bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuberculosis Diagnosis and Multidrug Resistance Testing by Direct Sputum Culture in Selective Broth without Decontamination or Centrifugation
Authors: Grandjean Louis , Martin Laura , Gilman Robert H. , Valencia Teresa , Herrera Beatriz , Quino Willi , Ramos Eric , Rivero Maribel , Montoya Rosario , Escombe A. Roderick , Coleman David , Mitchison Denis , Evans Carlton A. 
Published: May 2008

ABSTRACT

Tuberculosis culture usually requires sputum decontamination and centrifugation to prevent cultures from being overgrown by contaminating bacteria and fungi. However, decontamination destroys many tuberculous bacilli, and centrifugation often is not possible in resource-poor settings. We therefore assessed the performance of
Mycobacterium tuberculosis
culture with unprocessed samples plated directly by using tuberculosis-selective media and compared this procedure to conventional culture using centrifuge decontamination. Quadruplicate aliquots of strain H37RV were cultured in 7H9 broth with and without selective antimicrobials and after centrifuge decontamination. The subsequent comparison was made with 715 sputum samples. Split paired sputum samples were cultured conventionally with centrifuge decontamination and by direct culture in tuberculosis-selective media containing antibiotics. Centrifuge decontamination reduced tuberculosis H37RV colonies by 78% (
P
< 0.001), whereas direct culture in tuberculosis-selective media had no inhibitory effect. Similarly, in sputum cultures that were not overgrown by contaminants, conventional culture yielded fewer tuberculosis colonies than direct culture (
P
< 0.001). However, the sensitivity of conventional culture was greater than that of direct culture, because samples were less affected by contamination. Thus, of the 340 sputum samples that were tuberculosis culture positive, conventional culture detected 97%, whereas direct culture detected 81% (
P
< 0.001). Conventional and direct cultures both took a median of 8.0 days to diagnose tuberculosis (
P
= 0.8). In those direct cultures that detected drug resistance or susceptibility, there was a 97% agreement with the results of conventional culture (Kappa agreement statistic, 0.84;
P
< 0.001). Direct culture is a simple, low-technology, and rapid technique for diagnosing tuberculosis and determining drug susceptibility. Compared to that of conventional culture, direct culture has reduced sensitivity because of bacterial overgrowth, but in basic laboratories this deficit may be outweighed by the ease of use.
Multifunctional T-Cell Characteristics Induced by a Polyvalent DNA Prime/Protein Boost Human Immunodeficiency Virus Type 1 Vaccine Regimen Given to Healthy Adults Are Dependent on the Route and Dose of Administration
Authors: Bansal Anju , Jackson Bethany , West Kim , Wang Shixia , Lu Shan , Kennedy Jeffrey S. , Goepfert Paul A. 
Published: May 2008

ABSTRACT

A phase I clinical vaccine study of a human immunodeficiency virus type 1 (HIV-1) vaccine regimen comprising a DNA prime formulation (5-valent
env
and monovalent
gag
) followed by a 5-valent Env protein boost for seronegative adults was previously shown to induce HIV-1-specific T cells and anti-Env antibodies capable of neutralizing cross-clade viral isolates. In light of these initial findings, we sought to more fully characterize the HIV-1-specific T cells by using polychromatic flow cytometry. Three groups of participants were vaccinated three times with 1.2 mg of DNA administered intradermally (i.d.; group A), 1.2 mg of DNA administered intramuscularly (i.m.; group B), or 7.2 mg of DNA administered i.m. (high-dose group C) each time. Each group subsequently received one or two doses of 0.375 mg each of the gp120 protein boost vaccine (i.m.). Env-specific CD4 T-cell responses were seen in the majority of participants; however, the kinetics of responses differed depending on the route of DNA administration. The high i.m. dose induced the responses of the greatest magnitude after the DNA vaccinations, while the i.d. group exhibited the responses of the least magnitude. Nevertheless, after the second protein boost, the magnitude of CD4 T-cell responses in the i.d. group was indistinguishable from those in the other two groups. After the DNA vaccinations and the first protein boost, a greater number of polyfunctional Env-specific CD4 T cells (those with ≥2 functions) were seen in the high-dose group than in the other groups. Gag-specific CD4 T cells and Env-specific CD8 T cells were seen only in the high-dose group. These findings demonstrate that the route and dose of DNA vaccines significantly impact the quality of immune responses, yielding important information for future vaccine design.
The Hepatitis E Virus ORF3 Protein Modulates Epidermal Growth Factor Receptor Trafficking, STAT3 Translocation, and the Acute-Phase Response
Authors: Chandra Vivek , Kar-Roy Anindita , Kumari Sudha , Mayor Satyajit , Jameel Shahid 
Published: May 2008

ABSTRACTThe hepatitis E virus (HEV) causes acute viral hepatitis, but its characterization is hampered by the lack of an efficient in vitro infection system that can be used to study the effects of HEV proteins on cellular processes. Previous studies suggest that the viral ORF3 protein (pORF3) is essential for infection in vivo and is likely to modulate the host response. Here, we report that pORF3 localizes to early and recycling endosomes and causes a delay in the postinternalization trafficking of epidermal growth factor receptor (EGFR) to late endosomes/lysosomes. The cytoplasmic phosphorylated signal transducer and activator of transcription 3 (pSTAT3) proteins require growth factor receptor endocytosis for their translocation from the cytoplasm to nucleus. Consequently, lower levels of pSTAT3 were found in the nuclei of ORF3-expressing Huh7 human hepatoma cells stimulated with EGF. This results in downregulation of the acute-phase response, a major determinant of inflammation in the host. We propose that through its effects on EGFR trafficking, pORF3 prolongs endomembrane growth factor signaling and promotes cell survival. The effects on STAT3 translocation would result in a reduced inflammatory response. Both of these events are likely to contribute positively to viral replication.
Cell Adhesion Promotes Ebola Virus Envelope Glycoprotein-Mediated Binding and Infection
Authors: Dube Derek , Schornberg Kathryn L. , Stantchev Tzanko S. , Bonaparte Matthew I. , Delos Sue E. , Bouton Amy H. , Broder Christopher C. , White Judith M. 
Published: May 2008

ABSTRACT
Ebola virus infects a wide variety of adherent cell types, while nonadherent cells are found to be refractory. To explore this correlation, we compared the ability of pairs of related adherent and nonadherent cells to bind a recombinant Ebola virus receptor binding domain (EboV RBD) and to be infected with Ebola virus glycoprotein (GP)-pseudotyped particles. Both human 293F and THP-1 cells can be propagated as adherent or nonadherent cultures, and in both cases adherent cells were found to be significantly more susceptible to both EboV RBD binding and GP-pseudotyped virus infection than their nonadherent counterparts. Furthermore, with 293F cells the acquisition of EboV RBD binding paralleled cell spreading and did not require new mRNA or protein synthesis.
Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing
Authors: Dumortier Jerome , Streblow Daniel N. , Moses Ashlee V. , Jacobs Jon M. , Kreklywich Craig N. , Camp David , Smith Richard D. , Orloff Susan L. , Nelson Jay A. 
Published: May 2008

ABSTRACT
Human cytomegalovirus (HCMV) is implicated in the acceleration of a number of vascular diseases including transplant vascular sclerosis (TVS), the lesion associated with chronic rejection (CR) of solid organ transplants. Although the virus persists in the allograft throughout the course of disease, few cells are directly infected by CMV. This observation is in contrast to the global effects that CMV has on the acceleration of TVS/CR, suggesting that CMV infection indirectly promotes the vascular disease process. Recent transcriptome analysis of CMV-infected heart allografts indicates that the virus induces cytokines and growth factors associated with angiogenesis (AG) and wound healing (WH), suggesting that CMV may accelerate TVS/CR through the induction and secretion of AG/WH factors from infected cells. We analyzed virus-free supernatants from HCMV-infected cells (HCMV secretomes) for growth factors, by mass spectrometry and immunoassays, and found that the HCMV secretome contains over 1,000 cellular proteins, many of which are involved in AG/WH. Importantly, functional assays demonstrated that CMV but not herpes simplex virus secretomes not only induce AG/WH but also promote neovessel stabilization and endothelial cell survival for 2 weeks. These findings suggest that CMV acceleration of TVS occurs through virus-induced growth factors and cytokines in the CMV secretome.
Neutralizing Antibody Blocks Adenovirus Infection by Arresting Microtubule-Dependent Cytoplasmic Transport
Authors: Smith Jason G. , Cassany Aurelia , Gerace Larry , Ralston Robert , Nemerow Glen R. 
Published: May 2008

ABSTRACT
Neutralizing antibodies are commonly elicited by viral infection. Most antibodies that have been characterized block early stages of virus entry that occur before membrane penetration, whereas inhibition of late stages in entry that occurs after membrane penetration has been poorly characterized. Here we provide evidence that the neutralizing antihexon monoclonal antibody 9C12 inhibits adenovirus infection by blocking microtubule-dependent translocation of the virus to the microtubule-organizing center following endosome penetration. These studies identify a previously undescribed mechanism by which neutralizing antibodies block virus infection, a situation that may be relevant for other nonenveloped viruses that use microtubule-dependent transport during cell entry.
Severe Acute Respiratory Syndrome Coronavirus Protein 6 Accelerates Murine Hepatitis Virus Infections by More than One Mechanism
Authors: Hussain Snawar , Perlman Stanley , Gallagher Thomas M. 
Published: May 2008

ABSTRACT
The severe acute respiratory syndrome coronavirus (SARS-CoV) encodes numerous accessory proteins whose importance in the natural infection process is currently unclear. One of these accessory proteins is set apart by its function in the context of a related murine hepatitis virus (MHV) infection. SARS-CoV protein 6 increases MHV neurovirulence and accelerates MHV infection kinetics in tissue culture. Protein 6 also blocks nuclear import of macromolecules from the cytoplasm, a process known to involve its C-terminal residues interacting with cellular importins. In this study, protein 6 was expressed from plasmid DNAs and accumulated in cells prior to infection by wild-type MHV. Output of MHV progeny was significantly increased by preexisting protein 6. Protein 6 with C-terminal deletion mutations no longer interfered with nuclear import processes but still retained much of the capacity to augment MHV infections. However, some virus growth-enhancing activity could be ascribed to the C-terminal end of protein 6. To determine whether this augmentation provided by the C terminus was derived from interference with nuclear import, we evaluated the virus-modulating effects of small interfering RNAs (siRNAs) directed against importin-β mRNAs, which down-regulated classical nuclear import pathways. The siRNAs did indeed prime cells for enhanced MHV infection. Our findings indicated that protein 6-mediated nuclear import blocks augmented MHV infections but is clearly not the only way that this accessory protein operates to create a milieu conducive to robust virus growth. Thus, the SARS-CoV protein 6 accelerates MHV infections by more than one mechanism.
N-symmetry direction field design
Authors: Ray Nicolas , Vallet Bruno , Li Wan Chiu , Lévy Bruno 
Published: May 2008

Many algorithms in computer graphics and geometry processing use two orthogonal smooth direction fields (unit tangent vector fields) defined over a surface. For instance, these direction fields are used in texture synthesis, in geometry processing or in nonphotorealistic rendering to distribute and orient elements on the surface. Such direction fields can be designed in fundamentally different ways, according to the symmetry requested: inverting a direction or swapping two directions might be allowed or not.
Despite the advances realized in the last few years in the domain of geometry processing, a unified formalism is still lacking for the mathematical object that characterizes these generalized direction fields. As a consequence, existing direction field design algorithms are limited to using nonoptimum local relaxation procedures.

In this article, we formalize
N
-symmetry direction fields, a generalization of classical direction fields. We give a new definition of their singularities to explain how they relate to the topology of the surface. Specifically, we provide an accessible demonstration of the Poincaré-Hopf theorem in the case of
N
-symmetry direction fields on 2-manifolds. Based on this theorem, we explain how to control the topology of
N
-symmetry direction fields on meshes. We demonstrate the validity and robustness of this formalism by deriving a highly efficient algorithm to design a smooth field interpolating user-defined singularities and directions.
Comparing the Vertical Structures of Weighting Functions and Adjoint Sensitivity of Radiance and Verifying Mesoscale Forecasts Using AIRS Radiance Observations
Authors: Carrier Matthew J. , Zou Xiaolei , Lapenta William M. 
Published: May 2008

Abstract
An adjoint sensitivity analysis is conducted using the adjoint of the hyperspectral radiative transfer model (RTM) that simulates the radiance spectrum from the Advanced Infrared Sounder (AIRS). It is shown, both theoretically and numerically, that the height of the maximum sensitivity of radiance in a channel could be higher or lower than the height of the maximum weighting function of that channel. It is shown that the discrepancy between the two heights is determined by the vertical structures of the atmospheric thermodynamic state. The sensitivity finds the level at which changes in temperature and/or moisture will have the largest influence on the simulated brightness temperature (BT), and the maximum weighting function (WF) height indicates the level where the model atmosphere contributes most significantly to the emission at the top of the atmosphere. Based on the above findings, an adjoint method for forecast verification using AIRS radiances is presented. In this method, model forecasts are first mapped into radiance space by an RTM so that they can be compared directly with the observed radiance values. The adjoint sensitivity analysis results are then used to connect the deviations of the model forecasts from observed radiances to the changes of temperature and moisture variables in model space. This adjoint sensitivity based model verification provides useful information on forecast model performances based on indirect observations from satellites.
Using Model Reduction Methods within Incremental Four-Dimensional Variational Data Assimilation
Authors: Lawless A. S. , Nichols N. K. , Boess C. , Bunse-Gerstner A. 
Published: May 2008

Abstract
Incremental four-dimensional variational data assimilation is the method of choice in many operational atmosphere and ocean data assimilation systems. It allows the four-dimensional variational data assimilation (4DVAR) to be implemented in a computationally efficient way by replacing the minimization of the full nonlinear 4DVAR cost function with the minimization of a series of simplified cost functions. In practice, these simplified functions are usually derived from a spatial or spectral truncation of the full system being approximated. In this paper, a new method is proposed for deriving the simplified problems in incremental 4DVAR, based on model reduction techniques developed in the field of control theory. It is shown how these techniques can be combined with incremental 4DVAR to give an assimilation method that retains more of the dynamical information of the full system. Numerical experiments using a shallow-water model illustrate the superior performance of model reduction to standard truncation techniques.
Bred Vectors and Tropical Pacific Forecast Errors in the NASA Coupled General Circulation Model
Authors: Yang Shu-Chih , Kalnay Eugenia , Cai Ming , Rienecker Michele M. 
Published: May 2008

AbstractThe breeding method has been implemented in the NASA Global Modeling and Assimilation Office coupled general circulation model (CGCM) in its operational configuration in which ocean data assimilation is used to initialize the coupled forecasts. Bred vectors (BVs), designed to capture the dominant growing errors in the atmosphere–ocean coupled system, are applied as initial ensemble perturbations. The potential improvement for ensemble prediction is investigated by comparing BVs with the oceanic growing errors, estimated by the one-month forecast error from the nonperturbed forecast. Results show that one-month forecast errors and BVs from the NASA CGCM share very similar features: BVs are clearly related to forecast errors in both SST and equatorial subsurface temperature—in particular, when the BV growth rate is large. Both the forecast errors and the BVs in the subsurface are dominated by large-scale structures near the thermocline. Results suggest that the forecast errors are dominated by dynamically evolving structures related to the variations of the background anomalous state, and that their shapes can be captured by BVs, especially during the strong 1997/98 El Niño. Hindcast experiments starting from January 1997 with one pair of BVs achieve a significant improvement relative to the control (unperturbed) hindcast by capturing many important features of this event, including the westerly wind burst in early 1997.
Assessing the Usefulness of Probabilistic Forecasts
Authors: Cusack Stephen , Arribas Alberto 
Published: May 2008

Abstract
The errors in both the initialization and simulated evolution of weather and climate models create significant uncertainties in forecasts at lead times beyond a few days. Modern prediction systems sample the sources of these uncertainties to produce a probability distribution function of future meteorological conditions to help end users in their risk assessment and decision-making processes. The performance of prediction systems is assessed using data from a set of historical forecasts and the corresponding observations. There are many aspects to the correspondence between forecasts and observations, and various summary scores have been created to measure the different features of forecast quality. The main concern for end users is the usefulness of forecasts. There are two independent and sufficient aspects for the assessment of the usefulness of forecasts to end users: 1) the statistical consistency of forecast statements with observations and 2) the extra information contained in the forecast relative to the situation in which such predictions are unavailable. In this paper two new scores, the full-pdf-reliability Rpdf and information quantity IQ, are proposed to measure these two independent aspects of usefulness. In contrast to all existing summary scores, both Rpdf and IQ depend upon all moments of the forecast pdf. When taken together, the values of Rpdf and IQ offer a general measure of the usefulness of ensemble predictions.
Testing the Annular Mode Autocorrelation Time Scale in Simple Atmospheric General Circulation Models
Authors: Gerber Edwin P. , Voronin Sergey , Polvani Lorenzo M. 
Published: May 2008

Abstract
A new diagnostic for measuring the ability of atmospheric models to reproduce realistic low-frequency variability is introduced in the context of Held and Suarez’s 1994 proposal for comparing the dynamics of different general circulation models. A simple procedure to compute τ, the e-folding time scale of the annular mode autocorrelation function, is presented. This quantity concisely quantifies the strength of low-frequency variability in a model and is easy to compute in practice. The sensitivity of τ to model numerics is then studied for two dry primitive equation models driven with the Held–Suarez forcings: one pseudospectral and the other finite volume. For both models, τ is found to be unrealistically large when the horizontal resolutions are low, such as those that are often used in studies in which long integrations are needed to analyze model variability on low frequencies. More surprising is that it is found that, for the pseudospectral model, τ is particularly sensitive to vertical resolution, especially with a triangular truncation at wavenumber 42 (a very common resolution choice). At sufficiently high resolution, the annular mode autocorrelation time scale τ in both models appears to converge around values of 20–25 days, suggesting the existence of an intrinsic time scale at which the extratropical jet vacillates in the Held and Suarez system. The importance of τ for computing the correct response of a model to climate change is explicitly demonstrated by perturbing the pseudospectral model with simple torques. The amplitude of the model’s response to external forcing increases as τ increases, as suggested by the fluctuation–dissipation theorem.
NASA Cold Land Processes Experiment (CLPX 2002/03): Field Measurements of Snowpack Properties and Soil Moisture
Authors: Elder Kelly , Cline Don , Liston Glen E. , Armstrong Richard 
Published: May 2008

Abstract
A field measurement program was undertaken as part NASA’s Cold Land Processes Experiment (CLPX). Extensive snowpack and soil measurements were taken at field sites in Colorado over four study periods during the two study years (2002 and 2003). Measurements included snow depth, density, temperature, grain type and size, surface wetness, surface roughness, and canopy cover. Soil moisture measurements were made in the near-surface layer in snow pits. Measurements were taken in the Fraser valley, North Park, and Rabbit Ears Pass areas of Colorado. Sites were chosen to gain a wide representation of snowpack types and physiographies typical of seasonally snow-covered regions of the world. The data have been collected with rigorous protocol to ensure consistency and quality, and they have undergone several levels of quality assurance to produce a high-quality spatial dataset for continued cold lands hydrological research. The dataset is archived at the National Snow and Ice Data Center (NSIDC) in Boulder, Colorado.