bluuebunny/crossref_metadata_2025_split huggingface dataset:
West Nile Virus Methyltransferase Catalyzes Two Methylations of the Viral RNA Cap through a Substrate-Repositioning Mechanism
Authors: Dong Hongping , Ren Suping , Zhang Bo , Zhou Yangsheng , Puig-Basagoiti Francesc , Li Hongmin , Shi Pei-Yong 
Published: February 2008

ABSTRACT

Flaviviruses encode a single methyltransferase domain that sequentially catalyzes two methylations of the viral RNA cap, GpppA-RNA→m
7
GpppA-RNA→m
7
GpppAm-RNA, by using
S
-adenosyl-
l
-methionine (SAM) as a methyl donor. Crystal structures of flavivirus methyltransferases exhibit distinct binding sites for SAM, GTP, and RNA molecules. Biochemical analysis of West Nile virus methyltransferase shows that the single SAM-binding site donates methyl groups to both N7 and 2′-O positions of the viral RNA cap, the GTP-binding pocket functions only during the 2′-O methylation, and two distinct sets of amino acids in the RNA-binding site are required for the N7 and 2′-O methylations. These results demonstrate that flavivirus methyltransferase catalyzes two cap methylations through a substrate-repositioning mechanism. In this mechanism, guanine N7 of substrate GpppA-RNA is first positioned to SAM to generate m
7
GpppA-RNA, after which the m
7
G moiety is repositioned to the GTP-binding pocket to register the 2′-OH of the adenosine with SAM, generating m
7
GpppAm-RNA. Because N7 cap methylation is essential for viral replication, inhibitors designed to block the pocket identified for the N7 cap methylation could be developed for flavivirus therapy.
Severe Acute Respiratory Syndrome Coronavirus nsp1 Suppresses Host Gene Expression, Including That of Type I Interferon, in Infected Cells
Authors: Narayanan Krishna , Huang Cheng , Lokugamage Kumari , Kamitani Wataru , Ikegami Tetsuro , Tseng Chien-Te K. , Makino Shinji 
Published: February 2008

ABSTRACT
The severe acute respiratory syndrome coronavirus (SARS-CoV) nsp1 protein has unique biological functions that have not been described in the viral proteins of any RNA viruses; expressed SARS-CoV nsp1 protein has been found to suppress host gene expression by promoting host mRNA degradation and inhibiting translation. We generated an nsp1 mutant (nsp1-mt) that neither promoted host mRNA degradation nor suppressed host protein synthesis in expressing cells. Both a SARS-CoV mutant virus, encoding the nsp1-mt protein (SARS-CoV-mt), and a wild-type virus (SARS-CoV-WT) replicated efficiently and exhibited similar one-step growth kinetics in susceptible cells. Both viruses accumulated similar amounts of virus-specific mRNAs and nsp1 protein in infected cells, whereas the amounts of endogenous host mRNAs were clearly higher in SARS-CoV-mt-infected cells than in SARS-CoV-WT-infected cells, in both the presence and absence of actinomycin D. Further, SARS-CoV-WT replication strongly inhibited host protein synthesis, whereas host protein synthesis inhibition in SARS-CoV-mt-infected cells was not as efficient as in SARS-CoV-WT-infected cells. These data revealed that nsp1 indeed promoted host mRNA degradation and contributed to host protein translation inhibition in infected cells. Notably, SARS-CoV-mt infection, but not SARS-CoV-WT infection, induced high levels of beta interferon (IFN) mRNA accumulation and high titers of type I IFN production. These data demonstrated that SARS-CoV nsp1 suppressed host innate immune functions, including type I IFN expression, in infected cells and suggested that SARS-CoV nsp1 most probably plays a critical role in SARS-CoV virulence.
Formation of the Arterivirus Replication/Transcription Complex: a Key Role for Nonstructural Protein 3 in the Remodeling of Intracellular Membranes
Authors: Posthuma Clara C. , Pedersen Ketil W. , Lu Zhengchun , Joosten Ruth G. , Roos Norbert , Zevenhoven-Dobbe Jessika C. , Snijder Eric J. 
Published: February 2008

ABSTRACT
The replication/transcription complex of the arterivirus equine arteritis virus (EAV) is associated with paired membranes and/or double-membrane vesicles (DMVs) that are thought to originate from the endoplasmic reticulum. Previously, coexpression of two putative transmembrane nonstructural proteins (nsp2 and nsp3) was found to suffice to induce these remarkable membrane structures, which are typical of arterivirus infection. Here, site-directed mutagenesis was used to investigate the role of nsp3 in more detail. Liberation of the hydrophobic N terminus of nsp3, which is normally achieved by cleavage of the nsp2/3 junction by the nsp2 protease, was nonessential for the formation of DMVs. However, the substitution of each of a cluster of four conserved cysteine residues, residing in a predicted luminal loop of nsp3, completely blocked DMV formation. Some of these mutant nsp3 proteins were also found to be highly cytotoxic, in particular, exerting a dramatic effect on the endoplasmic reticulum. The functionality of an engineered N glycosylation site in the cysteine-containing loop confirmed both its presence in the lumen and the transmembrane nature of nsp3. This mutant displayed an interesting intermediate phenotype in terms of DMV formation, with paired and curved membranes being formed, but DMV formation apparently being impaired. The effect of nsp3 mutations on replicase polyprotein processing was investigated, and several mutations were found to influence processing of the region downstream of nsp3 by the nsp4 main protease. When tested in an EAV reverse genetics system, none of the nsp3 mutations was tolerated, again underlining the crucial role of the protein in the arterivirus life cycle.
South African pediments and interfluves
Authors: King R. Bruce 
Published: February 2008

Abstract

From fifty 1:50,000 scale topographic maps of South Africa, the following attributes were recorded at every intersection of one minute longitude and latitude: basic land facet description, annual rainfall, rainfall concentration, rainfall seasonality, monthly rainfall, local relief, contour interval, rock type, vegetation, pediment length or interfluve width, stream order at valley bottom, local drainage pattern, altitude, terrain morphology, physiographic region and postulated age of planation surface as defined by King (
The Morphology of the Earth: a Study and Synthesis of World Scenery
, Oliver & Boyd, 1962) and Partridge & Maud (
South African Journal of Geology
,
90
, 179–208, 1987). A strong relationship was found between the propensity for concave slopes (or escarpments) where there is low annual rainfall and high local relief. The relationship with rock type was not so strong, but concave slopes are shown to be more likely on fine-textured rather than coarser-textured rock types. The relationship between drainage density and annual rainfall decreases in value from less than 200 mm annual rainfall up to 400–600 mm annual rainfall, and then increases above this value. Concave slopes are particularly prone in lightly vegetated areas, require some local relief, and are more common on easily eroded rocks and older land surfaces protected from recent drainage dissection. Sheetwash seems the most likely agent of erosion.
Modelling cockpit karst landforms
Authors: Fleurant C. , Tucker G. E. , Viles H. A. 
Published: February 2008

Abstract
The purpose of this article is to present a model of the formation processes of cockpit karst landscapes. The CHILD software was used to simulate landscape evolution including dissolution processes of carbonate rocks. After examining briefly how the CHILD model operates, two applications of this model involving dissolution of carbonate rocks are presented. The simulated landscapes are compared with real landscapes of the Cockpit Country, Jamaica, using morphometric criteria. The first application is based on the hypothesis that dissolution of carbonate rocks is isotropic over time and space. In this case, dissolution is constant throughout the whole area studied and for each time step. The simulated landscapes based on this hypothesis have morphometric features which are quite different from those of real landscapes. The second application considers that dissolution of carbonate rocks is anisotropic over time and space. In this case, it is necessary to take into account subsurface and underground processes, by coupling surface runoff and water infiltration into the fractured carbonates.
Debris flows as a factor of hillslope evolution controlled by a continuous or a pulse process?
Authors: Bardou Eric , Jaboyedoff Michel 
Published: February 2008

Abstract
Flood effectiveness observations imply that two families of processes describe the formation of debris flow volume. One is related to the rainfall–erosion relationship, and can be seen as a gradual process, and one is related to additional geological/geotechnical events, those named hereafter extraordinary events. In order to discuss the hypothesis of coexistence of two modes of volume formation, some methodologies are applied. Firstly, classical approaches consisting in relating volume to catchments characteristics are considered. These approaches raise questions about the quality of the data rather than providing answers concerning the controlling processes. Secondly, we consider statistical approaches (cumulative number of events distribution and cluster analysis) and these suggest the possibility of having two distinct families of processes. However the quantitative evaluation of the threshold differs from the one that could be obtained from the first approach, but they all agree in the sense of the coexistence of two families of events. Thirdly, a conceptual model is built exploring how and why debris flow volume in alpine catchments changes with time. Depending on the initial condition (sediment production), the model shows that large debris flows (i.e. with important volume) are observed in the beginning period, before a steady-state is reached. During this second period debris flow volume such as is observed in the beginning period is not observed again. Integrating the results of the three approaches, two case studies are presented showing: (1) the possibility to observe in a catchment large volumes that will never happen again due to a drastic decrease in the sediment availability, supporting its difference from gradual erosion processes; (2) that following a rejuvenation of the sediment storage (by a rock avalanche) the magnitude–frequency relationship of a torrent can be differentiated into two phases, the beginning one with large and frequent debris flow and a later one with debris flow less intense and frequent, supporting the results of the conceptual model. Although the results obtained cannot identify a clear threshold between the two families of processes, they show that some debris flows can be seen as pulse of sediment differing from that expected from gradual erosion.
Fluvial solar signals
Authors: Vita-Finzi C. 
Published: February 2008

Abstract

The fluvial history of the Mediterranean basin and the Near East includes depositional evidence for a latitudinally diachronous, locally bipartite, episode of aggradation by equable streams during the period AD 500–1900. According to the Leopold gullying model, the key requirement would have been an increase in the proportion of small, non-erosive rains. Theoretical considerations supported by general climate models suggest that a decrease in solar radiation at the UV wavelengths would lead to equatorward displacement of the subtropical jet streams and the associated mid-latitude depressions. Atmospheric Δ
14
C values show a gradual decline from
c
. 7000
bp
followed by a temporary resurgence after AD 500 which includes peaks corresponding to the Oort, Wolf, Spörer, Maunder, Dalton and other solar minima. Reduced irradiance could account for channel aggradation by favouring cyclonic at the expense of convectional precipitation. Confirmation of a solar–fluvial link would benefit both solar history and flood forecasting.
Enabling multimedia using resource-constrained video processing techniques
Authors: Zamora Nicholas H. , Hu Xiaoping , Ogras Umit Y. , Marculescu Radu 
Published: February 2008

Successful proliferation of multimedia-enabled devices and advances in very large-scale integration (VLSI) technology has spawned new research efforts in migrating video processing applications onto ever smaller and more inexpensive devices. This article focuses on the technical challenges associated with that migration.
Due to limitations in size, battery lifetime, and, ultimately, cost, mapping complex video applications onto resource-constrained systems is a very challenging proposition. To this end, we first consider a technique, region-of-interest (ROI) processing, of defining a window within a video frame and only operating on the data inside that window, ignoring the rest of the frame. By using this lossy technique, the processing requirements can be reduced by roughly 80% while the error introduced in the quality of the results is roughly 10%. The other technique is adaptive data partitioning (ADP) combined with a content-based power management algorithm. By distributing video processing among multiple processors and shutting them down when they are not needed, the energy consumed per processor can be reduced by 60% without sacrificing the performance of the underlying video-based application.
Taken together, these novel techniques enable ambient multimedia systems and maintain the needed overall efficiency in video processing.
B-trees, shadowing, and clones
Authors: Rodeh Ohad 
Published: February 2008

B-trees are used by many file systems to represent files and directories. They provide guaranteed logarithmic time key-search, insert, and remove. File systems like WAFL and ZFS use shadowing, or copy-on-write, to implement snapshots, crash recovery, write-batching, and RAID. Serious difficulties arise when trying to use b-trees and shadowing in a single system.
This article is about a set of b-tree algorithms that respects shadowing, achieves good concurrency, and implements cloning (writeable snapshots). Our cloning algorithm is efficient and allows the creation of a large number of clones.
We believe that using our b-trees would allow shadowing file systems to better scale their on-disk data structures.
VISA
Authors: Assent Ira , Krieger Ralph , Müller Emmanuel , Seidl Thomas 
Published: February 2008

To gain insight into today's large data resources, data mining extracts interesting patterns. To generate knowledge from patterns and benefit from human cognitive abilities, meaningful visualization of patterns are crucial. Clustering is a data mining technique that aims at grouping data to patterns based on mutual (dis)similarity. For high dimensional data, subspace clustering searches patterns in any subspace of the attributes as patterns are typically obscured by many irrelevant attributes in the full space. For visual analysis of subspace clusters, their comparability has to be ensured. Existing subspace clustering approaches, however, lack interactive visualization and show bias with respect to the dimensionality of subspaces.
In this work, dimensionality unbiased subspace clustering and a novel distance function for subspace clusters are proposed. We suggest two visualization techniques that allow users to browse the entire subspace clustering, to zoom into individual objects, and to analyze subspace cluster characteristics in-depth. Bracketing of different parameter settings enable users to immediately see the effect of parameters on their data and hence to choose the best clustering result for further analysis. Usage of user analysis for feedback to the subspace clustering algorithm directly improves the subspace clustering. We demonstrate our visualization techniques on real world data and confirm results through additional accuracy measurements and comparison with existing subspace clustering algorithms.
The MAGS Water and Energy Budget Study
Authors: Szeto K. K. , Tran H. , MacKay M. D. , Crawford R. , Stewart R. E. 
Published: February 2008

Abstract
This study represents the first attempt at developing a comprehensive climatology of atmospheric and surface water and energy budgets for the Mackenzie River basin (MRB). Different observed, remotely sensed, (re)analyzed, and modeled datasets were used to obtain independent estimates of the budgets. In particular, assimilated datasets, including the National Centers for Environmental Prediction Global Reanalysis 2 (NCEP-R2), the global 40-yr European Centre for Medium-Range Weather Forecasts Re-Analysis (ERA-40), the NCEP North American Regional Reanalysis (NARR), and the Canadian Meteorological Centre (CMC) operational regional analysis as well as results from the Canadian Regional Climate Model (CRCM) simulations, are used in the study. Apart from the development of state-of-the-art budget estimates for the MRB, the relative merits of current models, data assimilation systems, and global blended datasets in representing aspects of the water and energy cycle of this northern and data-sparse region were also assessed. In addition, the levels of uncertainty in assessing the budgets as well as their sources are discussed. The regional water budget for the MRB is closed within 10% of the observed runoff by using the moisture flux convergence from ERA-40, NARR, CMC, or CRCM. While these are noted improvements over previous water closure assessments for the region, magnitudes of the residuals in balancing the budgets are often comparable to the budget terms themselves in all the model and analysis datasets, and the spreads of budget estimates from the different datasets are also typically large, suggesting that substantial improvements to the models and observations are needed before the assessments of water and energy budgets for this northern region can be vastly improved.
Evaluation of the Surface Radiation Budget in the Atmospheric Component of the Hadley Centre Global Environmental Model (HadGEM1)
Authors: Bodas-Salcedo A. , Ringer M. A. , Jones A. 
Published: February 2008

Abstract
The partitioning of the earth radiation budget (ERB) between its atmosphere and surface components is of crucial interest in climate studies as it has a significant role in the oceanic and atmospheric general circulation. An analysis of the present-day climate simulation of the surface radiation budget in the atmospheric component of the new Hadley Centre Global Environmental Model version 1 (HadGEM1) is presented, and the simulations are assessed by comparing the results with fluxes derived from satellite data from the International Satellite Cloud Climatology Project (ISCCP) and ground measurements from the Baseline Surface Radiation Network (BSRN).
Comparisons against radiative fluxes from satellite and ground observations show that the model tends to overestimate the surface incoming solar radiation (Ss,d). The model simulates Ss,d very well over the polar regions. Consistency in the comparisons against BSRN and ISCCP-FD suggests that the ISCCP-FD database is a good test for the performance of the surface downwelling solar radiation in climate model simulations. Overall, the simulation of downward longwave radiation is closer to observations than its shortwave counterpart. The model underestimates the downward longwave radiation with respect to BSRN measurements by 6.0 W m−2.
Comparisons of land surface albedo from the model and estimates from the Moderate Resolution Imaging Spectroradiometer (MODIS) show that HadGEM1 overestimates the land surface albedo over deserts and over midlatitude landmasses in the Northern Hemisphere in January. Analysis of the seasonal cycle of the land surface albedo in different regions shows that the amplitude and phase of the seasonal cycle are not well represented in the model, although a more extensive validation needs to be carried out.
Two decades of coupled model simulations of the twentieth-century climate are used to look into the model’s simulation of global dimming/brightening. The model results are in line with the conclusions of the studies that suggest that global dimming is far from being a uniform phenomenon across the globe.
Barotropic Zonal Jets Induced by Islands in the Southwest Pacific
Authors: Couvelard Xavier , Marchesiello Patrick , Gourdeau Lionel , Lefèvre Jerome 
Published: February 2008

Abstract
The oceanic circulation entering the tropical southwest Pacific (SWP) is dominated by the broad westward flow of the South Equatorial Current (SEC), which is forced by the trade winds. It has been argued that the numerous islands of the SWP are able to restructure the SEC into a series of deep and narrow zonal jets, which control important pathways connecting equatorial and extraequatorial signals. The primary objective of this paper is to improve the understanding of the structure and dynamics of SWP zonal jets, giving special attention to topographic effects. This study is based on the use of a high-resolution regional oceanic model, whose solution is compared with observations, as well as with solutions from global models and the Sverdrup relation. The model used here indicates that the regional topography drives a general equatorward shift of the SEC, which is beneficial to the North Fiji, North Vanuatu, and North Caledonian jets. A depth-integrated vorticity budget shows that this topographic effect is considerably attenuated by baroclinicity and advection processes, but not to the point of total compensation as often admitted for the interior ocean. The effect of nonlinear advection is to allow flow rectification of the jets fluctuations, taking the form of zonally elongated dipole circulations in the leeward side of the islands.
Life Events Associated With Major Depression in Ugandan Primary Healthcare (PHC) Patients: Issues of Cultural Specificity
Authors: Muhwezi Wilson Winstons , Ågren Hans , Neema Stella , Koma Maganda Albert , Musisi Seggane 
Published: February 2008

Objective: The study compared life events experienced by depressed patients seen at primary healthcare (PHC) centres with those among healthy community controls. Method: Data was collected from 74 depressed patients and 64 unmatched controls from village locales of patients. Interview instruments included the depression module of the Mini International Neuropsychiatric Interview (MINI) and Interview for Recent Life Events (IRLE). Associations between type of respondent and demographic variables were examined. Statistical comparisons were done for the two groups on other variables. Results: Most depressed patients were single by marital status, lacked formal employment and had less post-primary education.They had experienced more life events; job changes, discomforting working hours, unfavourable working conditions, and job losses; personal health problems; loss of valuables; difficulties with intimate partners and family members' marital problems. Independent life events were more among depressed patients and clustered around work, health, bereavement and marriage. Most events reported by depressed patients had high negative impact ratings compared to controls. Conclusion: Compared to healthy community controls, depressed patients reported more undesirable life events. The relationship between life events and depression implies that in PHC settings of poor countries, deploying mental health-oriented workers to manage life events may lessen escalation of distress.