bluuebunny/crossref_metadata_2025 huggingface dataset:
Host‐parasitoid spatial dynamics in heterogeneous landscapes
Authors: H. Hirzel Alexandre , M. Nisbet Roger , W. Murdoch William
Published: October 2007

This paper explores the effect of spatial processes in a heterogeneous environment on the dynamics of a host‐parasitoid interaction. The environment consists of a lattice of favourable (habitat) and hostile (matrix) hexagonal cells, whose spatial distribution is measured by habitat proportion and spatial autocorrelation (inverse of fragmentation). At each time step, a fixed fraction of both populations disperses to the adjacent cells where it reproduces following the Nicholson‐Bailey model. Aspects of the dynamics analysed include extinction, stability, cycle period and amplitude, and the spatial patterns emerging from the dynamics.

We find that, depending primarily on the fraction of the host population that disperses in each generation and on the landscape geometry, five classes of spatio‐temporal dynamics can be objectively distinguished: spatial chaos, spirals, metapopulation, mainland‐island and spiral fragments. The first two are commonly found in theoretical studies of homogeneous landscapes. The other three are direct consequences of the heterogeneity and have strong similarities to dynamic patterns observed in real systems (e.g. extinction‐recolonisation, source‐sink, outbreaks, spreading waves).

We discuss the processes that generate these patterns and allow the system to persist. The importance of these results is threefold: first, our model merges into a same theoretical framework dynamics commonly observed in the field that are usually modelled independently. Second, these dynamics and patterns are explained by dispersal rate and common landscape statistics, thus linking in a practical way population ecology to landscape ecology. Third, we show that the landscape geometry has a qualitative effect on the length of the cycles and, in particular, we demonstrate how very long periods can be produced by spatial processes.
Predatory fish loss affects the structure and functioning of a model marine food web
Authors: O'Connor Nessa E. , Bruno John F.
Published: October 2007

The rate of species loss is increasing on a global scale and predators are most at risk from human‐induced extinction. The effects of losing predators are difficult to predict, even with experimental single species removals, because different combinations of species interact in unpredictable ways. We tested the effects of the loss of groups of common predators on herbivore and algal assemblages in a model benthic marine system. The predator groups were fish, shrimp and crabs. Each group was represented by at least two characteristic species based on data collected at local field sites. We examined the effects of the loss of predators while controlling for the loss of predator biomass. The identity, not the number of predator groups, affected herbivore abundance and assemblage structure. Removing fish led to a large increase in the abundance of dominant herbivores, such as Ampithoids and Caprellids. Predator identity also affected algal assemblage structure. It did not, however, affect total algal mass. Removing fish led to an increase in the final biomass of the least common taxa (red algae) and reduced the mass of the dominant taxa (brown algae). This compensatory shift in the algal assemblage appeared to facilitate the maintenance of a constant total algal biomass. In the absence of fish, shrimp at higher than ambient densities had a similar effect on herbivore abundance, showing that other groups could partially compensate for the loss of dominant predators. Crabs had no effect on herbivore or algal populations, possibly because they were not at carrying capacity in our experimental system. These findings show that contrary to the assumptions of many food web models, predators cannot be classified into a single functional group and their role in food webs depends on their identity and density in ‘real’ systems and carrying capacities.
Osmosis and thermodynamics
Authors: Lachish Uri
Published: October 2007

The van’t Hoff formula for osmotic pressure, which is identical in form to the formula for ideal gas pressure, is a direct outcome of the second law of thermodynamics. The formula is derived by applying a closed cycle reversible and isothermal process, following an argument in Fermi’s book on thermodynamics.
Einstein’s 1934 two-blackboard derivation of energy-mass equivalence
Authors: Topper David , Vincent Dwight
Published: October 2007

We use a famous and a rare picture of Einstein to reconstruct the context of a lecture he gave on the derivation of the equivalence of energy and mass in Pittsburgh in 1934. This lecture is interesting from a historical and sociological point of view because, at the time, Einstein was at the height of his fame, the equivalence of energy and mass was being discussed in newspapers, and his presence in Pittsburgh created much attention among the general public. Einstein exhibited his well-known intuitive style of using only the most important physical information in the zero-momentum frame derivation. His method was simple and direct and is relevant to those who teach the zero-momentum frame idea. From the perspective of the nonspecialists in the Pittsburgh audience, it was presented at an expert level without allowing for many explanatory concessions we would take for granted today. A definitive picture of Einstein, in front of his famous energy equation, was missed by photographers who posed him with the wrong blackboard in the background.
Classical analytical mechanics and entropy production
Authors: Silverberg J. , Widom A.
Published: October 2007

The usual canonical Hamiltonian or Lagrangian formalism of classical mechanics applied to macroscopic systems describes energy conserving adiabatic motion. If irreversible diabatic processes are to be included, the law of increasing entropy must also be considered. The notion of entropy then enters into the classical mechanical formalism. The resulting general formulation and its physical consequences are explored.
Vertical bounce of two vertically aligned balls
Authors: Cross Rod
Published: October 2007

When a tennis ball rests on top of a basketball and both drop to the floor together, the tennis ball is projected vertically at high speed. A mass-spring model of the impact, as well as air track data, suggest that the tennis ball should be projected at relatively low speed. Measurements of the forces on each ball and the bounce of vertically aligned superballs are used to resolve the discrepancy.
Improvements in the analysis of diffraction phenomena by means of digital images
Authors: Ramil A. , López A. J. , Vincitorio F.
Published: October 2007

We introduce a simple methodology employing digital photography and image processing techniques to do a quantitative study of diffraction. To enhance the range of intensities recorded by a CCD camera without saturation, digital images of the diffraction patterns taken at different exposure times are combined pixel by pixel, and the measured values of the light intensity are fitted to theoretical curves. Diffraction by a single slit, a double slit, and a circular hole were analyzed to obtain quantitative results and demonstrate that the methodology is suitable for student laboratories.
Scientist as detective: Luis Alvarez and the pyramid burial chambers, the JFK assassination, and the end of the dinosaurs
Authors: Wohl Charles G.
Published: October 2007

Luis Alvarez (1911–1988) was one of the most brilliant and productive experimental physicists of the twentieth century. His investigations of three mysteries, all of them outside his normal areas of research, show what remarkable things a far-ranging imagination working with an immense store of knowledge can accomplish.
The effect of multiple internal representations on context-rich instruction
Authors: Lasry Nathaniel , Aulls Mark W.
Published: October 2007

We discuss n-coding, a theoretical model of multiple internal mental representations. The n-coding construct is developed from a review of cognitive and imaging data that demonstrates the independence of information processed along different modalities such as verbal, visual, kinesthetic, logico-mathematic, and social modalities. A study testing the effectiveness of the n-coding construct in classrooms is presented. Four sections differing in the level of n-coding opportunities were compared. Besides a traditional-instruction section used as a control group, each of the remaining three sections were given context-rich problems, which differed by the level of n-coding opportunities designed into their laboratory environment. To measure the effectiveness of the construct, problem-solving skills were assessed as conceptual learning using the force concept inventory. We also developed several new measures that take students’ confidence in concepts into account. Our results show that the n-coding construct is useful in designing context-rich environments and can be used to increase learning gains in problem solving, conceptual knowledge, and concept confidence. Specifically, when using props in designing context-rich problems, we find n-coding to be a useful construct in guiding which additional dimensions need to be attended to.
Comment on "Emergence of Novel Color Vision in Mice Engineered to Express a Human Cone Photopigment"
Authors: Makous Walter
Published: October 2007

Jacobs
et al
. (Reports, 23 March 2007, p. 1723) reported that plasticity in the mammalian visual system permitted the emergence of “a new dimension of sensory experience” in mice genetically engineered to express a human long-wavelength–sensitive cone photopigment. However, neither neural plasticity nor a new dimension of sensory experience is required to explain their results.
Lyso-Phosphatidylcholine Is a Signal in the Arbuscular Mycorrhizal Symbiosis
Authors: Drissner David , Kunze Gernot , Callewaert Nico , Gehrig Peter , Tamasloukht M'Barek , Boller Thomas , Felix Georg , Amrhein Nikolaus , Bucher Marcel
Published: October 2007

The arbuscular mycorrhizal (AM) symbiosis represents the most widely distributed mutualistic root symbiosis. We report that root extracts of mycorrhizal plants contain a lipophilic signal capable of inducing the phosphate transporter genes
StPT3
and
StPT4
of potato (
Solanum tuberosum
L.), genes that are specifically induced in roots colonized by AM fungi. The same signal caused rapid extracellular alkalinization in suspension-cultured tomato (
Solanum lycopersicum
L.) cells and induction of the mycorrhiza-specific phosphate transporter gene
LePT4
in these cells. The active principle was characterized as the lysolipid lyso-phosphatidylcholine (LPC) via a combination of gene expression studies, alkalinization assays in cell cultures, and chromatographic and mass spectrometric analyses. Our results highlight the importance of lysophospholipids as signals in plants and in particular in the AM symbiosis.
Response to Comment on "Emergence of Novel Color Vision in Mice Engineered to Express a Human Cone Photopigment"
Authors: Jacobs Gerald H. , Nathans Jeremy
Published: October 2007

Makous suggests that the novel color vision documented in knock-in mice neither requires visual system plasticity nor implies the emergence of a new dimension of sensory experience. We explain why we disagree.
Polymers with Cavities Tuned for Fast Selective Transport of Small Molecules and Ions
Authors: Park Ho Bum , Jung Chul Ho , Lee Young Moo , Hill Anita J. , Pas Steven J. , Mudie Stephen T. , Van Wagner Elizabeth , Freeman Benny D. , Cookson David J.
Published: October 2007

Within a polymer film, free-volume elements such as pores and channels typically have a wide range of sizes and topologies. This broad range of free-volume element sizes compromises a polymer's ability to perform molecular separations. We demonstrated free-volume structures in dense vitreous polymers that enable outstanding molecular and ionic transport and separation performance that surpasses the limits of conventional polymers. The unusual microstructure in these materials can be systematically tailored by thermally driven segment rearrangement. Free-volume topologies can be tailored by controlling the degree of rearrangement, flexibility of the original chain, and judicious inclusion of small templating molecules. This rational tailoring of free-volume element architecture provides a route for preparing high-performance polymers for molecular-scale separations.
Excitation of Lunar Eccentricity by Planetary Resonances
Authors: Ćuk Matija
Published: October 2007

The origin of the Moon's nonnegligible orbital eccentricity of 0.053 has no theoretical explanation. Lunar laser ranging indicates that tides on Earth are currently increasing the Moon's eccentricity. However, ocean tides were likely much weaker during the first billion years, allowing lunar tides to damp any primordial lunar eccentricity very early on. During the tidally driven expansion of its orbit, the Moon must have been affected by two substantial resonances related to Jupiter and Venus, passage through which may have generated today's lunar eccentricity.
Diverse Plasma Populations and Structures in Jupiter's Magnetotail
Authors: McComas D. J. , Allegrini F. , Bagenal F. , Crary F. , Ebert R. W. , Elliott H. , Stern A. , Valek P.
Published: October 2007

Jupiter's magnetotail is the largest cohesive structure in the solar system and marks the loss of vast numbers of heavy ions from the Jupiter system. The New Horizons spacecraft traversed the magnetotail to distances exceeding 2500 jovian radii (
R
J
) and revealed a remarkable diversity of plasma populations and structures throughout its length. Ions evolve from a hot plasma disk distribution at ∼100
R
J
to slower, persistent flows down the tail that become increasingly variable in flux and mean energy. The plasma is highly structured—exhibiting sharp breaks, smooth variations, and apparent plasmoids—and contains ions from both Io and Jupiter's ionosphere with intense bursts of H
+
and H
+
3
. Quasi-periodic changes were seen in flux at ∼450 and ∼1500
R
J
with a 10-hour period. Other variations in flow speed at ∼600 to 1000
R
J
with a 3- to 4-day period may be attributable to plasmoids moving down the tail.
Io's Atmospheric Response to Eclipse: UV Aurorae Observations
Authors: Retherford K. D. , Spencer J. R. , Stern S. A. , Saur J. , Strobel D. F. , Steffl A. J. , Gladstone G. R. , Weaver H. A. , Cheng A. F. , Parker J. Wm. , Slater D. C. , Versteeg M. H. , Davis M. W. , Bagenal F. , Throop H. B. , Lopes R. M. C. , Reuter D. C. , Lunsford A. , Conard S. J. , Young L. A. , Moore J. M.
Published: October 2007

The New Horizons (NH) spacecraft observed Io's aurora in eclipse on four occasions during spring 2007. NH Alice ultraviolet spectroscopy and concurrent Hubble Space Telescope ultraviolet imaging in eclipse investigate the relative contribution of volcanoes to Io's atmosphere and its interaction with Jupiter's magnetosphere. Auroral brightness and morphology variations after eclipse ingress and egress reveal changes in the relative contribution of sublimation and volcanic sources to the atmosphere. Brightnesses viewed at different geometries are best explained by a dramatic difference between the dayside and nightside atmospheric density. Far-ultraviolet aurora morphology reveals the influence of plumes on Io's electrodynamic interaction with Jupiter's magnetosphere. Comparisons to detailed simulations of Io's aurora indicate that volcanoes supply 1 to 3% of the dayside atmosphere.
Jupiter's Nightside Airglow and Aurora
Authors: Gladstone G. Randall , Stern S. Alan , Slater David C. , Versteeg Maarten , Davis Michael W. , Retherford Kurt D. , Young Leslie A. , Steffl Andrew J. , Throop Henry , Parker Joel Wm. , Weaver Harold A. , Cheng Andrew F. , Orton Glenn S. , Clarke John T. , Nichols Jonathan D.
Published: October 2007

Observations of Jupiter's nightside airglow (nightglow) and aurora obtained during the flyby of the New Horizons spacecraft show an unexpected lack of ultraviolet nightglow emissions, in contrast to the case during the Voyager flybys in 1979. The flux and average energy of precipitating electrons generally decrease with increasing local time across the nightside, consistent with a possible source region along the dusk flank of Jupiter's magnetosphere. Visible emissions associated with the interaction of Jupiter and its satellite Io extend to a surprisingly high altitude, indicating localized low-energy electron precipitation. These results indicate that the interaction between Jupiter's upper atmosphere and near-space environment is variable and poorly understood; extensive observations of the day side are no guide to what goes on at night.
... and a Partridge in Allopatry
Authors: Rieseberg Loren H.
Published: October 2007

Speciation in Birds
.
By Trevor Price
. Roberts and Company, Greenwood Village, CO, 2007. 480 pp. Paper, $59.95. ISBN 9780974707785.

Price examines the behavioral and genetic causes and consequences of speciation in birds.
Energetic Particles in the Jovian Magnetotail
Authors: McNutt R. L. , Haggerty D. K. , Hill M. E. , Krimigis S. M. , Livi S. , Ho G. C. , Gurnee R. S. , Mauk B. H. , Mitchell D. G. , Roelof E. C. , McComas D. J. , Bagenal F. , Elliott H. A. , Brown L. E. , Kusterer M. , Vandegriff J. , Stern S. A. , Weaver H. A. , Spencer J. R. , Moore J. M.
Published: October 2007

When the solar wind hits Jupiter's magnetic field, it creates a long magnetotail trailing behind the planet that channels material out of the Jupiter system. The New Horizons spacecraft traversed the length of the jovian magnetotail to >2500 jovian radii (
R
J
; 1
R
J
≡71,400 kilometers), observing a high-temperature, multispecies population of energetic particles. Velocity dispersions, anisotropies, and compositional variation seen in the deep-tail (≳ 500
R
J
) with a ∼3-day periodicity are similar to variations seen closer to Jupiter in Galileo data. The signatures suggest plasma streaming away from the planet and injection sites in the near-tail region (∼200 to 400
R
J
) that could be related to magnetic reconnection events. The tail structure remains coherent at least until it reaches the magnetosheath at 1655
R
J
.
Matters of the Heart
Authors: Wells A. J.
Published: October 2007

Heartfelt Emotions
. A Symposium. Presented by the Wellcome Collection, London, 7-8 September 2007.
www.wellcomecollection.org/assets/wtx041078.pdf

The Heart
.
James Peto, Ed.
. Yale University Press, New Haven, CT, and Wellcome Collection, London, 2007. 272 pp. $35, £16.99. ISBN 9780300125108.

The symposium, arranged in conjunction with The Heart exhibition, explored the concept of emotions through approaches ranging from Victorian poetry to neuroscience.
New Surprises in the Largest Magnetosphere of Our Solar System
Authors: Krupp Norbert
Published: October 2007

En route to its ultimate rendezvous with Pluto, the New Horizons spacecraft passed through the magnetic and plasma environment of Jupiter in February 2007. Onboard instruments collected high-resolution images, spectroscopic data, and information about charged particles. The results have revealed unusual structure and variation in Jupiter's plasma and large plasmoids that travel down the magnetotail. Data on Jupiter's aurora provide details of the interaction with the solar wind, and a major volcanic eruption from the moon Io was observed during the encounter.
DNA Fingerprinting Analysis of Breakthrough Outbreaks in Vaccine-Protected Poultry Stocks
Authors: Kardos G. , Turcsányi I. , Bistyák A. , Nagy J. , Kiss I.
Published: October 2007

We report recurrent outbreaks of
Yersinia pseudotuberculosis
conjunctivitis in ducks and of fowl cholera in geese, occurring in stocks previously vaccinated with inactivated autogenous vaccines. Enterobacterial repetitive intergenic consensus sequence-based PCR and pulsed-field gel electrophoresis indicated reinfection with a new
Y. pseudotuberculosis
strain and vaccine evasion by the same
Pasteurella multocida
strain.
Molecular Epidemiology of TwoKlebsiella pneumoniaeMastitis Outbreaks on a Dairy Farm in New York State
Authors: Munoz Marcos A. , Welcome Francis L. , Schukken Ynte H. , Zadoks Ruth N.
Published: October 2007

Klebsiellaspp. have become an important cause of clinical mastitis in dairy cows in New York State. We describe the occurrence of twoKlebsiellamastitis outbreaks on a single dairy farm.Klebsiellaisolates from milk, feces, and environmental sources were compared using random amplified polymorphic DNA (RAPD)-PCR typing. The first mastitis outbreak was caused by a single strain ofKlebsiella pneumoniae, RAPD type A, which was detected in milk from eight cows. RAPD type A was also isolated from the rubber liners of milking machine units after milking of infected cows and from bedding in the outbreak pen. Predominance of a single strain could indicate contagious transmission of the organism or exposure of multiple cows to an environmental point source. No new cases with RAPD type A were observed after implementation of intervention measures that targeted the prevention of transmission via the milking machine as well as improvement of environmental hygiene. A second outbreak ofKlebsiellamastitis that occurred several weeks later was caused by multiple RAPD types, which rules out contagious transmission and indicates opportunistic infections originating from the environment. The diversity ofKlebsiellastrains as quantified with Simpson's index of discrimination was significantly higher for isolates from fecal, feed, and water samples than for isolates from milk samples. Several isolates from bedding material that had the phenotypic appearance ofKlebsiellaspp. were identified as beingRaoultella planticolaandRaoultella terrigenabased onrpoBsequencing.
Ebola Virus VP24 Proteins Inhibit the Interaction of NPI-1 Subfamily Karyopherin α Proteins with Activated STAT1
Authors: Reid St. Patrick , Valmas Charalampos , Martinez Osvaldo , Sanchez Freddy Mauricio , Basler Christopher F.
Published: October 2007

The
Zaire ebolavirus
protein VP24 was previously demonstrated to inhibit alpha/beta interferon (IFN-α/β)- and IFN-γ-induced nuclear accumulation of tyrosine-phosphorylated STAT1 (PY-STAT1) and to inhibit IFN-α/β- and IFN-γ-induced gene expression. These properties correlated with the ability of VP24 to interact with the nuclear localization signal receptor for PY-STAT1, karyopherin α1. Here, VP24 is demonstrated to interact not only with overexpressed but also with endogenous karyopherin α1. Mutational analysis demonstrated that VP24 binds within the PY-STAT1 binding region located in the C terminus of karyopherin α1. In addition, VP24 was found to inhibit PY-STAT1 binding to both overexpressed and endogenous karyopherin α1. We assessed the binding of both PY-STAT1 and the VP24 proteins from Zaire, mouse-adapted Zaire, and Reston Ebola viruses for interaction with all six members of the human karyopherin α family. We found, in contrast to previous studies, that PY-STAT1 can interact not only with karyopherin α1 but also with karyopherins α5 and α6, which together comprise the NPI-1 subfamily of karyopherin αs. Similarly, all three VP24s bound and inhibited PY-STAT1 interaction with karyopherins α1, α5, and α6. Consistent with their ability to inhibit the karyopherin-PY-STAT1 interaction, Zaire, mouse-adapted Zaire, and Reston Ebola virus VP24s displayed similar capacities to inhibit IFN-β-induced gene expression in human and mouse cells. These findings suggest that VP24 inhibits interaction of PY-STAT1 with karyopherins α1, α5, or α6 by binding within the PY-STAT1 binding region of the karyopherins and that this function is conserved among the VP24 proteins of different Ebola virus species.
The U95 Protein of Human Herpesvirus 6B Interacts with Human GRIM-19: Silencing of U95 Expression Reduces Viral Load and Abrogates Loss of Mitochondrial Membrane Potential
Authors: Yeo W. M. , Isegawa Yuji , Chow Vincent T. K.
Published: October 2007

To better understand the pathogenesis of human herpesvirus 6 (HHV-6), it is important to elucidate the functional aspects of immediate-early (IE) genes at the initial phase of the infection. To study the functional role of the HHV-6B IE gene encoding U95, we generated a U95-Myc fusion protein and screened a pretransformed bone marrow cDNA library for U95-interacting proteins, using yeast-two hybrid analysis. The most frequently appearing U95-interacting protein identified was GRIM-19, which belongs to the family of genes associated with retinoid-interferon mortality and serves as an essential component of the oxidative phosphorylation system. This interaction was verified by both coimmunoprecipitation and confocal microscopic coimmunolocalization. Short-term HHV-6B infection of MT-4 T-lymphocytic cells induced syncytial formation, resulted in decreased mitochondrial membrane potential, and led to progressively pronounced ultrastructural changes, such as mitochondrial swelling, myelin-like figures, and a loss of cristae. Compared to controls, RNA interference against U95 effectively reduced the U95 mRNA copy number and abrogated the loss of mitochondrial membrane potential. Our results indicate that the high affinity between U95 early viral protein and GRIM-19 may be closely linked to the detrimental effect of HHV-6B infection on mitochondria. These findings may explain the alternative cell death mechanism of expiration, as opposed to apoptosis, observed in certain productively HHV-6B-infected cells. The interaction between U95 and GRIM-19 is thus functionally and metabolically significant in HHV-6B-infected cells and may be a means through which HHV-6B modulates cell death signals by interferon and retinoic acid.
Binding Kinetics of Darunavir to Human Immunodeficiency Virus Type 1 Protease Explain the Potent Antiviral Activity and High Genetic Barrier
Authors: Dierynck Inge , De Wit Mieke , Gustin Emmanuel , Keuleers Inge , Vandersmissen Johan , Hallenberger Sabine , Hertogs Kurt
Published: October 2007

The high incidence of cross-resistance between human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) limits their sequential use. This necessitates the development of PIs with a high genetic barrier and a broad spectrum of activity against PI-resistant HIV, such as tipranavir and darunavir (TMC114). We performed a surface plasmon resonance-based kinetic study to investigate the impact of PI resistance-associated mutations on the protease binding of five PIs used clinically: amprenavir, atazanavir, darunavir, lopinavir, and tipranavir. With wild-type protease, the binding affinity of darunavir was more than 100-fold higher than with the other PIs, due to a very slow dissociation rate. Consequently, the dissociative half-life of darunavir was much higher (>240 h) than that of the other PIs, including darunavir's structural analogue amprenavir. The influence of protease mutations on the binding kinetics was tested with five multidrug-resistant (MDR) proteases derived from clinical isolates harboring 10 to 14 PI resistance-associated mutations with a decreased susceptibility to various PIs. In general, all PIs bound to the MDR proteases with lower binding affinities, caused mainly by a faster dissociation rate. For amprenavir, atazanavir, lopinavir, and tipranavir, the decrease in affinity with MDR proteases resulted in reduced antiviral activity. For darunavir, however, a nearly 1,000-fold decrease in binding affinity did not translate into a weaker antiviral activity; a further decrease in affinity was required for the reduced antiviral effect. These observations provide a mechanistic explanation for darunavir's potent antiviral activity and high genetic barrier to the development of resistance.
Discrete Clusters of Virus-Encoded MicroRNAs Are Associated with Complementary Strands of the Genome and the 7.2-Kilobase Stable Intron in Murine Cytomegalovirus
Authors: Buck Amy H. , Santoyo-Lopez Javier , Robertson Kevin A. , Kumar Diwakar S. , Reczko Martin , Ghazal Peter
Published: October 2007

The prevalence and importance of microRNAs (miRNAs) in viral infection are increasingly relevant. Eleven miRNAs were previously identified in human cytomegalovirus (HCMV); however, miRNA content in murine CMV (MCMV), which serves as an important in vivo model for CMV infection, has not previously been examined. We have cloned and characterized 17 novel miRNAs that originate from at least 12 precursor miRNAs in MCMV and are not homologous to HCMV miRNAs. In parallel, we applied a computational analysis, using a support vector machine approach, to identify potential precursor miRNAs in MCMV. Four of the top 10 predicted precursor sequences were cloned in this study, and the combination of computational and cloning analysis demonstrates that MCMV has the capacity to encode miRNAs clustered throughout the genome. On the basis of drug sensitivity experiments for resolving the kinetic class of expression, we show that the MCMV miRNAs are both early and late gene products. Notably, the MCMV miRNAs occur on complementary strands of the genome in specific regions, a feature which has not previously been observed for viral miRNAs. One cluster of miRNAs occurs in close proximity to the 5′ splice site of the previously identified 7.2-kb stable intron, implying a variety of potential regulatory mechanisms for MCMV miRNAs.
Venezuelan Equine Encephalitis Virus Replicon Particles Encoding Respiratory Syncytial Virus Surface Glycoproteins Induce Protective Mucosal Responses in Mice and Cotton Rats
Authors: Mok Hoyin , Lee Sujin , Utley Thomas J. , Shepherd Bryan E. , Polosukhin Vasiliy V. , Collier Martha L. , Davis Nancy L. , Johnston Robert E. , Crowe James E.
Published: October 2007

Respiratory syncytial virus (RSV) is an important viral pathogen that causes severe lower respiratory tract infection in infants, the elderly, and immunocompromised individuals. There are no licensed RSV vaccines to date. To prevent RSV infection, immune responses in both the upper and lower respiratory tracts are required. Previously, immunization with Venezuelan equine encephalitis virus replicon particles (VRPs) demonstrated effectiveness in inducing mucosal protection against various pathogens. In this study, we developed VRPs encoding RSV fusion (F) or attachment (G) glycoproteins and evaluated the immunogenicity and efficacy of these vaccine candidates in mice and cotton rats. VRPs, when administered intranasally, induced surface glycoprotein-specific virus neutralizing antibodies in serum and immunoglobulin A (IgA) antibodies in secretions at the respiratory mucosa. In addition, fusion protein-encoding VRPs induced gamma interferon (IFN-γ)-secreting T cells in the lungs and spleen, as measured by reaction with an
H-2K

d

-restricted CD8
+
T-cell epitope. In animals vaccinated with F protein VRPs, challenge virus replication was reduced below the level of detection in both the upper and lower respiratory tracts following intranasal RSV challenge, while in those vaccinated with G protein VRPs, challenge virus was detected in the upper but not the lower respiratory tract. Close examination of histopathology of the lungs of vaccinated animals following RSV challenge revealed no enhanced inflammation. Immunization with VRPs induced balanced Th1/Th2 immune responses, as measured by the cytokine profile in the lungs and antibody isotype of the humoral immune response. These results represent an important first step toward the use of VRPs encoding RSV proteins as a prophylactic vaccine for RSV.
Enzymatically Active APOBEC3G Is Required for Efficient Inhibition of Human Immunodeficiency Virus Type 1
Authors: Miyagi Eri , Opi Sandrine , Takeuchi Hiroaki , Khan Mohammad , Goila-Gaur Ritu , Kao Sandra , Strebel Klaus
Published: October 2007

APOBEC3G (APO3G) is a cellular cytidine deaminase with potent antiviral activity. Initial studies of the function of APO3G demonstrated extensive mutation of the viral genome, suggesting a model in which APO3G's antiviral activity is due to hypermutation of the viral genome. Recent studies, however, found that deaminase-defective APO3G mutants transiently expressed in virus-producing cells exhibited significant antiviral activity, suggesting that the antiviral activity of APO3G could be dissociated from its deaminase activity. To directly compare the antiviral activities of wild-type (wt) and deaminase-defective APO3G, we used two approaches: (i) we titrated wt and deaminase-defective APO3G in transient-transfection studies to achieve similar levels of virus-associated APO3G and (ii) we constructed stable cell lines and selected clones expressing comparable amounts of wt and deaminase-defective APO3G. Viruses produced under these conditions were tested for viral infectivity. The results from the two approaches were consistent and suggested that the antiviral activity of deaminase-defective APO3G was significantly lower than that of wt APO3G. We conclude that efficient inhibition of
vif
-defective human immunodeficiency virus type 1 requires catalytically active APO3G.
Primary Human Splenic Macrophages, but Not T or B Cells, Are the Principal Target Cells for Dengue Virus Infection In Vitro
Authors: Blackley Shanley , Kou Zhihua , Chen Huiyuan , Quinn Matthew , Rose Robert C. , Schlesinger Jacob J. , Coppage Myra , Jin Xia
Published: October 2007

Understanding the pathogenesis of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) requires the precise identification of dengue virus (DV)-permissive target cells. In a previous study using unfractionated human peripheral blood mononuclear cells, we found that monocytes, but not B or T cells, were the principal DV-permissive cells in the absence of DV-immune pooled human sera (PHS) and the major mediators of antibody-dependent enhancement in the presence of PHS. To further identify DV-permissive target cells in other tissues and organs, we isolated human splenic mononuclear cells (MNCs), inoculated them with DV type 2 (strain 16681) in the presence or absence of PHS, and assessed their infection either directly using flow cytometry and reverse transcription-PCR (RT-PCR) assays or indirectly by plaque assay. We found that in the absence of PHS, a small proportion of splenic macrophages appeared to be positive for DV antigens in comparison to staining controls by the flow cytometric assay (0.77% ± 1.00% versus 0.18% ± 0.12%;P= 0.07) and that viral RNA was detectable by the RT-PCR assay in MNCs exposed to DV. Additionally, supernatants from cultures of DV-exposed MNCs contained infectious virions that were readily detectable by plaque assay. The magnitude of infection was significantly enhanced in splenic macrophages in the presence of highly diluted PHS (5.41% ± 3.53% versus 0.77% ± 1.00%;P= 0.001). In contrast, primary T and B cells were not infected in either the presence or absence of PHS. These results provide evidence, for the first time, that human primary splenic macrophages, rather than B or T cells, are the principal DV-permissive cells in the spleen and that they may be uniquely important in the initial steps of immune enhancement that leads to DHF/DSS in some DV-infected individuals.
The 29-Nucleotide Deletion Present in Human but Not in Animal Severe Acute Respiratory Syndrome Coronaviruses Disrupts the Functional Expression of Open Reading Frame 8
Authors: Oostra Monique , de Haan Cornelis A. M. , Rottier Peter J. M.
Published: October 2007

One of the most striking and dramatic genomic changes observed in the severe acute respiratory syndrome coronavirus (SARS-CoV) isolated from humans soon after its zoonotic transmission from palm civets was the acquisition of a characteristic 29-nucleotide deletion. This occurred in open reading frame 8 (ORF8), one of the accessory genes unique to the SARS-CoV. The function of ORF8 and the significance of the deletion are unknown. The intact ORF8 present in animal and some early human isolates encodes a 122-amino-acid polypeptide (8ab
+
), which we expressed in cells using the vaccinia virus T7 expression system. It was found to contain a cleavable signal sequence, which directs the precursor to the endoplasmic reticulum (ER) and mediates its translocation into the lumen. The cleaved protein became N-glycosylated, assembled into disulfide-linked homomultimeric complexes, and remained stably in the ER. The 29-nucleotide deletion splits ORF8 into two ORFs, 8a and 8b, encoding 39- and 84-residue polypeptides. The 8a polypeptide is likely to remain in the cytoplasm, as it is too small for its signal sequence to function and will therefore be directly released from the ribosome. However, we could not confirm this experimentally due to the lack of proper antibodies. ORF8b appeared not to be expressed in SARS-CoV-infected cells or when expressed from mRNA's mimicking mRNA8. This was due to the context of the internal AUG initiation codon, as we demonstrated after placing the ORF8b immediately behind the T7 promoter. A soluble, unmodified and monomeric 8b protein was now expressed in the cytoplasm, which was highly unstable and rapidly degraded. Clearly, the 29-nucleotide deletion disrupts the proper expression of the SARS-CoV ORF8, the implications of which are discussed.
Identification of Functional Domains within the Essential Large Tegument Protein pUL36 of Pseudorabies Virus
Authors: Böttcher Sindy , Granzow Harald , Maresch Christina , Möhl Britta , Klupp Barbara G. , Mettenleiter Thomas C.
Published: October 2007

Proteins of the capsid proximal tegument are involved in the transport of incoming capsids to the nucleus and secondary envelopment after nuclear egress. Homologs of the essential large capsid proximal tegument protein pUL36 are conserved within the
Herpesviridae
. They interact with another tegument component, pUL37, and contain a deubiquitinating activity in their N termini which, however, is not essential for virus replication. Whereas an internal deletion of 709 amino acids (aa) within the C-terminal half of the alphaherpesvirus pseudorabies virus (PrV) pUL36 does not impair its function (S. Böttcher, B. G. Klupp, H. Granzow, W. Fuchs, K. Michael, and T. C. Mettenleiter, J. Virol. 80:9910-9915, 2006), deletion of the very C terminus does (J. Lee, G. Luxton, and G. A. Smith, J. Virol. 80:12086-12094, 2006). For further characterization we deleted several predicted functional and structural motifs within PrV pUL36 and analyzed the resulting phenotypes in cell culture and a mouse infection model. Extension of the internal deletion to encompass aa 2087 to 2981 exerted only minor effects on virus replication but resulted in prolonged mean survival times of infected mice. Any additional extension did not yield viable virus. Deletion of an N-terminal region containing the deubiquitinating activity (aa 22 to 248) only slightly impaired viral replication in cell culture but slowed neuroinvasion in our mouse model, whereas a strong impairment of viral replication was observed after simultaneous removal of both nonessential domains. Absence of a region containing two predicted leucine zipper motifs (aa 748 to 991) also strongly impaired virus replication and spread. Thus, we identify several domains within the PrV UL36 protein, which, though not essential, are nevertheless important for virus replication.
RADON TRANSFORM ON H-TYPE AND SIEGEL-TYPE NILPOTENT GROUPS
Authors: PENG LIZHONG , ZHANG GENKAI
Published: October 2007

Let N = V ⊕ Z be a step-two nilpotent group. We study the Radon transform on functions on N defined by integration over the orbits {(z, t)(v, 0); v ∈ V} of the points (z, t) by the action of the subspace V ⊕ 0 of N. For N being of H-type, Siegel-type defined as the Shilov boundary of a complex Siegel domain, or Type F2r, b, a real analogue of the Siegel type, we find an inversion and a Plancherel formula for the Radon transform. We prove certain Lp- Lqboundedness properties for the transform. This generalizes earlier works of Geller–Stein and Strichartz for the Heisenberg groups.
MULTIPLE SOLUTIONS FOR NONLINEAR ELLIPTIC EQUATIONS ON COMPACT RIEMANNIAN MANIFOLDS
Authors: VÉTOIS JÉRÔME
Published: October 2007

Let (M,g) be a smooth compact Riemannian n-manifold, n ≥ 4, and h be a Holdër continuous function on M. We prove multiplicity of changing sign solutions for equations like Δg u + hu = |u|2* - 2 u, where Δg is the Laplace–Beltrami operator and 2* = 2n/(n - 2) is critical from the Sobolev viewpoint.
A METHODOLOGY FOR THE ESTIMATION OF CAPACITIVE CROSSTALK-INDUCED SHORT-CIRCUIT ENERGY
Authors: MONDAL MOSIN , MASSOUD YEHIA
Published: October 2007

In the nanometer regime, crosstalk significantly impacts the dynamic power consumption of a chip. In this paper, we present a methodology for analyzing crosstalk-induced short-circuit power dissipation in cell-based digital designs. We introduce a new cell pre-characterization technique for facilitating the estimation of crosstalk-induced short-circuit power. Examples demonstrate that the presented methodology is three orders of magnitude faster than circuit simulators while the average error is as low as 3.5%.
COMPASES: AN OPTIMIZED DESIGN FOR TESTABILITY SCHEME TO REDUCE THE COST OF TEST APPLICATION USING PARALLEL-SERIAL SCAN DESIGN
Authors: SOLANA JOSÉ M.
Published: October 2007

A full-scan structure is described, in which the classic single serial scan-path and the parallel-in/serial-out scan (PASE-Scan) designs coexist. It requires only one extra pin and a small hardware overhead with respect to the single serial scan-path approach, and is compatible with a test scheme of this type. A method for the structure design is outlined and a structure-oriented optimized procedure for obtaining the test is proposed which considerably reduces the test application cost with respect to the serial scan case, improving the previous results for parallel-serial designs. The experiments performed with the ISCAS89 benchmarks show average reductions in test length of 60.6% with respect to its full serial scan counterpart and of 58.7%, with respect to a conventional full serial scan test with normal compaction. The advantage of the COMPASES scheme in testing some circuits with multiple PASE-Scan structures is also outlined.
LOCATION-AIDED RESOURCE RESERVATION FOR HANDOFF BASED ON MOBILITY PREDICTION
Authors: ZHU HUAMIN , YANG QINGHAI , KWAK KYUNG SUP
Published: October 2007

In this paper, a location-aided resource reservation scheme for handoff based on mobility prediction is proposed for wireless cellular networks. We analyze the performance of the proposed scheme and propose a two-dimensional random walk model for simulation. Performance evaluation is done by computing several key performance criteria, i.e., prediction accuracy, average number of reservation per call, reservation efficiency, and reservation time overhead. The influences of threshold distance, average distance where the mobile station moves along a straight line, location error and sample time are investigated, and the effectiveness of mobility prediction is also evaluated. Performance comparison reveals that the proposed scheme performs better than a solely distance-based scheme without mobility prediction.
STOCHASTIC MODELING OF LOSS- AND GAIN-OF-FUNCTION MUTATIONS IN CANCER
Authors: KOMAROVA NATALIA L.
Published: October 2007

Here we review some spatial and non-spatial stochastic methods developed to study the dynamics of cancer progression. We illustrate the methodology with applications to the two most common patterns in cancer initiation and progression: loss-of-function and gain-of-function mutations. An example of a gain-of-function mutation is an activation of an oncogene; for such mutations we are interested in the process of mutant take-over. An example of a loss-of-function mutation is an inactivation of a tumor suppressor gene; for such processes we calculate the rate of production of double-hit mutants. We consider three stochastic models of cell populations with a constant size: a simple mass-action model, a spatial model and a hierarchical model which contains stem cells and daughter cells. Interestingly, the process of mutation accumulation and spread develops differently in different models. This suggests that simple mass-action models can be misleading when studying cancer dynamics. Moreover, our results also allow us to think about various types of tissue architecture and its protective role against cancer. In particular, we show that hierarchical tissue organization lowers the risk of cancerous transformations. Also, cellular motility and long-range signaling can decrease the risk of cancer in solid tissues.
MODELLING OF EARLY LUNG CANCER PROGRESSION: INFLUENCE OF GROWTH FACTOR PRODUCTION AND COOPERATION BETWEEN PARTIALLY TRANSFORMED CELLS
Authors: MARCINIAK-CZOCHRA ANNA , KIMMEL MAREK
Published: October 2007

The generally accepted Moolgavkar's theory of carcinogenesis assumes that all cancers are clonal, i.e. that they arise from progressive genetic deregulation in a cell pedigree originating from a single ancestral cell.18 However, recently the clonal theory has been challenged by the field theory of carcinogenesis, which admits the possibility of simultaneous changes in tissue subject to carcinogenic agents, such as tobacco smoke in lung cancer. Axelrod et al.1 formulated a more detailed framework, in which partially transformed cells depend in a mutualistic way on growth factors they produce, in this way enabling these cells to proliferate and undergo further transformations. On the other hand, the field theory assumes spatial distribution of precancerous cells and indeed there exists evidence that early-stage precancerous lesions in lung cancer progress along linear, tubular, or irregular surface structures. This seems to be the case for the atypical adenomatous hyperplasia (AAH),10 a likely precursor of adenocarcinoma of the lung. In this paper we explore the consequences of linking the model of spatial growth of precancerous cells,12 with the mutualistic hypothesis. We investigate the solutions of the model using analytical and computational techniques. The picture emerging from our modelling indicates that production of growth factors by cells considered may lead to diffusion-driven instability, which in turn may lead either to decay of both population, or to emergence of local growth foci, represented by spike-like solutions. Mutualism may, in some situations, increase the stability of solutions. One important conclusion is that models of field carcinogenesis, which include spatial effects, generally have very different behaviour compared to ODE models.
PERTURBING SINGULAR SOLUTIONS OF THE GELFAND PROBLEM
Authors: DÁVILA J. , DUPAIGNE L.
Published: October 2007

The equation -Δu = λeuposed in the unit ball B ⊆ ℝN, with homogeneous Dirichlet condition u|∂B= 0, has the singular solution [Formula: see text] when λ = 2(N - 2). If N ≥ 4 we show that under small deformations of the ball there is a singular solution (u,λ) close to (U,2(N - 2)). In dimension N ≥ 11 it corresponds to the extremal solution — the one associated to the largest λ for which existence holds. In contrast, we prove that if the deformation is sufficiently large then even when N ≥ 10, the extremal solution remains bounded in many cases.
MULTIPLE POSITIVE SOLUTIONS OF A ONE-DIMENSIONAL PRESCRIBED MEAN CURVATURE PROBLEM
Authors: HABETS PATRICK , OMARI PIERPAOLO
Published: October 2007

We discuss existence, non-existence and multiplicity of positive solutions of the Dirichlet problem for the one-dimensional prescribed curvature equation [Formula: see text] in connection with the changes of concavity of the function f. The proofs are based on an upper and lower solution method, we specifically develop for this problem, combined with a careful analysis of the time-map associated with some related autonomous equations.
EXPONENTIAL DECAY OF THE SOLUTIONS FOR NONLINEAR BIHARMONIC EQUATIONS
Authors: DENG YINBIN , LI YI
Published: October 2007

The purpose of this paper is to establish the exponential decay properties of the solutions for the nonlinear biharmonic equation [Formula: see text] We introduce the fundamental solutions for the linear biharmonic operator Δ2 - λ if λ < 0. By applying some properties of Hankel functions, which are the solutions of Bessel's equation, we obtain the asymptotic representation of the fundamental solution of Δ2 - λ at ∞ and 0. Asymptotic estimates of the solutions of (*) can be obtained from the properties of the fundamental solutions of Δ2 - λ.