bluuebunny/crossref_metadata_2025_split huggingface dataset:
TheStaphylococcus aureusGGDEF Domain-Containing Protein, GdpS, Influences Protein A Gene Expression in a Cyclic Diguanylic Acid-Independent Manner
Authors: Shang Fei , Xue Ting , Sun Haipeng , Xing Lei , Zhang Shuo , Yang Zhenjun , Zhang Lihe , Sun Baolin 
Published: April 2009

ABSTRACTStaphylococcus aureusis an important human pathogen that is the principal cause of a variety of diseases, ranging from localized skin infections to life-threatening systemic infections. The success of the organism as a pathogen and its ability to cause such a wide range of infections are due to its extensive virulence factors. In this study, we identified the role of the only GGDEF domain protein (GdpS [GGDEFdomainprotein fromStaphylococcus]) in the virulence ofS. aureusNCTC8325. Inactivation ofgdpSresults in an alteration in the production of a range of virulence factors, such as serine and cysteine proteases, fibrinogen-binding proteins, and, specifically, protein A (Spa), a major surface protein ofS. aureus. The transcript level ofspadecreases eightfold in thegdpSmutant compared with the parental NCTC8325 strain. Furthermore, the transcript level ofsarS, which encodes a direct positive regulator ofspa, also decreases in thegdpSmutant compared with the wild type, while the transcript levels ofagr,sarA,sarT, androtdisplay no apparent changes in thegdpSmutant, suggesting that GdpS affects the expression ofspathrough interaction with SarS by unknown mechanisms. Furthermore, the complementation assays show that the influences of GdpS onspaandsarSdepend on its N-terminal domain, which is predicted to be the sensor of a two-component system, rather than its C-terminal GGDEF domain with conserved GGDEF, suggesting that GdpS functions inS. aureusby an unknown mechanism independent of 3′,5′-cyclic diguanylic acid signaling.
Novel Subtilase Cytotoxin Produced by Shiga-Toxigenic
Escherichia coli
Induces Apoptosis in Vero Cells via Mitochondrial Membrane Damage
Authors: Matsuura Gen , Morinaga Naoko , Yahiro Kinnosuke , Komine Reiko , Moss Joel , Yoshida Hideo , Noda Masatoshi 
Published: April 2009

ABSTRACT

Subtilase cytotoxin (SubAB) is an AB
5
cytotoxin produced by some strains of Shiga-toxigenic
Escherichia coli
. The A subunit is a subtilase-like serine protease and cleaves an endoplasmic reticulum chaperone, BiP, leading to transient inhibition of protein synthesis and cell cycle arrest at G
1
phase. Here we show that SubAB, but not the catalytically inactive mutant SubAB(S272A), induced apoptosis in Vero cells, as detected by DNA fragmentation and annexin V binding. SubAB induced activation of caspase-3, -7, and -8. Caspase-3 appeared earlier than caspase-8, and by use of specific caspase inhibitors, it was determined that caspase-3 may be upstream of caspase-8. A general caspase inhibitor blocked SubAB-induced apoptosis, detected by annexin V binding. SubAB also stimulated cytochrome
c
release from mitochondria, which was not suppressed by caspase inhibitors. In HeLa cells, Apaf-1 small interfering RNA inhibited caspase-3 activation, suggesting that cytochrome
c
might form an apoptosome, leading to activation of caspase-3. These data suggested that SubAB induced caspase-dependent apoptosis in Vero cells through mitochondrial membrane damage.
M-Cell Targeting of Whole Killed Bacteria Induces Protective Immunity against Gastrointestinal Pathogens
Authors: Chionh Yok-Teng , Wee Janet L. K. , Every Alison L. , Ng Garrett Z. , Sutton Philip 
Published: April 2009

ABSTRACT

As the majority of human pathogens infect via a mucosal surface, delivery of killed vaccines by mucosal routes could potentially improve protection against many such organisms. Our ability to develop effective killed mucosal vaccines is inhibited by a lack of adjuvants that are safe and effective in humans. The
Ulex europaeus
agglutinin I (UEA-I) lectin specifically binds M cells lining the murine gastrointestinal tract. We explored the potential for M-cell-targeted vaccination of whole, killed
Helicobacter pylori
, the main causative agent of peptic ulcer disease and gastric cancer, and
Campylobacter jejuni
, the most common cause of diarrhea. Oral delivery of UEA-I-agglutinated
H. pylori
or
C. jejuni
induced a significant increase in both serum and intestinal antibody levels. This elevated response (i) required the use of whole bacteria, as it did not occur with lysate; (ii) was not mediated by formation of particulate clumps, as agglutination with a lectin with a different glycan specificity had no effect; and (iii) was not due to lectin-mediated, nonspecific immunostimulatory activity, as UEA-I codelivery with nonagglutinated bacteria did not enhance the response. Vaccination with UEA-I-agglutinated, killed whole
H. pylori
induced a protective response against subsequent live challenge that was as effective as that induced by cholera toxin adjuvant. Moreover, vaccination against
C. jejuni
by this approach resulted in complete protection against challenge in almost all animals. We believe that this is the first demonstration that targeting of whole killed bacteria to mucosal M cells can induce protective immunity without the addition of an immunostimulatory adjuvant.
Memory allocation for embedded systems with a compile-time-unknown scratch-pad size
Authors: Nguyen Nghi , Dominguez Angel , Barua Rajeev 
Published: April 2009

This article presents the first memory allocation scheme for embedded systems having a scratch-pad memory whose size is unknown at compile time. A scratch-pad memory (SPM) is a fast compiler-managed SRAM that replaces the hardware-managed cache. All existing memory allocation schemes for SPM require the SPM size to be known at compile time. Unfortunately, because of this constraint, the resulting executable is tied to that size of SPM and is not portable to other processor implementations having a different SPM size. Size-portable code is valuable when programs are downloaded during deployment either via a network or portable media. Code downloads are used for fixing bugs or for enhancing functionality. The presence of different SPM sizes in different devices is common because of the evolution in VLSI technology across years. The result is that SPM cannot be used in such situations with downloaded codes.
To overcome this limitation, our work presents a compiler method whose resulting executable is portable across SPMs of any size. Our technique is to employ a customized installer software, which decides the SPM allocation just before the program's first run, since the SPM size can be discovered at that time. The installer then, based on the decided allocation, modifies the program executable accordingly. The resulting executable places frequently used objects in SPM, considering both code and data for placement. To keep the overhead low, much of the preprocessing for the allocation is done at compile time. Results show that our benchmarks average a 41% speedup versus an all-DRAM allocation, while the optimal static allocation scheme, which knows the SPM size at compile time and is thus an unachievable upper-bound and is only slightly faster (45% faster than all-DRAM). Results also show that the overhead from our customized installer averages about 1.5% in code size, 2% in runtime, and 3% in compile time for our benchmarks.
Expanding network communities from representative examples
Authors: Mehler Andrew , Skiena Steven 
Published: April 2009

We present an approach to leverage a small subset of a coherent community within a social network into a much larger, more representative sample. Our problem becomes identifying a small conductance subgraph containing many (but not necessarily all) members of the given seed set. Starting with an initial seed set representing a sample of a community, we seek to discover as much of the full community as possible.
We present a general method for network community expansion, demonstrating that our methods work well in expanding communities in real world networks starting from small given seed groups (20 to 400 members). Our approach is marked by incremental expansion from the seeds with retrospective analysis to determine the ultimate boundaries of our community. We demonstrate how to increase the robustness of the general approach through bootstrapping multiple random partitions of the input set into seed and evaluation groups.
We go beyond statistical comparisons against gold standards to careful subjective evaluations of our expanded communities. This process explains the causes of most disagreement between our expanded communities and our gold-standards—arguing that our expansion methods provide more reliable communities than can be extracted from reference sources/gazetteers such as Wikipedia.
Biophysical Evaluation of Land-Cover Products for Land–Climate Modeling
Authors: Ge Jianjun , Torbick Nathan , Qi Jiaguo 
Published: April 2009

Abstract
The need for accurate characterization of the land surface as boundary conditions in climate models has been recognized widely in the climate modeling community. A large number of land-cover datasets are currently used in climate models either to better represent surface conditions or to study the impacts of surface changes. Deciding upon land-cover datasets can be challenging because the datasets are made with different sensors, ranging methodologies, and varying classification objectives. A new statistical measure Q was developed to evaluate land-cover datasets in land–climate interaction research. This measure calculates biophysical precision of land-cover datasets using 1-km monthly Moderate Resolution Imaging Spectroradiometer (MODIS) leaf area index (LAI) product. This method aggregates within-class biophysical consistency, calculated as LAI variation, across a study domain and over multiple years into a single statistic. A smaller mean Q value for a land-cover product indicates more precise biophysical characterization within the classes. As an illustration, four land-cover products were assessed in the East Africa region: Global Land Cover 2000 (GLC2000), MODIS land cover, Olson Global Ecosystems (OGE), and Land Ecosystem–Atmosphere Feedback (LEAF) model. The evaluation was conducted at three different spatial scales corresponding to 30 × 30, 50 × 50, and 100 × 100 km quadrates. The Q measure found that GLC2000 ranked higher compared to the other three land-cover products for every quadrate size. For the 30 × 30 km quadrate size GLC2000 was significantly better than LEAF, which is currently used in the Regional Atmospheric Modeling System. The statistic ranks MODIS land cover above OGE, which is above LEAF. As quadrate size increases, differences between Q decrease indicating greater uncertainty at coarser resolution. The utility of the measure is that it can be applied to any continuous parameter over any scale (space or time) to evaluate the biophysical precision of any land-cover dataset.
The Soil Moisture–Precipitation Feedback in Simulations with Explicit and Parameterized Convection
Authors: Hohenegger Cathy , Brockhaus Peter , Bretherton Christopher S. , Schär Christoph 
Published: April 2009

Abstract
Moist convection is a key aspect of the extratropical summer climate and strongly affects the delicate balance of processes that determines the surface climate in response to larger-scale forcings. Previous studies using parameterized convection have found that the feedback between soil moisture and precipitation is predominantly positive (more precipitation over wet soils) over Europe. Here this feedback is investigated for one full month (July 2006) over the Alpine region using two different model configurations. The first one employs regional climate simulations performed with the Consortium for Small-Scale Modeling Model in Climate Mode (CCLM) on a grid spacing of 25 km. The second one uses the same model but integrated on a cloud-resolving grid of 2.2 km, allowing an explicit treatment of convection. Each configuration comprises one control and two sensitivity experiments. The latter start from perturbed soil moisture initial conditions.
Comparison of the simulated soil moisture–precipitation feedback reveals significant differences between the two systems. The 25-km simulations sustain a strong positive feedback, while those at 2.2-km resolution are associated with a predominantly negative feedback. Thus the two systems yield not only different strengths of this key feedback but also different signs. This has important implications, with the cloud-resolving model exhibiting a shorter soil moisture memory and a smaller soil moisture–temperature feedback.
Analysis shows that the different feedback signs relate to the sensitivity of the simulated convective development to the presence of a stable layer sitting on top of the planetary boundary layer. In the 2.2-km integrations, dry initial soil moisture conditions yield more vigorous thermals (owing to stronger daytime heating), which can more easily break through the stable air barrier, thereby leading to deep convection and ultimately to a negative soil moisture–precipitation feedback loop. In the 25-km integrations, deep convection is much less sensitive to the stable layer because of the design of the employed convective parameterization. The authors also show that there are considerable differences in the simulated soil moisture–precipitation feedback between low-resolution modeling frameworks using different cloud convection schemes.
Interannual Variability of the Upper Ocean in the Southeast Pacific Stratus Cloud Region
Authors: Shinoda Toshiaki , Lin Jialin 
Published: April 2009

Abstract
Persistent stratus/stratocumulus cloud decks in the southeast Pacific near the coasts of Peru and northern Chile play an important role in regional and global climate variability. Interannual variability of the upper ocean under stratus cloud decks in the southeast Pacific is investigated using ocean general circulation model (OGCM) experiments. The model was first forced with daily surface fluxes based on the NCEP–NCAR reanalysis and satellite-derived surface shortwave and longwave radiation for the period of 1979–2004. Gridded surface heat flux estimates used in the model integration agree well with those based on Woods Hole Oceanographic Institution (WHOI) Improved Meteorology (IMET) buoy measurements at 20°S, 85°W. Also, the OGCM is able to reproduce well the observed interannual SST and sea surface height variations in this region. The results suggest that the interannual variation of the upper ocean north of 20°S is mostly associated with ENSO variability. Additional model experiments were conducted to examine the relative importance of ocean dynamics and surface heat fluxes in determining the interannual variation in SST. The results of these experiments indicate that upper-ocean dynamics play a dominant role in controlling the interannual variation of SST north of 20°S in the stratus cloud region. The upper-ocean heat budget analysis shows that meridional heat advection associated with ENSO events primarily controls the interannual SST variation in the stratus cloud region north of 20°S.
Estimating Oceanic Heat Content Change Using Isotherms
Authors: Palmer Matthew D. , Haines Keith 
Published: April 2009

AbstractThis paper presents a new analysis of ocean heat content changes over the last 50 yr using isotherms by calculating the mean temperature above the 14°C isotherm and the depth of the 14°C isotherm as separate variables. A new quantity called the “relative heat content” (“RHC”) is introduced, which represents the minimum local heat content change over time, relative to a fixed isotherm. It is shown how mean temperature and isotherm depth changes make separable and additive contributions to changes in RHC.Maps of RHC change between 1970 and 2000 show similar spatial patterns to a traditional fixed-depth ocean heat content change to 220 m. However, the separate contributions to RHC suggest a more spatially uniform contribution from warming above the isotherm, while isotherm depth changes show wind-driven signals, of which some are identifiable as being related to the North Atlantic Oscillation. The time series show that the warming contribution to RHC dominates the global trend, while the depth contribution only dominates on the basin scale in the North Atlantic. The RHC shows minima associated with the major volcanic eruptions (particularly in the Indian Ocean), and these are entirely contributed by mean temperature changes rather than isotherm depth changes. The depth change contributions to RHC are strongly affected by the recently reported XBT fall-rate bias, whereas the mean temperature contributions are not. Therefore, only the isotherm depth change contributions to RHC will need to be reassessed as fall-rate-corrected data become available.
Structure and Evolution of Precipitation along a Cold Front in the Northeastern United States
Authors: Zhang Yan , Smith James A. , Ntelekos Alexandros A. , Baeck Mary Lynn , Krajewski Witold F. , Moshary Fred 
Published: April 2009

Abstract
Heavy precipitation in the northeastern United States is examined through observational and numerical modeling analyses for a weather system that produced extreme rainfall rates and urban flash flooding over the New York–New Jersey region on 4–5 October 2006. Hydrometeorological analyses combine observations from Weather Surveillance Radar-1988 Doppler (WSR-88D) weather radars, the National Lightning Detection Network, surface observing stations in the northeastern United States, a vertically pointing lidar system, and a Joss–Waldvogel disdrometer with simulations from the Weather Research and Forecasting Model (WRF). Rainfall analyses from the Hydro-Next Generation Weather Radar (NEXRAD) system, based on observations from WSR-88D radars in State College, Pennsylvania, and Fort Dix, New Jersey, and WRF model simulations show that heavy rainfall was organized into long-lived lines of convective precipitation, with associated regions of stratiform precipitation, that develop along a frontal zone.
Structure and evolution of convective storm elements that produced extreme rainfall rates over the New York–New Jersey urban corridor were influenced by the complex terrain of the central Appalachians, the diurnal cycle of convection, and the history of convective evolution in the frontal zone. Extreme rainfall rates and flash flooding were produced by a “leading line–trailing stratiform” system that was rapidly dissipating as it passed over the New York–New Jersey region. Radar, disdrometer, and lidar observations are used in combination with model analyses to examine the dynamical and cloud microphysical processes that control the spatial and temporal structure of heavy rainfall. The study illustrates key elements of the spatial and temporal distribution of rainfall that can be used to characterize flash flood hazards in the urban corridor of the northeastern United States.
Enhanced Diapycnal Mixing in the South China Sea
Authors: Tian Jiwei , Yang Qingxuan , Zhao Wei 
Published: April 2009

Abstract
Profiles of current velocity, temperature, and salinity were obtained in the Internal Wave and Mixing Experiment in the South China Sea (SCS), the Luzon Strait, and the North Pacific. The observations are examined for evidence of enhanced diapycnal mixing in the SCS, which reaches O(10−3 m2 s−1) in magnitude. Results from independent casts reveal that diapycnal diffusivity in the SCS and the Luzon Strait is elevated by two orders of magnitude over that of the smooth bathymetry in the North Pacific, which are typical of background values in an open ocean. The vertical distribution of diapycnal diffusivity is nonuniform in the SCS, exhibiting higher values at depths greater than about 1000 m. This result compares favorably with the direct microstructure measurements at four stations in the SCS. Velocity and density profiles are combined to estimate the internal tide energy flux generated in the Luzon Strait and directed into the SCS. The energy amounts to 10 GW, most of which is rationalized to be the potential energy source for enhanced mixing in the SCS.
Hydraulic Criticality of the Exchange Flow through the Strait of Gibraltar
Authors: Sannino Gianmaria , Pratt Lawrence , Carillo Adriana 
Published: April 2009

Abstract
The hydraulic state of the exchange circulation through the Strait of Gibraltar is defined using a recently developed critical condition that accounts for cross-channel variations in layer thickness and velocity, applied to the output of a high-resolution three-dimensional numerical model simulating the tidal exchange. The numerical model uses a coastal-following curvilinear orthogonal grid, which includes, in addition to the Strait of Gibraltar, the Gulf of Cadiz and the Alboran Sea. The model is forced at the open boundaries through the specification of the surface tidal elevation that is characterized by the two principal semidiurnal and two diurnal harmonics: M2, S2, O1, and K1. The simulation covers an entire tropical month.
The hydraulic analysis is carried out approximating the continuous vertical stratification first as a two-layer system and then as a three-layer system. In the latter, the transition zone, generated by entrainment and mixing between the Atlantic and Mediterranean flows, is considered as an active layer in the hydraulic model. As result of these vertical approximations, two different hydraulic states have been found; however, the simulated behavior of the flow only supports the hydraulic state predicted by the three-layer case. Thus, analyzing the results obtained by means of the three-layer hydraulic model, the authors have found that the flow in the strait reaches maximal exchange about 76% of the tropical monthlong period.
The Salinity, Heat, and Buoyancy Budgets of a Coastal Current in a Marginal Sea
Authors: Wåhlin A. K. , Johnson H. L. 
Published: April 2009

Abstract
The Atlantic overturning circulation has conventionally been pictured in the meridional–vertical plane, but a significant densification of the water masses involved also occurs as the surface branch of the circulation flows in boundary currents around the subpolar gyre and northern marginal seas. Here an analytical model of the heat and salt budget for an idealized coastal boundary current in a marginal sea is presented. The boundary current exchanges heat and freshwater with the atmosphere as well as with the interior of the basin through eddy and Ekman transports. Its along-coast volume transport is assumed to be constant and independent of buoyancy; it is set, for example, by the wind forcing. Because the atmospheric fluxes of heat and freshwater are different, the temperature and salinity of the boundary current adjust on different length scales. The size of these length scales compared with the circumference of the basin determines the properties of the water that flows over the sill. Furthermore, the relative size of the two length scales determines the evolution of the density as the current moves around the basin. If temperature and salinity adjust on the same length scale (or if the density forcing is represented by a single component), then the density will increase or decrease monotonically from the inflow to the outflow. However, when the adjustment length scale for temperature is shorter than that for salinity, a warm and salty inflow can cool significantly before it freshens. As a result, the density first increases to a local maximum before decreasing again. Therefore, when salinity as well as temperature is included in the buoyancy forcing, the outflow from the basin can be significantly denser than for the equivalent single-component density forcing and can be more sensitive to the forcing parameters. The relevance and implications for the Nordic seas are discussed.