bluuebunny/crossref_metadata_2025_split huggingface dataset:
Injection of
Staphylococcus aureus
EDIN by the
Bacillus anthracis
Protective Antigen Machinery Induces Vascular Permeability
Authors: Rolando Monica , Munro Patrick , Stefani Caroline , Auberger Patrick , Flatau Gilles , Lemichez Emmanuel 
Published: June 2009

ABSTRACT

Systemic injection of
Bacillus anthracis
lethal toxin (LT) produces vascular leakage and animal death. Recent studies suggest that LT triggers direct endothelial cell cytotoxicity that is responsible for the vascular leakage. LT is composed of heptamers of protective antigen (PA), which drives the endocytosis and translocation into host cells of the lethal factor (LF), a mitogen-activated protein kinase kinase protease. Here we investigated the consequences of injection of an endothelium-permeabilizing factor using LT as a “molecular syringe.” To this end, we generated the chimeric factor LE, corresponding to the PA-binding domain of LF (LF
1-254
) fused to EDIN exoenzyme. EDIN ADP ribosylates RhoA, leading to actin cable disruption and formation of transcellular tunnels in endothelial cells. We report that systemic injection of LET (LE plus PA) triggers a PA-dependent increase in the pulmonary endothelium permeability. We also report that native LT induces a progressive loss of endothelium barrier function. We established that there is a direct correlation between the extent of endothelium permeability induced by LT and the cytotoxic activity of LT. This suggests new ways to design therapeutic drugs against anthrax directed toward vascular permeability.
Decreased Expression of Colonic Slc26a3 and Carbonic Anhydrase IV as a Cause of Fatal Infectious Diarrhea in Mice
Authors: Borenshtein Diana , Schlieper Katherine A. , Rickman Barry H. , Chapman Jeannie M. , Schweinfest Clifford W. , Fox James G. , Schauer David B. 
Published: June 2009

ABSTRACTCitrobacter rodentiumcauses epithelial hyperplasia and colitis and is used as a model for enteropathogenic and enterohemorrhagicEscherichia coliinfections. Little or no mortality develops in most inbred strains of mice, but C3H and FVB/N mice exhibit fatal outcomes of infection. Here we test the hypothesis that decreased intestinal transport activity duringC. rodentiuminfection results in fatality in C3H/HeOu and FVB/N mice. Susceptible strains were compared to resistant C57BL/6 mice and to inbred strains SWR and SJL of Swiss origin, which have not been previously characterized for outcomes ofC. rodentiuminfection. Mortality in susceptible strains C3H/HeOu and FVB/N was associated with significant fluid loss in feces, a remarkable downregulation of Slc26a3 and carbonic anhydrase IV (CAIV) message and protein expression, retention of chloride in stool, and hypochloremia, suggesting defects in intestinal chloride absorption. SWR, SJL, and C57BL/6 mice were resistant and survived the infection. Fluid therapy fully prevented mortality in C3H/HeOu and FVB/N mice without affecting clinical disease. Common pathogenic mechanisms, such as decreased levels of expression of Slc26a3 and CAIV, affect intestinal ion transport inC. rodentium-infected FVB and C3H mice, resulting in profound electrolyte loss, dehydration, and mortality. Intestinal chloride absorption pathways are likely a potential target for the treatment of infectious diarrhea.
Outer Membrane Protein Expression Profile in
Helicobacter pylori
Clinical Isolates
Authors: Odenbreit Stefan , Swoboda Kirstin , Barwig Iris , Ruhl Stefan , Borén Thomas , Koletzko Sibylle , Haas Rainer 
Published: June 2009

ABSTRACT

The gram-negative gastric pathogen
Helicobacter pylori
is equipped with an extraordinarily large set of outer membrane proteins (OMPs), whose role in the infection process is not well understood. The Hop (
Helicobacter o
uter membrane
p
orins) and Hor (
Ho
p-
r
elated proteins) groups constitute a large paralogous family consisting of 33 members. The OMPs AlpA, AlpB, BabA, SabA, and HopZ have been identified as adhesins or adherence-associated proteins. To better understand the relevance of these and other OMPs during infection, we analyzed the expression of eight different
omp
genes (
alpA
,
alpB
,
babA
,
babB
,
babC
,
sabA
,
hopM
, and
oipA
) in a set of 200 patient isolates, mostly from symptomatic children or young adults. Virtually all clinical isolates produced the AlpA and AlpB proteins, supporting their essential function. All other OMPs were produced at extremely variable rates, ranging from 35% to 73%, indicating a function in close adaptation to the individual host or gastric niche. In 11% of the isolates, BabA was produced, and SabA was produced in 5% of the isolates, but the strains failed to bind their cognate substrates. Interleukin-8 (IL-8) expression in gastric cells was strictly dependent on the presence of the
cag
pathogenicity island, whereas the presence of OipA clearly enhanced IL-8 production. The presence of the translocated effector protein CagA correlated well with BabA and OipA production. In conclusion, we found unexpectedly diverse
omp
expression profiles in individual
H. pylori
strains and hypothesize that this reflects the selective pressure for adhesion, which may differ across different hosts as well as within an individual over time.
TheAcinetobacter baylyi hfqGene Encodes a Large Protein with an Unusual C Terminus
Authors: Schilling Dominik , Gerischer Ulrike 
Published: June 2009

ABSTRACTIn gammaproteobacteria the Hfq protein shows a great variation in size, especially in its C-terminal part. Extremely large Hfq proteins consisting of almost 200 amino acid residues and more are found within the gammaproteobacterial familyMoraxellaceae. The difference in size compared to other Hfq proteins is due to a glycine-rich domain near the C-terminal end of the protein.Acinetobacter baylyi, a nonpathogenic soil bacterium and member of theMoraxellaceaeencodes a large 174-amino-acid Hfq homologue containing the unique and repetitive amino acid pattern GGGFGGQ within the glycine-rich domain. Despite the presence of the C-terminal extension,A. baylyiHfq complemented anEscherichia coli hfqmutant in vivo. By using polyclonal anti-Hfq antibodies, we detected the largeA. baylyiHfq that corresponds to its annotated size indicating the expression and stability of the full protein. Deletion of the completeA. baylyi hfqopen reading frame resulted in severe reduction of growth. In addition, a deletion or overexpression of Hfq was accompanied by the loss of cell chain assembly. The glycine-rich domain was not responsible for growth and cell phenotypes.hfqgene localization inA. baylyiis strictly conserved within themutL-miaA-hfqoperon, and we show thathfqexpression starts within the precedingmiaAgene or further upstream.
Exposure–response relationship between lung cancer and polycyclic aromatic hydrocarbons (PAHs)
Authors: Armstrong B G , Gibbs G 
Published: June 2009

Objectives:To estimate the exposure–response function associating polycyclic aromatic hydrocarbon (PAH) exposure and lung cancer, with consideration of smoking.Methods:Mortality, occupational exposure and smoking histories were ascertained for a cohort of 16 431 persons (15 703 men and 728 women) who had worked in one of four aluminium smelters in Quebec from 1950 to 1999. A variety of exposure–response functions were fitted to the cohort data using generalised relative risk models.Results:In 677 lung cancer cases there was a clear trend of increasing risk with increasing cumulative exposure to PAH measured as benzo(a)pyrene (BaP). A linear model predicted a relative risk of 1.35 (95% CI 1.22 to 1.51) at 100 μg/m−3BaP years, but there was a significant departure from linearity in the direction of decreasing slope with increasing exposures. Among the models tried, the best fitting were a two-knot cubic spline and a power curve (RR = (1+bx)p), the latter predicting a relative risk of 2.68 at 100 μg/m−3BaP years. Additive models and multiplicative models for combining risks from occupational PAH and smoking fitted almost equally well, with a slight advantage to the additive.Conclusion:Despite the large cohort with long follow-up, the shape of the exposure–response function and the mode of combination of risks due to occupational PAH and smoking remains uncertain. If a linear exposure–response function is assumed, the estimated slope is broadly in line with the estimate from a previous follow-up of the same cohort, and somewhat higher than the average found in a recent meta-analysis of lung cancer studies.
MATHEMATICAL FRAMEWORK OF THE WELL PRODUCTIVITY INDEX FOR FAST FORCHHEIMER (NON-DARCY) FLOWS IN POROUS MEDIA
Authors: AULISA EUGENIO , IBRAGIMOV AKIF , VALKO PETER , WALTON JAY 
Published: June 2009

Motivated by the reservoir engineering concept of the well Productivity Index, we introduced and analyzed a functional, denoted as "diffusive capacity", for the solution of the initial-boundary value problem (IBVP) for a linear parabolic equation.21 This IBVP described laminar (linear) Darcy flow in porous media; the considered boundary conditions corresponded to different regimes of the well production. The diffusive capacities were then computed as steady state invariants of the solutions to the corresponding time-dependent boundary value problem. Here similar features for fast or turbulent nonlinear flows subjected to the Forchheimer equations are analyzed. It is shown that under some hydrodynamic and thermodynamic constraints, there exists a so-called pseudo steady state regime for the Forchheimer flows in porous media. In other words, under some assumptions there exists a steady state invariant over a certain class of solutions to the transient IBVP modeling the Forchheimer flow for slightly compressible fluid. This invariant is the diffusive capacity, which serves as the mathematical representation of the so-called well Productivity Index. The obtained results enable computation of the well Productivity Index by resolving a single steady state boundary value problem for a second-order quasilinear elliptic equation. Analytical and numerical studies highlight some new relations for the well Productivity Index in linear and nonlinear cases. The obtained analytical formulas can be potentially used for the numerical well block model as an analog of Piecemann.
DFT STUDY OF BOND ENERGIES AND ATTACHMENT SITES OF SAMPLE DIVALENT CATIONS (Mg2+, Ca2+, Zn2+) TO HISTIDINE IN THE GAS PHASE
Authors: TAVASOLI ELHAM , FATTAHI ALIREZA 
Published: June 2009

In view of better understanding interactions of amino acids and peptides with metallic cations in the isolated state, the model system histidine– M 2+ ( M 2+ = Mg 2+, Ca 2+, Zn 2+) has been studied theoretically. The computations have been performed with the help of the density functional theory (DFT) and the B3LYP functional. The extended basis set was the standard 6-311++G**. All the molecular complexes obtained by the interaction between several energetically low-lying tautomers/conformers/zwitterions of histidine and the cations on different binding sites were considered. Our study shows that complexes of histidine with Mg 2+, Ca 2+, Zn 2+ are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with oxygen and two nitrogen atoms: one from the terminal NH 2 and one from the imidazole ring. All computations indicate that the metal ion affinity (MIA) decreases on going from Zn 2+ to Mg 2+ and Ca 2+, for the considered amino acid. This indicates that histidine prefers to bind to the transition metal cation rather than alkali earth metals. The influence of theses cations on the acidity of histidine were also considered. As expected, upon metal complexation, proton dissociation of histidine becomes much more favorable, that is, its acidity becomes much less endothermic.
DFT STUDY ON GAS-PHASE INTERACTION BETWEEN HISTIDINE AND ALKALI METAL IONS (Li+, Na+, K+); AND INFLUENCE OF THESE IONS ON HISTIDINE ACIDITY
Authors: TAVASOLI ELHAM , FATTAHI ALIREZA 
Published: June 2009

The gas-phase metal affinities of histidine Li +, Na + and K + ions have been determined theoretically employing the hybrid B3LYP exchange–correlation functional and using 6-311++G** basis sets. All computations indicate that the metal ion affinity decreases on going from Li + to Na + and K + for the considered amino acid. Different types of M + coordinations on several histidine conformers/tautomers were considered in detail. The optimized structures indicate that Li + and Na + prefer a tri-dentate coordination, bonding with a nitrogen atom of imidazole ring ( N τ), – NH 2, and an oxygen atom of a carbonyl, while in the K +-histidine lowest-energy conformer, the cation appears to be bi-coordinated to both oxygen atoms of the zwitterionic form by the energy values not too far from that of tri-coordination. We also performed the DFT calculations for proton dissociation energy of histidine both in the presence and absence of alkali metal ions. Our results also reveal that the acidity of histidine dramatically increases upon metal ion complexation.
NEW PRODUCT DEVELOPMENT WITH DYNAMIC DECISION SUPPORT
Authors: VENTER JACOBUS PETRUS , VAN WAVEREN CORNELIS CRISTO 
Published: June 2009

The development of new and improved management methods for new product development is important. Existing methods suffer from a number of shortcomings, especially their inability to deal with a mixture of quantitative and qualitative data. The objective of this study is to apply decision support techniques (especially Bayesian networks) to the area of new product development management in order to address some of the shortcomings. The research approach is one of decision structuring and modeling. The literature shows the criteria that are important during the management of new product development. These criteria are used in a three-step decision structuring framework to develop a conceptual model based on a Bayesian network, in support of new product development management. The result is a Bayesian network that incorporates the knowledge of experts into a decision support model. The model is shown to be requisite because it contains all the essential elements of the problem on which decision-makers can base their action. The model can be used to perform 'what-if' analyses in various ways, thereby supporting the management of risk in new product development. This research not only contributes a model to support new product development management, but also provides insight into how decision support — especially Bayesian networks — can enhance technology management methods.
CRUSTAL DEFORMATION STUDIES IN JAVA (INDONESIA) USING GPS
Authors: ABIDIN HASANUDDIN Z. , ANDREAS HERI , KATO TERUYUKI , ITO TAKEO , MEILANO IRWAN , KIMATA FUMIAKI , NATAWIDJAYA DANNY H. , HARJONO HERY 
Published: June 2009

Along the Java trench the Australian–Oceanic plate is moving and pushing onto and subducting beneath the Java continental crust at a relative motion of about 70 mm/yr in NNE direction. This subduction-zone process imposed tectonic stresses on the fore-arc region offshore and on the land of Java, thus causing the formation of earthquake fault zones to accommodate the plate movement. Historically, several large earthquakes happened in Java, including West Java. This research use GPS surveys method to study the inter-seismic deformation of three active faults in West Java region (i.e. Cimandiri, Lembang and Baribis faults), and the co-seismic and post-seismic deformation related to the May 2006 Yogyakarta and the July 2006 South Java earthquakes.Based on GPS surveys results it was found that the area around Cimandiri, Lembang and Baribis fault zones have the horizontal displacements of about 1 to 2 cm/yr or less. Further research is however still needed to extract the real inter-seismic deformation of the faults from those GPS-derived displacements. GPS surveys have also estimated that the May 2006 Yogyakarta earthquake was caused by the sinistral movement of the (Opak) fault with horizontal co-seismic deformation that generally was less than 10 cm. The post-seismic horizontal deformation of the July 2006 South Java tsunami earthquake has also been estimated using GPS surveys data. In the first year after the earthquake (2006 to 2007), the post-seismic deformation is generally less than 5 cm; and it becomes generally less than 3 cm in the second year (2007 to 2008).
EARTHQUAKE AND TSUNAMI HAZARD IN MYANMAR
Authors: THEIN MAUNG , MYINT THAN , TUN SOE THURA , SWE TINT LWIN 
Published: June 2009

Myanmar, lying in a major seismic belt, is indeed earthquake-prone and is vulnerable to hazards from moderate and large magnitude earthquakes, including tsunami hazards along its long coastal areas. The seismotectonics of the region indicates that earthquakes in Myanmar mostly have originated along an active subduction zone (Andaman Megathrust Zone) in the west and along a large transform fault zone (Sagaing Fault Zone) in the middle part of the country. In the past, at least two large magnitude earthquakes along that subduction zones were tsunamigenic. Of course, the tsunami generated by the giant 2004 Sumatra Earthquake also caused moderate damage in some parts of the Myanmar Coast. Thus, it is evident that Myanmar is vulnerable to hazards from moderate and large magnitude earthquakes, including tsunami hazards along its long coastline.The active fault studies (from paleoseismological survey through tectonic geodesy), upgrade and newly installation of seismic station networks, public awareness and curriculum development, building code development and technical training program are priority requirements in the country. Recently, researchers on tectonic geology recognize some active segments of the Sagaing, Kyaukkyan and Kabaw faults, as well as marine and fluvial terraces which seemed to be associated with subduction of India and Burma (Myanmar) plates along the Bengal tectonic boundary. Their study should be extended by providing some instrumentation schemes like global positioning system (GPS) network. Myanmar Earthquake Committee (MEC) has developed a seismic zone map of Myanmar in deterministic approach in 2006, for the sake of providing general information to the user for various purposes, and for public information. Technical development is needed for the completeness of the next generation of seismic zone map of Myanmar which is to be incorporated in Building Code, which in turn requires researches and findings on tectonics of Myanmar.
The Role of Pacific Climate on Low-Frequency Hydroclimatic Variability and Predictability in Southern Alberta, Canada
Authors: Gobena Adam K. , Gan Thian Y. 
Published: June 2009

Abstract
Wavelet and rank correlation analysis were used to identify the links between primary Pacific climate variability modes and low-frequency hydroclimatic variability in the South Saskatchewan River basin (SSRB) of southern Alberta. The April–September average streamflow shows strong interdecadal oscillations with dominant scales of 19–22, 41–42, and 62 yr whereas statistically significant wavelet power in the interannual scale was organized on a background scale of approximately 20–25 yr. At interannual scales, strong coherency is observed between streamflow and the Niño-3 index prior to the 1940s, and in the 1950s, 1970s, and 1980s. However, a change in the phase difference from near 0° in the 1950s to near 180° in the 1980s indicates that the relationship between streamflow and the El Niño–Southern Oscillation (ENSO) is not consistent. Streamflow–Pacific–North America pattern (PNA) and streamflow–Pacific decadal oscillation (PDO) relationships at interannual scales also exhibit similar inconsistencies in phase difference. At interdecadal scales, PDO and streamflow exhibited consistently strong coherence with a stable phase difference of 180° for scales &gt;20 yr. From the period of 1913–2001, the median partial correlation between streamflow and PDO|Niño-3 (read as PDO given Niño-3) was −0.36, whereas it was zero between streamflow and Niño-3|PDO, suggesting that PDO is the primary mode of importance in streamflow variability and predictability in the SSRB. Precipitation variability was also dominated by interdecadal oscillations; however, there is less spatial coherence for dominant scales. Correlations between the basin’s winter precipitation and climate indices are also weaker than with streamflow.
The Description of Mixing in Stratified Layers without Shear in Large-Scale Ocean Models
Authors: Umlauf Lars 
Published: June 2009

Abstract
Large-scale geophysical flows often exhibit layers with negligible vertical shear and infinite gradient Richardson number Ri. It is well known that these layers may be regions of active mixing, even in the absence of local shear production of turbulence because, among other processes, turbulence may be supplied by vertical turbulent transport from neighboring regions. This observation is contrasted by the behavior of most turbulence parameterizations used in ocean climate modeling, predicting the collapse of mixing of mass and matter if the Richardson number exceeds a critical threshold. Here, the performance of a simple model without critical Richardson number is evaluated, taking into account the diffusion of turbulence into layers without shear production and therefore avoiding the suppression of mixing at large values of Ri. The model is based on the framework of second-moment turbulence closures, focusing on the consistent modeling of the turbulent length scale for strongly stratified turbulence. Results are compared to eddy-resolving simulations of stratified shear flows that have recently become available. The model is simple enough for inclusion in ocean climate models.
Energy Flux to a Cyclonic Eddy off Cabo Frio, Brazil
Authors: Mano Manlio F. , Paiva Afonso M. , Torres Audalio R. , Coutinho Alvaro L. G. A. 
Published: June 2009

Abstract
To evaluate the energy flux from the mean flow of South Atlantic western boundary currents toward typical Cabo Frio eddies (at Brazilian southeast coast), the southwestern Atlantic circulation was simulated with the Princeton Ocean Model. Throughout the study period, the vertical profile of eddy available potential energy direction was monitored.
The results indicated that baroclinic instability eddies first appear in intermediate depths and then its signal propagates upward, draining energy from the Brazil Current (BC), until it reaches the surface, 30 days after its formation. The depth of eddy formation is related to the vertical profile of the mean potential vorticity cross-current gradient (∂q/∂s). The beginning of the potential energy flux toward the perturbation and the origin of the eddy occurred at a similar depth and time.
The observed pattern suggests the following cycle: 1) a well-defined southwestward-flowing BC in the beginning of the period, with a baroclinically unstable profile of ∂q/∂s; 2) energy flux from the mean flow toward perturbation at intermediate depth; 3) current destabilization and meandering; 4) formation and growth of the cyclonic eddy; 5) potential energy flux progressively shallower; 6) propagation of the eddy signal upward; and 7) stabilization of the water column.