bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Regulation and Functional Alterations Induced by Kaposi's Sarcoma-Associated Herpesvirus-Encoded
ORFK13/vFLIP
in Endothelial Cells
Authors: Sakakibara Shuhei , Pise-Masison Cynthia A. , Brady John N. , Tosato Giovanna 
Published: December 2008

ABSTRACT

Kaposi's sarcoma (KS) is an angioproliferative inflammatory disorder induced by endothelial cell infection with the KS-associated herpesvirus (KSHV).
ORFK13/vFLIP
, one of the KSHV genes expressed in KS, encodes a 188-amino-acid protein which binds to the Iκb kinase (IKK) complex to activate NF-κB. We examined
ORFK13/vFLIP
contribution to KS phenotype and potential for therapeutic targeting. Retroviral transduction of
ORFK13/vFLIP
into primary human endothelial cells induces the spindle morphology distinctive of KS cells and promotes the formation of abnormal vascular networks typical of KS vasculature; upregulates the expression of proinflammatory cytokines, chemokines, and interferon-responsive genes; and stimulates the adhesion of inflammatory cells characteristic of KS lesions. Thymidine phosphorylase, a cellular enzyme markedly induced by
ORFK13/vFLIP
, can metabolize the prodrug 5-fluoro-5-deoxyuridine (5-dFUrd) to 5-fluouridine (5-FU), a potent thymidine synthase inhibitor, which blocks DNA and RNA synthesis. When tested for cytotoxicity, 5-dFUrd (0.1 to 1 μM) selectively killed
ORFK13/vFLIP
-expressing endothelial cells while sparing control cells. These results demonstrate that
ORFK13/vFLIP
directly and indirectly contributes to the inflammatory and vascular phenotype of KS and identify 5-dFUrd as a potential new drug that targets KSHV latency for the treatment of KS and other KSHV-associated malignancies.
Comprehensive Profiling of Epstein-Barr Virus MicroRNAs in Nasopharyngeal Carcinoma
Authors: Cosmopoulos Katherine , Pegtel Michiel , Hawkins Jared , Moffett Howell , Novina Carl , Middeldorp Jaap , Thorley-Lawson David A. 
Published: December 2008

ABSTRACT

Epstein-Barr Virus (EBV) establishes a long-term latent infection and is associated with a number of human malignancies that are thought to arise from deregulation of different stages of the viral life cycle. Recently, a large number of microRNAs (miRNAs) have been described for EBV, and it has been suggested that their expression may vary between the different latency states found in normal and malignant tissue. To date, however, no technique has been utilized to comprehensively and quantitatively test this idea by profiling expression of the EBV miRNAs in primary infected tissues. We describe here a multiplex reverse transcription-PCR assay that allows the profiling of 39 of the 40 known mature EBV miRNAs from as little as 250 ng of RNA. With this approach, we present a comprehensive profile of EBV miRNAs in primary nasopharyngeal carcinoma (NPC) tumors including estimates of miRNA copy number per tumor cell. This is the first comprehensive profiling of EBV miRNAs in any EBV-associated tumor. In contrast to previous suggestions, we show that the BART-derived miRNAs are present in a wide range of copy numbers from ≤10
3
per cell in both primary tumors and the widely used NPC-derived C666-1 cell line. However, we confirm the hypothesis that the BHRF1 miRNAs are not expressed in NPC. Lastly, we demonstrate that EBV miRNA expression in the widely used NPC line C666-1 is, with some caveats, broadly representative of primary NPC tumors.
Genome Comparison of a Nonpathogenic Myxoma Virus Field Strain with Its Ancestor, the Virulent Lausanne Strain
Authors: Morales Mónica , Ramírez Miguel A. , Cano María J. , Párraga Mario , Castilla Joaquín , Pérez-Ordoyo Luis I. , Torres Juan M. , Bárcena Juan 
Published: December 2008

ABSTRACT
One of the best-studied examples of host-virus coevolution is the release of myxoma virus (MV) for biological control of European rabbits in Australia and Europe. To investigate the genetic basis of MV adaptation to its new host, we sequenced the genome of 6918, an attenuated Spanish field strain, and compared it with that of Lausanne, the strain originally released in Europe in 1952. Although isolated 43 years apart, the genomes were highly conserved (99.95% identical). Only 32 of the 159 MV predicted proteins revealed amino acid changes. Four genes (M009L, M036L, M135R, and M148R) in 6918 were disrupted by frameshift mutations.
Continuous, diurnally fluctuating turbidity currents in Kluane Lake, Yukon Territory
Authors: Crookshanks Sarah , Gilbert Robert 
Published: December 2008

Modern sedimentary processes were studied in Kluane Lake, Yukon Territory, to determine the spatial and temporal patterns of sediment distribution in a large, dynamic, glacier-fed lake. Data from a river monitoring station, moored instruments, sediment traps, and water-column profiles in the lake were used to document lacustrine sedimentary processes in 2006 and 2007. During the peak melt season, the suspended sediment concentration of Slims River is weakly dependent on river discharge and can reach up to 5 g L–1, although a diurnal range between 1 and 2 g L–1 is more commonly observed. The high suspended sediment load in the river generates continuous, diurnally fluctuating turbidity currents in Kluane Lake with maximum velocities up to 0.6 m s–1. During times of peak flow, variations in velocity can be traced to beyond 4 km from the river mouth. The vertical concentration profiles, mass accumulation rates, and suspended sediment loads show distinctive longitudinal variations; the highest rate of accumulation occurs ∼1 km from the point of inflow, which is concurrent with a distinct change in flow structure. Diurnal laminations are apparent in sediment traps close to the point of inflow and can be directly linked to variations in current velocity; however, these laminations do not occur consistently over space or time. These results suggest that long-term measurement records of lacustrine turbidity currents provide valuable insights regarding the multiple scales of environmental variability and have important implications for paleoenvironmental reconstruction using lacustrine sediments.
A spatiotemporal Ripley’sK-function to analyze interactions between spruce budworm and fire in British Columbia, Canada
Authors: Lynch Heather J. , Moorcroft Paul R. 
Published: December 2008

In this paper, we extend traditional methods of spatial statistics to study spatiotemporal correlations between two different point processes. After introducing the methodology, we apply this analysis to a particular case study of interest in ecology, the interaction between damage by a particular forest pest (western spruce budworm ( Choristoneura occidentalis )) and forest fires. Our analysis, which covers parts of British Columbia in the 26-year period from 1970 to 1995, indicates that areas affected by budworm infestation have a significantly decreased risk of forest fire for the 7 years following the infestation. Conversely, forest fires decrease the risk of infestation for at least 6 years after the fire. These temporal correlations extend over a spatial range of at least 25 km. Our study rejects the common assumption that insect infestation necessarily results in increased fire risk. This case study illustrates the utility of point process modeling and spatial statistics to understanding ecosystem dynamics extending over both space and time.
Long-term recovery of vegetation communities after harvesting in the coastal temperate rainforests of northern British Columbia
Authors: Banner Allen , LePage Philip 
Published: December 2008

We sampled second-growth forests ranging in age from 28 to 98 years and compared them with old-growth forests to quantify rates of terrestrial vegetation recovery following harvesting on the northcentral coast of British Columbia. Species richness approximately doubles, while Simpson’s index of diversity increases from 0.81 to 0.91 from young to old forests. Nonmetric multidimensional scaling ordinations showed differentiation, with some overlap, of old-growth and second-growth forests and a fairly strong correlation of stand age with plot scores, driven by plant species presence and cover. Vegetation succession following logging disturbance is driven primarily by predisturbance species composition; most species found in the young forests are present in old forests and the higher species richness typical of old growth is largely due to the establishment of additional cryptogam and herb species of low cover and constancy. Significantly higher cover of shrub, herb, and bryophyte species differentiates old forests from second-growth forests. Forests 41–100 years old average 63%–73% similarity (depending on site type) to old-growth forests based on species presence–absence and 53%–58% similarity based on species cover. The scarcity of western redcedar ( Thuja plicata Donn ex D. Don) in second-growth stands is of particular concern because of the high ecological, cultural, and economic importance of this tree species.
Do decomposing Scots pine, Norway spruce, and silver birch stems retain nitrogen?
Authors: Palviainen Marjo , Laiho Raija , Mäkinen Harri , Finér Leena 
Published: December 2008

The contents of nitrogen (N) have generally been observed to increase in the early stages of decomposition in coarse woody debris and then to decrease slowly. This is potentially an important mechanism of nutrient retention in ecosystems after disturbances. We studied N dynamics in decomposing Scots pine ( Pinus sylvestris L.), Norway spruce ( Picea abies (L.) Karst.), and silver birch ( Betula pendula Roth.) stems in Finland. The oldest stems had decomposed for 34 (spruce and birch) or 45 (pine) years. Concentrations of N in both fallen logs and standing snags increased and C/N ratios decreased with time, and birch had significantly higher N concentrations and lower C/N ratios than pine and spruce. Even though increased N contents were observed in some cases, N was generally already released in the early stages of decomposition and more rapidly from birch than from conifers. Based on model analysis, from 40% (pine and spruce) to 50% (birch) of initial N was released within 30 years. The results suggest that decomposing stems of especially Scots pine and Norway spruce retain N rather effectively in boreal forest ecosystems and form a long-term, small but steady N pool with a slow release rate.
Real-Time Water Vapor Maps from a GPS Surface Network: Construction, Validation, and Applications
Authors: de Haan Siebren , Holleman Iwan , Holtslag Albert A. M. 
Published: December 2008

Abstract
In this paper the construction of real-time integrated water vapor (IWV) maps from a surface network of global positioning system (GPS) receivers is presented. The IWV maps are constructed using a two-dimensional variational technique with a persistence background that is 15 min old. The background error covariances are determined using a novel two-step method, which is based on the Hollingsworth–Lonnberg method. The quality of these maps is assessed by comparison with radiosonde observations and IWV maps from a numerical weather prediction (NWP) model. The analyzed GPS IWV maps have no bias against radiosonde observations and a small bias against NWP analysis and forecasts up to 9 h. The standard deviation with radiosonde observations is around 2 kg m−2, and the standard deviation with NWP increases with increasing forecast length (from 2 kg m−2 for the NWP analysis to 4 kg m−2 for a forecast length of 48 h). To illustrate the additional value of these real-time products for nowcasting, three thunderstorm cases are discussed. The constructed GPS IWV maps are combined with data from the weather radar, a lightning detection network, and surface wind observations. All cases show that the location of developing thunderstorms can be identified 2 h prior to initiation in the convergence of moist air.
Influence of ENSO on the West African Monsoon: Temporal Aspects and Atmospheric Processes
Authors: Joly Mathieu , Voldoire Aurore 
Published: December 2008

Abstract
A significant part of the West African monsoon (WAM) interannual variability can be explained by the remote influence of El Niño–Southern Oscillation (ENSO). Whereas the WAM occurs in the boreal summer, ENSO events generally peak in late autumn. Statistics show that, in the observations, the WAM is influenced either during the developing phase of ENSO or during the decay of some long-lasting La Niña events. The timing of ENSO thus seems essential to the teleconnection process. Composite maps for the developing ENSO illustrate the large-scale mechanisms of the teleconnection. The most robust features are a modulation of the Walker circulation and a Kelvin wave response in the high troposphere.
In the Centre National de Recherches Météorologiques Coupled Global Climate Model, version 3 (CNRM-CM3), the teleconnection occurs unrealistically at the end of ENSO events. An original sensitivity experiment is presented in which the ocean component is forced with a reanalyzed wind stress over the tropical Pacific. This allows for the reproduction of the observed ENSO chronology in the coupled simulation. In CNRM-CM3, the atmospheric response to ENSO is slower than in the reanalysis data, so the influence on the WAM is delayed by a year.
The two principal features of the teleconnection are the timing of ENSO onsets and the time lag of the atmospheric response. Both are assessed separately in 16 twentieth-century simulations of the third phase of the Coupled Model Intercomparison Project (CMIP3). The temporal aspects of the ENSO teleconnection are reproduced with difficulty in state-of-the-art coupled models. Only four models simulate an impact of ENSO on the WAM during the developing phase.
Independent Component Analysis of Climate Data: A New Look at EOF Rotation
Authors: Hannachi A. , Unkel S. , Trendafilov N. T. , Jolliffe I. T. 
Published: December 2008

AbstractThe complexity inherent in climate data makes it necessary to introduce more than one statistical tool to the researcher to gain insight into the climate system. Empirical orthogonal function (EOF) analysis is one of the most widely used methods to analyze weather/climate modes of variability and to reduce the dimensionality of the system. Simple structure rotation of EOFs can enhance interpretability of the obtained patterns but cannot provide anything more than temporal uncorrelatedness. In this paper, an alternative rotation method based on independent component analysis (ICA) is considered. The ICA is viewed here as a method of EOF rotation. Starting from an initial EOF solution rather than rotating the loadings toward simplicity, ICA seeks a rotation matrix that maximizes the independence between the components in the time domain. If the underlying climate signals have an independent forcing, one can expect to find loadings with interpretable patterns whose time coefficients have properties that go beyond simple noncorrelation observed in EOFs. The methodology is presented and an application to monthly means sea level pressure (SLP) field is discussed. Among the rotated (to independence) EOFs, the North Atlantic Oscillation (NAO) pattern, an Arctic Oscillation–like pattern, and a Scandinavian-like pattern have been identified. There is the suggestion that the NAO is an intrinsic mode of variability independent of the Pacific.
The Effect of Large-Scale Atmospheric Uncertainty on Streamflow Predictability
Authors: Hou Dingchen , Mitchell Kenneth , Toth Zoltan , Lohmann Dag , Wei Helin 
Published: December 2008

Abstract
Hydrological processes are strongly coupled with atmospheric processes related, for example, to precipitation and temperature, and a coupled atmosphere–land surface system is required for a meaningful hydrological forecast. Since the atmosphere is a chaotic system with limited predictability, ensemble forecasts offer a practical tool to predict the future state of the coupled system in a probabilistic fashion, potentially leading to a more complete and informative hydrologic prediction. As ensemble forecasts with coupled meteorological–hydrological models are operationally running at major numerical weather prediction centers, it is currently possible to produce a gridded streamflow prognosis in the form of a probabilistic forecast based on ensembles. Evaluation and improvement of such products require a comprehensive assessment of both components of the coupled system.
In this article, the atmospheric component of a coupled ensemble forecasting system is evaluated in terms of its ability to provide reasonable forcing to the hydrological component and the effect of the uncertainty represented in the atmospheric ensemble system on the predictability of streamflow as a hydrological variable. The Global Ensemble Forecast System (GEFS) of NCEP is evaluated following a “perfect hydrology” approach, in which its hydrological component, including the Noah land surface model and attached river routing model, is considered free of errors and the initial conditions in the hydrological variables are assumed accurate. The evaluation is performed over the continental United States (CONUS) domain for various sizes of river basins. The results from the experiment suggest that the coupled system is capable of generating useful gridded streamflow forecast when the land surface model and the river routing model can successfully simulate the hydrological processes, and the ensemble strategy significantly improves the forecast. The expected forecast skill increases with increasing size of the river basin. With the current GEFS system, positive skill in short-range (one to three days) predictions can be expected for all significant river basins; for the major rivers with mean streamflow more than 500 m3 s−1, significant skill can be expected from extended-range (the second week) predictions. Possible causes for the loss of skills, including the existence of systematic error and insufficient ensemble spread, are discussed and possible approaches for the improvement of the atmospheric ensemble forecast system are also proposed.
Forecasting Lightning Threat Using Cloud-Resolving Model Simulations
Authors: McCaul Eugene W. , Goodman Steven J. , LaCasse Katherine M. , Cecil Daniel J. 
Published: December 2008

Abstract
Two new approaches are proposed and developed for making time- and space-dependent, quantitative short-term forecasts of lightning threats, and a blend of these approaches is devised that capitalizes on the strengths of each. The new methods are distinctive in that they are based entirely on the ice-phase hydrometeor fields generated by regional cloud-resolving numerical simulations, such as those produced by the Weather Research and Forecasting (WRF) model. These methods are justified by established observational evidence linking aspects of the precipitating ice hydrometeor fields to total flash rates. The methods are straightforward and easy to implement, and offer an effective near-term alternative to the incorporation of complex and costly cloud electrification schemes into numerical models.
One method is based on upward fluxes of precipitating ice hydrometeors in the mixed-phase region at the −15°C level, while the second method is based on the vertically integrated amounts of ice hydrometeors in each model grid column. Each method can be calibrated by comparing domain-wide statistics of the peak values of simulated flash-rate proxy fields against domain-wide peak total lightning flash-rate density data from observations. Tests show that the first method is able to capture much of the temporal variability of the lightning threat, while the second method does a better job of depicting the areal coverage of the threat. The blended solution proposed in this work is designed to retain most of the temporal sensitivity of the first method, while adding the improved spatial coverage of the second.
Simulations of selected diverse North Alabama cases show that the WRF can distinguish the general character of most convective events, and that the methods employed herein show promise as a means of generating quantitatively realistic fields of lightning threat. However, because the models tend to have more difficulty in predicting the instantaneous placement of storms, forecasts of the detailed location of the lightning threat based on single simulations can be in error. Although these model shortcomings presently limit the precision of lightning threat forecasts from individual runs of current generation models, the techniques proposed herein should continue to be applicable as newer and more accurate physically based model versions, physical parameterizations, initialization techniques, and ensembles of forecasts become available.
Connecting Intonation Labels to Mathematical Descriptions of Fundamental Frequency
Authors: Grabe Esther , Kochanski Greg , Coleman John 
Published: December 2008

The mathematical models of intonation used in speech technology are often inaccessible to linguists. By the same token, phonological descriptions of intonation are rarely used by speech technologists, as they cannot be implemented directly in applications. Consequently, these research communities do not benefit much from each other's insights. In this paper, we explore the interface between the disciplines, in search of bridges between intonational phonology and speech technology. In a corpus of speech data from seven dialects of English, we hand-labeled over 700 sentences and identified seven nuclear accent types. Then we fitted a third-order polynomial to the fundamental frequency (F0) contour in the region around the accent mark. The polynomial captures the local shape (time-dependence) of F0 in a few numbers, in our case, four coefficients. The coefficients were subjected to statistical analysis. Nineteen of the 21 pairs of accent types differed significantly in one or more coefficients. Our approach bridges the gap between intonational phonology and speech technology. It provides quantitative, empirically testable models of intonation labels that can be implemented in applications.