bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Barotropic Envelope Rossby Soliton Model for Block–Eddy Interaction. Part III: Wavenumber Conservation Theorems for Isolated Blocks and Deformed Eddies
Authors: Luo Dehai 
Published: November 2005

AbstractIn a series of previous papers, an envelope Rossby soliton theory was formulated to investigate the interaction between a preexisting planetary wave and synoptic-scale eddies leading to a typical blocking flow. In this paper, numerical and analytical studies are presented in order to examine the interactive relationship between an isolated vortex pair block and deformed synoptic-scale eddies during their interaction. The deformed blocked flow and eddies are found to satisfy the wavenumber conservation theorem. It is shown that the feedback by a blocked flow on the preexisting synoptic eddies gives rise to two types of eddies: one is the Z-type eddies with a meridional monopole structure that appears at the middle of the channel and the other is the M-type eddies with a meridional tripole structure that have long wavelength and large amplitude. Both the total wavenumber of the blocked flow and M-type eddies and the total wavenumber of the Z- and M-type eddies are conserved. The M- and Z-type eddies are compressed and elongated, respectively, as the blocked flow is elongated zonally during its onset phase, but the reverse is observed during the decay phase. The zonally elongated Z-type eddies are found to counteract the compressed M-type eddies in the blocking region, but strengthen the M-type eddies upstream, causing the split of eddies around the blocking region.In addition, it is also verified theoretically that the blocked flow and synoptic-eddy activity are symbiotically dependent upon one another. The deformed (Z and M type) eddies also display a low-frequency oscillation in amplitude, wavenumber, group velocity, and phase speed, consistent with the blocked flow by the eddy forcing. Thus, it appears that the low-frequency eddy forcing is responsible for the low-frequency variability of the blocked flow and synoptic-eddy activity.
Dynamic Instabilities of Simulated Hurricane-like Vortices and Their Impacts on the Core Structure of Hurricanes. Part I: Dry Experiments
Authors: Kwon Young C. , Frank William M. 
Published: November 2005

Abstract
A series of numerical simulations of dry, axisymmetric hurricane-like vortices is performed to examine the growth of barotropic and baroclinic eddies and their potential impacts on hurricane core structure and intensity. The numerical experiments are performed using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) with a 6-km horizontal grid. To examine internal effects on the stability of vortices, all external forcings are eliminated. Axisymmetric vortices that resemble observed hurricane structures are constructed on an f plane, and the experiments are performed without moist and boundary layer processes.
Three vortices are designed for this study. A balanced control vortex is built based on the results of a full-physics simulation of Hurricane Floyd (1999). Then, two other axisymmetric vortices, EXP-1 and EXP-2, are constructed by modifying the wind and mass fields of the control vortex. The EXP-1 vortex is designed to satisfy the necessary condition of baroclinic instability, while the EXP-2 vortex satisfies the necessary condition of barotropic instability. These modified vortices are thought to lie within the natural range of structural variability of hurricanes.
The EXP-1 and EXP-2 vortices are found to be unstable with respect to small imposed perturbations, while the control vortex is stable. Small perturbations added to the EXP-1 and EXP-2 vortices grow exponentially at the expense of available potential energy and kinetic energy of the primary vortex, respectively. The most unstable normal modes of both vortices are obtained via a numerical method. The most unstable mode of the EXP-1 (baroclinically unstable) vortex vertically tilts against shear, and the maximum growth occurs near a height of 14 km and a radius of 20 km. On the other hand, the most unstable normal mode of the EXP-2 (barotropically unstable) vortex has horizontal tilting against the mean angular velocity shear, and the maximum perturbations are located at a lower altitude (around 4 km) and at larger radius (around 100 km). Despite these differences, the normal modes of both vortices have a wavenumber-1 structure.
The energy budget analysis shows that the growing baroclinic and barotropic perturbations have opposite effects on the vortex intensity in terms of kinetic energy. Baroclinic eddies strengthen, whereas barotropic eddies weaken, the primary vortex. It is hypothesized that fluctuations in hurricane core structure and intensity can occur due to eddy processes triggered by alternating periods of barotropic and baroclinic eddy growth in the core. Once formed, these eddies may interact with the intense diabatic energy sources in real hurricanes. A similar study of eddy behaviors in a more realistic hurricane, which includes moist and boundary layer processes and uses a finer grid mesh, will be the topic of Part II.
Study of the Aerosol Indirect Effect by Large-Eddy Simulation of Marine Stratocumulus
Authors: Lu Miao-Ling , Seinfeld John H. 
Published: November 2005

Abstract
A total of 98 three-dimensional large-eddy simulations (LESs) of marine stratocumulus clouds covering both nighttime and daytime conditions were performed to explore the response of cloud optical depth (τ) to various aerosol number concentrations (Na = 50–2500 cm−3) and the covarying meteorological conditions (large-scale divergence rate and SST). The idealized First International Satellite Cloud Climatology Project (ISCCP) Regional Experiment (FIRE) and the Atlantic Stratocumulus Transition Experiment (ASTEX) Lagrangian 1 sounding profiles were used to represent the lightly and heavily drizzling cases, respectively. The first and second aerosol indirect effects are identified. Through statistical analysis, τ is found be to both positively correlated with Na and cloud liquid water path (LWP) with a higher correlation associated with LWP, which is predominantly regulated by large-scale subsidence and SST. Clouds with high LWP occur under low SST or weak large-scale subsidence. Introduction of a small amount of giant sea salt aerosol into the simulation lowers the number of cloud droplets activated, results in larger cloud droplets, and initiates precipitation for nondrizzling polluted clouds or precedes the precipitation process for drizzling clouds. However, giant sea salt aerosol is found to have a negligible effect on τ for lightly precipitating cases, while resulting in a relative reduction of τ of 3%–77% (increasing with Na, for Na = 1000–2500 cm−3) for heavily precipitating cases, suggesting that the impact of giant sea salt is only important for moist and potentially convective clouds. Finally, a regression analysis of the simulations shows that the second indirect effect is more evident in clear than polluted cases. The second indirect effect is found to enhance (reduce) the overall aerosol indirect effect for heavily (lightly) drizzling clouds; that is, τ is larger (smaller) for the same relative change in Na than considering the Twomey (first indirect) effect alone. The aerosol indirect effect (on τ) is lessened in the daytime afternoon conditions and is dominated by the Twomey effect; however, the effect in the early morning is close but slightly smaller than that in the nocturnal run. Diurnal variations of the aerosol indirect effect should be considered to accurately assess its magnitude.
Supplying Local Microphysics Parameterizations with Information about Subgrid Variability: Latin Hypercube Sampling
Authors: Larson Vincent E. , Golaz Jean-Christophe , Jiang Hongli , Cotton William R. 
Published: November 2005

Abstract
One problem in computing cloud microphysical processes in coarse-resolution numerical models is that many microphysical processes are nonlinear and small in scale. Consequently, there are inaccuracies if microphysics parameterizations are forced with grid box averages of model fields, such as liquid water content. Rather, the model needs to determine information about subgrid variability and input it into the microphysics parameterization.
One possible solution is to assume the shape of the family of probability density functions (PDFs) associated with a grid box and sample it using the Monte Carlo method. In this method, the microphysics subroutine is called repeatedly, once with each sample point. In this way, the Monte Carlo method acts as an interface between the host model’s dynamics and the microphysical parameterization. This avoids the need to rewrite the microphysics subroutines.
A difficulty with the Monte Carlo method is that it introduces into the simulation statistical noise or variance, associated with the finite sample size. If the family of PDFs is tractable, one can sample solely from cloud, thereby improving estimates of in-cloud processes. If one wishes to mitigate the noise further, one needs a method for reduction of variance. One such method is Latin hypercube sampling, which reduces noise by spreading out the sample points in a quasi-random fashion.
This paper formulates a sampling interface based on the Latin hypercube method. The associated family of PDFs is assumed to be a joint normal/lognormal (i.e., Gaussian/lognormal) mixture. This method of variance reduction has a couple of advantages. First, the method is general: the same interface can be used with a wide variety of microphysical parameterizations for various processes. Second, the method is flexible: one can arbitrarily specify the number of hydrometeor categories and the number of calls to the microphysics parameterization per grid box per time step.
This paper performs a preliminary test of Latin hypercube sampling. As a prototypical microphysical formula, this paper uses the Kessler autoconversion formula. The PDFs that are sampled are extracted diagnostically from large-eddy simulations (LES). Both stratocumulus and cumulus boundary layer cases are tested. In this diagnostic test, the Latin hypercube can produce somewhat less noisy time-averaged estimates of Kessler autoconversion than a traditional Monte Carlo estimate, with no additional calls to the microphysics parameterization. However, the instantaneous estimates are no less noisy. This paper leaves unanswered the question of whether the Latin hypercube method will work well in a prognostic, interactive cloud model, but this question will be addressed in a future manuscript.
Biology and Management of Histologic Transformation of Indolent Lymphoma
Authors: Freedman Arnold S. 
Published: November 2005

Abstract
The evolution of indolent lymphomas to aggressive histologies, known as histologic transformation (HT), is a frequent occurrence for all subtypes of low grade B cell lymphoproliferative disorders. The risk of developing HT is approximately 3% per year for patients with indolent lymphoma. Clinically these present with a rapid change in the behavior of the disease, with evidence of a highly proliferative malignancy with a propensity to involve extranodal sites. The prognosis of patients following transformation is generally poor, with median survival of about 12 months. Recent studies suggest that the development of HT is very complex with the acquisition of multiple cytogenetic abnormalities in the low-grade lymphoma cells prior to HT. To date, there are no biologic or genetic parameters predictive of the development of HT. A myriad of genetic lesions have been identified in HT, and provide insight into its pathogenesis. These include genes regulating proliferation (C-MYC and C-MYC-regulated genes); control of the cell cycle (CDKN2a and CDKN2B); and programmed cell death (TP53, C-MYC, and BCL2). Gene expression profiling has been applied to the study of HT and has increased our understanding of the transformation process. There has been limited progress in the treatment of patients with HT. Conventional chemotherapy is generally of limited benefit, although a subset of patients are long-term survivors following high-dose therapy and autologous stem cell transplantation. The use of radioimmunotherapy and new agents targeting specific lesions or aberrant pathways may impact on the management of these aggressive diseases.
Umbilical Cord Blood Transplantation: A New Alternative Option
Authors: Tse William , Laughlin Mary J. 
Published: November 2005

Abstract
Allogeneic hematopoietic stem cell transplantation is a life-saving procedure for hematopoietic malignancies, marrow failure syndromes, and hereditary immunodeficiency disorders. However, wide application of this procedure is limited by availability of suitably HLA-matched adult donors. Umbilical cord blood (UCB) has being increasingly used as an alternative hematopoietic stem cell source for these patients. To date, over 6000 UCB transplant procedures in children and adults have been performed worldwide using UCB donors. Broader use of UCB for adult patients is however limited by the available infused cell dose. This has prompted intensive research on ex vivo expansion of UCB stem cells and UCB graft-engineering including accessory cells able to improve UCB engraftment and reconstitution and for tissue regenerative potential. Recently, two large European and North American retrospective studies demonstrated that UCB is an acceptable alternative source of hematopoietic stem cells for adult recipients who lack HLA-matched adult donors. UCB is anticipated to address needs in both transplantation and regenerative medicine fields. It has advantages of easy procurement, no risk to donors, low risk of transmitting infections, immediate availability and immune tolerance allowing successful transplantation despite HLA disparity.
Haploidentical Stem Cell Transplantation: The Always Present but Overlooked Donor
Authors: Spitzer Thomas R. 
Published: November 2005

Abstract
Haploidentical stem cell transplantation is a treatment option for the approximately 70% of patients who do not have an HLA-identical sibling donor. The availability of a haploidentical donor in most families is a potential advantage, both for avoiding the need to find an alternative unrelated donor, and for the potentially more potent graft-versus-tumor effect that can be induced. The early complications of severe graft-versus-host disease (GVHD) following T-cell replete stem cell transplantation (SCT), and graft failure and recurrent malignancy (after T-cell depleted SCT) have limited the applications of this approach. Newer strategies employing T-cell depletion of the graft, using either very high-dose peripheral blood stem cells and/or more intensive conditioning therapy have overcome some of the problems of conventional transplantation. Nonmyeloablative SCT approaches have overcome some of the morbidity and mortality associated with the early complications of SCT and have been associated with favorable engraftment and GVHD profiles. Induction of mixed lymphohematopoietic chimerism as a platform for adoptive cellular immunotherapy (via delayed donor lymphocyte infusions) may have important application in avoiding early GVHD, while ultimately capturing a very potent graft-versus-tumor effect. Current strategies are focusing on improvement of immune reconstitution and prevention of recurrence of the underlying malignancy.
Acquired Risk Factors for Venous Thromboembolism in Medical Patients
Authors: Prandoni Paolo 
Published: November 2005

Abstract
Acute venous thromboembolism (VTE) is a serious and potentially fatal disorder, which often complicates the course of hospitalized patients, but may also affect ambulatory and otherwise healthy people. While the introduction of thromboprophylactic measures is expected to have reduced the occurrence of postoperative VTE, there is an increasing awareness of the importance of medical conditions in determining thromboembolic events. Among the conditions that predispose patients to VTE are increasing age, cancer and its treatment, prolonged immobility, stroke or paralysis, previous VTE, congestive heart failure, acute infection, pregnancy or puerperium, dehydration, hormonal treatment, varicose veins, long air travel, acute inflammatory bowel disease, rheumatologic disease, and nephrotic syndrome. Other factors that have recently been associated with an increased risk of VTE disorders include persistent elevation of D-dimer and atherosclerotic disease. Recognition of the incidence and clinical importance of thrombosis will most likely encourage more widespread use of antithrombotic prophylaxis in medical patients.
Efficient gene-driven germ-line point mutagenesis of C57BL/6J mice
Authors: Michaud Edward J , Culiat Cymbeline T , Klebig Mitchell L , Barker Paul E , Cain KT , Carpenter Debra J , Easter Lori L , Foster Carmen M , Gardner Alysyn W , Guo ZY , Houser Kay J , Hughes Lori A , Kerley Marilyn K , Liu Zhaowei , Olszewski Robert E , Pinn Irina , Shaw Ginger D , Shinpock Sarah G , Wymore Ann M , Rinchik Eugene M , Johnson Dabney K 
Published: November 2005

Abstract

Background
Analysis of an allelic series of point mutations in a gene, generated by N-ethyl-N-nitrosourea (ENU) mutagenesis, is a valuable method for discovering the full scope of its biological function. Here we present an efficient gene-driven approach for identifying ENU-induced point mutations in any gene in C57BL/6J mice. The advantage of such an approach is that it allows one to select any gene of interest in the mouse genome and to go directly from DNA sequence to mutant mice.

Results
We produced the Cryopreserved Mutant Mouse Bank (CMMB), which is an archive of DNA, cDNA, tissues, and sperm from 4,000 G1 male offspring of ENU-treated C57BL/6J males mated to untreated C57BL/6J females. Each mouse in the CMMB carries a large number of random heterozygous point mutations throughout the genome. High-throughput Temperature Gradient Capillary Electrophoresis (TGCE) was employed to perform a 32-Mbp sequence-driven screen for mutations in 38 PCR amplicons from 11 genes in DNA and/or cDNA from the CMMB mice. DNA sequence analysis of heteroduplex-forming amplicons identified by TGCE revealed 22 mutations in 10 genes for an overall mutation frequency of 1 in 1.45 Mbp. All 22 mutations are single base pair substitutions, and nine of them (41%) result in nonconservative amino acid substitutions. Intracytoplasmic sperm injection (ICSI) of cryopreserved spermatozoa into B6D2F1 or C57BL/6J ova was used to recover mutant mice for nine of the mutations to date.

Conclusions
The inbred C57BL/6J CMMB, together with TGCE mutation screening and ICSI for the recovery of mutant mice, represents a valuable gene-driven approach for the functional annotation of the mammalian genome and for the generation of mouse models of human genetic diseases. The ability of ENU to induce mutations that cause various types of changes in proteins will provide additional insights into the functions of mammalian proteins that may not be detectable by knockout mutations.
Functional inaccessibility of quiescent herpes simplex virus genomes
Authors: Minaker Rebecca L , Mossman Karen L , Smiley James R 
Published: November 2005

Abstract

Background
Newly delivered herpes simplex virus genomes are subject to repression during the early stages of infection of human fibroblasts. This host defence strategy can limit virus replication and lead to long-term persistence of quiescent viral genomes. The viral immediate-early protein ICP0 acts to negate this negative regulation, thereby facilitating the onset of the viral replication cycle. Although few mechanistic details are available, the host repression machinery has been proposed to assemble the viral genome into a globally inaccessible configuration analogous to heterochromatin, blocking access to most or all trans-acting factors. The strongest evidence for this hypothesis is that ICP0-deficient virus is unable to reactivate quiescent viral genomes, despite its ability to undergo productive infection given a sufficiently high multiplicity of infection. However, recent studies have shown that quiescent infection induces a potent antiviral state, and that ICP0 plays a key role in disarming such host antiviral responses. These findings raise the possibility that cells containing quiescent viral genomes may be refractory to superinfection by ICP0-deficient virus, potentially providing an alternative explanation for the inability of such viruses to trigger reactivation. We therefore asked if ICP0-deficient virus is capable of replicating in cells that contain quiescent viral genomes.

Results
We found that ICP0-deficient herpes simplex virus is able to infect quiescently infected cells, leading to expression and replication of the superinfecting viral genome. Despite this productive infection, the resident quiescent viral genome was neither expressed nor replicated, unless ICP0 was provided in trans.

Conclusion
These data document that quiescent HSV genomes fail to respond to the virally modified host transcriptional apparatus or viral DNA replication machinery provided in trans by productive HSV infection in the absence of ICP0. These results point to global repression as the basis for HSV genome quiescence, and indicate that ICP0 induces reactivation by overcoming this global barrier to the access of trans-acting factors.
Stimulation of poliovirus RNA synthesis and virus maturation in a HeLa cell-free in vitro translation-RNA replication system by viral protein 3CDpro
Authors: Franco David , Pathak Harsh B , Cameron Craig E , Rombaut Bart , Wimmer Eckard , Paul Aniko V 
Published: November 2005

Abstract
Poliovirus protein 3CDpro possesses both proteinase and RNA binding activities, which are located in the 3Cpro domain of the protein. The RNA polymerase (3Dpol) domain of 3CDpro modulates these activities of the protein. We have recently shown that the level of 3CDpro in HeLa cell-free in vitro translation-RNA replication reactions is suboptimal for efficient virus production. However, the addition of either 3CDpro mRNA or of purified 3CDpro protein to in vitro reactions, programmed with viral RNA, results in a 100-fold increase in virus yield. Mutational analyses of 3CDpro indicated that RNA binding by the 3Cpro domain and the integrity of interface I in the 3Dpol domain of the protein are both required for function. The aim of these studies was to determine the exact step or steps at which 3CDpro enhances virus yield and to determine the mechanism by which this occurs. Our results suggest that the addition of extra 3CDpro to in vitro translation RNA-replication reactions results in a mild enhancement of both minus and plus strand RNA synthesis. By examining the viral particles formed in the in vitro reactions on sucrose gradients we determined that 3CDpro has only a slight stimulating effect on the synthesis of capsid precursors but it strikingly enhances the maturation of virus particles. Both the stimulation of RNA synthesis and the maturation of the virus particles are dependent on the presence of an intact RNA binding site within the 3Cpro domain of 3CDpro. In addition, the integrity of interface I in the 3Dpol domain of 3CDpro is required for efficient production of mature virus. Surprisingly, plus strand RNA synthesis and virus production in in vitro reactions, programmed with full-length transcript RNA, are not enhanced by the addition of extra 3CDpro. Our results indicate that the stimulation of RNA synthesis and virus maturation by 3CDpro in vitro is dependent on the presence of a VPg-linked RNA template.