bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Integrated Approach to Mid- and Upper-Level Turbulence Forecasting
Authors: Sharman R. , Tebaldi C. , Wiener G. , Wolff J. 
Published: June 2006

AbstractAn automated procedure for forecasting mid- and upper-level turbulence that affects aircraft is described. This procedure, termed the Graphical Turbulence Guidance system, uses output from numerical weather prediction model forecasts to derive many turbulence diagnostics that are combined as a weighted sum with the relative weights computed to give best agreement with the most recent available turbulence observations (i.e., pilot reports of turbulence or PIREPs). This procedure minimizes forecast errors due to uncertainties in individual turbulence diagnostics and their thresholds. Thorough statistical verification studies have been performed that focused on the probabilities of correct detections of yes and no PIREPs by the forecast algorithm. Using these statistics as a guide, the authors have been able to intercompare individual diagnostic performance, and test various diagnostic threshold and weighting strategies. The overall performance of the turbulence forecast and the effect of these strategies on performance are described.
The Use of Global and Mesoscale Meteorological Model Data to Predict the Transport and Dispersion of Tracer Plumes over Washington, D.C.
Authors: Draxler Roland R. 
Published: June 2006

Abstract
The data from a yearlong tracer dispersion experiment over Washington, D.C., in 1984 were used to evaluate Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) dispersion model calculations using coarse global meteorological reanalysis data [NCEP–NCAR and 40-Yr ECMWF Re-Analysis (ERA-40)] and calculations using meteorological data fields created by running a high-resolution meteorological model [fifth-generation Pennsylvania State University–NCAR Mesoscale Model (MM5)]. None of the meteorological models were optimized for urban environments. The dispersion calculation using the ERA-40 data showed better performance than those using the NCEP–NCAR data and comparable performance to those using MM5 data fields. Calculations with MM5 data that used shorter-period forecasts were superior to calculations that used forecast data that extended beyond 24 h. Daytime dispersion model calculations using the MM5 data showed an underprediction bias not evident in calculations using the ERA-40 data or for nighttime calculations using either meteorological dataset. It was found that small changes in the wind direction for all meteorological model data resulted in dramatic improvements in dispersion model performance. All meteorological data modeled plume directions were biased 10°–20° clockwise to the measured plume direction. This bias was greatest when using the global meteorological data. A detailed analysis of the wind observations during the November intensive, which had the greatest difference between the model and measured plume directions, showed that only the very lowest level of observed winds could account for the transport direction of the measured plume. In the Northern Hemisphere, winds tend to turn clockwise with height resulting in positive directional transport bias if the lowest-level winds are not represented in sufficient detail by the meteorological model.
DIgR2, dendritic cell-derived immunoglobulin receptor 2, is one representative of a family of IgSF inhibitory receptors and mediates negative regulation of dendritic cell-initiated antigen-specific T-cell responses
Authors: Shi Liyun , Luo Kun , Xia Dajing , Chen Taoyong , Chen Guoyou , Jiang Yingming , Li Nan , Cao Xuetao 
Published: June 2006

AbstractDendritic cells (DCs) are specialized antigen-presenting cells that play crucial roles in the initiation and regulation of immune responses. Maturation and activation of DCs are controlled by a balance of the inhibitory and activating signals transduced through distinct surface receptors. Many inhibitory receptors expressed by DCs have been identified, whereas the new members and their functions need further investigation. In this study, we functionally characterized DC-derived immunoglobulin receptor 2 (DIgR2) as a novel representative of a family of inhibitory receptors belonging to the immunoglobulin superfamily. We show that DIgR2 contains 2 immunoreceptor tyrosine-based inhibitory motifs (ITIMs) within its cytoplasmic region and that DIgR2 associates with Src homology-2 domain-containing protein tyrosine phosphatases-1 (SHP-1). Blockade of DIgR2 on DCs by pretreatment with DIgR2-Ig fusion protein or by silencing with specific small interfering RNA enhances DC-initiated T-cell proliferation and antigen-specific T-cell responses both in vitro and in vivo. Furthermore, immunization of mice with antigen-pulsed, DIgR2-silenced DCs elicits more potent antigen-specific CD4+ and CD8+ T-cell responses, thus protecting the vaccinated mice from tumor challenge more effectively. Our data suggest that DIgR2 is a functionally inhibitory receptor and can mediate negative signaling to regulate DC-initiated antigen-specific T-cell responses.
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
Authors: Petřek Martin , Otyepka Michal , Banáš Pavel , Košinová Pavlína , Koča Jaroslav , Damborský Jiří 
Published: June 2006

AbstractBackgroundThe main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.ResultsThe algorithm to perform a skeleton search was based on a reciprocal distance function grid that was developed and implemented for the CAVER program. The program identifies and visualizes routes from the interior of the protein to the bulk solvent. CAVER was primarily developed for proteins, but the algorithm is sufficiently robust to allow the analysis of any molecular system, including nucleic acids or inorganic material. Calculations can be performed using discrete structures from crystallographic analysis and NMR experiments as well as with trajectories from molecular dynamics simulations. The fully functional program is available as a stand-alone version and as plug-in for the molecular modeling program PyMol. Additionally, selected functions are accessible in an online version.ConclusionThe algorithm developed automatically finds the path from a starting point located within the interior of a protein. The algorithm is sufficiently rapid and robust to enable routine analysis of molecular dynamics trajectories containing thousands of snapshots. The algorithm is based on reciprocal metrics and provides an easy method to find a centerline, i.e. the spine, of complicated objects such as a protein tunnel. It can also be applied to many other molecules. CAVER is freely available from the web sitehttp://loschmidt.chemi.muni.cz/caver/.
PSMIX: an R package for population structure inference via maximum likelihood method
Authors: Wu Baolin , Liu Nianjun , Zhao Hongyu 
Published: June 2006

AbstractBackgroundInference of population stratification and individual admixture from genetic markers is an integrative part of a study in diverse situations, such as association mapping and evolutionary studies. Bayesian methods have been proposed for population stratification and admixture inference using multilocus genotypes and widely used in practice. However, these Bayesian methods demand intensive computation resources and may run into convergence problem in Markov Chain Monte Carlo based posterior samplings.ResultsWe have developed PSMIX, an R package based on maximum likelihood method using expectation-maximization algorithm, for inference of population stratification and individual admixture.ConclusionCompared with software based on Bayesian methods (e.g., STRUCTURE), PSMIX has similar accuracy, but more efficient computations.PSMIX and its supplemental documents are freely available athttp://bioinformatics.med.yale.edu/PSMIX.
Differentiated evolutionary rates in alternative exons and the implications for splicing regulation
Authors: Plass Mireya , Eyras Eduardo 
Published: June 2006

Abstract

Background
Alternatively spliced exons play an important role in the diversification of gene function in most metazoans and are highly regulated by conserved motifs in exons and introns. Two contradicting properties have been associated to evolutionary conserved alternative exons: higher sequence conservation and higher rate of non-synonymous substitutions, relative to constitutive exons. In order to clarify this issue, we have performed an analysis of the evolution of alternative and constitutive exons, using a large set of protein coding exons conserved between human and mouse and taking into account the conservation of the transcript exonic structure. Further, we have also defined a measure of the variation of the arrangement of exonic splicing enhancers (ESE-conservation score) to study the evolution of splicing regulatory sequences. We have used this measure to correlate the changes in the arrangement of ESEs with the divergence of exon and intron sequences.

Results
We find evidence for a relation between the lack of conservation of the exonic structure and the weakening of the sequence evolutionary constraints in alternative and constitutive exons. Exons in transcripts with non-conserved exonic structures have higher synonymous (dS) and non-synonymous (dN) substitution rates than exons in conserved structures. Moreover, alternative exons in transcripts with non-conserved exonic structure are the least constrained in sequence evolution, and at high EST-inclusion levels they are found to be very similar to constitutive exons, whereas alternative exons in transcripts with conserved exonic structure have a dS significantly lower than average at all EST-inclusion levels. We also find higher conservation in the arrangement of ESEs in constitutive exons compared to alternative ones. Additionally, the sequence conservation at flanking introns remains constant for constitutive exons at all ESE-conservation values, but increases for alternative exons at high ESE-conservation values.

Conclusion
We conclude that most of the differences in dN observed between alternative and constitutive exons can be explained by the conservation of the transcript exonic structure. Low dS values are more characteristic of alternative exons with conserved exonic structure, but not of those with non-conserved exonic structure. Additionally, constitutive exons are characterized by a higher conservation in the arrangement of ESEs, and alternative exons with an ESE-conservation similar to that of constitutive exons are characterized by a conservation of the flanking intron sequences higher than average, indicating the presence of more intronic regulatory signals.
PHOG: a database of supergenomes built from proteome complements
Authors: Merkeev Igor V , Novichkov Pavel S , Mironov Andrey A 
Published: June 2006

Abstract

Background
Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships are often based on manual revision of clusters of orthologous groups and/or lack any rigorous evolutionary base.

Description
We developed a completely automated procedure that creates clusters of orthologous groups at each node of the taxonomy tree (PHOGs – Phylogenetic Orthologous Groups). As a result of this procedure, a tree of orthologous groups was obtained. Each cluster is a "supergene" and it is represented by an "ancestral" sequence obtained from the multiple alignment of orthologous and paralogous genes.
The procedure has been applied to the taxonomy tree of organisms from all three domains of life. Protein complements from 50 bacterial, archaeal and eukaryotic species were used to create PHOGs at all tree nodes. 51367 PHOGs were obtained at the root node.

Conclusion
The PHOG database demonstrates that it is possible to automatically process any number of sequenced genomes and to reconstruct orthologous and paralogous relationships between genomes using a rigorous evolutionary approach. This database can become a very useful tool in various areas of comparative genomics.
Does a preceding hand wash and drying time after surgical hand disinfection influence the efficacy of a propanol-based hand rub?
Authors: Hübner Nils-Olaf , Kampf Günter , Kamp Philipp , Kohlmann Thomas , Kramer Axel 
Published: June 2006

Abstract

Background
Recently, a propanol-based hand rub has been described to exceed the efficacy requirements of the European standard EN 12791 in only 1.5 min significantly. But the effect of a 1 min preceding hand wash and the effect of one additional minute for evaporation of the alcohol after its application on the efficacy after a 1.5 min application time has never been studied.

Methods
We have investigated a propanol-based hand rub (Sterillium®, based on 45% propan-2-ol, 30% propan-1-ol and 0.2% mecetronium etilsulfate) in three variations: with (A) and without (B) a 1 min hand wash before the disinfection of 1.5 min with immediate sampling after the disinfection; and (C) without a hand wash before the disinfection but with sampling 1 min after the disinfection. The efficacy of the three variations was compared to the reference treatment of EN 12791. All experiments were performed in a Latin-square design with 20 volunteers. Pre- and post-values (immediate and after 3 hr) were obtained according to EN 12791.

Results
The 3 min reference disinfection reduced resident hand bacteria on average by 1.8 log10 steps (immediate effect) and 1.4 log10-steps (sustained effect) respectively. Method A was equally effective as the reference (immediate efficacy: 1.5 log10-steps; sustained efficacy: 1.6 log10-steps). Method B seemed to be more effective (immediate efficacy: 2.3 log10-steps; sustained efficacy: 1.7 log10-steps). Method C revealed the best efficacy (immediate efficacy: 2.3 log10-steps; sustained efficacy: 2.0 log10-steps). A comparison of all three treatment variations and the reference treatment revealed a significant difference for the immediate efficacy (p = 0.026; Friedman test), but not for the sustained efficacy (p = 0.430). A post-hoc-test for the immediate efficacy indicated a significant difference between methods A and C (p < 0.05; Wilcoxon-Wilcox test). Hence, none of the treatment variations was significantly less effective than the reference treatment.

Conclusion
An application of the propanol-based hand rub for 1.5 min after 1 min hand wash fulfills the efficacy requirements of EN 12791. The efficacy can be improved to some extent by omitting the preceding hand wash and by awaiting the evaporation of the alcohol which is clinical practice anyway. The preceding hand wash has the most negative effect on the immediate effect. Based on our data hands should not be routinely washed before the disinfection period unless there is a good reason for it such as visible soiling.
Insulin-like growth factor-1 (IGF-1) induces the activation/phosphorylation of Akt kinase and cAMP response element-binding protein (CREB) by activating different signaling pathways in PC12 cells
Authors: Zheng Wen-Hua , Quirion Rémi 
Published: June 2006

AbstractBackgroundInsulin-like growth factor-1 (IGF-1) is a polypeptide growth factor with a variety of functions in both neuronal and non-neuronal cells. IGF-1 plays anti-apoptotic and other functions by activating multiple signaling pathways including Akt kinase, a serine/threonine kinase essential for cell survival. The nuclear transcription factor cAMP response element-binding protein (CREB) may also be involved although relationships between these two proteins in IGF-1 receptor signaling and protection is not clear, especially in neuronal cells.ResultsIGF-1, in a concentration- and time-dependent manner, induces the activation/phosphorylation of Akt and CREB in PC12 cells by activating different signaling pathways. IGF-1 induced a sustained phosphorylation of Akt while only a transient one was seen for CREB. The phosphorylation of Akt is mediated by the PI3 kinase pathway while that of CREB is dependent on the activation of both MAPK kinase and p38 MAPK. Moreover, the stimulation of PKC attenuated the phosphorylation of Akt induced by IGF-1 while enhancing that of CREB. Survival assays with various kinase inhibitors suggested that the activation/phosphorylation of both Akt and CREB contributes to IGF-1 mediated cell survival in PC12 cells.ConclusionThese data suggest that IGF-1 induced the activation of Akt and CREB using distinct pathways in PC12 cells.
Endothelial progenitor cells display clonal restriction in multiple myeloma
Authors: Braunstein Marc , Özçelik Tayfun , Bağişlar Sevgi , Vakil Varsha , Smith Eric LP , Dai Kezhi , Akyerli Cemaliye B , Batuman Olcay A 
Published: June 2006

Abstract

Background
In multiple myeloma (MM), increased neoangiogenesis contributes to tumor growth and disease progression. Increased levels of endothelial progenitor cells (EPCs) contribute to neoangiogenesis in MM, and, importantly, covary with disease activity and response to treatment. In order to understand the mechanisms responsible for increased EPC levels and neoangiogenic function in MM, we investigated whether these cells were clonal by determining X-chromosome inactivation (XCI) patterns in female patients by a human androgen receptor assay (HUMARA). In addition, EPCs and bone marrow cells were studied for the presence of clonotypic immunoglobulin heavy-chain (IGH) gene rearrangement, which indicates clonality in B cells; thus, its presence in EPCs would indicate a close genetic link between tumor cells in MM and endothelial cells that provide tumor neovascularization.

Methods
A total of twenty-three consecutive patients who had not received chemotherapy were studied. Screening in 18 patients found that 11 displayed allelic AR in peripheral blood mononuclear cells, and these patients were further studied for XCI patterns in EPCs and hair root cells by HUMARA. In 2 patients whose EPCs were clonal by HUMARA, and in an additional 5 new patients, EPCs were studied for IGH gene rearrangement using PCR with family-specific primers for IGH variable genes (VH).

Results
In 11 patients, analysis of EPCs by HUMARA revealed significant skewing (≥ 77% expression of a single allele) in 64% (n = 7). In 4 of these patients, XCI skewing was extreme (≥ 90% expression of a single allele). In contrast, XCI in hair root cells was random. Furthermore, PCR amplification with VH primers resulted in amplification of the same product in EPCs and bone marrow cells in 71% (n = 5) of 7 patients, while no IGH rearrangement was found in EPCs from healthy controls. In addition, in patients with XCI skewing in EPCs, advanced age was associated with poorer clinical status, unlike patients whose EPCs had random XCI.

Conclusion
Our results suggest that EPCs in at least a substantial subpopulation of MM patients are related to the neoplastic clone and that this is an important mechanism for upregulation of tumor neovascularization in MM.
Histological response of peritoneal carcinomatosis after hyperthermic intraperitoneal chemoperfusion (HIPEC) in experimental investigations
Authors: Pelz Joerg OW , Doerfer J , Dimmler A , Hohenberger W , Meyer T 
Published: June 2006

Abstract

Background
In selected patients with peritoneal carcinomatosis from colorectal cancer prognosis can be improved by hyperthermic intraperitoneal chemotherapy (HIPEC) after cytoreductive surgery. The aim of this study was to evaluate the tumor response of peritoneal carcinomatosis in tumor-bearing rats treated with HIPEC.

Methods
CC531 colon carcinoma (2,5 × 106 cells), implanted intraperitoneally in Wag/Rija rats, was treated by hyperthermic intraperitoneal chemotherapy. After 10 days of tumor growth the animals were randomized into five groups of six animals each: group I: control (n = 6), group II: sham operated animals (n = 6), group III: hyperthermic intraperitoneal perfusion (HIP) without cytostatic drugs, group IV: HIPEC with mitomycin C in a concentration of 15 mg/m2 (n = 6), group V: mitomycin C i.p. alone in a concentration of 10 mg/m2 (n = 6). After 10 days the extent of tumor spread and histological outcome were analysed by autopsy.

Results
All control animals developed extensive intraperitoneal tumor growth. Histological tumor load was significantly reduced in group III and group V and was lowest in group IV. In group II tumor load was significantly higher than in group I. Implanted metastases were significantly decreased in group IV compared with group I and group II.

Conclusion
These findings indicate that HIPEC is an effective treatment for peritoneal carcinomatosis in this animal model. HIPEC reduced macroscopic and microscopic intraperitoneal tumor spread.
The prevalence of pseudoexfoliation syndrome in Pakistan. Hospital based study
Authors: Rao Rashad Qamar , Arain Tariq Mehmood , Ahad Muhammad Ali 
Published: June 2006

Abstract

Background
Pseudoexfoliation syndrome (PXS) is the most common identifiable cause of secondary glaucoma, the prevalence of which varies considerably among different ethnicities. The aim of this study was to assess the prevalence of pseudoexfoliation syndrome in Pakistan.

Methods
A prospective study conducted in the period from January 2003 to June 2004 in a teaching hospital serving a population of about 7.6 million. 1860 patients aged 45 or above attending the general ophthalmic clinics were recruited for this study. A detailed evaluation including ophthalmic and general history, slit lamp biomicroscopy, intraocular pressure measurement, gonioscopy and dilated eye examination was performed on all patients.

Results
120(6.45%) subjects were found to have PXS with a male to female ratio of 1.5:1. All 120 (100%) cases were bilateral and 48(40%) patients had high intraocular pressure.

Conclusion
To the best of our knowledge, this is the first study conducted in a Pakistani population to determine the prevalence of PXS. The prevalence rate of 6.45% is similar to other studies conducted in south Asia, however all cases were bilateral and quite a high percentage of patients had high intra-ocular pressure.
In planta production of two peptides of the Classical Swine Fever Virus (CSFV) E2 glycoprotein fused to the coat protein of potato virus X
Authors: Marconi Gianpiero , Albertini Emidio , Barone Pierluigi , De Marchis Francesca , Lico Chiara , Marusic Carla , Rutili Domenico , Veronesi Fabio , Porceddu Andrea 
Published: June 2006

Abstract

Background
Classical Swine Fever (CSFV) is one of the most important viral infectious diseases affecting wild boars and domestic pigs. The etiological agent of the disease is the CSF virus, a single stranded RNA virus belonging to the family Flaviviridae.
All preventive measures in domestic pigs have been focused in interrupting the chain of infection and in avoiding the spread of CSFV within wild boars as well as interrupting transmission from wild boars to domestic pigs. The use of plant based vaccine against CSFV would be advantageous as plant organs can be distributed without the need of particular treatments such as refrigeration and therefore large areas, populated by wild animals, could be easily covered.

Results
We report the in planta production of peptides of the classical swine fever (CSF) E2 glycoprotein fused to the coat protein of potato virus X. RT-PCR studies demonstrated that the peptide encoding sequences are correctly retained in the PVX construct after three sequential passage in Nicotiana benthamiana plants. Sequence analysis of RT-PCR products confirmed that the epitope coding sequences are replicated with high fidelity during PVX infection. Partially purified virions were able to induce an immune response in rabbits.

Conclusion
Previous reports have demonstrated that E2 synthetic peptides can efficiently induce an immunoprotective response in immunogenized animals. In this work we have showed that E2 peptides can be expressed in planta by using a modified PVX vector. These results are particularly promising for designing strategies for disease containment in areas inhabited by wild boars.