bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpreting Century-Scale Changes in Southern North Sea Storm Surge Climate Derived from Coupled Model Simulations
Authors: Howard Tom , Lowe Jason , Horsburgh Kevin 
Published: August 2010

Abstract
This paper describes numerical experiments using a climate–storm surge simulation system for the coast of the United Kingdom, with a particular focus on the southern North Sea and the Thames estuary in southeastern England.
Time series of surges simulated in the southern North Sea by a surge model driven by atmospheric data from a regional climate model and surges simulated by the same surge model driven by atmospheric data from a global climate model are compared. A strong correspondence is demonstrated, and a linear scaling factor relating them is derived. This factor varies slowly with location. Around the Thames estuary, extreme surges are compared in the same way, and the linear scaling factor for the extremes is found to be similar to that for the full time series. The authors therefore assert that in seeking significant trends in surge at this location using this model arrangement, the regional model downscaling stage could be avoided, if observations were used to establish a suitable scaling factor for each location.
The influence of the tide–surge phase relationship is investigated, and extreme sea levels at the mouth of the River Thames from regional-model-driven simulations are compared to the extreme event of 1953. Although the simulated levels are slightly lower, they are found to be comparable given the observational uncertainty.
The assumption that time-mean sea level changes can be added linearly to surge changes is investigated at this location for large changes in time-mean sea level. The authors find that the primary effect of such an increase is on the speed of propagation of tide and surge, supporting the case for a simple linear addition of mean and extreme sea level changes.
The Effect of Milankovitch Variations in Insolation on Equatorial Seasonality
Authors: Ashkenazy Yosef , Eisenman Ian , Gildor Hezi , Tziperman Eli 
Published: August 2010

Abstract
Although the sun crosses the equator 2 times per year at the equinoxes, at times in the past the equatorial insolation has had only one maximum and one minimum throughout the seasonal cycle because of Milankovitch orbital variations. Here a state-of-the-art coupled atmosphere–ocean general circulation model is used to study the effect of such insolation forcing on equatorial surface properties, including air and sea temperature, salinity, winds, and currents. It is shown that the equatorial seasonality is altered according to the insolation with, for example, either maximum sea surface temperature (SST) close to the vernal equinox and minimum SST close to the autumnal equinox or vice versa. The results may have important implications for understanding tropical climate as well as for the interpretation of proxy data collected from equatorial regions.
NARR’s Atmospheric Water Cycle Components. Part II: Summertime Mean and Diurnal Interactions
Authors: Ruane Alex C. 
Published: August 2010

Abstract
Summertime interactions in the North American Regional Reanalysis (NARR) atmospheric water cycle are examined from a user’s perspective over the 1980–99 period with a particular emphasis on the diurnal cycle, the nocturnal maximum of precipitation over the Midwest, and the impacts of precipitation assimilation. NARR’s full-year mean atmospheric water cycle and its annual variations are examined in Part I of this study. North American summertime (June–August) features substantial convective activity that is often organized on a diurnal scale, although diverse regional diurnal features are evident to various extents in high-resolution precipitation products. NARR’s hourly assimilation of precipitation observations over the continental United States allows it to resolve diurnal effects on the water cycle, but in other regions the diurnal cycle of precipitation is imposed from an external reanalysis model. The prominent nocturnal maximum in precipitation across the upper Midwest is captured in NARR, but different precipitation assimilation sources disrupt the propagation of convective systems across the Canadian border. Normalized covariances of NARR’s diurnal water cycle component interactions in the nocturnal maximum region reveal a strong relationship between moisture convergence and precipitation, and also measure the way in which the precipitable water column holds a lagged response between evaporation and precipitation. In many regions the diurnal cycle of rainfall is driven by interactions with water cycle components that differ from those driving the seasonal cycle. A comparison between NARR’s precipitation and an estimate of the model precipitation prior to precipitation assimilation distinguishes the portion of the water cycle captured in full by the model and that which is value added by the assimilation routine. The nocturnal rainfall maximum is not present in the model precipitation estimate, leading to diurnal-scale biases in the evaporation and moisture flux convergence fields that are not directly modified by precipitation assimilation.
On the Merits of Using a 3D-FGAT Assimilation Scheme with an Outer Loop for Atmospheric Situations Governed by Transport
Authors: Massart Sébastien , Pajot Benjamin , Piacentini Andrea , Pannekoucke Olivier 
Published: August 2010

Abstract
Three-dimensional variational data assimilation (3D-Var) with the first guess at appropriate time (FGAT) appears to be an attractive compromise between accuracy and overall computing time. It is computationally cheaper than four-dimensional (4D)-Var as the increment is not propagated back and forth in time by a model, yet the comparison between the model and the observations is still computed at the right observation time. An interesting feature of the 4D-Var is the iterative process known as the outer loop. This outer-loop approach can also be used in conjunction with 3D-FGAT. But it requires the application of the 3D-FGAT analysis increment at the beginning of the assimilation window.
The pros and cons of using this unusual 3D-FGAT variant are illustrated in this paper on two applications focused on the transport, one of the main phenomena governing the atmospheric evolution. The first one is the one-dimensional advection of a passive tracer. By three representative situations, it shows the benefits of the outer loop, except for practical situations driven by very rapid dynamics such as a zonal wind of 50 m s−1 on the earth’s great circle, when the assimilation window has a size of 3 h. The second application is the 3D-FGAT assimilation of true ozone measurements into a chemical–transport model. It confirms the previous results, showing that the 3D-FGAT analysis with the outer loop produces an overestimation of the ozone increment in regions where the wind speed is high compared to the time length of the assimilation window.
A Coupled Atmosphere–Wave–Ocean Modeling System: Simulation of the Intensity of an Idealized Tropical Cyclone
Authors: Liu Bin , Liu Huiqing , Xie Lian , Guan Changlong , Zhao Dongliang 
Published: August 2010

Abstract
A coupled atmosphere–wave–ocean modeling system (CAWOMS) based on the integration of atmosphere–wave, atmosphere–ocean, and wave–current interaction processes is developed. The component models consist of the Weather Research and Forecasting (WRF) model, the Simulating Waves Nearshore (SWAN) model, and the Princeton Ocean Model (POM). The coupling between the model components is implemented by using the Model Coupling Toolkit. The CAWOMS takes into account various wave-related effects, including wave state and sea-spray-affected sea surface roughness, sea spray heat fluxes, and dissipative heating in atmosphere–wave coupling. It also considers oceanic effects such as the feedback of sea surface temperature (SST) cooling and the impact of sea surface current on wind stress in atmosphere–ocean coupling. In addition, wave–current interactions, including radiation stress and wave-induced bottom stress, are also taken into account. The CAWOMS is applied to the simulation of an idealized tropical cyclone (TC) to investigate the effects of atmosphere–wave–ocean coupling on TC intensity. Results show that atmosphere–wave coupling strengthens the TC system, while the thermodynamic coupling between the atmosphere and ocean weakens the TC as a result of the negative feedback of TC-induced SST cooling. The overall effects of atmosphere–wave–ocean coupling on TC intensity are determined by the balance between wave-related positive feedback and the negative feedback attributable to TC-induced SST cooling.
Photodepletion differentially affects CD4+ Tregs versus CD4+ effector T cells from patients with chronic graft-versus-host disease
Authors: Bastien Jean-Philippe , Krosl Gorazd , Therien Cynthia , Rashkovan Marissa , Scotto Christian , Cohen Sandra , Allan David S. , Hogge Donna , Egeler R. Maarten , Perreault Claude , Roy Denis Claude 
Published: August 2010

AbstractEven the most potent immunosuppressive drugs often fail to control graft-versus-host disease (GVHD), the most frequent and deleterious posttransplantation complication. We previously reported that photodepletion using dibromorhodamine (TH9402) eliminates T cells from healthy donors activated against major histocompatibility complex–incompatible cells and spares resting T cells. In the present study, we identified photodepletion conditions selectively eradicating endogenous proliferating T cells from chronic GVHD patients, with the concomittant sparing and expansion of CD4+CD25+ forkhead box protein 3–positive T cells. The regulatory T-cell (Treg) nature and function of these photodepletion-resistant cells was demonstrated in coculture and depletion/repletion experiments. The mechanism by which Tregs escape photodepletion involves active P-glycoprotein–mediated drug efflux. This Treg-inhibitory activity is attributable to interleukin-10 secretion, requires cell-cell contact, and implies binding with cytotoxic T-lymphocyte antigen 4 (CTLA-4). Preventing CTLA-4 ligation abrogated the in vitro generation of Tregs, thus identifying CTLA-4–mediated cell-cell contact as a crucial priming event for Treg function. Moreover, the frequency of circulating Tregs increased in chronic GVHD patients treated with TH9402 photodepleted cells. In conclusion, these results identify a novel approach to both preserve and expand Tregs while selectively eliminating CD4+ effector T cells. They also uncover effector pathways that could be used advantageously for the treatment of patients with refractory GVHD.
Novel strong tissue specific promoter for gene expression in human germ cells
Authors: Kuzmin Denis , Gogvadze Elena , Kholodenko Roman , Grzela Dawid P , Mityaev Maxim , Vinogradova Tatyana , Kopantzev Eugene , Malakhova Galina , Suntsova Maria , Sokov Dmitry , Ivics Zoltán , Buzdin Anton 
Published: August 2010

Abstract

Background
Tissue specific promoters may be utilized for a variety of applications, including programmed gene expression in cell types, tissues and organs of interest, for developing different cell culture models or for use in gene therapy. We report a novel, tissue-specific promoter that was identified and engineered from the native upstream regulatory region of the human gene NDUFV1 containing an endogenous retroviral sequence.

Results
Among seven established human cell lines and five primary cultures, this modified NDUFV1 upstream sequence (mNUS) was active only in human undifferentiated germ-derived cells (lines Tera-1 and EP2102), where it demonstrated high promoter activity (~twice greater than that of the SV40 early promoter, and comparable to the routinely used cytomegaloviral promoter). To investigate the potential applicability of the mNUS promoter for biotechnological needs, a construct carrying a recombinant cytosine deaminase (RCD) suicide gene under the control of mNUS was tested in cell lines of different tissue origin. High cytotoxic effect of RCD with a cell-death rate ~60% was observed only in germ-derived cells (Tera-1), whereas no effect was seen in a somatic, kidney-derived control cell line (HEK293). In further experiments, we tested mNUS-driven expression of a hyperactive Sleeping Beauty transposase (SB100X). The mNUS-SB100X construct mediated stable transgene insertions exclusively in germ-derived cells, thereby providing further evidence of tissue-specificity of the mNUS promoter.

Conclusions
We conclude that mNUS may be used as an efficient promoter for tissue-specific gene expression in human germ-derived cells in many applications. Our data also suggest that the 91 bp-long sequence located exactly upstream NDUFV1 transcriptional start site plays a crucial role in the activity of this gene promoter in vitro in the majority of tested cell types (10/12), and an important role - in the rest two cell lines.
Modeling the epidemiological history of plague in Central Asia: Palaeoclimatic forcing on a disease system over the past millennium
Authors: Kausrud Kyrre Linné , Begon Mike , Ari Tamara Ben , Viljugrein Hildegunn , Esper Jan , Büntgen Ulf , Leirs Herwig , Junge Claudia , Yang Bao , Yang Meixue , Xu Lei , Stenseth Nils Chr 
Published: August 2010

Abstract

Background
Human cases of plague (Yersinia pestis) infection originate, ultimately, in the bacterium's wildlife host populations. The epidemiological dynamics of the wildlife reservoir therefore determine the abundance, distribution and evolution of the pathogen, which in turn shape the frequency, distribution and virulence of human cases. Earlier studies have shown clear evidence of climatic forcing on contemporary plague abundance in rodents and humans.

Results
We find that high-resolution palaeoclimatic indices correlate with plague prevalence and population density in a major plague host species, the great gerbil (Rhombomys opimus), over 1949-1995. Climate-driven models trained on these data predict independent data on human plague cases in early 20th-century Kazakhstan from 1904-1948, suggesting a consistent impact of climate on large-scale wildlife reservoir dynamics influencing human epidemics. Extending the models further back in time, we also find correspondence between their predictions and qualitative records of plague epidemics over the past 1500 years.

Conclusions
Central Asian climate fluctuations appear to have had significant influences on regional human plague frequency in the first part of the 20th century, and probably over the past 1500 years. This first attempt at ecoepidemiological reconstruction of historical disease activity may shed some light on how long-term plague epidemiology interacts with human activity. As plague activity in Central Asia seems to have followed climate fluctuations over the past centuries, we may expect global warming to have an impact upon future plague epidemiology, probably sustaining or increasing plague activity in the region, at least in the rodent reservoirs, in the coming decades.
See commentary: http://www.biomedcentral.com/1741-7007/8/108
Serological characterization of guinea pigs infected with H3N2 human influenza or immunized with hemagglutinin protein
Authors: Bushnell Ruth V , Tobin John K , Long Jinxue , Schultz-Cherry Stacey , Chaudhuri A Ray , Nara Peter L , Tobin Gregory J 
Published: August 2010

AbstractBackgroundRecent and previous studies have shown that guinea pigs can be infected with, and transmit, human influenza viruses. Therefore guinea pig may be a useful animal model for better understanding influenza infection and assessing vaccine strategies. To more fully characterize the model, antibody responses following either infection/re-infection with human influenza A/Wyoming/03/2003 H3N2 or immunization with its homologous recombinant hemagglutinin (HA) protein were studied.ResultsSerological samples were collected and tested for anti-HA immunoglobulin by ELISA, antiviral antibodies by hemagglutination inhibition (HI), and recognition of linear epitopes by peptide scanning (PepScan). Animals inoculated with infectious virus demonstrated pronounced viral replication and subsequent serological conversion. Animals either immunized with the homologous HA antigen or infected, showed a relatively rapid rise in antibody titers to the HA glycoprotein in ELISA assays. Antiviral antibodies, measured by HI assay, were detectable after the second inoculation. PepScan data identified both previously recognized and newly defined linear epitopes.ConclusionsInfection and/or recombinant HA immunization of guinea pigs with H3N2 Wyoming influenza virus resulted in a relatively rapid production of viral-specific antibody thus demonstrating the strong immunogenicity of the major viral structural proteins in this animal model for influenza infection. The sensitivity of the immune response supports the utility of the guinea pig as a useful animal model of influenza infection and immunization.
SICTIN: Rapid footprinting of massively parallel sequencing data
Authors: Enroth Stefan , Andersson Robin , Wadelius Claes , Komorowski Jan 
Published: August 2010

Abstract

Background
Massively parallel sequencing allows for genome-wide hypothesis-free investigation of for instance transcription factor binding sites or histone modifications. Although nucleotide resolution detailed information can easily be generated, biological insight often requires a more general view of patterns (footprints) over distinct genomic features such as transcription start sites, exons or repetitive regions. The construction of these footprints is however a time consuming task.

Methods
The presented software generates a binary representation of the signals enabling fast and scalable lookup. This representation allows for footprint generation in mere minutes on a desktop computer. Several different input formats are accepted, e.g. the SAM format, bed-files and the UCSC wiggle track.

Conclusions
Hypothesis-free investigation of genome wide interactions allows for biological data mining at a scale never before seen. Until recently, the main focus of analysis of sequencing data has been targeted on signal patterns around transcriptional start sites which are in manageable numbers. Today, focus is shifting to a wider perspective and numerous genomic features are being studied. To this end, we provide a system allowing for fast querying in the order of hundreds of thousands of features.
Swimming behavior and prey retention of the polychaete larvaePolydora ciliata(Johnston)
Authors: Hansen B. W. , Jakobsen H. H. , Andersen A. , Almeda R. , Pedersen T. M. , Christensen A. M. , Nilsson B. 
Published: August 2010

SUMMARYThe behavior of the ubiquitous estuarine planktotrophic spionid polychaete larvae Polydora ciliata was studied. We describe ontogenetic changes in morphology, swimming speed and feeding rates and have developed a simple swimming model using low Reynolds number hydrodynamics. In the model we assumed that the ciliary swimming apparatus is primarily composed of the prototroch and secondarily by the telotroch. The model predicted swimming speeds and feeding rates that corresponded well with the measured speeds and rates. Applying empirical data to the model, we were able to explain the profound decrease in specific feeding rates and the observed increase in the difference between upward and downward swimming speeds with larval size. We estimated a critical larval length above which the buoyancy-corrected weight of the larva exceeds the propulsion force generated by the ciliary swimming apparatus and thus forces the larva to the bottom. This modeled critical larval length corresponded to approximately 1 mm, at which, according to the literature, competence for metamorphosis and no more length increase is observed. These findings may have general implications for all planktivorous polychaete larvae that feed without trailing threads. We observed bell shaped particle retention spectra with a minimum prey size of approximately 4 μm equivalent spherical diameter, and we found that an ontogenetic increase in maximum prey size add to a reduction in intra-specific food competition in the various larval stages. In a grazing experiment using natural seawater, ciliates were cleared approximately 50% more efficiently than similar sized dinoflagellates. The prey sizes retainable for P. ciliata larvae covers the microplankton fraction and includes non-motile as well as motile prey items, which is why the larvae are trophically positioned among the copepods and dinoflagellates. Not only do larval morphology and behavior govern larval feeding, prey behavior also influences the feeding efficiency of Polydora ciliata.
The orientation-dependent visual spatial cut-off frequency in a spider
Authors: Fenk Lisa M. , Schmid Axel 
Published: August 2010

SUMMARY
Cupiennius salei (Araneae, Ctenidae) has, like most spiders, eight camera-type eyes. The anterior median eyes are called principal eyes and have a movable retina; all of the other eyes are referred to as secondary eyes and are equipped with a reflecting tapetum. The photoreceptors in the secondary eyes are arranged in rows on the tapetum and the inter-receptor angle along such a row is smaller than normal to it. In this study, the vertical and horizontal spatial cut-off frequencies of moving gratings were measured for the posterior median (PM) eyes, and the data were then compared with the anatomical data reported in the literature. Detection of moving objects in the secondary eyes enhances the eye muscle potential frequency in the principal eyes. We thus recorded the eye muscle activity with a telemetric unit as a monitor for motion detection while moving stimuli – sinusoidally modulated bright and dark stripes – were presented to the PM eyes on a computer screen. A significant increase in the eye muscle activity was measured for gratings at an angular wavelength of 2.0 deg in the vertical orientation and of 2.7 deg in the horizontal direction. In the vertical orientation the critical wavelength is twice the inter-receptor angle; in the horizontal orientation the spiders responded to wavelengths that are smaller than twice the corresponding inter-receptor angle. The cut-off frequency seems thus to be limited by the visual field of the photoreceptors rather than the inter-receptor angle. The relative intensity modulations modelled for the two different grating orientations in single photoreceptor cells were in line with our data.