bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the Value of Radar Rainfall Nowcasts in Flood Forecasting and Warning in Flashy Catchments
Authors: Werner Micha , Cranston Michael 
Published: February 2009

AbstractProviding flood forecasts in flashy catchments poses significant challenges to the hydrologist. This is particularly the case when the prediction of high intensity rainfall at small spatial scales is difficult. Radar rainfall nowcasts, such as those provided by the Met Office Nimrod system, provide short range predictions at these spatial scales, and can be used as an input to hydrological models for the prediction of flood flows. Such short term forecasts are, however, considerably uncertain, and this uncertainty will influence the reliability of hydrological forecasts used in flood warning and forecasting. In this paper the value and benefit of the use of radar rainfall nowcasts in three small catchments in central Scotland is assessed through the evaluation of a large sample of forecasts. Both the reliability of the catchment rainfall predictions and the forecast flows are assessed. Whilst it is demonstrated that the rainfall predictions provided by Nimrod are uncertain and at times biased, it is also shown that there is considerable benefit in their use for flood forecasting when compared to the alternative of using no future prediction of rainfall. To deal with the uncertainty in the forecast, a method is shown that can help the hydrologist and forecaster to understand the structure of the uncertainties, allowing them to use the guidance provided by the forecasts more effectively in the provision of flood warnings. Copyright © 2009 Royal Meteorological Society
New developments in the spatial encoding of spin interactions for single‐scan 2D NMR
Authors: Shrot Yoav , Tal Assaf , Frydman Lucio 
Published: February 2009

AbstractSingle‐scan 2D NMR relies on a spatial axis for encoding the indirect‐domain internal spin interactions. Various strategies have been demonstrated for fulfilling the needs underlying this procedure. All such schemes use gradient‐echoed sequences that leave at their conclusion solely the effects of the internal interactions along the indirect domain; they also include a real‐time scheme that though simple, yields in general mixed‐phase line shapes. The present paper introduces two new proposals geared up for easing the spatial encoding underlying single‐scan 2D NMR methodologies. One of these is capable of delivering dispersive‐free peaks along the indirect domain, and thereby purely‐absorptive 2D line shapes, in amplitude‐encoded experiments. The other demonstrates for the first time, the possibility to obtain single‐scan 2D spectra without echoing the effects of the encoding gradient–simply by applying a single‐pulse frequency sweep to encode the interactions. Both of these modes are compatible with homo‐ and heteronuclear correlations, and exhibit a number of complementary features vis‐à‐vis encoding alternatives that have so far been presented. The overall principles underlying these new spatially encoding protocols are derived, and their performance demonstrated with single‐scan 2D NMR TOCSY and HSQC experiments on model compounds. Copyright © 2009 John Wiley & Sons, Ltd.
Regional pulmonary blood flow: Comparison of dynamic contrast‐enhanced MR perfusion and phase‐contrast MR
Authors: van Amerom Joshua F.P. , Vidarsson Logi , Wu Shengping , Tessler Rogerio , Yoo Shi‐Joon , Belik Jaques , Macgowan Christopher K. 
Published: February 2009

AbstractRegional pulmonary blood flow can be assessed using both dynamic contrast‐enhanced (DCE) MR and phase‐contrast (PC) MR. These methods provide somewhat complementary information: DCE MR can assess flow over the entire lung while PC MR can detect rapid changes in flow to a targeted region. Although both methods are considered accurate, one may be more feasible than the other depending on pathology, patient condition, and availability of an intravenous route. The objective of this study was to establish a consensus between the two methods by comparing paired DCE MR and PC MR measurements of relative blood flow in Yorkshire piglets (N = 5, age = 7 days, weight = 3.3 ± 0.6 kg) under various physiological states including regional lung collapse. A strong correlation (R2 = 0.71, P < 0.01) was observed between the methods. In conclusion, DCE MR and PC MR provide a consistent measure of changes in regional pulmonary blood flow. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
In vivo 31P magnetic resonance spectroscopy using a needle microcoil
Authors: Howe Franklyn A. , Syms Richard R.A. , Ahmad Munir M. , Rodrigues Loreta M. , Griffiths John R. , Young Ian R. 
Published: February 2009

AbstractBatch fabrication methods have been used to produce low‐cost microcoils for magnetic resonance spectroscopy (MRS) that could be discarded after applications such as insertion into tissue during interventional surgery. Needle‐shaped microcoils were constructed using electroplated conductors buried in shafts formed with different combinations of silicon and plastic and used to acquire in vivo 31P spectra of rat thigh muscle at 81 MHz. The designs in this study achieved a maximum signal‐to‐noise ratio (SNR) for phosphocreatine (PCr) of 10.4 in a 10‐min acquisition, with the three adenosine triphosphate (ATP) multiplets also clearly visible. An average 20% reduction in PCr occurred over a 60‐min period, and intracellular pH was estimated to be 6.6, which are both evidence of ischemia. A needle microcoil design could have applications in real‐time MRS of tumors or in evaluating pathology in general during surgical investigations. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Three‐dimensional, in vivo MRI with self‐gating and image coregistration in the mouse
Authors: Nieman Brian J. , Szulc Kamila U. , Turnbull Daniel H. 
Published: February 2009

AbstractMotion during magnetic resonance imaging (MRI) scans routinely results in undesirable image artifact or blurring. Since high‐resolution, three‐dimensional (3D) imaging of the mouse requires long scan times for satisfactory signal‐to‐noise ratio (SNR) and image quality, motion‐related artifacts are likely over much of the body and limit applications of mouse MRI. In this investigation, we explored the use of self‐gated imaging methods and image coregistration for improving image quality in the presence of motion. Self‐gated signal results from a modified 3D gradient‐echo sequence showed detection of periodic respiratory and cardiac motion in the adult mouse—with excellent comparison to traditional measurements, sensitivity to respiration‐induced tissue changes in the brain, and even detection of embryonic cardiac motion in utero. Serial image coregistration with rapidly‐acquired, low‐SNR volumes further enabled detection and correction of bulk changes in embryo location during in utero imaging sessions and subsequent reconstruction of high‐quality images. These methods, in combination, are shown to expand the range of applications for 3D mouse MRI, enabling late‐stage embryonic heart imaging and introducing the possibility of longitudinal developmental studies from embryonic stages through adulthood. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Comparison of amyloid plaque contrast generated by T2‐weighted, T‐weighted, and susceptibility‐weighted imaging methods in transgenic mouse models of Alzheimer's disease
Authors: Chamberlain Ryan , Reyes Denise , Curran Geoffrey L. , Marjanska Malgorzata , Wengenack Thomas M. , Poduslo Joseph F. , Garwood Michael , Jack Clifford R. 
Published: February 2009

AbstractOne of the hallmark pathologies of Alzheimer's disease (AD) is amyloid plaque deposition. Plaques appear hypointense on T2‐weighted and T‐weighted MR images probably due to the presence of endogenous iron, but no quantitative comparison of various imaging techniques has been reported. We estimated the T1, T2, T, and proton density values of cortical plaques and normal cortical tissue and analyzed the plaque contrast generated by a collection of T2‐weighted, T‐weighted, and susceptibility‐weighted imaging (SWI) methods in ex vivo transgenic mouse specimens. The proton density and T1 values were similar for both cortical plaques and normal cortical tissue. The T2 and T values were similar in cortical plaques, which indicates that the iron content of cortical plaques may not be as large as previously thought. Ex vivo plaque contrast was increased compared to a previously reported spin‐echo sequence by summing multiple echoes and by performing SWI; however, gradient echo and SWI were found to be impractical for in vivo imaging due to susceptibility interface–related signal loss in the cortex. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Visualization of free radical reactions in an aqueous sample irradiated by 290 MeV carbon beam
Authors: Matsumoto Ken‐ichiro , Nagata Katsura , Yamamoto Haruhiko , Endo Kazutoyo , Anzai Kazunori , Aoki Ichio 
Published: February 2009

AbstractThe detection of free radical reactions in a gelatin sample irradiated by a heavy‐ion beam was tested using electron paramagnetic resonance (EPR) spectroscopic and MRI methods. Geometry and the amount of free radical generation in a sample are described. A reaction mixture containing glutathione and a nitroxyl radical, TEMPOL, was caked with gelatin, and then irradiated with a 290 MeV carbon beam. The amount of free radical generation in a solid sample was almost flat from the surface to the beam end, except for a small peak, the peak radioactivation profile, and then steeply decreased approaching the beam end. Total free radical reactions obtained with carbon‐beam irradiation were expected to be less than one‐third of X‐ray irradiation, when the same dose for a deeper target was considered. Both EPR and MRI are useful tools to visualize free radical generation in samples irradiated by a heavy‐ion beam. The EPR‐based method is more sensitive and quantitative than the MRI‐based method; however, the MRI method can achieve high spatial resolution. This study gives the rationale for a redox regulation trial using antioxidant drugs to reduce the side effects on normal tissues in carbon‐beam therapy. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Evaluation of hepatic fibrosis with portal pressure gradient in rats
Authors: Wang Yuenan , Booth Carmen J. , Kim Hyeonjin , Qiu Maolin , Constable R. Todd 
Published: February 2009

AbstractMRI has the potential of providing a noninvasive assessment of liver pathology. This work introduces a portal pressure gradient (PPG) model derived from fluid mechanics, where the PPG is proportional to the average velocity and inversely proportional to the vessel area in the upper part of portal vein. Using a phase‐contrast spoiled gradient echo sequence, the PPG model was verified in a phantom study and was tested in an animal study using 35 rats with various degrees of hepatic fibrosis induced by carbon tetrachloride (CCl4). Histological examination was conducted to determine the severity of hepatic fibrosis. The fibrosis score monotonically increased with the duration of CCl4 treatment. The PPG was highly correlated with nonzero fibrosis scores (r2 = 0.90, P < 0.05). There was a significant difference between control and cirrhosis groups (P < 0.0006, α < 0.0018). The difference between control and fibrosis (noncirrhosis) groups (P < 0.002, α < 0.006) was also significant. Without the administration of any contrast agent, the MRI‐PPG approach shows promise as a noninvasive means of evaluating liver fibrosis. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Group‐theoretic exploitations of symmetry in computational solid and structural mechanics
Authors: Zingoni A. 
Published: February 2009

AbstractThe use of group theory in simplifying the study of problems involving symmetry is a well‐established approach in various branches of physics and chemistry, and major applications in these areas date back more than 70 years. Within the engineering disciplines, the search for more systematic and more efficient strategies for exploiting symmetry in the computational problems of solid and structural mechanics has led to the development of group‐theoretic methods over the past 40 years. This paper reviews the advances made in the application of group theory in areas such as bifurcation analysis, vibration analysis and finite element analysis, and summarizes the various implementation procedures currently available. Illustrative examples of typical solution procedures are drawn from recent work of the author. It is shown how the group‐theoretic approach, through the characteristic vector‐space decomposition, enables considerable simplifications and reductions in computational effort to be achieved. In many cases, group‐theoretic considerations also allow valuable insights on the behaviour or properties of a system to be gained, before any actual calculations are carried out. Copyright © 2009 John Wiley & Sons, Ltd.
Unrelated stem cell transplant for infantile idiopathic myelofibrosis
Authors: Domm Jennifer , Calder Cassie , Manes Becky , Crossno Christine , Correa Hernan , Frangoul Haydar 
Published: February 2009

AbstractIdiopathic myelofibrosis (IMF) is a rare disease in children that can present during infancy and have a protracted course. The only known curative approach for this disease in adult patients is allogeneic stem cell transplant. We present two cases of IMF during infancy that did not resolve with supportive care measures. Both patients underwent unrelated stem cell transplant with complete resolution of their hematologic manifestations and resolution of the bone marrow fibrosis. Pediatr Blood Cancer 2009;52:893–895. © 2009 Wiley‐Liss, Inc.
Subcellular fractionation of TGF‐β1‐stimulated lung epithelial cells: A novel proteomic approach for identifying signaling intermediates
Authors: Milosevic Jadranka , Bulau Patrick , Mortz Ejvind , Eickelberg Oliver 
Published: February 2009

AbstractMembers of the transforming growth factor (TGF)‐β superfamily are key regulators of lung development and homeostasis, in particular by controlling alveolar/bronchial epithelial cell function. TGF‐β signaling involves ligand‐dependent activation of receptor serine/threonine kinases, activation and subsequent nuclear translocation of pathway‐specific transcription factors (Smads), and ultimately, modulation of gene expression. While Smad‐dependent responses represent the primary signaling components activated by TGF‐β receptors, their function is controlled by a variety of cofactors. In addition, alternative signaling systems mediating TGF‐β‐induced effects have recently been described such as MAP kinase pathways. To uncover novel proteins that participate in TGF‐β signaling via nuclear/cytoplasmic shuttling in lung epithelial cells, we have analyzed A549 human lung epithelial cells, using subcellular fractionation combined with 2‐D PAGE, tryptic digestion, and MS. We identified a rapid increase in the cytosolic localization of KH‐type splicing regulatory protein (KHSRP), far upstream element‐binding protein (FUBP1), hnRNP‐L, and hnRNP‐H1, concomitant with a decrease in their nuclear localization in response to TGF‐β1. Proteomic data were confirmed by immunofluorescence and immunoblot analyses. In summary, we represent a powerful novel technology for the identification of previously unknown signaling intermediates.
Identification of glycoprotein receptors within the human salivary proteome for the lectin‐like BabA and SabA adhesins of Helicobacter pylori by fluorescence‐based 2‐D bacterial overlay
Authors: Walz Anke , Odenbreit Stefan , Stühler Kai , Wattenberg Andreas , Meyer Helmut E. , Mahdavi Jafar , Borén Thomas , Ruhl Stefan 
Published: February 2009

AbstractBecause gastric infection by Helicobacter pylori takes place via the oral route, possible interactions of this bacterium with human salivary proteins could occur. By using modified 1‐ and 2‐D bacterial overlay, binding of H. pylori adhesins BabA and SabA to the whole range of salivary proteins was explored. Bound salivary receptor molecules were identified by MALDI‐MS and by comparison to previously established proteome maps of whole and glandular salivas. By use of adhesin‐deficient mutants, binding of H. pylori to MUC7 and gp‐340 could be linked to the SabA and BabA adhesins, respectively, whereas binding to MUC5B was associated with both adhesins. Binding of H. pylori to the proline‐rich glycoprotein was newly detected and assigned to BabA adhesin whereas the SabA adhesin was found to mediate binding to newly detected receptor molecules, including carbonic anhydrase VI, secretory component, heavy chain of secretory IgA1, parotid secretory protein and zinc‐α2‐glycoprotein. Some of these salivary glycoproteins are known to act as scavenger molecules or are involved in innate immunity whereas others might come to modify the pathogenetic properties of this organism. In general, this 2‐D bacterial overlay technique represents a useful supplement in adhesion studies of bacteria with complex protein mixtures.
The cost of resistance to colistin in Acinetobacter baumannii: a proteomic perspective
Authors: Fernández‐Reyes María , Rodríguez‐Falcón Manuel , Chiva Cristina , Pachón Jerónimo , Andreu David , Rivas Luis 
Published: February 2009

AbstractColistin resistance in Acinetobacter baumannii, a pathogen of clinical concern, was induced in the susceptible strain ATCC 19606 by growth under increasing pressure of the antibiotic, the only drug universally active against multi‐resistant clinical strains. In 2‐D difference gel electrophoresis (DIGE) experiments, 35 proteins with differences in expression between both phenotypes were identified, most of them appearing as down regulated in the colistin‐resistant strain. These include outer membrane (OM) proteins, chaperones, protein biosynthesis factors, and metabolic enzymes, all suggesting substantial loss of biological fitness in the resistant phenotype, as substantiated by complementary experiments in the absence of colistin. Results shed light on the scarcity of widespread clinical outbreaks for resistant phenotypes.
POSTMan (POST‐translational modification analysis), a software application for PTM discovery
Authors: Arntzen Magnus Ø. , Osland Christoffer Leif , Raa Christopher Rasch‐Olsen , Kopperud Reidun , Døskeland Stein‐Ove , Lewis Aurélia E. , D'Santos Clive S. 
Published: February 2009

AbstractPost‐translationally modified peptides present in low concentrations are often not selected for CID, resulting in no sequence information for these peptides. We have developed a software POSTMan (POST‐translational Modification analysis) allowing post‐translationally modified peptides to be targeted for fragmentation. The software aligns LC‐MS runs (MS1 data) between individual runs or within a single run and isolates pairs of peptides which differ by a user defined mass difference (post‐translationally modified peptides). The method was validated for acetylated peptides and allowed an assessment of even the basal protein phosphorylation of phenylalanine hydroxylase (PHA) in intact cells.
How specific is my SRM?: The issue of precursor and product ion redundancy
Authors: Sherman Jamie , McKay Matthew J. , Ashman Keith , Molloy Mark P. 
Published: February 2009

AbstractSelected reaction monitoring (SRM) MS is proving to be a popular approach for targeted quantitative proteomics. The use of proteotypic peptides as candidates for SRM analysis is a wise first step in SRM method design. The obvious reason for this is the need to avoid redundancy at the sequence level, however this is incidental. The true reason is that homologous peptides result in redundancy in the mass‐to‐charge domain. This may seem like a trivial subtlety, however, we believe this is an issue of far greater significance than the proteomic community is aware. This VIEWPOINT article serves to highlight the complexity associated with designing SRM assays in light of potential ion redundancy.
Proteome responses to stable hepatitis B virus transfection and following interferon alpha treatment in human liver cell line HepG2
Authors: Wang Jianghua , Jiang Dong , Zhang Henghui , Lv Sa , Rao Huiying , Fei Ran , Wei Lai 
Published: February 2009

AbstractHepatitis B virus (HBV) infection is a worldwide health problem and may develop to liver fibrosis, cirrhosis, and even hepatocellular carcinoma. To investigate the global proteome responses of liver‐derived cells to HBV infection and IFNα treatment, 2‐DE and MS‐based analysis were performed to compare the proteome changes between HBV stably transfected cell line HepG2.2.15 and its parental cell line HepG2, as well as HepG2.2.15 before and after IFNα treatment (5000 IU/mL for 72 h). Compared to HepG2, 12 of 18 down‐regulated and 27 of 32 up‐regulated proteins were identified in HepG2.2.15. After IFNα treatment, 6 of 7 down‐regulated and 11 of 14 up‐regulated proteins were identified. Differentially expressed proteins caused by HBV infection were involved with cytoskeletal matrix, heat shock stress, kinases/signal transduction, protease/proteasome components, etc. Prohibitin showed a dose‐dependent up‐regulation during IFNα treatment and might play a potent role in anti‐HBV activities of IFNα by enhancing the crossbinding p53 expression to achieve the apoptosis of HBV infected liver cells. Down‐regulation of interferon‐stimulated gene 15 (ISG15) in HepG2.2.15 and recovery by IFNα suggested its relationship with IFNα's anti‐HBV effect.
Proteome analysis ofEdwardsiella ictaluri
Authors: Dumpala Pradeep R. , Lawrence Mark L. , Karsi Attila 
Published: February 2009

AbstractEdwardsiella ictaluriis a facultative intracellular Gram‐negative bacterium causing enteric septicemia of catfish (ESC), the most prevalent disease affecting farm‐raised channel catfish in the United States. Despite its economic importance, studies addressing high‐throughput proteomics were not possible because of lack of comprehensive protein database. Here, we report the first high‐throughput proteomics analysis ofE. ictaluriusing 2‐D LC ESI MS/MS and 2‐DE MALDI TOF/TOF MS. Proteins identified in this study and predicted from the wholeE. ictalurigenome were clustered into functional groups using clusters of orthologous groups (COG), and their subcellular locations were predicted. Possible functional relationships among proteins were determined using pathway analysis. The total number of uniqueE. ictaluriproteins identified using both 2‐D LC and 2‐DE approaches was 788, of which 15.48% (122) were identified by both methods while 78.43% (618) and 6.09% (48) were unique in 2‐D LC and 2‐DE, respectively. COG groupings and subcellular localizations were quite similar between our data set and proteins predicted from the whole genome. Twelve pathways were significantly represented in our dataset (p<0.05). Results from this study provided experimental evidence for many proteins that were predicted from theE. ictalurigenome annotation, and they should accelerate future functional and comparative studies aimed at understanding virulence mechanisms of this important pathogen.