bluuebunny/crossref_metadata_2025 huggingface dataset:
Vortex formation in a cavity with oscillating walls
Authors: Ovando G. , Juárez H. , Huelsz G. , Ramos E.
Published: February 2009

The vortex formation in a two-dimensional Cartesian cavity, which their vertical walls move simultaneously with an oscillatory velocity and the horizontal walls are fixed pistons, is studied numerically. The governing equations were solved with a finite element method combined with an operator splitting scheme. We analyzed the behavior of vortical structures occurring inside a cavity with an aspect ratio of height-to-width of 1.5 for three different displacement amplitudes of the vertical oscillatory walls (amplitude/width=Y=0.2, 0.4, and 0.8) and Reynolds numbers based on the cavity width of 50, 500, and 1000. Two vortex formation mechanisms are identified: (a) the shear, oscillatory motion of the moving boundaries coupled with the fixed walls that provide a translational symmetry-breaking effect and (b) the sharp changes in the flow motion when the flow meets the corners of the cavity. The vortex cores were identified using the Jeong–Hussain criterion and it is found that the area occupied by the cores decreases as the Reynolds number increases and increases as Y increases. All flows studied are cyclic symmetric and for low Y and Re values they are also symmetric with respect to the vertical axis dividing the cavity in two sides. In asymmetric flows, the unbalance between the vortices on each side of the midvertical line generates a vortex that occupies the central part of the cavity. The breakdown of the axial symmetry was studied for a fixed value of the oscillation amplitude, Y=0.8, taking Re as the bifurcation parameter. The results indicate that the symmetry is broken through a supercritical pitchfork bifurcation.
Phenomenological analysis for spin-Seebeck effect in metallic magnets
Authors: Uchida K. , Takahashi S. , Ieda J. , Harii K. , Ikeda K. , Koshibae W. , Maekawa S. , Saitoh E.
Published: February 2009

The two-band spin diffusion model has been extended to nonequilibrium systems to investigate the recently discovered spin-Seebeck effect in a ferromagnetic metal. A calculation using this model well reproduces the experimental results for a Ni81Fe19 film; the gradient of electrochemical potential is different between up- and down-spin bands affected by a temperature difference between the ends of the film.
Mechanism of room temperature ferromagnetism in ZnO doped with Al
Authors: Ma Y. W. , Ding J. , Yi J. B. , Zhang H. T. , Ng C. M.
Published: February 2009

ZnO recently receives extensive interest owing to its potential applications in the dilute magnetic semiconductor. In this work, Al was deposited onto the surface of ZnO film followed by high vacuum annealing. The film showed the room temperature ferromagnetism (RTF). The saturation magnetization (Ms) highly depends on both the thickness of the Al top layer and the thickness of the ZnO film. The RTF disappeared when the film was further annealed in air atmosphere. The detailed structure characterizations (x-ray diffraction and x-ray photoelectron spectroscopy) revealed that the RTF was associated with a charge transfer between Al and Zn.
The anisotropic magnetoresistance in epitaxial thin films and polycrystalline samples of La0.65Ca0.35MnO3
Authors: Egilmez M. , Ma Rongchao , Chow K. H. , Jung J.
Published: February 2009

We report measurements of the anisotropic magnetoresistance (AMR) of epitaxial thin film and polycrystalline samples of La0.65Ca0.35MnO3. Near the metal-insulator transition (MIT) temperature the AMR of both polycrystalline and thin film samples exhibit a peak. However at temperatures well below the MIT, the AMR of the polycrystalline samples is much larger than that of the epitaxial films, suggesting that the anisotropy of the spin-polarized tunneling of the charge carriers across grain boundaries in a magnetic field is responsible for the observed low temperature behavior.
Granular L10 FePt–X (X=C, TiO2, Ta2O5) (001) nanocomposite films with small grain size for high density magnetic recording
Authors: Chen J. S. , Lim B. C. , Ding Y. F. , Hu J. F. , Chow G. M. , Ju G.
Published: February 2009

Fe Pt – X (X=C, TiO2, Ta2O5) nanocomposite films were deposited on MgO∕CrRu∕glass substrates at 350°C by magnetron cosputtering. The comparison investigations on the magnetic properties and microstructure of FePt–X films with various dopants were conducted. All FePt–X films showed (001) preferred orientation and oxide dopants promoted the formation of magnetically soft fcc FePt phase. With 15vol% C doping, FePt–C film with columnar grains of 7.5nm was obtained and the out-of-plane coercivity measured at room temperature was as high as 14.4kOe. The increase in carbon volume fraction to 20% caused the formation of two-layer structure, whereas for the 20vol% TiO2 and Ta2O5 doping, the columnar structure of the FePt films remained and the corresponding grain sizes were 5 and 10nm, respectively. Ta2O5 doping showed better grain isolation than the others. The out-of-plane coercivities of FePt–TiO2 and FePt–Ta2O5 films were 7.5 and 8.8kOe, respectively.
Magnetic phase transitions in CePtSn under ambient and hydrostatic pressures
Authors: Prokleška Jan , Míšek Martin , Sechovský Vladimír , Javorský Pavel
Published: February 2009

CePtSn belongs to the group of orthorhombic CeTX compounds. Similar to some other CeTX companions, it exhibits a pronounced anisotropy of electronic and elastic properties with respect to the direction of an applied magnetic field. We report on our study of the temperature and magnetic field evolution of the thermal expansion and magnetostriction, acquiring all the major components of the corresponding tensors. Also, the evolution of the electrical resistivity across the H-T-p space was investigated in order to confirm and extend the information on physics of the studied material. We have observed a significant dependence of elastic properties on the magnetic history for the magnetic field applied along the b-axis, which is reflecting a nontrivial evolution of magnetic ordering. Consequently, these results are discussed within the framework of the appearance of magnetism in the Ce(Pt,Ni)Sn system and the relationship between the elastic properties and the results of the investigation of pressure induced effects.
ZnO:Co diluted magnetic semiconducting single crystalline films by hydrothermal epitaxy
Authors: Zhang Y. B. , Li S. , Goh G. K. L.
Published: February 2009

Epitaxial ZnO:Co films with room-temperature ferromagnetism have been hydrothermally grown in water at 90°C using a ZnO seed layer on MgAl2O4 (111) substrates. The ZnO:Co films are single crystalline with out-of-plane orientations of ZnO:Co⟨001⟩∥MgAl2O4⟨111⟩ and in-plane orientations of ZnO:Co[110]∥MgAl2O4[1¯1¯2] and ZnO:Co[1¯10]∥MgAl2O4[1¯10] in spite of numerous threading dislocations at the boundaries of crystal mosaic. Saturation magnetizations of 0.83, 0.77, and 0.08emu∕cm3 and coercivities of 40, 22, and 22Oe were obtained for the epitaxial Zn1−xCoxO (x=0.02, 0.05, and 0.10) films, respectively, at room temperature. Hydrogen unintentionally incorporated in the hydrothermal synthesis may contribute to the ferromagnetic properties in ZnO:Co by enhancing carrier concentration as a shallow donor.
Dielectric window breakdown in oxygen gas: Global model and particle-in-cell approach
Authors: Nam Sang Ki , Lim Chul-hyun , Verboncoeur John P.
Published: February 2009

Dielectric window breakdown is a major issue in the transmission of high power microwave (HPM) radiation. Breakdown at the dielectric window decreases the power transmitted to a target, and if the electron density increases significantly, it can reflect a large fraction of HPM radiation to the source. Dielectric window breakdown from vacuum multipactor to collisional microwave discharge was previously investigated using the particle-in-cell Monte Carlo collision (PIC-MCC) model for noble gases. A global model (GM) with pressure-independent enhanced electron energy distribution function (EEDF) was also developed to study the breakdown in noble gases. In this work, the previous PIC-MCC model and GM are extended to include oxygen cross sections, and used to study microwave breakdown in oxygen. The GM with pressure-independent enhanced EEDF enables more efficient study of parameter space due to its simplicity and speed. The PIC-MCC model and GM indicate that the breakdown time for oxygen is less than that for argon below 500Torr. Above 500Torr, the high collision frequency reduces the effective electron temperature, and the depleted tail leads to faster reduction of ionization than dissociative attachment, and hence longer breakdown times.
Dependence of the liquid-vapor surface tension on the range of interaction: A test of the law of corresponding states
Authors: Grosfils Patrick , Lutsko James F.
Published: February 2009

The validity of the principle of corresponding states is investigated for the case of a potential with more than one intrinsic length scale. The planar surface tension of coexisting liquid and vapor phases of a fluid of Lennard–Jones atoms is studied as a function of the range of the potential using both Monte Carlo simulations and density functional theory (DFT). The interaction range is varied from rc*=2.5 to rc*=6 and the surface tension is determined for temperatures ranging from T*=0.7 up to the critical temperature in each case. The simulation results are consistent with previous studies and are shown to obey the law of corresponding states even though the potential has two intrinsic length scales. It is further shown that the corresponding states principle can also be used to enhance the accuracy of some, but not all, DFT calculations of the surface tension. The results show that most of the cutoff dependence of the surface tension can be explained as a result of changes in the cutoff-dependent phase diagram and that corresponding states can be a useful tool for explaining differences between theory and simulation.
Comment on “Entropy of polydisperse chains: Solution on the Bethe lattice” [J. Chem. Phys. 128, 184904 (2008)]
Authors: Gujrati P. D.
Published: February 2009

The results presented in the above-mentioned recent paper by Neto and Stilck [J. Chem. Phys.128, 184904 (2008)] represent special cases of a more general investigation by Gujrati on recursive lattices and have already appeared either in this journal or elsewhere. Even the methodology adopted by these authors is almost identical to that of Gujrati. We show that their Eq. (27) remains valid even when interactions are present.
Characteristics of polycrystalline silicon Schottky barrier thin film transistors fabricated using metallic junction source/drain with erbium silicide and platinum silicide
Authors: Shin Jin-Wook , Cho Won-Ju , Choi Chel-Jong , Jang Moongyu
Published: February 2009

Polycrystalline silicon (poly-Si) Schottky barrier thin film transistors (SB-TFTs) were fabricated using platinum and erbium silicided source/drain for p- and n-channel SB-TFTs, respectively. High quality poly-Si films were obtained by crystallizing the amorphous Si films with the excimer laser annealing method. Poly-Si SB-TFTs with metallic source/drain junctions showed a large on/off current ratio and a low leakage current. Significant improvements in electrical characteristics were obtained by additional forming gas annealing in 2% H2/N2 gas ambient due to the termination of dangling bonds at the grain boundaries of the poly-Si film as well as the reduction in interface trap states at gate oxide/poly-Si channel.
Optical pumping as artificial doping in quantum dots-in-a-well infrared photodetectors
Authors: Höglund L. , Holtz P. O. , Pettersson H. , Asplund C. , Wang Q. , Malm H. , Almqvist S. , Petrini E. , Andersson J. Y.
Published: February 2009

Resonant optical pumping across the band gap was used as artificial doping in InAs/In0.15Ga0.85As/GaAs quantum dots-in-a-well infrared photodetectors. A selective increase in the electron population in the different quantum dot energy levels enabled the low temperature photocurrent peaks observed at 120 and 148 meV to be identified as intersubband transitions emanating from the quantum dot ground state and the quantum dot excited state, respectively. The response was increased by a factor of 10 through efficient filling of the quantum dot energy levels by simultaneous optical pumping into the ground states and the excited states of the quantum dots.
Molecular dynamics investigation of interfacial mixing behavior in transition metals (Fe, Co, Ni)-Al multilayer system
Authors: Lee Soon-Gun , Chung Yong-Chae
Published: February 2009

The interface and surface structure of transition metal (TM) (Fe, Co, and Ni) thin film deposited on Al(001) substrate at atomic level were investigated by molecular dynamics simulation. In spite of the low adatom incident energy of 0.1 eV, TM-Al intermixing occurred actively at the surface of Al(001) at room temperature. At the interface region of TM/Al(001), an intermetallic compound was formed and found to be of B2 structure. The Co/Al system showed different layer coverage and pair correlation function characteristics, in comparison with Fe/Al and Ni/Al systems. The different structural and intermixing characteristics at the interface were successfully explained in terms of lattice matching, cohesive energy, and local acceleration effect.
Oxygen induced strain field homogenization in AlN nucleation layers and its impact on GaN grown by metal organic vapor phase epitaxy on sapphire: An x-ray diffraction study
Authors: Bläsing J. , Krost A. , Hertkorn J. , Scholz F. , Kirste L. , Chuvilin A. , Kaiser U.
Published: February 2009

This paper presents an x-ray study of GaN, which is grown on nominally undoped and oxygen-doped AlN nucleation layers on sapphire substrates by metal organic vapor phase epitaxy. Without additional oxygen doping a trimodal nucleation distribution of AlN is observed leading to inhomogeneous in-plane strain fields, whereas in oxygen-doped layers a homogeneous distribution of nucleation centers is observed. In both types of nucleation layers extremely sharp correlation peaks occur in transverse ω-scans which are attributed to a high density of edge-type dislocations having an in-plane Burgers vector. The correlation peaks are still visible in the (0002) ω-scans of 500 nm GaN which might mislead an observer to conclude incorrectly that there exists an extremely high structural quality. For the undoped nucleation layers depth-sensitive measurements in grazing incidence geometry reveal a strong thickness dependence of the lattice parameter a, whereas no such dependence is observed for doped samples. For oxygen-doped nucleation layers, in cross-sectional transmission electron microscopy images a high density of stacking faults parallel to the substrate surface is found in contrast to undoped nucleation layers where a high density of threading dislocations is visible. GaN of 2.5 μm grown on top of 25 nm AlN nucleation layers with an additional in situ SiN mask show full widths at half maximum of 160″ and 190″ in (0002) and (10–10) high-resolution x-ray diffraction ω-scans, respectively.
A thermal emitter with selective wavelength: Based on the coupling between photonic crystals and surface plasmon polaritons
Authors: Fu Han-Kuei , Jiang Yu-Wei , Tsai Ming-Wei , Lee Si-Chen , Chen Yang-Fang
Published: February 2009

A thermal emitter with selective wavelength has been demonstrated in which the dielectric layers formed one-dimensional photonic crystals are sandwiched between two Ag films. The top Ag film is perforated periodically with hexagonal hole array. The selected thermal radiation of the photonic crystals resonates between two metal films and surface plasmon polaritons are generated on the top Ag and converted to light radiation. It is found that when leakage modes adjacent to the optic band gap of photonic crystals meet the resonant modes of surface plasmom polaritons, an enhanced thermal emission with maximum intensity can be obtained. The hybrid photonic and plasmonic thermal emitters are selective, which should be very useful for the creation of high power infrared light sources.
Characteristics of In(Ga)As quantum ring infrared photodetectors
Authors: Ling H. S. , Wang S. Y. , Lee C. P. , Lo M. C.
Published: February 2009

Characteristics of In(Ga)As quantum ring infrared photodetectors (QRIPs) were investigated under normal incidence configuration. Compared with quantum dot infrared photodetectors (QDIPs), QRIPs showed wider photocurrent spectra, more stable responsivity with temperature change, and lower dark current activation energy. The wide detection band comes from the transitions from the quantum ring (QR) ground states to different excited states. The shallow confinement states generate higher dark current and enhance the carrier flow between the QRs within the same QR layer. This carrier flow averages out the repulsive potential and makes QRIPs behave similarly to the quantum well infrared photodetectors instead of QDIPs. With an Al0.27Ga0.73As current blocking layer, the performance of QRIPs was greatly enhanced.
Studies on the transport of high intensity laser-generated hot electrons in cone coupled wire targets
Authors: King J. A. , Akli K. U. , Freeman R. R. , Green J. , Hatchett S. P. , Hey D. , Jamangi P. , Key M. H. , Koch J. , Lancaster K. L. , Ma T. , MacKinnon A. J. , MacPhee A. , Norreys P. A. , Patel P. K. , Phillips T. , Stephens R. B. , Theobald W. , Town R. P. J. , Van Woerkom L. , Zhang B. , Beg F. N.
Published: February 2009

Experimental results showing hot electron penetration into Cu wires using Kα fluorescence imaging are presented. A 500 J, 1 ps laser was focused at f/3 into hollow aluminum cones joined at their tip to Cu wires of diameters from 10 to 40 μm. Comparison of the axially diminishing absolute intensity of Cu Kα with modeling shows that the penetration of the electrons is consistent with one dimensional Ohmic potential limited transport. The laser coupling efficiency to electron energy within the wire is shown to be proportional to the cross sectional area of the wire, reaching 15% for 40 μm wires. Further, we find the hot electron temperature within the wire to be about 750 keV. The relevance of these data to cone coupled fast ignition is discussed.
Photoacoustic guidance of high intensity focused ultrasound with selective optical contrasts and time-reversal
Authors: Funke Arik R. , Aubry Jean-François , Fink Mathias , Boccara Albert-Claude , Bossy Emmanuel
Published: February 2009

The authors present a method of focusing high intensity ultrasound by time-reversing the photoacoustic response of an optically selective target in a nonselective background. The target’s photoacoustic response was isolated from the background by subtracting the photoacoustic waveforms obtained at different optical wavelengths and convolved with a continuous signal. It was found that the focus produced was comparable in quality to that obtained by delay-law beam-forming. The method holds the promise of allowing precise targeting of high intensity focused ultrasound on nonechogenic targets, in moving environments, independently of the presence of aberrating layers.
Phonon anomalies in Pb1−xLax(Zr0.9Ti0.1)O3 ceramics
Authors: Buixaderas E. , Gregora I. , Kamba S. , Kužel P. , Reaney I.
Published: February 2009

The lattice dynamics of Pb1−xLax(Zr0.9Ti0.1)O3 (PLZT X/90/10) with X=0, 2, 4, 10% of La was studied by means of Far Infrared, Raman and terahertz spectroscopies in the temperature range of 20–800 K. Infrared active soft phonons with anomalies near the paraelectric-ferroelectric phase transition were found for all the samples. Some Raman active phonons show anomalies ∼200 K below TC, due to another phase transition to a ferroelectric state with doubled unit cell. Samples with higher La content (X=4,10) display nonclassical phonon softening described by ω2=a(T−TC)γ with γ=2/3.
Room-temperature-operating carbon nanotube single-hole transistors with significantly small gate and tunnel capacitances
Authors: Ohno Yasuhide , Asai Yoshihiro , Maehashi Kenzo , Inoue Koichi , Matsumoto Kazuhiko
Published: February 2009

Carbon nanotube single-hole transistors operating at room temperature were realized. To obtain large charging energy, a 25-nm-long carbon nanotube channel was formed by shadow evaporation for small gate capacitance and an insulator was inserted between the channel and electrodes for small tunnel capacitances. A significantly small gate capacitance (0.06 aF) and a small tunnel capacitance (0.3 aF) were obtained. The estimated charging energy of a carbon nanotube single quantum dot was 108 meV. Drain current oscillation as a function of gate voltage was clearly observed while typical p-type field effect transistor characteristics were obtained for the device without insulator. These results indicate that the small tunnel capacitance is necessary for the room-temperature-operating carbon nanotube single-charge transistors.
Tapered Sommerfeld wire terahertz near-field imaging
Authors: Awad M. , Nagel M. , Kurz H.
Published: February 2009

We explore the potential of tapered Sommerfeld wire waveguides for terahertz near-field imaging. The electric field confinement in the vicinity of the tapered wire tip is exploited to achieve subwavelength resolution. After coupling onto the Sommerfeld wire, terahertz pulses propagate as surface-plasmon waves along the waveguide and subsequently reflect at the imaging target surface. The reflected signal is then detected at the waveguide surface using a freestanding photoconductive terahertz probe. The resolution achieved is on the order of the tip diameter. This subwavelength resolution is demonstrated in a proof-of-principle experiment.
Surface leakage reduction in narrow band gap type-II antimonide-based superlattice photodiodes
Authors: Huang Edward Kwei-wei , Hoffman Darin , Nguyen Binh-Minh , Delaunay Pierre-Yves , Razeghi Manijeh
Published: February 2009

Inductively coupled plasma (ICP) dry etching rendered structural and electrical enhancements on type-II antimonide-based superlattices compared to those delineated by electron cyclotron resonance (ECR) with a regenerative chemical wet etch. The surface resistivity of 4×105 Ω cm is evidence of the surface quality achieved with ICP etching and polyimide passivation. By only modifying the etching technique in the fabrication steps, the ICP-etched devices with a 9.3 μm cutoff wavelength revealed a diffusion-limited dark current density of 4.1×10−6 A/cm2 and a maximum differential resistance at zero bias in excess of 5300 Ω cm2 at 77 K, which are an order of magnitude better in comparison to the ECR-etched devices.
In situ small-angle x-ray scattering study of nanostructure evolution during decomposition of arc evaporated TiAlN coatings
Authors: Odén M. , Rogström L. , Knutsson A. , Terner M. R. , Hedström P. , Almer J. , Ilavsky J.
Published: February 2009

Small-angle x-ray scattering was used to study in situ decomposition of an arc evaporated TiAlN coating into cubic-TiN and cubic-AlN particles at elevated temperature. At the early stages of decomposition particles with ellipsoidal shape form, which grow and change shape to spherical particles at higher temperatures. The spherical particles grow at a rate of 0.18 Å/°C while coalescing.
Simultaneous generation and detection of ultrashort voltage pulses in low-temperature grown GaAs with below-bandgap laser pulses
Authors: Bieler Mark , Pierz Klaus , Siegner Uwe
Published: February 2009

We present a method that allows for the simultaneous generation and detection of ultrashort voltage pulses, which propagate on a planar transmission line, in the same material with laser pulses of the same wavelength. The generation is accomplished by exciting band-tail states below the fundamental bandgap of a low-temperature grown GaAs layer, while the detection takes advantage of the electro-optic effect in the GaAs material. This simple scheme considerably enhances previous measurement techniques and is capable of generating and measuring frequencies exceeding 1 THz. The optimum wavelength for the combined generation and detection technique is found at ∼900 nm.
Casimir forces between solids can be repulsive
Authors: Miller Johanna
Published: February 2009

A decades-old prediction—that materials with certain combinations of optical properties can reverse a quantum force’s direction—has been experimentally verified.
Commercial optical traps emerge from biophysics labs
Authors: Matthews Jermey N. A.
Published: February 2009

Traditionally custom-built, optical tweezers are now available off-the-shelf for single-molecule research and clinical applications.
Beyond quantum jumps: Blinking nanoscale light emitters
Authors: Stefani Fernando D. , Hoogenboom Jacob P. , Barkai Eli
Published: February 2009

On the nanoscale, almost all light sources blink. Surprisingly, such blinking occurs on time scales much larger than predicted by quantum mechanics and has statistics governed by nonergodicity.
The no-cloning theorem
Authors: Wootters William K. , Zurek Wojciech H.
Published: February 2009

People gather, copy, and distribute information all the time. But in the quantum world, the laws of physics impose a severe restriction on copying: It is impossible to make a perfect copy of an unknown state.
MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles
Authors: Sasaki Yasnory T. F. , Ideue Takashi , Sano Miho , Mituyama Toutai , Hirose Tetsuro
Published: February 2009

Recent transcriptome analyses have shown that thousands of noncoding RNAs (ncRNAs) are transcribed from mammalian genomes. Although the number of functionally annotated ncRNAs is still limited, they are known to be frequently retained in the nucleus, where they coordinate regulatory networks of gene expression. Some subnuclear organelles or nuclear bodies include RNA species whose identity and structural roles are largely unknown. We identified 2 abundant overlapping ncRNAs, MENε and MENβ (MENε/β), which are transcribed from the corresponding site in the multiple endocrine neoplasia (MEN) I locus and which localize to nuclear paraspeckles. This finding raises the intriguing possibility that MENε/β are involved in paraspeckle organization, because paraspeckles are, reportedly, RNase-sensitive structures. Successful removal of MENε/β by a refined knockdown method resulted in paraspeckle disintegration. Furthermore, the reassembly of paraspeckles disassembled by transcriptional arrest appeared to be unsuccessful in the absence of MENε/β. RNA interference and immunoprecipitation further revealed that the paraspeckle proteins p54/nrb and PSF selectively associate with and stabilize the longer MENβ, thereby contributing to the organization of the paraspeckle structure. The paraspeckle protein PSP1 is not directly involved in either MENε/β stabilization or paraspeckle organization. We postulate a model for nuclear paraspeckle body organization where specific ncRNAs and RNA-binding proteins cooperate to maintain and, presumably, establish the structure.
The feeding biomechanics and dietary ecology of
Australopithecus africanus
Authors: Strait David S. , Weber Gerhard W. , Neubauer Simon , Chalk Janine , Richmond Brian G. , Lucas Peter W. , Spencer Mark A. , Schrein Caitlin , Dechow Paul C. , Ross Callum F. , Grosse Ian R. , Wright Barth W. , Constantino Paul , Wood Bernard A. , Lawn Brian , Hylander William L. , Wang Qian , Byron Craig , Slice Dennis E. , Smith Amanda L.
Published: February 2009

The African Plio-Pleistocene hominins known as australopiths evolved a distinctive craniofacial morphology that traditionally has been viewed as a dietary adaptation for feeding on either small, hard objects or on large volumes of food. A historically influential interpretation of this morphology hypothesizes that loads applied to the premolars during feeding had a profound influence on the evolution of australopith craniofacial form. Here, we test this hypothesis using finite element analysis in conjunction with comparative, imaging, and experimental methods. We find that the facial skeleton of the
Australopithecus
type species,
A. africanus
, is well suited to withstand premolar loads. However, we suggest that the mastication of either small objects or large volumes of food is unlikely to fully explain the evolution of facial form in this species. Rather, key aspects of australopith craniofacial morphology are more likely to be related to the ingestion and initial preparation of large, mechanically protected food objects like large nuts and seeds. These foods may have broadened the diet of these hominins, possibly by being critical resources that australopiths relied on during periods when their preferred dietary items were in short supply. Our analysis reconciles apparent discrepancies between dietary reconstructions based on biomechanics, tooth morphology, and dental microwear.
Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning
Authors: Jones Thouis R. , Carpenter Anne E. , Lamprecht Michael R. , Moffat Jason , Silver Serena J. , Grenier Jennifer K. , Castoreno Adam B. , Eggert Ulrike S. , Root David E. , Golland Polina , Sabatini David M.
Published: February 2009

Many biological pathways were first uncovered by identifying mutants with visible phenotypes and by scoring every sample in a screen via tedious and subjective visual inspection. Now, automated image analysis can effectively score many phenotypes. In practical application, customizing an image-analysis algorithm or finding a sufficient number of example cells to train a machine learning algorithm can be infeasible, particularly when positive control samples are not available and the phenotype of interest is rare. Here we present a supervised machine learning approach that uses iterative feedback to readily score multiple subtle and complex morphological phenotypes in high-throughput, image-based screens. First, automated cytological profiling extracts hundreds of numerical descriptors for every cell in every image. Next, the researcher generates a rule (i.e., classifier) to recognize cells with a phenotype of interest during a short, interactive training session using iterative feedback. Finally, all of the cells in the experiment are automatically classified and each sample is scored based on the presence of cells displaying the phenotype. By using this approach, we successfully scored images in RNA interference screens in 2 organisms for the prevalence of 15 diverse cellular morphologies, some of which were previously intractable.
Female rats learn trace memories better than male rats and consequently retain a greater proportion of new neurons in their hippocampi
Authors: Dalla Christina , Papachristos Efstathios B. , Whetstone Abigail S. , Shors Tracey J.
Published: February 2009

Learning increases the survival of new cells that are generated in the hippocampal formation before the training experience, especially if the animal learns to associate stimuli across time [Gould E, Beylin A, Tanapat P, Reeves A, Shors TJ (1999)
Nat Neurosci
2:260–265]. All relevant studies have been conducted on male rats, despite evidence for sex differences in this type of learning. In the present study, we asked whether sex differences in learning influence the survival of neurons generated in the adult hippocampus. Male and female adult rats were injected with one dose of bromodeoxyuridine (BrdU; 200 mg/kg), to label one population of dividing cells. One week later, half of the animals were trained with a temporal learning task of trace eyeblink conditioning, while the other half were not trained. Animals were killed 1 day after training (12 days after the BrdU injection). Hippocampal tissue was stained for BrdU and a marker of immature neurons, doublecortin. Both sexes learned to emit the conditioned eyeblink response during the trace interval. As a consequence, more new neurons remained in their hippocampi than in sex-matched controls. In individual animals, the number of surviving cells correlated positively with asymptotic performance; those that expressed more learned responses retained more new neurons. However, animals that learned very well retained even more new cells if they required many trials to do so. Because females emitted more learned responses than males did, they retained nearly twice as many new cells per unit volume of tissue. This effect was most evident in the ventral region of the hippocampal formation. Thus, sex differences in learning alter the anatomical structure of the hippocampus. As a result, male and female brains continue to differentiate in adulthood.
Conditional deletion of the MHC class I-related receptor FcRn reveals the sites of IgG homeostasis in mice
Authors: Montoyo Héctor Pérez , Vaccaro Carlos , Hafner Martin , Ober Raimund J. , Mueller Werner , Ward E. Sally
Published: February 2009

The MHC class I-related receptor FcRn regulates the levels and persistence of IgG in vivo. This receptor salvages IgG from lysosomal degradation within cells, and the binding properties of an IgG for FcRn correlate with in vivo half-life. FcRn is expressed at multiple different sites throughout adult life. However, the cell types and sites at which FcRn maintains IgG homeostasis are not well defined. Toward understanding the sites of FcRn function, we have generated a mouse strain in which this Fc receptor can be conditionally deleted. In combination with mice that express Cre recombinase under the control of the Tie2 promoter (Tie2-Cre), the effect of site-specific deletion of floxed FcRn in endothelial and hematopoietic cells on IgG persistence was analyzed. The pharmacokinetics and steady-state levels of IgG in Tie2-Cre mice that are homozygous for the floxed FcRn allele reveal a complete loss of FcRn function in regulating the half-lives of wild-type IgG. The primary sites for the maintenance of endogenous IgGs in mice are therefore endothelial and hematopoietic cells.
Melanin-concentrating hormone neurons discharge in a reciprocal manner to orexin neurons across the sleep–wake cycle
Authors: Hassani Oum Kaltoum , Lee Maan Gee , Jones Barbara E.
Published: February 2009

Neurons containing melanin-concentrating hormone (MCH) are codistributed with neurons containing orexin (Orx or hypocretin) in the lateral hypothalamus, a peptide and region known to be critical for maintaining wakefulness. Evidence from knockout and c-Fos studies suggests, however, that the MCH neurons might play a different role than Orx neurons in regulating activity and sleep–wake states. To examine this possibility, neurons were recorded across natural sleep–wake states in head-fixed rats and labeled by using the juxtacellular technique for subsequent immunohistochemical identification. Neurons identified as MCH+ did not fire during wake (W); they fired selectively during sleep, occasionally during slow wave sleep (SWS) and maximally during paradoxical sleep (PS). As W-Off/Sleep-On, the MCH neurons discharged in a reciprocal manner to the W-On/Sleep-Off Orx neurons and could accordingly play a complementary role to Orx neurons in sleep–wake state regulation and contribute to the pathophysiology of certain sleep disorders, such as narcolepsy with cataplexy.
Genome-wide association analysis reveals aSOD1mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis
Authors: Awano Tomoyuki , Johnson Gary S. , Wade Claire M. , Katz Martin L. , Johnson Gayle C. , Taylor Jeremy F. , Perloski Michele , Biagi Tara , Baranowska Izabella , Long Sam , March Philip A. , Olby Natasha J. , Shelton G. Diane , Khan Shahnawaz , O'Brien Dennis P. , Lindblad-Toh Kerstin , Coates Joan R.
Published: February 2009

Canine degenerative myelopathy (DM) is a fatal neurodegenerative disease prevalent in several dog breeds. Typically, the initial progressive upper motor neuron spastic and general proprioceptive ataxia in the pelvic limbs occurs at 8 years of age or older. If euthanasia is delayed, the clinical signs will ascend, causing flaccid tetraparesis and other lower motor neuron signs. DNA samples from 38 DM-affected Pembroke Welsh corgi cases and 17 related clinically normal controls were used for genome-wide association mapping, which produced the strongest associations with markers on CFA31 in a region containing the canineSOD1gene.SOD1was considered a regional candidate gene because mutations in humanSOD1can cause amyotrophic lateral sclerosis (ALS), an adult-onset fatal paralytic neurodegenerative disease with both upper and lower motor neuron involvement. The resequencing ofSOD1in normal and affected dogs revealed a G to A transition, resulting in an E40K missense mutation. Homozygosity for the A allele was associated with DM in 5 dog breeds: Pembroke Welsh corgi, Boxer, Rhodesian ridgeback, German Shepherd dog, and Chesapeake Bay retriever. Microscopic examination of spinal cords from affected dogs revealed myelin and axon loss affecting the lateral white matter and neuronal cytoplasmic inclusions that bind anti-superoxide dismutase 1 antibodies. These inclusions are similar to those seen in spinal cord sections from ALS patients withSOD1mutations. Our findings identify canine DM to be the first recognized spontaneously occurring animal model for ALS.
Thymic stromal lymphopoietin overproduced by keratinocytes in mouse skin aggravates experimental asthma
Authors: Zhang Zhikun , Hener Pierre , Frossard Nelly , Kato Shigeaki , Metzger Daniel , Li Mei , Chambon Pierre
Published: February 2009

Atopic dermatitis (AD) is often the initial step in the “atopic march,” given that more than half of AD patients with moderate to severe AD develop asthma later in life. Both AD and asthma share a similar “atopy” phenotype that includes T helper type 2 inflammation with eosinophilia and hyper-IgE immunoglobulinemia, but the molecular mechanisms underlying the “atopic march” remain elusive. In the present study, we show that induced expression of thymic stromal lymphopoietin (TSLP) in mouse epidermal keratinocytes upon topical application of MC903 (a low calcemic analogue of vitamin D3) not only triggers AD as we previously reported but also aggravates experimental allergic asthma induced by ovalbumin sensitization and challenge. Our study, which provides a mouse model to study human “atopic march,” indicates that keratinocyte-produced TSLP may represent an important factor in the link of atopic dermatitis to asthma.
Climate change and health costs of air emissions from biofuels and gasoline
Authors: Hill Jason , Polasky Stephen , Nelson Erik , Tilman David , Huo Hong , Ludwig Lindsay , Neumann James , Zheng Haochi , Bonta Diego
Published: February 2009

Environmental impacts of energy use can impose large costs on society. We quantify and monetize the life-cycle climate-change and health effects of greenhouse gas (GHG) and fine particulate matter (PM
2.5
) emissions from gasoline, corn ethanol, and cellulosic ethanol. For each billion ethanol-equivalent gallons of fuel produced and combusted in the US, the combined climate-change and health costs are $469 million for gasoline, $472–952 million for corn ethanol depending on biorefinery heat source (natural gas, corn stover, or coal) and technology, but only $123–208 million for cellulosic ethanol depending on feedstock (prairie biomass,
Miscanthus
, corn stover, or switchgrass). Moreover, a geographically explicit life-cycle analysis that tracks PM
2.5
emissions and exposure relative to U.S. population shows regional shifts in health costs dependent on fuel production systems. Because cellulosic ethanol can offer health benefits from PM
2.5
reduction that are of comparable importance to its climate-change benefits from GHG reduction, a shift from gasoline to cellulosic ethanol has greater advantages than previously recognized. These advantages are critically dependent on the source of land used to produce biomass for biofuels, on the magnitude of any indirect land use that may result, and on other as yet unmeasured environmental impacts of biofuels.
Loss of cryptochrome reduces cancer risk in
p53
mutant mice
Authors: Ozturk Nuri , Lee Jin Hyup , Gaddameedhi Shobhan , Sancar Aziz
Published: February 2009

It is commonly thought that disruption of the circadian clock increases the cancer incidence in humans and mice. However, it was found that disruption of the clock by the
Cryptochrome
(
Cry
) mutation in mice did not increase cancer rate in the mutant mice even after exposing the animals to ionizing radiation. Therefore, in this study we tested the effect of the
Cry
mutation on carcinogenesis in a mouse strain prone to cancer because of a
p53
mutation, with the expectation that clock disruption in this sensitized background would further increase cancer risk. Paradoxically, we find that the
Cry
mutation protects
p53
mutant mice from the early onset of cancer and extends their median lifespan ≈50%, in part by sensitizing
p53
mutant cells to apoptosis in response to genotoxic stress. These results suggest alternative therapeutic approaches in management of cancers associated with a
p53
mutation.
Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
Authors: Sims Gregory E. , Jun Se-Ran , Wu Guohong A. , Kim Sung-Hou
Published: February 2009

For comparison of whole-genome (genic + nongenic) sequences, multiple sequence alignment of a few selected genes is not appropriate. One approach is to use an alignment-free method in which feature (or
l
-mer) frequency profiles (FFP) of whole genomes are used for comparison—a variation of a text or book comparison method, using word frequency profiles. In this approach it is critical to identify the optimal resolution range of
l
-mers for the given set of genomes compared. The optimum FFP method is applicable for comparing whole genomes or large genomic regions even when there are no common genes with high homology. We outline the method in 3 stages: (
i
) We first show how the optimal resolution range can be determined with English books which have been transformed into long character strings by removing all punctuation and spaces. (
ii
) Next, we test the robustness of the optimized FFP method at the nucleotide level, using a mutation model with a wide range of base substitutions and rearrangements. (
iii
) Finally, to illustrate the utility of the method, phylogenies are reconstructed from concatenated mammalian intronic genomes; the FFP derived intronic genome topologies for each
l
within the optimal range are all very similar. The topology agrees with the established mammalian phylogeny revealing that intron regions contain a similar level of phylogenic signal as do coding regions.
Substitutional alloy of Ce and Al
Authors: Zeng Qiao-Shi , Ding Yang , Mao Wendy L. , Luo Wei , Blomqvist Andreas , Ahuja Rajeev , Yang Wenge , Shu Jinfu , Sinogeikin Stas V. , Meng Yue , Brewe Dale L. , Jiang Jian-Zhong , Mao Ho-kwang
Published: February 2009

The formation of substitutional alloys has been restricted to elements with similar atomic radii and electronegativity. Using high-pressure at 298 K, we synthesized a face-centered cubic disordered alloy of highly dissimilar elements (large Ce and small Al atoms) by compressing the Ce
3
Al intermetallic compound >15 GPa or the Ce
3
Al metallic glass >25 GPa. Synchrotron X-ray diffraction, Ce

L
3

-edge absorption spectroscopy, and ab initio calculations revealed that the pressure-induced Kondo volume collapse and 4
f
electron delocalization of Ce reduced the differences between Ce and Al and brought them within the Hume-Rothery (HR) limit for substitutional alloying. The alloy remained after complete release of pressure, which was also accompanied by the transformation of Ce back to its ambient 4
f
electron localized state and reversal of the Kondo volume collapse, resulting in a non-HR alloy at ambient conditions.
Mesenchymal cells reactivate Snail1 expression to drive three-dimensional invasion programs
Authors: Rowe R. Grant , Li Xiao-Yan , Hu Yuexian , Saunders Thomas L. , Virtanen Ismo , de Herreros Antonio Garcia , Becker Karl-Friedrich , Ingvarsen Signe , Engelholm Lars H. , Bommer Guido T. , Fearon Eric R. , Weiss Stephen J.
Published: February 2009

Epithelial–mesenchymal transition (EMT) is required for mesodermal differentiation during development. The zinc-finger transcription factor, Snail1, can trigger EMT and is sufficient to transcriptionally reprogram epithelial cells toward a mesenchymal phenotype during neoplasia and fibrosis. Whether Snail1 also regulates the behavior of terminally differentiated mesenchymal cells remains unexplored. Using a Snai1 conditional knockout model, we now identify Snail1 as a regulator of normal mesenchymal cell function. Snail1 expression in normal fibroblasts can be induced by agonists known to promote proliferation and invasion in vivo. When challenged within a tissue-like, three-dimensional extracellular matrix, Snail1-deficient fibroblasts exhibit global alterations in gene expression, which include defects in membrane type-1 matrix metalloproteinase (MT1-MMP)-dependent invasive activity. Snail1-deficient fibroblasts explanted atop the live chick chorioallantoic membrane lack tissue-invasive potential and fail to induce angiogenesis. These findings establish key functions for the EMT regulator Snail1 after terminal differentiation of mesenchymal cells.
Kinetochore stretching inactivates the spindle assembly checkpoint
Authors: Uchida Kazuhiko S.K. , Takagaki Kentaro , Kumada Kazuki , Hirayama Youko , Noda Tetsuo , Hirota Toru
Published: February 2009

The spindle assembly checkpoint (SAC) monitors the attachment of microtubules to the kinetochore and inhibits anaphase when microtubule binding is incomplete. The SAC might also respond to tension; however, how cells can sense tension and whether its detection is important to satisfy the SAC remain controversial. We generated a HeLa cell line in which two components of the kinetochore, centromere protein A and Mis12, are labeled with green and red fluorophores, respectively. Live cell imaging of these cells reveals repetitive cycles of kinetochore extension and recoiling after biorientation. Under conditions in which kinetochore stretching is suppressed, cells fail to silence the SAC and enter anaphase after a delay, regardless of centromere stretching. Monitoring cyclin B levels as a readout for anaphase-promoting complex/cyclosome activity, we find that suppression of kinetochore stretching delays and decelerates cyclin B degradation. These observations suggest that the SAC monitors stretching of kinetochores rather than centromeres and that kinetochore stretching promotes silencing of the SAC signal.
The antigen-specific CD8+ T cell repertoire in unimmunized mice includes memory phenotype cells bearing markers of homeostatic expansion
Authors: Haluszczak Catherine , Akue Adovi D. , Hamilton Sara E. , Johnson Lisa D.S. , Pujanauski Lindsey , Teodorovic Lenka , Jameson Stephen C. , Kedl Ross M.
Published: February 2009

Memory T cells exhibit superior responses to pathogens and tumors compared with their naive counterparts. Memory is typically generated via an immune response to a foreign antigen, but functional memory T cells can also be produced from naive cells by homeostatic mechanisms. Using a recently developed method, we studied CD8 T cells, which are specific for model (ovalbumin) and viral (HSV, vaccinia) antigens, in unimmunized mice and found a subpopulation bearing markers of memory cells. Based on their phenotypic markers and by their presence in germ-free mice, these preexisting memory-like CD44hi CD8 T cells are likely to arise via physiological homeostatic proliferation rather than a response to environmental microbes. These antigen-inexperienced memory phenotype CD8 T cells display several functions that distinguish them from their CD44lo counterparts, including a rapid initiation of proliferation after T cell stimulation and rapid IFN-γ production after exposure to proinflammatory cytokines. Collectively, these data indicate that the unprimed antigen-specific CD8 T cell repertoire contains antigen-inexperienced cells that display phenotypic and functional traits of memory cells.