bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality and Kinetics of the Antibody Response in Mice after Three Different Low-Dose Influenza Virus Vaccination Strategies
Authors: Hauge Solveig , Madhun Abdullah , Cox Rebecca Jane , Haaheim Lars Reinhardt 
Published: June 2007

ABSTRACT
The threat of a new influenza pandemic has led to renewed interest in dose-sparing vaccination strategies such as intradermal immunization and the use of adjuvanted vaccines. In this study we compared the quality and kinetics of the serum antibody response elicited in mice after one or two immunizations with a split influenza A (H3N2) virus, using three different low-dose vaccination strategies. The mice were divided into four groups, receiving either a low-dose vaccine (3 μg hemagglutinin [HA]) intradermally or intramuscularly with or without aluminum adjuvant or the normal human vaccine dose (15 μg HA) intramuscularly. Sera were collected weekly after vaccination and tested in the hemagglutination inhibition, virus neutralization, and enzyme-linked immunosorbent assays. The antibody responses induced after intradermal or intramuscular low-dose vaccinations were similar and lower than those observed after the human vaccine dose. However, low-dose adjuvanted vaccine elicited a serum antibody response comparable to that elicited by the human dose, although the second immunization did not result in any increase in cross-reactive hemagglutination inhibition antibodies, and the peak serum antibody response was observed 1 week later than in the other vaccination groups. Our murine data suggest that the low-dose intradermal route does not show any obvious advantage over the low-dose intramuscular route in inducing a serum antibody response and that none of the low-dose vaccination strategies is as effective as intramuscular vaccination with the normal human dose. However, the low-dose aluminum-adjuvanted vaccine could present a feasible alternative in case of limited vaccine supply.
Comparison of Four Methods Using Throat Swabs To Confirm Rubella Virus Infection
Authors: Zhu Zhen , Xu Wenbo , Abernathy Emily S. , Chen Min-Hsin , Zheng Qi , Wang Tongzhan , Zhang Zhenying , Li Congyong , Wang Changyin , He Weikuan , Zhou Shujie , Icenogle Joseph 
Published: June 2007

ABSTRACTLaboratory tests are essential for confirming sporadic cases and outbreaks of rubella. Detection of rubella virus is often necessary to confirm rubella cases and to identify specimens to be used to characterize wild-type rubella viruses. The sensitivities of four methods for detecting rubella virus infection using throat swabs, which had been collected in Henan and Anhui provinces in China, were evaluated. The methods used were reverse transcription (RT)-PCR followed by Southern hybridization using RNA extracted directly from clinical specimens, virus growth in tissue culture followed by virus detection by RT-PCR, low-background immunofluorescence in infected tissue culture cells using monoclonal antibodies to the structural proteins of rubella virus, and a replicon-based method of detecting infectious virus. Among these four methods, direct RT-PCR followed by hybridization was the most sensitive method; the replicon-based method was the least difficult to perform.
First Contemporary Case of Human Infection with
Cryptococcus gattii
in Puget Sound: Evidence for Spread of the Vancouver Island Outbreak
Authors: Upton Arlo , Fraser James A. , Kidd Sarah E. , Bretz Camille , Bartlett Karen H. , Heitman Joseph , Marr Kieren A. 
Published: June 2007

ABSTRACT

We report a case of cryptococcosis due to
C. gattii
which appears to have been acquired in the Puget Sound region, Washington State. Genotyping confirmed identity to the predominant Vancouver Island genotype. This is the first documented case of human disease by the major Vancouver Island emergence strain acquired within the United States.
Spectrum of Clinically RelevantExophialaSpecies in the United States
Authors: Zeng J. S. , Sutton D. A. , Fothergill A. W. , Rinaldi M. G. , Harrak M. J. , de Hoog G. S. 
Published: June 2007

ABSTRACTNumerous members of the genusExophialaare potential agents of human and animal mycoses. The majority of these infections are cutaneous and superficial, but also fatal systemic infections are known. We re-identified 188 clinical isolates from the United States, which had a preliminary morphological identification ofExophialaspecies, by sequencing internal transcribed spacer (ITS) region of the rRNA. Molecular identifications of the strains were as follows, in order of frequency: 55E. dermatitidis(29.3%), 37E. xenobiotica(19.7%), 35E. oligosperma(18.6%), 13E. lecanii-corni(6.9%), 12E. phaeomuriformis(6.4%), 7E. jeanselmei(3.7%), 7E. bergeri(3.7%), 6E. mesophila(3.2%), 5E. spinifera(2.7%), 3Exophialasp. 1 (1.6%), 3E. attenuata(1.6%), 3Phialophora europaea(1.3%), 1E. heteromorpha(0.5%), and 1Exophialasp. 2 (0.5%) strains.Exophialastrains were repeatedly isolated from deep infections (39.9%) involving lung, pleural fluid, sputum, digestive organs (stomach, intestines, bile), heart, brain, spleen, bone marrow, blood, dialysis fluid, lymph node, joint, breast, middle ear, throat, and intraocular tissues. About 38.3% of theExophialaspp. strains were agents of cutaneous infections including skin, mucous membranes, nail, and corneal epithelium lesions. The other strains caused superficial infections (0.5%, including hair) or subcutaneous infection (12.0%, including paranasal sinusitis, mycetoma, and subcutaneous cyst). The systemic infections were preponderantly caused byE. dermatitidis,E. oligosperma,E. phaeomuriformis,E. xenobiotica, andE. lecanii-corni. Strains ofE. bergeri,E. spinifera,E. jeanselmei,E. mesophila, andE. attenuatamainly induced cutaneous and subcutaneous infections. Since relatively few unknown ITS motifs were encountered, we suppose that the list of opportunisticExophialaspecies in temperate climates is nearing completion, but a number of species still have to be described.
The RNA Binding Domain of Influenza A Virus NS1 Protein Affects Secretion of Tumor Necrosis Factor Alpha, Interleukin-6, and Interferon in Primary Murine Tracheal Epithelial Cells
Authors: Newby Celeste M. , Sabin Leah , Pekosz Andrew 
Published: June 2007

ABSTRACT
Primary differentiated respiratory epithelial cell cultures closely model the in vivo environment and allow for studies of innate immune responses generated specifically by epithelial cells, the primary cell type infected by human influenza A virus strains. We used primary murine tracheal epithelial cell (mTEC) cultures to investigate antiviral and cytokine responses to influenza A virus infection, focusing on the contribution of the RNA binding domain of the NS1 protein. rWSN NS1 R38A replication is attenuated in mTEC cultures; however, viral antigen is detected predominantly in ciliated cells, similar to wild-type virus. NS1 and NS1 R38A proteins display a primarily cytoplasmic localization in infected mTEC cultures. Increased production of tumor necrosis factor alpha, interleukin-6, and beta interferon is observed during rWSN NS1 R38A infection, and cytokines are secreted in a directional manner. Cytokine pretreatment of mTEC cultures and Vero cells suggest that rWSN NS1 R38A is more sensitive to the presence of antiviral/inflammatory cytokines than wild-type virus. Our results demonstrate that the RNA binding domain is a critical regulator of both cytokine production and cytokine sensitivity during influenza A virus infection of primary tracheal epithelial cells.
Simulated Seasonal and Interannual Variability of the Mixed Layer Heat Budget in the Northern Indian Ocean*
Authors: Montégut Clémentde Boyer , Vialard Jérôme , Shenoi S. S. C. , Shankar D. , Durand Fabien , Ethé Christian , Madec Gurvan 
Published: June 2007

AbstractA global ocean general circulation model (OGCM) is used to investigate the mixed layer heat budget of the northern Indian Ocean (NIO). The model is validated against observations and shows fairly good agreement with mixed layer depth data in the NIO. The NIO has been separated into three subbasins: the western Arabian Sea (AS), the eastern AS, and the Bay of Bengal (BoB). This study reveals strong differences between the western and eastern AS heat budget, while the latter basin has similarities with the BoB. Interesting new results on seasonal time scales are shown. The penetration of solar heat flux needs to be taken into account for two reasons. First, an average of 28 W m−2 is lost beneath the mixed layer over the year. Second, the penetration of solar heat flux tends to reduce the effect of solar heat flux on the SST seasonal cycle in the AS because the seasons of strongest flux are also seasons with a thin mixed layer. This enhances the control of SST seasonal variability by latent heat flux. The impact of salinity on SST variability is demonstrated. Salinity stratification plays a clear role in maintaining a high winter SST in the BoB and eastern AS while not in the western AS. The presence of freshwater near the surface allows heat storage below the surface layer that can later be recovered by entrainment warming during winter cooling (with a winter contribution of +2.1°C in the BoB). On an interannual time scale, the eastern AS and BoB are strongly controlled by the winds through the latent heat flux anomalies. In the western AS, vertical processes, as well as horizontal advection, contribute significantly to SST interannual variability, and the wind is not the only factor controlling the heat flux forcing.
The Years of El Niño, La Niña, and Interactions with the Tropical Indian Ocean
Authors: Meyers Gary , McIntosh Peter , Pigot Lidia , Pook Mike 
Published: June 2007

Abstract
The Indian Ocean zonal dipole is a mode of variability in sea surface temperature that seriously affects the climate of many nations around the Indian Ocean rim, as well as the global climate system. It has been the subject of increasing research, and sometimes of scientific debate concerning its existence/nonexistence and dependence/independence on/from the El Niño–Southern Oscillation, since it was first clearly identified in Nature in 1999. Much of the debate occurred because people did not agree on what years are the El Niño or La Niña years, not to mention the newly defined years of the positive or negative dipole. A method that identifies when the positive or negative extrema of the El Niño–Southern Oscillation and Indian Ocean dipole occur is proposed, and this method is used to classify each year from 1876 to 1999. The method is statistical in nature, but has a strong basis on the oceanic physical mechanisms that control the variability of the near-equatorial Indo-Pacific basin. Early in the study it was found that some years could not be clearly classified due to strong decadal variation; these years also must be recognized, along with the reason for their ambiguity. The sensitivity of the classification of years is tested by calculating composite maps of the Indo-Pacific sea surface temperature anomaly and the probability of below median Australian rainfall for different categories of the El Niño–Indian Ocean relationship.
Impacts of ENSO and Indian Ocean Dipole Events on the Southern Hemisphere Storm-Track Activity during Austral Winter
Authors: Ashok Karumuri , Nakamura Hisashi , Yamagata Toshio 
Published: June 2007

Abstract
Impacts of the ENSO and Indian Ocean dipole (IOD) phenomena on winter storm-track activity over the Southern Hemisphere are examined on the basis of the observed and reanalysis data for 1979–2003. The partial correlation technique is utilized to distinguish the impact of one phenomenon from that of the other. During an El Niño event, the subtropical jet stream tends to strengthen substantially, enhancing the jet bifurcation and thereby reducing storm-track activity over the midlatitude South Pacific and to the south of Australia. During a positive IOD event, the westerlies and storm-track activity also tend to weaken over southern Australia and portions of New Zealand. Thus both the positive IOD and, to a lesser extent, El Niño events act to reduce winter rainfall significantly over some portions of South Australia and New Zealand. Precipitation over the southeastern portion of the continent and over the northern portions of the two main islands of New Zealand is more sensitive to IOD. Significant reduction in precipitation associated with an El Niño event is seen over Tasmania. Over midlatitude South America, in contrast, the enhancement of the westerlies and storm-track activity tends to be more significant in a positive IOD event than in an El Niño event. It is demonstrated that despite the dominant influence of the Southern Hemispheric Annular Mode from a hemispheric viewpoint, the remote influence of ENSO and/or IOD on local storm-track activity can be detected in winter as a significant signal in particular midlatitude regions, including South Australia and New Zealand.
Annual, Seasonal, and Interannual Variability of Air–Sea Heat Fluxes in the Indian Ocean
Authors: Yu Lisan , Jin Xiangze , Weller Robert A. 
Published: June 2007

Abstract
This study investigated the accuracy and physical representation of air–sea surface heat flux estimates for the Indian Ocean on annual, seasonal, and interannual time scales. Six heat flux products were analyzed, including the newly developed latent and sensible heat fluxes from the Objectively Analyzed Air–Sea Heat Fluxes (OAFlux) project and net shortwave and longwave radiation results from the International Satellite Cloud Climatology Project (ISCCP), the heat flux analysis from the Southampton Oceanography Centre (SOC), the National Centers for Environmental Prediction reanalysis 1 (NCEP1) and reanalysis-2 (NCEP2) datasets, and the European Centre for Medium-Range Weather Forecasts operational (ECMWF-OP) and 40-yr Re-Analysis (ERA-40) products.
This paper presents the analysis of the six products in depicting the mean, the seasonal cycle, and the interannual variability of the net heat flux into the ocean. Two time series of in situ flux measurements, one taken from a 1-yr Arabian Sea Experiment field program and the other from a 1-month Joint Air–Sea Monsoon Interaction Experiment (JASMINE) field program in the Bay of Bengal were used to evaluate the statistical properties of the flux products over the measurement periods. The consistency between the six products on seasonal and interannual time scales was investigated using a standard deviation analysis and a physically based correlation analysis.
The study has three findings. First of all, large differences exist in the mean value of the six heat flux products. Part of the differences may be attributable to the bias in the numerical weather prediction (NWP) models that underestimates the net heat flux into the Indian Ocean. Along the JASMINE ship tracks, the four NWP modeled mean fluxes all have a sign opposite to the observations, with NCEP1 being underestimated by 53 W m−2 (the least biased) and ECMWF-OP by 108 W m−2 (the most biased). At the Arabian Sea buoy site, the NWP mean fluxes also have an underestimation bias, with the smallest bias of 26 W m−2 (ERA-40) and the largest bias of 69 W m−2 (NCEP1). On the other hand, the OAFlux+ISCCP has the best comparison at both measurement sites. Second, the bias effect changes with the time scale. Despite the fact that the mean is biased significantly, there is no major bias in the seasonal cycle of all the products except for ECMWF-OP. The latter does not have a fixed mean due to the frequent updates of the model platform. Finally, among the four products (OAFlux+ISCCP, ERA-40, NCEP1, and NCEP2) that can be used for studying interannual variability, OAFlux+ISCCP and ERA-40 Qnet have good consistency as judged from both statistical and physical measures. NCEP1 shows broad agreement with the two products, with varying details. By comparison, NCEP2 is the least representative of the Qnet variabilities over the basin scale.
Termination of Indian Ocean Dipole Events in a Coupled General Circulation Model
Authors: Rao Suryachandra A. , Masson Sebastien , Luo Jing-Jia , Behera Swadhin K. , Yamagata Toshio 
Published: June 2007

Abstract
Using 200 yr of coupled general circulation model (CGCM) results, causes for the termination of Indian Ocean dipole (IOD) events are investigated. The CGCM used here is the Scale Interaction Experiment-Frontier Research Center for Global Change (SINTEX-F1) model, which consists of a version of the European Community–Hamburg (ECHAM4.6) atmospheric model and a version of the Ocean Parallelise (OPA8.2) ocean general circulation model. This model reproduces reasonably well the present-day climatology and interannual signals of the Indian and Pacific Oceans. The main characteristics of the intraseasonal disturbances (ISDs)/oscillations are also fairly well captured by this model. However, the eastward propagation of ISDs in the model is relatively fast in the Indian Ocean and stationary in the Pacific compared to observations.
A sudden reversal of equatorial zonal winds is observed, as a result of significant intraseasonal disturbances in the equatorial Indian Ocean in November–December of IOD events, which evolve independently of ENSO. A majority of these IOD events (15 out of 18) are terminated mainly because of the 20–40-day ISD activity in the equatorial zonal winds. Ocean heat budget analysis in the upper 50 m clearly shows that the initial warming after the peak of the IOD phenomenon is triggered by increased solar radiation owing to clear-sky conditions in the eastern Indian Ocean. Subsequently, the equatorial jets excited by the ISD deepen the thermocline in the southeastern equatorial Indian Ocean. This deepening of the thermocline inhibits the vertical entrainment of cool waters and therefore the IOD is terminated. IOD events that co-occur with ENSO are terminated owing to anomalous incoming solar radiation as a result of prevailing cloud-free skies. Further warming occurs seasonally through the vertical convergence of heat due to a monsoonal wind reversal along Sumatra–Java. On occasion, strong ISD activities in July–August terminated short-lived IOD events by triggering downwelling intraseasonal equatorial Kelvin waves.
Clinical relevance of airway remodelling in airway diseases
Authors: James A. L. , Wenzel S. 
Published: June 2007

Asthma and chronic obstructive pulmonary disease (COPD) are characterised by airflow obstruction, airway remodelling (measurable structural change) and inflammation. The present review will examine the relationship between airway remodelling in these two conditions with respect to symptoms, abnormal lung function, airway hyperresponsiveness and decline in lung function. The potential for remodelling to be a protective response will also be discussed.Asthma is associated with variable symptoms and changes in lung function and also fixed abnormalities of lung function and an increased rate of decline in lung function with age. There is a relative preservation of the relaxed airway lumen dimensions, prominent thickening of the smooth muscle layer and reduced airway distensibility. The severity of asthma is related to the degree of airway remodelling, which is most marked in cases of fatal asthma.In COPD, symptoms are persistent and predictable but also progressive and are related to fixed abnormalities of lung function. Remodelling is associated with narrowing of the airway lumen and an increased thickness of the airway wall, although not usually to the extent seen in asthma. COPD is most often due to smoking where there is also remodelling of the parenchyma that may contribute to symptoms.
Leisure time activity and new onset of wheezing during adolescence
Authors: Vogelberg C. , Hirsch T. , Radon K. , Dressel H. , Windstetter D. , Weinmayr G. , Weiland S. K. , von Mutius E. , Nowak D. , Leupold W. 
Published: June 2007

Asthma prevalence is increasing in adult and paediatric patients. In the present study, the association between different leisure time activities and new onset of wheezing was analysed in adolescents aged 16–18 yrs taking part in a questionnaire-based follow-up of the International Study on Asthma and Allergies in Childhood in Munich and Dresden, Germany.Of the 3,785 adolescents who took part in the follow-up (76% response), 2,910 adolescents without earlier episodes of wheezing in childhood were included in the analyses. Of these, 330 (11.3%) reported new onset of wheeze during the previous 12 months.In the bivariate analyses, exercising more than once per week or performing computer work >1 h·day−1were inversely related to new onset of wheeze. In contrast, visiting discotheques on a regular basis increased the risk of new onset of wheeze (12.9versus9.9%). The observed inverse relationship between physical activity and new onset of wheeze was not an independent effect but mediated by differences in active smoking.The association between physical activity and new onset of wheeze disappeared when active smoking was taken into account. However, the present data do not allow for determining whether smoking operated as a confounder or as an intermediate factor,i.e.whether physical activities prevented active smoking.
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
Authors: Fujita Masashi , Mihara Hisaaki , Goto Susumu , Esaki Nobuyoshi , Kanehisa Minoru 
Published: June 2007

Abstract

Background
Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completely sequenced to date, it is tempting to ask whether the 23rd amino acid is left undiscovered in these genomes. Recently, a computational study addressed this question and reported that no tRNA gene for unknown amino acid was found in genome sequences available. However, performance of the tRNA prediction program on an unknown tRNA family, which may have atypical sequence and structure, is unclear, thereby rendering their result inconclusive. A protein-level study will provide independent insight into the novel amino acid.

Results
Assuming that the 23rd amino acid is also encoded by a stop codon, we systematically predicted proteins that contain stop-codon-encoded amino acids from 191 prokaryotic genomes. Since our prediction method relies only on the conservation patterns of primary sequences, it also provides an opportunity to search novel selenoproteins and other readthrough proteins. It successfully recovered many of currently known selenoproteins and pyrrolysine proteins. However, no promising candidate for the 23rd amino acid was detected, and only one novel selenoprotein was predicted.

Conclusion
Our result suggests that the unknown amino acid encoded by stop codons does not exist, or its phylogenetic distribution is rather limited, which is in agreement with the previous study on tRNA. The method described here can be used in future studies to explore novel readthrough events from complete genomes, which are rapidly growing.