bluuebunny/crossref_metadata_2025_split huggingface dataset:
Staphylococcus aureus
Rbf Activates Biofilm Formation In Vitro and Promotes Virulence in a Murine Foreign Body Infection Model
Authors: Luong Thanh T. , Lei Mei G. , Lee Chia Y. 
Published: October 2008

ABSTRACT

We previously identified Rbf as an activator for biofilm formation on polystyrene surfaces in
Staphylococcus aureus
strain 8325-4. However, strain 8325-4 contains genetic mutations that may affect biofilm formation. To extend the observation to other strains, we used strain Newman, a weak biofilm producer, and strain UAMS-1, an osteomyelitis clinical strain, in this study. We found that mutations in the chromosomal
rbf
gene did not affect biofilm formation on polystyrene surfaces in these strains, but transformants of these strains carrying a multiple-copy plasmid containing the
rbf
gene formed stronger biofilms than the wild-type strains and the mutant strains. Using the flow cell method, we found that the chromosomal mutation in the
rbf
gene delayed biofilm formation, whereas strains with a plasmid containing the
rbf
gene accelerated biofilm formation in strains Newman and UAMS-1. These results led us to conclude that
rbf
is an activator of biofilm formation in different strains of
S. aureus
, although the degree of activation varies among strains. In a murine model of foreign body infection, the
rbf
mutations in strain Newman, but not in strain UAMS-1, reduced the bacterial survival rate in catheter lumen. However, UAMS-1 carrying multiple copies of
rbf
in a plasmid increased the bacterial survival rate. The animal studies therefore suggest that Rbf has a role in
S. aureus
virulence.
Genome-Wide Screen in
Francisella novicida
for Genes Required for Pulmonary and Systemic Infection in Mice
Authors: Kraemer Petra S. , Mitchell Allison , Pelletier Mark R. , Gallagher Larry A. , Wasnick Mike , Rohmer Laurence , Brittnacher Mitchell J. , Manoil Colin , Skerett Shawn J. , Salama Nina R. 
Published: October 2008

ABSTRACT

Francisella tularensis
is a gram-negative, highly infectious, aerosolizable facultative intracellular pathogen that causes the potentially life-threatening disease tularemia. To date there is no approved vaccine available, and little is known about the molecular mechanisms important for infection, survival, and dissemination at different times of infection. We report the first whole-genome screen using an inhalation mouse model to monitor infection in the lung and dissemination to the liver and spleen. We queried a comprehensive library of 2,998 sequence-defined transposon insertion mutants in
Francisella novicida
strain U112 using a microarray-based negative-selection screen. We were able to track the behavior of 1,029 annotated genes, equivalent to a detection rate of 75% and corresponding to ∼57% of the entire
F. novicida
genome. As expected, most transposon mutants retained the ability to colonize, but 125 candidate virulence genes (12%) could not be detected in at least one of the three organs. They fell into a variety of functional categories, with one-third having no annotated function and a statistically significant enrichment of genes involved in transcription. Based on the observation that behavior during complex pool infections correlated with the degree of attenuation during single-strain infection we identified nine genes expected to strongly contribute to infection. These included two genes, those for ATP synthase C (FTN_1645) and thioredoxin (FTN_1415), that when mutated allowed increased host survival and conferred protection in vaccination experiments.
Multiple Functional Domains of
Enterococcus faecalis
Aggregation Substance Asc10 Contribute to Endocarditis Virulence
Authors: Chuang Olivia N. , Schlievert Patrick M. , Wells Carol L. , Manias Dawn A. , Tripp Timothy J. , Dunny Gary M. 
Published: October 2008

ABSTRACT

Aggregation substance proteins encoded by sex pheromone plasmids increase the virulence of
Enterococcus faecalis
in experimental pathogenesis models, including infectious endocarditis models. These large surface proteins may contain multiple functional domains involved in various interactions with other bacterial cells and with the mammalian host. Aggregation substance Asc10, encoded by plasmid pCF10, is induced during growth in the mammalian bloodstream, and pCF10 carriage gives
E. faecalis
a significant selective advantage in this environment. We employed a rabbit model to investigate the role of various functional domains of Asc10 in endocarditis. The data suggested that the bacterial load of the infected tissue was the best indicator of virulence. Isogenic strains carrying either no plasmid, wild-type pCF10, a pCF10 derivative with an in-frame deletion of the
prgB
gene encoding Asc10, or pCF10 derivatives expressing other alleles of
prgB
were examined in this model. Previously identified aggregation domains contributed to the virulence associated with the wild-type protein, and a strain expressing an Asc10 derivative in which glycine residues in two RGD motifs were changed to alanine residues showed the greatest reduction in virulence. Remarkably, this strain and the strain carrying the pCF10 derivative with the in-frame deletion of
prgB
were both significantly less virulent than an isogenic plasmid-free strain. The data demonstrate that multiple functional domains are important in Asc10-mediated interactions with the host during the course of experimental endocarditis and that in the absence of a functional
prgB
gene, pCF10 carriage is actually disadvantageous in vivo.
MP1
Authors: Brosgol Ben 
Published: October 2008

Level - Intermediate.
This intermediate-level tutorial is aimed at people with a technical background in software development. No previous experience with safety-critical standards is required. Some familiarity with one or more of C, C++, Ada, or Java would be useful.

Safety-critical systems (whose anomalous behavior could cause catastrophic or major failure involving loss of life) are becoming increasingly prevalent. Standards such as
DO-178B
, originally developed for commercial avionics, are attracting attention in other segments. The requirement to comply with such standards imposes constraints (on quality assurance, traceability, etc.) much beyond what is typical for Commercial-Off-The-Shelf Software. One of the major decisions that affects safety certification is the choice of programming language(s). Specific language features, either by their presence of absence, may make certification easier or harder. (Practicalities such as tool support and programmer experience are of course also important but are outside the scope of the tutorial).

This tutorial first summarizes existing safety standards, with a focus on DO-178B, and explains how they affect the requirements on a programming language. It specifically addresses the challenges imposed by Object-Oriented Technology and summarizes the work currently underway on DO-178C. The tutorial then assesses three language technologies - C (including C++), Ada, and Java - with respect to suitability for meeting these requirements through appropriate subsetting. MISRA C, SPARK, and the in-progress Safety-Critical Java Technology are specifically identified and reviewed.
Re-ADA
Authors: Liang Sheldon X. , Reibling Lyle A. , Betts John 
Published: October 2008

Military commands must respond to a variety of situations by quickly assembling and organizing coalition forces consisting of different components from several countries. Dependable interoperability of their C4ISR systems is vital to the success of many military applications where pressing new requirements quickly emerge and undergo rapid change.
In order to achieve dependable interoperability, a reliable infrastructure is critical to incorporating operational components into C4ISR systems. Software architectures and related techniques hold the answer to interoperable, reliable and evolvable C4ISR systems. This paper analyzes the major aspects of dependable interoperability for C4ISR, and presents a Quantitative Interoperating Model (QIM) for enabling seamless interconnection, effective intercommunication and dependable interoperation between heterogeneous components over the network. Based on the QIM, an approach is synthesized toward Reliable Ada-based Descriptive Architecture (re-ADA) for C4ISR. As an executable architectural framework, re-ADA can directly be mapped into Ada95 code and constructed on the basis of CORBA to support distributed computing over-the-network. In particular, the well-formalized QIM - through mapping dependability into quantitative attributes that are attached to architectural artifacts - makes it possible to statically verify quantitative attributes during architectural design, and dynamically monitor them at runtime.
Ada and software engineering education
Authors: McCormick John W. 
Published: October 2008

How do you select a programming language for your project? Few developers have the luxury of coding the same design in multiple languages to compare language merits. For over twenty years my undergraduate students have implemented the same large (10-15K lines), multi-tasking, real-time embedded system. In one 15 week semester, student teams specify, design, and implement software to control a substantial model railroad layout.
Students implement everything from device drivers for custom I/O hardware to high-level decision making algorithms. Student teams have implemented the project in both Ada and C. This paper describes the course, the laboratory, the project, and an analysis of the results achieved with each of the implementation languages.
Implementing the extended return statement for Ada 2005
Authors: Taft S. Tucker 
Published: October 2008

Ada 2005 adds an important capability to the language by allowing the construction and return of an object of a limited type by a function. New syntax for an extended return statement was added to enhance this capability further. This capability to return newly constructed objects of a limited type from a function, when combined with the additional capability to use aggregates to construct objects of a limited type, goes a long way to making use of limited types far more friendly and effective.
Although the extended return statement and the associated ability to construct and return objects of a limited type brings new power to Ada, it also brings new choices and challenges to the Ada compiler implementor, when trying to decide how best to implement this feature. This presentation will review some of these alternatives, and present a high-level description of one particular approach based on the notion of an object creation context (OCC) which is designed to minimize the complexity of the generated code while providing an efficient and flexible implementation.
Evaluation of Turbulence Closure Models for Large-Eddy Simulation over Complex Terrain: Flow over Askervein Hill
Authors: Chow Fotini Katopodes , Street Robert L. 
Published: October 2008

Abstract
The evaluation of turbulence closure models for large-eddy simulation (LES) has primarily been performed over flat terrain, where comparisons with theory and observations are simplified. The authors have previously developed improved closure models using explicit filtering and reconstruction, together with a dynamic eddy-viscosity model and a near-wall stress term. This dynamic reconstruction model (DRM) is a mixed model, combining scale-similarity and eddy-viscosity components. The DRM gave improved results over standard eddy-viscosity models for neutral boundary layer flow over flat but rough terrain, yielding the expected logarithmic velocity profiles near the wall. The results from the studies over flat terrain are now extended to flow over full-scale topography. The test case is flow over Askervein Hill, an isolated hill in western Scotland, where a field campaign was conducted in 1983 with the purpose of capturing wind data representing atmospheric episodes under near-neutral stratification and steady wind conditions. This widely studied flow provides a more challenging test case for the new turbulence models because of the sloping terrain and separation in the lee of the hill. Since an LES formulation is used, a number of simulation features are different than those typically used in the Askervein literature. The simulations are inherently unsteady, the inflow conditions are provided by a separate turbulent flow database, and (uniquely herein) ensemble averages of the turbulent flow results are used in comparisons with field data. Results indicate that the DRM can improve the predictions of flow speedup and especially turbulent kinetic energy (TKE) over the hill when compared with the standard TKE-1.5 model. This is the first study, to the authors’ knowledge, in which explicit filtering and reconstruction (scale similarity) and dynamic turbulence models have been applied to full-scale simulations of the atmospheric boundary layer over terrain. Simulations with the lowest level of reconstruction are straightforward. Increased levels of reconstruction, however, present difficulties when used with a dynamic eddy-viscosity model. An alternative mixed model is proposed to avoid the complexities associated with the dynamic procedure and to allow higher levels of reconstruction; this mixed model combines a standard TKE-1.5 eddy-viscosity closure with velocity reconstruction to form a simple and efficient turbulence model that gives good results for both mean flow and turbulence over Askervein Hill. The results indicate that significant improvements in LES over complex terrain can be obtained by the use of mixed models that combine scale-similarity and eddy-viscosity components.
Zonal Flow Regime Changes in a GCM and in a Simple Quasigeostrophic Model: The Role of Stratospheric Dynamics
Authors: Bordi Isabella , Fraedrich Klaus , Ghil Michael , Sutera Alfonso 
Published: October 2008

Abstract
The atmospheric general circulation is characterized by both single- and double-jet patterns. The double-jet structure of the zonal mean zonal wind is analyzed in Southern Hemisphere observations for the two calendar months of November and April. The observed features are studied further in an idealized quasigeostrophic and a simplified general circulation model (GCM). Results suggest that capturing the bimodality of the zonal mean flow requires the parameterization of momentum and heat fluxes associated with baroclinic instability of the three-dimensional fields.
The role of eddy heat fluxes in generating the observed double-jet pattern is ascertained by using an analytical Eady model with stratospheric easterlies, in which a single wave disturbance interacts with the mean flow. In this model, the dual jets are generated by the zonal mean flow correction. Sensitivity of the results to the tropospheric vertical wind shear (or, equivalently, the meridional temperature gradient in the basic state’s troposphere) is also studied in the Eady model and compared to related experiments using the simplified GCM.
Predictability of Rotating Stratified Turbulence
Authors: Ngan K. , Bartello P. , Straub D. N. 
Published: October 2008

Abstract
Although predictability represents one of the fundamental problems in atmospheric science, gaps in our knowledge remain. Theoretical understanding of the inverse error cascade is limited mostly to homogeneous, isotropic turbulence, whereas numerical simulations have focused on highly complex numerical weather prediction models. These results cannot be easily reconciled.
This paper describes selected aspects of the predictability behavior of rotating stratified turbulence. The objective is to determine how the predictability varies with scale when the dynamics are more realistic than the idealized models that underlie the classical picture of predictability and yet are free of the parameterizations that complicate interpretation of NWP models. Using a numerical model of the nonhydrostatic Boussinesq equations, it is shown that the predictability decay, as diagnosed by the relative error, is slower for subsynoptic flow. The dependence on the deformation radius, differences between balanced and unbalanced modes, and implications for NWP models are discussed.
Evaluation of MJO Forecast Skill from Several Statistical and Dynamical Forecast Models
Authors: Seo Kyong-Hwan , Wang Wanqiu , Gottschalck Jon , Zhang Qin , Schemm Jae-Kyung E. , Higgins Wayne R. , Kumar Arun 
Published: October 2008

Abstract
This work examines the performance of Madden–Julian oscillation (MJO) forecasts from NCEP’s coupled and uncoupled general circulation models (GCMs) and statistical models. The forecast skill from these methods is evaluated in near–real time. Using a projection of El Niño–Southern Oscillation (ENSO)-removed variables onto the principal patterns of MJO convection and upper- and lower-level circulations, MJO-related signals in the dynamical model forecasts are extracted. The operational NCEP atmosphere–ocean fully coupled Climate Forecast System (CFS) model has useful skill (&gt;0.5 correlation) out to ∼15 days when the initial MJO convection is located over the Indian Ocean. The skill of the CFS hindcast dataset for the period from 1995 to 2004 is nearly comparable to that from a lagged multiple linear regression model, which uses information from the previous five pentads of the leading two principal components (PCs). In contrast, the real-time analysis for the MJO forecast skill for the period from January 2005 to February 2006 using the lagged multiple linear regression model is reduced to ∼10–12 days. However, the operational CFS forecast for this period is skillful out to ∼17 days for the winter season, implying that the coupled dynamical forecast has some usefulness in predicting the MJO compared to the statistical model.
It is shown that the coupled CFS model consistently, but only slightly, outperforms the uncoupled atmospheric model (by one to two days), indicating that only limited improvement is gained from the inclusion of the coupled air–sea interaction in the MJO forecast in this model. This slight improvement may be the result of the existence of a propagation barrier around the Maritime Continent and the far western Pacific in the NCEP Global Forecast System (GFS) and CFS models, as shown in several previous studies. This work also suggests that the higher horizontal resolution and finer initial data might contribute to improving the forecast skill, presumably as a result of an enhanced representation of the Maritime Continent region.
An Analysis of ENSO Prediction Skill in the CFS Retrospective Forecasts
Authors: Wu Renguang , Kirtman Ben P. , van den Dool Huug 
Published: October 2008

Abstract
The present study documents the so-called spring prediction and persistence barriers in association with El Niño–Southern Oscillation (ENSO) in the National Centers for Environmental Prediction (NCEP) Climate Forecast System (CFS) retrospective forecasts. It is found that the spring prediction and persistence barriers in the eastern equatorial Pacific sea surface temperature (SST) are preceded by a boreal winter barrier in the western equatorial Pacific zonal wind stress. The time of the persistence barrier is closely related to the time of the ENSO phase transition, but may differ from the time of the lowest variance. The seasonal change of the signal-to-noise ratio cannot explain the persistence barrier. While the noise may lead to a drop of skill around boreal spring in the western equatorial Pacific zonal wind stress, its impacts on the skill of eastern equatorial Pacific SST is small. The equatorial Pacific zonal winds display an excessive response to ENSO-related SST anomalies, which leads to a longer persistence in the equatorial Pacific thermocline depth anomalies and a delayed transition of the eastern equatorial Pacific SST anomalies. This provides an interpretation for the prediction skill drop in boreal spring in the eastern equatorial Pacific SST. The results suggest that improving the atmospheric model wind response to SST anomalies may reduce the spring prediction barrier.
A Finite-Volume Icosahedral Shallow-Water Model on a Local Coordinate
Authors: Lee Jin-Luen , MacDonald Alexander E. 
Published: October 2008

Abstract
An icosahedral-hexagonal shallow-water model (SWM) on the sphere is formulated on a local Cartesian coordinate based on the general stereographic projection plane. It is discretized with the third-order Adam–Bashforth time-differencing scheme and the second-order finite-volume operators for spatial derivative terms. The finite-volume operators are applied to the model variables defined on the nonstaggered grid with the edge variables interpolated using polynomial interpolation. The projected local coordinate reduces the solution space from the three-dimensional, curved, spherical surface to the two-dimensional plane and thus reduces the number of complete sets of basis functions in the Vandermonde matrix, which is the essential component of the interpolation. The use of a local Cartesian coordinate also greatly simplifies the mathematic formulation of the finite-volume operators and leads to the finite-volume integration along straight lines on the plane, rather than along curved lines on the spherical surface. The SWM is evaluated with the standard test cases of Williamson et al. Numerical results show that the icosahedral SWM is free from Pole problems. The SWM is a second-order finite-volume model as shown by the truncation error convergence test. The lee-wave numerical solutions are compared and found to be very similar to the solutions shown in other SWMs. The SWM is stably integrated for several weeks without numerical dissipation using the wavenumber 4 Rossby–Haurwitz solution as an initial condition. It is also shown that the icosahedral SWM achieves mass conservation within round-off errors as one would expect from a finite-volume model.
Identification of a Steap3 endosomal targeting motif essential for normal iron metabolism
Authors: Lambe Teresa , Simpson Robert J. , Dawson Sara , Bouriez-Jones Tiphaine , Crockford Tanya L. , Lepherd Michelle , Latunde-Dada Gladys O. , Robinson Hannah , Raja Kishor B. , Campagna Dean R. , Villarreal Guadalupe , Ellory J. Clive , Goodnow Christopher C. , Fleming Mark D. , McKie Andrew T. , Cornall Richard J. 
Published: October 2008

Abstract
Hereditary forms of iron-deficiency anemia, including animal models, have taught us much about the normal physiologic control of iron metabolism. However, the discovery of new informative mutants is limited by the natural mutation frequency. To address this limitation, we have developed a screen for heritable abnormalities of red blood cell morphology in mice with single-nucleotide changes induced by the chemical mutagen ethylnitrosourea (ENU). We now describe the first strain, fragile-red, with hypochromic microcytic anemia resulting from a Y228H sub-stitution in the ferrireductase Steap3 (Steap3Y288H). Analysis of the Steap3Y288H mutant identifies a conserved motif required for targeting Steap3 to internal compartments and highlights how phenotypic screens linked to mutagenesis can identify new functional variants in erythropoiesis and ascribe function to previously unidentified motifs.