bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Density Current Parameterization Coupled with Emanuel’s Convection Scheme. Part II: 1D Simulations
Authors: Grandpeix Jean-Yves , Lafore Jean-Philippe , Cheruy Frédérique 
Published: November 2009

Abstract
The density current parameterization coupled with Emanuel’s convection scheme, described in Part I of this series of papers, is tested in a single-column framework for continental and maritime convective systems. The case definitions and reference simulations are provided by cloud-resolving models (CRMs). For both cases, the wake scheme yields cold pools with temperature and humidity differences relative to the environment in reasonable agreement with observations (with wake depth on the order of 2 km over land and 1 km over ocean). The coupling with the convection scheme yields convective heating, drying, and precipitation similar to those simulated by the CRM. Thus, the representation of the action of the wakes on convection in terms of available lifting energy (ALE) and available lifting power (ALP) appears satisfactory. The sensitivity of the wake–convection system to the basic parameters of the parameterization is widely explored. A range of values for each parameter is recommended to help with implementing the scheme in a full-fledged general circulation model.
A Bayesian Algorithm for Reconstructing Climate Anomalies in Space and Time. Part II: Comparison with the Regularized Expectation–Maximization Algorithm
Authors: Tingley Martin P. , Huybers Peter 
Published: November 2009

AbstractPart I presented a Bayesian algorithm for reconstructing climate anomalies in space and time (BARCAST). This method involves specifying simple parametric forms for the spatial covariance and temporal evolution of the climate field as well as “observation equations” describing the relationships between the data types and the corresponding true values of the climate field. As this Bayesian approach to reconstructing climate fields is new and different, it is worthwhile to compare it in detail to the more established regularized expectation–maximization (RegEM) algorithm, which is based on an empirical estimate of the joint data covariance matrix and a multivariate regression of the instrumental time series onto the proxy time series. The differing assumptions made by BARCAST and RegEM are detailed, and the impacts of these differences on the analysis are discussed. Key distinctions between BARCAST and RegEM include their treatment of spatial and temporal covariance, the prior information that enters into each analysis, the quantities they seek to impute, the end product of each analysis, the temporal variance of the reconstructed field, and the treatment of uncertainty in both the imputed values and functions of these imputations. Differences between BARCAST and RegEM are illustrated by applying the two approaches to various surrogate datasets. If the assumptions inherent to BARCAST are not strongly violated, then in scenarios comparable to practical applications BARCAST results in reconstructions of both the field and the spatial mean that are more skillful than those produced by RegEM, as measured by the coefficient of efficiency. In addition, the uncertainty intervals produced by BARCAST are narrower than those estimated using RegEM and contain the true values with higher probability.
Errors in Cloud Detection over the Arctic Using a Satellite Imager and Implications for Observing Feedback Mechanisms
Authors: Liu Yinghui , Ackerman Steven A. , Maddux Brent C. , Key Jeffrey R. , Frey Richard A. 
Published: November 2009

Abstract
Arctic sea ice extent has decreased dramatically over the last 30 years, and this trend is expected to continue through the twenty-first century. Changes in sea ice extent impact cloud cover, which in turn influences the surface energy budget. Understanding cloud feedback mechanisms requires an accurate determination of cloud cover over the polar regions, which must be obtained from satellite-based measurements. The accuracy of cloud detection using observations from space varies with surface type, complicating any assessment of climate trends as well as the understanding of ice–albedo and cloud–radiative feedback mechanisms. To explore the implications of this dependence on measurement capability, cloud amounts from the Moderate Resolution Imaging Spectroradiometer (MODIS) are compared with those from the CloudSat and Cloud–Aerosol Lidar and Infrared Pathfinder (CALIPSO) satellites in both daytime and nighttime during the time period from July 2006 to December 2008. MODIS is an imager that makes observations in the solar and infrared spectrum. The active sensors of CloudSat and CALIPSO, a radar and lidar, respectively, provide vertical cloud structures along a narrow curtain.
Results clearly indicate that MODIS cloud mask products perform better over open water than over ice. Regional changes in cloud amount from CloudSat/CALIPSO and MODIS are categorized as a function of independent measurements of sea ice concentration (SIC) from the Advanced Microwave Scanning Radiometer for Earth Observing System (AMSR-E). As SIC increases from 10% to 90%, the mean cloud amounts from MODIS and CloudSat–CALIPSO both decrease; water that is more open is associated with increased cloud amount. However, this dependency on SIC is much stronger for MODIS than for CloudSat–CALIPSO, and is likely due to a low bias in MODIS cloud amount. The implications of this on the surface radiative energy budget using historical satellite measurements are discussed. The quantified ice–water difference in MODIS cloud detection can be used to adjust estimated trends in cloud amount in the presence of changing sea ice cover from an independent dataset. It was found that cloud amount trends in the Arctic might be in error by up to 2.7% per decade. The impact of these errors on the surface net cloud radiative effect (“forcing”) of the Arctic can be significant, as high as 8.5%.
Robust Characterization of Model Physics Uncertainty for Simulations of Deep Moist Convection
Authors: Posselt Derek J. , Vukicevic Tomislava 
Published: November 2009

AbstractThis study explores the functional relationship between model physics parameters and model output variables for the purpose of 1) characterizing the sensitivity of the simulation output to the model formulation and 2) understanding model uncertainty so that it can be properly accounted for in a data assimilation framework. A Markov chain Monte Carlo algorithm is employed to examine how changes in cloud microphysical parameters map to changes in output precipitation, liquid and ice water path, and radiative fluxes for an idealized deep convective squall line. Exploration of the joint probability density function (PDF) of parameters and model output state variables reveals a complex relationship between parameters and model output that changes dramatically as the system transitions from convective to stratiform. Persistent nonuniqueness in the parameter–state relationships is shown to be inherent in the construction of the cloud microphysical and radiation schemes and cannot be mitigated by reducing observation uncertainty. The results reinforce the importance of including uncertainty in model configuration in ensemble prediction and data assimilation, and they indicate that data assimilation efforts that include parameter estimation would benefit from including additional constraints based on known physical relationships between model physics parameters to render a unique solution.
Diet-Specific Family Support and Glucose Control Among Korean Immigrants With Type 2 Diabetes
Authors: Choi Sarah E. 
Published: November 2009

Purpose The purpose of this study was to examine the influence of diet family support on glucose outcome in Korean immigrants with type 2 diabetes, taking into consideration patient gender. Methods A total of 143 Korean immigrants with type 2 diabetes were recruited from a West Coast Koreatown. On com- pleting questionnaires (demographic, health history, and the Diabetes Family Behavior Checklist-II [DFBC]), a participant was given a finger stick blood test for glyco-sylated hemoglobin (A1C). Body mass index (BMI) and waist-to-hip ratio (WHR) were calculated after measurements were taken. Analyses assessed the independent associations of diet family support, gender, and diet fam- ily support by gender interactions with glucose outcome. Results A higher level of diet family support was significantly associated with lower A1C, indicating the beneficial effect of diet family support on glucose control. Although the main effect of gender on A1C was not significant, the effect of the product term of family support and gender was, indicating that the significant beneficial impact of diet family support on A1C depends on gender. The impact is much more pronounced in men (B = -.516) than women (B = -.038). Conclusions Family support, specific to diet, is significantly associ- ated with glucose outcomes in Korean immigrants with type 2 diabetes. That is, more perceived family support was associated with better glucose control. The positive impact of family support on glucose outcome was sig- nificantly stronger in men than in women, even after other factors were taken into consideration
Lithium treatment — moderate dose use study (LiTMUS) for bipolar disorder: rationale and design
Authors: Nierenberg Andrew A , Sylvia Louisa G , Leon Andrew C , Reilly-Harrington Noreen A , Ketter Terence A , Calabrese Joseph R , Thase Michael E , Bowden Charles L , Friedman Edward S , Ostacher Michael J , Novak Lena , Iosifescu Dan V ,   Litmus Study Group
Published: November 2009

Background Recent data indicate that lithium use for bipolar disorder has declined over the last decade and that lithium largely has been replaced with alternate, commercially promoted medications that may or may not result in better outcomes. Purpose This article describes the rationale and study design of LiTMUS, a multi-site, prospective, randomized clinical trial of outpatients with bipolar disorder. LiTMUS seeks to address whether initiating therapy at lower doses of lithium as part of optimized treatment (OPT, guideline-informed, evidence-based, and personalized pharmacotherapy) improves outcomes and decreases the need for other medication changes across 6 months of therapy. Methods LiTMUS will randomize 284 adults with bipolar disorder (Type I or II) across 6 study sites. The co-primary outcomes are overall illness severity on clinical global improvement scale for bipolar disorder and a novel measure, necessary clinical adjustments. This metric provides a composite that reflects both clinical response and tolerability. Other relevant outcomes include full symptomatic recovery, quality of life, suicidal behaviors, and moderators of suicidality. Results As of August 28th, 2009, we have consented 338 patients and randomized 281 for this study. Limitations The potential limitations of the study include an arbitrary definition of ‘low, but effective’ doses of lithium, lack of a placebo-controlled group, open treatment, and use of a new outcome measure (i.e., necessary clinical adjustments). Conclusion We expect that this study will inform our understanding of the effectiveness of low to moderate doses of lithium therapy for individuals with bipolar disorder. Clinical Trials 2009; 6: 637—648. http://ctj.sagepub.com
A small molecule inhibitor of Pim protein kinases blocks the growth of precursor T-cell lymphoblastic leukemia/lymphoma
Authors: Lin Ying-Wei , Beharry Zanna M. , Hill Elizabeth G. , Song Jin H. , Wang Wenxue , Xia Zuping , Zhang Zhenhua , Aplan Peter D. , Aster Jon C. , Smith Charles D. , Kraft Andrew S. 
Published: November 2009

Abstract
The serine/threonine Pim kinases are up-regulated in specific hematologic neoplasms, and play an important role in key signal transduction pathways, including those regulated by MYC, MYCN, FLT3-ITD, BCR-ABL, HOXA9, and EWS fusions. We demonstrate that SMI-4a, a novel benzylidene-thiazolidine-2, 4-dione small molecule inhibitor of the Pim kinases, kills a wide range of both myeloid and lymphoid cell lines with precursor T-cell lymphoblastic leukemia/lymphoma (pre–T-LBL/T-ALL) being highly sensitive. Incubation of pre–T-LBL cells with SMI-4a induced G1 phase cell-cycle arrest secondary to a dose-dependent induction of p27Kip1, apoptosis through the mitochondrial pathway, and inhibition of the mammalian target of rapamycin C1 (mTORC1) pathway based on decreases in phospho-p70 S6K and phospho-4E-BP1, 2 substrates of this enzyme. In addition, treatment of these cells with SMI-4a was found to induce phosphorylation of extracellular signal-related kinase1/2 (ERK1/2), and the combination of SMI-4a and a mitogen-activated protein kinase kinase 1/2 (MEK1/2) inhibitor was highly synergistic in killing pre–T-LBL cells. In immunodeficient mice carrying subcutaneous pre–T-LBL tumors, treatment twice daily with SMI-4a caused a significant delay in the tumor growth without any change in the weight, blood counts, or chemistries. Our data suggest that inhibition of the Pim protein kinases may be developed as a therapeutic strategy for the treatment of pre–T-LBL.
Histone modifications are specifically relocated during gene activation and nuclear differentiation
Authors: Heyse Katharina Sarah , Weber Susanne Erika , Lipps Hans-Joachim 
Published: November 2009

Abstract

Background
Post-translational histone modifications (PTMs) and their specific distribution on genes play a crucial role in the control of gene expression, but the regulation of their dynamics upon gene activation and differentiation is still poorly understood. Here, we exploit the unique genome organization of ciliates to analyse PTM dynamics during gene activation in the differentiated cell and during nuclear differentiation. In the macronucleus of these cells the DNA is organized into nanochromosomes which represent independent functional units. Therefore, ciliated protozoa represent a simplistic model system to analyse the relevance of histone modifications and their localization for gene expression and differentiation.

Results
We analysed the distribution of three PTMs on six individual nanochromosomes, two of which are silenced in the vegetative cell and only activated during sexual reproduction. We show that a specific relocation of these PTMs correlates with gene activation. Moreover, macronuclear-destined sequences in the differentiating macronucleus display a distribution of PTMs which differs significantly from the PTM patterns of actively transcribed genes.

Conclusion
We show for the first time that a relocation of specific histone modifications takes place during activation of genes. In addition, we demonstrate that genes in a differentiating nucleus are characterised by a specific distribution and composition of PTMs. This allows us to propose a mechanistic model about the relevance of PTMs for gene activation, gene silencing and nuclear differentiation. Results described here will be relevant for eukaryotic cells in general.
Combining next-generation pyrosequencing with microarray for large scale expression analysis in non-model species
Authors: Bellin Diana , Ferrarini Alberto , Chimento Antonio , Kaiser Olaf , Levenkova Natasha , Bouffard Pascal , Delledonne Massimo 
Published: November 2009

Abstract

Background
The next generation sequencing technologies provide new options to characterize the transcriptome and to develop affordable tools for functional genomics. We describe here an innovative approach for this purpose and demonstrate its potential also for non-model species.

Results
The method we developed is based on 454 sequencing of 3' cDNA fragments from a normalized library constructed from pooled RNAs to generate, through de novo reads assembly, a large catalog of unique transcripts in organisms for which a comprehensive collection of transcripts or the complete genome sequence, is not available. This "virtual transcriptome" provides extensive coverage depth, and can be used for the setting up of a comprehensive microarray based expression analysis. We evaluated the potential of this approach by monitoring gene expression during berry maturation in Vitis vinifera as if no other sequence information was available for this species. The microarray designed on the berries' transcriptome derived from half of a 454 run detected the expression of 19,609 genes, and proved to be more informative than one of the most comprehensive grape microarrays available to date, the GrapeArray 1.2 developed by the Italian-French Public Consortium for Grapevine Genome Characterization, which could detect the expression of 15,556 genes in the same samples.

Conclusion
This approach provides a powerful method to rapidly build up an extensive catalog of unique transcripts that can be successfully used to develop a microarray for large scale analysis of gene expression in any species, without the need for prior sequence knowledge.
An ongoing process: A qualitative study of how the alcohol-dependent free themselves of addiction through progressive abstinence
Authors: Yeh Mei-Yu , Che Hui-Lian , Wu Shu-Mei 
Published: November 2009

Abstract

Background
Most people being treated for alcoholism are unable to successfully quit drinking within their treatment programs. In few cases do we know the full picture of how abstinence is achieved in Taiwan. We tracked processes of abstinence in alcohol-dependency disorders, based on study evidence and results. This research explores the process of recovery from the viewpoint of the alcohol-dependent.

Methods
Semi-structured interviews were conducted in two different settings, using purpose sampling, during 2003-2004. The data were analyzed using content analysis. Participants were 32 adults, purposefully selected from an Alcoholics Anonymous group and a psychiatric hospital in North Taiwan.

Results
We found that the abstinence process is an ongoing process, in which the alcohol-dependent free themselves of addiction progressively. This process never ends or resolves in complete recovery. We have identified three stages in the struggle against alcoholism: the Indulgence, Ambivalence and Attempt (IAA) cycle, in which the sufferer is trapped in a cycle of attempting to give up and failing; the Turning Point, in which a Personal Nadir is reached, and the Ongoing Process of abstinence, in which a constant effort is made to remain sober through willpower and with the help of support groups. We also discuss Influencing Factors that can derail abstinence attempts, pushing the sufferer back into the IAA cycle.

Conclusion
This study provides important points of reference for alcohol and drug service workers and community healthcare professionals in Taiwan, casting light on the abstinence process and providing a basis for intervention or rehabilitation services.
Glycosylated VCAM-1 isoforms revealed in 2D western blots of HUVECs treated with tumoral soluble factors of breast cancer cells
Authors: Montes-Sánchez Delina , Ventura Jose Luis , Mitre Irma , Frías Susana , Michán Layla , Espejel-Nuñez Aurora , Vadillo-Ortega Felipe , Zentella Alejandro 
Published: November 2009

Abstract

Background
Several common aspects of endothelial phenotype, such as the expression of cell adhesion molecules, are shared between metastasis and inflammation. Here, we analyzed VCAM-1 variants as biological markers of these two types of endothelial cell activation. With the combination of 2-DE and western blot techniques and the aid of tunicamycin, we analyzed N-glycosylation variants of VCAM-1 in primary human endothelial cells stimulated with either TNF or tumoral soluble factors (TSF's) derived from the human breast cancer cell line ZR75.30.

Results
Treatments induced a pro-adhesive endothelial phenotype. 2D western blots analysis of cells subjected to both treatments revealed the expression of the two known VCAM-1 isoforms and of previously unknown isoforms. In particular TSFZR75.30 induced an isoform with a relative molecular mass (Mr) and isoelectric point (pI) of 75-77 kDa and 5.0, respectively.

Conclusion
The unknown isoforms of VCAM-1 that were found to be overexpressed after treatment with TSF's compared with TNF, could serve as biomarkers to discriminate between inflammation and metastasis. 2D western blots revealed three new VCAM-1 isoforms expressed in primary human endothelial cells in response to TSF stimulation. Each of these isoforms varies in Mr and pI and could be the result of differential glycosylation states.
Multi-body simulation of a canine hind limb: model development, experimental validation and calculation of ground reaction forces
Authors: Helms Gabriele , Behrens Bernd-Arno , Stolorz Martin , Wefstaedt Patrick , Nolte Ingo 
Published: November 2009

AbstractBackgroundAmong other causes the long-term result of hip prostheses in dogs is determined by aseptic loosening. A prevention of prosthesis complications can be achieved by an optimization of the tribological system which finally results in improved implant duration. In this context a computerized model for the calculation of hip joint loadings during different motions would be of benefit. In a first step in the development of such an inverse dynamic multi-body simulation (MBS-) model we here present the setup of a canine hind limb model applicable for the calculation of ground reaction forces.MethodsThe anatomical geometries of the MBS-model have been established using computer tomography- (CT-) and magnetic resonance imaging- (MRI-) data. The CT-data were collected from the pelvis, femora, tibiae and pads of a mixed-breed adult dog. Geometric information about 22 muscles of the pelvic extremity of 4 mixed-breed adult dogs was determined using MRI. Kinematic and kinetic data obtained by motion analysis of a clinically healthy dog during a gait cycle (1 m/s) on an instrumented treadmill were used to drive the model in the multi-body simulation.Results and DiscussionAs a result the vertical ground reaction forces (z-direction) calculated by the MBS-system show a maximum deviation of 1.75%BW for the left and 4.65%BW for the right hind limb from the treadmill measurements. The calculated peak ground reaction forces in z- and y-direction were found to be comparable to the treadmill measurements, whereas the curve characteristics of the forces in y-direction were not in complete alignment.ConclusionIn conclusion, it could be demonstrated that the developed MBS-model is suitable for simulating ground reaction forces of dogs during walking. In forthcoming investigations the model will be developed further for the calculation of forces and moments acting on the hip joint during different movements, which can be of help in context with thein silicodevelopment and testing of hip prostheses.