bluuebunny/crossref_metadata_2025 huggingface dataset:
Ethylene-styrene copolymerization with constrained geometry catalysts: A density functional study
Authors: Ramos Javier , Muñoz-Escalona Antonio , Martínez Sonia , Martínez-Salazar Javier , Cruz Victor
Published: February 2005

A density functional theory (DFT) study of the ethylene-styrene copolymerization process with titanium-based constrained geometry catalyst (CGC) is presented. To establish the difference between simplified CGC or real CGC models, i.e., considering all ligands of the catalyst, we have performed calculations for ethylene and styrene insertions in both models. Thus, we have used two different DFT functional, BP86 and B3L YP along with two basis set, LANL 2DZ (without polarization functions) and DZVP (including polarization functions). We have noted certain differences between theoretical results published by other authors and our theoretical and experimental data.
Rotational distributions following van der Waals molecule dissociation:  Comparison between experiment and theory for benzene–Ar
Authors: Sampson Rebecca K. , Bellm Susan M. , McCaffery Anthony J. , Lawrance Warren D.
Published: February 2005

The translational energy release distribution for dissociation of benzene–Ar has been measured and, in combination with the 610 rotational contour of the benzene product observed in emission, used to determine the rotational J,K distribution of 00 benzene products formed during dissociation from 61¯. Significant angular momentum is transferred to benzene on dissociation. The 00 rotational distribution peaks at J=31 and is skewed to low K:Javerage=27, ∣K∣average=10.3. The average angle between the total angular momentum vector and the unique rotational axis is determined to be 68°. This indicates that benzene is formed tumbling about in-plane axes rather than in a frisbeelike motion, consistent with Ar “pushing off” benzene from an off-center position above or below the plane. The J distribution is very well reproduced by angular momentum model calculations based on an equivalent rotor approach [A. J. McCaffery, M. A. Osborne, R. J. Marsh, W. D. Lawrance, and E. R. Waclawik, J. Chem. Phys. 121, 1694 (2004)], indicating that angular momentum constraints control the partitioning of energy between translation and rotation. Calculations for p-difluorobenzene–Ar suggest that the equivalent rotor model can provide a reasonable prediction of both J and K distributions in prolate (or near prolate) tops when dissociation leads to excitation about the unique, in-plane axis. Calculations for s-tetrazine–Ar require a small maximum impact parameter to reproduce the comparatively low J values seen for the s-tetrazine product. The three sets of calculations show that the maximum impact parameter is not necessarily equal to the bond length of the equivalent rotor and must be treated as a variable parameter. The success of the equivalent rotor calculations argues that angular momentum constraints control the partitioning between rotation and translation of the products.
A 3000K laboratory emission spectrum of water
Authors: Coheur Pierre-François , Bernath Peter F. , Carleer Michel , Colin Reginald , Polyansky Oleg L. , Zobov Nikolai F. , Shirin Sergei V. , Barber Robert J. , Tennyson Jonathan
Published: February 2005

An emission spectrum of hot water with a temperature of about 3000K is obtained using an oxy-acetylene torch. This spectrum contains a very large number of transitions. The spectrum, along with previous cooler laboratory emission spectra and an absorption spectrum recorded from a sunspot, is analyzed in the 500–2000cm−1 region. Use of a calculated variational linelist for water allows significant progress to be made on assigning transitions involving highly excited vibrational and rotational states. In particular emission from rotationally excited states up to J=42 and vibrational levels with up to eight quanta of bending motion are assigned.
Theoretical mechanistic study on the ion-molecule reaction of SiCN+/SiNC+ with H2O
Authors: Wang Jian , Ding Yi-hong , Sun Chia-chung
Published: February 2005

The gas-phase ion-molecule reactions play very important roles in interstellar and in plasma chemistry. Motivated by recent astrophysical detection of the SiCN/SiNC radicals and laboratory characterization of some SiCN-containing species, we carried out a detailed potential energy survey on the SiCN+/SiNC++H2O reaction at the Becke's three-parameter Lee–Yang–Parr-B3LYP/6-311G(d,p) and coupled cluster with single, double, and triple excitations-CCSD(T)/6-311+G(2df,p) (single-point) levels as an attempt towards understanding the SiCN+/SiNC+ reaction mechanisms. In contrast to the carbene-featured analogous CCN+/CNC++H2X (X=O,S) reactions, the title reaction SiCN+/SiNC++H2O are not associated with any competitive silylene-insertion characters. Moreover, the –CN↔–NC interconversion has a low barrier and plays an important role in determining the final product distributions. This is also in marked difference from the CCN+/CNC+ reaction. It is shown that the isomeric sila-cations SiCN+ and SiNC+ can both react with H2O to barrierlessly generate the major product P1HOSi++HCN and the minor one P3HOSi++HNC, whereas other low-lying products such as P2SiNCO++H2, and P0H2NSi++CO are kinetically unfeasible. The high efficiency of the SiCN+/SiNC+ reaction towards H2O and the potential importance of SiCN+/SiNC+ ion chemistry in interstellar and SiCN-based microelectric and photoelectric processes strongly appeals for future laboratory investigations on the SiCN+/SiNC+ chemical reactivity.
Mechanisms of electron transport through bellows-shaped fullerene tubes
Authors: Tsukamoto Shigeru , Nakayama Tomonobu
Published: February 2005

A bellows-shaped fullerene tube is featured by diameter modulation along the tube, where C60 molecules polymerize with tubular linkages between the molecules. The electronic structures of two types of bellows-shaped fullerene tube are theoretically found to exhibit band gaps indicating semiconducting characteristics. Although the effective masses of the conduction states of the two tubes are similar, these states have different spatial distributions. One of the two tubes is expected to exhibit thermally assisted electron transport.
Method of variation of constants for difference equations and its application to the calculation of atomic integrals
Authors: Zamastil J. , Šimánek M. , Čížek J. , Skála L.
Published: February 2005

In this paper we extend the method for numerically stable calculation of the atomic integrals suggested in our previous paper for the S-states of two-electron atoms to the states with arbitrary total angular momenta. The extension consists in finding numerically stable forms of the solution of difference equations appearing in the calculation of the radial part of the atomic integrals. These equations become for some value of the independent variable homogenous and their solution in that region is described by one of the two linearly independent solutions. Modification of the method of the variation of constants for this special type of linear second order inhomogenous difference equations is suggested and applied.
Photodissociation spectroscopy of trapped protonated tryptophan
Authors: Talbot Francis O. , Tabarin Thibault , Antoine Rodolphe , Broyer Michel , Dugourd Philippe
Published: February 2005

We have coupled a quadrupole ion trap with a frequency doubled optical parametric oscillator laser. The photodissociation spectrum of the protonated tryptophan ion from 215 to 320 nm is reported. The yields of fragmentation on each mass channel as a function of the laser wavelength were obtained. We also report experiments involving multiple stages of laser induced dissociation and discuss possible structures for the fragmentation products.
Electronic spectroscopy of small toluene clusters
Authors: Musgrave Adam , Wright Timothy G.
Published: February 2005

Small clusters of toluenen (n=1–8) were created in a supersonic expansion of toluene with argon as a carrier gas. Mass-selected resonance enhanced multiphoton ionization spectra of these clusters were recorded for each n. For the dimer, the appearance of the spectrum under warm and very cold conditions was studied. We discuss previous results in the light of the present spectra. For n>2, the spectra resemble very closely that of the dimer.
Study of vibrational energy localization and redistribution in hydrogen peroxide H2O2 at low energy
Authors: Joyeux Marc
Published: February 2005

Vibrational energy localization and/or redistribution in hydrogen peroxide H2O2 is studied at about 4000cm−1 above the quantum mechanical ground state using the ab initio potential energy surface of Koput, Carter, and Handy [J. Phys. Chem. A 102, 6325 (1998)]. In this work, the recently derived canonical perturbation procedure for floppy molecules serves two purposes. First, from the quantum mechanical point of view, it is shown that the energies of the lowest 130 states are reproduced with an average error smaller than 1.5cm−1 by a two-dimensional Hamiltonian, which is a function of the torsion and OO-stretch coordinates and momenta, while the other four degrees of freedom contribute only through powers of good quantum numbers. Moreover, the canonical perturbation procedure is also used in classical mechanics calculations, in order to define meaningful local modes, for which the ingoing and outgoing energy flows are monitored. Almost all the individual trajectories launched on the ab initio surface display the same behavior, that is, the superposition of (a) rapid (few hundreds of femtoseconds) and quasiperiodic energy exchanges between the two OH stretches and between the torsion and OO-stretch, and (b) slower (few to several picoseconds) but erratic-looking energy flows between all degrees of freedom. When averaging over large numbers of trajectories with the same local mode energies at time t=0, one observes instead a smooth and irreversible energy flow between all degrees of freedom, which usually thermalize in the range of several tens of picoseconds, that is, on time scales larger than the 5ps period associated with the quantum density of states.
On the thermodynamic stability and structural transition of clathrate hydrates
Authors: Koyama Yuji , Tanaka Hideki , Koga Kenichiro
Published: February 2005

Gas mixtures of methane and ethane form structure II clathrate hydrates despite the fact that each of pure methane and pure ethane gases forms the structure I hydrate. Optimization of the interaction potential parameters for methane and ethane is attempted so as to reproduce the dissociation pressures of each simple hydrate containing either methane or ethane alone. An account for the structural transitions between type I and type II hydrates upon changing the mole fraction of the gas mixture is given on the basis of the van der Waals and Platteeuw theory with these optimized potentials. Cage occupancies of the two kinds of hydrates are also calculated as functions of the mole fraction at the dissociation pressure and at a fixed pressure well above the dissociation pressure.
Energy decompositions according to physical space partitioning schemes
Authors: Alcoba Diego R. , Torre Alicia , Lain Luis , Bochicchio Roberto C.
Published: February 2005

This work describes simple decompositions of the energy of molecular systems according to schemes that partition the three-dimensional space. The components of those decompositions depend on one and two atomic domains thus providing a meaningful chemical information about the nature of different bondings among the atoms which compose the system. Our algorithms can be applied at any level of theory (correlated or uncorrelated wave functions). The results reported here, obtained at the Hartree–Fock level in selected molecules, show a good agreement with the chemical picture of molecules and require a low computational cost in comparison with other previously reported decompositions.
Calculation of Verdet constants with time-dependent density functional theory: Implementation and results for small molecules
Authors: Krykunov Mykhaylo , Banerjee Arup , Ziegler Tom , Autschbach Jochen
Published: February 2005

We report the implementation of a method by which to calculate Verdet constants for molecules. The method is based on gauge-including atomic orbitals (GIAOs) and density functional theory. Calculations based on this method afford magneto-optical rotations of the right magnitude for the molecules H2, N2, CO, HF, CH4, C2H2, H2O, and CS2. The results are in satisfactory agreement with experiment. We investigate the dependency of the results on the gauge origin if GIAOs are not chosen, the convergence of the results with the size of the basis set for AOs and GIAOs, and for H2O and CS2 a comparison of gas-phase and liquid phase values. For the small molecules studied here, large polarized basis sets with diffuse functions are required to obtain well converged results. The use of an asymptotically correct Kohn–Sham potential is advantageous.
The He–LiH potential energy surface revisited. II. Rovibrational energy transfer on a three-dimensional surface
Authors: Taylor Brian K. , Hinde Robert J.
Published: February 2005

We use our rigid rotor He–LiH potential energy surface [B. K. Taylor and R. J. Hinde, J. Phys. Chem. 111, 973 (1999)] as a starting point to develop a three-dimensional potential surface that describes the interaction between He and a rotating and vibrating LiH molecule. We use a fully quantum treatment of the collision dynamics on the current potential surface to compute rovibrational state-to-state cross sections. We compute excitation and relaxation vibrational rate constants as a function of temperature by integrating these cross sections over a Maxwell–Boltzmann translational energy distribution and summing over Boltzmann-weighted initial rotational levels. The rate constants for vibrational excitatation of LiH are very small for temperatures below 300 K. Rate constants for vibrational relaxation of excited LiH molecules, however, are several orders of magnitude larger and show very little temperature dependence, suggesting that the collisions that result in vibrational relaxation are governed by long-range attractive interactions.
Clusters of glycolic acid with three to six water molecules
Authors: Roy Amlan K. , Hu Shaowen , Thakkar Ajit J.
Published: February 2005

Semiempirical, ab initio, and density functional theory calculations are used to locate many low-energy minima on the potential energy surfaces of the CH2OHCOOH–(H2O)n complexes with n=3,4,5,6. In the clusters with three, four, and five water molecules, the lowest-energy structure consists of a (H2O)n complex, not necessarily of lowest energy, hydrogen bonded to the carboxylic group of the glycolic acid. The lowest-energy structure for n=6 is similar except that the water hexamer is hydrogen bonded to both the carboxylic and α-hydroxyl groups of the acid. In all the lowest-energy clusters, the intramolecular hydrogen bond remains intact in the glycolic acid.
Anomalous Kerr effect relaxation in an alternating field
Authors: Déjardin Jean-Louis , Jadzyn Jan
Published: February 2005

Perturbation theory is used to derive the complex harmonic components (stationary regime) arising in Kerr effect relaxation for an assembly of nonelectrically interacting, polar, and polarizable symmetric-top molecules acted on by a strong dc bias electric field superimposed on a weak ac electric field. The approach starts from a fractional kinetic equation written in configuration space and represents an extension of the Smoluchowski equation to fractional dynamics. This equation is solved in the context of a subdiffusive process characterized by an anomalous exponent α ranging from 0 to 1, the Brownian limit. By using a perturbation procedure restricted to the second order in the ac field strength, analytic expressions for the electric birefringence spectra representing the frequency dependence of the first (in ω) and the second (in 2ω) harmonic components are obtained. Various Cole–Cole-like diagrams are presented in order to illustrate the results so obtained and to emphasize the role played by the fractal parameter α in the anomalous diffusion collision process. A comparison of our theoretical model with experimental measurements of the ac Kerr effect response of a dilute polymer solution [poly(3-hexylthiophene)] appears to be quite satisfactory.
Size-selective deposition of particles combining liquid and particulate dielectrophoresis
Authors: King M. R. , Lomakin O. A. , Ahmed R. , Jones T. B.
Published: February 2005

Rapid, size-based, deposition of particles from liquid suspension has been demonstrated using the nonuniform electric field created by coplanar microelectrode strips patterned on an insulating substrate. The scheme uses the dielectrophoretic force both to distribute aqueous liquid containing particles and, simultaneously, to separate the particles. Tests conducted with solutions containing equal volume fractions of 0.53 and 0.93μm polystyrene beads, tagged with different fluorescent dyes, reveal size-based separation within nanoliter droplets formed along the structure after voltage removal. The relative volume ratio of the two sizes varies smoothly from 1:1 to ∼3:1 (favoring the smaller particles) along the electrodes. Using the Clausius–Mossotti factor Ḵ as the only adjustable parameter, the experimental data correlate to a numerical simulation of the process at Re[Ḵ]≈0.5, a value consistent with expectation for polystyrene beads at ∼100kHz in aqueous suspension.
Correlations between low-field microwave absorption and magnetoimpedance in Co-based amorphous ribbons
Authors: Montiel H. , Alvarez G. , Betancourt I. , Zamorano R. , Valenzuela R.
Published: February 2005

Microwave power absorption measurements at 9.4 GHz were carried out on as-cast amorphous ribbons of nominal composition Co66Fe4B12Si13Nb4Cu. Two absorptions were observed: a small signal at a low dc field (<0.01T) and another one at a high dc field (∼0.1682T). The high-field signal shows all the features corresponding to ferromagnetic resonance. The low-field absorption (LFA) signal exhibits different characteristics such as hysteresis and a minimum in power absorption at zero magnetic field. A correlation between this LFA signal and magnetoimpedance measurements showed that both electromagnetic processes are associated with the same phenomenon.
Formation and evolution of epitaxial Co5Ge7 on Ge(001) surface by reactive deposition inside an ultrahigh-vacuum transmission electron microscope
Authors: Sun H. P. , Chen Y. B. , Pan X. Q. , Chi D. Z. , Nath R. , Foo Y. L.
Published: February 2005

Cobalt was deposited on single-crystal Ge(001) surface at ∼350°C by electron-beam evaporation in an ultrahigh-vacuum transmission electron microscope. The deposited Co reacts with Ge to form nanosized islands with the cobalt germanide Co5Ge7 phase. The Co5Ge7 islands show square and rectangular shapes. Two epitaxial orientation relationships between Co5Ge7 and Ge were observed: Co5Ge7 ⟨110⟩(001)‖Ge⟨100⟩(001) and Co5Ge7⟨001⟩(110)‖Ge⟨100⟩(001).
Fabrication and electric-field-dependent transport measurements of mesoscopic graphite devices
Authors: Zhang Yuanbo , Small Joshua P. , Pontius William V. , Kim Philip
Published: February 2005

We have developed a unique micromechanical method to extract extremely thin graphite samples. Graphite crystallites with thicknesses ranging from 10 to 100nm and lateral size ∼2μm are extracted from bulk. Mesoscopic graphite devices are fabricated from these samples for electric field-dependent conductance measurements. Strong conductance modulation as a function of gate voltage is observed in the thinner crystallite devices. The temperature-dependent resistivity measurements show more boundary scattering contribution in the thinner graphite samples.
Resonant tunneling in (110) oriented interband diodes
Authors: Zinck J. J. , Chow D. H. , Holabird K. S. , Schulman J. N. , Hall K. C. , Boggess T. F.
Published: February 2005

Growth of high-quality Sb-based resonant tunneling diodes in the (110) orientation is demonstrated. The room-temperature current–voltage characteristics of the diodes are studied as a function of GaSb well width. Electronic band structure calculations including spin support the conclusion that the position of the GaSb light hole band with respect to the InAs conduction band is responsible for the strength of the negative differential resistance observed. The spin splitting of the heavy hole band is calculated to be larger than the light hole band suggesting that the observation of negative differential resistance may not be necessary or desirable for spin transport in these structures.
Fabrication of nanoscale charge density wave systems
Authors: Inagaki Katsuhiko , Toshima Takeshi , Tanda Satoshi , Yamaya Kazuhiko , Uji Shinya
Published: February 2005

Nanoscale charge density wave systems of quasi-one-dimensional o-TaS3 crystals were fabricated. Gold electrodes 400 nm wide were made by standard lift-off technique on o-TaS3 nanocrystals prepared by deposition on silicon substrates. Interface resistance was higher than 100GΩ just after evaporation, and were significantly reduced by electron-beam irradiation. The electrodes were tested down to 80 mK, and were found quite durable for cryogenic measurement. The temperature dependence of the resistance of the nanocrystal was represented as the variable-range-hopping-type conduction with one dimension over the wide range of temperature, from 4.2 to 100 K. This behavior was different from that of conventional bulk samples.
Blue semiconductor nanocrystal laser
Authors: Chan Yinthai , Steckel Jonathan S. , Snee Preston T. , Caruge J.-Michel , Hodgkiss Justin M. , Nocera Daniel G. , Bawendi Moungi G.
Published: February 2005

We demonstrate tunable room-temperature amplified spontaneous emission and lasing from blue-emitting core-shell CdS∕ZnS nanocrystals (NCs) stabilized in a sol-gel derived silica matrix. Variable stripe length measurements show that these NC-silica composites have a modal gain of ∼100cm−1 at room temperature. Coating microspheres with a NC-silica composite film via a facile process resulted in uniform resonators that exhibit room-temperature lasing over long periods of continuous excitation. This work opens up a spectral window for emission tunable, microscale NC-based lasers.
Intrinsic and extrinsic contributions to the lattice parameter of GaMnAs
Authors: Zhao L. X. , Staddon C. R. , Wang K. Y. , Edmonds K. W. , Campion R. P. , Gallagher B. L. , Foxon C. T.
Published: February 2005

We report on measurements of the crystal structure and hole density in a series of as-grown and annealed GaMnAs samples. The measured hole densities are used to obtain the fraction of incorporated Mn atoms occupying interstitial and substitutional sites. This allows us to make a direct comparison of the measured lattice parameters with recent density-functional theory (DFT) predictions. We find that the decrease in lattice constant observed on annealing is smaller than that predicted due to the out-diffusion of interstitial Mn during annealing. The measured lattice parameters after annealing are still significantly larger than that of GaAs even in samples with very low compensation. This indicates that the intrinsic lattice parameter of GaMnAs is significantly larger than that of GaAs, in contradiction to the DFT prediction.
X-ray diffraction measurements of internal strain in Si nanowires fabricated using a self-limiting oxidation process
Authors: Shimura Takayoshi , Yasutake Kiyoshi , Umeno Masataka , Nagase Masao
Published: February 2005

We demonstrate x-ray diffraction measurements of internal strain in Si nanowires that were fabricated using a self-limiting oxidation process. Rod-shaped scattering around the 111 Bragg point due to interference effects from the Si nanowires were observed, which are robust reflections for incoherent displacement of the wires. From the shifts of the scattering in reciprocal space, the strain was estimated to be 1.0–1.5×10−3 for the sample oxidized at 800°C for 300min.
High-density self-assembled GaN nanoislands on SiC (0001) by molecular-beam epitaxy
Authors: Jeganathan K. , Shimizu M. , Okumura H.
Published: February 2005

We report the fabrication of self-assembled coherent GaN nanoislands on Ga-adsorbed √3×√3R30° 6H–SiC(0001) surfaces via Stranski–Krastanov (SK) growth mode by molecular-beam epitaxy at 760°C. The initial GaN deposition reveals a stable two-dimensional growth (2D) mode under Ga-rich growth conditions (Ga∕N⪢1), as evidenced by the variation of in-plane misfit strain (Δa∕a0). We show that above ∼2.2 monolayer (ML) surface coverage, the 2D layer spontaneously transformed into SK islands by the accommodation of elastic strain in the epitaxial lattice misfit under a vacuum. The SK islands density is found to be ∼4×1011cm−2 and the mean height and diameter is 2±0.5nm and 20±5nm for 3.2 ML surface coverage, respectively.
n
-type carbon nanotube field-effect transistors fabricated by using Ca contact electrodes
Authors: Nosho Yosuke , Ohno Yutaka , Kishimoto Shigeru , Mizutani Takashi
Published: February 2005

We have fabricated n-type carbon nanotube field effect transistors by choosing the contact metal. Single-walled carbon nanotubes were grown directly on a SiO2∕Si substrate by chemical vapor deposition using patterned metal catalysts. Following the nanotube growth, Ca contacts with a small work function were formed by evaporating and lifting off the metal. The devices showed n-type transfer characteristics without any doping into the nanotube channel. In contrast, the devices with Pd contacts showed p-type conduction. These results can be explained by taking into account the work functions of the contact metals.
Effects of progressive catchment harvesting on stream invertebrates in two contrasting regions of New Zealand's North Island
Authors: Collier K. J. , Smith B. J.
Published: February 2005

We examined changes in stream habitat and benthic invertebrate communities in two contrasting regions of New Zealand’s North Island over a 9–10-year period as pine forest harvesting progressed through the catchments. Increases in streambed cover by sand/silt, wood and macrophytes were recorded as harvesting progressed, but little change was observed in qualitative periphyton abundance. Despite similar high-level taxonomic structure of invertebrate communities between the two regions, differences in percentage and log-transformed abundance indicated an effect of landscape context that reflected different hydrologies and bed-substratum stabilities. Within regions, ordination plots indicated broadly distinct site clusters that persisted through time and reflected variations in stream size, substratum composition, periphyton abundance and degree of catchment harvesting. Generally, few of the invertebrate community metrics examined showed clear responses to progressive catchment or onsite harvesting relative to previous intra- and inter-annual variation. The most noticeable exceptions were percentage Ephemeroptera, Plecoptera and Trichoptera (excluding Hydroptilidae) abundance and percentage Elmidae abundance, which were negatively and positively correlated, respectively, with percentage catchment harvested. We identify three broad response categories to catchment harvesting that reflect subsidy–stress effects as logging progressed and discuss the relevance of these findings to potential pine forest harvesting effects in southern Australia.
Investigations into the taxonomy, toxicity and ecology of benthic cyanobacterial accumulations in Myall Lake, Australia
Authors: Dasey Matthew , Ryan Natasha , Wilson Joanne , McGregor Glenn , Fabbro Larelle , Neilan Brett A. , Burns Brendan P. , Kankaanpää Harri , Morrison Louise F. , Codd Geoffrey A. , Rissik Dave , Bowling Lee
Published: February 2005

Large benthic accumulations of cyanobacteria occur in sheltered embayments within Myall Lake, New South Wales, Australia. The lake is shallow, with the entire bottom within the euphotic zone, and it is generally considered pristine, having low nutrient concentrations. The accumulations are highly organic and contain a mix of species mainly from the order Chroococcales, with two forms of Aphanothece being dominant. However polymerase chain reaction (PCR) analysis indicates a close similarity to Microcystis flos-aquae. The cells appear to lack aerotopes and form sticky mucilaginous amalgamations, which may enhance their benthic habit. Although Chroococcales also dominate the planktonic cyanobacterial community, the benthic species are seldom, if ever, found entrained within the water column. Some hepatotoxicity was indicated by mouse bioassay, protein phosphatase inhibition assay, enzyme-linked immuno-sorbent assay (ELISA) for microcystins, PCR and by chromatographic evidence for a microcystin. Ecological aspects of the distribution, gross morphology of the organisms and management implications for recreational water-users are discussed.
Methodological and conceptual issues in the search for a relationship between animal body-size distributions and benthic habitat architecture
Authors: Robson B. J. , Barmuta L. A. , Fairweather P. G.
Published: February 2005

Benthic ecologists have studied the distribution of animal body sizes because it is a form of ‘taxon-free’ classification that may be a useful metric for describing variation within and between ecological communities. In particular, the idea that the allometry of physiological and life-history traits may control species composition and relative abundances implies a functional link between body-size distributions and communities. The physical structure of aquatic habitats has often been cited as the mechanism by which habitat may determine body-size distributions in communities. However, further progress is hindered by a lack of theoretical clarity regarding the mechanisms that connect body size to the characteristics of ecological communities, leading to methods that may obscure interesting trends in body-size data. This review examines the methodological and conceptual issues hindering progress in the search for a relationship between animal body size and habitat architecture and suggests ways to resolve these issues. Problems are identified with current methods for the measurement of animal body size, the data and measures used to quantify body-size distributions and the methods used to identify patterns therein. Fundamentally, renewed emphasis on the mechanisms by which animal body sizes are influenced by habitat architecture is required to refine methodology and synthesise results from pattern-seeking and mechanistic studies.
Habitat use by the hymenosomatid crab Amarinus lacustris (Chilton) in two south-eastern Australian rivers
Authors: Johnston Kerrylyn , Robson Belinda J.
Published: February 2005

The hymenosomatid crab Amarinus lacustris is abundant in some south-eastern Australian rivers; however, little is known of its ecology. Patterns of habitat use by crabs in rivers may be affected by seasonal changes in river discharge. This study investigates population characteristics, timing of reproduction and patterns of habitat use by A. lacustris in five riffle and pool habitats from each of the Hopkins and Merri Rivers in south-west Victoria, Australia, sampled over a twelve-month period. Distribution of Amarinus lacustris was similar between the two rivers, but log-linear modelling showed that there was a strong association between crab sex, habitat occupied and time of year because female A. lacustris showed a shift from riffle to pool habitats during March and April, coinciding with the non-gravid period of the year. Male crabs also showed a change in relative occurrence, occurring most often in riffles during winter–spring (July–November) but being equally common in both habitats in summer–autumn (January–May). These patterns are probably the result of the reproductive cycle of A. lacustris, which appears to show both ontogenetic and sex-related changes in habitat use during its life cycle, taking advantage of seasonal fluctuations in flow regime that may assist egg/larval development and dispersal.
Harshness: characterisation of intermittent stream habitat over space and time
Authors: Fritz Ken M. , Dodds Walter K.
Published: February 2005

Frequently disturbed environments, such as intermittent streams, are ecologically useful for studying how disturbance characteristics (e.g. frequency, magnitude) affect community structure and succession. We developed a harshness index that quantifies ecologically pertinent spatial and temporal characteristics of prairie intermittent streams that may limit or reduce diversity and abundance to predict benthic macroinvertebrate assemblage characteristics. The index incorporates 11 variables that describe the hydrological regime (e.g. average flow, flow variability, drying and flooding) and distance to perennial surface water. We started with 27 variables, but removed 16 that did not increase the predictive value of the index. The relationships among index values and annual mean macroinvertebrate assemblage characteristics (taxonomic richness, diversity, evenness and abundance) were tested over two years using seven sites that represent a range of flow permanence (recent and historical), flood magnitude (recent and historical) and surface-water connectivity. Mean annual taxonomic richness was significantly related to the harshness index. Evenness and abundance were not related to harshness. Further analyses indicated that distance to the nearest permanent habitat was less important than annual or historical hydrological parameters, even though prior research had documented higher rates of colonisation at sites that were closer to nearest permanent habitat. Both annual factors that can alter abundance and colonisation immediately (e.g. floods, drought in each year) and historical factors (e.g. probability of drying, average length of dry period over decades) may influence assemblage characteristics. Historical factors may influence evolutionary adaptations of invertebrates and may predominate when relative disturbance rates are lower such as in years with less flooding.
Analysis of congenital hypomyelinating Egr2
Lo/Lo
nerves identifies Sox2 as an inhibitor of Schwann cell differentiation and myelination
Authors: Le Nam , Nagarajan Rakesh , Wang James Y. T. , Araki Toshiyuki , Schmidt Robert E. , Milbrandt Jeffrey
Published: February 2005

Egr2 is a transcription factor required for peripheral nerve myelination in rodents, and mutations in Egr2 are associated with congenital hypomyelinating neuropathy (CHN) in humans. To further study its role in myelination, we generated mice harboring a hypomorphic Egr2 allele (Egr2
Lo
) that survive for up to 3 weeks postnatally, a period of active myelination in rodents. These Egr2
Lo/Lo
mice provided the opportunity to study the molecular effects of Egr2 deficiency on Schwann cell biology, an analysis that was not possible previously, because of the perinatal lethality of Egr2-null mice. Egr2
Lo/Lo
mice phenocopy CHN, as evidenced by the severe hypomyelination and increased numbers of proliferating Schwann cells of the peripheral nerves. Comparison of sciatic nerve gene expression profiles during development and after crush injury with those of Egr2
Lo/Lo
Schwann cells revealed that they are developmentally arrested, with down-regulation of myelination-related genes and up-regulation of genes associated with immature and promyelinating Schwann cells. One of the abnormally elevated genes in Egr2
Lo/Lo
Schwann cells, Sox2, encodes a transcription factor that is crucial for maintenance of neural stem cell pluripotency. Wild-type Schwann cells infected with Sox2 adenovirus or lentivirus inhibited expression of myelination-associated genes (e.g., myelin protein zero; Mpz), and failed to myelinate axons
in vitro
, but had an enhanced proliferative response to β-neuregulin. The characterization of a mouse model of CHN has provided insight into Schwann cell differentiation and allowed the identification of Sox2 as a negative regulator of myelination.
Proteolysis of SNARE proteins alters facilitation and depression in a specific way
Authors: Young Samuel M.
Published: February 2005

The molecular mechanisms of short-term plasticity observed during synaptic transmission are unknown. To determine whether the soluble
N
-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins play a role in short-term plasticity, Botulinum toxins A, E, and F, were used to disrupt SNARE protein function in cultured hippocampal neurons. Although low concentrations of all of the toxins significantly reduced evoked release, they differentially affected short-term plasticity as assessed by the paired-pulse ratio, regardless of the initial release probability and size of the readily releasable pool of the synapse. The toxin effects on the paired-pulse ratio resulted in different phenotypes dependent on the toxin cleavage site. Together, these data indicate proteolysis of SNARE proteins alters facilitation and depression in a specific way.
Suppressor of cytokine signaling (SOCS)-5 is a potential negative regulator of epidermal growth factor signaling
Authors: Nicholson Sandra E. , Metcalf Donald , Sprigg Naomi S. , Columbus Ruth , Walker Francesca , Silva Anabel , Cary Dale , Willson Tracy A. , Zhang Jian-Guo , Hilton Douglas J. , Alexander Warren S. , Nicola Nicos A.
Published: February 2005

The suppressors of cytokine signaling (SOCS) proteins are a family of SH2 domain-containing intracellular inhibitors of cytokine signal transduction that act by several different mechanisms. Recent evidence suggests that the action of the SOCS proteins may extend beyond the cytokine receptors to signaling initiated by members of the tyrosine kinase receptor family. In this study, the ability of SOCS-5 to negatively regulate signaling cascades downstream of the epidermal growth factor receptor (EGF-R) has been examined by using an EGF-responsive cell line engineered to constitutively express the EGF-R and SOCS-5 or SOCS-5 mutants. SOCS-5 associated with the EGF-R complex in an EGF-independent manner, and the mitogenic response to EGF of all SOCS-5-expressing cell lines was dramatically inhibited when compared with control cell lines. Furthermore, this effect was abrogated after deletion of the SOCS-5 SOCS box. This result suggests that the inhibition of signaling occurs through enhanced proteasomal degradation of the EGF-R through SOCS box recruitment of E3 ubiquitin ligase activity.
Abnormal GABA
A
receptors from the human epileptic hippocampal subiculum microtransplanted to
Xenopus
oocytes
Authors: Palma Eleonora , Spinelli Gabriele , Torchia Gregorio , Martinez-Torres A. , Ragozzino Davide , Miledi Ricardo , Eusebi Fabrizio
Published: February 2005

We studied the properties of GABA
A
receptors microtransplanted from the human temporal lobe epilepsy (TLE)-associated brain regions to
Xenopus
oocytes. Cell membranes, isolated from surgically resected brain specimens of drug-resistant TLE patients, were injected into frog oocytes, which rapidly incorporated human GABA
A
receptors, and any associated proteins, into their surface membrane. The receptors originating from different epileptic brain regions had a similar run-down but an affinity for GABA that was ≈60% lower for the subiculum receptors than for receptors issuing from the hippocampus proper or the temporal lobe neocortex. Moreover, GABA currents recorded in oocytes injected with membranes from the subiculum had a more depolarized reversal potential compared with the hippocampus proper or neocortex of the same patients. Quantitative RT-PCR analysis was performed of the GABA
A
receptor α1- to α5-, β1- to β3-, γ2- to γ3-, and δ-subunit mRNAs. The levels of expression of the α3-, α5-, and β1- to β3- subunit mRNAs are significantly higher, with the exception of γ2-subunit whose expression is lower, in subiculum compared with neocortex specimens. Our results suggest that an abnormal GABA-receptor subunit transcription in the TLE subiculum leads to the expression of GABA
A
receptors with a relatively low affinity. This abnormal behavior of the subiculum GABA
A
receptors may contribute to epileptogenesis.
RNA interference rescue by bacterial artificial chromosome transgenesis in mammalian tissue culture cells
Authors: Kittler Ralf , Pelletier Laurence , Ma Chunling , Poser Ina , Fischer Steffi , Hyman Anthony A. , Buchholz Frank
Published: February 2005

RNA interference (RNAi) is a widely used method for analysis of gene function in tissue culture cells. However, to date there has been no reliable method for testing the specificity of any particular RNAi experiment. The ideal experiment is to rescue the phenotype by expression of the target gene in a form refractory to RNAi. The transgene should be expressed at physiological levels and with its different splice variants. Here, we demonstrate that expression of murine bacterial artificial chromosomes in human cells provides a reliable method to create RNAi-resistant transgenes. This strategy should be applicable to all eukaryotes and should therefore be a standard technology for confirming the specificity of RNAi. We show that this technique can be extended to allow the creation of tagged transgenes, expressed at physiological levels, for the further study of gene function.
Comparative Hepatic Toxicity: Prechronic/Chronic Liver Toxicity in Rodents
Authors: Hardisty Jerry F. , Brix Amy E.
Published: February 2005

The morphologic assessment of the gross and microscopic appearance of the liver can provide a broad base of knowledge concerning the potential toxicity of a drug or chemical. This information may either lead to an understanding of the underlying mechanism of toxicity or guide further study to discern the mode of action of the hepatotoxicity. In standard regulatory bioassays, toxicity studies are conducted during phase 1 and phase 2 of the development process to define the acute, subchronic and chronic toxicity of the test compound. In the liver, there are a limited number of morphologic changes that can be identified using conventional light microscopy. These morphologic alterations are often characterized as “adaptive,” consisting of an exaggerated normal physiologic response; “pharmacologic,” consisting of an expected alteration in response to the desired action of the test article; or “adverse,” consisting of morphologic alterations that are generally undesired, progressive and deleterious to the normal function of the cell(s) involved. Morphologic evidence of adverse effects may involve hepatocytes, the biliary system, hepatic vasculature, Kupffer cells, or stellate cells (Ito cells). In drug discovery and development programs, it is necessary to utilize a multidisciplinary approach, using different endpoints, to investigate the same or similar biological responses in the liver. This results in large amounts of data that must be organized in a retrievable fashion. In order for such a multidisciplinary approach to succeed, each discipline must organize and generate their data in a manner that is easily used by others in the process. The toxicologic pathologist must develop and use standardized nomenclature and diagnostic criteria when examining the liver so that data from various investigators can be compared in a useful manner.
Do Preclinical Testing Strategies Help Predict Human Hepatotoxic Potentials?
Authors: Peters Terry S.
Published: February 2005

Overt hepatotoxicity due to drug administration is a real and present issue in drug development and regulatory circles. Preclinical drug development is intended to identify potential risks and target tissues prior to introduction of new molecular entities into the human population. The standard regimen is testing at various multiples of the intended human therapeutic dose in at least 2 species of animals, one rodent (rats or mice), one non-rodent (dogs, nonhuman primates, minipigs, and rabbits, as examples) for at least two weeks of repeated dosing. Experience has shown that this regimen “works” most of the time. However, preclinical models are not infallible and are not always predictive. Whether the lack of predictivity is due to individual human genetic sensitivities, immunologically mediated phenomena, disease mediation or idiosyncratic reactions, the animal models are limited in detecting these characteristics and other low incidence phenomena. While it is uncommon for drug developers to continue development with products that elicit overt hepatic toxicity early in the animal testing, some products have made it through the approval process and then shown significant adverse effects. Some of the drugs (acetaminophen, isoniazid, trovafloxacin, troglitazone, bromfenac, clarithromycin, telithromycin) that have shown this propensity will be discussed in detail from early preclinical development to marketing and, in some instances, to limitations to usage or removal from the U.S. marketplace.
Variation in the Hepatic Gene Expression in Individual Male Fischer Rats
Authors: Boorman Gary A. , Irwin Richard D. , Vallant Molly K. , Gerken Diane K. , Lobenhofer Edward K. , Hejtmancik Milton R. , Hurban Patrick , Brys April M. , Travlos Greg S. , Parker Joel S. , Portier Christopher J.
Published: February 2005

A new tool beginning to have wider application in toxicology studies is transcript profiling using microarrays. Microarrays provide an opportunity to directly compare transcript populations in the tissues of chemical-exposed and unexposed animals. While several studies have addressed variation between microarray platforms and between different laboratories, much less effort has been directed toward individual animal differences especially among control animals where RNA samples are usually pooled. Estimation of the variation in gene expression in tissues from untreated animals is essential for the recognition and interpretation of subtle changes associated with chemical exposure. In this study hepatic gene expression as well as standard toxicological parameters were evaluated in 24 rats receiving vehicle only in 2 independent experiments. Unsupervised clustering demonstrated some individual variation but supervised clustering suggested that differentially expressed genes were generally random. The level of hepatic gene expression under carefully controlled study conditions is less than 1.5-fold for most genes. The impact of individual animal variability on microarray data can be minimized through experimental design.
New Technologies and Screening Strategies for Hepatotoxicity: Use of In Vitro Models
Authors: Dambach Donna M. , Andrews Barbara A. , Moulin Frederic
Published: February 2005

Hepatotoxicity remains a significant cause for drug failures during clinical trials. This is due, in part, to the idiosyncratic nature of toxicity in humans and inherent physiological differences between humans and preclinical species leading to limited correct prediction of adverse responses in humans. To address this issue, robust screening assays are being developed, which have heightened predictive capacity for human hepatotoxicity, and may be utilized throughout the discovery and development phases in conjunction with traditional in vivo methods, for decision making during drug selection and risk assessment. This manuscript describes an example application of in vitro-based strategies using human hepatocyte cultures in lead optimization screening in conjunction with ADME profiling, for evaluation of compound-associated CYP450 induction potential, and the identification of potentially useful biomarkers as predictors of hepatotoxicity for use in vitro, and in preclinical species and humans.