bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of shape and size in micro-/nanodimples adhesion
Authors: Gissi Ruggiero , Decuzzi Paolo
Published: July 2005

Stiction is of major concern in the design of micro-nanoscale systems as microelectromechanical switches, micromotors, and hard-disk drives, affecting both manufacturing (release stiction) and operation (in use stiction). A current strategy to alleviate stiction relies on the microfabrication of dimples of different shape and size distributed over the interacting surfaces. In this paper, the interaction of an axisymmetric dimple with a half-space is modeled using a Lennard-Jones potential. The traction distribution at the interface is derived as a function of (i) the approach between the dimple and the half-space, (ii) the material properties (elastic modulus E and surface energy γ), and (iii) the dimple geometry. It is shown that, for a fixed tip radius, the pull-off force reduces dramatically as the lateral surface of the dimple becomes steeper. Even a small deviation from the classical parabolic profile leads to a 50% drop of the pull-off force, alleviating stiction, and to a smoother transition from the no-contact to the contact conditions (jump into contact).
Thermal characterization and analysis of phase change random access memory
Authors: Giraud V. , Cluzel J. , Sousa V. , Jacquot A. , Dauscher A. , Lenoir B. , Scherrer H. , Romer S.
Published: July 2005

The cross-plane thermal conductivity of Ge2Sb2Te5, either in its amorphous state or fcc crystallized state, and titanium nitride (TiN) thin films has been measured at room temperature by the 3ω method. These materials are involved in the fabrication of phase change random access memory (PC-RAM), Ge2Sb2Te5 and TiN being the PC and pseudoelectrode materials, respectively. The thermal conductivity of insulating SiO2 and ZnS:SiO2 layers was determined too. Each thermal conductivity measurement was performed by the means of at least two strip widths in order to check both the measurement self-consistency and the measurement accuracy. The performance of PC-RAM cells, i.e., the time needed to reach the melting temperature of the PC material and the cooling speed, has been evaluated as a function of both the measured thermal conductivity of the PC material and the reset current intensity independently of the thermal properties of the pseudoelectrodes by the way of analytical formula. The influence of the thickness and the thermal properties of the pseudoelectrodes on the performances have been determined by numerical simulations.
Pressure calibration to 20GPa by simultaneous use of ultrasonic and x-ray techniques
Authors: Li Baosheng , Kung Jennifer , Uchida Takeyuki , Wang Yanbin
Published: July 2005

Simultaneous measurements of elastic P- and S-wave travel times, density (specific volume), and sample length using a multianvil apparatus interfaced with ultrasonic interferometry and x-ray diffraction and radiography have enabled simultaneous determination of elastic properties and absolute pressure at high pressures and high temperatures. Experimental procedures and data analyses are demonstrated using data collected on polycrystalline samples of ferropericalse (MgFe) and wadsleyite Mg2SiO4 under quasihydrostatic conditions up to 20GPa. Compared with those derived from the internal pressure standard in the same experiments based on equations of state of NaCl, the directly determined pressure at 20GPa is ∼8% and ∼12% higher than those inferred from the Brown and Decker pressure scales, respectively. The discrepancy cannot be reconciled by uncertainties in the NaCl pressure scale and current experimental data. Until further results are available, the pressure determined in this study is believed to be a more accurate measurement of the effective pressure imposed on the sample than that inferred from NaCl based on previous pressure scales.
Charge-induced spin alignment in diradical donor molecules: Numerical calculations of correlated many-electron-spin systems
Authors: Huai Ping , Shimoi Yukihiro , Abe Shuji
Published: July 2005

The mechanism of charge-induced high spin is studied in π-conjugated molecules by means of a model-Hamiltonian approach. Intersite Coulomb interactions are taken into account in a π-conjugated moiety, which is coupled with two localized spins through exchange interactions. We clarify spin alignment in neutral and oxidized states by exact numerical calculations including all the correlation effects. In thianthrene-based molecules, one-electron oxidation induces strong ferromagnetic correlation between the localized spins irrespective of the spin alignment in the neutral state. The localized spins are coupled to the delocalized hole spin ferromagnetically, leading to a high-spin state in the oxidized molecule. Our calculations on structural dependence and effective exchange interaction are consistent with the recent experiment of thianthrene bis(nitronyl nitroxide). By comparing the thianthrene-based molecule with the anthracene-based one, we clarify the role of superexchange interactions via the sulfur atoms.
Nontrivial dependence of dielectric stiffness on bias field in relaxors and dipole glasses
Authors: Prosandeev S. A. , Raevski I. P. , Emelyanov A. S. , Colla Eugene V. , Dellis J-L. , El Marssi M. , Kapphan S. E. , Jastrabik L.
Published: July 2005

Dielectric permittivity studies in the field-cooled mode show a linear dependence of dielectric stiffness (inverse dielectric permittivity) on the dc bias in (1−x)PbMg1∕3Nb2∕3O3−xPbTiO3 crystals. We explain this unusual result in the framework of a theory of transverse, hydrodynamic-type instability of local polarization.
Structural determination of the low-coverage phase of Al on Si(001) surface
Authors: Park J. Y. , Seo J. H. , Whang C. N. , Kim S. S. , Choi D. S. , Chae K. H.
Published: July 2005

The atomic structure of Al layer on Si(001)-(2×1) surface has been studied by coaxial impact collision ion scattering spectroscopy. When 0.5 monolayer (ML) of Al atoms are adsorbed on Si(001) at room temperature, it is found that Al adatoms are dimerized and Al ad-dimers are oriented parallel to the underlying Si dimers at the position of centering T3 site with a height of 1.02 Å from the first layer of Si(001). The bond length of the Al dimer is 2.67 Å. With increasing Al coverage up to one ML, Al ad-dimers still occupied near T3 site and the next favorable site is near HH site.
Crack healing during molecular-beam-epitaxy growth of GaP∕GaAs thin films
Authors: Li Y. , Weatherly G. C. , Niewczas M.
Published: July 2005

A crack-healing phenomenon occurring during epitaxial growth of GaP films on a GaAs substrate was studied by transmission electron microscopy. The process is driven by a decrease in the surface energy of the cracked film. The results indicate that the fundamental mechanism operating during healing is the deposition and diffusion of Ga and P atoms onto the crack surface in the GaP lattice, combined with self-diffusion of GaAs within the crack tip in the GaAs substrate. This process is not fully completed in the GaP∕GaAs system; unhealed crack tips located in the GaAs substrate always remain in the structure. Development of cracks and subsequent crack healing during film growth lead to a decrease in residual stress in the film. New cracks are formed at an equilibrium spacing which increases with increasing film thickness. A modified expression for predicting the relation between crack spacing and film thickness in epitaxial films is proposed.
Precise measurement of the self-diffusion coefficient for poly(ethylene glycol) in aqueous solution using uniform oligomers
Authors: Shimada Kayori , Kato Haruhisa , Saito Takeshi , Matsuyama Shigetomo , Kinugasa Shinichi
Published: July 2005

Uniform poly(ethylene glycol) (PEG) oligomers, with a degree of polymerization n=1–40, were separated by preparative supercritical fluid chromatography from commercial monodispersed samples. Diffusion coefficients, D, for separated uniform PEG oligomers were measured in dilute solutions of deuterium oxide (D2O) at 30 ° C, using pulsed-field gradient nuclear magnetic resonance. The measured D for each molecular weight was extrapolated to infinite dilution. Diffusion coefficients obtained at infinite dilution follow the scaling behavior of Zimm-type diffusion, even in the lower molecular weight range. Molecular-dynamics simulations for PEG in H2O also showed this scaling behavior, and reproduced close hydrodynamic interactions between PEG and water. These findings suggest that diffusion of PEG in water is dominated by hydrodynamic interaction over a wide molecular weight range, including at low molecular weights around 1000.
A time-dependent wave-packet quantum scattering study of the reaction H2+(v=–2,4,6;j=1)+He→HeH++H
Authors: Chu Tian-Shu , Lu Rui-Feng , Han Ke-Li , Tang X.-N. , Xu H.-F. , Ng C. Y.
Published: July 2005

The quantum scattering dynamics calculation was carried out for the titled reaction in the collision energy range of 0.0–2.4 eV with reactant H2+ in the rotational state j=1 and vibrational states v=0–2, 4, and 6. The present time-dependent wave-packet calculation takes into account the Coriolis coupling (CC) and uses the accurate ab initio potential-energy surface of Palmieri et al. [Mol. Phys. 98, 1835 (2000)]. The importance of including the CC quantum scattering calculation has been revealed by the comparison between the CC calculation and the previous coupled state (CS) calculation. The CC total cross sections for the v=2, 4, and 6 states show collision energy-dependent behaviors different from those based on the CS calculation. Furthermore, the collision energy dependence of the total cross sections obtained in the present CC calculation only exhibits minor oscillations, indicating that the chance is slim for reactive resonances in total cross sections to survive through the partial-wave averaging. The magnitude and profile of the CC total cross sections for v=0–2 in the collision energy range of 0.0–2.5 eV are found to be consistent with experimental cross sections obtained recently by Tang et al. [J. Chem. Phys. 122, 164301 (2005)] after taking into account the experimental uncertainties.
Ab initio computed diabatic potential energy surfaces of OH–HCl
Authors: Wormer Paul E. S. , Kłos Jacek A. , Groenenboom Gerrit C. , van der Avoird Ad
Published: July 2005

The two four-dimensional diabatic potential energy surfaces (DPESs) for OH–HCl are computed that correlate with the twofold degenerate Π2 ground state of the free OH radical. About 20 000 points on the surface are obtained by the ab initio coupled-cluster and multi-reference configuration interaction methods. Analytic forms for the diabatic potential energy surfaces are derived as expansions in complete sets of orthogonal functions depending on the three intermolecular angles. The numeric computation of the angular expansion coefficients is discussed. The distance-dependence of the angular coefficients is represented by the reproducing kernel Hilbert space method. It is checked that both diabatic potentials converge for large intermolecular separations to the values computed directly from the electrostatic multipole expansion. The final DPESs are discussed and illustrated by some physically meaningful one- and two-dimensional cuts through them.
A dynamic model for the Lagrangian-averaged Navier-Stokes-α equations
Authors: Zhao Hongwu , Mohseni Kamran
Published: July 2005

A dynamic procedure for the Lagrangian-averaged Navier-Stokes-α (LANS-α) equations is developed where the variation in the parameter α in the direction of anisotropy is determined in a self-consistent way from the data contained in the simulation itself. In order to derive this model, the incompressible Navier-Stokes equations are Helmholtz filtered at the grid and test filter levels. A Germano-type identity is derived by comparing the filtered subgrid-scale stress terms with those given in the LANS-α equations. Assuming constant α in homogenous directions of the flow and averaging in these directions result in a nonlinear equation for the parameter α, which determines the variation of α in the nonhomogeneous directions or in time. Consequently, the parameter α is calculated during the simulation instead of a predefined value. The dynamic model is initially tested in forced and decaying isotropic turbulent flows where α is constant in space but it is allowed to vary in time. It is observed that by using the dynamic LANS-α procedure a more accurate simulation of the isotropic homogeneous turbulence is achieved. The energy spectra and the total kinetic-energy decay are captured more accurately as compared with the LANS-α simulations using a fixed α. In order to evaluate the applicability of the dynamic LANS-α model in anisotropic turbulence, a priori test of a turbulent channel flow is performed. It is found that the parameter α changes in the wall normal direction. Near a solid wall, the length scale α is seen to depend on the distance from the wall with a vanishing value at the wall. On the other hand, away from the wall, where the turbulence is more isotropic, α approaches an almost constant value. Furthermore, the behavior of the subgrid-scale stresses in the near-wall region is captured accurately by the dynamic LANS-α model. The dynamic LANS-α model has the potential to extend the applicability of the LANS-α equations to more complicated anisotropic flows.
Thermally widely tunable laser diodes with distributed feedback
Authors: Todt R. , Jacke T. , Meyer R. , Amann M.-C.
Published: July 2005

A thermally widely tunable buried heterostructure laser diode with distributed feedback (DFB) is demonstrated. This device requires only two tuning currents for wide quasicontinuous wavelength tuning, thereby facilitating easy and fast device calibration and control. Furthermore, being based on regular DFB laser fabrication technology, it is readily manufacturable. By using window structures instead of cleaved facets plus antireflection coatings, a regular tuning behavior has been achieved for a DFB-like widely tunable laser diode with only two tuning currents. The laser diode covers the wavelength range between 1552 and 1602 nm. Requiring side-mode suppression ratio and output power above 30 dB and 10 mW, respectively, a wavelength range of 43 nm is accessible.
Demonstration of chip-to-chip transmission of single-flux-quantum pulses at throughputs beyond 100 Gbps
Authors: Hashimoto Yoshihito , Yorozu Shinichi , Satoh Tetsuro , Miyazaki Toshiyuki
Published: July 2005

We report a demonstration of single-flux-quantum (SFQ) pulse transmission between superconductor chips at throughputs beyond 100 Gbps. A fabrication process with a high junction critical current density of 10kA∕cm2 was used to increase the operation speed of a pulse driver and receiver. The chips were flip-chip bonded on a passive microstrip carrier using small solder bumps with diameters of 30μm. With experiments based on a ring-shaped circuit, chip-to-chip SFQ pulse transmission has been demonstrated up to 117 Gbps with an error rate of less than 10−15. The power dissipated by the driver and receiver was only 0.24μW at 117 Gbps.
Fabrication of field-effect transistor device with higher fullerene, C88
Authors: Nagano Takayuki , Sugiyama Hiroyuki , Kuwahara Eiji , Watanabe Rie , Kusai Haruka , Kashino Yoko , Kubozono Yoshihiro
Published: July 2005

A fullerene field-effect transistor (FET) device has been fabricated with thin films of C88, and n-channel normally on depletion-type FET properties have been found in this FET device. The C88 FET exhibited a high mobility, μ, of 2.5×10−3cm2V−1s−1 at 300 K, in fullerene FETs. The carrier transport showed a thermally activated hopping transport. The n-channel normally on FET properties and the hopping transport reflect the small mobility gap and low carrier concentration in the channel region of C88 thin films.
High-intensity deer culling increases growth of mountain beech seedlings in New Zealand
Authors: Husheer Sean W. , Robertson Alastair W.
Published: July 2005

Browsing of mountain beech seedlings by introduced deer in the central North Island of New Zealand appears to have inhibited canopy regeneration over large areas. In 1998, a trial of high-, medium- and low-intensity deer-culling treatments was initiated in Kaimanawa and Kaweka Forest Parks to test whether mountain beech (Nothofagus solandri var. cliffortioides) forest regeneration could be restored by removing deer. Paired exclosure plots (one plot fenced to exclude deer and the other unfenced) were established within a high-intensity culling area, to monitor the benefits of recreational, commercial and aerial deer culling. Paired plots were also established within low- and medium-intensity culling areas. Medium-intensity culling was allowed through recreational and commercial deer culling. In two low-intensity culling treatment areas, deer management remained substantially unaltered. Annual relative growth rates of tagged seedlings from spring 1998 to spring 2001 from low-, medium- and high-intensity culling areas provide strong evidence that mountain beech seedling growth increases once browsing by deer is removed through fencing. Faecal pellet data indicated that high-intensity deer culling reduced deer abundance by 67% in comparison to medium- and low-intensity culling areas. This apparent reduction in deer abundance appears to have led to a doubling in mountain beech seedling growth in the high-intensity culling area outside fences, in comparison to low- and medium-intensity deer culling areas where there was little or no evidence of benefits for seedling growth.
Home range, activity and habitat use of European rabbits (Oryctolagus cuniculus) in arid Australia: implications for control
Authors: Moseby K. E. , De Jong S. , Munro N. , Pieck A.
Published: July 2005

The home range, activity and habitat use of wild European rabbits in northern South Australia were compared during winter and summer, and results used to suggest improvements to control techniques. Average home range was significantly smaller in summer (2.1 ha) than winter (4.2 ha) and there was no significant difference between the sexes. Rabbits used both dune and swale habitat but most warrens and more surface fixes were recorded in dune habitat in both seasons. Proportionally more surface fixes were found in swale habitat at night than during the day. The proportion of diurnal fixes on the surface was not significantly influenced by season, averaging 47% in winter and 62% in summer. Only 30% of radio-collared rabbits flushed by humans retreated to warrens. Comparable levels of diurnal surface activity in both winter and summer suggest that the death rate from fumigation or warren destruction may be similar in both seasons. High levels of diurnal surface activity suggest that warren fumigation may be ineffective unless rabbits can first be flushed to their warrens. The use of dogs to flush rabbits before fumigation or ripping should increase the efficacy of control. Activity data suggest that fumigation or ripping should be conducted between 0900 and 1600 hours in winter and 1100 and 1800 hours in summer when radio-collared rabbits were most likely to be down their warrens. Home-range data suggest that the effectiveness of poison baiting may be increased by placing bait lines closer together in summer and, although bait lines should be concentrated in dune habitat, some poison should also be placed in swale feeding areas remote from warrens. The most successful control method for radio-collared rabbits was fumigation with phosphine gas tablets, with 10 of 11 rabbits successfully killed. Pressure fumigation with chloropicrin was also successful but 1080 poisoning and warren destruction using shovels were all relatively unsuccessful.
Predation of artificial ground nests in Australian tropical savannas: inverse edge effects
Authors: Fraser Fiona J. , Whitehead Peter J.
Published: July 2005

Depredation of artificial ground nests was examined in tropical savanna in northern Australia to assess potential predation pressures on nests of the partridge pigeon (Geophaps smithii), a declining tropical granivore. Predation rates were examined at two sites, Kakadu National Park (which supported a relatively high density of partridge pigeons) and Berry Springs (which had greater habitat fragmentation and comparatively low partridge pigeon density). The effects of distance from road, understorey structure, topography and nest-microsite concealment on nest predation rates were examined. Artificial-nest predation rates were greater at 150 m from roads than <1 m from the roadside. Predation rates did not vary with understorey structure, topography, or level of nest concealment. There was marked variation between sites, with predation levels at Kakadu more than double those recorded for Berry Springs. Discerning predator identity, or even the size of a predator, from marks left in clay eggs proved difficult and was possible for ~35% of predation events. Of these, 42% of predation events involved predators of a size we considered too small to take a natural partridge pigeon nest. We suggest that extrapolation from artificial to natural ground-nest predation rates be undertaken with caution for landscapes such as Australia’s tropical savanna, which supports a high diversity and abundance of small potential predators of artificial nests. There was no evidence of predation by birds, and the methodology proved inadequate for identifying predation by feral cats (Felis catus).
A comparison of three trap designs for capturing brown treesnakes on Guam
Authors: Vice Daniel S. , Engeman Richard M. , Vice Diane L.
Published: July 2005

The accidental introduction of the brown treesnake (Boiga irregularis) to Guam has resulted in the extirpation of most native terrestrial vertebrates on the island, thousands of power outages, and significant ecological changes. In addition, Guam now serves as a source population for the dispersal of snakes to other islands. Control of the brown treesnake is dependent upon the use of traps in a variety of settings, including port environments and in forested habitat. A variety of snake traps have been used on Guam; most consist of a modified crawfish or minnow trap, housing a live mouse that serves as a lure. We compared the efficacy of three trap styles: (1) a two-piece design with a separate internal mouse chamber; (2) a one-piece trap, with design improvements aimed at decreasing handling; and (3) the same one-piece trap, fitted with a PVC-coated wire-mesh entrance flap. Data collected included snake capture rates, snake size distribution, mouse survival, and trap maintenance time. Snake capture rates did not differ between the one-piece and the two-piece traps, although capture rates were significantly lower in the PVC-flap traps. The average snake size or distribution of snake sizes did not differ between the one-piece and two-piece traps. Handling times, both with and without a snake in the trap, were significantly lower for the one-piece trap. Mouse survival did not differ between the one-piece and two-piece trap styles. Our results indicate that the modified one-piece trap design provides several advantages over previous trap designs.
Dietary ecology of the Australian freshwater turtle (Elseya sp.: Chelonia:Chelidae) in the Burnett River, Queensland
Authors: Armstrong Graeme , Booth David T.
Published: July 2005

The Burnett River snapping turtle (Elseya sp.) from the Burnett, Mary and Fitzroy river systems is an undescribed Australian freshwater turtle, of which very little ecological information is known. This paper describes the dietary ecology of the species in the Burnett River catchment. Stomach and faecal samples were collected from turtles and an index of relative importance was used to rank food items found in stomach samples. This index indicated that algae and aquatic ribbon weed (Vallisneria) were the dominant food items consumed. No difference in diet was found between males and females. Although the sample size was small, diet appeared to vary slightly seasonally, with Elseya sp. selectively feeding on the flower buds of the Chinese elm tree (Celtis chinensis) and the seeds of the blackbean tree (Castanospermum australe) when these food items were seasonally available. Faecal samples suggest that the most ingested foods (algae and aquatic ribbon weed) were also the most digestible. Although predominantly herbivorous, Elseya sp. was seen to eat carrion once in the wild.
Vaccinating against zoonotic parasitic diseases: myth or reality?
Authors: Zarlenga Dante S.
Published: July 2005

The largely unanticipated difficulties of parasite vaccine development have led us to a renewed awareness of the survival strategies evolutionarily embedded within parasites over hundreds of millions of years. We have grown to appreciate that efforts to disrupt parasite–host relationships are substantially compounded by our incomplete understanding of the complex immune responses that occur in the naturally infected host. Given the inability to transfer laboratory successes to field trials, research is leading us to conclude that genetically defined animal models may not be good predictors of the unique and disparate protective immune responses one can expect from the genetically heterogeneous populations of animals that represent the parasite's natural environment. This is further compounded by the abundance of mechanisms parasites have created for themselves to defend against immune intervention. Thus, in the never-ending saga of vaccine development, it is only appropriate that pitfalls and advancements be critiqued as they apply across parasite groups, with a look towards promising technologies that may propel this field to the level of scientific achievement once envisaged.
Commercialization of veterinary viral vaccines
Authors: Flore P. H.
Published: July 2005

If vaccines are to reliably prevent disease, they must be developed, produced and quality-controlled according to very strict regulations and procedures. Veterinary viral vaccine registrations are governed by different rules in different countries, but these rules all emphasize that the quality of the raw materials—the cells, eggs, animals or plants that are used in production—need to be carefully controlled. The veterinary vaccine business is also very cost-conscious. Emphasis over the last 5–10 years has therefore been to develop culture systems that minimize labor and sterility problems and thus provide for reliable and cost-effective production. Implementing these often more complex systems in a production environment takes considerable effort, first in scale-up trials and further down the line in convincing production personnel to change their familiar system for something new and possibly untried. To complete scale-up trials successfully, it is absolutely necessary to understand the biochemistry of the cells and the influence of the virus on the cells under scale-up and later production conditions. Once a viral product can be produced on a large scale, it is imperative that the quality of the end-product is controlled in an intelligent way. One needs to know whether the end-product performs in the animal as was intended during its conception in the research and development department. The development of the appropriate tests to demonstrate this plays an important role in the successful development of a vaccine.
Oral vaccines for finfish: academic theory or commercial reality?
Authors: Vandenberg Grant W.
Published: July 2005

Aquaculture is the fastest growing food-producing sector, providing an acceptable supplement to and substitute for wild fish and plants. Increased production intensification, particularly in high-value species, involves substantial stress, which, as in other captive livestock species, has resulted in outbreaks of major diseases and related mortalities. Widespread use of antibiotics has led to the development of antibiotic-resistant bacteria and the accumulation of antibiotics in the environment and the flesh of fish. Thus, recently effort has been dedicated to vaccine development. Vaccination in fish is complicated by their aquatic environment. Individual injections are labor-intensive and stressful, since fish have to be removed from the water and anaesthetized. Some vaccines offer a limited duration of protection, and thus booster applications are required. In salmonid species, many commercial vaccines use oil-based adjuvants, resulting in a greatly improved duration of protection. However, oil-based adjuvants have been related to significant growth depression, internal adhesions and injection site melanization, resulting in carcass downgrading. Oral administration to aquatic species is by far the most appealing method of vaccine delivery: there is no handling of the fish, which reduces stress; and administration is easy and suitable for mass immunization. However, few oral vaccines have been commercialized, due in part to the increased quantity of antigen required to provoke an immune response, and the lack of an adequate duration of protection. For effective oral delivery, protective antigens must avoid digestive hydrolysis and be taken up in the hindgut in order to induce an effective protective immune response. Antigen encapsulation technologies have been used to protect antigen; however, such strategies can be expensive and are not always effective. Alternative approaches, currently under development, are discussed.
The molecular biology of bovine immunodeficiency virus: a comparison with other lentiviruses
Authors: St-Louis Marie-Claude , Cojocariu Mihaela , Archambault Denis
Published: July 2005

Bovine immunodeficiency virus (BIV) was first isolated in 1969 from a cow, R-29, with a wasting syndrome. The virus isolated induced the formation of syncytia in cell cultures and was structurally similar to maedi-visna virus. Twenty years later, it was demonstrated that the bovine R-29 isolate was indeed a lentivirus with striking similarity to the human immunodeficiency virus. Like other lentiviruses, BIV has a complex genomic structure characterized by the presence of several regulatory/accessory genes that encode proteins, some of which are involved in the regulation of virus gene expression. This manuscript aims to review biological and, more particularly, molecular aspects of BIV, with emphasis on regulatory/accessory viral genes/proteins, in comparison with those of other lentiviruses.
Bovine torovirus (Breda virus) revisited
Authors: Hoet Armando E. , Saif Linda J.
Published: July 2005

Bovine torovirus (BoTV) is a pleomorphic virus with a spike-bearing envelope and a linear, non-segmented, positive-sense single-stranded RNA genome. This kidney-shaped virus is associated with diarrhea in calves and apparently has a worldwide distribution. This review provides details of the history and taxonomy of BoTV since its discovery in 1979. Information about virion morphology and architecture, antigenic and biological properties, viral genome, protein composition, thermal and chemical stability, and pH and proteolytic enzymes resistance is also summarized. A major focus of this review is to postulate a possible epidemiological cycle for BoTV, based on epidemiological data obtained in our studies and other published data, and progressing from the newborn calf to the adult animal. The distribution, host range, pathogenesis, disease and clinical signs (under experimental and natural exposure), pathology, diagnosis, prevention, treatment and control of BoTV infections are also described. In addition, a discussion of the zoonotic implications of torovirus-like particles detected in patients with gastroenteritis that resemble and cross-react with BoTV is presented. Hopefully, the findings described here will alert others to the existence of BoTV in cattle and its contribution to the diarrheal disease complex. This review also highlights the need for continual vigilance for potential zoonotic viruses belonging to the orderNidovirales, such as the SARS coronavirus.
Advances in PCR technology
Authors: Lauerman Lloyd H.
Published: July 2005

Since the discovery of the polymerase chain reaction (PCR) 20 years ago, an avalanche of scientific publications have reported major developments and changes in specialized equipment, reagents, sample preparation, computer programs and techniques, generated through business, government and university research. The requirement for genetic sequences for primer selection and validation has been greatly facilitated by the development of new sequencing techniques, machines and computer programs. Genetic libraries, such as GenBank, EMBL and DDBJ continue to accumulate a wealth of genetic sequence information for the development and validation of molecular-based diagnostic procedures concerning human and veterinary disease agents. The mechanization of various aspects of the PCR assay, such as robotics, microfluidics and nanotechnology, has made it possible for the rapid advancement of new procedures. Real-time PCR, DNA microarray and DNA chips utilize these newer techniques in conjunction with computer and computer programs. Instruments for hand-held PCR assays are being developed. The PCR and reverse transcription–PCR (RT–PCR) assays have greatly accelerated the speed and accuracy of diagnoses of human and animal disease, especially of the infectious agents that are difficult to isolate or demonstrate. The PCR has made it possible to genetically characterize a microbial isolate inexpensively and rapidly for identification, typing and epidemiological comparison.
Urea nitrogen salvage mechanisms and their relevance to ruminants, non-ruminants and man
Authors: Stewart Gavin S. , Smith Craig P.
Published: July 2005

Maintaining a correct balance of N is essential for life. In mammals, the major sources of N in the diet are amino acids and peptides derived from ingested proteins. The immediate endproduct of mammalian protein catabolism is ammonia, which is toxic to cells if allowed to accumulate. Therefore, amino acids are broken down in the liver as part of the ornithine–urea cycle, which results in the formation of urea – a highly soluble, biochemically benign molecule. Mammals cannot break down urea, which is traditionally viewed as a simple waste product passed out in the urine. However, urea from the bloodstream can pass into the gastrointestinal tract, where bacteria expressing urease cleave urea into ammonia and carbon dioxide. The bacteria utilise the ammonia as an N source, producing amino acids and peptides necessary for growth. Interestingly, these microbial products can be reabsorbed back into the host mammalian circulation and used for synthetic processes. This entire process is known as ‘urea nitrogen salvaging’ (UNS). In this review we present evidence supporting a role for this process in mammals – including ruminants, non-ruminants and man. We also explore the possible mechanisms involved in UNS, including the role of specialised urea transporters.
Calreticulin signals upstream of calcineurin and MEF2C in a critical Ca2+-dependent signaling cascade
Authors: Lynch Jeffrey , Guo Lei , Gelebart Pascal , Chilibeck Kaari , Xu Jian , Molkentin Jeffery D. , Agellon Luis B. , Michalak Marek
Published: July 2005

We uncovered a new pathway of interplay between calreticulin and myocyte-enhancer factor (MEF) 2C, a cardiac-specific transcription factor. We establish that calreticulin works upstream of calcineurin and MEF2C in a Ca2+-dependent signal transduction cascade that links the endoplasmic reticulum and the nucleus during cardiac development. In the absence of calreticulin, translocation of MEF2C to the nucleus is compromised. This defect is reversed by calreticulin itself or by a constitutively active form of calcineurin. Furthermore, we show that expression of the calreticulin gene itself is regulated by MEF2C in vitro and in vivo and that, in turn, increased expression of calreticulin affects MEF2C transcriptional activity. The present findings provide a clear molecular explanation for the embryonic lethality observed in calreticulin-deficient mice and emphasize the importance of calreticulin in the early stages of cardiac development. Our study illustrates the existence of a positive feedback mechanism that ensures an adequate supply of releasable Ca2+ is maintained within the cell for activation of calcineurin and, subsequently, for proper functioning of MEF2C.
FcεRI-mediated mast cell degranulation requires calcium-independent microtubule-dependent translocation of granules to the plasma membrane
Authors: Nishida Keigo , Yamasaki Satoru , Ito Yukitaka , Kabu Koki , Hattori Kotaro , Tezuka Tohru , Nishizumi Hirofumi , Kitamura Daisuke , Goitsuka Ryo , Geha Raif S. , Yamamoto Tadashi , Yagi Takeshi , Hirano Toshio
Published: July 2005

The aggregation of high affinity IgE receptors (Fcε receptor I [FcεRI]) on mast cells is potent stimulus for the release of inflammatory and allergic mediators from cytoplasmic granules. However, the molecular mechanism of degranulation has not yet been established. It is still unclear how FcεRI-mediated signal transduction ultimately regulates the reorganization of the cytoskeleton and how these events lead to degranulation. Here, we show that FcεRI stimulation triggers the formation of microtubules in a manner independent of calcium. Drugs affecting microtubule dynamics effectively suppressed the FcεRI-mediated translocation of granules to the plasma membrane and degranulation. Furthermore, the translocation of granules to the plasma membrane occurred in a calcium-independent manner, but the release of mediators and granule–plasma membrane fusion were completely dependent on calcium. Thus, the degranulation process can be dissected into two events: the calcium-independent microtubule-dependent translocation of granules to the plasma membrane and calcium-dependent membrane fusion and exocytosis. Finally, we show that the Fyn/Gab2/RhoA (but not Lyn/SLP-76) signaling pathway plays a critical role in the calcium-independent microtubule-dependent pathway.
Hydrogen peroxide regulation of endothelial exocytosis by inhibition of N-ethylmaleimide sensitive factor
Authors: Matsushita Kenji , Morrell Craig N. , Mason Rebecca J.A. , Yamakuchi Munekazu , Khanday Firdous A. , Irani Kaikobad , Lowenstein Charles J.
Published: July 2005

Although an excess of reactive oxygen species (ROS) can damage the vasculature, low concentrations of ROS mediate intracellular signal transduction pathways. We hypothesized that hydrogen peroxide plays a beneficial role in the vasculature by inhibiting endothelial exocytosis that would otherwise induce vascular inflammation and thrombosis. We now show that endogenous H2O2 inhibits thrombin-induced exocytosis of granules from endothelial cells. H2O2 regulates exocytosis by inhibiting N-ethylmaleimide sensitive factor (NSF), a protein that regulates membrane fusion events necessary for exocytosis. H2O2 decreases the ability of NSF to hydrolyze adenosine triphosphate and to disassemble the soluble NSF attachment protein receptor complex. Mutation of NSF cysteine residue C264T eliminates the sensitivity of NSF to H2O2, suggesting that this cysteine residue is a redox sensor for NSF. Increasing endogenous H2O2 levels in mice decreases exocytosis and platelet rolling on venules in vivo. By inhibiting endothelial cell exocytosis, endogenous H2O2 may protect the vasculature from inflammation and thrombosis.
αvβ3-dependent cross-presentation of matrix metalloproteinase–2 by melanoma cells gives rise to a new tumor antigen
Authors: Godefroy Emmanuelle , Moreau-Aubry Agnes , Diez Elisabeth , Dreno Brigitte , Jotereau Francine , Guilloux Yannick
Published: July 2005

A large array of antigens that are recognized by tumor-specific T cells has been identified and shown to be generated through various processes. We describe a new mechanism underlying T cell recognition of melanoma cells, which involves the generation of a major histocompatibility complex class I–restricted epitope after tumor-mediated uptake and processing of an extracellular protein—a process referred to as cross-presentation—which is believed to be restricted to immune cells. We show that melanoma cells cross-present, in an αvβ3-dependent manner, an antigen derived from secreted matrix metalloproteinase–2 (MMP-2) to human leukocyte antigen A*0201-restricted T cells. Because MMP-2 activity is critical for melanoma progression, the MMP-2 peptide should be cross-presented by most progressing melanomas and represents a unique antigen for vaccine therapy of these tumors.
Selective activation of STAT5 unveils its role in stem cell self-renewal in normal and leukemic hematopoiesis
Authors: Kato Yuko , Iwama Atsushi , Tadokoro Yuko , Shimoda Kazuya , Minoguchi Mayu , Akira Shizuo , Tanaka Minoru , Miyajima Atsushi , Kitamura Toshio , Nakauchi Hiromitsu
Published: July 2005

Although the concept of a leukemic stem cell system has recently been well accepted, its nature and the underlying molecular mechanisms remain obscure. Constitutive activation of signal transducers and activators of transcription 3 (STAT3) and STAT5 is frequently detected in various hematopoietic tumors. To evaluate their role in normal and leukemic stem cells, we took advantage of constitutively active STAT mutants to activate STAT signaling selectively in hematopoietic stem cells (HSCs). Activation of STAT5 in CD34–c-Kit+Sca-1+ lineage marker– (CD34–KSL) HSCs led to a drastic expansion of multipotential progenitors and promoted HSC self-renewal ex vivo. In sharp contrast, STAT3 was demonstrated to be dispensable for the HSC maintenance in vivo, and its activation facilitated lineage commitment of HSCs in vitro. In a mouse model of myeloproliferative disease (MPD), sustained STAT5 activation in CD34–KSL HSCs but not in CD34+KSL multipotential progenitors induced fatal MPD, indicating that the capacity of STAT5 to promote self-renewal of hematopoietic stem cells is crucial to MPD development. Our findings collectively establish a specific role for STAT5 in self-renewal of normal as well as leukemic stem cells.
Restricted MHC–peptide repertoire predisposes to autoimmunity
Authors: Logunova Nadezda N. , Viret Christophe , Pobezinsky Leonid A. , Miller Sara A. , Kazansky Dmitri B. , Sundberg John P. , Chervonsky Alexander V.
Published: July 2005

MHC molecules associated with autoimmunity possess known structural features that limit the repertoire of peptides that they can present. Such limitation gives a selective advantage to TCRs that rely on interaction with the MHC itself, rather than with the peptide residues. At the same time, negative selection is impaired because of the lack of negatively selecting peptide ligands. The combination of these factors may predispose to autoimmunity. We found that mice with an MHC class II–peptide repertoire reduced to a single complex demonstrated various autoimmune reactions. Transgenic mice bearing a TCR (MM14.4) cloned from such a mouse developed severe autoimmune dermatitis. Although MM14.4 originated from a CD4+ T cell, dermatitis was mediated by CD8+ T cells. It was established that MM14.4+ is a highly promiscuous TCR with dual MHC class I/MHC class II restriction. Furthermore, mice with a limited MHC–peptide repertoire selected elevated numbers of TCRs with dual MHC class I/MHC class II restriction, a likely source of autoreactivity. Our findings may help to explain the link between MHC class I responses that are involved in major autoimmune diseases and the well-established genetic linkage of these diseases with MHC class II.
Notch1 modulates timing of G1-S progression by inducing SKP2 transcription and p27Kip1 degradation
Authors: Sarmento Leonor M. , Huang Hui , Limon Ana , Gordon William , Fernandes Jacquenilson , Tavares Maria J. , Miele Lucio , Cardoso Angelo A. , Classon Marie , Carlesso Nadia
Published: July 2005

Cyclin-dependent kinase inhibitors (CKIs) and Notch receptor activation have been shown to influence adult stem cells and progenitors by altering stem cell self-renewal and proliferation. Yet, no interaction between these molecular pathways has been defined. Here we show that ligand-independent and ligand-dependent activation of Notch1 induces transcription of the S phase kinase–associated protein 2 (SKP2), the F-box subunit of the ubiquitin-ligase complex SCFSKP2 that targets proteins for degradation. Up-regulation of SKP2 by Notch signaling enhances proteasome-mediated degradation of the CKIs, p27Kip1 and p21Cip1, and causes premature entry into S phase. Silencing of SKP2 by RNA interference in G1 stabilizes p27Kip1 and p21Cip1 and abolishes Notch effect on G1-S progression. Thus, SKP2 serves to link Notch1 activation with the cell cycle machinery. This novel pathway involving Notch/SKP2/CKIs connects a cell surface receptor with proximate mediators of cell cycle activity, and suggests a mechanism by which a known physiologic mediator of cell fate determination interfaces with cell cycle control.
Habitat selection determines abundance, richness and species composition of beetles in aquatic communities
Authors: Binckley Christopher A , Resetarits William J
Published: July 2005

Distribution and abundance patterns at the community and metacommunity scale can result from two distinct mechanisms. Random dispersal followed by non-random, site-specific mortality (species sorting) is the dominant paradigm in community ecology, while habitat selection provides an alternative, largely unexplored, mechanism with different demographic consequences. Rather than differential mortality, habitat selection involves redistribution of individuals among habitat patches based on perceived rather than realized fitness, with perceptions driven by past selection. In particular, habitat preferences based on species composition can create distinct patterns of positive and negative covariance among species, generating more complex linkages among communities than with random dispersal models. In our experiments, the mere presence of predatory fishes, in the absence of any mortality, reduced abundance and species richness of aquatic beetles by up to 80% in comparison with the results from fishless controls. Beetle species' shared habitat preferences generated distinct patterns of species richness, species composition and total abundance, matching large-scale field patterns previously ascribed to random dispersal and differential mortality. Our results indicate that landscape-level patterns of distribution and species diversity can be driven to a large extent by habitat selection behaviour, a critical, but largely overlooked, mechanism of community and metacommunity assembly.
Ultraviolet reflecting photonic microstructures in the King Penguin beak
Authors: Dresp Birgitta , Jouventin Pierre , Langley Keith
Published: July 2005

King and emperor penguins (Aptenodytes patagonicusandAptenodytes forsteri) are the only species of marine birds so far known to reflect ultraviolet (UV) light from their beaks. Unlike humans, most birds perceive UV light and several species communicate using the near UV spectrum. Indeed, UV reflectance in addition to the colour of songbird feathers has been recognized as an important signal when choosing a mate. The king penguin is endowed with several highly coloured ornaments, notably its beak horn and breast and auricular plumage, but only its beak reflects UV, a property considered to influence its sexual attraction. Because no avian UV-reflecting pigments have yet been identified, the origin of such reflections is probably structural. In an attempt to identify the structures that give rise to UV reflectance, we combined reflectance spectrophotometry and morphological analysis by both light and electron microscopy, after experimental removal of surface layers of the beak horn. Here, we characterize for the first time a multilayer reflector photonic microstructure that produces the UV reflections in the king penguin beak.