bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-neoplastic action of aspirin against a T-cell lymphoma involves an alteration in the tumour microenvironment and regulation of tumour cell survival
Authors: Kumar Anjani , Vishvakarma Naveen Kumar , Tyagi Abhishek , Bharti Alok Chandra , Singh Sukh Mahendra
Published: July 2011

The present study explores the potential of the anti-neoplastic action of aspirin in a transplantable murine tumour model of a spontaneously originated T-cell lymphoma designated as Dalton's lymphoma. The antitumour action of aspirin administered to tumour-bearing mice through oral and/or intraperitoneal (intratumoral) routes was measured via estimation of survival of tumour-bearing mice, tumour cell viability, tumour progression and changes in the tumour microenvironment. Intratumour administration of aspirin examined to assess its therapeutic potential resulted in retardation of tumour progression in tumour-bearing mice. Oral administration of aspirin to mice as a prophylactic measure prior to tumour transplantation further primed the anti-neoplastic action of aspirin administered at the tumour site. The anti-neoplastic action of aspirin was associated with a decline in tumour cell survival, augmented induction of apoptosis and nuclear shrinkage. Tumour cells of aspirin-treated mice were found arrested in G0/G1 phase of the cell cycle and showed nuclear localization of cyclin B1. Intratumoral administration of aspirin was accompanied by alterations in the biophysical, biochemical and immunological composition of the tumour microenvironment with respect to pH, level of dissolved O2, glucose, lactate, nitric oxide, IFNγ (interferon γ), IL-4 (interleukin-4), IL-6 and IL-10, whereas the TGF-β (tumour growth factor-β) level was unaltered. Tumour cells obtained from aspirin-treated tumour-bearing mice demonstrated an altered expression of pH regulators monocarboxylate transporter-1 and V-ATPase along with alteration in the level of cell survival regulatory molecules such as survivin, vascular endothelial growth factor, heat-shock protein 70, glucose transporter-1, SOCS-5 (suppressor of cytokine signalling-5), HIF-1α (hypoxia-inducible factor-1α) and PUMA (p53 up-regulated modulator of apoptosis). The study demonstrates a possible indirect involvement of the tumour microenvironment in addition to a direct but limited anti-neoplastic action of aspirin in the retardation of tumour growth.
Radiosensitization in human breast carcinoma cells by thymoquinone: role of cell cycle and apoptosis
Authors: Velho‐Pereira Reelma , Kumar Amit , Pandey Badri N. , Jagtap Aarti G. , Mishra Kaushala P.
Published: July 2011

TQ (thymoquinone), the bioactive constituent of black seed (Nigella sativa), has been shown to inhibit the growth of various human cancers both in vitro and in vivo. This study reports the radiosensitizing effect of TQ on human breast carcinoma cells (MCF7 and T47D). TQ in combination with single dose of ionizing radiation (2.5 Gy) was found to exert supra‐additive cytotoxic effects on both the carcinomas as measured by cell proliferation and colony‐formation assays. Annexin V binding and FACS analysis revealed the role of enhanced apoptosis and cell cycle modulation in the mechanism of TQ‐mediated radiosensitization, thus supporting TQ as an adjuvant for preclinical testing in cancer chemo‐radiotherapy.
Curvature factor and membrane solubilization, with particular reference to membrane rafts
Authors: Mrówczyńska Lucyna , Salzer Ulrich , Iglič Aleš , Hägerstrand Henry
Published: July 2011

The composition of membrane rafts (cholesterol/sphingolipid‐rich domains) cannot be fully deduced from the analysis of a detergent‐resistant membrane fraction after solubilization in Triton X‐100 at 4°C. It is hypothesized that the membrane curvature‐dependent lateral distribution of membrane components affects their solubilization. The stomatocytogenic, Triton X‐100, cannot effectively solubilize membrane components, especially with regard to the outward membrane curvature.
Plasma proprotein convertase subtilisin kexin type 9 is a heritable trait of familial combined hyperlipidaemia
Authors: Brouwers Martijn C.G.J. , van Greevenbroek Marleen M.J. , Troutt Jason S. , Bonner Freeman Angela , Lu Ake , Schaper Nicolaas C. , Konrad Robert J. , Stehouwer Coen D.A.
Published: July 2011

The aim of the present study was to investigate the relationship between circulating PCSK9 (proprotein convertase subtilisin kexin type 9) and FCHL (familial combined hyperlipidaemia) and, when positive, to determine the strength of its heritability. Plasma PCSK9 levels were measured in FCHL patients (n=45), NL (normolipidaemic) relatives (n=139) and their spouses (n=72). In addition, 11 FCHL patients were treated with atorvastatin to study the response in PCSK9 levels. PCSK9 levels were higher in FCHL patients compared with NL relatives and spouses: 96.1 compared with 78.7 and 82.0 ng/ml (P=0.004 and P=0.002 respectively). PCSK9 was significantly associated with both TAG (triacylglycerol) and apolipoprotein B levels (P<0.001). The latter relationship was accounted for by LDL (low-density lipoprotein)–apolipoprotein B (r=0.31, P=0.02), not by VLDL (very-low-density lipoprotein)–apolipoprotein B (r=0.09, P=0.49) in a subgroup of subjects (n=59). Heritability calculations for PCSK9 using SOLAR and FCOR software yielded estimates of 67–84% respectively (P<0.0001). PCSK9 increased from 122 to 150 ng/ml in 11 FCHL patients treated with atorvastatin (40 mg) once daily for 8 weeks (P=0.018). In conclusion, plasma PCSK9 is a heritable trait associated with both FCHL diagnostic hallmarks. These results, combined with the significant rise in PCSK9 levels after statin therapy, warrant further studies in order to unravel the exact role of PCSK9 in the pathogenesis and treatment of this highly prevalent genetic dyslipidaemia.
Acute simvastatin increases endothelial nitric oxide synthase phosphorylation via AMP-activated protein kinase and reduces contractility of isolated rat mesenteric resistance arteries
Authors: Rossoni Luciana V. , Wareing Mark , Wenceslau Camilla F. , Al-Abri Mahmood , Cobb Chris , Austin Clare
Published: July 2011

Statins can have beneficial cholesterol-independent effects on vascular contractility, which may involve increases in the bioavailability of NO (nitric oxide) as a result of phosphorylation of eNOS (endothelial NO synthase). Although this has been attributed to phosphorylation of Akt (also known as protein kinase B), studies in cultured cells have shown that statins can phosphorylate AMPK (AMP-activated protein kinase); it is unknown whether this has functional effects in intact arteries. Thus we investigated the acute effects of simvastatin on resistance arterial contractile function, evaluating the involvement of NO, Akt and AMPK. Isolated rat mesenteric resistance arteries were mounted on a wire myograph. The effects of incubation (1 and 2 h) with simvastatin (0.1 or 1 μM) on contractile responses were examined in the presence and absence of L-NNA (N-nitro-L-arginine; 10 μM) or mevalonate (1 mM). Effects on eNOS, phospho-eNOS (Ser1177), and total and phospho-Akt and -AMPK protein expression were investigated using Western blotting. The effect of AMPK inhibition (compound C, 10 μM) on eNOS phosphorylation and contractile responses were also studied. Simvastatin (1 μM, 2 h) significantly reduced constriction to U46619 and phenylephrine and enhanced dilations to ACh (acetylcholine) in depolarized, but not in U46619-pre-constricted arteries. These effects were completely and partially prevented by L-NNA and mevalonate respectively. Simvastatin increased eNOS and AMPKα phosphorylation, but had no effect on Akt protein expression and phosphorylation after 2 h incubation. Compound C prevented the effects of simvastatin on eNOS phosphorylation and contractility. Thus simvastain can acutely modulate resistance arterial contractile function via mechanisms that involve the AMPK/phospho-eNOS (Ser1177)/NO-dependent pathway.
Dynamic response of a turbulent cylinder wake to sinusoidal inflow perturbations across the vortex lock-on range
Authors: Konstantinidis Efstathios , Liang Chunlei
Published: July 2011

Large-eddy simulations are employed to investigate the dynamic response of the turbulent wake of a circular cylinder to sinusoidal perturbations in the inflow velocity superposed on a mean component. The perturbation frequency is varied across the vortex lock-on range at a constant amplitude of 5% of the mean velocity corresponding to a Reynolds number of 2580. The effect on the instantaneous, time-averaged and phase-averaged characteristics of the near-wake flow and fluid forces on the cylinder is reported. Comparisons of the present simulations to experimental realizations show that the physics of the unsteady three-dimensional separated flow are well reproduced. The simulations capture the modification of the wake structure including the shrinking of the recirculation bubble and vortex-formation region and the enhancement of the wake fluctuations and vortex strength in the lock-on regime. These wake effects are accompanied by an increase in the steady and unsteady drag and the unsteady lift acting on the cylinder. An empirical formula for the amplification of the mean drag coefficient due to inflow perturbations and equivalent oscillations of the cylinder in a steady flow is provided from compilation of available data. Particular attention is given to the change in the timing of vortex shedding with respect to the imposed perturbation across the lock-on range in order to reveal the link between the vortex dynamics and the fluid-induced forces on the cylinder. It is shown that the phase at which vortices are shed from the cylinder shifts monotonically as a function of the perturbation frequency resulting in corresponding changes in the phase of the unsteady forces. It is further shown that the phase of the lift is directly linked to that of vortex shedding but the phase of the drag is biased by inertial forces due to added mass and induced pressure waves. Decomposition of the total in-line force to inviscid “potential-flow” and viscous “vortex-drag” components indicates that the latter exhibits a behavior which is not physically consistent. The stochastic character of vortex synchronization in turbulent wakes and the implications of the present findings for vortex-induced free in-line vibrations are also discussed.
Secondary electron dopant contrast imaging of compound semiconductor junctions
Authors: Chung Suk , Wheeler Virginia , Myers-Ward Rachael , Nyakiti Luke O. , Eddy Charles R. , Gaskill D. Kurt , Skowronski Marek , Picard Yoosuf N.
Published: July 2011

Secondary electron imaging combined with immersion lens and through-the-lens detection has been used to analyze various semiconductor junctions. Dopant contrast imaging was applied for multi-doped 4H–SiC, growth-interrupted n+/p and n/n+ homoepitaxial interfaces, and an AlGaAs/GaAs p-n junction light-emitting diode structure. Dopant contrast was explained by the local variation in secondary electron escape energies resulting from the built-in potential difference. The effect of varying electron affinity on contrast for the heterostructures is also discussed. The contrast profile of the n-doped AlGaAs compared reasonably well to the simulated valence bandedge energy using a previously determined efficiency of dopant ionization.
Spectroscopic identification of reactive porphyrin motions
Authors: Barabanschikov Alexander , Demidov Alexander , Kubo Minoru , Champion Paul M. , Sage J. Timothy , Zhao Jiyong , Sturhahn Wolfgang , Alp E. Ercan
Published: July 2011

Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, 57Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.
Electrical characterization of (Ni/Au)/Al0.25Ga0.75N/GaN/SiC Schottky barrier diode
Authors: Saadaoui Salah , Mongi Ben Salem Mohamed , Gassoumi Malek , Maaref Hassen , Gaquière Christophe
Published: July 2011

In this work we report on the characteristics of a (Ni/Au)/AlGaN/GaN/SiC Schottky barrier diode (SBD). A variety of electrical techniques, such as gate current-voltage (I-V), capacitance-voltage (C-V), and deep level transient spectroscopy (DLTS) measurements have been used to characterize the diode. The behavior study of the series resistance, RS, the ideality factor, n, the effective barrier height, Φb, and the leakage current with the temperature have emphasized an inhomogeneity of the barrier height and a tunneling mechanism assisted by traps in the SBD. Hence, C-V measurements successively sweeping up and down the voltage have demonstrate a hysteresis phenomenon which is more pronounced in the temperature range of 240 to 320 K, with a maximum at ∼300 K. This parasitic effect can be attributed to the presence of traps activated at the same range of temperature in the SBD. Using the DLTS technique, we have detected one hole trap having an activation energy and a capture cross-section of 0.75 eV and 1.09 × 10−13cm2, respectively, seems to be responsible for the appearance of the hysteresis phenomenon.
Prediction of a superconductive superhard material: Diamond-like BC7
Authors: Xu Lifang , Zhao Zhisheng , Wang Qianqian , Wang Li-Min , Xu Bo , He Julong , Tian Yongjun
Published: July 2011

Through particle swarm optimization algorithm and first-principles structural optimizations, we have predicted two novel low-energy structures of BC7: graphite-like Amm2 structure and diamond-like P-4m2 structure. Structural stability of the proposed BC7 polymorphs was confirmed by calculating the elastic constants and phonon frequencies. Phase transition pressure from Amm2 to P-4m2 was determined to be at 2.2 GPa. Calculations for the electronic band structures demonstrated hole-type conductivity of the two novel phases. Ideal tensile strength along the 〈001〉 direction for the diamond-like BC7 was 155.2 GPa, which was approximately 52% higher than that of the recently predicted diamond-like BC5. Theoretical Vickers hardness of the diamond-like BC7 was 78.0 GPa, indicating that it is a superhard material. Electron-phonon coupling calculations revealed that diamond-like BC7 was superconducting with a critical temperature of ∼11.4 K.
A comparison of emissive probe techniques for electric potential measurements in a complex plasma
Authors: Sheehan J. P. , Raitses Y. , Hershkowitz N. , Kaganovich I. , Fisch N. J.
Published: July 2011

The major emissive probe techniques are compared to better understand the floating potential of an electron emitting surface in a plasma. An overview of the separation point technique, floating point technique, and inflection point in the limit of zero emission technique is given, addressing how each method works as well as the theoretical basis and limitations of each. It is shown that while the floating point method is the most popular, it is expected to yield a value ∼1.5Te/e below the plasma potential due to a virtual cathode forming around the probe. The theoretical predictions were checked with experiments performed in a 2 kW annular Hall thruster plasma (ne ∼ 109−1010 cm−3and Te ∼ 10−50 eV). The authors find that the floating point method gives a value around 2Te/e below the inflection point method, which is shown to be a more accurate emissive probe technique than other techniques used in this work for measurements of the plasma potential.
Non-Gaussian properties of global momentum and particle fluxes in a cylindrical laboratory plasma
Authors: Nagashima Yoshihiko , Itoh Sanae -I. , Inagaki Shigeru , Arakawa Hiroyuki , Kasuya Naohiro , Fujisawa Akihide , Kamataki Kunihiro , Yamada Takuma , Shinohara Shunjiro , Oldenbürger Stella , Yagi Masatoshi , Takase Yuichi , Diamond Patrick H. , Itoh Kimitaka
Published: July 2011

Non-Gaussian statistical properties of the azimuthally averaged momentum and particle fluxes driven by turbulence have been simultaneously observed in inhomogeneous magnetized plasmas for the first time. We identified the stretched Gaussian distribution of the both fluxes and the transition from the point-wise distribution to averaged ones was confirmed. The change of the particle flux precedes that of the momentum flux, demonstrating that the momentum flux is induced by the relaxation of density gradient.
Energy measurement in nonlinearly coupled nanomechanical modes
Authors: Gaidarzhy Alexei , Dorignac Jérôme , Zolfagharkhani Guiti , Imboden Matthias , Mohanty Pritiraj
Published: July 2011

We report direct measurements of average vibration energy in a high frequency flexural resonance mode achieved via an-harmonic elastic coupling to a fundamental vibration mode of a nanomechanical resonator. The second order coupling effect produces a frequency shift of the read-out mode as a function of the mean square of the excitation amplitude of the high order mode. We measure frequency shifts at the lowest driving amplitudes, down to the noise floor of the experimental setup. With implementation of existing ultra-sensitive amplifiers, the reported technique will enable direct measurements of quantized energy transitions in low-thermal occupation number nanomechanical resonators.
Similarity solutions of a class of perturbative Fokker-Planck equation
Authors: Lin Wen-Tsan , Ho Choon-Lin
Published: July 2011

In a previous work, a perturbative approach to a class of Fokker-Planck equations, which have constant diffusion coefficients and small time-dependent drift coefficients, was developed by exploiting the close connection between the Fokker-Planck equations and the Schrödinger equations. In this work, we further explore the possibility of similarity solutions of such a class of Fokker-Planck equations. These solutions possess definite scaling behaviors and are obtained by means of the so-called similarity method.
Charge transport in various dimensions of small networks composed of gold nanoparticles and terthiophene wire-molecules
Authors: Noguchi Yutaka , Terui Toshifumi , Katayama Takuya , Matsushita Michio M. , Sugawara Tadashi
Published: July 2011

We report the charge transport properties of networks composed of several to tens of gold nanoparticles (GNPs) linked by dithiolated terthiophene (3T) molecules. A large activation energy was observed for the conductance of networks with lesser dimensions. This bahavior is explained in terms of the charging energy of the GNPs in the current path. The Efros-Shklovskii variable range hopping model [A. L. Efros and B. I. Shklovskii, J. Phys. C 8, L49 (1975)] qualitatively describes the transport properties, where the dimensionality of the network and the small tunneling resistance of 3T serve as important factors.
Free volume holes diffusion to describe physical aging in poly(mehtyl methacrylate)/silica nanocomposites
Authors: Cangialosi Daniele , Boucher Virginie M. , Alegría A. , Colmenero J.
Published: July 2011

The spontaneous thermodynamically driven densification, the so-called physical aging, of glassy poly(mehtyl methacrylate) (PMMA) and its nanocomposites with silica has been described by means of the free volume holes diffusion model. This mechanism is able to account for the partial decoupling between physical aging and segmental dynamics of PMMA in nancomposites. The former has been found to be accelerated in PMMA/silica nanocomposites in comparison to “bulk” PMMA, whereas no difference between the segmental dynamics of bulk PMMA and that of the same polymer in nanocomposites has been observed. Thus, the rate of physical aging also depends on the amount of interface polymer/nanoparticles, where free volume holes disappear after diffusing through the polymer matrix. The free volume holes diffusion model is able to nicely capture the phenomenology of the physical aging process with a structure dependent diffusion coefficient.
Edge effect on band gap shift in Si nanowires with polygonal cross-sections
Authors: Zhu Ziming , Zhang Ai , Ouyang Gang , Yang Guowei
Published: July 2011

The strain-dependent band gap shift of Si nanowires (SiNWs) induced by the edge effect has been investigated by taking into account the shell-core configurations. It was found that the geometry of SiNWs plays the dominant effect for their band structures due to the appearance of strain in the self-equilibrium state. Theoretical analyses demonstrated that the derived relation is applicable for the band gap shift of SiNWs with polygonal cross-sections. The results were validated by compared them with the available evidences, implying that the developed method is helpful for clarifying physical mechanisms on tunable optical-electronics properties of semiconductor nanostructures.
Note: Achieving quasi-hydrostatic conditions in large-volume toroidal anvils for neutron scattering to pressures of up to 18 GPa
Authors: Bull C. L. , Bocian A. , Hamidov H. , Kamenev K. V. , Nelmes R. J. , Loveday J. S.
Published: July 2011

We present developments that allow neutron-scattering experiments to be performed, with both single-crystal and powder samples, under quasi-hydrostatic conditions to pressures beyond previous limits. Samples of sodium chloride and squaric acid (H2C4O4) have been loaded with argon as the pressure-transmitting medium in encapsulated gaskets redesigned for double-toroidal anvils, using a gas-loading method at ambient temperature. These samples have been compressed up to 18 GPa in a Paris-Edinburgh press, and no evidence of peak broadening in either the single-crystal or the powder experiments was observed.
Ultracold Bose gases deviate from the textbook picture
Authors: Miller Johanna L.
Published: July 2011

Interactions among identical bosons remove the upper bound on the number of particles in excited states.
Current-driven magnetic domain walls gather speed
Authors: Smart Ashley G.
Published: July 2011

The key, according to new experiments, is to house the walls in a sandwich of platinum, cobalt,and aluminum oxide.
Scientists help make deserts into solar-energy hubs
Authors: Feder Toni
Published: July 2011

Enthusiasm is high for collecting solar energy in the Middle East and North Africa, with some to be exported to Europe. But doing so requires overcoming political, social, legal, technical, and financial obstacles.
Europe to invest billions in multinational science initiatives
Authors: Feder Toni
Published: July 2011

Coordinating fragmented efforts in selected research areas is expected to provide a strong basis for future technological innovation, economic growth, and other benefits for society.
Developing-world academy of sciences has new leader
Authors: Matthews Jermey N. A.
Published: July 2011

The mathematical physicist looks to increase the number of PhD scientists in economically challenged countries.
Supercomputing has a future in clean energy
Authors: Kramer David
Published: July 2011

As national laboratories tout their high-performance computing for energy applications, the path to more powerful computers may be blocked by prohibitive electricity requirements.
Magnetic dynamos in the lab
Authors: Lathrop Daniel P. , Forest Cary B.
Published: July 2011

There is as yet no predictive theory of planetary or astrophysical dynamos. But theorists, numerical modelers, and experimenters are on the case.
Velar and dental stop consonant softening in Romance
Authors: Recasens Daniel
Published: July 2011

Experimental and descriptive evidence from the Romance languages suggests that velar and dental stop consonant softening, i.e., the process by which stops of these places of articulation turn mostly into palatoalveolar or alveolar affricates or fricatives, has proceeded gradually through intermediate (alveolo)palatal stop realizations. Several arguments are adduced in support of this interpretation: the presence of (alveolo)palatal stops and of (alveolo)palatal consonants of other manners of articulation in Romance languages and dialects, whether through gestural blending, gestural strengthening or other production strategies; alternations between (alveolo)palatal stops and affricates in several dialectal areas; variability in closure location for (alveolo)palatal stops in general, which accounts for their confusion with dental or velar stops; experimental evidence from speech production and perception studies. Moreover, there appears to be a plausible relationship between (alveolo)palatal stop realizations differing in closure fronting, and differences in fronting in the affricate and fricative outcomes of original Latin dental and velar stops. Historically, those differences depend mainly on place of articulation and voicing for the original stop as well as on the contextual and position conditions in which the stop occurred. The present investigation reveals that fine articulatory detail needs to be taken into consideration in the formulation of phonetic explanations of sound change.
Interdiscursivity between political and religious discourses in a speech by Sadat
Authors: Abdul-Latif Emad
Published: July 2011

Religion and politics have a complicated relationship in the Arab world. Interdiscursivity within political speeches between religious and political discourses is a manifestation of this complexity. This article argues that this sort of interdiscursivity imposes hard restrictions on the responses of Muslim addressees. Muslims’ responses to Islamic sacred texts are inherently restricted because disagreement with divine texts amounts to heresy. Accordingly, their responses to political speeches that present themselves as semi-religious texts are highly restricted as well. I will analyze a speech by the late Egyptian president Sadat to show how potential and actual responses could be controlled by creating intertextual links with the Qur’an and adopting the genre of Islamic religious sermons. I combine analytical tools from critical discourse analysis and what I refer to as “addressee rhetoric” to investigate the relationship between interdiscursivity and addressee response.
False dichotomies of disability politics
Authors: Grue Jan
Published: July 2011

This article discusses the relationship between the social and medical models of disability and between the academic and NGO communities in that field. Interviews with professionals from Norwegian disability NGOs show that while they share some of the political goals of the social model, they have a somewhat narrow understanding of the model’s critical potential. A false dichotomy has emerged in NGO discourse: The medical model, which originated as a negative construct within the social model, is reinterpreted as a legitimate conceptual alternative. This hinders dialogue between academe and the NGO community, and hampers the critical potential of the NGOs. In order to eliminate the dichotomy, it is necessary to develop the social model more extensively in discourse contexts outside the academic field.
Simulating CALUMA (CAssino Low‐Cost hUMAnoid) Robot Carrying a Load
Authors: Nava Rodriguez Nestor Eduardo , Carbone Giuseppe , Ceccarelli Marco
Published: July 2011

In this paper, the operation of CALUMA (CAssino Low‐cost hUMAnoid) robot has been investigated for a task while carrying a load. CALUMA robot is the result of a design project that has been elaborated for designing and building a low‐cost easy‐operation humanoid robot by summarizing experiences and prototypes that have been developed at LARM. Dynamic simulations have been computed by using ADAMS software in order to study dynamical aspects of CALUMA operation while carrying a load. The dynamic simulations have also been used for studying the manipulation performance of CALUMA robot. Simulations have given results that confirm the feasibility of the proposed design, as shown in the reported examples.
Minimizing Human Intervention in the Development of Basal Ganglia‐Inspired Robot Control
Authors: Montes-Gonzalez F. , Prescott T. J. , Negrete-Martinez J.
Published: July 2011

A biologically inspired mechanism for robot action selection, based on the vertebrate basal ganglia, has been previously presented (Prescott et al. 2006, Montes Gonzalez et al. 2000). In this model the task confronting the robot is decomposed into distinct behavioural modules that integrate information from multiple sensors and internal state to form ‘salience’ signals. These signals are provided as inputs to a computational model of the basal ganglia whose intrinsic processes cause the selection by disinhibition of a winning behaviour. This winner is then allowed access to the motor plant whilst losing behaviours are suppressed. In previous research we have focused on the development of this biomimetic selection architecture, and have therefore used behavioural modules that were hand‐coded as algorithmic procedures. In the current article, we demonstrate the use of genetic algorithms and gradient–descent learning to automatically generate/tune some of the modules that generate the model behaviour.
3D Image Modelling and Specific Treatments in Orthodontics Domain
Authors: Goularas Dionysis , Djemal Khalifa , Mannoussakis Yannis
Published: July 2011

In this article, we present a 3D specific dental plaster treatment system for orthodontics. From computer tomography scanner images, we propose first a 3D image modelling and reconstruction method of the Mandible and Maxillary based on an adaptive triangulation allowing management of contours meant for the complex topologies. Secondly, we present two specific treatment methods directly achieved on obtained 3D model allowing the automatic correction for the setting in occlusion of the Mandible and the Maxillary, and the teeth segmentation allowing more specific dental examinations. Finally, these specific treatments are presented via a client/server application with the aim of allowing a telediagnosis and treatment.
Influence of lower leg muscle fatigue on the centre of pressure in a static upright posture
Authors: Noda Masahiro , Demura Shin‐Ichi
Published: July 2011

We examined the influence of fatigue in the lower leg muscles on the centre of pressure sway during a static upright posture. Twelve healthy young men and women completed the exercise stress test on the triceps surae muscle and continued the exercise until their muscles were fatigued. A centre of pressure sway of 1 min was carried out in a Romberg posture at rest and at different instants after fatiguing exercise: immediately after, 5 min after, and 10 min after exercise. Blood lactate concentration was measured from fingertip samples taken before and immediately after exercise. To evaluate body sway, the following four centre of pressure sway factors were selected: unit time sway, front–back sway, left–right sway, and high‐frequency band power spectrum. The measurement device used was an Anima stabilometer (G5500). The data sampling frequency was 20 Hz. After exercise, blood lactate concentration was increased. Significant differences were observed in unit time sway, front–back sway, and high‐frequency band power spectrum immediately after exercise. These values eventually returned to baseline levels 5 min after fatiguing exercise.
TotalReCaller: improved accuracy and performance via integrated alignment and base-calling
Authors: Menges Fabian , Narzisi Giuseppe , Mishra Bud
Published: July 2011

Motivation: Currently, re-sequencing approaches use multiple modules serially to interpret raw sequencing data from next-generation sequencing platforms, while remaining oblivious to the genomic information until the final alignment step. Such approaches fail to exploit the full information from both raw sequencing data and the reference genome that can yield better quality sequence reads, SNP-calls, variant detection, as well as an alignment at the best possible location in the reference genome. Thus, there is a need for novel reference-guided bioinformatics algorithms for interpreting analog signals representing sequences of the bases ({A, C, G, T}), while simultaneously aligning possible sequence reads to a source reference genome whenever available.

Results: Here, we propose a new base-calling algorithm, TotalReCaller, to achieve improved performance. A linear error model for the raw intensity data and Burrows–Wheeler transform (BWT) based alignment are combined utilizing a Bayesian score function, which is then globally optimized over all possible genomic locations using an efficient branch-and-bound approach. The algorithm has been implemented in soft- and hardware [field-programmable gate array (FPGA)] to achieve real-time performance. Empirical results on real high-throughput Illumina data were used to evaluate TotalReCaller's performance relative to its peers—Bustard, BayesCall, Ibis and Rolexa—based on several criteria, particularly those important in clinical and scientific applications. Namely, it was evaluated for (i) its base-calling speed and throughput, (ii) its read accuracy and (iii) its specificity and sensitivity in variant calling.

Availability: A software implementation of TotalReCaller as well as additional information, is available at: http://bioinformatics.nyu.edu/wordpress/projects/totalrecaller/

Contact:  fabian.menges@nyu.edu
Tissue-specific prediction of directly regulated genes
Authors: McLeay Robert C. , Leat Chris J. , Bailey Timothy L.
Published: July 2011

Direct binding by a transcription factor (TF) to the proximal promoter of a gene is a strong evidence that the TF regulates the gene. Assaying the genome-wide binding of every TF in every cell type and condition is currently impractical. Histone modifications correlate with tissue/cell/condition-specific (‘tissue specific’) TF binding, so histone ChIP-seq data can be combined with traditional position weight matrix (PWM) methods to make tissue-specific predictions of TF–promoter interactions.

Results: We use supervised learning to train a naïve Bayes predictor of TF–promoter binding. The predictor's features are the histone modification levels and a PWM-based score for the promoter. Training and testing uses sets of promoters labeled using TF ChIP-seq data, and we use cross-validation on 23 such datasets to measure the accuracy. A PWM+histone naïve Bayes predictor using a single histone modification (H3K4me3) is substantially more accurate than a PWM score or a conservation-based score (phylogenetic motif model). The naïve Bayes predictor is more accurate (on average) at all sensitivity levels, and makes only half as many false positive predictions at sensitivity levels from 10% to 80%. On average, it correctly predicts 80% of bound promoters at a false positive rate of 20%. Accuracy does not diminish when we test the predictor in a different cell type (and species) from training. Accuracy is barely diminished even when we train the predictor without using TF ChIP-seq data.

Availability: Our tissue-specific predictor of promoters bound by a TF is called Dr Gene and is available at http://bioinformatics.org.au/drgene.

Contact:  t.bailey@imb.uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ultrafast magnetization dynamics of spintronic nanostructures
Authors: Keatley P. S. , Kruglyak V. V. , Gangmei P. , Hicken R. J.
Published: July 2011

The ultrafast (sub-nanosecond) magnetization dynamics of ferromagnetic thin films and elements that find application in spintronic devices is reviewed. The major advances in the understanding of magnetization dynamics in the two decades since the discovery of giant magnetoresistance and the prediction of spin-transfer torque are discussed, along with the plethora of new experimental techniques developed to make measurements on shorter length and time scales. Particular consideration is given to time-resolved measurements of the magneto-optical Kerr effect, and it is shown how a succession of studies performed with this technique has led to an improved understanding of the dynamics of nanoscale magnets. The dynamics can be surprisingly rich and complicated, with the latest studies of individual nanoscale elements showing that the dependence of the resonant mode spectrum upon the physical structure is still not well understood. Finally, the article surveys the prospects for development of high-frequency spintronic devices and highlights areas in which further study of fundamental properties will be required within the coming decade.
Nanopillar junctions
Authors: Blamire M. G. , Aziz A. , Robinson J. W. A.
Published: July 2011

The fabrication of nanopillar devices has been essential to the understanding and development of metallic spin electronics. This paper discusses the processes that can be used for the fabrication of such structures and the challenges in which they present, with particular emphasis on extreme sub-micrometre pillar structures suitable for the study of spin-transfer torque effects.
Manipulation of spin currents in metallic systems
Authors: Otani Yoshichika , Kimura Takashi
Published: July 2011

The transport properties of diffusive spin currents have been investigated in lateral ferromagnetic/non-magnetic metal hybrid structures. The spin diffusion processes were found to be strongly dependent on the magnitude of the spin resistances of connected materials. Efficient spin injection and detection are accomplished by optimizing the junction structures on the basis of the spin resistance circuitry. The magnetization switching of a nanoscale ferromagnetic particle and also room temperature spin Hall effect measurements were realized by using an efficient pure-spin-current injection.
Antiferromagnetic metal spintronics
Authors: MacDonald A. H. , Tsoi M.
Published: July 2011

In this brief review, we explain the theoretical basis for the notion that spin-transfer torques (STTs) and giant-magnetoresistance effects can, in principle, occur in circuits containing only normal and antiferromagnetic (AFM) materials, and for the notion that antiferromagnets can play a role in STT phenomena in circuits containing both ferromagnetic and AFM elements. We review the experimental literature that provides partial evidence for these AFM spintronic effects but demonstrates that, like exchange-bias effects, they are sensitive to details of interface structure that are not always under experimental control. Finally, we speculate briefly on some strategies that might advance progress.
Switching on pluripotency: a perspective on the biological requirement of Nanog
Authors: Theunissen Thorold W. , Silva José C. R.
Published: July 2011

Pluripotency is a transient cellular state during early development which can be recreated
in vitro
by direct reprogramming. The molecular mechanisms driving entry into and exit from the pluripotent state are the subject of intense research interest. Here, we review the role of the homeodomain-containing transcription factor Nanog in mammalian embryology and induced pluripotency. Nanog was originally thought to be confined to the maintenance of pluripotency, but recent insights from genetic studies uncovered a new biological function. Embryonic stem cells deficient in
Nanog
alleles are more prone to differentiate but do not lose pluripotency
per se
. Instead, Nanog is transiently required for the specification of the naive pluripotent epiblast and development of primordial germ cells. Nanog is also essential to finalize somatic cell reprogramming during induction of pluripotency. We propose that this unique transcription factor acts as a molecular switch to turn on the naive pluripotent programme in mammalian cells. In this context, the capacity of Nanog to resist differentiation can be regarded as recapitulation of effects normally associated with the specification of pluripotency. Pertinent questions are how Nanog specifies naive pluripotency and whether this mechanism is evolutionarily conserved.
Immunological considerations for embryonic and induced pluripotent stem cell banking
Authors: Taylor Craig J. , Bolton Eleanor M. , Bradley J. Andrew
Published: July 2011

Recent advances in stem cell technology have generated enthusiasm for their potential to study and treat a diverse range of human disease. Pluripotent human stem cells for therapeutic use may, in principle, be obtained from two sources: embryonic stem cells (hESCs), which are capable of extensive self-renewal and expansion and have the potential to differentiate into any somatic tissue, and induced pluripotent stem cells (iPSCs), which are derived from differentiated tissue such as adult skin fibroblasts and appear to have the same properties and potential, but their generation is not dependent upon a source of embryos. The likelihood that clinical transplantation of hESC- or iPSC-derived tissues from an unrelated (allogeneic) donor that express foreign human leucocyte antigens (HLA) may undergo immunological rejection requires the formulation of strategies to attenuate the host immune response to transplanted tissue. In clinical practice, individualized iPSC tissue derived from the intended recipient offers the possibility of personalized stem cell therapy in which graft rejection would not occur, but the logistics of achieving this on a large scale are problematic owing to relatively inefficient reprogramming techniques and high costs. The creation of stem cell banks comprising HLA-typed hESCs and iPSCs is a strategy that is proposed to overcome the immunological barrier by providing HLA-matched (histocompatible) tissue for the target population. Estimates have shown that a stem cell bank containing around 10 highly selected cell lines with conserved homozygous HLA haplotypes would provide matched tissue for the majority of the UK population. These simulations have practical, financial, political and ethical implications for the establishment and design of stem cell banks incorporating cell lines with HLA types that are compatible with different ethnic populations throughout the world.
Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces
Authors: Kitahara Maki , Sakamoto Mitsuo , Tsuchida Sayaka , Kawasumi Koh , Amao Hiromi , Benno Yoshimi , Ohkuma Moriya
Published: July 2011

Strains of Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces, and three strains, ST161T, ST33 and ST37T, were investigated taxonomically. Based on phylogenetic analyses and specific phenotypic characteristics, the three strains were allocated to the genus

Bacteroides

. Phylogenetic analyses of their 16S rRNA gene sequences revealed that strain ST161T formed a distinct line of descent, with highest sequence similarity to strain ST33 (98.7 %) and

Bacteroides oleiciplenus

JCM 16102T (97.7 %). High levels of DNA–DNA relatedness (79–89 %) were found between strains ST161T and ST33, but low levels were found between strain ST161T and

B. oleiciplenus

JCM 16102T (33–37 %) and between strain ST33 and

B. oleiciplenus

JCM 16102T (33–37 %). These data clearly indicated that strains ST161T and ST33 represent a single novel species. 16S rRNA gene sequence analyses showed that strain ST37T also formed a distinct line of descent, with highest sequence similarity to

Bacteroides acidifaciens

JCM 10556T (96.5 %) and

Bacteroides caccae

JCM 9498T (95.6 %). Analysis of hsp60 gene sequences also supported these relationships. Based on phenotypic and phylogenetic characteristics, two novel species, Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., are thus proposed. The type strains of B. stercorirosoris and B. faecichinchillae are ST161T ( = JCM 17103T = CCUG 60872T) and ST37T ( = JCM 17102T = CCUG 60873T), respectively. The DNA G+C contents of strains ST161T and ST37T were 45.7 and 41.0 mol%, respectively.
HSulf‐1 inhibits cell proliferation and invasion in human gastric cancer
Authors: Li Jie , Mo Min‐Li , Chen Zhao , Yang Jie , Li Qiu‐Shi , Wang Dian‐Jun , Zhang Hui , Ye Ying‐Jiang , Xu Jun‐Pu , Li Hai‐Long , Zhang Fang , Zhou Hai‐Meng
Published: July 2011

The HSulf‐1 gene encodes an extracellular 6‐O‐endosulfatase and regulates the sulfation status of heparan sulfate proteoglycans (HSPG). We have demonstrated that promoter hypermethylation is correlated with the HSulf‐1 silencing in gastric cancer. To investigate the functional importance of HSulf‐1 silencing in gastric cancer, we restored HSulf‐1 expression in the gastric cancer cell line MKN28, which lacks endogenous HSulf‐1. Following restoration of expression, HSulf‐1 inhibited cell proliferation, motility, and invasion in vitro, as well as significantly suppressing the MKN28 xenograft model (P < 0.05). No noticeable changes in proliferation and motility were observed following restoration of HSulf‐1 in another gastric cancer cell line, namely AGS cells. Interestingly, in MKN28 cells, which have been reported to be dependent on extracellular Wnt signaling, we found that HSulf‐1 inhibited the transcriptional activity of the Wnt/β‐catenin pathway and downregulated its targeted genes. Conversely, in AGS cells, in the constitutive Wnt/β‐catenin pathway is active, HSulf‐1 had no effect on the activity of the Wnt/β‐catenin pathway. Furthermore, transfection of Wnt3a cDNA or β‐catenin shRNA resulted in rescue or enhancement, respectively, of the effects of HSulf‐1 in MKN28 cells. Furthermore, HSPG epitope analysis confirmed that HSulf‐1 affected the structure of heparan sulfate on the cell surface. Together, the results of the present study suggest that extracellular HSulf‐1 may function as a negative regulator of proliferation and invasion in gastric cancer by suppressing Wnt/β‐catenin signaling at the cell surface. (Cancer Sci 2011; 102: 1815–1821)
An examination of information‐processing skills among inhalant‐using adolescents
Authors: Scott K. D. , Scott A. A.
Published: July 2011

Background  This study investigates the association between inhalant use and information processing (IP) in adjudicated polysubstance users. Polysubstance users who used inhalants (n= 158) were compared with polysubstance users who did not use inhalants (n= 303). Hispanic Americans comprised 72% of the participants; European Americans, African Americans and Asian Americans comprised 28% of the participants.

Method  Standardized intelligence and achievement tests were used to assess information‐processing constructs of working memory and processing speed. Psychosocial and substance abuse standardized surveys were used to assess drug use severity and psychosocial problems associated with substance use.

Results  Polysubstance users who used inhalants (PSI users) were younger, used more drugs more frequently and had more psychiatric admissions than non‐inhalant polysubstance users (PSO users). Statistical analysis also shows that PSI users performed worse on measures of IP selected tests in comparison with the PSO users.

Conclusion  Inhalant users begin abusing substances at a younger age and suffer from more verbal and non‐verbal processing, behavioural, language and memory problems than non‐inhalant users.