bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Importance of High-Frequency Sea Surface Temperature Variability to the Intraseasonal Oscillation of Indian Monsoon Rainfall
Authors: Klingaman Nicholas P. , Inness Peter M. , Weller Hilary , Slingo Julia M. 
Published: June 2008

AbstractWhile the Indian monsoon exhibits substantial variability on interannual time scales, its intraseasonal variability (ISV) is of greater magnitude and hence of critical importance for monsoon predictability. This ISV comprises a 30–50-day northward-propagating oscillation (NPISO) between active and break events of enhanced and reduced rainfall, respectively, over the subcontinent. Recent studies have implied that coupled general circulation models (CGCMs) were better able to simulate the NPISO than their atmosphere-only counterparts (AGCMs). These studies have forced their AGCMs with SSTs from coupled integrations or observations from satellite-based infrared sounders, both of which underestimate the ISV of tropical SSTs.The authors have forced the 1.25° × 0.83° Hadley Centre Atmospheric Model (HadAM3) with a daily, high-resolution, observed SST analysis from the United Kingdom National Center for Ocean Forecasting that contains greater ISV in the Indian Ocean than past products. One ensemble of simulations was forced by daily SSTs, a second with monthly means, and a third with 5-day means. The ensemble with daily SSTs displayed significantly greater variability in 30–50-day rainfall across the monsoon domain than the ensemble with monthly mean SSTs, variability similar to satellite-derived precipitation analyses. Individual ensemble members with daily SSTs contained intraseasonal events with a strength, a propagation speed, and an organization that closely matched observed events. When ensemble members with monthly mean SSTs displayed power in intraseasonal rainfall, the events were weak and disorganized, and they propagated too quickly. The ensemble with 5-day means had less intraseasonal rainfall variability than the ensemble with daily SSTs but still produced coherent NPISO-like events, indicating that SST variability at frequencies higher than 5 days contributes to but is not critical for simulations of the NPISO.It is concluded that high-frequency SST anomalies not only increased variance in intraseasonal rainfall but helped to organize and maintain coherent NPISO-like convective events. Further, the results indicate that an AGCM can respond to realistic and frequent SST forcing to generate an NPISO that closely resembles observations. These results have important implications for simulating the NPISO in AGCMs and coupled climate models, as well as for predicting tropical ISV in short- and medium-range weather forecasts.
Global Decadal Upper-Ocean Heat Content as Viewed in Nine Analyses
Authors: Carton James A. , Santorelli Anthony 
Published: May 2008

Abstract
This paper examines nine analyses of global ocean 0-/700-m temperature and heat content during the 43-yr period of warming, 1960–2002. Among the analyses are two that are independent of any numerical model, six that rely on sequential data assimilation, including an ocean general circulation model, and one that uses four-dimensional variational data assimilation (4DVAR), including an ocean general circulation model and its adjoint. Most analyses show gradual warming of the global ocean with an ensemble trend of 0.77 × 108 J m−2 (10 yr)−1 (=0.24 W m−2) as the result of rapid warming in the early 1970s and again beginning around 1990. One proposed explanation for these variations is the effect of volcanic eruptions in 1963 and 1982. Examination of this hypothesis suggests that while there is an oceanic signal, it is insufficient to explain the observed heat content variations.
A second potential cause of decadal variations in global heat content is the uncorrelated contribution of heat content variations in individual ocean basins. The subtropical North Atlantic is warming at twice the global average, with accelerated warming in the 1960s and again beginning in the late 1980s and extending through the end of the record. The Barents Sea region of the Arctic Ocean and the Gulf of Mexico have also warmed, while the western subpolar North Atlantic has cooled. Heat content variability in the North Pacific differs significantly from the North Atlantic. There the spatial and temporal patterns are consistent with the decadal variability previously identified through observational and modeling studies examining SST and surface winds. In the Southern Hemisphere large heat content anomalies are evident, and while there is substantial disagreement among analyses on average the band of latitudes at 30°–60°S contribute significantly to the global warming trend. Thus, the uncorrelated contributions of heat content variations in the individual basins are a major contributor to global heat content variations.
A third potential contributor to global heat content variations is the effect of time-dependent bias in the set of historical observations. This last possibility is examined by comparing the analyses to the unbiased salinity–temperature–depth dataset and finding a very substantial warm bias in all analyses in the 1970s relative to the latter decades. This warm bias may well explain the rapid increase in analysis heat content in the early 1970s, but not the more recent increase, which began in the early 1990s.
Finally, this study provides information about the similarities and differences between analyses that are independent of a model and those that use sequential assimilation and 4DVAR. The comparisons provide considerable encouragement for the use of the sequential analyses for climate research despite the presence of erroneous variability (also present in the no-model analyses) resulting from instrument bias. The strengths and weaknesses of each analysis need to be considered for a given application.
Changes in Water Vapor Transport and the Production of Precipitation in the Eastern Fertile Crescent as a Result of Global Warming
Authors: Evans J. P. 
Published: May 2008

Abstract
This study investigates changes in the types of storm events occurring in the Fertile Crescent as a result of global warming. Regional climate model [fifth-generation Pennsylvania State University–National Center for Atmospheric Research Mesoscale Model (MM5)–Noah] simulations are run for the first and last five years of the twenty-first century following the Special Report on Emissions Scenarios (SRES) A2 experiment. Then the precipitation events are classified according to the water vapor fluxes that created them. At present most of the region’s precipitation is from westerly water vapor fluxes. Results indicate that the region will increasingly get its precipitation from large events that are dominated by southerly water vapor fluxes. The increase in these events will occur in the transition seasons, especially autumn.
Correction of Angular Response Error in Brewer UV Irradiance Measurements
Authors: Antón Manuel , Serrano Antonio , Cancillo María L. , Vilaplana JoséM. , Cachorro Victoria E. , Gröbner Julian 
Published: May 2008

Abstract
Ultraviolet spectral irradiance measured by spectroradiometers usually presents high deviations from the ideal angular response due to imperfections in the entrance optics. In this paper a methodology to correct the angular error in the global UV spectral measurements of a Brewer MKIII spectroradiometer under all weather conditions is presented. This methodology calculates the global correction factor as a function of three variables: the direct irradiance correction factor, the diffuse irradiance correction factor, and a factor depending on the direct-to-global irradiance ratio. This work contributes to better measuring the UV radiation by improving the parameterization of the clouds effects.
Depending mainly on wavelength, solar zenith angle, and cloud optical thickness, the angular correction obtained ranges from 2% to 9%. The accuracy of this correction is limited by the uncertainties in the measured angular response and in the ratio of direct to global radiation. The original and the corrected Brewer measurements are compared with simultaneous values of the transportable Quality Assurance of Spectral Ultraviolet Measurements in Europe through the Development of a Transportable Unit (QASUME) reference spectroradiometer. A notable decrease (about a factor higher than 2) in the relative differences between the two instruments is obtained when Brewer-corrected measurements are considered.
An Alternative Tropical Cyclone Intensity Forecast Verification Technique
Authors: Aberson Sim D. 
Published: May 2008

Abstract
The National Hurricane Center (NHC) does not verify official or model forecasts if those forecasts call for a tropical cyclone to dissipate or if the real tropical cyclone dissipates. A new technique in which these forecasts are included in a contingency table with all other forecasts is presented. Skill scores and probabilities are calculated. Forecast verifications with the currently used technique have shown a slight improvement in intensity forecasts. The new technique, taking into account all forecasts, suggests that the probability of a forecast having a large (&gt;30 kt) error is decreasing, and the likelihood of the error being less than about 10 kt is increasing in time, at all forecast lead times except 12 h when the forecasts are already quite good.
Self-rated physical health predicts change in disability in multiple sclerosis
Authors: Drulovic J , Riise T , Nortvedt M , Pekmezovic T , Manigoda M 
Published: May 2008

Objective To examine whether self-rated physical health, as measured by the Physical Functioning Scale (PF) and the Role-physical Scale (RF) of the SF-36 Health Survey, could predict change in disability measured by the Expanded Disability Status Scale (EDSS) in patients with multiple sclerosis (MS) over a follow-up period of 3 years. Methods A group of 156 clinically definite MS patients (Poser criteria), who had never been treated with disease-modifying therapies, were recruited consecutively from an outpatient clinic setting at the Institute of Neurology, Belgrade. The self-rated physical health was measured by using PF and RF of the SF-36. Results At follow-up, 33 out of 156 patients (21%) had dropped out. The mean EDSS score had increased from 3.7 to 4.5. Multiple regression analyses using change in EDSS as the dependent variable and baseline scores of EDSS and RF as independent variables showed a significant effect for RF (standardized beta = –0.21). A similar but non-significant effect was found for PF. Dichotomizing change in disability according to clinically meaningful deterioration and using logistic regression, an odds ratio of 1.27 (95% confidence interval 1.01–1.62) was found for the smallest unit of change in the self-rated scale. This means that patients who rated their own physical health as poor had a higher increase in disability compared with patients with the same level of disability at baseline who rated their physical health better. Conclusions MS patients’ perception of their health comprises information predictive for disease development not included in the more objective measure of disability status.
Interferon-β stabilizes barrier characteristics of the blood–brain barrier in four different species in vitro
Authors: Kraus J , Voigt K , Schuller AM , Scholz M , Kim KS , Schilling M , Schäbitz WR , Oschmann P , Engelhardt B 
Published: May 2008

Background Blood–brain barrier (BBB) breakdown is an early event in the pathogenesis of multiple sclerosis (MS). In a previous study we have found a direct stabilization of barrier characteristics after treatment of bovine brain capillary endothelial cells (BCECs) with human recombinant interferon-β-1a (IFN-β-1a) in an in vitro BBB model. In the present study we examined the effect of human recombinant IFN-β-1a on the barrier properties of BCECs derived from four different species including humans to predict treatment efficacy of IFN-β-1a in MS patients. Methods We used primary bovine and porcine BCECs, as well as human and murine BCEC cell lines. We investigated the influence of human recombinant IFN-β-1a on the paracellular permeability for 3H-inulin and 14C-sucrose across monolayers of bovine, human, and murine BCECs. In addition, the transendothelial electrical resistance (TEER) was determined in in vitro systems applying porcine and murine BCECS. Results We found a stabilizing effect on the barrier characteristics of BCECs after pretreatment with IFN-β-1a in all applied in vitro models: addition of IFN-β-1a resulted in a significant decrease of the paracellular permeability across monolayers of human, bovine, and murine BCECs. Furthermore, the TEER was significantly increased after pretreatment of porcine and murine BCECs with IFN-β-1a. Conclusion Our data suggest that BBB stabilization by IFN-β-1a may contribute to its beneficial effects in the treatment of MS. A human in vitro BBB model might be useful as bioassay for testing the treatment efficacy of drugs in MS.
Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists
Authors: Deng Xutao , Xu Jun , Wang Charles 
Published: May 2008

Abstract

Background
In DNA microarray gene expression profiling studies, a fundamental task is to extract statistically significant genes that meet certain research hypothesis. Currently, Venn diagram is a frequently used method for identifying overlapping genes that meet the investigator's research hypotheses. However this simple operation of intersecting multiple gene lists, known as the Intersection-Union Tests (IUTs), is performed without knowing the incurred changes in Type 1 error rate and can lead to loss of discovery power.

Results
We developed an IUT adjustment procedure, called Relaxed IUT (RIUT), which is proved to be less conservative and more powerful for intersecting independent tests than the traditional Venn diagram approach. The advantage of the RIUT procedure over traditional IUT is demonstrated by empirical Monte-Carlo simulation and two real toxicogenomic gene expression case studies. Notably, the enhanced power of RIUT enables it to identify overlapping gene sets leading to identification of certain known related pathways which were not detected using the traditional IUT method.

Conclusion
We showed that traditional IUT via a Venn diagram is generally conservative, which may lead to loss discovery power in DNA microarray studies. RIUT is proved to be a more powerful alternative for performing IUTs in identifying overlapping genes from multiple gene lists derived from microarray gene expression profiling.
Comparative analyses of bidirectional promoters in vertebrates
Authors: Yang Mary Qu , Taylor James , Elnitski Laura 
Published: May 2008

Abstract

Background
Orthologous genes with deep phylogenetic histories are likely to retain similar regulatory features. In this report we utilize orthology assignments for pairs of genes co-regulated by bidirectional promoters to map the ancestral history of the promoter regions.

Results
Our mapping of bidirectional promoters from humans to fish shows that many such promoters emerged after the divergence of chickens and fish. Furthermore, annotations of promoters in deep phylogenies enable detection of missing data or assembly problems present in higher vertebrates. The functional importance of bidirectional promoters is indicated by selective pressure to maintain the arrangement of genes regulated by the promoter over long evolutionary time spans. Characteristics unique to bidirectional promoters are further elucidated using a technique for unsupervised classification, known as ESPERR.

Conclusion
Results of these analyses will aid in our understanding of the evolution of bidirectional promoters, including whether the regulation of two genes evolved as a consequence of their proximity or if function dictated their co-regulation.
Control over the morphology and segregation of Zebrafish germ cell granules during embryonic development
Authors: Strasser Markus J , Mackenzie Natalia C , Dumstrei Karin , Nakkrasae La-Iad , Stebler Jürg , Raz Erez 
Published: May 2008

AbstractBackgroundZebrafish germ cells contain granular-like structures, organized around the cell nucleus. These structures share common features with polar granules in Drosophila, germinal granules in Xenopus and chromatoid bodies in mice germ cells, such as the localization of the zebrafish Vasa, Piwi and Nanos proteins, among others. Little is known about the structure of these granules as well as their segregation in mitosis during early germ-cell development.ResultsUsing transgenic fish expressing a fluorescently labeled novel component of Zebrafish germ cell granules termed Granulito, we followed the morphology and distribution of the granules. We show that whereas these granules initially exhibit a wide size variation, by the end of the first day of development they become a homogeneous population of medium size granules. We investigated this resizing event and demonstrated the role of microtubules and the minus-end microtubule dependent motor protein Dynein in the process. Last, we show that the function of the germ cell granule resident protein the Tudor domain containing protein-7 (Tdrd7) is required for determination of granule morphology and number.ConclusionOur results suggest that Zebrafish germ cell granules undergo a transformation process, which involves germ cell specific proteins as well as the microtubular network.
RPS4Ygene family evolution in primates
Authors: Andrés Olga , Kellermann Thomas , López-Giráldez Francesc , Rozas Julio , Domingo-Roura Xavier , Bosch Montserrat 
Published: May 2008

AbstractBackgoundTheRPS4gene codifies for ribosomal protein S4, a very well-conserved protein present in all kingdoms. In primates,RPS4is codified by two functional genes located on both sex chromosomes: theRPS4XandRPS4Ygenes. In humans,RPS4Yis duplicated and the Y chromosome therefore carries a third functional paralog:RPS4Y2, which presents a testis-specific expression pattern.ResultsDNA sequence analysis of the intronic and cDNA regions ofRPS4Ygenes from species covering the entire primate phylogeny showed that the duplication event leading to the second Y-linked copy occurred after the divergence of New World monkeys, about 35 million years ago. Maximum likelihood analyses of the synonymous and non-synonymous substitutions revealed that positive selection was acting onRPS4Y2gene in the human lineage, which represents the first evidence of positive selection on a ribosomal protein gene. Putative positive amino acid replacements affected the three domains of the protein: one of these changes is located in the KOW protein domain and affects the unique invariable position of this motif, and might thus have a dramatic effect on the protein function.ConclusionHere, we shed new light on the evolutionary history ofRPS4Ygene family, especially on that ofRPS4Y2. The results point that theRPS4Y1gene might be maintained to compensate gene dosage between sexes, whileRPS4Y2might have acquired a new function, at least in the lineage leading to humans.
Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth
Authors: Lee Ju-Hoon , Karamychev VN , Kozyavkin SA , Mills D , Pavlov AR , Pavlova NV , Polouchine NN , Richardson PM , Shakhova VV , Slesarev AI , Weimer B , O'Sullivan DJ 
Published: May 2008

AbstractBackgroundBifidobacteria are frequently proposed to be associated with good intestinal health primarily because of their overriding dominance in the feces of breast fed infants. However, clinical feeding studies with exogenous bifidobacteria show they don't remain in the intestine, suggesting they may lose competitive fitness when grown outside the gut.ResultsTo further the understanding of genetic attenuation that may be occurring in bifidobacteria cultures, we obtained the complete genome sequence of an intestinal isolate,Bifidobacterium longumDJO10A that was minimally cultured in the laboratory, and compared it to that of a culture collection strain,B. longumNCC2705. This comparison revealed colinear genomes that exhibited high sequence identity, except for the presence of 17 unique DNA regions in strain DJO10A and six in strain NCC2705. While the majority of these unique regions encoded proteins of diverse function, eight from the DJO10A genome and one from NCC2705, encoded gene clusters predicted to be involved in diverse traits pertinent to the human intestinal environment, specifically oligosaccharide and polyol utilization, arsenic resistance and lantibiotic production. Seven of these unique regions were suggested by a base deviation index analysis to have been precisely deleted from strain NCC2705 and this is substantiated by a DNA remnant from within one of the regions still remaining in the genome of NCC2705 at the same locus. This targeted loss of genomic regions was experimentally validated when growth of the intestinalB. longumin the laboratory for 1,000 generations resulted in two large deletions, one in a lantibiotic encoding region, analogous to a predicted deletion event for NCC2705. A simulated fecal growth study showed a significant reduced competitive ability of this deletion strain againstClostridium difficileandE. coli. The deleted region was between two IS30elements which were experimentally demonstrated to be hyperactive within the genome. The other deleted region bordered a novel class of mobile elements, termed mobile integrase cassettes (MIC) substantiating the likely role of these elements in genome deletion events.ConclusionDeletion of genomic regions, often facilitated by mobile elements, allows bifidobacteria to adapt to fermentation environments in a very rapid manner (2 genome deletions per 1,000 generations) and the concomitant loss of possible competitive abilities in the gut.