bluuebunny/crossref_metadata_2025_split huggingface dataset:
Properties of El Niño–Southern Oscillation in Different Equilibrium Climates with HadCM3
Authors: Toniazzo Thomas 
Published: October 2006

Abstract
The ENSO variability in three long, stable, steady-state integrations of the Third Hadley Centre Coupled Ocean–Atmosphere GCM (HadCM3) is analyzed, relevant to climatic conditions of the Last Glacial Maximum (LGM), of the preindustrial period [control (CTL)], and of a greenhouse stabilization scenario (GHS) at 4 times the preindustrial CO2 concentration. It is found that progressively from LGM to CTL and GHS, the SST variability pattern associated with ENSO is centered farther west, and the oscillation acquires a shorter dominant period. While there are no large changes in total SST variability, very strong events become less frequent, and El Niño events develop over a narrower period within the seasonal cycle. The westward ENSO pattern shift is concurrent with a similar shift in the climatological wind stress distribution and with increased convective activity over the west equatorial Pacific. The wind response to anomalous SSTs follows this shift and increases in strength. The thermocline feedback becomes stronger in the 4 × CO2 integration, but the largest SST anomalies are associated with surface processes. The role of surface flux damping for the decay of anomalous SSTs is reduced in LGM and increased in GHS. From the analysis, the principal changes in mean climate that appear to affect the evolution of ENSO-related SST anomalies in HadCM3 are thus the changes in zonal wind stress over the equator, the depth of the equatorial thermocline, and the sensitivity of atmospheric convection to equatorial SST anomalies.
A New Blocking Index and Its Application: Blocking Action in the Northern Hemisphere
Authors: Diao Yina , Li Jianping , Luo Dehai 
Published: October 2006

Abstract
In this paper, a new two-dimensional blocking index is proposed by defining a difference between the daily 500-hPa geopotenial heights at the reference latitude and its north side. The reference latitude is determined by a composite latitude-dependent 500-hPa geopotenial height of blocking events in different seasons and sectors. The new index can take account of the duration, intensity, propagation, and spatial structure of a blocking event. Using this index, the characteristics (frequency, duration, intensity, and preferred occurrence region) of the blocking action in the North Hemisphere (NH) are investigated using a 42-yr sample of blocking events from the NCEP–NCAR reanalyses.
It is found that blocking events in the NH are more frequent in the Atlantic–Europe sector than in the Pacific sector in winter and spring and autumn, but more persistent in the Atlantic–Europe sector than in the Pacific sector for all seasons. Blocking events in the Pacific sector tend to have larger amplitudes than the Atlantic counterparts. In addition, it is shown that in the NH independently occurring blocking events are most frequent, but simultaneously occurring blockings are rather rare, indicating that the blocking events in the NH should be a local phenomenon.
On the other hand, a comparison with the existing indices [e.g., Tibaldi and Molteni (TM) index] indicates that in summer and autumn the new index shows similar longitudinal dependency of NH blocking events as does the TM index, but it shows two distinct action centers of blocking events in the Atlantic sector in winter and spring (in which the most frequent one is situated more westward) and an eastward blocking action center in the Pacific sector in spring and autumn, compared to the TM index.
In addition, it is found that the new blocking index proposed here shows relatively low blocking frequency for all seasons compared to the TM index, especially in the Atlantic sector in spring and in the Pacific sector in winter and spring, which seems to be in agreement with the result obtained by Pelly and Hoskins using the PV–θ index.
Local Air–Sea Relationship in Observations and Model Simulations
Authors: Wu Renguang , Kirtman Ben P. , Pegion Kathy 
Published: October 2006

Abstract
The present study compares the local simultaneous correlation between rainfall–evaporation and sea surface temperature (SST)–SST tendency among observations, coupled general circulation model (CGCM) simulations, and stand-alone atmospheric general circulation model (AGCM) simulations. The purpose is to demonstrate to what extent the model simulations can reproduce the observed air–sea relationship. While the model-simulated correlation agrees with the observations in the tropical eastern Pacific, large discrepancies are found in the subtropics, midlatitudes, and tropical Indo-western Pacific Ocean regions. In tropical Indo-western Pacific Ocean regions and the midlatitudes where the atmosphere contributes to the observed SST changes, the specified SST simulations produce excessive SST forcing, whereas the CGCM captures the atmospheric feedback on the SST, but with somewhat of an overestimation. In the subtropics, both the AGCM and CGCM produce unrealistic positive rainfall–SST correlations. In the tropical western-central Pacific and the North Indian Ocean, the CGCM-simulated evaporation–SST correlation is opposite to that observed because of an excessive dependence of the sea–air humidity difference on the SST.
A New Perspective on the Climate Prediction of Asian Summer Monsoon Precipitation
Authors: Lim Young-Kwon , Kim Kwang-Yul 
Published: October 2006

Abstract
A new paradigm for climate (one month and longer) prediction is developed and is applied to the 5-day-averaged Asian summer monsoon (ASM) precipitation. The foundation of the method is to identify climate signals (deterministic components) that constitute the ASM system and predict the temporal fluctuations of the amplitudes (stochastic components) of the individual signals. Climate signals were identified via cyclostationary empirical orthogonal function (CSEOF) analysis of the Xie–Arkin pentad precipitation in this study and include the annual cycle, El Niño/La Niña, and the intraseasonal oscillations of the 40–50-day period band (the Madden–Julian oscillation). Prediction is much facilitated by forecasting the slowly undulating amplitude time series of each climate signal rather than the raw precipitation data directly. The new prediction method results in reasonable forecasts of the pentad precipitation for the test period of 1999–2001. Specifically, the propagation of the intraseasonal oscillations is predicted successfully 60 days in advance. The performance of the new method is significantly better than persistence and that of conventional prediction methods in which raw data is predicted directly.
Climate and Tropical Cyclone Activity: A New Model Downscaling Approach
Authors: Emanuel Kerry 
Published: October 2006

Abstract
While there is a pressing need to understand and predict the response of tropical cyclones to climate change, global climate models are at present too coarse to resolve tropical cyclones to the extent necessary to simulate their intensity, and their ability to simulate genesis is questionable. For these reasons, a “downscaling” approach to modeling the effect of climate change on tropical cyclones is desirable. Here a new approach to downscaling is introduced that consists of generating a large set of synthetic storm tracks whose statistics are consistent with the large-scale general circulation of the climate model, and then running a deterministic, coupled tropical cyclone model along each track, with atmospheric and upper-ocean thermodynamic conditions taken from the global climate model. As a first step in this direction, this paper explores the sensitivity of the intensity of a large sample of tropical cyclones to changes in potential intensity, shear, and ocean mixed layer depth, fixing other variables, including the space–time probability distribution of storm genesis. It is shown that a 10% increase in potential intensity leads to a 65% increase in the “power dissipation index,” a measure of the total amount of mechanical energy generated by tropical cyclones over their life spans. This is consistent with the observed increase of power dissipation over the past 50 yr. Storms are somewhat less influenced by equivalent fractional changes in environmental wind shear or ocean mixed layer depth.
Effects of Ekman Transport on the NAO Response to a Tropical Atlantic SST Anomaly
Authors: Peng Shiling , Robinson Walter A. , Li Shuanglin , Alexander Michael A. 
Published: October 2006

Abstract
A recent study showed that a tropical Atlantic sea surface temperature (SST) anomaly induces a significant coupled response in late winter [February–April (FMA)] in a coupled model, in which an atmospheric general circulation model is coupled to a slab mixed layer ocean model (AGCM_ML). The coupled response comprises a dipole in the geopotential height, like the North Atlantic Oscillation (NAO), and a North Atlantic tripole in the SST. The simulated NAO response developed 1 or 2 months later in the model than in observations. To determine the possible effects of Ekman heat transport on the development of the coupled response to the tropical forcing, an extended coupled model (AGCM_EML), including Ekman transport in the slab mixed layer ocean, is now used. Large ensembles of AGCM_EML experiments are performed, parallel to the previous AGCM_ML experiments, with the model forced by the same tropical Atlantic SST anomaly over the boreal winter months (September–April).
The inclusion of Ekman heat transport is found to result in an earlier development of the coupled NAO–SST tripole response in the AGCM_EML, compared to that in the AGCM_ML. The mutual reinforcement between the anomalous Ekman transport and the surface heat flux causes the tropical forcing to induce an extratropical SST response in November–January (NDJ) in the AGCM_EML that is twice as strong as that in the AGCM_ML. The feedback of this stronger extratropical SST response on the atmosphere in turn drives the development of the NAO response in NDJ. In FMA, the sign of the anomalous surface heat flux is reversed in the Gulf Stream region such that it opposes the anomalous Ekman transport. The resulting equilibrium NAO response in the AGCM_EML is similar to that in the AGCM_ML, but it is reached 1–2 months sooner in the AGCM_EML. Hence, the presence of Ekman transport causes a seasonal shift in the evolution of the coupled response. The faster development of the NAO response in the AGCM_EML suggests that tropical Atlantic SST anomalies should be able to influence the NAO, in nature, on the seasonal time scale, and that efficient interactions with the extratropical ocean play a significant role in determining the coupled response.
Characteristics of Satellite-Derived Clear-Sky Atmospheric Temperature Inversion Strength in the Arctic, 1980–96
Authors: Liu Yinghui , Key Jeffrey R. , Schweiger Axel , Francis Jennifer 
Published: October 2006

Abstract
The low-level atmospheric temperature inversion is a dominant feature of the Arctic atmosphere throughout most of the year. Meteorological stations that provide radiosonde data are sparsely distributed across the Arctic, and therefore provide little information on the spatial distribution of temperature inversions. Satellite-borne sensors provide an opportunity to fill the observational gap. In this study, a 17-yr time series, 1980–96, of clear-sky temperature inversion strength during the cold season is derived from High Resolution Infrared Radiation Sounder (HIRS) data using a two-channel statistical method. The satellite-derived clear-sky inversion strength monthly mean and trends agree well with radiosonde data. Both increasing and decreasing trends are found in the cold season for different areas. It is shown that there is a strong coupling between changes in surface temperature and changes in inversion strength, but that trends in some areas may be a result of advection aloft rather than warming or cooling at the surface.
XRate: a fast prototyping, training and annotation tool for phylo-grammars
Authors: Klosterman Peter S , Uzilov Andrew V , Bendaña Yuri R , Bradley Robert K , Chao Sharon , Kosiol Carolin , Goldman Nick , Holmes Ian 
Published: October 2006

AbstractBackgroundRecent years have seen the emergence of genome annotation methods based on thephylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists.ResultsWe have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures.ConclusionOur results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools.
Construction of a multiple fluorescence labelling system for use in co-invasion studies of Listeria monocytogenes
Authors: Andersen Jens B , Roldgaard Bent B , Lindner Ariel B , Christensen Bjarke B , Licht Tine R 
Published: October 2006

Abstract

Background
Existing virulence models are often difficult to apply for quantitative comparison of invasion potentials of Listeria monocytogenes. Well-to-well variation between cell-line based in vitro assays is practically unavoidable, and variation between individual animals is the cause of large deviations in the observed capacity for infection when animal models are used.
One way to circumvent this problem is to carry out virulence studies as competition assays between 2 or more strains. This, however, requires invasion-neutral markers that enable easy discrimination between the different strains.

Results
A fluorescent marker system, allowing visualization and identification of single L. monocytogenes cells as well as colonies in a non-destructive manner, was developed. Five different fluorescent labels are available, and allowed simultaneous visual discrimination between three differently labelled strains at the single cell level by use of fluorescence microscopy. More than 90% of the L. monocytogenes host cells maintained the fluorescence tags for 40 generations.
The fluorescence tags did not alter the invasive capacity of the L. monocytogenes cells in a traditional Caco-2 cell invasion assay, and visual discrimination between invaded bacteria carrying different fluorescent labels inside the cells was possible.

Conclusion
The constructed fluorescent marker system is stable, easy to use, does not affect the virulence of L. monocytogenes in Caco-2 cell assays, and allows discrimination between differently labelled bacteria after internalization in these cells.
High-resolution analysis of HLA class I alterations in colorectal cancer
Authors: Dierssen Jan Willem F , de Miranda Noel FCC , Mulder Arend , van Puijenbroek Marjo , Verduyn Willem , Claas Frans HJ , van de Velde Cornelis JH , Jan Fleuren Gert , Cornelisse Cees J , Corver Willem E , Morreau Hans 
Published: October 2006

AbstractBackgroundPrevious studies indicate that alterations in Human Leukocyte Antigen (HLA) class I expression are frequent in colorectal tumors. This would suggest serious limitations for immunotherapy-based strategies involving T-cell recognition. Distinct patterns of HLA surface expression might conceal different immune escape mechanisms employed by the tumors and are worth further study.MethodWe applied four-color multiparameter flow cytometry (FCM), using a large panel of alloantigen-specific anti-HLA-A and -B monoclonal antibodies, to study membranous expression of individual HLA alleles in freshly isolated colorectal cancer cell suspensions from 21 patients.ResultsAlterations in HLA class I phenotype were observed in 8 (38%) of the 21 tumors and comprised loss of a single A or B alleles in 4 cases, and loss of all four A and B alleles in the other 4 cases. Seven of these 8 tumors were located on the right side of the colon, and those showing loss of both HLA-A and -B membranous expression were all of the MSI-H phenotype.ConclusionFCM allows the discrimination of complex phenotypes related to the expression of HLA class I. The different patterns of HLA class I expression might underlie different tumor behavior and influence the success rate of immunotherapy.
The CF-CIRC study: a French collaborative study to assess the accuracy of Cystic Fibrosis diagnosis in neonatal screening
Authors: Sermet-Gaudelus Isabelle , Roussel Delphine , Bui Stéphanie , Deneuville Eric , Huet Frédéric , Reix Philippe , Bellon Gabriel , Lenoir Gérard , Edelman Aleksander 
Published: October 2006

Abstract

Background
Cystic fibrosis (CF) is caused by mutations in the gene encoding for the CF transmembrane conductance regulator (CFTR) protein, which acts as a chloride channel after activation by cyclic AMP (cAMP). Newborn screening programs for CF usually consist of an immunoreactive trypsinogen (IRT) assay, followed when IRT is elevated by testing for a panel of CF-causing mutations. Some children, however, may have persistent hypertrypsinogenemia, only one or no identified CFTR gene mutation, and sweat chloride concentrations close to normal values. In vivo demonstration of abnormal CFTR protein function would be an important diagnostic aid in this situation. Measurements of transepithelial nasal potential differences (NPD) in adults accurately characterize CFTR-related ion transport. The aim of the present study is to establish reference values for NPD measurements for healthy children and those with CF aged 3 months to 3 years, the age range of most difficult-to-diagnose patients with suspected CF. The ultimate goal of our study is to validate NPD testing as a diagnostic tool for children with borderline results in neonatal screening.

Methods/Design
We adapted the standard NPD protocol for young children, designed a special catheter for them, used a slower perfusion rate, and shortened the protocol to include only measurement of basal PD, transepithelial sodium (Na+) transport in response to the Na+ channel inhibitor amiloride, and CFTR-mediated chloride (Cl-) secretion in response to isoproterenol, a β-agonist in a Cl- free solution.
The study will include 20 children with CF and 20 healthy control children. CF children will be included only if they carry 2 CF-causing mutations in the CFTR gene or have sweat chloride concentrations > 60 mEq/L or both. The healthy children will be recruited among the siblings of the CF patients, after verification that they do not carry the familial mutation.

Discussion
A preliminary study of 3 adult control subjects and 4 children older than 12 years with CF verified that the new protocol was well tolerated and produced NPD measurements that did not differ significantly from those obtained with the standard protocol. This preliminary study will provide a basis for interpreting NPD measurements in patients with suspected CF after neonatal screening. Earlier definitive diagnosis should alleviate parental distress and allow earlier therapeutic intervention and genetic counseling.
Nordic Walking and chronic low back pain: design of a randomized clinical trial
Authors: Morsø Lars , Hartvigsen Jan , Puggaard Lis , Manniche Claus 
Published: October 2006

AbstractBackgroundLow Back Pain is a major public health problem all over the western world. Active approaches including exercise in the treatment of low back pain results in better outcomes for patients, but it is not known exactly which types of back exercises are most beneficial or whether general physical activity provide similar benefits.Nordic Walking is a popular and fast growing type of exercise in Northern Europe. Initial studies have demonstrated that persons performing Nordic Walking are able to exercise longer and harder compared to normal walking thereby increasing their cardiovascular metabolism. Until now no studies have been performed to investigate whether Nordic Walking has beneficial effects in relation to low back pain.The primary aim of this study is to investigate whether supervised Nordic Walking can reduce pain and improve function in a population of chronic low back pain patients when compared to unsupervised Nordic Walking and advice to stay active. In addition we investigate whether there is an increase in the cardiovascular metabolism in persons performing supervised Nordic Walking compared to persons who are advised to stay active. Finally, we investigate whether there is a difference in compliance between persons receiving supervised Nordic Walking and persons doing unsupervised Nordic Walking.MethodsOne hundred and fifty patients with low back pain for at least eight weeks and referred to a specialized secondary sector outpatient back pain clinic are included in the study. After completion of the standard back centre treatment patients are randomized into one of three groups: A) Nordic Walking twice a week for eight weeks under supervision of a specially trained instructor; B) Unsupervised Nordic Walking for eight weeks after one training session with an instructor; C) A one hour motivational talk including advice to stay active. Outcome measures are pain, function, overall health, cardiovascular ability and activity level.ResultsNo results available at this point.DiscussionThis study will investigate the effect of Nordic Walking on pain and function in a population of people with chronic LBP.Trial Registrationhttp://www.ClinicalTrials.govregistration # NCT00209820
Distribution of hepatitis C virus genotypes in patients infected by different sources and its correlation with clinical and virological parameters: a preliminary study
Authors: Kabir Ali , Alavian Seyed-Moayed , Keyvani Hussein 
Published: October 2006

AbstractBackgroundInformation about genotypes and associated risk factors in hepatitis C virus (HCV) infected patients in Iran is limited. The aim of this study was to identify the HCV genotypes and associated risk factors in a group of HCV infected patients from Iran.ResultsGenotyping analysis was performed in 156 patients with positive anti-HCV and HCV-RNA. Patients were questioned concerning documented risk factors. Genotypes 1 and 3 were found in 87 (55.8%) and 45 (28.8%) patients, respectively. The most frequent HCV subtype was 1a (37.8), followed by 3a (28.9%) and 1b (16.7%). There was no statistically significant difference between the risk factors analyzed and the acquisition of HCV infection. We further found that 18 (40%) and 17 (37.8%) patients that were intravenous drug users (IVDU) had genotype 1a and 3a respectively.ConclusionGenotypes 3a and 1a in Iran are less prevalent in IVDU than in Europe and USA, but there is a high similarity between the pattern of genotype in IVDU in both Europe and United States, and Iran. However, in this case it can not be due to people migration among countries since history of travel abroad existed only in 6 cases (13.3%).