bluuebunny/crossref_metadata_2025 huggingface dataset:
Analytical spatiotemporal soliton solutions to (3+1)-dimensional cubic-quintic nonlinear Schrödinger equation with distributed coefficients
Authors: Kumar Hitender , Malik Anand , Chand Fakir
Published: October 2012

We obtain exact spatiotemporal periodic traveling wave solutions to the generalized (3+1)-dimensional cubic-quintic nonlinear Schrödinger equation with spatial distributed coefficients. For restrictive parameters, these periodic wave solutions acquire the form of localized spatial solitons. Such solutions exist under certain conditions, and impose constraints on the functions describing dispersion, nonlinearity, and gain (or loss). We then demonstrate the nonlinear tunneling effects and controllable compression technique of three-dimensional bright and dark solitons when they pass unchanged through the potential barriers and wells affected by special choices of the diffraction and/or the nonlinearity parameters. Direct numerical simulation has been performed to show the stable propagation of bright soliton with 5% white noise perturbation.
Tunability of intersubband transition wavelength in the atmospheric window in AlGaN/GaN multi-quantum wells grown on different AlGaN templates by metalorganic chemical vapor deposition
Authors: Tian W. , Yan W. Y. , Hui Xiong , Li S. L. , Ding Y. Y. , Li Y. , Tian Y. , Dai J. N. , Fang Y. Y. , Wu Z. H. , Yu C. H. , Chen C. Q.
Published: October 2012

The properties of intersubband transition in AlGaN/GaN multi-quantum wells (MQWs) grown on different AlGaN templates by metalorganic chemical vapor deposition are investigated. The strain states of GaN wells are studied by Raman spectra and reciprocal space mappings, which shows that the GaN wells are compressively strained and the compressive strain is increased when the Al mole composition is varied from 0 to 0.3. The Fourier transform infrared spectrometer results show that the intersubband transition wavelength in the AlGaN/GaN MQWs can be tuned from 5.14 μm to 4.65 μm when the Al mole composition of the AlGaN template is increased. The results can be attributed to the quantum confined Stark effect.
Numerical simulation of drop deformations and breakup modes caused by direct current electric fields
Authors: Paknemat H. , Pishevar A. R. , Pournaderi P.
Published: October 2012

A drop suspended in another fluid shows different dynamic behaviors in an electric field that depends on its physical properties. The phenomenon of drop deformation under the application of an electric field, in the absence of a net volume charge, is simply caused by the surface stresses. Therefore, an accurate method is required for numerical modeling of the electric driving force at the interface to handle all of the discontinuities involved in the model. For this purpose, in this study the level set method is used along with the ghost fluid method to investigate the responses of three types of drop in the presence of an electric field. Moreover, to demonstrate the accuracy of the method, the breakup modes of each electric model are carefully simulated. Finally, the results of the simulations are compared with similar numerical and experimental results from the literature. The simulation results indicate the accuracy of the method for modeling of the phenomenon over a wide range of electric capillary numbers, and particularly for the capture of the drop profile at the instant of disintegration.
Controllability of femtosecond laser-induced impulse in water evaluated by local force measurement system using atomic force microscopy
Authors: Iino Takanori , Hosokawa Yoichiroh
Published: October 2012

A micro-sized impulse is generated in water by tightly focusing a femtosecond laser through an objective lens. Pulse energy dependence of the impulse was investigated for application as an external force to analyze single biological cells. The impulse proportionally increased between threshold (Eth) and 2 × Eth, and then it was saturated above 2 × Eth. In the proportional region, control precision of the impulse was 2.5 × 10−14 Ns, which was smaller than the uncertainty of the cell-cell adhesion force previously evaluated. This result indicates the impulse can be applied as a promising tool to estimate cell adhesion force.
Magnetization reversal and magnetoresistance behavior of perpendicularly magnetized [Co/Pd]4/Au/[Co/Pd]2 nanowires
Authors: Liu X. M. , Ho P. , Chen J. S. , Adeyeye A. O.
Published: October 2012

We present a systematic investigation of the magnetization reversal mechanism and magnetoresistance behavior of perpendicularly magnetized Co/Pd multilayer films and nanowires (NWs) as a function of Cu buffer layer thickness and temperature. The effect of interlayer coupling is studied by varying the Au spacer layer thickness in between two Co/Pd multilayer stacks in the [Co/Pd]4/Au/[Co/Pd]2 structure. We observed that compared with continuous (un-patterned) films deposited at the same time, the NWs display much stronger temperature dependent interlayer coupling due to magnetostatic interactions through the stray fields. At low temperature, the competition between the interlayer coupling and coercive field difference between the soft and hard Co/Pd multilayer stacks determines the overall magnetization reversal process and magnetoresistance behavior.
Transformation reactions of copper centers in the space-charge region of a copper-diffused silicon crystal measured by deep-level transient spectroscopy
Authors: Nakamura Minoru , Murakami Susumu , Udono Haruhiko
Published: October 2012

The transformation reactions of copper centers by annealing in Schottky electrode-formed (EL-formed) silicon crystals diffused with copper were measured by deep-level transient spectroscopy (DLTS) and the results were compared with those measured in samples without electrode (EL-free). The dissociation speeds of the dominant center (denoted as the CuDLB center) to the dissociation product (denoted as the CuDLA center) in the EL-formed samples were more than two orders faster than those in EL-free samples at respective annealing temperatures, although the dissociation energy of the former center was identical in both samples. An extended copper center, which was never observed in EL-free samples, was formed in the EL-formed samples at the cost of the CuDLA center. The origins of these specialties in the EL-formed samples were attributed to the actions of the electric field on the copper species in the space-charge region of the samples. The easy dissociation of the CuDLA center in the EL-formed samples was explained by the change in the charge state of the center in the space-charge region of the samples. From this analysis, the positively charged copper bonded at the bond center (CuBC+) was proposed as the most probable model for the CuDLA center.
State and species selective energy flow in gas ensembles containing vibrationally excited O2
Authors: McCaffery Anthony J.
Published: October 2012

State-to-state, collision-induced, energy transfer is followed to equilibrium through sequences of collision cycles in gas ensembles containing vibrationally excited oxygen molecules (v = 8 and 1) in several different atomic and molecular bath gases. Quantum state distributions for each of the constituent species are available at each stage of the ensemble's evolution and enable the dominant energy exchange mechanisms to be identified. Equilibration is generally a complex process that evolves through several phases of inter- and intra-molecular events, each with their characteristic response rate to collisions. The results suggest that single quantum state population loss rate constants, however precisely determined, may miss key features of the overall equilibration process.
A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin
Authors: Elenewski Justin E. , Hackett John C
Published: October 2012

High-valent oxo-metal complexes exhibit correlated electronic behavior on dense, low-lying electronic state manifolds, presenting challenging systems for electronic structure methods. Among these species, the iron-oxo (IV) porphyrin denoted Compound I occupies a privileged position, serving a broad spectrum of catalytic roles. The most reactive members of this family bear a thiolate axial ligand, exhibiting high activity toward molecular oxygen activation and substrate oxidation. The default approach to such systems has entailed the use of hybrid density functionals or multi-configurational/multireference methods to treat electronic correlation. An alternative approach is presented based on the GGA+U approximation to density functional theory, in which a generalized gradient approximation (GGA) functional is supplemented with a localization correction to treat on-site correlation as inspired by the Hubbard model. The electronic structure of thiolate-ligated iron-oxo (IV) porphyrin and corresponding Coulomb repulsion U are determined both empirically and self-consistently, yielding spin-distributions, state level splittings, and electronic densities of states consistent with prior hybrid functional calculations. Comparison of this detailed electronic structure with model Hamiltonian calculations suggests that the localized 3d iron moments induce correlation in the surrounding electron gas, strengthening local moment formation. This behavior is analogous to strongly correlated electronic systems such as Mott insulators, in which the GGA+U scheme serves as an effective single-particle representation for the full, correlated many-body problem.
Note: Quasi-real-time analysis of dynamic near field scattering data using a graphics processing unit
Authors: Cerchiari G. , Croccolo F. , Cardinaux F. , Scheffold F.
Published: October 2012

We present an implementation of the analysis of dynamic near field scattering (NFS) data using a graphics processing unit. We introduce an optimized data management scheme thereby limiting the number of operations required. Overall, we reduce the processing time from hours to minutes, for typical experimental conditions. Previously the limiting step in such experiments, the processing time is now comparable to the data acquisition time. Our approach is applicable to various dynamic NFS methods, including shadowgraph, Schlieren and differential dynamic microscopy.
Phase transitions and domain evolution in (Pb, La)(Zr, Sn, Ti)O3 single crystal
Authors: Li Yuanyuan , Li Qiang , Yan Qingfeng , Zhang Yiling , Xi Xiaoqing , Chu Xiangcheng , Cao Wenwu
Published: October 2012

Antiferroelectric (Pb, La)(Zr, Sn, Ti)O3 (PLZST) single crystal has been grown and characterized. From dielectric measurements, x-ray diffraction analysis, and in situ observation of domain structures, we found two first-order phase transitions during heating from room temperature to 250 °C: orthorhombic (O) → rhombohedral (R) → cubic. Coexistence of O and R phases, with the R phase region strongly restricted inside the O phase matrix, has been observed within a broad temperature range above 123 °C. In addition, much denser domain walls appeared in the PLZST crystal when the O-R transition takes place.
Photophoretic trampoline—Interaction of single airborne absorbing droplets with light
Authors: Esseling Michael , Rose Patrick , Alpmann Christina , Denz Cornelia
Published: October 2012

We present the light-induced manipulation of absorbing liquid droplets in air. Ink droplets from a printer cartridge are used to demonstrate that absorbing liquids—just like their solid counterparts—can interact with regions of high light intensity due to the photophoretic force. It is shown that droplets follow a quasi-ballistic trajectory after bouncing off a high intensity light sheet. We estimate the intensities necessary for this rebound of airborne droplets and change the droplet trajectories through a variation of the manipulating light field.
The role of micro-shorts and electrode-film interface in the electrical transport of ultra-thin metallophthalocyanine capacitive devices
Authors: Monton C. , Valmianski I. , Schuller Ivan K.
Published: October 2012

The transport properties of metallophthalocyanine thin films are important ingredients in many technological applications. Ohmic conductance of thin film (15 nm to 90 nm) Co-phthalocyanine (CoPc) capacitive devices has been investigated in the temperature range of 40 K to 300 K. For Pd and V electrodes, the electrode-film (E-F) interface and metallic micro-shorts contribute substantially to the conductance with decrease in CoPc layer thickness. A quantitative model which describes E-F interface, CoPc roughness, micro-shorts, and the exponential temperature and thickness dependence of conductance was developed. Parameters obtained from this model are in good quantitative agreement with independent measurements. The model predicts a 15-20 nm lower limit for capacitive device thickness, below which the conduction is mainly controlled by shorts. In this regime, small changes in mean CoPc thickness result in drastic variation in device conductance.
Temporal and spectral evolution of runaway electron bursts in TEXTOR disruptions
Authors: Forster M. , Finken K. H. , Kudyakov T. , Lehnen M. , Willi O. , Xu Y. , Zeng L. ,   the TEXTOR Team
Published: October 2012

Novel observations of the burst-like runaway electron losses in tokamak disruptions are reported. The runaway bursts are temporally resolved and first-time measurements of the corresponding runaway energy spectra are presented. A characteristic shape and burst to burst changes of the spectra are found. The runaway energy content of the disruptions and the conversion of the predisruptive magnetic energy are estimated. The radial decay of the runaways can be approximated by an exponential distribution. Deriving from the measurements, resistive tearing modes or kink modes are suggested to trigger the formation of the bursts.
Minimum energy structures of faceted, incoherent interfaces
Authors: Kang K. , Wang J. , Zheng S. J. , Beyerlein I. J.
Published: October 2012

In this article, we describe a method for quantifying the dislocation distribution in incoherent faceted fcc/bcc interfaces, including details such as the facet length and crystallography and the location, Burgers vector, and line orientation of each interface dislocation. The method is applied to a variety of relaxed equilibrium interface structures obtained from atomistic simulations. The results show that minimum energy forms of faceted interfaces are achieved when the serrated interface planes of the natural lattice are optimally matched such that when joined and relaxed, extended facet faces can form with minimum density of interface dislocations. With a proposed dislocation-based model for the formation energy, we demonstrate that optimal matching corresponds to minimal self-energies of the interfacial dislocations and extended facets (terrace planes). Most importantly, the formation energy of faceted interfaces is found to have no correlation with the net Burgers vector of the interface, which further emphasizes the importance of characterizing the interfacial dislocation distribution.
Self-excited chaotic dynamics of a nonlinear thermo-visco-elastic system that is subject to laser irradiation
Authors: Hollander E. , Gottlieb O.
Published: October 2012

We derive and investigate a continuum mechanics based low-order dynamical system for a nonlinear thermo-visco-elastic cantilever that is subject to laser irradiation. The model consists of a Fabry–Pérot interferometer where heat transfer between cantilever layers creates a photothermal effect that triggers self-excited oscillations. Model validation is demonstrated by comparison of results to those of a benchmark experiment [K. Hane and K. Suzuki, Sens. Actuators, A 51, 179–182 (1996)] that exhibited periodic oscillations near a subcritical Hopf bifurcation. A numerical analysis reveals a dense chaotic bifurcation structure foliated by multiple periodic solutions. This analysis of a validated continuum based model culminates with a photothermal strange attractor where radiation pressure is negligible.
Inference of oxygen vacancies in hydrothermal Na0.5Bi0.5TiO3
Authors: O'Brien Aoife , Woodward David I. , Sardar Kripasindhu , Walton Richard I. , Thomas Pam A.
Published: October 2012

A high-resolution x-ray powder diffraction study has been made of pseudo-rhombohedral and tetragonal phases in Na0.5Bi0.5TiO3 (NBT), produced via hydrothermal and conventional solid-state methods. Hydrothermal NBT exhibits significantly greater structural distortion at room temperature than solid-state NBT. Peak widths and superstructure peak intensities show a phase transition at ∼305 °C, with trends suggesting that the structure tends towards cubic symmetry at this temperature. Structural refinements indicate that the transition occurs via a phase coexistence region with no clear intermediate phase. Piezoelectric data show evidence of polarisation pinning in hydrothermal NBT, interpreted as a high proportion of oxygen vacancies.
Path derivation for a wave scattered model to estimate height correlation function of rough surfaces
Authors: Zamani M. , Fazeli S. M. , Salami M. , Vasheghani Farahani S. , Jafari G. R.
Published: October 2012

The long standing problem on finding the height correlation function is studied by the inverse scattering problem. We propose a method in the frame work of Kirchhoff theory which we call “path derivation of scattered wave” in order to obtain an expression for direct measurements of the height correlation function. This would provide adequate insight to rough surfaces. The efficiency of this method is due to the fact that the height correlation function could be estimated directly by measurements of the scattered intensity on a suggested path. The model is tested numerically and an experimental setup is suggested.
Direct visualization method of the atomic structure of light and heavy atoms with double-detector Cs-corrected scanning transmission electron microscopy
Authors: Kotaka Yasutoshi
Published: October 2012

The advent of Cs-corrected scanning transmission electron microscopy (STEM) has advanced the observation of atomic structures in materials and nanotechnology devices. High-angle annular dark-field (HAADF)-STEM using an annular detector visualizes heavy elements as bright spots at atomic resolution that can be observed with the Z-contrast technique. In this study, the atomic column of light elements is directly observed as bright spots by middle-angle bright-field (MABF)-STEM imaging. Therefore, a double-detector STEM imaging method was developed, exploiting the advantage of both MABF-STEM and HAADF-STEM to maximum, which consists of multiple exposures of simultaneously observed MABF- and HAADF-STEM images in red-green-blue color.
The reduction of efficiency droop by Al0.82In0.18N/GaN superlattice electron blocking layer in (0001) oriented GaN-based light emitting diodes
Authors: Chung Roy B. , Han Changseok , Pan Chih-Chien , Pfaff Nathan , Speck James S. , DenBaars Steven P. , Nakamura Shuji
Published: October 2012

To investigate the effect of Al0.82In0.18N electron blocking layer (EBL) on the efficiency droop, (0001) oriented InGaN light emitting diodes (LEDs) were grown with two different types of EBLs—single Al0.82In0.18N:Mg layer and Al0.82In0.18N:Mg (2 nm)/GaN:Mg (2 nm) superlattice (SL) structure with 7 periods. It was found that the output power and operating voltage of single Al0.82In0.18N EBL LED were sensitive to EBL thickness due to the difficulty in growing high quality Mg doped Al0.82In0.18N. On the other hand, LED with SL EBL showed no deterioration of optical power and operating voltage while its efficiency droop (17% at 300 A/cm2) reduced by more than a half compared to a conventional Al0.2Ga0.8N (20 nm) EBL LED (36% at 300 A/cm2).
Condensation heat transfer on two-tier superhydrophobic surfaces
Authors: Cheng Jiangtao , Vandadi Aref , Chen Chung-Lung
Published: October 2012

We investigated water vapor condensation on a two-tier superhydrophobic surface in an environmental scanning electron microscope (ESEM) and in a customer-designed vapor chamber. We have observed continuous dropwise condensation (DWC) on the textured surface in ESEM. However, a film layer of condensate was formed on the multiscale texture in the vapor chamber. Due to the filmwise condensation, the condensation heat transfer coefficient of the superhydrophobic surface is lower than that of a flat hydrophobic surface especially under high heat flux situations. Our studies indicate that adaptive and prompt condensate droplet purging is the dominant factor for sustaining long-term DWC.
Surface wettability of titania thin films with increasing Nb content
Authors: Mardare Diana , Yildiz Abdullah , Girtan Mihaela , Manole Alina , Dobromir Marius , Irimia Mihaela , Adomnitei Catalin , Cornei Nicoleta , Luca Dumitru
Published: October 2012

TiO2 and TiO2/Nb amorphous thin films were grown on glass substrates by a sol-gel technique (spin coating). Films' surface composition, structure, and morphology were derived from x-ray photoelectron spectroscopy, x-ray diffraction, and atomic force microscopy data. The investigated films showed a smooth surface (roughness values below 5 nm). A separate surface wettability investigation showed that by increasing the Nb amount in pristine titania films results in a decrease of contact angle (CA) values from 40° to nearly 0°, thus, indicating a super-hydrophilic conversion under UV illumination. This conversion rate is greatly enhanced by increasing the Nb content, the surface super-hydrophilic behavior occurring after a couple of minutes in the TiO2/Nb samples, but after 4 h in the pristine titania specimen. The current results are discussed in terms of the optical band gap shift towards higher energies, by increasing the Nb content in the films, a process explained based on small polaron hopping model.
Localized surface plasmon-enhanced ultraviolet electroluminescence from n-ZnO/i-ZnO/p-GaN heterojunction light-emitting diodes via optimizing the thickness of MgO spacer layer
Authors: Liu W. Z. , Xu H. Y. , Zhang L. X. , Zhang C. , Ma J. G. , Wang J. N. , Liu Y. C.
Published: October 2012

Localized surface plasmon (LSP)-enhanced ultraviolet light-emitting diodes were manufactured by introducing Ag nanoparticles and MgO spacer layer into n-ZnO/i-ZnO/p-GaN heterostructures. By optimizing the MgO thickness, which can suppress the undesired charge transfer and nonradiative Förster resonant energy transfer between Ag and ZnO, a 7-fold electroluminescence enhancement was achieved. Time-resolved and temperature-dependent photoluminescence measurements reveal that both spontaneous emission rate and internal quantum efficiency are increased as a result of coupling between ZnO excitons and Ag LSPs, and simple calculations, based on experimental data, also indicate that most of LSP's energy can be converted into the photon energy.
Thermal behavior of bovine serum albumin after exposure to barrier discharge helium plasma jet
Authors: Jijie R. , Pohoata V. , Topala I.
Published: October 2012

Non-thermal plasma jets at atmospheric pressure are useful tools nowadays in plasma medicine. Various applications are tested such as cauterization, coagulation, wound healing, natural and artificial surfaces decontamination, and sterilization. In order to know more about the effects of gas plasma on biological supramolecules, we exposed protein powders to a barrier discharge helium plasma jet. Then, spectroscopic investigations were carried out in order to obtain information on protein secondary, tertiary, and quaternary structures. We obtained a reduction of the protein alpha-helix content after the plasma exposure and a different behavior, for both thermal denaturation/renaturation kinetics and thermal aggregation process.
A mysterious player on the atmospheric stage
Authors: Miller Johanna L.
Published: October 2012

The unidentified molecule’s reaction with sulfur dioxide has implications for climate and human health.
Fenbendazole as a method for measuring supplement intake in grazing sheep
Authors: Fishpool F. J. , Kahn L. P. , Tucker D. J. , Nolan J. V. , Leng R. A.
Published: October 2012

Currently there is a need for an accurate and non-hazardous method to measure individual intake of a supplement in grazing sheep over a prolonged period. This paper examines the potential of fenbendazole (FBZ) as a marker of intake. The following five experiments aim to determine the relationship between oral ingestion of FBZ and the plasma concentrations of FBZ and its metabolites oxfendazole (OFZ) and FBZ-sulfone (SUL) after single, multiple and daily doses both in housed and grazing sheep and sheep infected with internal parasites. The results from these experiments indicate that OFZ+SUL concentrations in plasma are dependent on FBZ dose rate in housed and grazing animals with differences evident between different dose rates (P < 0.001). Variability of OFZ and SUL concentrations increase in grazing compared with housed animals. Area under the curve of metabolite concentrations was also shown to indicate dose rate regardless of the timing and frequency of dose. Stepwise regressions indicated that sampling every 48 h gave a good representation of area under the curve for different dose rates (R2 = 0.951, P < 0.001). A significant separation of treatment means was achieved when samples were taken every 48 h and pooled during daily dosing with FBZ (P < 0.001). Finally gastrointestinal nematode infection did not affect OFZ and SUL concentrations after daily doses of FBZ. The results from these experiments indicate that FBZ is a useful and accurate marker of supplement intake in grazing animals.
Vascular contributions to early ovarian development: potential roles of VEGFA isoforms
Authors: McFee Renee M. , Cupp Andrea S.
Published: October 2012

Vascularisation is an essential component of ovarian morphogenesis; however, little is known regarding factors regulating the establishment of vasculature in the ovary. Angiogenesis involving extensive endothelial cell migration is a critical component of vessel formation in the embryonic testis but vasculogenic mechanisms appear to play a prominent role in ovarian vascularisation. Vasculature has a strong influence on the formation of ovarian structures, and the early developmental processes of ovigerous cord formation, primordial follicle assembly and follicle activation are all initiated in regions of the ovary that are in close association with the highly vascular medulla. The principal angiogenic factor, vascular endothelial growth factor A (VEGFA), has an important role in both endothelial cell differentiation and vascular pattern development. Expression of VEGFA has been localised to ovigerous cords and follicles in developing ovaries and an increased expression of pro-angiogenic Vegfa isoform mRNA in relation to anti-angiogenic isoform mRNA occurs at the same time-point as the peak of primordial follicle assembly in perinatal rats. Elucidation of specific genes that affect vascular development within the ovary may be critical for determining not only the normal mechanisms of ovarian morphogenesis, but also for understanding certain ovarian reproductive disorders.
An Individual‐Based Model of Ontogenetic Migration in Reef Fish Using a Biased Random Walk
Authors: Saul Steven , Die David , Brooks Elizabeth N. , Burns Karen
Published: October 2012

Migration is an important component of the life history and ontogeny of reef fish. On the west coast of Florida, the interaction between ontogenetically migrating reef fish and fishing effort is an important contributor to the pattern of fishing mortality. A biased random walk model was developed to represent the movement of red grouper Epinephelus morio from the inshore nursery habitat occupied by juveniles to the offshore reef habitat inhabited by adults on the West Florida Shelf. A simulated tagging study was conducted to develop distributions of movement speed. Time at large, release location, and input movement speed from conventional tagging data were used to parameterize the simulation. Maturity at age, determined when fish began moving, and directional movement behavior were modeled as functions of preferential habitat. The results suggest that the general movement of tagged fish can be represented using simple assumptions. Comparison of the tagging study and the tagging simulation showed no statistical differences between these two in terms of movement speed, distance traveled, mean size of fish at release, and mean size of fish at recapture. Furthermore, the age distribution of the fish arriving at the reef in the model matched the observed age distribution in the commercial catch.
Empirical Evidence of Fall Spawning by Atlantic Sturgeon in the James River, Virginia
Authors: Balazik Matthew T. , Garman Greg C. , Van Eenennaam Joel P. , Mohler Jerre , Woods L. Curry
Published: October 2012

Due to overfishing and habitat alteration, the anadromous Atlantic sturgeon Acipenser oxyrinchus oxyrinchus is severely depleted across its historic range. The James and York rivers in Virginia are the two rivers comprising the Chesapeake Bay distinct population segment, where Atlantic sturgeon reproduction has been confirmed. It is widely recognized that Atlantic sturgeon spawn in the spring throughout their range; however, there is debate over whether they also spawn in the fall. To determine if Atlantic sturgeon spawn in the fall, independent of the spring spawn, large‐mesh gill netting in the freshwater portion of the James River (above river kilometer 108) was conducted in the spring (April–June) and fall (August–October) for 3 years (2009–2011), resulting in the capture of 125 adult Atlantic sturgeon (three were recaptures) during the fall sampling, but none were captured during the spring. Field examination for sex and stage of maturity identified 106 mature males and one postspawned female. Sex was not determined for four fish, and due to time constraints, 11 were not examined. Forty mature males were externally tagged with Vemco© ultrasonic passives tags and movements were monitored with a Vemco© VR2W passive receiver array. Collection and tracking data showed that mature Atlantic sturgeon aggregate in the freshwater portion of the James River during the fall season, entering during August and out‐migrating by the end of November. No tagged fish were detected in the freshwater area of the river during the subsequent spring months. Though James River Atlantic sturgeon may spawn in the spring, we suggest there is strong evidence for an independent fall spawn, which should be considered in future management and recovery actions.
Short-Term Retention Rates of Passive Integrated Transponders Surgically Implanted in Burbot and the Effects on Survival
Authors: Gardunio E. I. , Myrick C. A.
Published: October 2012

Passive integrated transponder tags are commonly used in fisheries science to individually identify fish in studies that assume high fish survival and tag retention rates, and have recently been used in studies on burbot Lota lota, although information on retention and survival rates is unavailable. Burbot (310–676-mm TL) surgically implanted with 23-mm PIT tags had 93% survival and 100% retention over 60 d; the survival of these burbot was not significantly different from that of a control group. This suggests that this marking method is a viable means of individually identifying burbot for short-term studies.

Received January 21, 2012; accepted July 4, 2012
Spatial and Temporal Variation of Whirling Disease Risk in Montana Spring Creeks and Rivers
Authors: Neudecker Ryen A. , McMahon Thomas E. , Vincent E. Richard
Published: October 2012

Spring creeks are important spawning and rearing areas for wild trout, but the stable flows, cool temperatures, and high nutrient levels that characterize these unique habitats may also make them highly susceptible to establishment and proliferation of the whirling disease pathogen Myxobolus cerebralis. We evaluated the spatial and temporal dynamics in whirling disease risk by using sentinel rainbow trout Oncorhynchus mykiss fry in nine different spring creeks and their conjoining rivers or reservoirs in Montana over a 20-month period. Whirling disease risk was high in five of the seven pathogen-positive spring creek study sites; at these sites, prevalence levels exceeded 90% and over 50% of sentinel fry had moderate to high infection severity scores. Spring creeks generally had higher disease prevalence and severity than paired river or reservoir sites. Fine sediment levels varied widely among springs creeks with high and low whirling disease risk, and we found no significant association between fine sediment level and infection severity. The low risk measured for some spring creeks was likely attributable to the pathogen invasion being in its early stages rather than to environmental characteristics limiting the severity of infection. High whirling disease risk occurred over a wide range of temperatures at spring creek sites (4.5–13°C) and river sites (1.7–12.5°C). There was an unusual seasonal cycle of infection in spring creeks, with peak infection levels occurring from late fall to early spring and declining to near zero in late spring to early fall. The low infection risk during spring suggests that spring-spawning trout would be at a low risk of infection, even in spring creeks with otherwise high disease severity. In contrast, fry of fall-spawning trout may be much more susceptible to infection in spring creek environments.

Received November 22, 2011; accepted May 7, 2012
Effect of Dietary Supplementation with Achyranthes aspera Seed on Larval Rohu Labeo rohita Challenged with Aeromonas hydrophila
Authors: Chakrabarti R. , Srivastava P. K.
Published: October 2012

Larval rohu Labeo rohita were fed four different diets: three of the diets contained Achyranthes aspera (prickly chaff-flower) seeds at 0.10% (D1), 0.25% (D2), or 0.50% (D3); the fourth diet was a control diet (D4; no A. aspera supplementation). After 70 d, the rohu were injected intraperitoneally with live Aeromonas hydrophila. Mortality of fish was recorded for 7 d. In the D4 group, the first mortality was observed within 12 h of exposure, whereas in the D1–D3 treatment groups, mortality was first observed at 24 h postexposure. In the D4 group, 50% of fish died within 72 h of exposure, whereas in the D3 group, 10–15% mortality occurred between 72 and 84 h. The cumulative mortality rate was 50% for D4, 40% for D1, 35% for D2, and 15% for D3. Total tissue protein level in the larvae was higher for the D2 and D3 groups than for the other groups. Glutamic oxaloacetic transaminase, glutamate pyruvate transaminase, and thiobarbituric acid reactive substance levels were significantly lower in D3 larvae than in the other groups, whereas lysozyme and nitric oxide synthase levels were significantly higher in D3 larvae compared with the other groups. Dietary supplementation with A. aspera seeds at the 0.50% level provided protection against oxidative stress, prevented tissue damage, and enhanced disease resistance in rohu larvae.

Received December 26, 2011; accepted May 7, 2012
Can Copper-Based Substrates Be Used to Protect Hatcheries from Invasion by the New Zealand Mudsnail?
Authors: Hoyer S A , Myrick C A
Published: October 2012

Copper sheet (abbreviated SC), copper mesh (MC), copper-based ablative antifouling paint (AP), and copper-based nonablative antifouling paint (NP) were tested to determine each material's ability to serve as contact deterrents to the invasive New Zealand mudsnail Potamopyrgus antipodarum. Mudsnail responses to each surface treatment was measured across a range of water temperatures (8, 12, 18, and 24°C), hardness levels (75, 125, 175, and 300 mg/L as CaCO3), pH values (6, 7, and 8.5), water velocities (0, 9, and 33 cm/s), and levels of surface fouling (0, 6, and 10 weeks of exposure). Mean crawling distances (MCD) by the mudsnails in the temperature, hardness, and pH experiments were significantly lower on the SC and MC surface treatment than the NP treatment. In the velocity experiment, static, nonflowing conditions produced the lowest MCD, whereas increasing water velocity from 9 cm/s to 33 cm/s did not produce a significant change in MCD on either the SC or MC surfaces. Finally, MCD did increase significantly on the AP surface treatment after exposure to surface fouling; fouling had no significant effect on MCD on the MC or SC surface. Overall, MC and SC were determined to be the most effective surfaces in limiting the locomotor activity of the mudsnail. By lining the inside surface of effluent pipes with either material, hatcheries may be able to eliminate a potential invasion pathway for this organism. Based on the maximum observed crawling distance observed throughout these experiments, we recommend that barriers constructed of MC or SC be a minimum length of 250 cm to provide a satisfactory level of protection against mudsnail invasion. Additional considerations include design and integration with other types of barriers.
Using Golf Balls to Keep Screens Clean in Circular Rearing Tanks
Authors: Irvine James R , Gaetz Harley
Published: October 2012

Screens on bottom-draining circular tanks typically require daily cleaning with a brush. The addition of three golf balls to 9,000-L tanks virtually eliminated the need for cleaning, saving money and potentially reducing the risk of damage to fish during cleaning. Circular moving water kept the golf balls in perpetual motion on top of the screens, crushing entrained feces and waste food, which then exited the tanks. Golf balls typically require replacement after 6 months.
Cell biology: At the center of modern biomedicine
Authors: Budde Priya Prakash , Williams Elizabeth H. , Misteli Tom
Published: October 2012

How does basic cell biology contribute to biomedicine? A new series of Features in JCB provides a cross section of compelling examples of how basic cell biology findings can lead to therapeutics. These articles highlight the fruitful, essential, and increasingly prominent bridge that exists between cell biology and the clinic.
HiCNorm: removing biases in Hi-C data via Poisson regression
Authors: Hu Ming , Deng Ke , Selvaraj Siddarth , Qin Zhaohui , Ren Bing , Liu Jun S.
Published: October 2012

Summary: We propose a parametric model, HiCNorm, to remove systematic biases in the raw Hi-C contact maps, resulting in a simple, fast, yet accurate normalization procedure. Compared with the existing Hi-C normalization method developed by Yaffe and Tanay, HiCNorm has fewer parameters, runs >1000 times faster and achieves higher reproducibility.

Availability: Freely available on the web at: http://www.people.fas.harvard.edu/∼junliu/HiCNorm/.

Contact:  jliu@stat.harvard.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Advanced Complex Trait Analysis
Authors: Gray A. , Stewart I. , Tenesa A.
Published: October 2012

Motivation: The Genome-wide Complex Trait Analysis (GCTA) software package can quantify the contribution of genetic variation to phenotypic variation for complex traits. However, as those datasets of interest continue to increase in size, GCTA becomes increasingly computationally prohibitive. We present an adapted version, Advanced Complex Trait Analysis (ACTA), demonstrating dramatically improved performance.

Results: We restructure the genetic relationship matrix (GRM) estimation phase of the code and introduce the highly optimized parallel Basic Linear Algebra Subprograms (BLAS) library combined with manual parallelization and optimization. We introduce the Linear Algebra PACKage (LAPACK) library into the restricted maximum likelihood (REML) analysis stage. For a test case with 8999 individuals and 279 435 single nucleotide polymorphisms (SNPs), we reduce the total runtime, using a compute node with two multi-core Intel Nehalem CPUs, from ∼17 h to ∼11 min.

Availability and implementation: The source code is fully available under the GNU Public License, along with Linux binaries. For more information see http://www.epcc.ed.ac.uk/software-products/acta.

Contact:  a.gray@ed.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
The ortho : para ratio of H
3
+
in laboratory and astrophysical plasmas
Authors: Crabtree Kyle N. , McCall Benjamin J.
Published: October 2012

In diffuse molecular clouds, the nuclear spin temperature of

(approx. 30 K) is much lower than the cloud kinetic temperature (approx. 70 K). To understand this temperature discrepancy, we have measured the ratio of the hop to exchange pathways (
α
) in the

reaction (which interconverts ortho- and para-

) using high-resolution spectroscopy of the
ν
2
fundamental band of

in a hydrogenic plasma. We find that
α
decreases from 1.6±0.1 at 350 K to its statistical value of 0.5±0.1 at 135 K. We use this result to model the steady-state chemistry of diffuse molecular clouds, finding good agreement with astronomical data provided the dissociative recombination rates of ortho- and para-

are equal and the identity branching fraction for the

reaction is large. Our results highlight the need for further studies of the

reaction as well as state-selective measurements of

dissociative recombination.
Using deuterated H
3
+
and other molecular species to understand the formation of stars and planets
Authors: van der Tak F. F. S.
Published: October 2012

The

ion plays a key role in the chemistry of dense interstellar gas clouds where stars and planets are forming. The low temperatures and high extinctions of such clouds make direct observations of

impossible, but lead to large abundances of H
2
D
+
and D
2
H
+
that are very useful probes of the early stages of star and planet formation. Maps of H
2
D
+
and D
2
H
+
pure rotational line emission towards star-forming regions show that the strong deuteration of

is the result of near-complete molecular depletion of CNO-bearing molecules onto grain surfaces, which quickly disappears as cores warm up after stars have formed. In the warmer parts of interstellar gas clouds,

transfers its proton to other neutrals such as CO and N
2
, leading to a rich ionic chemistry. The abundances of such species are useful tracers of physical conditions such as the radiation field and the electron fraction. Recent observations of HF line emission towards the Orion Bar imply a high electron fraction, and we suggest that observations of OH
+
and H
2
O
+
emission may be used to probe the electron density in the nuclei of external galaxies.
H
2
, H
3
+
and the age of molecular clouds and prestellar cores
Authors: Pagani L. , Lesaffre P. , Roueff E. , Jorfi M. , Honvault P. , González-Lezana T. , Faure A.
Published: October 2012

Measuring the age of molecular clouds and prestellar cores is a difficult task that has not yet been successfully accomplished although the information is of paramount importance to help in understanding and discriminating between different formation scenarios. Most chemical clocks suffer from unknown initial conditions and are therefore difficult to use. We propose a new approach based on a subset of deuterium chemistry that takes place in the gas phase and for which initial conditions are relatively well known. It relies primarily on the conversion of H
3
+
into H
2
D
+
to initiate deuterium enrichment of the molecular gas. This conversion is controlled by the ortho/para ratio of H
2
that is thought to be produced with the statistical ratio of 3 and subsequently slowly decays to an almost pure para-H
2
phase. This slow decay takes approximately 1 Myr and allows us to set an upper limit on the age of molecular clouds. The deuterium enrichment of the core takes longer to reach equilibrium and allows us to estimate the time necessary to form a dense prestellar core, i.e. the last step before the collapse of the core into a protostar. We find that the observed abundance and distribution of DCO
+
and N
2
D
+
argue against quasi-static core formation and favour dynamical formation on time scales of less than 1 Myr. Another consequence is that ortho-H
2
remains comparable to para-H
2
in abundance outside the dense cores.
Belnapia soli sp. nov., a proteobacterium isolated from grass soil
Authors: Jin Long , Lee Hyung-Gwan , No Kui-Jung , Ko So-Ra , Kim Hee-Sik , Ahn Chi-Yong , Oh Hee-Mock
Published: October 2012

A Gram-negative, aerobic, non-motile, non-spore-forming, cocci-shaped, red-pigmented bacterium, designated strain PB-K8T, was isolated from grass soil sampled in Daejeon, Republic of Korea. Comparative 16S rRNA gene sequence studies showed that the isolate was clearly affiliated with the class

Alphaproteobacteria

, and was most closely related to

Belnapia moabensis

DSM 16746T and

Belnapia rosea

DSM 23312T, showing a 16S rRNA gene sequence similarity to the type strains of each species of 98.4 and 97.2 %, respectively. The cells of strain PB-K8T formed red colonies on R2A agar, contained Q-9 as the predominant ubiquinone and included summed feature 3 (C16 : 1ω7c C16 : 1ω6c), C16 : 0, summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C18 : 1 2-OH and C19 : 0 cyclo ω8c as the major fatty acids. The G+C content of the genomic DNA of strain PB-K8T was 72.1 mol%. Thus, the combined genotypic and phenotypic data supported the conclusion that strain PB-K8T represents a novel species of the genus

Belnapia

, for which the name Belnapia soli sp. nov. is proposed. The type strain is PB-K8T ( = KCTC 23765T = JCM 18033T).
Sphingobium fontiphilum sp. nov., isolated from a freshwater spring
Authors: Sheu Shih-Yi , Shiau Yu-Wen , Wei Yan-Ting , Chen Wen-Ming
Published: October 2012

To investigate the biodiversity of bacteria in the spring water of the Chengcing Lake Park in Taiwan, a Gram-stain-negative, rod-shaped, non-motile, non-spore-forming and aerobic bacterial strain, designated strain Chen16-4T, was isolated and characterized in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain Chen16-4T were

Sphingobium amiense

YTT,

Sphingobium yanoikuyae

GIFU 9882T and

Sphingobium scionense

WP01T, with sequence similarities of 97.6, 97.1 and 97.0 %, respectively. A phylogenetic tree obtained with 16S rRNA gene sequences indicated that strain Chen16-4T and these three closest relatives formed an independent phylogenetic clade within the genus

Sphingobium

. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of C18 : 1ω7c in the cellular fatty acid profile and the DNA G+C content also supported affiliation of the isolate to the genus

Sphingobium

. The DNA–DNA relatedness of strain Chen16-4T with respect to recognized species of the genus

Sphingobium

was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Chen16-4T represents a novel species in the genus

Sphingobium

, for which the name Sphingobium fontiphilum sp. nov. is proposed. The type strain is Chen16-4T ( = BCRC 80308T = LMG 26342T = KCTC 23559T).