bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Annual Cycle of the Axial Angular Momentum of the Atmosphere
Authors: Egger Joseph , Hoinka Klaus-Peter 
Published: March 2005

Abstract
Earlier analyses of the annual cycle of the axial angular momentum (AAM) are extended to include mass flows and vertical transports as observed, and to establish angular momentum budgets for various control volumes, using the European Centre for Medium-Range Forecasts (ECMWF) Re-Analyses (ERA) for the years 1979–92, transformed to height coordinates. In particular, the role of the torques is examined. The annual cycle of the zonally averaged angular momentum is large in the latitude belt 20° ⩽ |ϕ| ⩽ 45°, with little attenuation in the vertical up to a height of ∼12 km. The oscillation of the mass term (AAM due to the earth’s rotation) dominates in the lower troposphere, but that of the wind term (relative AAM) is more important elsewhere. The cycle of the friction torque as related to the trade winds prevails in the Tropics. Mountain torque and friction torque are equally important in the extratropical latitudes of the Northern Hemisphere.
The annual and the semiannual cycle of the global angular momentum are in good balance with the global mountain and friction torques. The addition of the global gravity wave torque destroys this agreement. The transports must be adjusted if budgets of domains of less than global extent are to be considered. Both a streamfunction, representing the nondivergent part of the fluxes, and a flux potential, describing the divergences/convergences, are determined. The streamfunction pattern mainly reflects the seasonal shift of the Hadley cell. The flux potential links the annual oscillations of the angular momentum with the torques. It is concluded that the interaction of the torques with the angular momentum is restricted to the lower troposphere, in particular, in the Tropics. The range of influence is deeper in the Northern Hemisphere than in the Southern Hemisphere, presumably because of the mountains. The angular momentum cycle in the upper troposphere and stratosphere is not affected by the torques and reflects interhemispheric flux patterns. Budgets for the polar as well as for the midlatitude domains show that fluxes in the stratosphere are important.
Topographic Effects on the Eastward Propagation and Initiation of the Madden–Julian Oscillation
Authors: Hsu Huang-Hsiung , Lee Ming-Ying 
Published: March 2005

Abstract
This study investigates the relationship between deep convection (and heating anomaly) in the Madden–Julian oscillation (MJO) and the tropical topography. The eastward propagation of the deep heating anomalies is confined to two regions: the Indian Ocean and the western Pacific warm pool. Superimposed on the eastward propagation is a series of quasi-stationary deep heating anomalies that occur sequentially and discretely downstream in a leapfrog manner in the central Indian Ocean, the Maritime Continent, tropical South America, and tropical Africa.
The deep heating anomaly, usually preceded by near-surface moisture convergence and shallow heating anomalies, tends to occur on the windward side of the tropical topography in these regions (except the central Indian Ocean) under the prevailing surface easterly anomaly of the MJO. It is suggested that the lifting and frictional effects of the tropical topography and landmass induce the near-surface moisture convergence anomaly, which in turn triggers the deep heating anomaly. Subsequently, the old heating anomaly located to the west of the tropical topography weakens and the new heating anomaly east of the topography develops because of the eastward shift in the major moisture convergence center to the east of the mountains. Therefore, the deep heating anomaly shifts eastward from one region to another. The equatorial Kelvin wave, which is forced by the tropical heating anomaly and propagates quickly across the ocean basins in the lower troposphere, plays an important role by helping to strengthen the easterly anomaly and lowering the surface pressure.
This process is proposed to further our understanding of the shift in the deep convection from the Indian Ocean to the western Pacific, the reappearance of the deep convection in tropical South America, and the initiation of the MJO in the western Indian Ocean. It is suggested that the fast eastward propagation and the slow development of quasi-stationary convection together determine the quasi-periodicity of the MJO.
The Forced and Intrinsic Low-Frequency Modes in the North Pacific*
Authors: An Soon-Il , Wang Bin 
Published: March 2005

Abstract
Conditional maximum covariance analysis is applied to investigate the coherent patterns between the tropical and North Pacific SST and the North Pacific 500-hPa geopotential height anomalies. Two leading modes are identified. One is an intrinsic midlatitude mode, the North Pacific (NP) mode, for which SST anomalies are mainly confined to the extratropical North Pacific. The other is a tropical ocean–atmosphere coupled mode, the ENSO mode, in which an ENSO-like SST pattern dominates the Tropics but extratropical SST anomalies are relatively weak.
The NP and ENSO modes exhibit distinct spatial and temporal characteristics. For the NP mode, atmospheric variation leads to changes in SST, while for the ENSO mode the opposite is true. The NP mode displays a persistence barrier during August–September whereas the ENSO mode has a March–April persistence barrier. The upper-tropospheric jet stream associated with the NP and ENSO mode intensifies, respectively, over the central North Pacific and the subtropical northeastern Pacific; consequently, the transient activities maximize in their corresponding jet exit regions. The expansion coefficients of the 500-hPa geopotential height associated with the two modes appear to be significantly correlated. However, by reducing the high-frequency part (e.g., shorter than the interannual time scale) in expansion coefficients, the correlation becomes insignificant, indicating that the significant correlation results from high-frequency signals that are unrelated to the corresponding SST variation. The results presented here suggest that the intrinsic coupled mode in the midlatitude North Pacific may be distinguished from the forced mode by remote ENSO, especially on the interannual time scale.
“Eyeballing” Trends in Climate Time Series: A Cautionary Note
Authors: Percival Donald B. , Rothrock D. Andrew 
Published: March 2005

Abstract
In examining a plot of a time series of a scalar climate variable for indications of climate change, an investigator might pick out what appears to be a linear trend commencing near the end of the record. Visual determination of the starting time of the trend can lead to an incorrect conclusion that the trend is significant when the assessment is based on standard linear regression analysis; in fact, a presumed level of significance of 5% can be smaller than the actual level by up to an order of magnitude. An alternative procedure is suggested that is more appropriate for assessing the significance of a trend in which the starting point is identified visually.
Variability in the Characteristics of Precipitation Systems in the Tropical Pacific. Part I: Spatial Structure
Authors: Masunaga Hirohiko , L’Ecuyer Tristan S. , Kummerow Christian D. 
Published: March 2005

Abstract
Regional and temporal variability in the vertical and horizontal characteristics of tropical precipitating clouds are investigated using the Precipitation Radar (PR) and the Visible and Infrared Scanner (VIRS) on board the Tropical Rainfall Measuring Mission (TRMM) satellite. The present study focuses on the three oceanic regions (west, central, and east Pacific) together with two continental regions for comparison and the two separate time periods (February 1998 and February 2000) under different phases of the El Niño–Southern Oscillation (ENSO) in order to examine regional and ENSO-related variations. The height spectrums of storms are investigated in terms of radar echo-top height and infrared brightness temperature. The variability in the spectrum clearly correlates with the large-scale circulation and its ENSO-related change. On the basis of the height spectrum, storm systems are classified into the four categories of shallow, cumulus congestus, deep stratiform, and deep convective. The deep stratiform and deep convective categories, both of which have very cold cloud tops, are differentiated by radar echo-top heights so that deep convective systems are accompanied with an appreciable amount of large frozen particles aloft. While shallow events are dominant in the probability of occurrence over relatively cold oceans, deep convective systems take their place for warmer sea surface temperatures (SSTs). The turnover occurs at the SST threshold of 28°–29°C for all the oceanic regions and years investigated except the west Pacific in 2000, for which deep convective systems prevail over the entire range of SST. Rain correlation-scale length (RCSL) and cloud correlation-scale length (CCSL) are introduced as statistical indicators of the horizontal scale of storms. While the RCSL is 8–18 km for shallow- and cumulus congestus–type clouds without significant regional and temporal variations, the RCSL and CCSL associated with deep stratiform and deep convective systems consistently exceed 100 km and exhibit a systematic variability. The RCSL and CCSL in the central and east Pacific, particularly, increase significantly in the El Niño year.
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
Authors: Marinescu Voichita D , Kohane Isaac S , Riva Alberto 
Published: March 2005

Abstract
Background
Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity.

Results
We describe the implementation of a search method for putative transcription factor binding sites (TFBSs) based on hidden Markov models built from alignments of known sites. We built 1,079 models of TFBSs using experimentally determined sequence alignments of sites provided by the TRANSFAC and JASPAR databases and used them to scan sequences of the human, mouse, fly, worm and yeast genomes. In several cases tested the method identified correctly experimentally characterized sites, with better specificity and sensitivity than other similar computational methods. Moreover, a large-scale comparison using synthetic data showed that in the majority of cases our method performed significantly better than a nucleotide weight matrix-based method.

Conclusion
The search engine, available at http://mapper.chip.org, allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, fly, worm and yeast genomes. In addition it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. Due to its extensive database of models, powerful search engine and flexible interface, MAPPER represents an effective resource for the large-scale computational analysis of transcriptional regulation.
Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails
Authors: Koene Joris M , Schulenburg Hinrich 
Published: March 2005

Abstract
Background
Evolutionary conflicts of interest between the sexes often lead to co-evolutionary arms races consisting of repeated arisal of traits advantageous for one sex but harmful to the other sex, and counter-adaptations by the latter. In hermaphrodites, these antagonistic interactions are at least an equally important driving force. Here, we investigate the evolution of one of the most striking examples of sexual conflict in hermaphrodites, the so-called shooting of love-darts in land snails. Stabbing this calcareous dart through the partner's skin ultimately increases paternity. This trait is obviously beneficial for the shooter, but it manipulates sperm storage in the receiver. Hence, an arms race between the love-dart and the spermatophore receiving organs may be expected.

Results
We performed a detailed phylogenetic analysis of 28S ribosomal RNA gene sequences from dart-possessing land snail species. Both the Shimodaira-Hasegawa test and Bayesian posterior probabilities rejected a monophyletic origin of most reproductive structures, including the love-dart, indicating that most traits arose repeatedly. Based on the inferred phylogenetic trees, we calculated phylogenetically independent contrasts for the different reproductive traits. Subsequent principal component and correlation analyses demonstrated that these contrasts covary, meaning that correlated evolution of these traits occurred.

Conclusion
Our study represents the first comprehensive comparative analysis of reproductive organ characteristics in simultaneous hermaphrodites. Moreover, it strongly suggests that co-evolutionary arms races can result from sexual conflict in these organisms and play a key role in the evolution of hermaphroditic mating systems.
Effect of testosterone replacement or duration of castration on baroreflex bradycardia in conscious rats
Authors: Ward Gregg R , Abdel-Rahman Abdel A 
Published: March 2005

Abstract
Background
In this study, we tested the hypothesis that 17β-estradiol contributes to testosterone-mediated restoration of baroreflex-mediated bradycardia in short-term (3 weeks) castrated rats. Further, a reported increase in serum testosterone after long-term (6 weeks) castration constituted a basis for testing the hypothesis that a spontaneous increase in serum testosterone or androstenedione in this model causes a commensurate increase in baroreflex-mediated bradycardia.

Results
Testosterone (1 week) replacement enhanced baroreflex-mediated bradycardia in short-term castrated rats without changing 17β-estradiol level. A spontaneous recovery of baroreflex-mediated bradycardia occurred following long-term castration, although circulating testosterone and androstenedione remained suppressed.

Conclusion
The data suggest: 1) 17β-Estradiol does not contribute to testosterone restoration of the baroreflex-mediated bradycardia in short-term castrated rats. 2) The long-term modulation of baroreflex-mediated bradycardia occurs independent of androgens, or the baroreflex mechanism may become adapted to low levels of circulating androgens.
Floral gene resources from basal angiosperms for comparative genomics research
Authors: Albert Victor A , Soltis Douglas E , Carlson John E , Farmerie William G , Wall P Kerr , Ilut Daniel C , Solow Teri M , Mueller Lukas A , Landherr Lena L , Hu Yi , Buzgo Matyas , Kim Sangtae , Yoo Mi-Jeong , Frohlich Michael W , Perl-Treves Rafael , Schlarbaum Scott E , Bliss Barbara J , Zhang Xiaohong , Tanksley Steven D , Oppenheimer David G , Soltis Pamela S , Ma Hong , dePamphilis Claude W , Leebens-Mack James H 
Published: March 2005

Abstract
Background
The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants.

Results
Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms.

Conclusion
Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.
The measurement of response shift in patients with advanced prostate cancer and their partners
Authors: Rees Jonathan , Clarke Michael G , Waldron Dympna , O'Boyle Ciaran , Ewings Paul , MacDonagh Ruaraidh P 
Published: March 2005

Abstract

Background
There is increasing evidence to support the phenomenon of response shift (RS) in quality of life (QoL) studies, with many current QoL measures failing to allow for this. If significant response shift occurs amongst prostate cancer patients, it will be necessary to allow for this in the design of future clinical research and to reassess the conclusions of previous studies that have not allowed for this source of bias. This study therefore aimed to assess the presence of RS and psychosocial morbidity in patients with advanced prostate cancer and their partners.

Methods
55 consecutive advanced prostate cancer patients and their partners completed the Prostate Cancer Patient & Partner questionnaire (PPP), shortly after diagnosis and again at 3 months and 6 months. At the follow-up visits, both patients and partners also completed a then-test in order to assess RS.

Results
Partners consistently showed greater psychological morbidity than patients in relation to the prostate cancer. This was most marked on the General Cancer Distress (GCD) subscale (p < 0.001, paired t-test), and regarding worries about treatment (p = 0.01). Significant RS was identified in partners and patients by the use of the then-test technique, particularly on the GCD subscale, the concerns about treatment and the concerns about urinary symptoms items.

Conclusion
These results suggest the presence of RS in patients with advanced prostate cancer and their partners, with higher levels of psychosocial morbidity noted amongst partners. This is the first study to identify RS in partners and calls into question the interpretation of all studies assessing changes in QoL that fail to allow for this phenomenon.
Mathematical model of blunt injury to the vascular wall via formation of rouleaux and changes in local hemodynamic and rheological factors. Implications for the mechanism of traumatic myocardial infarction
Authors: Ismailov Rovshan M 
Published: March 2005

AbstractBackgroundBlood viscosity is fundamentally important in clinical practice yet the apparent viscosity at very low shear rates is not well understood. Various conditions such as blunt trauma may lead to the appearance of zones inside the vessel where shear stress equals zero. The aim of this research was to determine the blood viscosity and quantitative aspects of rouleau formation from erythrocytes at yield velocity (and therefore shear stress) equal to zero. Various fundamental differential equations and aspects of multiphase medium theory have been used. The equations were solved by a method of approximation. Experiments were conducted in an aerodynamic tube.ResultsThe following were determined: (1) The dependence of the viscosity of a mixture on volume fraction during sedimentation of a group of particles (forming no aggregates), confirmed by published experimental data on the volume fractions of the second phase (f2) up to 0.6; (2) The dependence of the viscosity of the mixture on the volume fraction of erythrocytes during sedimentation of rouleaux when yield velocity is zero; (3) The increase in the viscosity of a mixture with an increasing erythrocyte concentration when yield velocity is zero; (4) The dependence of the quantity of rouleaux on shear stress (the higher the shear stress, the fewer the rouleaux) and on erythrocyte concentration (the more erythrocytes, the more rouleaux are formed).ConclusionsThis work represents one of few attempts to estimate extreme values of viscosity at low shear rate. It may further our understanding of the mechanism of blunt trauma to the vessel wall and therefore of conditions such as traumatic acute myocardial infarction. Such estimates are also clinically significant, since abnormal values of blood viscosity have been observed in many pathological conditions such as traumatic crush syndrome, cancer, acute myocardial infarction and peripheral vascular disease.
Synergistic effect of SCF and TNF-α on the up-regulation of cell-surface expression of ICAM-1 on human leukemic mast cell line (HMC)-1 cells
Authors: Tsang Chi-Man , Wong Chun-Kwok , Ip Wai-Ki , Lam Christopher Wai-Kei 
Published: March 2005

AbstractIntercellular adhesion molecule-1 (ICAM-1) has been shown to play crucial roles in mast cell interaction with other inflammatory cells and recruitment into the inflamed tissue. In the present study, human mast cell line-1 (HMC-1) was stimulated with different cytokines including stem cell factor (SCF), tumor necrosis factor α (TNF-α), interleukin (IL)-13, IL-18, and IL-25. Cell-surface expression of ICAM-1 was assessed by flow cytometry. To elucidate the intracellular signal transduction regulating the ICAM-1 expression, phosphorylated extracellular signal-regulated kinase (ERK), phosphorylated p38 mitogen-activated protein kinase (MAPK), and nuclear factor (NF)-κB translocation were assessed by enzyme-linked immunosorbent assay. Results showed that SCF, TNF-α, and IL-13 but not IL-18 and IL-25 could up-regulate the surface expression of ICAM-1 on HMC-1 cells. A synergistic effect of SCF and TNF-α on ICAM-1 expression was demonstrated. This synergistic effect was shown to be dose-dependently enhanced by SCF but not TNF-α. Results indicated that SCF activated ERK, and TNF-α activated the p38 MAPK and NF-κB pathway. Selective inhibitor of ERK, PD098059, and c-kit inhibitors, STI571 and PP1, suppressed the combined SCF and TNF-α-induced ICAM-1 expression. BAY117082 but not SB203580, which are the inhibitors of NF-κB and p38 MAPK, respectively, suppressed the TNF-α-induced ICAM-1 expression. Therefore, SCF and TNF-α acted through ERK and the NF-κB pathway to regulate the ICAM-1 expression and elicited the synergistic effect. In conclusion, our results provide insight for cross-talk between different signaling pathways that can help in understanding the fine control of adhesion molecule expression under the concerted effects of cytokines.