward Rossby wave breaking for the appearance of inertia–gravity waves in the midlatitudes.
Advanced Doubling–Adding Method for Radiative Transfer in Planetary Atmospheres
Authors: Liu Quanhua , Weng Fuzhong 
Published: December 2006

The doubling–adding method (DA) is one of the most accurate tools for detailed multiple-scattering calculations. The principle of the method goes back to the nineteenth century in a problem dealing with reflection and transmission by glass plates. Since then the doubling–adding method has been widely used as a reference tool for other radiative transfer models. The method has never been used in operational applications owing to tremendous demand on computational resources from the model. This study derives an analytical expression replacing the most complicated thermal source terms in the doubling–adding method. The new development is called the advanced doubling–adding (ADA) method. Thanks also to the efficiency of matrix and vector manipulations in FORTRAN 90/95, the advanced doubling–adding method is about 60 times faster than the doubling–adding method. The radiance (i.e., forward) computation code of ADA is easily translated into tangent linear and adjoint codes for radiance gradient calculations. The simplicity in forward and Jacobian computation codes is very useful for operational applications and for the consistency between the forward and adjoint calculations in satellite data assimilation. ADA is implemented into the Community Radiative Transfer Model (CRTM) developed at the U.S. Joint Center for Satellite Data Assimilation.
High-Resolution Simulation of Shallow-to-Deep Convection Transition over Land
Authors: Khairoutdinov Marat , Randall David 
Published: December 2006

Results are presented from a high-resolution three-dimensional simulation of shallow-to-deep convection transition based on idealization of observations made during the Large-Scale Biosphere–Atmosphere (LBA) experiment in Amazonia, Brazil, during the Tropical Rainfall Measuring Mission (TRMM)-LBA mission on 23 February. The doubly periodic grid has 1536 × 1536 × 256 grid cells with horizontal grid spacing of 100 m, thus covering an area of 154 × 154 km2. The vertical resolution varies from 50 m in the boundary layer to 100 m in the free troposphere and gradually coarsens to 250 m near the domain top at 25.4 km. The length of the simulation is 6 h, starting from an early morning sounding corresponding to 0730 local time. Convection is forced by prescribed surface latent and sensible heat fluxes and prescribed horizontally uniform radiative heating Despite a considerable amount of convective available potential energy (CAPE) in the range of 1600–2400 J kg−1, and despite virtually no convective inhibition (CIN) in the mean sounding throughout the simulation, the cumulus convection starts as shallow, gradually developing into congestus, and becomes deep only toward the end of simulation. Analysis shows that the reason is that the shallow clouds generated by the boundary layer turbulence are too small to penetrate deep into the troposphere, as they are quickly diluted by mixing with the environment. Precipitation and the associated cold pools are needed to generate thermals big enough to support the growth of deep clouds. This positive feedback involving precipitation is supported by a sensitivity experiment in which the cold pools are effectively eliminated by artificially switching off the evaporation of precipitation; in the experiment, the convection remains shallow throughout the entire simulation, with a few congestus but no deep clouds. The probability distribution function (PDF) of cloud size during the shallow, congestus, and deep phases is analyzed using a new method. During each of the three phases, the shallow clouds dominate the mode of the PDFs at about 1-km diameter. During the deep phase, the PDFs show cloud bases as wide as 4 km. Analysis of the joint PDFs of cloud size and in-cloud variables demonstrates that, as expected, the bigger clouds are far less diluted above their bases than their smaller counterparts. Also, thermodynamic properties at cloud bases are found to be nearly identical for all cloud sizes, with the moist static energy exceeding the mean value by as much as 4 kJ kg−1. The width of the moist static energy distribution in the boundary layer is mostly due to variability of water vapor; therefore, clouds appear to grow from the air with the highest water vapor content available. No undiluted cloudy parcels are found near the level of neutral buoyancy. It appears that a simple entraining-plume model explains the entrainment rates rather well. The least diluted plumes in the simulation correspond to an entrainment parameter of about 0.1 km−1.
Representing Convective Organization in Prediction Models by a Hybrid Strategy
Authors: Moncrieff Mitchell W. , Liu Changhai 
Published: December 2006

The mesoscale organization of precipitating convection is highly relevant to next-generation global numerical weather prediction models, which will have an intermediate horizontal resolution (grid spacing about 10 km). A primary issue is how to represent dynamical mechanisms that are conspicuously absent from contemporary convective parameterizations. A hybrid parameterization of mesoscale convection is developed, consisting of convective parameterization and explicit convectively driven circulations. This kind of problem is addressed for warm-season convection over the continental United States, although it is argued to have more general application. A hierarchical strategy is adopted: cloud-system-resolving model simulations represent the mesoscale dynamics of convective organization explicitly and intermediate resolution simulations involve the hybrid approach. Numerically simulated systems are physically interpreted by a mechanistic dynamical model of organized propagating convection. This model is a formal basis for approximating mesoscale convective organization (stratiform heating and mesoscale downdraft) by a first-baroclinic heating couplet. The hybrid strategy is implemented using a predictor–corrector strategy. Explicit dynamics is the predictor and the first-baroclinic heating couplet the corrector. The corrector strengthens the systematically weak mesoscale downdrafts that occur at intermediate resolution. When introduced to the Betts–Miller–Janjic convective parameterization, this new hybrid approach represents the propagation and dynamical structure of organized precipitating systems. Therefore, the predictor–corrector hybrid approach is an elementary practical framework for representing organized convection in models of intermediate resolution.