bluuebunny/crossref_metadata_2025 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

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

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

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.
Litter mass-loss rates in late stages of decomposition in a climatic transect of pine forests. Long-term decomposition in a Scots pine forest. IX.
Authors: Johansson Maj-Britt , Berg Björn , Meentemeyer Vernon
Published: February 2008

We investigated rate-regulating factors for decomposition rates of Scots pine needle litter at 22 sites over a 2000-km long transect ranging from the Arctic Circle in Scandinavia to northern continental Europe. We found very different patterns for rate-regulating factors in the early stages of decomposition as compared to later stages (> 20% accumulated mass loss). The initial decomposition rates (measured over the 1st year) ranged from about 10.9%/year close to the Arctic Circle to about 43.7%/year in south Sweden. The dominant rate-regulating factor was climate (average annual temperature, and actual evapotranspiration), and none of the substrate-quality factors was significant. In the later stages, the annual mass loss varied from 2.2%/year to 41.5%/year. The rate-regulating factors were climate and the litter's concentration of lignin. We found that the effect of lignin concentration on litter mass-loss rate varied with site and this relative effect was negatively related with actual evapotranspiration. The effect of lignin concentration on mass-loss rates near the Arctic Circle was thus low (at low values for actual evapotranspiration) whereas in Southern Sweden and on the continent the rate-regulating effect of lignin was higher. Key words: foliar litter, decomposition, lignin, climatic transect, rate-regulating factors, climate change.
Are Synthyris and Besseya closely related to Wulfenia (Scrophulariaceae – Veroniceae)? Evidence from floral development
Authors: Kampny Christine M.
Published: February 2008

Within the tribe Veroniceae (Scrophulariaceae), Synthyris and Besseya have been grouped at times with Wulfenia, because of their rosette habit, and with cauline-leaved Veronica, because of similarities of pollen and seed morphology. Floral development patterns of Synthyris reniformis, Besseya alpina, and Wulfenia carinthiaca were studied with quantitative methods to contribute additional evidence towards resolving the phylogenetic relationships of those genera. For each species, 19 flower organ measurements were taken on each of 50 buds from all stages of development. Compared to the fast early corolla development observed in most Scrophulariaceae, all species examined shared a delay in early corolla tube growth which was less extreme than that observed in Veronica. A strong delay in early corolla lobe growth was shared only between Veronica, Synthyris, and Besseya. This derived attribute is a possible synapomorphy supporting hypotheses of monophyly of those genera. Summarizing all measurements with multigroup principal components analysis showed that the overall floral allometries of Wulfenia have more similarity with those of Digitalis than with Veronica and relatives; this concurs with evidence from vegetative and reproductive morphology. Key words: floral development, allometry, phylogeny.
Late Quaternary sedimentation in Baffin Bay
Authors: Aksu A. E. , Piper David J. W.
Published: February 2008

Baffin Bay is a small ocean basin that connects the Arctic and Atlantic oceans. The adjacent continental shelves have been extensively reworked during Quaternary glaciation. The shelf break generally lies between 200 and 500 m. The continental slope passes directly into the abyssal plain of Baffin Bay basin without any major submarine canyon – deep-sea fan system being present, except for a large smooth sediment apron in northern Baffin Bay.On the basis of over 50 piston cores, six Quaternary sediment facies are distinguished from detrital mineralogy (reflected in colour) and sediment texture. Facies A, B, and C are predominantly ice-rafted or are debris flow deposits, each with a distinct mineralogy. Facies D is turbidites and bottom-current sorted sands, silts, and muds. Facies E is hemipelagic sediment. Facies F consists of sediments ranging from slumps, through debris flow deposits, to fine-grained turbidites, with a distinctive provenance in northern Baffin Bay.These sediment facies appear to be partly controlled by glacial conditions. Hemipelagic facies E predominates during the present interglacial. During glacial stages, facies D turbidites were deposited. They resulted from slumping of proglacial sediments on the continental slopes off Greenland and Baffin Island. Facies C and F occurred on the continental slopes at these times. Ice-rafted facies A and B predominate at several horizons, reflecting a rapid breakup of ice shelves in northern Baffin Bay and increased rates of iceberg melting within the Bay. Overall sedimentation rates are relatively low, reflecting dry-base ice sheets in source areas.Deep-sea channel systems floored by sorted coarse sediments and bounded by muddy levees are absent in Baffin Bay, in contrast to mid-latitude glaciated continental margins off eastern Canada. These channel systems are the result of melting of wet-base glaciers, which provide a localized supply of sediment that is sorted by ice margin processes. In Baffin Bay, most glacial sediments are derived by calving of icebergs, probably from dry-base glaciers. Sediments are gradually released over large areas as the bergs melt, and are subsequently redistributed by debris flows.
Productivity in the pulp and paper industries of the United States and Canada: a nonparametric analysis
Authors: Hseu Jiing-Shyang , Buongiorno Joseph
Published: February 2008

Partial and total measures of factor productivity are presented for the pulp and paper industries of the United States and Canada, from 1959 to 1987. Total factor productivity was measured with (1) a Tornqvist–Theil index, (2) a nonparametric index with translating hypothesis, and (3) a nonparametric index with distance functions. Method 1 implied a constant return to scale translog production function. Methods 2 and 3 removed any assumption on the functional form of the production function. Furthermore, method 3 allowed for fully disaggregated outputs. Methods 1 and 3 gave similar results within countries: an increase in total factor productivity of 0.7% per year in the United States and of 0.5% per year in Canada. Method 2 gave rates of growth of total factor productivity that were twice as high, but unreliable because of the assumptions of the method. From 1961 to 1984, when comparable data are available, methods 1 and 3 gave growth rates of total factor productivity that were significantly higher, statistically, in the United States than in Canada. Nevertheless, the differences seem to be too small to be of economic significance.
Effects of phosphorus deficiency and recovery fertilization on growth, mineral concentration, and ultrastructure of Scots pine needles
Authors: Palomäki V. , Holopainen T.
Published: February 2008

During the first year of a 2-year field experiment (1989–1990), 3-year-old Scots pine (Pinussylvestris L.) seedlings were watered with phosphorus-deficient nutrient solutions containing no phosphorus (0%) or 30% of the optimal phosphorus supply. A complete nutrient solution was used as the control. In the second growing period, the seedlings were divided into two groups, a deficiency and a recovery treatment, to follow the further development of, and recovery from, symptoms. Phosphorus contents in both current- and previous-year needles in both deficiency groups decreased clearly during the first growing period. Limited growth was observed at both deficiency levels after 10 weeks of treatment. The first ultrastructural symptom, swelling of cristae and subsequent dilatation of whole mitochondria, was observed after 16 weeks of treatment in the current-year needles. In addition to this symptom, the previous-year needles had an increase in the number and translucency of plastoglobuli, a decrease of granum thylakoids, and an increase in the density of the stroma in chloroplasts. After the second growing period, the same changes were observable in the phosphorus-deficient seedlings. In the young needles grown during the recovery fertilization period, slight swelling of mitochondria was detected and recovery of the previous-year needles was not complete. The results of this experiment suggest that the swelling of mitochondria is a characteristic symptom of phosphorus deficiency at the ultrastructural level in different needle generations. All the symptoms, when occurring together, may be used in identifying a moderate phosphorus-deficiency stress in seedlings.
The relationship between water content and frost tolerance in shoots of hardwood seedlings
Authors: Calmé Sophie , Margolis Hank A. , Mailly Daniel , Bigras Francine J.
Published: February 2008

Two experiments were designed to test the relationship between water content and frost tolerance in stems of hardwood seedlings during the frost hardening process. In the first experiment, 3-month-old container-grown yellow birch (Betulaalleghaniensis Britton) seedlings were submitted to a decreasing temperature regime in a 8-h (short day, SD) or 16-h (long day, LD) photoperiod in growth chambers. In the second experiment, 3-month-old container-grown red oak (Quercusrubra L.), bur oak (Quercusmacrocarpa Michx.), and yellow birch seedlings were naturally cold hardened in a production polyhouse. To estimate frost tolerance, freezing tests were performed on whole seedlings (experiment 1) or on the upper 5 cm of the stem apex (experiment 2), and stem damage was visually estimated. Water content of the apex (5 cm) was expressed as the ratio of dry mass over fresh mass (DM/FM) for both experiments. Frost tolerance and DM/FM increased during the course of both experiments. In the growth-chamber experiment, SD seedlings hardened deeper than LD ones (−19.2 °C for SD versus −15.7 °C for LD), and DM/FM was higher for SD after 60 days of photoperiod treatment. In the polyhouse experiment, bur oak, yellow birch, and red oak reached a frost tolerance of −26.7, −25.1, and −20.4 °C, respectively, on November 2. The three species had DM/FM ratios of about 50% on November 2. For both experiments, DM/FM values higher than 45% corresponded to seedlings with a frost tolerance of −10 °C or lower.
The influence of mountain laurel on regeneration in pitch pine canopy gaps of the Coweeta Basin, North Carolina, U.S.A.
Authors: Waterman Jayson R. , Gillespie Andrew R. , Vose James M. , Swank Wayne T.
Published: February 2008

Because of its dense nature, mountain laurel (Kalmialatifolia L.) understories may be retarding the regeneration of xeric pitch pine (Pinusrigida Mill.) sites in the southern Appalachians and thereby influencing successional dynamics. This study examined the impact of the laurel understory on hardwood successional ecology in living pitch pine stands and pine gaps at their upper and lower elevational distribution. The laurel understory was physically removed from half the plots; the remaining plots served as a control. The plots were inventoried and all seedlings were tagged and measured to determine importance values, recruitment, survivorship, and biomass for 2 years following treatment. The results indicate that the presence or absence of the laurel understory does not affect initial seedling recruitment, survivorship, or their relative competitiveness. However, mountain laurel does suppress growth of smaller seedlings. Given the higher importance value, recruitment, and survivorship of red maple (Acerrubrum L.), the regeneration layer in these pitch pine sites is currently dominated by red maple, with scarlet oak (Quercuscoccinea Muenchh.) and other xeric-site hardwoods as associates. With the adaptive ability of red maple to take advantage of openings, red maple will continue to dominate and ultimately regenerate these communities with other hardwoods as minor associates.
A comparative study of the anatomy of the iris and ciliary body in aquatic mammals
Authors: West J. A. , Sivak J. G. , Murphy C. J. , Kovacs K. M.
Published: February 2008

The ciliary muscle exhibits considerable variation in its development among the vertebrates. The muscle is considered to be well developed in humans, primates, ungulates, and aquatic carnivores, and the extent of development is thought to correspond to the amplitude of accommodation. The recent finding of a well-developed ciliary muscle in the hooded seal (Cystophora cristata) has initiated interest in an accommodative mechanism for vision in air and in water. This study is a comparative investigation of the ciliary muscle in a number of aquatic mammals. The methods include gross inspection of the ciliary region and histological examination of the ciliary body and iris by means of light microscopy. The results indicate that in completely aquatic mammals the ciliary muscle is rudimentary, and in fact, appears to be lacking in one species (beluga whale). The ciliary muscle appears to be better developed in the amphibious pinnipeds (California sea lion, elephant seal, and walrus). The presence of circular muscle bundles suggests that the muscle is more developed in the elephant seal and California sea lion than in the walrus. The degree of ciliary muscle development and the need for accommodation can be related to the natural history of each species.
A comparison of population characteristics and reproductive success of resident and immigrant meadow voles
Authors: Pugh Stephen R. , Tamarin Robert H.
Published: February 2008

We used a radionuclide technique combined with a minimum-weight criterion to identify resident and immigrant meadow voles, Microtus pennsylvanicus, on an open grid in South Natick, Massachusetts. Using the same techniques with populations on two fenced grids, we calculated an error rate of 7.2% in residency assignment. Immigrants were not a random subset of the resident population. Among immigrant voles the sex ratio was significantly male biased, whereas among residents it did not differ from 1:1. Immigrants had genotypic ratios that differed significantly from those of residents at three of five allozyme loci examined electrophoretically. Although immigrant males resided on the grid significantly longer than resident adult males, they did not differ significantly in reproductive success, maximum weight, or distance moved between trapping periods. Immigrants seemed to be as successful as residents during a period of low or declining density.
A method for assessing clearance rates in suspension-feeding organisms by means of a fiber-optic colorimeter
Authors: Hornbach Daniel J. , Wilcox Thomas , Layne John , Powers Lindsay , Davis Timothy
Published: February 2008

A method for determining the clearance rates of suspension-feeding organisms by means of a fiber-optic colorimeter is discussed. The fiber-optic probe facilitates direct measurement of the turbidity of solutions without the need for removing subsamples. This allows for continuous monitoring and overcomes problems associated with calculating clearance rates if subsamples are removed. Standard curves are provided for plastic microspheres of six sizes (0.497–45.8 μm diameter), at concentrations of 0.8–100 mg/L, for each of four light-path lengths (1, 2, 5, and 10 cm). An experiment using the freshwater unionid mussel Truncilla truncata is described as an example of the use of this method.
ELECTRICAL TRANSPORT AND MAGNETORESISTANCE PROPERTIES OF La0.67Ca0.33MnO3 FILM COATED ON PYREX GLASS SUBSTRATE
Authors: GENCER H. , GOKTAS A. , GUNES M. , MUTLU H. I. , ATALAY S.
Published: February 2008

The electrical transport and magnetoresistance properties of the polycrystalline La 0.67 Ca 0.33 MnO 3 film produced on a Pyrex substrate were investigated for the first time. X-ray powder diffraction indicated that the film sample has a perovskite structure. Scanning electron microscope indicated that La 0.67 Ca 0.33 MnO 3 film thickness is approximately 500 nm, and the average grain size of this sample varies between 40 and 50 nm. La 0.67 Ca 0.33 MnO 3 film showed a phase transition from paramagnetic to ferromagnetic at (TC) 80 K and a metal–insulator transition at (T MI ) 77.5 K and at 2 mT magnetic field. The upturn of the resistance observed at low temperatures (<36 K) was attributed to the Coulomb blockade, and the strong structural disorder is due to the large lattice mismatch and strain relaxation. A large magnetoresistance ratio [MR (%)] of 780% was observed at 100 K and 6 T magnetic field.
South African pediments and interfluves
Authors: King R. Bruce
Published: February 2008

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

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

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

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.
Boosting interpolation with dynamic localized abstraction and redundancy removal
Authors: Cabodi Gianpiero , Murciano Marco , Nocco Sergio , Quer Stefano
Published: February 2008

SAT--based Unbounded Model Checking based on Craig Interpolants is often able to overcome BDDs and other SAT--based techniques on large verification instances. Based on refutation proofs generated by SAT solvers, interpolants provide compact circuit representations of state sets, as they abstract away several nonrelevant details of the proofs. We propose three main contributions, aimed at controlling interpolant size and traversal depth. First of all, we introduce interpolant--based dynamic abstraction to reduce the support of computed interpolants. Subsequently, we propose new advances in interpolant compaction by redundancy removal. Finally, we introduce interpolant computation exploiting circuit quantification, instead of SAT refutation proofs. These techniques heavily rely on an effective application of the incremental SAT paradigm. The experimental results proposed in this paper are specifically oriented to prove properties, rather than disproving them, i.e., they target complete verification instead of simply hunting bugs. They show how this methodology is able to stretch the applicability of interpolant--based Model Checking to larger and deeper verification instances.
Probabilistic transfer matrices in symbolic reliability analysis of logic circuits
Authors: Krishnaswamy Smita , Viamontes George F. , Markov Igor L. , Hayes John P.
Published: February 2008

We propose the probabilistic transfer matrix (PTM) framework to capture nondeterministic behavior in logic circuits. PTMs provide a concise description of both normal and faulty behavior, and are well-suited to reliability and error susceptibility calculations. A few simple composition rules based on connectivity can be used to recursively build larger PTMs (representing entire logic circuits) from smaller gate PTMs. PTMs for gates in series are combined using matrix multiplication, and PTMs for gates in parallel are combined using the tensor product operation. PTMs can accurately calculate joint output probabilities in the presence of reconvergent fanout and inseparable joint input distributions. To improve computational efficiency, we encode PTMs as algebraic decision diagrams (ADDs). We also develop equivalent ADD algorithms for newly defined matrix operations such as
eliminate_variables
and
eliminate_redundant_variables
, which aid in the numerical computation of circuit PTMs. We use PTMs to evaluate circuit reliability and derive polynomial approximations for circuit error probabilities in terms of gate error probabilities. PTMs can also analyze the effects of logic and electrical masking on error mitigation. We show that ignoring logic masking can overestimate errors by an order of magnitude. We incorporate electrical masking by computing error attenuation probabilities, based on analytical models, into an extended PTM framework for reliability computation. We further define a susceptibility measure to identify gates whose errors are not well masked. We show that hardening a few gates can significantly improve circuit reliability.
ReChannel
Authors: Raabe Andreas , Hartmann Philipp A. , Anlauf Joachim K.
Published: February 2008

With the ongoing integration of (dynamic) reconfiguration into current system models, new methodologies and tools are needed to help the designer during the development process. This article introduces a language extension for SystemC along with a design methodology for describing and simulating dynamically reconfigurable systems at all levels of abstraction. The presented library provides maximum freedom of description of reconfiguration behavior and its control, while featuring simulation of runtime configuration, removal, and exchange of custom modules as well as third-party IP-cores during the complete architecture refinement process. When designing at RT-level, the resulting hardware description can easily be synthesized by standard synthesis tools.
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.
Low-power gated and buffered clock network construction
Authors: Chao Wei-Chung , Mak Wai-Kei
Published: February 2008

We propose an efficient algorithm to construct a low-power zero-skew gated clock network, given the module locations and activity information. Unlike previous works, we consider masking logic insertion and buffer insertion simultaneously, and guarantee to yield a zero-skew clock tree. Both the logical and physical information of the modules are carefully taken into consideration when determining where masking logic should be inserted. We also account for the power overhead of the control signals so that the total average power consumption of the constructed zero-skew gated clock network can be minimized. To this end, we present a recursive approach to compute the effective switched capacitance of a general gated and buffered clock network, accounting for both the clock tree's and controller tree's switched capacitance. The power consumptions of the gated clock networks constructed by our algorithm are 20 to 36% lower than those reported in the best previous work in the literature.
Survey of graph database models
Authors: Angles Renzo , Gutierrez Claudio
Published: February 2008

Graph database models can be defined as those in which data structures for the schema and instances are modeled as graphs or generalizations of them, and data manipulation is expressed by graph-oriented operations and type constructors. These models took off in the eighties and early nineties alongside object-oriented models. Their influence gradually died out with the emergence of other database models, in particular geographical, spatial, semistructured, and XML. Recently, the need to manage information with graph-like nature has reestablished the relevance of this area. The main objective of this survey is to present the work that has been conducted in the area of graph database modeling, concentrating on data structures, query languages, and integrity constraints.
Nearcast
Authors: Tu Xuping , Jin Hai , Liao Xiaofei , Cao Jiannong
Published: February 2008

Peer-to-peer (P2P) live video streaming has been widely used in distance education applications to deliver the captured video courses to a large number of online students. By allowing peers serving each other in the network, P2P technology overcomes many limitations in the traditional client-server paradigm to achieve user and bandwidth scalabilities. However, existing systems do not perform well when the number of online students increases, and the system performance degrades seriously. One of the reasons is that the construction of the peer overlay in existing P2P systems has not considered the underlying physical network topology and can cause serious topology mismatch between the P2P overlay network and the physical network. The topology mismatch problem brings great link stress (unnecessary traffic) in the Internet infrastructure and greatly degrades the system performance. In this article, we address this problem and propose a locality-aware P2P overlay construction method, called
Nearcast
, which builds an efficient overlay multicast tree by letting each peer node choose physically closer nodes as its logical children.

We have conducted extensive simulations to evaluate the performance of Nearcast in comparison with the existing RTT and NICE protocols. Also, Nearcast has been deployed on a wide-area network testbed to delivery video coursed to about 7200 users distributed across 100 collages in 32 cities in China. The experimental results show that Nearcast leads to lower link stress and shorter end-to-end latencies compared with the RTT and NICE protocols.
A multimedia broker to support accessible and mobile learning through learning objects adaptation
Authors: Salomoni Paola , Mirri Silvia , Ferretti Stefano , Roccetti Marco
Published: February 2008

The large diffusion of e-learning technologies represents a great opportunity for underserved segments of population. This is particularly true for people with disabilities for whom digital barriers should be overstepped with the aim of reengaging them back into society to education. In essence, before a mass of learners can be engaged in a collective educational process, each single member should be put in the position to enjoy accessible and customized educational experiences, regardless of the wide diversity of their personal characteristics and technological equipment. To respond to this demand, we developed LOT (Learning Object Transcoder), a distributed PHP-based service-oriented system designed to deliver flexible and customized educational services for a multitude of learners, each with his/her own diverse preferences and needs. The main novelty of LOT amounts to a broking service able to manage the transcoding activities needed to convert multimedia digital material into the form which better fits a given student profile. Transcoding activities are performed based on the use of Web service technologies. Experimental results gathered from several field trials with LOT (available online at http://137.204.74.83/∼lot/) have confirmed the viability of our approach.
The inaccurate conception
Authors: Armour Phillip G.
Published: February 2008

Some thoughts on the accuracy of estimates.
Location-based services
Authors: Junglas Iris A. , Watson Richard T.
Published: February 2008

Evaluating user perceptions of location-tracking and location-awareness services.
Role of word of mouth in online store loyalty
Authors: Gauri Dinesh K. , Bhatnagar Amit , Rao Raghav
Published: February 2008

Comparing online store ratings with other e-store loyalty factors.
Energy-efficient on-demand reprogramming of large-scale sensor networks
Authors: Krasniewski Mark D. , Panta Rajesh Krishna , Bagchi Saurabh , Yang Chin-Lung , Chappell William J.
Published: February 2008

As sensor networks operate over long periods of deployment in difficult to reach places, their requirements may change or new code may need to be uploaded to them. The current state-of-the-art protocols (Deluge and MNP) for network reprogramming perform the code dissemination in a multihop manner using a three-way handshake where metadata is exchanged prior to code exchange to suppress redundant transmissions. The code image is also pipelined through the network at the granularity of pages. In this article we propose a protocol called Freshet for optimizing the energy for code upload and speeding up the dissemination if multiple sources of code are available. The energy optimization is achieved by equipping each node with limited nonlocal topology information which it uses to determine the time when it can go to sleep since code is not being distributed in its vicinity. The protocol to handle multiple sources provides a loose coupling of nodes to a source and disseminates code in waves each originating at a source with a mechanism to handle collisions when the waves meet. The protocol's performance with respect to reliability, delay, and energy consumed is demonstrated through analysis, simulation, and implementation on the Berkeley mote platform.
Efficient gathering of correlated data in sensor networks
Authors: Gupta Himanshu , Navda Vishnu , Das Samir , Chowdhary Vishal
Published: February 2008

In this article, we design techniques that exploit data correlations in sensor data to minimize communication costs (and hence, energy costs) incurred during data gathering in a sensor network. Our proposed approach is to select a small subset of sensor nodes that may be sufficient to reconstruct data for the entire sensor network. Then, during data gathering only the selected sensors need to be involved in communication. The selected set of sensors must also be connected, since they need to relay data to the data-gathering node. We define the problem of selecting such a set of sensors as the
connected correlation-dominating set
problem, and formulate it in terms of an appropriately defined correlation structure that captures general data correlations in a sensor network.

We develop a set of energy-efficient distributed algorithms and competitive centralized heuristics to select a connected correlation-dominating set of small size. The designed distributed algorithms can be implemented in an asynchronous communication model, and can tolerate message losses. We also design an exponential (but nonexhaustive) centralized approximation algorithm that returns a solution within
O
(log
n
) of the optimal size. Based on the approximation algorithm, we design a class of centralized heuristics that are empirically shown to return near-optimal solutions. Simulation results over randomly generated sensor networks with both artificially and naturally generated data sets demonstrate the efficiency of the designed algorithms and the viability of our technique—even in dynamic conditions.
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.
Workload-based generation of administrator hints for optimizing database storage utilization
Authors: Dutta Kaushik , Rangaswami Raju , Kundu Sajib
Published: February 2008

Database storage management at data centers is a manual, time-consuming, and error-prone task. Such management involves regular movement of database objects across storage nodes in an attempt to balance the I/O bandwidth utilization across disk drives. Achieving such balance is critical for avoiding I/O bottlenecks and thereby maximizing the utilization of the storage system. However, manual management of the aforesaid task, apart from increasing administrative costs, encumbers the greater risks of untimely and erroneous operations. We address the preceding concerns with STORM, an automated approach that combines low-overhead information gathering of database access and storage usage patterns with efficient analysis to generate accurate and timely hints for the administrator regarding data movement operations. STORM's primary objective is minimizing the volume of data movement required (to minimize potential down-time or reduction in performance) during the reconfiguration operation, with the secondary constraints of space and balanced I/O-bandwidth-utilization across the storage devices. We analyze and evaluate STORM theoretically, using a simulation framework, as well as experimentally. We show that the dynamic data layout reconfiguration problem is NP-hard and we present a heuristic that provides an approximate solution in
O
(
Nlog
(
N
/
M
) + (
N
/
M
)
2
) time, where
M
is the number of storage devices and
N
is the total number of database objects residing in the storage devices. A simulation study shows that the heuristic converges to an acceptable solution that is successful in balancing storage utilization with an accuracy that lies within 7% of the ideal solution. Finally, an experimental study demonstrates that the STORM approach can improve the overall performance of the TPC-C benchmark by as much as 22%, by reconfiguring an initial random, but evenly distributed, placement of database objects.
A formal foundation for XrML
Authors: Halpern Joseph Y. , Weissman Vicky
Published: February 2008

XrML is becoming a popular language in industry for writing software licenses. The semantics for XrML is implicitly given by an algorithm that determines if a permission follows from a set of licenses. We focus on a fragment of the language and use it to highlight some problematic aspects of the algorithm. We then correct the problems, introduce formal semantics, and show that our semantics captures the (corrected) algorithm. Next, we consider the complexity of determining if a permission is implied by a set of XrML licenses. We prove that the general problem is undecidable, but it is polynomial-time computable for an expressive fragment of the language. We extend XrML to capture a wider range of licenses by adding negation to the language. Finally, we discuss the key differences between XrML and MPEG-21, an international standard based on XrML.
Passive-Logging Attacks Against Anonymous Communications Systems
Authors: Wright Matthew K. , Adler Micah , Levine Brian Neil , Shields Clay
Published: February 2008

Using analysis, simulation, and experimentation, we examine the threat against anonymous communications posed by passive-logging attacks. In previous work, we analyzed the success of such attacks under various assumptions. Here, we evaluate the effects of these assumptions more closely. First, we analyze the Onion Routing-based model used in prior work in which a fixed set of nodes remains in the system indefinitely. We show that for this model, by removing the assumption of uniformly random selection of nodes for placement in the path, initiators can greatly improve their anonymity. Second, we show by simulation that attack times are significantly lower in practice than bounds given by analytical results from prior work. Third, we analyze the effects of a dynamic membership model, in which nodes are allowed to join and leave the system; we show that all known defenses fail more quickly when the assumption of a static node set is relaxed. Fourth, intersection attacks against peer-to-peer systems are shown to be an additional danger, either on their own or in conjunction with the predecessor attack. Finally, we address the question of whether the regular communication patterns required by the attacks exist in real traffic. We collected and analyzed the Web requests of users to determine the extent to which basic patterns can be found. We show that, for our study, frequent and repeated communication to the same Web site is common.