bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assimilation of GPS Radio Occultation Data for an Intense Atmospheric River with the NCEP Regional GSI System
Authors: Ma Zaizhong , Kuo Ying-Hwa , Ralph F. Martin , Neiman Paul J. , Wick Gary A. , Sukovich Ellen , Wang Bin 
Published: April 2011

Abstract
This paper uses a case study to explore the potential of Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC) and Challenging Minisatellite Payload (CHAMP) global positioning system (GPS) radio occultation (RO) satellite data over the eastern Pacific Ocean to improve analyses and mesoscale forecasts of landfalling atmospheric rivers (ARs) along the U.S. West Coast. The case study is from early November 2006 and was a very high-impact event in the Pacific Northwest where it created torrential rainfall and severe flooding. Recent studies have shown that the COSMIC data offshore have the ability to better define the vertical and horizontal structure of the strong AR. This paper extends the earlier work by assessing the impact of assimilating the COSMIC data into the Advanced Research Weather Research and Forecasting (ARW-WRF) mesoscale numerical model (using a nested mode with 36-, 12-, and 4-km grid sizes) on a key 24-h forecast.
The data are assimilated using NCEP’s Gridpoint Statistical Interpolation (GSI), and impacts are evaluated using Special Sensor Microwave Imager (SSM/I) satellite observations over the ocean and precipitation observations over land. The assimilation of GPS RO soundings made use of a local refractivity observation operator as well as an advanced nonlocal excess phase observation operator that considers the effects of atmospheric horizontal gradients. The results show that the assimilation of GPS RO soundings improved the moisture analysis for this AR event. This result supports conclusions from earlier observing systems simulation experiment (OSSE) studies, but in a real event. The use of a nonlocal excess phase observation operator can produce larger and more robust analysis increments. Although this is a single case study, the results are likely representative of the potential impacts of assimilating COSMIC data in other extreme AR and precipitation events and in other regions affected by landfalling ARs, for example, western Europe, western South America, and New Zealand.
A Stability Analysis of Divergence Damping on a Latitude–Longitude Grid
Authors: Whitehead Jared P. , Jablonowski Christiane , Rood Richard B. , Lauritzen Peter H. 
Published: April 2011

The dynamical core of an atmospheric general circulation model is engineered to satisfy a delicate balance between numerical stability, computational cost, and an accurate representation of the equations of motion. It generally contains either explicitly added or inherent numerical diffusion mechanisms to control the buildup of energy or enstrophy at the smallest scales. The diffusion fosters computational stability and is sometimes also viewed as a substitute for unresolved subgrid-scale processes. A particular form of explicitly added diffusion is horizontal divergence damping. In this paper a von Neumann stability analysis of horizontal divergence damping on a latitude–longitude grid is performed. Stability restrictions are derived for the damping coefficients of both second- and fourth-order divergence damping. The accuracy of the theoretical analysis is verified through the use of idealized dynamical core test cases that include the simulation of gravity waves and a baroclinic wave. The tests are applied to the finite-volume dynamical core of NCAR’s Community Atmosphere Model version 5 (CAM5). Investigation of the amplification factor for the divergence damping mechanisms explains how small-scale meridional waves found in a baroclinic wave test case are not eliminated by the damping.
Vertical Diabatic Heating Structure of the MJO: Intercomparison between Recent Reanalyses and TRMM Estimates
Authors: Jiang Xianan , Waliser Duane E. , Olson William S. , Tao Wei-Kuo , L’Ecuyer Tristan S. , Li King-Fai , Yung Yuk L. , Shige Shoichi , Lang Stephen , Takayabu Yukari N. 
Published: April 2011

Abstract
Capitalizing on recently released reanalysis datasets and diabatic heating estimates based on Tropical Rainfall Measuring Mission (TRMM), the authors have conducted a composite analysis of vertical anomalous heating structures associated with the Madden–Julian oscillation (MJO). Because diabatic heating lies at the heart of prevailing MJO theories, the intention of this effort is to provide new insights into the fundamental physics of the MJO. However, some discrepancies in the composite vertical MJO heating profiles are noted among the datasets, particularly between three reanalyses and three TRMM estimates. A westward tilting with altitude in the vertical heating structure of the MJO is clearly evident during its eastward propagation based on three reanalysis datasets, which is particularly pronounced when the MJO migrates from the equatorial eastern Indian Ocean (EEIO) to the western Pacific (WP). In contrast, this vertical tilt in heating structure is not readily seen in the three TRMM products. Moreover, a transition from a shallow to deep heating structure associated with the MJO is clearly evident in a pressure–time plot over both the EEIO and WP in three reanalysis datasets. Although this vertical heating structure transition is detectable over the WP in two TRMM products, it is weakly defined in another dataset over the WP and in all three TRMM datasets over the EEIO.
The vertical structures of radiative heating QR associated with the MJO are also analyzed based on TRMM and two reanalysis datasets. A westward vertical tilt in QR is apparent in all these datasets: that is, the low-level QR is largely in phase of convection, whereas QR in the upper troposphere lags the maximum convection. The results also suggest a potentially important role of radiative heating for the MJO, particularly over the Indian Ocean. Caveats in heating estimates based on both the reanalysis datasets and TRMM are briefly discussed.
The prostate exam
Authors: Romero Frederico R , Romero Antonio W , Filho Thadeu Brenny , Kulysz David , Oliveira Fernando C , Filho Renato Tambara 
Published: April 2011

Objective: To help students, residents, and general practitioners to improve the technique, skills, and reproducibility of their prostate examination. Methods: We developed a comprehensive guideline outlining prostate anatomy, indications, patient preparation, positioning, technique, findings, and limitations of this ancient art of urological evaluation. Results: The prostate exam was the first diagnostic test used for prostate cancer screening and other urological conditions. Although several alternative procedures have been developed in the past century, the prostate exam is still an important part of genital–pelvic evaluation because of its simplicity, cost and time effectiveness, and relatively minimal patient discomfort experienced. Conclusion: With an aging population and increasing incidence of prostate diseases, it is imperative that healthcare professionals possess the knowledge, skills, and attitudes to make the prostate exam a routine part of a complete physical examination.
Visual and auditory perceptual rivalry in migraine
Authors: McKendrick Allison M , Battista Josephine , Snyder Joel S , Carter Olivia L 
Published: April 2011

Introduction: Recent evidence demonstrates that perceptual rivalry rate can be modulated by perturbation of the serotonergic system. Specifically, pharmacologically lowering the availability of serotonin results in slower rivalry rates. As it has been suggested that brain serotonin is low during the interictal phase of migraine, we hypothesized that perceptual rivalry rates would be reduced in individuals with migraine. Methods: Visual and auditory perceptual rivalry measures were obtained for a group of 30 participants with migraine (15 migraine with aura, 15 migraine without aura) and 20 non-headache control individuals. Results: Our experiments reveal fewer perceptual rivalry switches within both visual and auditory domains for our migraine without aura group, while the with-aura group performed similarly to non-headache controls. Dividing the data by headache frequency rather than headache subtype classification revealed fewer perceptual switches in those with more frequent headaches. Conclusions: Our data provides further support for interictal differences in brain sensory reactivity in migraine, with the observed effects being in the same direction as those caused by pharmacologically reducing brain availability of serotonin in normal observers.
Incidence of multiple sclerosis in Iceland, 2002–2007: a population-based study
Authors: Eliasdottir Olöf Jona , Olafsson Elias , Kjartansson Olafur 
Published: April 2011

Background: We conducted a study to determine the incidence of multiple sclerosis (MS) among the whole Icelandic population during a 6-year period (2002–2007). Methods: We included all Icelandic residents diagnosed with MS during the study period. Cases were identified from records of the only neurology department in Iceland, plus the records of all practicing neurologists and all radiology departments. All patients had experienced at least two confirmed MS relapses (i.e. clinically definite MS) or had primary progressive MS as defined by the Poser criteria. Results:We identified 136 individuals who met the inclusion criteria, including 102 (75%) women. The mean age at diagnosis was 36.3 years (women 35.7 years, men 38.3 years). Average annual incidence was 7.6 per 100,000 population. All but one patient (99%) had an MRI study done at diagnosis and 61% of these (83/135) fulfilled the Barkhof criteria for diagnosis of MS; one had a normal MRI. A visual evoked potential test was done in 68% (93/136) at the time of diagnosis and 44% (41/93) were abnormal. Spinal fluid was obtained from 78% (106/136), and 75% (80/106) had oligoclonal bands. Conclusion:A total population study is the most reliable method of determining the spectrum of clinical symptoms and the results of investigations in MS patients at diagnosis.
A functional p.82G>S polymorphism in the RAGE gene is associated with multiple sclerosis in the Chinese population
Authors: Li Keshen , Zhao Bin , Dai Dawei , Yao Songpo , Liang Wandong , Yao Lifen , Yang Ze 
Published: April 2011

Background: The receptor for advanced glycation end products (RAGE) and its proinflammatory ligand, S100-calgranulins, are critically implicated in the pathological progression of multiple sclerosis (MS). A functional polymorphism within the V-type immunoglobulin domain of RAGE gene, p.82G>S (c.557G>A), has been shown to affect ligand binding affinity and thus may affect susceptibility to MS. Methods: The RAGE p.82G>S polymorphism was genotyped in 144 MS patients and 156 healthy controls using polymerase chain reaction – restriction fragment length polymorphism. A replication study was performed on a second cohort comprising 138 patients and 150 controls. The relationship between the RAGE p.82G>S polymorphism and circulating levels of soluble RAGE (sRAGE), a secreted decoy receptor against RAGE signaling, was also investigated. Results: In both initial and replication cohorts, an increased MS risk was detected in RAGE p.82G>S variant allele carriers (odds ratio [OR] = 1.786, p = 0.0134 and OR = 1.732, p = 0.0210, respectively). This association signal persisted in subgroups of women and patients with relapsing–remitting MS. Moreover, compared with the wild-type 82GG carriers, carriers of the variant allele presented a faster progression of disability and a reduced serum sRAGE level. Conclusions: The present study provides preliminary evidence that the gain-of-function p.82G>S polymorphism in the RAGE gene is associated with an increased risk of MS in the Chinese population.
Occurrence of antibodies against natalizumab in relapsing multiple sclerosis patients treated with natalizumab
Authors: Sørensen Per Soelberg , Hyldgaard Jensen Poul Erik , Haghikia Aiden , Lundkvist Malin , Vedeler Christian , Sellebjerg Finn , Koch-Henriksen Nils , Fogdell-Hahn Anna , Myhr Kjell-Morten , Hillert Jan , Gold Ralf 
Published: April 2011

Background: In the clinical trials about 9% of natalizumab treated multiple sclerosis (MS) patients generated anti-natalizumab antibodies, of which 6% were persistent and 3% transient. The occurrence of antibodies reduced serum levels of natalizumab, decreased bio-efficacy, and abrogated the therapeutic efficacy. Objective: The objective was to assess the frequency of anti-natalizumab antibodies in an unselected cohort of patients from four different countries. Methods: We measured anti-natalizumab antibodies in a large cohort of 4881 unselected patients from four MS centres that systematically measured antibodies in patients treated with natalizumab. We applied the same ELISA assay developed by Biogen Idec and used in the pivotal trials of natalizumab. Results: Antibodies occurred in 4.5% (95% confidence interval, CI: 4.0–5.1%) of the patients, and were persistent in 3.5% (95% CI: 3.0–4.0%) and transient in 1.0% (95% CI: 0.7–1.3%) of the patients. The frequencies of permanently antibody positive patients did not show statistically significant differences between the four centres, whereas the frequencies of transiently antibody positive patients showed some variations. Conclusion: The frequencies of antibodies appeared to be of the same magnitude in the four centres, but might be less than in the pivotal studies of natalizumab.
Quantitative evaluation of single-arm versus randomized phase II cancer clinical trials
Authors: Pond Gregory R , Abbasi Saqib 
Published: April 2011

Background There is a debate among cancer researchers about the use of single-arm or randomized phase II clinical trial designs; however, there is limited published objective evaluation of this issue. Purpose To objectively quantify the impact on phase III clinical trials of a policy of all single-arm versus all randomized phase II trials. Methods A simulation study was performed comparing optimal single-arm and randomized phase II trial designs with a variety of commonly used α and β error rates. Parameters modeled included: between-institution variability in the standard of care response rate, between-institution variability in the treatment effect, between-institution variability in the estimate of historical control rate (for selecting H0), presence of historical bias, and proportion of phase II trials conducted using active agents. Results Using single-arm phase II trials resulted in a higher percentage of phase III trials conducted using active agents when there was minimal standard of care activity, or in the presence of a positive historical bias (H0 estimated to be greater than truth). Randomized phase II trials performed better in the presence of a negative historical bias, in the presence of high variability, and were more consistent across variation of historical bias. The proportion of phase III trials conducted using active agents was increased by reducing the α error. Presence of historical bias and the proportion of active agents studied in phase II had the greatest influence on results. Limitations It was estimated that between 5% and 20% of agents studied in phase II trials are active; however, the conclusions could change if this estimate is incorrect. This study did not account for the possibility of a new drug application submission immediately following phase II. The primary outcome looked at was response rate, although some investigators have suggested that time-to-event outcomes should be used in phase II, particularly for randomized phase II trials. Conclusions Both single-arm and randomized phase II trials appear warranted in certain situations. Investigators should increase consideration of the potential impact on phase III trials to optimally select the proper trial design prior to phase II study implementation.
Activated protein C cofactor function of protein S: a novel role for a γ-carboxyglutamic acid residue
Authors: Ahnström Josefin , Andersson Helena M. , Canis Kevin , Norstrøm Eva , Yu Yao , Dahlbäck Björn , Panico Maria , Morris Howard R. , Crawley James T. B. , Lane David A. 
Published: April 2011

AbstractProtein S has an important anticoagulant function by acting as a cofactor for activated protein C (APC). We recently reported that the EGF1 domain residue Asp95 is critical for APC cofactor function. In the present study, we examined whether additional interaction sites within the Gla domain of protein S might contribute to its APC cofactor function. We examined 4 residues, composing the previously reported “Face1” (N33S/P35T/E36A/Y39V) variant, as single point substitutions. Of these protein S variants, protein S E36A was found to be almost completely inactive using calibrated automated thrombography. In factor Va inactivation assays, protein S E36A had 89% reduced cofactor activity compared with wild-type protein S and was almost completely inactive in factor VIIIa inactivation; phospholipid binding was, however, normal. Glu36 lies outside the ω-loop that mediates Ca2+-dependent phospholipid binding. Using mass spectrometry, it was nevertheless confirmed that Glu36 is γ-carboxylated. Our finding that Gla36 is important for APC cofactor function, but not for phospholipid binding, defines a novel function (other than Ca2+ coordination/phospholipid binding) for a Gla residue in vitamin K–dependent proteins. It also suggests that residues within the Gla and EGF1 domains of protein S act cooperatively for its APC cofactor function.
Identification of CCR9− murine plasmacytoid DC precursors with plasticity to differentiate into conventional DCs
Authors: Schlitzer Andreas , Loschko Jakob , Mair Katrin , Vogelmann Roger , Henkel Lynette , Einwächter Henrik , Schiemann Matthias , Niess Jan-Hendrik , Reindl Wolfgang , Krug Anne 
Published: April 2011

AbstractWhereas the final differentiation of conventional dendritic cells (CDCs) from committed precursors occurs locally in secondary lymphoid or peripheral tissues, plasmacytoid dendritic cells (PDCs) are thought to fully develop in the bone marrow from common DC progenitors before migrating to the periphery. In our study, we define, for the first time, a subpopulation of CCR9− major histocompatibility complex class IIlow PDCs in murine bone marrow, which express E2-2 and are immediate precursors of CCR9+ fully differentiated PDCs. However, CCR9− PDCs have the plasticity to acquire the phenotype and function of CD11b+ CD8α− major histocompatibility complex class IIhigh CDC-like cells under the influence of soluble factors produced by intestinal epithelial cells or recombinant GM-CSF. This deviation from the PDC lineage commitment is regulated on the level of transcription factors reflected by down-regulation of E2-2 and up-regulation of ID2, PU.1, and BATF3. Thus, CCR9− PDCs are immediate PDC precursors that can be reprogrammed to differentiate into CDC-like cells with higher antigen-presenting and cytokine-producing capacity under the influence of the local tissue microenvironment.
A multi gene sequence-based phylogeny of the Musaceae (banana) family
Authors: Christelová Pavla , Valárik Miroslav , Hřibová Eva , De Langhe Edmond , Doležel Jaroslav 
Published: April 2011

AbstractBackgroundThe classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes.ResultsThe 19 gene sequences represented a sample of ~16 kb of genome sequence (~73% intronic). The sequence data were also used to obtain estimates for the divergence times of the Musaceae genera andMusasections. Nucleotide variation within the sample confirmed the close relationship ofAustralimusaandCallimusasections and showed thatEumusaandRhodochlamyssections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Divergence time analysis supported the previous dating of the Musaceae crown age to the Cretaceous/Tertiary boundary (~ 69 Mya), and the evolution ofMusato ~50 Mya. The first estimates for the divergence times of the fourMusasections were also obtained.ConclusionsThe gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.
Differences in TCDD-elicited gene expression profiles in human HepG2, mouse Hepa1c1c7 and rat H4IIE hepatoma cells
Authors: Dere Edward , Lee Andrea W , Burgoon Lyle D , Zacharewski Timothy R 
Published: April 2011

Abstract

Background
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is an environmental contaminant that elicits a broad spectrum of toxic effects in a species-specific manner. Current risk assessment practices routinely extrapolate results from in vivo and in vitro rodent models to assess human risk. In order to further investigate the species-specific responses elicited by TCDD, temporal gene expression responses in human HepG2, mouse Hepa1c1c7 and rat H4IIE cells were compared.

Results
Microarray analysis identified a core set of conserved gene expression responses across species consistent with the role of AhR in mediating adaptive metabolic responses. However, significant species-specific as well as species-divergent responses were identified. Computational analysis of the regulatory regions of species-specific and -divergent responses suggests that dioxin response elements (DREs) are involved. These results are consistent with in vivo rat vs. mouse species-specific differential gene expression, and more comprehensive comparative DRE searches.

Conclusions
Comparative analysis of human HepG2, mouse Hepa1c1c7 and rat H4IIE TCDD-elicited gene expression responses is consistent with in vivo rat-mouse comparative gene expression studies, and more comprehensive comparative DRE searches, suggesting that AhR-mediated gene expression is species-specific.