bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of human disease‐associated phosphorylation sites with combined feature selection approach and support vector machine
Authors: Xu Xiaoyi , Li Ao , Wang Minghui
Published: April 2015

Phosphorylation is a crucial post‐translational modification, which regulates almost all cellular processes in life. It has long been recognised that protein phosphorylation has close relationship with diseases, and therefore many researches are undertaken to predict phosphorylation sites for disease treatment and drug design. However, despite the success achieved by these approaches, no method focuses on disease‐associated phosphorylation sites prediction. Herein, for the first time the authors propose a novel approach that is specially designed to identify associations between phosphorylation sites and human diseases. To take full advantage of local sequence information, a combined feature selection method‐based support vector machine (CFS‐SVM) that incorporates minimum‐redundancy‐maximum‐relevance filtering process and forward feature selection process is developed. Performance evaluation shows that CFS‐SVM is significantly better than the widely used classifiers including Bayesian decision theory, k nearest neighbour and random forest. With the extremely high specificity of 99%, CFS‐SVM can still achieve a high sensitivity. Besides, tests on extra data confirm the effectiveness and general applicability of CFS‐SVM approach on a variety of diseases. Finally, the analysis of selected features and corresponding kinases also help the understanding of the potential mechanism of disease‐phosphorylation relationships and guide further experimental validations.
Osteogenesis Imperfecta Diagnosed from Mandibular and Lower Limb Fractures: A Case Report
Authors: Kobayashi Yoshikazu , Satoh Koji , Mizutani Hideki
Published: April 2015

Osteogenesis imperfecta (OI) is a congenital disease characterized by bone fragility and low bone mass. Despite the variety of its manifestation and severity, facial fractures occur very infrequently. Here, we report a case of an infant diagnosed with OI after mandibular and lower limb fractures. A boy aged 1 year and 3 months was brought to his neighboring hospital with a complaint of facial injury. He was transferred to our hospital to undergo operation 3 days later. Computed tomography images revealed multiple mandibular fractures including complete fracture in the symphysis and dislocated condylar fracture on the right side. Open reduction and internal fixation with absorbable implants was performed 7 days after injury. He fractured his right lower limb 2 months later. He was diagnosed with OI type IA by an orthopedist. He will be administered bone-modifying agents if he suffers from frequent fractures.
Ultrafast core-loss spectroscopy in four-dimensional electron microscopy
Authors: van der Veen Renske M. , Penfold Thomas J. , Zewail Ahmed H.
Published: April 2015

We demonstrate ultrafast core-electron energy-loss spectroscopy in four-dimensional electron microscopy as an element-specific probe of nanoscale dynamics. We apply it to the study of photoexcited graphite with femtosecond and nanosecond resolutions. The transient core-loss spectra, in combination with ab initio molecular dynamics simulations, reveal the elongation of the carbon-carbon bonds, even though the overall behavior is a contraction of the crystal lattice. A prompt energy-gap shrinkage is observed on the picosecond time scale, which is caused by local bond length elongation and the direct renormalization of band energies due to temperature-dependent electron–phonon interactions.
Magneto-optical visualization by Bi:YIG thin films prepared at low temperatures
Authors: Galstyan Ogsen , Lee Hanju , Babajanyan Arsen , Hakhoumian Arsen , Friedman Barry , Lee Kiejin
Published: April 2015

A device for the imaging of magnetic fields and domain structures based on the Faraday effect has been developed using garnet thin films prepared by the metal-organic decomposition method as indicators. The sensitivity was improved by using high concentration bismuth substituted yttrium iron garnet thin films with in-plane magnetic anisotropy. Low temperature synthesis of the films (BixY3−xFe5O12; x = 2) on glass substrates of thickness about 0.8 μm is described and the Faraday rotation angle is measured to be about −11°/μm.
Discontinuous non-equilibrium phase transition in a threshold Schloegl model for autocatalysis: Generic two-phase coexistence and metastability
Authors: Wang Chi-Jen , Liu Da-Jiang , Evans James W.
Published: April 2015

Threshold versions of Schloegl’s model on a lattice, which involve autocatalytic creation and spontaneous annihilation of particles, can provide a simple prototype for discontinuous non-equilibrium phase transitions. These models are equivalent to so-called threshold contact processes. A discontinuous transition between populated and vacuum states can occur selecting a threshold of N ≥ 2 for the minimum number, N, of neighboring particles enabling autocatalytic creation at an empty site. Fundamental open questions remain given the lack of a thermodynamic framework for analysis. For a square lattice with N = 2, we show that phase coexistence occurs not at a unique value but for a finite range of particle annihilation rate (the natural control parameter). This generic two-phase coexistence also persists when perturbing the model to allow spontaneous particle creation. Such behavior contrasts both the Gibbs phase rule for thermodynamic systems and also previous analysis for this model. We find metastability near the transition corresponding to a non-zero effective line tension, also contrasting previously suggested critical behavior. Mean-field type analysis, extended to treat spatially heterogeneous states, further elucidates model behavior.
Enhanced performance of branched TiO2 nanorod based Mn-doped CdS and Mn-doped CdSe quantum dot-sensitized solar cell
Authors: Kim Soo-Kyoung , Gopi Chandu V. V. M. , Lee Jae-Cheol , Kim Hee-Je
Published: April 2015

TiO2 branched nanostructures could be efficient as photoanodes for quantum dot-sensitized solar cells (QDSCs) due to their large surface area for QD deposition. In this study, Mn-doped CdS/Mn-doped CdSe deposited branched TiO2 nanorods were fabricated to enhance the photovoltaic performance of QDSCs. Mn doping in CdS and CdSe retards the recombination losses of electrons, while branched TiO2 nanorods facilitate effective electron transport and compensate for the low surface area of the nanorod structure. As a result, the charge-transfer resistance (RCT), electron lifetime (τe), and the amount of QD deposition were significantly improved with branched TiO2 nanorod based Mn-doped CdS/Mn-doped CdSe quantum dot-sensitized solar cell.
Negative-T InGaN laser diodes and their degradation
Authors: Bojarska Agata , Marona Łucja , Makarowa Irina , Czernecki Robert , Leszczynski Mike , Suski Tadeusz , Perlin Piotr
Published: April 2015

We studied the InGaN laser diode, emitting in the blue region of the spectrum and characterized by a negative characteristic temperature T0. The corresponding decrease in the threshold current with the increase in temperature for this device is caused by the increased distance between the electron-blocking layer and the quantum wells. Because of the non-monotonic temperature dependence of laser parameters, we can demonstrate a correlation of the degradation rate with nonradiative part of the total device current. This result indicates the potential importance of the recombination processes occurring outside of the active region for the reliability of InGaN laser diodes.
The tunable negative permittivity and negative permeability of percolative Fe/Al2O3 composites in radio frequency range
Authors: Sun K. , Fan R. H. , Zhang Z. D. , Yan K. L. , Zhang X. H. , Xie P. T. , Yu M. X. , Pan S. B.
Published: April 2015

The electromagnetic properties including ac conductivity, permittivity, and permeability of percolative Fe/Al2O3 composites, which were prepared by in-situ synthesis process, are investigated in the radio frequency range. There is an obvious percolation transition with the increase of iron contents. When iron content is beyond but near the percolation threshold, the negative permittivity and permeability are simultaneously obtained from 631 MHz to 1 GHz in sample FA30. Further increasing iron content, the Fano-like resonances are observed, and the resonance frequency where the permittivity changes from negative to positive shifts to lower frequency. In addition, the frequency region of negative permittivity and negative permeability are not overlapped any more. Hopefully, the percolative Fe/Al2O3 composites with tunable negative permittivity and negative permeability can be used as electromagnetic wave absorber.
Magneto-optical properties of Nd0.5Bi2.5Fe4GaO12 thin films on glass substrates with various thicknesses prepared using metal-organic decomposition
Authors: Lou Gengjian , Yoshida Tomohiko , Ishibashi Takayuki
Published: April 2015

Nd0.5Bi2.5Fe4GaO12 (Bi2.5:NIGG) thin films with thicknesses of d = 200–1200 nm are prepared on Nd2BiFe4GaO12 (Bi1:NIGG) buffer layers on glass substrates using metal-organic decomposition. The shapes of the Faraday rotation spectra and hysteresis did not change with an increasing film thickness. The Faraday rotation angles increased in proportion with the film thickness, indicating that Bi2.5:NIGG grew without any deterioration for thicknesses up to 1200 nm.
Ultra-broadband 2D electronic spectroscopy of carotenoid-bacteriochlorophyll interactions in the LH1 complex of a purple bacterium
Authors: Maiuri Margherita , Réhault Julien , Carey Anne-Marie , Hacking Kirsty , Garavelli Marco , Lüer Larry , Polli Dario , Cogdell Richard J. , Cerullo Giulio
Published: April 2015

We investigate the excitation energy transfer (EET) pathways in the photosynthetic light harvesting 1 (LH1) complex of purple bacterium Rhodospirillum rubrum with ultra-broadband two-dimensional electronic spectroscopy (2DES). We employ a 2DES apparatus in the partially collinear geometry, using a passive birefringent interferometer to generate the phase-locked pump pulse pair. This scheme easily lends itself to two-color operation, by coupling a sub-10 fs visible pulse with a sub-15-fs near-infrared pulse. This unique pulse combination allows us to simultaneously track with extremely high temporal resolution both the dynamics of the photoexcited carotenoid spirilloxanthin (Spx) in the visible range and the EET between the Spx and the B890 bacterio-chlorophyll (BChl), whose Qx and Qy transitions peak at 585 and 881 nm, respectively, in the near-infrared. Global analysis of the one-color and two-color 2DES maps unravels different relaxation mechanisms in the LH1 complex: (i) the initial events of the internal conversion process within the Spx, (ii) the parallel EET from the first bright state S2 of the Spx towards the Qx state of the B890, and (iii) the internal conversion from Qx to Qy within the B890.
A multi-scale approach to characterize pure CH4, CF4, and CH4/CF4 mixtures
Authors: Chattoraj Joyjit , Risthaus Tobias , Rubner Oliver , Heuer Andreas , Grimme Stefan
Published: April 2015

In this study, we develop three intermolecular potentials for methane (CH4), tetrafluoromethane (CF4), and CH4/CF4 dimers using a novel ab initio method. The ultimate goal is to understand microscopically the phase-separation in CH4/CF4 systems, which takes place in the liquid states near their freezing points. Monte-Carlo (MC) simulations of the pure CH4 system are performed using the ab initio energies to verify the potential. The simulations reproduce quite well the experimentally known liquid densities, the internal energies, the second virial coefficients, and the radial distribution function. The essentially six-dimensional (6D) ab initio potential is then reduced to a one-dimensional (1D) effective potential using the inverse Monte-Carlo technique. This potential, too, successfully reproduces the experimental results. Interestingly, the MC study cannot be extended to the pure CF4 system and the CH4/CF4 mixed system because the two respective ab initio potentials present very rough potential landscapes. This renders the interpolation of energies for the MC simulations and thus the multi-scale approach unreliable. It suggests, however, a possible driving force for the experimentally observed phase separation of the CH4/CF4 system at low temperatures. Furthermore, we carefully study the determination of 1D effective potentials via inverse MC techniques. We argue that to a good approximation the temperature dependence of the 1D potentials can be estimated via reweighting techniques for a fixed temperature.
Layered structure and related magnetic properties for annealed Fe/Ir(111) ultrathin films
Authors: Jiang Pei-Cheng , Chen Wei-Hsiang , Hsieh Chen-Yuan , Tsay Jyh-Shen
Published: April 2015

After annealing treatments for fcc-Fe/Ir(111) below 600 K, the surface layers remain pseudomorphic. The Ir(111) substrate plays an important role on the expanded Fe lattice. At temperatures between 750 and 800 K, the surface composition shows a stable state and a c(2 × 4) structure is observed. We discover a layered structure composed of some Fe atoms on the top of a Fe0.5Ir0.5 interfacial alloy supported on the Ir(111) substrate. The competition between the negative formation heat of Fe0.5Ir0.5 and surface free energy of Fe causes the formation of layered structure. The existence of ferromagnetic dead layer coincides with the formation of fcc-Fe for ultrathin Fe on Fe0.5Ir0.5/Ir(111). For Fe films thicker than three monolayers, the linear increase of the Kerr intensity versus the Fe coverage is related to the growing of bcc-Fe on the surface where the Fe layer is incoherent to the underlying Fe0.5Ir0.5/Ir(111). These results emphasize the importance of the substrate induced strain and layered structure of Fe/Fe0.5Ir0.5/Ir(111) on the magnetic properties and provide valuable information for future applications.
Rate-dependent shear-band initiation in a metallic glass
Authors: Tönnies D. , Samwer K. , Derlet P. M. , Volkert C. A. , Maaß R.
Published: April 2015

A statistical analysis of the rate-dependent pop-in behavior during spherical nanoindentation of a metallic glass is presented. Since the first pop-in of a test corresponds to the initiation of plasticity, this method provides insights into the fundamentals of shear-banding behavior. In this study, test series with different applied loading rates reveal that the initiation of a shear band is thermally activated with a rate- and stress-dependent activation volume. We further find a spatial inhomogeneity of the elastic modulus at the micrometer scale. This long-range structural heterogeneity does not strongly correlate with the shear-band initiation stress.
Broadband acoustic trapping of a particle by a soft plate with a periodic deep grating
Authors: He Hailong , Ouyang Shiliang , He Zhaojian , Deng Ke , Zhao Heping
Published: April 2015

We investigated the acoustic radiation force (ARF) acting on a cylindrical brass particle near an acoustically soft plate patterned with a periodic deep grating. The existence of a negative ARF by which the particle can be pulled towards the sound source is confirmed. In addition, the bandwidth for negative ARF in this soft-plate system is found to be considerably broader than in the stiff-plate systems typically used in previous studies. It is further demonstrated by field distribution analysis that the negative ARF is caused by the gradient force induced by the gradient vortex velocity field near the surface, which stems from the collective resonance excitation of the antisymmetric coupling of Scholte surface waves in the thin plate. The effects of particle location and size on the ARF were also investigated in detail. The negative ARF has potential use in applications requiring particle manipulation using acoustic waves.
The atomic details of the interfacial interaction between the bottom electrode of Al/AlOx/Al Josephson junctions and HF-treated Si substrates
Authors: Zeng L. J. , Krantz P. , Nik S. , Delsing P. , Olsson E.
Published: April 2015

The interface between the Al bottom contact layer and Si substrates in Al based Josephson junctions is believed to have a significant effect on the noise observed in Al based superconducting devices. We have studied the atomic structure of it by transmission electron microscopy. An amorphous layer with a thickness of ∼5 nm was found between the bottom Al electrode and HF-treated Si substrate. It results from intermixing between Al, Si, and O. We also studied the chemical bonding states among the different species using energy loss near edge structure. The observations are of importance for the understanding of the origin of decoherence mechanisms in qubits based on these junctions.
Effect of L12 ordering in antiferromagnetic Ir-Mn epitaxial layer on exchange bias of FePd films
Authors: Chang Y. C. , Hsiao S. N. , Liu S. H. , Su S. H. , Chiu K. F. , Hsieh W. C. , Chen S. K. , Lin Y. G. , Lee H. Y. , Sung C. K. , Duh J. G.
Published: April 2015

Two series of samples of single-layer IrMn and IrMn/FePd bilayer films, deposited on a single-crystal MgO substrate at different IrMn deposition temperatures (Ts = 300–700 °C), were investigated using magnetron sputtering. L12 ordering was revealed for the 30 nm-thick IrMn epitaxial (001) films with Ts ≥ 400 °C, determined by synchrotron radiation x-ray diffractometry (XRD). XRD results also provide evidence of the epitaxial growth of the IrMn films on MgO substrate. Increasing Ts from 400 to 700 °C monotonically increases the ordering parameter of L12 phases from 0.17 to 0.81. An in-plane exchange bias field (Heb) of 22 Oe is obtained in a 10 nm-thick FePd film that is deposited on the disordered IrMn films. As the L12 ordering of the IrMn layers increases, the Heb gradually decreases to 0 Oe, meaning that the exchange bias behavior vanishes. The increased surface roughness, revealed by atomic force microscopy, of the epitaxial IrMn layers with increasing Ts cannot be the main cause of the decrease in Heb due to the compensated surface spins regardless of the disordered and ordered (001) IrMn layers. The change of antiferromagnetic structure from the A1 to the L12 phase was correlated with the evolution of Heb.
Structural stability and defect energetics of ZnO from diffusion quantum Monte Carlo
Authors: Santana Juan A. , Krogel Jaron T. , Kim Jeongnim , Kent Paul R. C. , Reboredo Fernando A.
Published: April 2015

We have applied the many-body ab initio diffusion quantum Monte Carlo (DMC) method to study Zn and ZnO crystals under pressure and the energetics of the oxygen vacancy, zinc interstitial, and hydrogen impurities in ZnO. We show that DMC is an accurate and practical method that can be used to characterize multiple properties of materials that are challenging for density functional theory (DFT) approximations. DMC agrees with experimental measurements to within 0.3 eV, including the band-gap of ZnO, the ionization potential of O and Zn, and the atomization energy of O2, ZnO dimer, and wurtzite ZnO. DMC predicts the oxygen vacancy as a deep donor with a formation energy of 5.0(2) eV under O-rich conditions and thermodynamic transition levels located between 1.8 and 2.5 eV from the valence band maximum. Our DMC results indicate that the concentration of zinc interstitial and hydrogen impurities in ZnO should be low under n-type and Zn- and H-rich conditions because these defects have formation energies above 1.4 eV under these conditions. Comparison of DMC and hybrid functionals shows that these DFT approximations can be parameterized to yield a general correct qualitative description of ZnO. However, the formation energy of defects in ZnO evaluated with DMC and hybrid functionals can differ by more than 0.5 eV.
Comparison of volume distribution of magnetic nanoparticles obtained from M-H curve with a mixture of log-normal distributions
Authors: Sasayama T. , Yoshida T. , Saari M. M. , Enpuku K.
Published: April 2015

We studied the distributions of the magnetic moment and magnetic volume of magnetic nanoparticles (MNPs). These distributions were estimated by applying the singular value decomposition method to the M-H curve measured in the liquid phase. The estimated distributions were compared with a mixture of log-normal distributions, and two results agree well with each other. Using the estimated distribution of the magnetic moment, we also analyzed the M-H curve of immobilized MNPs in order to estimate the average value of the anisotropy energy constant Ku and the characteristic time τON that determines the Neel relaxation of immobilized MNPs. The values Ku and τON are estimated as 4 kJ/m3 and 1×10−9 s, respectively, for Resovist MNPs.
A beam-membrane structure micromachined differential pressure flow sensor
Authors: Chen P. , Zhao Y. L. , Tian B. , Li C. , Li Y. Y.
Published: April 2015

A beam-membrane structure micromachined flow sensor is designed, depending on the principle of differential pressure caused by the mass flow, which is directly proportional to the square flow rate. The FSI (fluid structure interaction) characteristics of the differential pressure flow sensor are investigated via numerical analysis and analog simulation. The working mechanism of the flow sensor is analyzed depending on the FSI results. Then, the flow sensor is fabricated and calibrated. The calibration results show that the beam-membrane structure differential pressure flow sensor achieves ideal static characteristics and works well in the practical applications.
Structure factor of a Gaussian chain confined between two parallel plates
Authors: Liao Yi , Miao Bing
Published: April 2015

We study the structure factor of a single Gaussian chain confined between two macroscopic parallel plates theoretically. The chain propagator is constructed in terms of the eigen-spectrum of the Laplace operator under the Dirichlet boundary condition enforced at the two plates, by which the confinement effect enters the treatment through size-dependent eigen-spectrum. In terms of the series expansion solution for the chain propagator, we first calculate the confinement free energy and the confinement force for an arbitrary confinement strength. It is found that the confinement force scales to the distance between the two confining surfaces with a power of −3 for strong confinements and of −2 for weak confinements. Based on the ground state dominance approximation for strong confinements and the Euler-Maclaurin formula for weak confinements, we develop approximation theories for the two limit situations, which agree with the numerical results well. We further calculate the structure factor of the confined Gaussian chain in this slit geometry. While the scattering function of the transverse chain fluctuations perpendicular to the confinement direction is still a Debye function form, the structure factor for the longitudinal fluctuations along the confinement dimension starts with the monotonic Debye function behavior for weak confinements and develops a decaying oscillation behavior with the increase of confinements. The numerical results for the structure factor are also interpreted by developing approximation theories in different confinement regimes. Finally, the orientational average of the anisotropic structure factor is performed and an analytic expression for the averaged structure factor is derived under the ground state dominance approximation for strong confinements.
(100)-Textured KNN-based thick film with enhanced piezoelectric property for intravascular ultrasound imaging
Authors: Zhu Benpeng , Zhang Zhiqiang , Ma Teng , Yang Xiaofei , Li Yongxiang , Shung K. Kirk , Zhou Qifa
Published: April 2015

Using tape-casting technology, 35 μm free-standing (100)-textured Li doped KNN (KNLN) thick film was prepared by employing NaNbO3 (NN) as template. It exhibited similar piezoelectric behavior to lead containing materials: a longitudinal piezoelectric coefficient (d33) of ∼150 pm/V and an electromechanical coupling coefficient (kt) of 0.44. Based on this thick film, a 52 MHz side-looking miniature transducer with a bandwidth of 61.5% at −6 dB was built for Intravascular ultrasound (IVUS) imaging. In comparison with 40 MHz PMN-PT single crystal transducer, the rabbit aorta image had better resolution and higher noise-to-signal ratio, indicating that lead-free (100)-textured KNLN thick film may be suitable for IVUS (>50 MHz) imaging.
Automated cell viability assessment using a microfluidics based portable imaging flow analyzer
Authors: Jagannadh Veerendra Kalyan , Adhikari Jayesh Vasudeva , Gorthi Sai Siva
Published: April 2015

In this work, we report a system-level integration of portable microscopy and microfluidics for the realization of optofluidic imaging flow analyzer with a throughput of 450 cells/s. With the use of a cellphone augmented with off-the-shelf optical components and custom designed microfluidics, we demonstrate a portable optofluidic imaging flow analyzer. A multiple microfluidic channel geometry was employed to demonstrate the enhancement of throughput in the context of low frame-rate imaging systems. Using the cell-phone based digital imaging flow analyzer, we have imaged yeast cells present in a suspension. By digitally processing the recorded videos of the flow stream on the cellphone, we demonstrated an automated cell viability assessment of the yeast cell population. In addition, we also demonstrate the suitability of the system for blood cell counting.
Filamentary resistance switching in phthalocyanine thin films observed by electroluminescence
Authors: Meng Qingyu , He Xiaochuan , Mao Qi , Weng Yuxiang , Yang Jianbing , Yan Donghang , Zhao Hongwu
Published: April 2015

Metal phthalocyanine heterojunctions with highly stable resistance switching characteristics have been prepared and the switching mechanism has been further investigated by electroluminescence (EL). The point-like EL emission has been observed during switching, demonstrating that the filamentary conduction gives rise to resistance switching. Furthermore, the high correlativity between EL emission sites and domain boundaries of phthalocyanine films has been established, which indicates that the switching process is favorable to occur within the disordered region of organic films. A band-based model has been proposed to describe the EL associated electrical switching mechanism.
The Nonvisual Illusion of Self-Touch: Misaligned Hands and Anatomical Implausibility
Authors: White Rebekah C , Weinberg Jennifer L , Davies Anne M Aimola
Published: April 2015

The self-touch illusion is elicited when the participant (with eyes closed) administers brushstrokes to a prosthetic hand while the examiner administers synchronous brushstrokes to the participant's other (receptive) hand. In three experiments we investigated the effects of misalignment on the self-touch illusion. In experiment 1 we manipulated alignment (0°, 45°, 90°, 135°, 180°) of the prosthetic hand relative to the participant's receptive hand. The illusion was equally strong at 0° and 45°: the two conditions in which the prosthetic hand was in an anatomically plausible orientation. To investigate whether the illusion was diminished at 90° (and beyond) by anatomical implausibility rather than by misalignment, in experiment 2 hand positioning was changed. The illusion was equally strong at 0°, 45°, and 90°, but diminished at 135° despite the prosthetic hand now being in an anatomically plausible orientation. Thus the illusion is diminished with misalignment of 135°, irrespective of anatomical plausibility. Having demonstrated that the illusion was equally strong with the hands aligned (0°) or misaligned by 45°, in experiment 3 we demonstrated that participants did not detect a 45° misalignment. Large degrees of misalignment prevent a compelling experience of the self-touch illusion, and the self-touch illusion prevents detection of small degrees of misalignment.
Theoretical Approaches to Lightness and Perception
Authors: Gilchrist Alan
Published: April 2015

Theories of lightness, like theories of perception in general, can be categorized as high-level, low-level, and mid-level. However, I will argue that in practice there are only two categories: one-stage mid-level theories, and two-stage low-high theories. Low-level theories usually include a high-level component and high-level theories include a low-level component, the distinction being mainly one of emphasis. Two-stage theories are the modern incarnation of the persistent sensation/perception dichotomy according to which an early experience of raw sensations, faithful to the proximal stimulus, is followed by a process of cognitive interpretation, typically based on past experience. Like phlogiston or the ether, raw sensations seem like they must exist, but there is no clear evidence for them. Proximal stimulus matches are postperceptual, not read off an early sensory stage. Visual angle matches are achieved by a cognitive process of flattening the visual world. Likewise, brightness (luminance) matches depend on a cognitive process of flattening the illumination. Brightness is not the input to lightness; brightness is slower than lightness. Evidence for an early (< 200 ms) mosaic stage is shaky. As for cognitive influences on perception, the many claims tend to fall apart upon close inspection of the evidence. Much of the evidence for the current revival of the ‘new look’ is probably better explained by (1) a natural desire of (some) subjects to please the experimenter, and (2) the ease of intuiting an experimental hypothesis. High-level theories of lightness are overkill. The visual system does not need to know the amount of illumination, merely which surfaces share the same illumination. This leaves mid-level theories derived from the gestalt school. Here the debate seems to revolve around layer models and framework models. Layer models fit our visual experience of a pattern of illumination projected onto a pattern of reflectance, while framework models provide a better account of illusions and failures of constancy. Evidence for and against these approaches is reviewed.
The effect of plant density in nickel-phytomining field experiments with Alyssum murale in Albania
Authors: Bani Aida , Echevarria Guillaume , Zhang Xin , Benizri Emile , Laubie Baptiste , Morel Jean Louis , Simonnot Marie-Odile
Published: April 2015

Ultramafic vertisols cover large areas in Albania and offer opportunities for phytomining. We undertook a field experiment with native Alyssum murale on two representative Vertisols at a distance of 20 km from each other (Pojskë and Domosdovë, Albania), to test the effect of planting density (transplanted seedlings) on a phytomining cropping system. Both areas were cleared in late summer 2012 and then ploughed and the soils were characterised. At Domosdovë, an area of 0.5 ha was planted with local native seedlings at a density of six plants per square metre in September 2012. Spontaneous plants that had germinated in Spring 2012 were left to grow without any competition from other plants on a second 0.1-ha plot at Domosdovë. All plots were weeded manually in the autumn of 2012 and spring of 2013. Individual plants occupied ~1 m2 at maturity. At Pojskë, an area of 0.3 ha was also planted in September 2012 with local native seedlings of A. murale at a density of four plants per square metre. Plants grown at initial densities of four and six plants per square metre did not fully cover the ground; gaps were filled in naturally by a second spontaneous generation of A. murale seedlings (recruits) that had germinated in Autumn 2012. Other weeds were eliminated with herbicides. At Domosdovë, at densities of one and six plants and at Pojskë of four plants per square metre, the biomass yield was 10, 5 and 10 t ha–1, respectively. Concentration of phytoextracted nickel was 77, 41 and 112 kg ha–1. We suggest that a density of four plants per square metre is suitable for phytoextraction with native populations of A. murale. A. murale can be a weed itself and lower the nickel phytoextraction yield. Plants responded differently in their native environment than in previous field trials in North America.
Interspecific competition between a non-native metal-hyperaccumulating plant (Noccaea caerulescens, Brassicaceae) and a native congener across a soil-metal gradient
Authors: Che-Castaldo Judy P. , Inouye David W.
Published: April 2015

Adaptive traits are hypothesised to incur fitness trade-offs, and a classical example is metal-tolerant plants that exhibit reduced competitive ability when grown on low-metal substrates. In the present study, we examined whether metal-hyperaccumulating plants exhibit a similar trade-off, by assessing competition across a soil-metal gradient in the context of phytoremediation. We studied the cadmium- and zinc-hyperaccumulator Noccaea caerulescens (J. Presl & C. Presl) F.K. Mey., which has been introduced to potential remediation sites contaminated with those metals, and the nickel- and zinc-hyperaccumulator Noccaea fendleri subsp. glauca (A. Nelson) Al-Shehbaz & M. Koch, which is native to our study sites. We performed a greenhouse experiment with a response-surface design to quantify their competitive interactions on higher- and lower-metal substrates from each of three mine sites. Overall competitive effects between the species were weak, but we did find evidence of competition on the substrates that supported the highest rates of plant growth and reproduction. Abiotic factors were more limiting than competitive interactions for both species, and both performed better on substrates containing higher zinc, lower cadmium and lower copper concentrations. A complementary field trial supported these findings. Our results also showed that substrates outside of contaminated mine tailings can still contain sufficiently high zinc concentrations to support N. caerulescens, suggesting that the use of these plants for phytoremediation should be monitored to prevent the unintentional establishment of non-native species.
Long-term cropping system studies support intensive and responsive cropping systems in the low-rainfall Australian Mallee
Authors: Whitbread A. M. , Davoren C. W. , Gupta V. V. S. R. , Llewellyn R. , Roget the late D.
Published: April 2015

Continuous-cropping systems based on no-till and crop residue retention have been widely adopted across the low-rainfall cereal belt in southern Australia in the last decade to manage climate risk and wind erosion. This paper reports on two long-term field experiments that were established in the late 1990s on texturally different soil types at a time of uncertainty about the profitability of continuous-cropping rotations in low-rainfall environments. Continuous-cereal systems significantly outyielded the traditional pasture–wheat systems in five of the 11 seasons at Waikerie (light-textured soil), resulting in a cumulative gross margin of AU$1600 ha–1 after the initial eight seasons, almost double that of the other treatments. All rotation systems at Kerribee (loam-textured soil) performed poorly, with only the 2003 season producing yields close to 3 t ha–1 and no profit achieved in the years 2004–08. For low-rainfall environments, the success of a higher input cropping system largely depends on the ability to offset the losses in poor seasons by capturing greater benefits from good seasons; therefore, strategies to manage climatic risk are paramount. Fallow efficiency, or the efficiency with which rainfall was stored during the period between crops, averaged 17% at Kerribee and 30% at Waikerie, also indicating that soil texture strongly influences soil evaporation. A ‘responsive’ strategy of continuous cereal with the occasional, high-value ‘break crop’ when seasonal conditions are optimal is considered superior to fixed or pasture–fallow rotations for controlling grass, disease or nutritional issues.
Culturally appropriate flipcharts improve the knowledge of common respiratory conditions among Northern Territory Indigenous families
Authors: Mckay Clare C. , Chang Anne B. , Versteegh Lesley A. , McCallum Gabrielle B.
Published: April 2015

Issue addressed

Flipcharts are widely used as education tools in Indigenous health but there is no published quantitative data on their use. As respiratory illness is the most frequent reason for hospitalisation of young children, we developed culturally sensitive flipcharts to educate carers of children on the 3 most common serious respiratory illness (bronchiolitis, pneumonia and bronchiectasis) affecting Indigenous children in the Northern Territory. In this study, we aimed to determine if use of these flipcharts improved the knowledge of these respiratory conditions among carers of Indigenous children admitted to the Royal Darwin Hospital.

Methods

We assessed the knowledge of 60 carers pre‐ and post‐flipchart education using a questionnaire. Pre‐ and postflipchart education scores for the three illnesses were combined and were compared using non‐parametric analyses.

Results

Most carers were mothers (n = 43, 72%) aged between 20–40 years (n = 54, 90%) and lived in a remote community (n = 53, 88%). Knowledge of all respiratory conditions improved post education: median scores pre = 8 (Interquartile range 6, 10); post = 12 (10, 14), P = <0.0001.

Conclusions

The use of culturally appropriate educational flipcharts improves the knowledge of respiratory conditions among carers of Indigenous children hospitalised with common serious respiratory illness.
Modular expression analysis reveals functional conservation between human Langerhans cells and mouse cross-priming dendritic cells
Authors: Artyomov Maxim N. , Munk Adiel , Gorvel Laurent , Korenfeld Daniel , Cella Marina , Tung Thomas , Klechevsky Eynav
Published: April 2015

Characterization of functionally distinct dendritic cell (DC) subsets in mice has fueled interest in whether analogous counterparts exist in humans. Transcriptional modules of coordinately expressed genes were used for defining shared functions between the species. Comparing modules derived from four human skin DC subsets and modules derived from the Immunological Genome Project database for all mouse DC subsets revealed that human Langerhans cells (LCs) and the mouse XCR1+CD8α+CD103+ DCs shared the class I–mediated antigen processing and cross-presentation transcriptional modules that were not seen in mouse LCs. Furthermore, human LCs were enriched in a transcriptional signature specific to the blood cross-presenting CD141/BDCA-3+ DCs, the proposed equivalent to mouse CD8α+ DCs. Consistent with our analysis, LCs were highly adept at inducing primary CTL responses. Thus, our study suggests that the function of LCs may not be conserved between mouse and human and supports human LCs as an especially relevant therapeutic target.
SIRT1 deacetylates RORγt and enhances Th17 cell generation
Authors: Lim Hyung W. , Kang Seung Goo , Ryu Jae Kyu , Schilling Birgit , Fei Mingjian , Lee Intelly S. , Kehasse Amanuel , Shirakawa Kotaro , Yokoyama Masaru , Schnölzer Martina , Kasler Herbert G. , Kwon Hye-Sook , Gibson Bradford W. , Sato Hironori , Akassoglou Katerina , Xiao Changchun , Littman Dan R. , Ott Melanie , Verdin Eric
Published: April 2015

The balance of effector and regulatory T cell function, dependent on multiple signals and epigenetic regulators, is critical to immune self-tolerance. Dysregulation of T helper 17 (Th17) effector cells is associated with multiple autoimmune diseases, including multiple sclerosis. Here, we report that Sirtuin 1 (SIRT1), a protein deacetylase previously reported to have an antiinflammatory function, in fact promotes autoimmunity by deacetylating RORγt, the signature transcription factor of Th17 cells. SIRT1 increases RORγt transcriptional activity, enhancing Th17 cell generation and function. Both T cell–specific Sirt1 deletion and treatment with pharmacologic SIRT1 inhibitors suppress Th17 differentiation and are protective in a mouse model of multiple sclerosis. Moreover, analysis of infiltrating cell populations during disease induction in mixed hematopoietic chimeras shows a marked bias against Sirt1-deficient Th17 cells. These findings reveal an unexpected proinflammatory role of SIRT1 and, importantly, support the possible therapeutic use of SIRT1 inhibitors against autoimmunity.
ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis
Authors: Moguche Albanus O. , Shafiani Shahin , Clemons Corey , Larson Ryan P. , Dinh Crystal , Higdon Lauren E. , Cambier C.J. , Sissons James R. , Gallegos Alena M. , Fink Pamela J. , Urdahl Kevin B.
Published: April 2015

Immune control of persistent infection with Mycobacterium tuberculosis (Mtb) requires a sustained pathogen-specific CD4 T cell response; however, the molecular pathways governing the generation and maintenance of Mtb protective CD4 T cells are poorly understood. Using MHCII tetramers, we show that Mtb-specific CD4 T cells are subject to ongoing antigenic stimulation. Despite this chronic stimulation, a subset of PD-1+ cells is maintained within the lung parenchyma during tuberculosis (TB). When transferred into uninfected animals, these cells persist, mount a robust recall response, and provide superior protection to Mtb rechallenge when compared to terminally differentiated Th1 cells that reside preferentially in the lung-associated vasculature. The PD-1+ cells share features with memory CD4 T cells in that their generation and maintenance requires intrinsic Bcl6 and intrinsic ICOS expression. Thus, the molecular pathways required to maintain Mtb-specific CD4 T cells during ongoing infection are similar to those that maintain memory CD4 T cells in scenarios of antigen deprivation. These results suggest that vaccination strategies targeting the ICOS and Bcl6 pathways in CD4 T cells may provide new avenues to prevent TB.
Association between Maturation and Aging and Pulmonary Responses in Animal Models of Lung Injury
Authors: Schouten Laura R. A. , Schultz Marcus J. , van Kaam Anton H. , Juffermans Nicole P. , Bos Albert P. , Wösten-van Asperen Roelie M.
Published: April 2015

AbstractAbstract

An investigation of the literature documents that the inflammatory response to injury is exaggerated in aged animals, and there is more edema and alveolar damage and a higher mortality.

Background:

Advanced age is associated with an increased susceptibility and mortality of the acute respiratory distress syndrome. This may be due to the progressive changes in innate immune responses and intrinsic properties of the lung that occur during the process of aging. Therefore, this study assesses the association between maturation and aging and pulmonary responses to injury in animal models of lung injury.

Methods:

A systematic search was conducted in PubMed, EMBASE (up to June 2014) and in the references of relevant articles to identify the studies using in vivo models of lung injury caused by an acute pulmonary insult, in which at least two age groups were compared. Because methodological diversity precluded combining these studies in a quantitative meta-analysis, data are presented based on the qualitative comparison with the adult group.

Results:

Of the 2,840 identified studies, 51 were included in this review. Most studies showed that, in response to a pulmonary insult, increasing age is associated with more pulmonary inflammation, edema, alveolar damage, and higher mortality. In addition, results indicate the existence of age-dependent changes in key components of the intracellular signaling pathways involved in the inflammatory response.

Conclusions:

Increasing age seems to be correlated with exaggerated pulmonary responses to injury, ultimately leading to more severe lung injury. Pulmonary inflammation seems relatively suppressed in infants/juveniles, whereas in the middle aged/elderly, the inflammatory response seems delayed but aggravated. This implies that investigators and clinicians need to use caution about extrapolating results from adolescent or youngadult animals to pediatric or elderly patients in clinical practice.
Ketamine—A Narrative Review of Its Uses in Medicine
Authors: Radvansky Brian M. , Puri Shawn , Sifonios Anthony N. , Eloy Jean D. , Le Vanny
Published: April 2015

One of the most fascinating drugs in the anesthesiologist's armament is ketamine, an N-methyl-D-aspartate receptor antagonist with a myriad of uses. The drug is a dissociative anesthetic and has been used more often as an analgesic in numerous hospital units, outpatient pain clinics, and in the prehospital realm. It has been used to treat postoperative pain, chronic pain, complex regional pain syndrome, phantom limb pain, and other neuropathic conditions requiring analgesia. Research has also demonstrated its efficacy as an adjunct in psychotherapy, as a treatment for both depression and posttraumatic stress disorder, as a procedural sedative, and as a treatment for respiratory and neurologic conditions. Ketamine is not without its adverse effects, some of which can be mitigated with certain efforts. Such effects make it necessary for the clinician to use the drug only in situations where it will provide the greatest benefit with the fewest adverse effects. To the best of our knowledge, none of the reviews regarding ketamine have taken a comprehensive look at the drug's uses in all territories of medicine. This review will serve to touch on its chemical data, pharmacokinetics and pharmacodynamics, medical uses, and adverse effects while focusing specifically on the drugs usage in anesthesia and analgesia.
Comparison Between Sequential Therapy and Modified Bismuth-Included Quadruple Therapy for Helicobacter pylori Eradication in Chinese Patients
Authors: Yang Xiuhong , Tan Pengsheng , Song Lianying , Lu Zhanying
Published: April 2015

To compare the efficacy and safety of sequential therapy and modified bismuth-included quadruple therapy as a first-line Helicobacter pylori eradication in China. The patients were randomized to receive sequential therapy [n = 90; rabeprazole (20 mg twice daily) and amoxicillin (1 g twice daily) for 5 days, followed by rabeprazole (20 mg twice daily), tinidazole (500 mg twice daily) plus clarithromycin (500 mg twice daily) for another 5 days] or modified bismuth-included quadruple therapy [n = 109; rabeprazole (20 mg twice daily), levofloxacin hydrochloride (400 mg twice daily), clarithromycin (500 mg twice daily), and colloidal bismuth pectin (200 mg 3 times a day) for 7 days]. A follow-up urea breath test was applied 4 weeks later. A total of 199 patients were diagnosed with H. pylori infection. The intention-to-treat and per-protocol (PP) eradication rates were 91.7% and 92.6%, respectively, in the modified bismuth-included quadruple therapy group, and 74.4% and 76.1%, respectively, in the sequential therapy group. The eradication rates were significantly higher in the modified bismuth-included quadruple therapy group, compared with the sequential therapy group (P = 0.001 for intention to treat and P = 0.001 for PP). Adverse effects were reported by patients from both groups, but the difference did not reach significant level (P = 0.280). The modified bismuth-included quadruple therapy seemed to be superior to the sequential therapy as the first-line regimen for H. pylori eradication in Chinese patients.