bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Break in the Mongolian Rainy Season and Its Relation to the Stationary Rossby Wave along the Asian Jet
Authors: Iwasaki Hiroyuki , Nii Tomomi 
Published: July 2006

Abstract
Seasonal and interannual variation of rainfall over Mongolia was investigated using 10-day rainfall data from 92 stations during 1993–2001 and NCEP–NCAR reanalysis data from 1979 to 2001. The break in the rainy season was found in the middle of July, and the meteorological stations with a clear break period were concentrated in eastern Mongolia where the plain prevails relative to western Mongolia without regard to the difference in annual precipitation.
Clear breaks in the rainy season were recognized in 5 yr among an analysis period of 9 yr. In the break period, the stationary Rossby wave trapped in the Asian jet was predominant at 200 hPa, and a barotropic ridge associated with the Rossby wave developed over Mongolia. Furthermore, interannual variation of the break also corresponded to the variation of the stationary Rossby wave. It is considered that the break of the Mongolian rainy season is caused by the stationary Rossby wave trapped in the Asian jet. The stationary Rossby wave was climatologically phase locked in seasonal evolution and, as a result, the break period was also concentrated around the middle of July.
DenseSLAM: Simultaneous Localization and Dense Mapping
Authors: Nieto Juan , Guivant Jose , Nebot Eduardo 
Published: July 2006

This paper addresses the problem of environment representation for Simultaneous Localization and Mapping (SLAM) algorithms. One of the main problems of SLAM is how to interpret and synthesize the external sensory information into a representation of the environment that can be used by the mobile robot to operate autonomously. Traditionally, SLAM algorithms have relied on sparse environment representations. However, for autonomous navigation, a more detailed representation of the environment is necessary, and the classic feature-based representation fails to provide a robot with sufficient information. While a dense representation is desirable, it has not been possible for SLAM paradigms. This paper presents DenseSLAM, an algorithm to obtain and maintain detailed environment representations. The algorithm represents different sensory information in dense multi-layered maps. Each layer can represent different properties of the environment, such as occupancy, traversability, elevation or each layer can describe the same environment property using different representations. Implementations of the algorithm with two different representations for the dense maps are shown. A rich representation has several potential advantages to assist the navigation process, for example to facilitate data association using multi-dimensional maps. This paper presents two particular applications to improve the localization process; the extraction of complex landmarks from the dense maps and the detection of areas with dynamic objects. The paper also presents an analysis of consistency of the maps obtained with DenseSLAM. The position error in the dense maps is analyzed and a method to select the landmarks in order to minimize these errors is explained. The algorithm was tested with outdoor experimental data taken with a ground vehicle. The experimental results show that the algorithm can obtain dense environment representations and that the detailed representation can be used to improve the vehicle localization process.
Stability of Phase-Based Gain Modulation with Designer-Chosen Switch Functions
Authors: Armstrong Brian S. R. , Gutierrez José A. , Wade Bruce A. , Joseph Ralph 
Published: July 2006

Phase-Based Gain-Modulation (PBGM) control is realized by modulating controller gains in response to the phase of the system state or tracking error. PBGM controllers have been applied to robotic hands, parallel manipulators and flexible mechanisms to give increased damping, reduced tracking error and friction compensation. A novel method is presented to establish Lyapunov stability for PBGM control. Prior PBGM stability results incorporated a constraint which limited the range of provably stable systems. The present result removes this constraint, establishing Lyapunov stability for a substantially broader class of systems. Additionally, the new approach decouples the selection of the Lyapunov function from the controller design, permitting the controls designer to independently specify a switch function which determines the application of gain modulation. The present results are applied to analyze PBGM control of the Sarcos dextrous manipulator, illuminating the stability properties of control experiments previously reported in the literature. Numerical methods for design calculations are also presented.
Action of chelators in iron-loaded cardiac cells: accessibility to intracellular labile iron and functional consequences
Authors: Glickstein Hava , El Rinat Ben , Link Gabi , Breuer William , Konijn Abraham M. , Hershko Chaim , Nick Hanspeter , Cabantchik Z. Ioav 
Published: July 2006

AbstractLabile iron in hemosiderotic plasma and tissue are sources of iron toxicity. We compared the iron chelators deferoxamine, deferiprone, and deferasirox as scavengers of labile iron in plasma and cardiomyocytes at therapeutic concentrations. This comprised chelation of labile plasma iron (LPI) in samples from thalassemia patients; extraction of total cellular iron; accessing labile iron accumulated in organelles and preventing formation of reactive-oxidant species; and restoring impaired cardiac contractility. Neonatal rat cardiomyocytes were used for monitoring chelator extraction of LCI (labile cell iron) as 59Fe; assessing in situ cell iron chelation by epifluorescence microscope imaging using novel fluorescent sensors for iron and reactive oxygen species (ROS) selectively targeted to organelles, and monitoring contractility by time-lapse microscopy. At plasma concentrations attained therapeutically, all 3 chelators eliminated LPI but the orally active chelators rapidly gained access to the LCI pools of cardiomyocytes, bound labile iron, attenuated ROS formation, extracted accumulated iron, and restored contractility impaired by iron overload. The effect of deferoxamine at therapeutically relevant concentrations was primarily by elimination of LPI. The rapid accessibility of the oral chelators deferasirox and deferiprone to intracellular labile iron compartments renders them potentially efficacious for protection from and possibly reversal of cardiac damage induced by iron overload.
STAT5 acts as a repressor to regulate early embryonic erythropoiesis
Authors: Schmerer Matthew , Torregroza Ingrid , Pascal Aude , Umbhauer Muriel , Evans Todd 
Published: July 2006

AbstractSTAT5 regulates definitive (adult stage) erythropoiesis through its ability to transduce signals from the erythropoietin receptor. A function for STAT-dependent signaling during primitive (embryonic) erythropoiesis has not been analyzed. We tested this in the Xenopus system, because STAT5 is expressed at the right time and place to regulate development of the embryonic primitive ventral blood island. Depletion of STAT5 activity results in delayed accumulation of the first globinexpressing cells, indicating that the gene does regulate primitive erythropoiesis. Our results suggest that in this context STAT5 functions as a repressor, since forced expression of an activator isoform blocks erythropoiesis, while embryos expressing a repressor isoform develop normally. The erythroid phenotype caused by the activator isoform of STAT5 resembles that caused by overexpression of fibroblast growth factor (FGF). We show that STAT5 isoforms can function epistatic to FGF and can be phosphorylated in response to hyperactivated FGF signaling in Xenopus embryos. Therefore, our data indicate that STAT5 functions in both primitive and definitive erythropoiesis, but by different mechanisms.
Blockade of αvβ3 and αvβ5 integrins by RGD mimetics induces anoikis and not integrin-mediated death in human endothelial cells
Authors: Maubant Sylvie , Saint-Dizier Dominique , Boutillon Morgane , Perron-Sierra Francoise , Casara Patrick J. , Hickman John A. , Tucker Gordon C. , Van Obberghen-Schilling Ellen 
Published: July 2006

Abstract
αv integrins are thought to play an important role in tumor angiogenesis. However, discrepancies between findings with Arg-Gly-Asp (RGD) mimetics, which block angiogenesis in animal models, and knockout mice, in which loss of some αv integrins enhances tumor angiogenesis, raise questions concerning the function of these integrins and the precise role of αv substrate mimetics in antiangiogenic therapies. We have examined the effects of a novel non–peptide RGD mimetic, S 36578-2, on human endothelial cells to elucidate its antagonist activity and to identify possible agonist functions. S 36578-2 is highly selective for αvβ3 and αvβ5 integrins and induces detachment, caspase-8 activation, and apoptosis in human umbilical endothelial cells (HUVECs) plated on vitronectin. Importantly, the compound has no effect on the morphology or survival of cells plated on interstitial matrix components such as fibronectin, and it does not potentiate the apoptotic process in suspended cells. Identical results were obtained with a cyclic RGD peptide with similar target specificity. In microvascular endothelial cells, S 36578-2–induced death was also linked to its antiadhesive effect, with established lines markedly more resistant than primary cultures to the antiadhesive and proapoptotic effects. Altogether, these findings have important implications for the development of this class of antiangiogenics.
Interleukin-6 induces hepcidin expression through STAT3
Authors: Wrighting Diedra M. , Andrews Nancy C. 
Published: July 2006

AbstractIron homeostasis is maintained through meticulous regulation of circulating hepcidin levels. Hepcidin levels that are inappropriately low or high result in iron overload or iron deficiency, respectively. Although hypoxia, erythroid demand, iron, and inflammation are all known to influence hepcidin expression, the mechanisms responsible are not well defined. In this report we show that the inflammatory cytokine interleukin-6 (IL-6) directly regulates hepcidin through induction and subsequent promoter binding of signal transducer and activator of transcription 3 (STAT3). STAT3 is necessary and sufficient for the IL-6 responsiveness of the hepcidin promoter. Our findings provide a mechanism by which hepcidin can be regulated by inflammation or, in the absence of inflammatory stimuli, by alternative mechanisms leading to STAT3 activation.
Tools for integrated sequence-structure analysis with UCSF Chimera
Authors: Meng Elaine C , Pettersen Eric F , Couch Gregory S , Huang Conrad C , Ferrin Thomas E 
Published: July 2006

Abstract

Background
Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a) provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b) facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit); (c) can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d) interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals.

Results
The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided.

Conclusion
The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is available for Microsoft Windows, Apple Mac OS X, Linux, and other platforms from http://www.cgl.ucsf.edu/chimera.
Similarities and differences of polyadenylation signals in human and fly
Authors: Retelska Dorota , Iseli Christian , Bucher Philipp , Jongeneel C Victor , Naef Felix 
Published: July 2006

Abstract

Background
Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage site containing a motif with consensus AAUAAA, followed by a U or UG rich region downstream of the cleavage site.

Results
We studied these signals using exhaustive databases of cleavage sites obtained from aligning raw expressed sequence tags (EST) sequences to genomic sequences in Homo sapiens and Drosophila melanogaster. These data show that the polyadenylation signal is highly conserved in human and fly. In addition, de novo motif searches generated a refined description of the U-rich downstream sequence (DSE) element, which shows more divergence between the two species. These refined motifs are applied, within a Hidden Markov Model (HMM) framework, to predict mRNA cleavage sites.

Conclusion
We demonstrate that the DSE is a specific motif in both human and Drosophila. These findings shed light on the sequence correlates of a highly conserved biological process, and improve in silico prediction of 3' mRNA cleavage and polyadenylation sites.
A novel flow cytometric assay for measurement of In Vivo pulmonary neutrophil phagocytosis
Authors: Vander Top Elizabeth A , Perry Greg A , Gentry-Nielsen Martha J 
Published: July 2006

Abstract

Background
Phagocytosis assays are traditionally performed in vitro using polymorphonuclear leukocytes (PMNs) isolated from peripheral blood or the peritoneum and heat-killed, pre-opsonized organisms. These assays may not adequately mimic the environment within the infected lung. Our laboratory therefore has developed a flow cytometric in vivo phagocytosis assay that enables quantification of PMN phagocytosis of viable bacteria within the lungs of rats. In these studies, rats are injected transtracheally with lipopolysaccharide (LPS) to recruit PMNs to their lungs. They are then infected with live 5(-and 6) carboxyfluorescein diacetate succinimidyl ester (CFDA/SE) labeled type 3 Streptococcus pneumoniae. Bronchoalveolar lavage is performed and resident alveolar macrophages and recruited PMNs are labeled with monoclonal antibodies specific for surface epitopes on each cell type. Three color flow cytometry is utilized to identify the cell types, quantify recruitment, and determine uptake of the labeled bacteria.

Results
The viability of the alveolar macrophages and PMNs isolated from the lavage fluid was >95%. The values of the percentage of PMNs in the lavage fluid as well as the percentage of PMNs associated with CFSE-labeled S. pneumoniae as measured through flow cytometry showed a high degree of correlation with the results from manual counting of cytospin slides.

Conclusion
This assay is suitable for measuring bacterial uptake within the infected lung. It can be adapted for use with other organisms and/or animal model systems.
Immunochemical characterization of polysaccharide antigens from six clinical strains of Enterococci
Authors: Hsu Carolyn T , Ganong Amanda L , Reinap Barbara , Mourelatos Zafiria , Huebner Johannes , Wang Julia Y 
Published: July 2006

Abstract

Background
Enterococci have become major nosocomial pathogens due to their intrinsic and acquired resistance to a broad spectrum of antibiotics. Their increasing drug resistance prompts us to search for prominent antigens to develop vaccines against enterococci. Given the success of polysaccharide-based vaccines against various bacterial pathogens, we isolated and characterized the immunochemical properties of polysaccharide antigens from five strains of Enterococcus faecalis and one strain of vancomycin-resistant E. faecium.

Results
We cultured large batches of each strain, isolated sufficient quantities of polysaccharides, analyzed their chemical structures, and compared their antigenic specificity. Three classes of polysaccharides were isolated from each strain, including a polyglucan, a teichoic acid, and a heteroglycan composed of rhamnose, glucose, galactose, mannosamine, and glucosamine. The polyglucans from all six strains are identical and appear to be dextran. Yields of the teichoic acids were generally low. The most abundant polysaccharides are the heteroglycans. The six heteroglycans are structurally different as evidenced by NMR spectroscopy. They also differ in their antigenic specificities as revealed by competitive ELISA. The heteroglycans are not immunogenic by themselves but conjugation to protein carriers significantly enhanced their ability to induce antibodies.

Conclusion
The six clinical strains of enterococci express abundant, strain-specific cell-surface heteroglycans. These polysaccharides may provide a molecular basis for serological typing of enterococcal strains and antigens for the development of vaccines against multi-drug resistant enterococci.
Carcinosarcoma of the colon: report of a case with morphological, ultrastructural and molecular analysis
Authors: Ambrosini-Spaltro Andrea , Vaira Valentina , Braidotti Paola , Rovati Marco PL , Ferrero Stefano , Bosari Silvano 
Published: July 2006

Abstract

Background
Carcinosarcoma of the colon is a rare histopathological entity with uncertain histogenesis, that shows both epithelial and mesenchymal malignant differentiation. Carcinosarcoma rarely affects the gastrointestinal tract and only few cases are reported in the colon. Herein we describe a carcinosarcoma of the ascending colon, with morphological, ultrastructural and molecular analysis.

Case presentation
An 81-year-old man was hospitalised for asthenia, weight loss and iron-deficiency anaemia. The patient underwent colonoscopy and adenocarcinoma was diagnosed by endoscopic biopsy. A right hemicolectomy was performed and, during surgical operation, liver metastases were detected. Histological examination of the surgical specimen revealed areas of both carcinomatous and sarcomatous differentiation, completely separated by fibrous septae. The sarcomatous component exhibited areas of smooth muscle and osteoblastic differentiation, with focal osteoid material deposition. Molecular analysis conducted separately on the epithelial and mesenchymal components revealed the same p53 gene mutation (R282W in exon 8) and identical polymorphisms in p53 exon 4, in EGFR exons 20 and 21, and in c-kit exon 17. Microsatellite markers analysis revealed a common loss of heterozygosis on 18q. Overall, the data are consistent with a common origin of the two tumor components. The patient was treated with 8 cycles of oral capecitabine (1250 mg/m2 twice a day for 14 days repeated every 28 days) and two years after surgery is alive with liver metastases.

Conclusion
Carcinosarcoma of the colon is a rare tumour with both epithelial and sarcomatous components. Molecular analysis of the current case suggests the histogenesis from a common cell progenitor.
Defining a common set of indicators to monitor road accidents in the European Union
Authors: Farchi Sara , Molino Nunzio , Giorgi Rossi Paolo , Borgia Piero , Krzyzanowski Michael , Dalbokova Dafina , Kim Rokho ,   the European Road Accident Indicator Working Group
Published: July 2006

Abstract

Background
currently road accidents are mostly monitored through mortality and injury rates. This paper reports the methodology and the results of a project set forth by the European Union (EU) and coordinated by the WHO aimed at identifying and evaluating a core set of indicators to monitor the causal chain of road accident health effects. The project is part of the ECOEHIS (Development of Environment and Health Indicators for European Union Countries).

Methods
a group of experts (WG), identified 14 indicators after a review of the information collected at the EU level, each of them representing a specific aspect of the DPSEEA (Driving, Pressure, State, Exposure, Effect, Action) model applied and adapted to the road accidents.
Each indicator was scored according to a list of 16 criteria chosen by the WG. Those found to have a high score were analysed to determine if they were compatible with EU legislation and then tested in the feasibility study.

Results
11 of the 14 indicators found to be relevant and compatible with the criteria of selection were proposed for the feasibility study. Mortality, injury, road accident rate, age of vehicle fleet, and distance travelled are the indicators recommended for immediate implementation.

Conclusion
after overcoming the limitations that emerged (absence of a common definition of death by road accident and injury severity, underestimation of injuries, differences in information quality) this core set of indicators will allow Member States to carry out effective internal/external comparisons over time.