bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Role of the Central Asian Mountains on the Midwinter Suppression of North Pacific Storminess
Authors: Park Hyo-Seok , Chiang John C. H. , Son Seok-Woo 
Published: June 2010

Abstract
The role of the central Asian mountains on North Pacific storminess is examined using an atmospheric general circulation model by varying the height and the areas of the mountains. A series of model integrations show that the presence of the central Asian mountains suppresses the North Pacific storminess by 20%–30% during boreal winter. Their impact on storminess is found to be small during other seasons. The mountains amplify stationary waves and effectively weaken the high-frequency transient eddy kinetic energy in boreal winter. Two main causes of the reduced storminess are diagnosed. First, the decrease in storminess appears to be associated with a weakening of downstream eddy development. The mountains disorganize the zonal coherency of wave packets and refract them more equatorward. As the zonal traveling distance of wave packets gets substantially shorter, downstream eddy development gets weaker. Second, the central Asian mountains suppress the global baroclinic energy conversion. The decreased baroclinic energy conversion, particularly over the eastern Eurasian continent, decreases the number of eddy disturbances entering into the western North Pacific. The “barotropic governor” does not appear to explain the reduced storminess in our model simulations.
On the Propagation of Information and the Use of Localization in Ensemble Kalman Filtering
Authors: Yoon Young-noh , Ott Edward , Szunyogh Istvan 
Published: June 2010

Abstract
Several localized versions of the ensemble Kalman filter have been proposed. Although tests applying such schemes have proven them to be extremely promising, a full basic understanding of the rationale and limitations of localization is currently lacking. It is one of the goals of this paper to contribute toward addressing this issue. The second goal is to elucidate the role played by chaotic wave dynamics in the propagation of information and the resulting impact on forecasts. To accomplish these goals, the principal tool used here will be analysis and interpretation of numerical experiments on a toy atmospheric model introduced by Lorenz in 2005. Propagation of the wave packets of this model is shown. It is found that, when an ensemble Kalman filter scheme is employed, the spatial correlation function obtained at each forecast cycle by averaging over the background ensemble members is short ranged, and this is in strong contrast to the much longer range correlation function obtained by averaging over states from free evolution of the model. Propagation of the effects of observations made in one region on forecasts in other regions is studied. The error covariance matrices from the analyses with localization and without localization are compared. From this study, major characteristics of the localization process and information propagation are extracted and summarized.
Transient Growth of Thermodynamically Coupled Variations in the Tropics under an Equatorially Symmetric Mean State*
Authors: Vimont Daniel J. 
Published: June 2010

Abstract
The dynamics of thermodynamically coupled disturbances in the tropics that bear a strong resemblance to observed meridional mode variations are investigated using two simple linear coupled models. Both models involve an ocean equation coupled to the atmosphere via the linearized effect of zonal wind variations on the surface bulk latent heat flux. The two models differ in their atmospheric components, which consist of (i) a Gill–Matsuno style model of the free troposphere in which atmospheric heating is parameterized to be linearly proportional to sea surface temperature and (ii) a reduced-gravity model of the tropical boundary layer in which SST anomalies are associated with hydrostatic pressure perturbations throughout the boundary layer. Both atmospheric models follow the standard shallow-water equations on an equatorial beta plane.
Growth rates and propagation of coupled disturbances are calculated and diagnosed via eigenanalysis of the linear models and singular value decomposition of the Green’s function for each model. It is found that the eigenvectors of either model are all damped, not orthogonal, and not particularly meaningful in understanding observed tropical coupled variability. The nonnormality of the system, however, leads to transient growth over a time period of about 100 days (based on the choice of parameters in this study). The idealized initial and final conditions that experience this transient growth resemble observed tropical meridional mode variations and tend to propagate equatorward and westward in accord with findings from previous theoretical and modeling studies. Instantaneous growth rates and propagation characteristics of idealized transient disturbances are diagnosed via the linearized atmospheric potential vorticity equation and via propagation characteristics of atmospheric equatorial Rossby waves.
Constraints on the poleward extent of initial conditions or imposed steady forcing that can lead to tropical meridional mode variations are identified through analysis of the steady coupled equations. Three constraints limit the poleward extent of forcing that can generate tropical meridional mode variations: (i) a dynamical constraint imposed by the damping rate of the temperature equation as well as the propagation speed of the mode along its wave characteristic; (ii) a constraint imposed by the effectiveness of zonal wind variations in generating surface latent heat flux anomalies; and (iii) the surface moisture convergence, which limits the poleward extent and strength of ocean to atmosphere coupling.
Observed Diurnal Cycle Climatology of Planetary Boundary Layer Height
Authors: Liu Shuyan , Liang Xin-Zhong 
Published: June 2010

Abstract
An observational climatology of the planetary boundary layer height (PBLH) diurnal cycle, specific to surface characteristics, is derived from 58 286 fine-resolution soundings collected in 14 major field campaigns around the world. An objective algorithm determining PBLH from sounding profiles is first developed and then verified by available lidar and sodar retrievals. The algorithm is robust and produces realistic PBLH as validated by visual examination of several thousand additional soundings. The resulting PBLH from all existing data is then subject to various statistical analyses. It is demonstrated that PBLH occurrence frequencies under stable, neutral, and unstable regimes follow a narrow, intermediate, and wide Gamma distribution, respectively, over both land and oceans. Over ice all exhibit a narrow distribution. The climatological PBLH diurnal cycle is strong over land and oceans, with a distinct peak at 1500 and 1200 LT, whereas the cycle is weak over ice. Relative to midlatitude land, the PBLH variability over tropical oceans is larger during the morning and at night but much smaller in the afternoon. This study provides a unique observational database for critical model evaluation on the PBLH diurnal cycle and its temporal/spatial variability.
The Tidally Averaged Momentum Balance in a Partially and Periodically Stratified Estuary
Authors: Stacey Mark T. , Brennan Matthew L. , Burau Jon R. , Monismith Stephen G. 
Published: June 2010

Abstract
Observations of turbulent stresses and mean velocities over an entire spring–neap cycle are used to evaluate the dynamics of tidally averaged flows in a partially stratified estuarine channel. In a depth-averaged sense, the net flow in this channel is up estuary due to interaction of tidal forcing with the geometry of the larger basin. The depth-variable tidally averaged flow has the form of an estuarine exchange flow (downstream at the surface, upstream at depth) and varies in response to the neap–spring transition. The weakening of the tidally averaged exchange during the spring tides appears to be a result of decreased stratification on the tidal time scale rather than changes in bed stress. The dynamics of the estuarine exchange flow are defined by a balance between the vertical divergence of the tidally averaged turbulent stress and the tidally averaged pressure gradient in the lower water column. In the upper water column, tidal stresses are important contributors, particularly during the neap tides. The usefulness of an effective eddy viscosity in the tidally averaged momentum equation is explored, and it is seen that the effective eddy viscosity on the subtidal time scale would need to be negative to close the momentum balance. This is due to the dominant contribution of tidally varying turbulent momentum fluxes, which have no specific relation to the subtidal circulation. Using a water column model, the validity of an effective eddy viscosity is explored; for periodically stratified water columns, a negative effective viscosity is required.
Measurement of Vertical Kinetic Energy and Vertical Velocity Skewness in Oceanic Boundary Layers by Imperfectly Lagrangian Floats
Authors: Harcourt Ramsey R. , D’Asaro Eric A. 
Published: June 2010

Abstract
The effects of upward buoyancy on the accuracy with which Lagrangian floats can measure the Eulerian mean variance 〈ww〉E and skewness SwE of vertical fluid velocity w in the wind-driven upper-ocean boundary layer is investigated using both simulated floats in large-eddy simulation (LES) models and two float datasets. Nearly neutrally buoyant floats are repeatedly advected by the turbulent velocities across the boundary layer. Their vertical position Z is determined from pressure measurements; their W variance 〈WW〉F and skewness SWE are determined from the time series of float W = dZ/dt. If the float buoyancy is small, then the simulated floats measure the Eulerian velocity accurately; that is, δW2 = 〈WW〉F − 〈ww〉E and δSW = SWF − SwE are small compared to 〈ww〉E and SwE respectively. If the floats are buoyant, and thus have an upward vertical velocity Wbias relative to the water, then δW2 and δSW can become significant. Buoyancy causes the floats to oversample both shallow depths and strong vertical velocities, leading to positive values of δW2 and negative values of δSW. The skewness SZ′F of depth measures the degree to which shallow depths are oversampled; it is shown to be a good predictor of Wbias/〈WW〉F1/2, δW2/〈WWF〉, and δSW/SWF over a wide range of float buoyancies and boundary layer forcings. Float data collected during two deployments confirm these results, but averaging times of several float days are typically required to obtain stable statistics. Significant differences in the magnitude of the effect may occur between datasets from different ocean forcing regimes and float designs. Other measures of float buoyancy are also useful predictors. These results can be used to correct existing float measurements of 〈ww〉E for the effects of buoyancy and also can be used as a means to operationally assess and control float buoyancy.
Analysis of electrical accidents in UK domestic properties
Authors: Barrett M. , O'Connell K. , Sung Cma , Stokes G. 
Published: June 2010

Electricity is one of the most convenient forms of energy that is used in every building today. However, it causes a number of fatalities every year and has the potential to cause harm to anyone exposed to it. This article, investigates the cause and effects of electrical accidents in domestic properties over a 3-year period (2000—2002) in the UK based on the 24th Report of the Home and Leisure Accident Surveillance System (HASS/LASS). The electrical accident data from this database was analysed to establish electrical injury trends for various categories and groups. This highlighted the high-risk activities, which led to receiving an electric shock in a domestic property and identified at-risk groups that could most benefit from electrical safety interventions. In order to enhance electrical safety and to aid in the formulation of the relevant national wiring regulations, it is imperative that the narrative reports and statistics presented in the HASS/LASS document and this article are considered by regulators, manufacturers, educators, safety officers and engineers so that the whole of society can benefit. Based on the evidence and analysis presented in this article, it was concluded that there are a number of recommended protective measures designers, installers and regulators could consider implementing to advance electrical safety in the home. Practical application: Engineers, educators, manufacturers and regulators can use the information highlighted in this article to improve electrical safety in the built environment.
Perceptions of Coronary Heart Disease Risk in African American Women With Type 2 Diabetes
Authors: McKenzie Carolyn , Skelly Anne H. 
Published: June 2010

Purpose The purpose of this study was to explore the perceptions of coronary heart disease (CHD) risk in a group of southern African American women with type 2 diabetes (T2DM). Methods Semistructured interviews were conducted in participants’ homes or setting of choice. The interviews were conducted with 6 participants from a larger study of 48 women who were stratified into levels of low, medium, and high perception of CHD risk, with 2 participants in each group. The interviews were analyzed using NVivo software; both investigators recoded and analyzed the data. Results African American women with T2DM do not believe they are at risk for CHD unless they are told specifically by their primary health care provider that they have heart disease. The African American women in the study expressed that managing their diabetes to prevent heart disease can be overwhelming. Participants identified faith beliefs called not claiming the illness as a reason they did not perceive themselves at risk for CHD. Conclusions Not claiming an illness may influence health and preventive behaviors. Many African American women with T2DM may not claim their illness. Diabetes educators should acknowledge and address women’s beliefs to create an appropriate plan of care.
Independent but coordinated trials: insights from the Practice-based Opportunities for Weight Reduction Trials Collaborative Research Group
Authors: Yeh Hsin-Chieh , Clark Jeanne M , Emmons Karen E , Moore Reneé H , Bennett Gary G , Warner Erica T , Sarwer David B , Jerome Gerald J , Miller Edgar R , Volger Sheri , Louis Thomas A , Wells Barbara , Wadden Thomas A , Colditz Graham A , Appel Lawrence J 
Published: June 2010

Background The National Heart, Lung, and Blood Institute (NHLBI) funded three institutions to conduct effectiveness trials of weight loss interventions in primary care settings. Unlike traditional multi-center clinical trials, each study was established as an independent trial with a distinct protocol. Still, efforts were made to coordinate and standardize several aspects of the trials. The three trials formed a collaborative group, the ‘Practice-based Opportunities for Weight Reduction (POWER) Trials Collaborative Research Group.’ Purpose We describe the common and distinct features of the three trials, the key characteristics of the collaborative group, and the lessons learned from this novel organizational approach. Methods The Collaborative Research Group consists of three individual studies: ‘Be Fit, Be Well’ (Washington University in St. Louis/Harvard University), ‘POWER Hopkins’ (Johns Hopkins), and ‘POWER-UP’ (University of Pennsylvania). There are a total of 15 participating clinics with ~1100 participants. The common primary outcome is change in weight at 24 months of follow-up, but each protocol has trial-specific elements including different interventions and different secondary outcomes. A Resource Coordinating Unit at Johns Hopkins provides administrative support. Results The Collaborative Research Group established common components to facilitate potential cross-site comparisons. The main advantage of this approach is to develop and evaluate several interventions, when there is insufficient evidence to test one or two approaches, as would be done in a traditional multi-center trial. Limitations The challenges of the organizational design include the complex decision-making process, the extent of potential data pooling, time intensive efforts to standardize reports, and the additional responsibilities of the DSMB to monitor three distinct protocols.
Milatuzumab immunoliposomes induce cell death in CLL by promoting accumulation of CD74 on the surface of B cells
Authors: Hertlein Erin , Triantafillou Georgia , Sass Ellen J. , Hessler Joshua D. , Zhang Xiaoli , Jarjoura David , Lucas David M. , Muthusamy Natarajan , Goldenberg David M. , Lee Robert J. , Byrd John C. 
Published: June 2010

Abstract
Chronic lymphocytic leukemia (CLL) is an incurable progressive disease for which new therapies are required. Therapy with monoclonal antibodies (mAbs) has improved the outcome of patients with CLL, making further investigation of novel antibodies directed against alternative and specific targets on B cells an important area of translational research. We now describe functional properties of an antagonistic humanized mAb to CD74, milatuzumab, showing that milatuzumab combined with a crosslinking antibody induces cytotoxicity in vitro in CLL cells in a caspase- and stromal-independent manner associated with aggregation of CD74 on the cell surface. Furthermore, incorporation of milatuzumab into an immunoliposome induces even more of a cytotoxic response than in vitro crosslinking, representing a novel therapeutic formulation for this mAb. Based on these data, future development of the milatuzumab-immunoliposome formulation as a therapeutic agent for CLL is warranted.
Autophagy contributes to therapy-induced degradation of the PML/RARA oncoprotein
Authors: Isakson Pauline , Bjørås Magnar , Bøe Stig Ove , Simonsen Anne 
Published: June 2010

Abstract
Treatment of acute promyelocytic leukemia (APL) with all-trans retinoic acid and/or arsenic trioxide represents a paradigm in targeted cancer therapy because these drugs cause clinical remission by affecting the stability of the fusion oncoprotein promyelocytic leukemia (PML)/retinoic acid receptor alpha (RARA). The authors of previous studies have implicated the ubiquitin-proteasome pathway as the main mechanism involved in therapy-induced PML/RARA degradation. Here we have investigated a role of autophagy, a protein degradation pathway that involves proteolysis of intracellular material within lysosomes. We found that both all-trans retinoic acid and arsenic trioxide induce autophagy via the mammalian target of rapamycin pathway in APL cells and that autophagic degradation contributes significantly both to the basal turnover as well as the therapy-induced proteolysis of PML/RARA. In addition, we observed a correlation between autophagy and therapy-induced differentiation of APL cells. Given the central role of the PML/RARA oncoprotein in APL pathogenesis, this study highlights an important role of autophagy in the development and treatment of this disease.
SOPRA: Scaffolding algorithm for paired reads via statistical optimization
Authors: Dayarian Adel , Michael Todd P , Sengupta Anirvan M 
Published: June 2010

AbstractBackgroundHigh throughput sequencing (HTS) platforms produce gigabases of short read (<100 bp) data per run. While these short reads are adequate for resequencing applications,de novoassembly of moderate size genomes from such reads remains a significant challenge. These limitations could be partially overcome by utilizing mate pair technology, which provides pairs of short reads separated by a known distance along the genome.ResultsWe have developed SOPRA, a tool designed to exploit the mate pair/paired-end information for assembly of short reads. The main focus of the algorithm is selecting a sufficiently large subset of simultaneously satisfiable mate pair constraints to achieve a balance between the size and the quality of the output scaffolds. Scaffold assembly is presented as an optimization problem for variables associated with vertices and with edges of the contig connectivity graph. Vertices of this graph are individual contigs with edges drawn between contigs connected by mate pairs. Similar graph problems have been invoked in the context of shotgun sequencing and scaffold building for previous generation of sequencing projects. However, given the error-prone nature of HTS data and the fundamental limitations from the shortness of the reads, the ad hoc greedy algorithms used in the earlier studies are likely to lead to poor quality results in the current context. SOPRA circumvents this problem by treating all the constraints on equal footing for solving the optimization problem, the solution itself indicating the problematic constraints (chimeric/repetitive contigs, etc.) to be removed. The process of solving and removing of constraints is iterated till one reaches a core set of consistent constraints. For SOLiD sequencer data, SOPRA uses a dynamic programming approach to robustly translate the color-space assembly to base-space. For assessing the quality of an assembly, we report the no-match/mismatch error rate as well as the rates of various rearrangement errors.ConclusionsApplying SOPRA to real data from bacterial genomes, we were able to assemble contigs into scaffolds of significant length (N50 up to 200 Kb) with very few errors introduced in the process. In general, the methodology presented here will allow better scaffold assemblies of any type of mate pair sequencing data.
An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database)
Authors: Lou Shao-Ke , Wong Ka-Lok , Li Ming , But Paul Pui-Hay , Tsui Stephen Kwok-Wing , Shaw Pang-Chui 
Published: June 2010

AbstractBackgroundThousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database.DescriptionWe have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD) for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed athttp://www.cuhk.edu.hk/icm/mmdbd.htm.ConclusionsThis work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.