bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Aerosol Radiative Forcing Uncertainty Based on a Radiative Perturbation Analysis
Authors: Loeb Norman G. , Su Wenying 
Published: June 2010

Abstract
To provide a lower bound for the uncertainty in measurement-based clear- and all-sky direct aerosol radiative forcing (DARF), a radiative perturbation analysis is performed for the ideal case in which the perturbations in global mean aerosol properties are given by published values of systematic uncertainty in Aerosol Robotic Network (AERONET) aerosol measurements. DARF calculations for base-state climatological cloud and aerosol properties over ocean and land are performed, and then repeated after perturbing individual aerosol optical properties (aerosol optical depth, single-scattering albedo, asymmetry parameter, scale height, and anthropogenic fraction) from their base values, keeping all other parameters fixed. The total DARF uncertainty from all aerosol parameters combined is 0.5–1.0 W m−2, a factor of 2–4 greater than the value cited in the Intergovernmental Panel on Climate Change’s (IPCC’s) Fourth Assessment Report. Most of the total DARF uncertainty in this analysis is associated with single-scattering albedo uncertainty. Owing to the greater sensitivity to single-scattering albedo in cloudy columns, DARF uncertainty in all-sky conditions is greater than in clear-sky conditions, even though the global mean clear-sky DARF is more than twice as large as the all-sky DARF.
Relationships between Barrier Jet Heights, Orographic Precipitation Gradients, and Streamflow in the Northern Sierra Nevada
Authors: Lundquist Jessica D. , Minder Justin R. , Neiman Paul J. , Sukovich Ellen 
Published: June 2010

Abstract
The rate of precipitation increase with elevation, termed the orographic precipitation gradient (OPG), is critically important for hydrologic forecasting in mountain basins that receive both rain and snow. Here, the following are examined to see how well they are able to predict the OPG and how it changes between storms and years: 1) a linear model of orographic precipitation forced by upstream radiosonde data, 2) monthly Parameter-Elevation Regressions on Independent Slopes Model (PRISM) precipitation data, and 3) seven years of hourly wind profiler data used to identify characteristics of the Sierra barrier jet (SBJ). These are compared against 124 daily resolution (four of which also had quality controlled, hourly resolution) precipitation gauge records in the northern Sierra Nevada. All methods represent the OPG well in the mean and during a year when less than 30% of the precipitation occurred on days with SBJs. However, the linear model and PRISM do not adequately capture annual variations in the OPG during years when more than 70% of the precipitation occurred on days with SBJs. Throughout all of the years, wind profiler data indicating the height of the SBJ provided additional, and necessary, information. The OPG is negatively correlated with the height of the SBJ. The SBJ height is lower, and hence, the OPG greater when the westerly winds are stronger, with more vertical wind shear. These westerly storms result in greater increases of precipitation with elevation, which act to increase snow storage in most storms but also to increase storm runoff during warmer-than-average storms.
On Turbulence Production by Swimming Marine Organisms in the Open Ocean and Coastal Waters
Authors: Rousseau Shani , Kunze Eric , Dewey Richard , Bartlett Kevin , Dower John 
Published: June 2010

AbstractMicrostructure and acoustic profile time series were collected near Ocean Station P in the eastern subarctic North Pacific and in Saanich Inlet at the south end of Vancouver Island, British Columbia, Canada, to examine production of turbulent dissipation by swimming marine organisms. At Ocean Station P, although a number of zooplankton species are large enough to generate turbulence with Reynolds numbers Re &gt; 1000, biomass densities are typically less than 103 individuals per cubic meter (&lt;0.01% by volume), and turbulent kinetic energy dissipation rates ɛ were better correlated with 16-m vertical shear than acoustic backscatter layers. In Saanich Inlet, where krill densities are up to 104 individuals per cubic meter (0.1% by volume), no dramatic elevation of dissipation rates ɛ was associated with dusk and dawn vertical migrations of the acoustic backscatter layer. Dissipation rates are a factor of 2 higher [〈ɛ〉 = 1.4 × 10−8 W kg−1, corresponding to buoyancy Re = 〈ɛ〉/(νN 2) ∼ 140] in acoustic backscatter layers than in acoustically quiet waters, regardless of whether they are vertically migrating. The O(1 m) thick turbulence patches have vertical wavenumber spectra for microscale shear commensurate with the Nasmyth model turbulence spectrum. However, the turbulence bursts of O(10−5 W kg−1) proposed to occur in such dense swarms appear to be rare. Thus far, intense turbulent bursts have been found infrequently, even in very dense aggregations O(104 individuals per cubic meter) characteristic of coastal and high-latitude environs. Based on sampling to date, this corresponds to a frequency of occurrence of less than 4%, suggesting that turbulence production by the marine biosphere is not efficient.
Eastern-Boundary Contribution to the Residual and Meridional Overturning Circulations
Authors: Cessi Paola , Wolfe Christopher L. , Ludka Bonnie C. 
Published: June 2010

Abstract
A model of the thermocline linearized around a specified stratification and the barotropic linear wind-driven Stommel solution is constructed. The forcings are both mechanical (the surface wind stress) and thermodynamical (the surface buoyancy boundary condition). The effects of diapycnal diffusivity and of eddy fluxes of buoyancy, parameterized in terms of the large-scale buoyancy gradient, are included. The eddy fluxes of buoyancy are especially important near the boundaries where they mediate the transport in and out of the narrow ageostrophic down-/upwelling layers. The dynamics of these narrow layers can be replaced by effective boundary conditions on the geostrophically balanced flow. The effective boundary conditions state that the residual flow normal to the effective coast vanishes. The separate Eulerian and eddy-induced components may be nonzero. This formulation conserves the total mass and the total buoyancy while permitting an exchange between the Eulerian and eddy transport of buoyancy within the down-/upwelling layers. In turn, this exchange allows buoyancy gradients along all solid boundaries, including the eastern one. A special focus is on the buoyancy along the eastern and western walls since east–west buoyancy difference determines the meridional overturning circulation.
The inclusion of advection of buoyancy by the barotropic flow allows a meaningful distinction between the meridional and the residual overturning circulations while retaining the simplicity of a linear model. The residual flow in both meridional and zonal directions reveals how the subsurface buoyancy distribution is established and, in particular, how the meridional buoyancy gradient is reversed at depth. In turn, the horizontal buoyancy gradient maintains stacked counterrotating cells in the meridional and residual overturning circulations. Quantitative scaling arguments are given for each of these cells, which show how the buoyancy forcing, the wind stress, and the diapycnal and eddy diffusivities, as well as the other imposed parameters, affect the strength of the overturn.
Numerical Simulations of Effects of Soil Moisture and Modification by Mountains over New Zealand in Summer
Authors: Yang Yang , Uddstrom Michael , Revell Mike , Andrews Phil , Oliver Hilary , Turner Richard , Carey-Smith Trevor 
Published: June 2010

Abstract
Historically most soil moisture–land surface impact studies have focused on continents because of the important forecasting and climate implications involved. For a relatively small isolated mountainous landmass in the ocean such as New Zealand, these impacts have received less attention. This paper addresses some of these issues for New Zealand through numerical experiments with a regional configuration of the Met Office Unified Model atmospheric model. Two pairs of idealized simulations with only contrasting dry or wet initial soil moisture over a 6-day period in January 2004 were conducted, with one pair using realistic terrain and the other pair flat terrain.
For the mean of the 6 days, the differences in the simulated surface air temperature between the dry and moist cases were 3–5 K on the leeside slopes and 1–2 K on the windward slopes and the central leeside coastal region of the South Island in the afternoon. This quite nonuniform response in surface air temperature to a uniformly distributed soil moisture content and soil type is mainly attributed to modification of the effects of soil moisture by mountains through two different processes: 1) spatial variation in cloud coverage across the mountains ranges leading to more shortwave radiation at ground surface on the leeside slope than the windward slope, and 2) the presence of a dynamically and thermally induced onshore flow on the leeside coast bringing in air with a lower sensitivity to soil moisture.
The response of local winds to soil moisture content is through direct or indirect effects. The direct effect is due to the thermal contrast between land and sea/land shown for the leeside solenoidal circulations, and the indirect effect is through the weakening of the upstream blocking of the South Island for dryer soils shown by the weakening and onshore shift of the upstream deceleration and forced ascent of incoming airflow.
Relationship between System Slope and Updraft Intensity in Squall Lines
Authors: Parker Matthew D. 
Published: June 2010

Abstract
In recent years there has been debate about whether squall lines have an “optimal state.” It has been repeatedly demonstrated that the slope of a squall line’s convective region is related to the comparative magnitudes of the squall line’s cold pool and the base-state vertical wind shear. The present work addresses a related assertion, that squall-line intensity ought to be maximized for an upright updraft zone. A simple demonstration shows that upright systems realize more of their buoyancy because their attendant downward-directed perturbation pressure gradient accelerations are weaker.
Effect of Omega-3 Fish Oil on Cardiovascular Risk in Diabetes
Authors: McEwen Brad , Morel-Kopp Marie-Christine , Tofler Geoffrey , Ward Christopher 
Published: June 2010

Purpose Diabetes and cardiovascular disease are major public health concerns worldwide and are leading causes of morbidity and mortality. People with type 2 diabetes are at an increased risk for cardiovascular disease. Diet has a substantial affect on the progression of many diseases, including diabetes, cardiovascular disease, osteoporosis, and arthritis. Omega-3 polyunsaturated fatty acids (long-chain polyunsaturated fatty acids [LC-PUFA]) have long been attributed to the maintenance of health and may be of benefit in reducing cardiovascular risk. The purpose of this review is to investigate the possible roles of omega-3 in reducing cardiovascular risk in patients with diabetes. Methods A literature search was conducted from the Medline, EBSCO, and EMBASE databases. Articles that addressed diabetes, cardiovascular disease, or omega-3 were included. Results Reviews and studies reported an association with fish and omega-3 LC-PUFA consumption and decreased total cardiovascular mortality (approximately 15%-19%), along with decreased platelet activation and aggregation, improved lipid profiles, including reduction of triglycerides and very low-density lipoprotein (VLDL), decreased inflammation, and lowered blood pressure. Conclusion Diets higher in fish and omega-3 LC-PUFA may reduce cardiovascular risk in diabetes by inhibiting platelet aggregation, improving lipid profiles, and reducing cardiovascular mortality. Fish and omega-3 LC-PUFA can be recommended to people with diabetes and included into a diabetes management program.
From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma
Authors: Thiberge Jean-Michel , Boursaux-Eude Caroline , Lehours Philippe , Dillies Marie-Agnès , Creno Sophie , Coppée Jean-Yves , Rouy Zoé , Lajus Aurélie , Ma Laurence , Burucoa Christophe , Ruskoné-Foumestraux Anne , Courillon-Mallet Anne , De Reuse Hilde , Boneca Ivo Gomperts , Lamarque Dominique , Mégraud Francis , Delchier Jean-Charles , Médigue Claudine , Bouchier Christiane , Labigne Agnès , Raymond Josette 
Published: June 2010

Abstract

Background

elicobacter pylori infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach.

Results
A set of 254 H. pylori genes was used to perform array-based comparative genomic hybridization among 120 French H. pylori strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with cag PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released H. pylori genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest H. pylori genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the vacA s2m2 allele and lacks the genes encoding the major virulence factors (absence of cag PAI, bab B, bab C, sab B, and hom B). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6 H. pylori sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38.

Conclusion
These isolates are deprived of the main H. pylori virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.
The inhibitory effect against collagen-induced arthritis by Schistosoma japonicum infection is infection stage-dependent
Authors: He YunKun , Li Jia , Zhuang WenJia , Yin Lan , Chen ChunXia , Li Jun , Chi FengLi , Bai YanShuang , Chen Xiao-Ping 
Published: June 2010

AbstractBackgroundA long-term existing schistosome infection can aid in maintaining immuno-homeostasis, thus providing protection against various types of autoimmune diseases to the infected host. Such benefits have often been associated with acute or egg stage infection and with the egg-induced Th2 response. However, since schistosome infection undergoes different stages, each associated with a specific induction of Th responses, the requirements for the ability of the different stages of schistosome infection to protect against autoimmune disease has not been elucidated. The present study was designed to study whether different stages of schistosome infection offer unique protection in collagen-induced arthritis and its mechanisms.ResultsArthritis susceptible strain DBA/1 male mice were infected withSchistosoma japonicumfor either 2 weeks resulting in early stage infection or for 7 weeks resulting in acute or egg stage infection. FollowingSchistosoma japonicuminfection, collagen II was administered to induce collagen-induced arthritis, an animal model for human rheumatoid arthritis. Infection bySchistosoma japonicumsignificantly reduced the severity and the incidence of experimental autoimmune collagen-induced arthritis. However, this beneficial effect can only be provided by a pre-established acute stage of infection but not by a pre-established early stage of the infection. The protection against collagen-induced arthritis correlated with reduced levels of anti-collagen II IgG, especially the subclass of IgG2a. Moreover, in protected mice increased levels of IL-4 were present at the time of collagen II injection together with sustained higher IL-4 levels during the course of arthritis development. In contrast, in unprotected mice minimal levels of IL-4 were present at the initial stage of collagen II challenge together with lack of IL-4 induction followingSchistosoma japonicuminfection.ConclusionThe protective effect against collagen-induced arthritis provided bySchistosoma japonicuminfection is infection stage-dependent. Furthermore, the ability of schistosomiasis to negatively regulate the onset of collagen-induced arthritis is associated with a dominant as well as long-lasting Th2 response at the initiation and development of autoimmune joint and systemic inflammation.
The Role of T cell PPAR γ in mice with experimental inflammatory bowel disease
Authors: Guri Amir J , Mohapatra Saroj K , Horne William T , Hontecillas Raquel , Bassaganya-Riera Josep 
Published: June 2010

Abstract

Background
Peroxisome proliferator-activated receptor γ (PPAR γ) is a nuclear receptor whose activation has been shown to modulate macrophage and T cell-mediated inflammation. The objective of this study was to investigate the mechanisms by which the deletion of PPAR γ in T cells modulates immune cell distribution and colonic gene expression and the severity of experimental IBD.

Methods
PPAR γ flfl; CD4 Cre+ (CD4cre) or Cre- (WT) mice were challenged with 2.5% dextran sodium sulfate in their drinking water for 0, 2, or 7 days. Mice were scored on disease severity both clinically and histopathologically. Flow cytometry was used to assess lymphocyte and macrophage populations in the blood, spleen, and mesenteric lymph nodes (MLN). Global gene expression in colonic mucosa was profiled using Affymetrix microarrays.

Results
The deficiency of PPAR γ in T cells accelerated the onset of disease and body weight loss. Examination of colon histopathology revealed significantly greater epithelial erosion, leukocyte infiltration, and mucosal thickening in the CD4cre mice on day 7. CD4cre mice had more CD8+ T cells than WT mice and fewer CD4+FoxP3+ regulatory T cells (Treg) and IL10+CD4+ T cells in blood and MLN, respectively. Transcriptomic profiling revealed around 3000 genes being transcriptionally altered as a result of DSS challenge in CD4cre mice. These included up-regulated mRNA expression of adhesion molecules, proinflammatory cytokines interleukin-6 (IL-6) and IL-1β, and suppressor of cytokine signaling 3 (SOCS-3) on day 7. Gene set enrichment analysis (GSEA) showed that the ribosome and Krebs cycle pathways were downregulated while the apoptosis pathway was upregulated in colons of mice lacking PPAR γ in T cells.

Conclusions
The expression of PPAR γ in T cells is involved in preventing gut inflammation by regulating colonic expression of adhesion molecules and inflammatory mediators at later stages of disease while favoring the recruitment of Treg to the mucosal inductive sites.
Symptoms and sources of Yersinia enterocolitica-infection: a case-control study
Authors: Huovinen Elisa , Sihvonen Leila M , Virtanen Mikko J , Haukka Kaisa , Siitonen Anja , Kuusi Markku 
Published: June 2010

AbstractBackgroundYersinia enterocolitica(YE) is the causative agent of yersiniosis. YE encompass strains of diverse pathogenicity: YE biotypes 1B and 2-5 are considered pathogenic, whereas biotype 1A is in general considered nonvirulent. Also YE-like species, which can sometimes be misidentified as YE, are considered nonvirulent.MethodsIn order to study differences in clinical picture caused by different YE types and their possible sources a case-control study was conducted in 2006. In this case-control study, 295 case-patients with YE or YE-like finding and their 758 controls responded to the questionnaire about symptoms and possible sources of infection.ResultsStrains of pathogenic YE bio/serotypes 3-4/O:3 or 2/O:9 were found in 18%, YE biotype 1A in 65% and YE -like strains of 17% of the patients. Patients infected with the strains of pathogenic YE bio/serotypes were younger and had fever more often than those with BT 1A who suffered more from vomiting. Symptoms of reactive arthritis were reported by 10% of pathogenic YE infections, 3% of YE BT 1A, and 0.3% of the controls. Eating or tasting raw or medium done pork was a significant risk factor for pathogenic YE bio/serotype infection (OR 6.6; 95% CI 1.7-24.9) as well as eating in a canteen (OR 3.5; 95% CI 1.6-7.9). Imported fruits and berries were associated with increased risk of YE BT 1A finding.ConclusionsThe symptoms of the patients with YE BT 1A differed from yersiniosis caused by the classic pathogenic YE bio/serotypes. In addition, the patients with YE BT 1A had more protracted gastrointestinal disorders and unspecific complaints. Small children were overrepresented in classic pathogenic bio/serotypes while in BT 1A or YE-like species were not found among children younger than two years. This suggests the lacking virulence of the BT 1A strains. We can not, however, rule out the possibility that some strains of genetically heterogeneous group of BT 1A may cause an illness.
The effect of accelerometer location on the classification of single-site forearm mechanomyograms
Authors: Alves Natasha , Sejdić Ervin , Sahota Bhupinder , Chau Tom 
Published: June 2010

AbstractBackgroundRecently, pattern recognition methods have been deployed in the classification of multiple activation states from mechanomyogram (MMG) signals for the purpose of controlling switching interfaces. Given the propagative properties of MMG signals, it has been suggested that MMG classification should be robust to changes in sensor placement. Nonetheless, this purported robustness remains speculative to date. This study sought to quantify the change in classification accuracy, if any, when a classifier trained with MMG signals from the muscle belly, is subsequently tested with MMG signals from a nearby location.MethodsAn arrangement of 5 accelerometers was attached to the flexor carpi radialis muscle of 12 able-bodied participants; a reference accelerometer was located over the muscle belly, two peripheral accelerometers were positioned along the muscle's transverse axis and two more were aligned to the muscle's longitudinal axis. Participants performed three classes of muscle activity: wrist flexion, wrist extension and semi-pronation. A collection of time, frequency and time-frequency features were considered and reduced by genetic feature selection. The classifier, trained using features from the reference accelerometer, was tested with signals from the longitudinally and transversally displaced accelerometers.ResultsClassification degradation due to accelerometer displacement was significant for all participants, and showed no consistent trend with the direction of displacement. Further, the displaced accelerometer signals showed task-dependent de-correlations with respect to the reference accelerometer.ConclusionsThese results indicate that MMG signal features vary with spatial location and that accelerometer displacements of only 1-2 cm cause sufficient feature drift to significantly diminish classification accuracy. This finding emphasizes the importance of consistent sensor placement between MMG classifier training and deployment for accurate control of switching interfaces.