bluuebunny/crossref_metadata_2025 huggingface dataset:
Guanosine supplementation reduces the antiproliferative and apoptotic effects of the IMPDH inhibitor gnidilatimonoein in K562 cells
Authors: Nouri Kazem , Yazdanparast Razieh , Sarafnejad Abdolfattah
Published: July 2011

IMPDH (inosine 5′‐monophosphate dehydrogenase) is the rate‐limiting enzyme in the de novo biosynthetic pathway of guanine nucleotides, which is usually up‐regulated in human leukaemia cell lines. Our previous studies have classified gnidilatimonoein, isolated from Daphne mucronata, as an IMPDH inhibitor and a strong antiproliferative agent among several types of leukaemia cells. In the present study, we investigated the effects of gnidilatimonoein on intracellular GTP pool size and its link to differentiation and apoptosis of K562 cells. It was found that gnidilatimonoein inhibited cell proliferation and induced G0/G1 cell cycle arrest in K562 cells after 24 h exposure to a single dose of gnidilatimonoein (1.5 μM), while no significant effects were observed on unstimulated and phytohaemagglutinin‐stimulated peripheral blood lymphocyte cells at the gnidilatimonoein dose (1.5 μM) used. Based on the morphological changes, Wright −Giemsa staining, benzidine assay and the expression of cell surface markers [GPIIb (glycoprotein IIb) and glycophorin A], as analysed by flow cytometry, we found that K562 cells had differentiated towards megakaryocytic lineage. In addition, gnidilatimonoein induced apoptosis among K562 cells based on Acridine Orange/ethidium bromide and annexin V/propidium iodide double‐staining observations. These changes, which were abrogated by the addition of guanosine, became evident when the intracellular GTP level decreased to approx. 20–35% of the untreated control level. Based on these findings, it can be concluded that gnidilatimonoein induces differentiation and apoptosis in K562 cells through perturbation of GTP metabolism, as one of its routes of action.
Identification of the VIL2 enhancer in human embryonic kidney cells
Authors: Gao Shu‐Ying , Dai Yan‐Peng , Long Xia , Zhang Fang‐Ting , Yu Jie
Published: July 2011

We previously demonstrated that the VIL2 −87/+134 region exhibited promoter activity in some human cells, and a region further upstream of this promoter might contain an enhancer. However, the properties and location of this VIL2 enhancer remain unclear. In this study, we cloned the VIL2 −1541/ −706 segment and investigated its transcriptional regulatory properties via luciferase assays in transiently transfected HEK‐293 cells (human embryonic kidney cells). The VIL2 −1541/ −706 was found to exhibit promoter activity. Furthermore, when this segment was located upstream of the VIL2 or SV40 (simian virus 40) promoters in the forward orientation, the expression levels of luciferase were dramatically enhanced. However, this transcriptional enhancement disappeared when this segment was located upstream of the promoter in the reverse orientation or downstream of the reporter gene in the forward or reverse orientation. In deletion experiments, we found several potential regulatory regions within the VIL2 −1541/ −706. When these regions were separately located upstream of the VIL2 or SV40 promoters, only the −1297/ −1186 considerably enhanced the activity of these promoters. Although the other regulatory regions exhibited significant transcriptional regulation in deletion experiments, they weakly enhanced VIL2 promoter activity and/or did not regulate SV40 promoter activity. These results suggest that the DNA sequence upstream of the VIL2 promoter functions as an enhancer in a position‐ and orientation‐dependent manner, and the VIL2 −1297/ −1186, which acts as a key enhancer, probably regulates VIL2 transcription in combination with other potential regulatory regions located upstream of the VIL2 promoter.
Doxorubicin-induced cardiac dysfunction is attenuated by ciclosporin treatment in mice through improvements in mitochondrial bioenergetics
Authors: Marechal Xavier , Montaigne David , Marciniak Camille , Marchetti Philippe , Hassoun Sidi Mohamed , Beauvillain Jean Claude , Lancel Steve , Neviere Remi
Published: July 2011

We tested whether inhibition of mitochondrial membrane potential dissipation by CsA (ciclosporin A) would prevent doxorubicin-induced myocardial and mitochondrial dysfunction. Acute and subchronic models of doxorubicin exposition were performed in mice with either a single intraperitoneal bolus (10 mg/kg of body weight, intraperitoneal) or one injection of 4 mg·kg−1 of body weight·week−1 during 5 weeks. Follow-up was at 1.5 weeks and 16 weeks in acute and subchronic models respectively. Mice received either CsA (1 mg/kg of body weight, intraperitoneal on alternate days) or saline until follow-up. Heart function was evaluated by echocardiography. Mitochondrial measurements included oxygen consumption, membrane potential and externally added calcium-induced mitochondrial permeability transition. Mitochondrial mass was evaluated by transmission electronic microscopy and mtDNA (mitochondrial DNA) content. Mitochondrial dynamics were detected as the expression of GTPases involved in mitochondrial fusion and fission. In both the acute and chronic models, doxorubicin decreased left ventricular fractional shortening and survival. Heart function and survival were improved by CsA, but not by tacrolimus (FK506), a ciclosporin derivative with no inhibitory effect on the mitochondrial transition pore. In the acute model, doxorubicin exposure was associated with increased mtDNA content, mitochondrial fragmentation and changes in mitochondrial fusion- and fission-related transcripts [increases in Mfn2 (mitofusin 2), Opa1 (optic atrophy 1 homologue) and Fis1 (fission 1 homologue), and no changes in Drp1 (dynamin 1-like)]. CsA did not alter mitochondrial biogenesis, but prevented mitochondrial fragmentation and partially restored the mitochondrial energy-producing capacity. These findings suggest that in vivo CsA treatment may limit MPTP (mitochondrial permeability transition pore) opening, mitochondrial potential loss and contractile depression in acute and chronic models of cardiac toxicity induced by doxorubicin.
Maternal antioxidant blocks programmed cardiovascular and behavioural stress responses in adult mice
Authors: Roghair Robert D. , Wemmie John A. , Volk Kenneth A. , Scholz Thomas D. , Lamb Fred S. , Segar Jeffrey L.
Published: July 2011

Intra-uterine growth restriction is an independent risk factor for adult psychiatric and cardiovascular diseases. In humans, intra-uterine growth restriction is associated with increased placental and fetal oxidative stress, as well as down-regulation of placental 11β-HSD (11β-hydroxysteroid dehydrogenase). Decreased placental 11β-HSD activity increases fetal exposure to maternal glucocorticoids, further increasing fetal oxidative stress. To explore the developmental origins of co-morbid hypertension and anxiety disorders, we increased fetal glucocorticoid exposure by administering the 11β-HSD inhibitor CBX (carbenoxolone; 12 mg·kg−1 of body weight·day−1) during the final week of murine gestation. We hypothesized that maternal antioxidant (tempol throughout pregnancy) would block glucocorticoid-programmed anxiety, vascular dysfunction and hypertension. Anxiety-related behaviour (conditioned fear) and the haemodynamic response to stress were measured in adult mice. Maternal CBX administration significantly increased conditioned fear responses of adult females. Among the offspring of CBX-injected dams, maternal tempol markedly attenuated the behavioural and cardiovascular responses to psychological stress. Compared with offspring of undisturbed dams, male offspring of dams that received daily third trimester saline injections had increased stress-evoked pressure responses that were blocked by maternal tempol. In contrast, tempol did not block CBX-induced aortic dysfunction in female mice (measured by myography and lucigenin-enhanced chemiluminescence). We conclude that maternal stress and exaggerated fetal glucocorticoid exposure enhance sex-specific stress responses, as well as alterations in aortic reactivity. Because concurrent tempol attenuated conditioned fear and stress reactivity even among the offspring of saline-injected dams, we speculate that antenatal stressors programme offspring stress reactivity in a cycle that may be broken by antenatal antioxidant therapy.
Cytochrome P450 metabolites of arachidonic acid are elevated in stroke patients compared with healthy controls
Authors: Ward Natalie C. , Croft Kevin D. , Blacker David , Hankey Graeme J. , Barden Anne , Mori Trevor A. , Puddey Ian B. , Beer Christopher D.
Published: July 2011

CYP450AAM [arachidonic acid metabolites of the CYP450 (cytochrome P450) enzyme system] have a range of biological functions. CYP450AAM are involved in the pathogenesis of hypertension, renal function and vascular function, yet their role in stroke has not been clarified. We aimed at determining the levels of circulating CYP450 metabolites in patients with acute ischaemic stroke (<96 h) compared with healthy age- and gender-matched controls. This was a retrospective case-controlled study of 44 acute ischaemic stroke patients and 44 matched controls. A subset of acute ischaemic stroke patients was available for follow-up. Acute ischaemic stroke patients had elevated plasma CYP450AAM, including 20-HETE (20-hydroxyeicosatetraenoic acid) (1921±170 compared with 1108±170 pmol/l, P<0.001), EETs (epoxyeicosatrienoic acids) (77.88±3.34 compared with 35.35±3.34 nmol/l, P<0.0001) and DiHETEs (dihydroxyeicosatetraenoic acids) (92.87±4.61 compared with 68.17±4.61 nmol/l, P<0.0001), as well as increased plasma F2-isoprostane levels (3754±538 compared with 1947±538 pmol/l, P<0.02), the latter a marker of oxidative stress, compared with controls. In a subset analysis of the stroke patients, plasma 20-HETE, EETs and F2-isoprostanes were attenuated 30 days after the stroke. Baseline 20-HETE levels were also associated with lesion size and functional indices within the stroke patients. The present study highlights the elevation in CYP450AAM and oxidative stress in acute ischaemic stroke patients. Further investigation of the effect this has on long-term clinical outcome or whether this can be modified by treatment is warranted.
Granular collapse in a fluid: Role of the initial volume fraction
Authors: Rondon L. , Pouliquen O. , Aussillous P.
Published: July 2011

The collapse of a granular column in a viscous liquid is experimentally investigated. The morphology of the deposits is shown to be mainly controlled by the initial volume fraction of the granular mass and not by the aspect ratio of the column, an observation which differs from dry granular collapse. Two different regimes are identified corresponding to initially loose and dense packings. Loose packings give rise to thin and long deposits, the dynamics being fast. A positive liquid pressure is measured below the column. For dense packings, the runout distance is twice less, the flow is slow, and a negative pore pressure is measured during the flow. These observations suggest that the dynamics of the granular collapse in a fluid is strongly affected by the dilatancy or contractancy behavior of the granular medium.
Magnetic properties and unusual exchange coupling in self-organized NdMnO3/Mn3O4 nanocomposite films
Authors: Hu Weijin , Zhou Gengheng , Ren Weijun , Li Da , Zhang Zhidong
Published: July 2011

The NdMnO3/Mn3O4 nanocomposite film was synthesized by spontaneous phase decomposition of NdMn2O5. NdMnO3 is a canted A-type antiferromagnet with a Néel temperature of about 75 K, while Mn3O4 is ferrimagnetic below its Curie temperature of 42 K. Ferromagnetic order of the Nd moments in NdMnO3 around 15 K has been confirmed. These moments are antiferromagnetically coupled with the Mn moments. The effect of the consecutive magnetic orderings of NdMnO3 on the exchange coupling between NdMnO3 and Mn3O4 has been investigated. The temperature dependence of the exchange bias manifests itself as a peak at 20 K, which is explained in terms of competing ferromagnetic and antiferromagnetic coupling of the Mn and Nd magnetic sublattices with Mn moments of Mn3O4, respectively.
Ultraviolet-infrared dielectric functions and electronic band structures of monoclinic VO2 nanocrystalline film: Temperature-dependent spectral transmittance
Authors: Li W. W. , Zhu J. J. , Xu X. F. , Jiang K. , Hu Z. G. , Zhu M. , Chu J. H.
Published: July 2011

Nanocrystalline vanadium dioxide (VO2) film on c-plane sapphire substrate has been prepared by direct-current magnetron sputter deposition. The electronic band structures of the VO2 film with monoclinic phase have been investigated by ultraviolet-infrared transmittance spectra in the temperature range of 5.3–300 K. It was found that the transmittance decreases while the dielectric functions slightly increase with the temperature. The optical bandgap decreases from 0.839±0.003 to 0.788±0.003 eV with increasing the temperature due to the variations of lattice constant and Vd-Op hybridization. Moreover, three higher-order interband electronic transitions can be uniquely distinguished and the temperature effects on the higher-order transition energy become much weaker.
Alternating current impedance spectroscopic analysis of biofunctionalized vertically-aligned silica nanospring surface for biosensor applications
Authors: Timalsina Yukta P. , Branen Joshua , Aston D. Eric , Noren Kenneth , Corti Giancarlo , Schumacher Randi , McIlroy David N.
Published: July 2011

In this study, alternating current impedance spectroscopic analysis of the biofunctionalization process of a vertically-aligned (silica) nanosprings (VANS) surface is presented. The VANS surface is functionalized with a biotinylated immunoglobulin G (B-IgG) layer formed by physisorption of B-IgG from the solution phase. Bovine serum albumin passivation of the B-IgG layer reduces additional surface adsorption by blocking the potential sites of weak bond formation via electrostatic and hydrophobic interactions. As avidin acts as a receptor of biotinylated compounds, avidin conjugated glucose oxidase (Av-GOx) binds to the B-IgG layer via biotin. This avidin-biotin bond is a stable bond with high association affinity (Ka = 1015 M−1) that withstands wide variations in chemistry and pH. An IgG layer without biotin shows no binding to the Av-GOx, indicating that bonding is through the avidin-biotin interaction. Finally, fluoroscein iso-thiocyanate (FITC) labeled biotinylated bovine serum albumin (B-BSA) added to the Av-GOx surface is used to fluorescently label Av-GOx for fluorescent measurements that allow for the correlation of surface binding with impedance measurements. Modeling of impedance spectra measured after the addition of each biological solution indicates that the bimolecular layers behave as insulating layers. The impedance spectra for the VANS-based sensor are compared to simple parallel capacitor sensors, sans VANS, and serve as controls. VANS-based sensors exhibit a greater magnitude of change between successive bio-layers relative to the controls below 10 kHz. Changes in the magnitudes of the components of the VANS equivalent circuit indicate that the addition of biological layers changes the effective dielectric response of the VANS via the impediment of ionic motion and biomolecule polarization.
RF phase control in a high-power high-efficiency klystron-like relativistic backward wave oscillator
Authors: Xiao Renzhen , Chen Changhua , Song Wei , Zhang Xiaowei , Sun Jun , Song Zhimin , Zhang Lijun , Zhang Ligang
Published: July 2011

The klystron-like relativistic backward wave oscillator (RBWO) with a dual-cavity extractor has demonstrated 10 GW output power with 48% efficiency in recent simulations. To realize radio-frequency (RF) phase control for the purpose of coherent power combining, a high-power high-efficiency klystron-like RBWO with an input signal is presented. In the device, an independent input cavity is introduced before the resonant reflector to reduce the leakage power from the input port, and the applied RF signal is injected into the input cavity through a mode convertor and a coaxial waveguide along the magnet, which avoids separating the magnet by the injection waveguide, and suppresses the asymmetric modes excited in the input cavity. For a frequency difference of 15 MHz between the input signal and free-running klystron-like RBWO, an input power of 10 MW is sufficient to control the phase of 10 GW output microwave.
Remarkable paramagnetic features of Fermi-Dirac-Pauli plasmas
Authors: Akbari-Moghanjoughi M.
Published: July 2011

In this paper by using the relativistic magnetic susceptibility of a Fermi-Dirac (relativistically degenerate) plasma, quantum magnetohydrodynamics model is used to investigate the propagation of spin-induced (SI) magnetosonic nonlinear excitations in a normally and relativistically degenerate dense electron-ion plasma in the presence of the spin magnetization effect. Based on the conventional pseudopotential method the matching criterion for the evolution of SI solitary structures is evaluated. It is found that, the plasma mass density and strength of the magnetic field have significant effects on excitation and evolution of magnetosonic nonlinear structures in Fermi-Dirac plasmas. Only rarefactive SI magnetosonic solitary structures are found to excite in such plasmas. Furthermore, fundamental differences are shown to exist in magnetosonic soliton dynamics in the two distinct plasma degeneracy regimes, which are due to interplay between the negative pressure-like paramagnetism and positive relativistic degeneracy pressure of electrons. Current investigation can help better understand the electron spin effects on nonlinear wave propagations in strongly magnetized dense astrophysical objects such as white dwarfs and pulsar magnetospheres.
Particle acceleration and energy conservation in particle in cell simulations
Authors: Lapenta Giovanni , Markidis Stefano
Published: July 2011

Particle acceleration is a process of great importance in all areas of plasma physics. In most cases, kinetic effects are dominant and require a full kinetic treatment, such as the particle in cell (PIC) method. PIC methods are widely used in all aspects of plasma physics, proving to be a precious and irreplaceable tool. Yet all methods in use and published conserve energy to a good approximation, but not exactly. A well known property of PIC methods, documented extensively in all textbooks, is that energy is not conserved exactly. In fact, the particle noise is a unphysical source of energy that, when insufficient resolution is used, can make the simulations go unstable. In the present paper, we apply a new exactly energy conserving scheme and demonstrate that indeed exact energy conservation plays a key role in determining the correct spectrum of the accelerated particles.
Stability and bifurcation diagram of Boussinesq thermal convection in a moderately rotating spherical shell
Authors: Kimura Keiji , Takehiro Shin-ichi , Yamada Michio
Published: July 2011

Stability and bifurcation of Boussinesq thermal convection in a moderately rotating spherical shell are investigated by obtaining finite-amplitude solutions with the Newton method instead of the numerical time integration. The ratio of the inner and outer radii of the shell and the Prandtl number are fixed to 0.4 and 1, respectively, while the Taylor number is varied from 522 to 5002 and the Rayleigh number is from about 1500 to 10 000. In this range of the Taylor number, the stable finite-amplitude solutions, which have four-fold symmetry in the longitudinal (azimuthal) direction, bifurcate supercritically at the critical points and become unstable when the Rayleigh number is increased up to about 1.2 to 2 times the critical values. When the Taylor number is larger than 3402, propagating direction of the solutions changes from prograde to retrograde continuously as the Rayleigh number is increased. The associated transition of the convection structure is also continuous.
Collision-induced dipole polarizability of helium dimer from explicitly correlated calculations
Authors: Cencek Wojciech , Komasa Jacek , Szalewicz Krzysztof
Published: July 2011

Large expansions in basis sets of explicitly correlated Gaussian functions and the variation-perturbation technique were used to calculate the static dipole polarizability of the helium dimer at 16 different internuclear separations from 1.0 to 9.0 bohrs. The convergence towards the complete basis set limit was analyzed in order to estimate uncertainties of all the calculated values. The results are significantly more accurate than literature data. Asymptotically correct analytic fits for the trace and anisotropy of collision-induced polarizability were obtained.
Excitation spectra of ABC-stacked graphene superlattice
Authors: Chiu Chih-Wei , Huang Yuan-Cheng , Shyu Feng-Lin , Lin Ming-Fa
Published: July 2011

The excitation spectra of ABC-stacked graphene superlattices are calculated by the gradient approximation. Based on the selection rule, only excitations between the conduction and valence bands of the same pairs are allowed. These excitations occur at the critical points in the energy-wave vector space. Different polarization directions induce different spectra. The spectra of a parallel polarization are stronger than those of a vertical polarization. The strong electron-hole excitations cause special structures in the electron-hole excitation and reflectance spectra. However, only one plasmon peak exists in the loss spectra of the parallel polarization. Some properties are consistent with the experimental measurements.
Field tunable localization of spin waves in antidot arrays
Authors: Hu C.-L. , Magaraggia R. , Yuan H.-Y. , Chang C. S. , Kostylev M. , Tripathy D. , Adeyeye A. O. , Stamps R. L.
Published: July 2011

We show that magnetic spin wave resonance modes in an antidot patterned array are sensitive to small changes in the magnetic configuration near dots, resulting in strong localization effects as the field is increased. Frequencies measured using ferromagnetic resonance from an antidot array patterned from a NiFe/IrMn bilayer are interpreted using micromagnetic calculations, and it is shown that the observed field dependence of the resonance response can be attributed to strong interdot localization of spin waves. This field tunable localization is created by stray fields produced by magnetic poles at the dot surfaces.
Iron-chalcogenide FeSe0.5Te0.5 coated superconducting tapes for high field applications
Authors: Si Weidong , Zhou Juan , Jie Qing , Dimitrov Ivo , Solovyov V. , Johnson P. D. , Jaroszynski J. , Matias V. , Sheehan C. , Li Qiang
Published: July 2011

The high upper critical field characteristic of the recently discovered iron-based superconducting chalcogenides opens the possibility of developing a new type of non-oxide high-field superconducting wires. In this work, we utilize a buffered metal template on which we grow a textured FeSe0.5Te0.5 layer, an approach developed originally for high temperature superconducting coated conductors. These tapes carry high critical current densities (>1 × 104 A/cm2) at about 4.2 K under magnetic field as high as 25 T, which are nearly isotropic to the field direction. This demonstrates a very promising future for iron chalcogenides for high field applications at liquid helium temperatures. Flux pinning force analysis indicates a point defect pinning mechanism, creating prospects for a straightforward approach to conductor optimization.
Adventures in scientific nuclear diplomacy
Authors: Hecker Siegfried S.
Published: July 2011

A former director of Los Alamos National Laboratory offers a first-person perspective on the important contributions scientists can make toward improving the safety and security of nuclear materials and reducing the global nuclear dangers in an evolving world.
Rethinking the genesis of the Romance periphrastic perfect
Authors: Acosta Diego de
Published: July 2011

The Romance languages all display periphrastic perfects that can be traced to Latin [habere “have” + noun + perfect participle]. A new survey of the Latin corpus reveals that this string had three distinct structures and values. I argue that the likeliest source of the perfects is a periphrasis denoting the achievement of a result or a persisting resultant state. This implies that the relationship between possessive and auxiliary habere is more complex than previously supposed. Finally, I examine the range of values that this periphrasis takes across the Romance languages. I maintain that the growth of the perfect at the expense of the preterite followed an orderly pattern, with requirements on the temporal denotation of the perfect successively relaxed.
Laryngeal stop systems in contact
Authors: Simon Ellen
Published: July 2011

This article examines the linguistic forces at work in present-day second language and bilingual acquisition of laryngeal contrasts, and to what extent these can give us insight into the origin of laryngeal systems of Germanic voicing languages like Dutch, with its contrast between prevoiced and unaspirated stops. The results of present-day child and adult second language acquisition studies reveal that both imposition and borrowing may occur when the laryngeal systems of a voicing and an aspirating language come into contact with each other. A scenario is explored in which socially dominant Germanic-speaking people came into contact with a Romance-speaking population, and borrowed the Romance stop system.
“We must agree on our vision”
Authors: Skilling Peter
Published: July 2011

From 1999–2008, New Zealand’s Labour-led coalition Government fashioned a specific discourse of globalisation and the nation. Within a representation of globalisation as a realm of hostile competition, New Zealanders were increasingly addressed as contributors to an urgently necessary and meaningfully shared national response. While there was nothing particularly unusual about this discourse, the history and structure of New Zealand society meant that its political and ethical implications could be seen particularly clearly in this setting. This article analyses three key features of the government’s discourse — its future-focussed orientation, its heavy use of imperative terms and its careful use of the first person plural — and shows how they led logically to a reductive address and positioning of individuals and sub-state groups. Drawing on elements of CDA and critical political theory, it explores how the discursive construction of a shared (national) purpose served an anti-political function by marginalising divergent perspectives, including the historically-based claims of the indigenous Maori.
Media construction of socio-political crises in Nigeria
Authors: Chiluwa Innocent
Published: July 2011

This paper attempts to show how social and political crises are constructed, represented/mediated in the Nigerian print media news headlines. Nigeria’s leading newsmagazines and newspapers namely The News, Newswatch, Tell, The Guardian and The Punch are selected for the study. From a corpus of thirty-two news headlines being the publications of the above news media between 2000 and 2006, fifteen headlines and their overlines covering the years that marked the end of military rule and the consolidation of democratic government in Nigeria are purposively selected and analyzed within the framework of the systemic model and critical linguistics. The study shows that socio-political crises have been frequent in Nigeria and that the much anticipated recovery associated with democracy has so far eluded the country. In fact the country has witnessed more social crises, national disasters and ethnic violence in the seven years of civil government than at other times. The study also shows that news headlines — an integral part of media discourse, is an instrument for molding social actions, attitudes and perceptions and are also used as an ideological tool for social criticism. Some of the headlines however, exaggerated the crises and indeed misinformed the general public about the identities and activities of certain people as well as the state of security in Nigeria.
A Potential Application of a Piezoelectric Atomiser for Ophthalmic Drug Delivery
Authors: Xia Wei , Hsu Hung-Yao , Kong Lingxue , Evans Allan , Lee Ryan
Published: July 2011

A liquid atomiser composed of a piezoelectric transducer and a metal plate with numerous micro‐apertures is studied to identify the most influential factors on its atomising performance. The Taguchi method is employed in the experiment design and analysis of the study on how each factor acts in the atomising process. An optimal condition is determined for producing a stream of droplets. The study shows that the droplet size and the spraying velocity are suitable for ophthalmic drug delivery application, with an even distribution of the drug over most of the eyeball surface area due to the controllable cross‐sectional area of the droplet stream. This greatly improves the treatment effectiveness and efficiency of eye therapy. Finally, a structure of the ophthalmic drug delivery system is proposed.
Estimating Shoulder‐Complex Mobility
Authors: Tondu Bertrand
Published: July 2011

Modeling shoulder motions is essential in understanding upper‐limb dynamic behavior. However, the mobility of the shoulder complex—in terms of degrees of freedom (DOFs)—is seldom quantified. In this paper we propose applying the theory of mechanisms and, especially, the powerful Grübler–Kutzbach formula to estimate it. This approach requires a rigorous kinematic analysis. So we suggest basing it on a bone schematisation derived from an extension of Dempster’s historical notation associated to mechanical interpretation of the physiological joints involved. In so doing, the proposed shoulder complex mobility leads to justifying a nine‐DOF serial‐chain upper‐limb mode, which extends the classical seven‐DOF arm–foream–wrist model and completing it by adding a clavicle‐like link with a two‐DOF mobility.
The New Method of Electroencephalogram Representation
Authors: Al-Kasasbeh R. T. , Shepovalnikov R. A.
Published: July 2011

A new method for visualization of electroencephalogram process is developed, using factorial analysis. This method permits data compression and visualization in a form adequate for humans to trace continuous change patterns, compare data from brain hemispheres and delete apparent artifacts using combined man‐computer mode for achieving additional reliability. Accordingly, this method is realized in software that allows an operator to select various modes of representation of results and speed of visualization.
Static Standing Trunk Sway Assessment in Amputees – Effects of Sub‐Threshold Stimulation
Authors: Ming-Yih L. , Kok-Soon S. , Chih-Feng L.
Published: July 2011

Sub‐threshold electrical stimulation can enhance the sensitivity of the human somatosensory system to improve the balance control capability of elderly was shown in recent rehabilitation articles. The purpose of this study was to evaluate the postural sway of trans‐tibial amputees when performing single leg quiet standing on firm surface. Four unilateral trans‐tibial amputees who consecutively wore prosthetics over 2 years were recruited in this study. Subjects performed single leg quiet standing trails with sub‐threshold electrical stimulation applied at the quadriceps muscle during the trails. Spatial co‐ordinates for the determination kinematic data (sway distance) of the center of mass (COM) on second sacral (S2) were collected using an ultrasound‐based Zebris CMS‐HS system. The single leg quiet standing test is measure considered to assess postural steadiness in a static position by a spatial measurement. The common notion is that a better postural steadiness, i.e. less postural sway, allows for longer time single leg quiet standing. However, there is lack of evidence how postural steadiness during single leg quiet standing changes over time. In this article, we hypothesized that the static balance of single leg quiet standing could be improved for providing proprioceptive neuromuscular facilitation using sub‐sensory stimulation in amputees. To test this hypothesis, a computerized sub‐threshold low‐level electrical stimulation device was developed and proposed for clinical study. Experimental results show that reduction in all of the postural sway indices (constant time sway length, max sway distance and average sway distance) and increase in single leg support time index during single leg quiet standing by applying sub‐sensory stimulation. The single leg quiet standing test findings suggest that sub‐threshold electrical stimulation rehabilitation strategies may be effective in improving static balance performance for amputees.
The Use of Evolution in a Central Action Selection Model
Authors: Montes-Gonzalez F. , Bautista-Cabrera P. , Escobar-Ruiz V.
Published: July 2011

The use of effective central selection provides flexibility in design by offering modularity and extensibility. In earlier papers we have focused on the development of a simple centralized selection mechanism. Our current goal is to integrate evolutionary methods in the design of non‐sequential behaviours and the tuning of specific parameters of the selection model. The foraging behaviour of an animal robot (animat) has been modelled in order to integrate the sensory information from the robot to perform selection that is nearly optimized by the use of genetic algorithms. In this paper we present how selection through optimization finally arranges the pattern of presented behaviours for the foraging task. Hence, the execution of specific parts in a behavioural pattern may be ruled out by the tuning of these parameters. Furthermore, the intensive use of colour segmentation from a colour camera for locating a cylinder sets a burden on the calculations carried out by the genetic algorithm.
Surface Approximation using Growing Self‐Organizing Nets and Gradient Information
Authors: Rivera-Rovelo Jorge , Bayro-Corrochano Eduardo
Published: July 2011

In this paper we show how to improve the performance of two self‐organizing neural networks used to approximate the shape of a 2D or 3D object by incorporating gradient information in the adaptation stage. The methods are based on the growing versions of the Kohonen′s map and the neural gas network. Also, we show that in the adaptation stage the network utilizes efficient transformations, expressed as versors in the conformal geometric algebra framework, which build the shape of the object independent of its position in space (coordinate free). Our algorithms were tested with several images, including medical images (CT and MR images). We include also some examples for the case of 3D surface estimation.
Integrating mechanisms of pulmonary fibrosis
Authors: Wynn Thomas A.
Published: July 2011

Pulmonary fibrosis is a highly heterogeneous and lethal pathological process with limited therapeutic options. Although research on the pathogenesis of pulmonary fibrosis has frequently focused on the mechanisms that regulate the proliferation, activation, and differentiation of collagen-secreting myofibroblasts, recent studies have identified new pathogenic mechanisms that are critically involved in the initiation and progression of fibrosis in a variety of settings. A more detailed and integrated understanding of the cellular and molecular mechanisms of pulmonary fibrosis could help pave the way for effective therapeutics for this devastating and complex disease.
Computational studies of a cut-wire pair and combined metamaterials
Authors: Nguyen Thanh Tung , Lievens Peter , Lee Young Pak , Vu Dinh Lam
Published: July 2011

The transfer-matrix method and finite-integration simulations show how the transmission properties of combined metamaterials, which consist of metallic cut-wire pairs and continuous wires, are affected by geometric parameters. The corresponding effective permittivity and permeability are retrieved from the complex scattering parameters using the standard retrieval procedure. The electromagnetic properties of the cut-wire pair as well as the left-handed behavior of the combined structure are understood by the effective medium theory. In addition, the dimensional dependence of transmission properties, the shapes of cut-wire pairs and continuous wire, and the impact of dielectric spacer are both examined. Finally, by expanding the results of previous research (Koschny et al 2003 Phys. Rev. Lett.
93 016608), we generalize the transmission picture of combined structures in terms of the correlation between electric and magnetic responses.
A negative feedback controlled hybrid mode locked Nd : YAG laser using a semiconductor quantum dot saturable absorber
Authors: Buganov Oleg V , Nguyen Dai Hung , Tikhomirov Sergei A , Onuschenko Alexei A
Published: July 2011

The parameters of a solid-state PbS quantum dot saturable absorber, optical elements, resonator and feedback circuit have been adjusted for stable and highly efficient hybrid mode-locking Nd : YAG laser operation. A highly stable microsecond pulse train (40–50 μs) containing about 5000 ps pulses and 3 mJ total train energy was generated with a repetition rate of 10 Hz. This all solid-state hybrid mode-locked Nd : YAG laser was used for synchronous pumping of a femtosecond Ti : sapphire laser.
MethylCoder: software pipeline for bisulfite-treated sequences
Authors: Pedersen Brent , Hsieh Tzung-Fu , Ibarra Christian , Fischer Robert L.
Published: July 2011

Motivation: MethylCoder is a software program that generates per-base methylation data given a set of bisulfite-treated reads. It provides the option to use either of two existing short-read aligners, each with different strengths. It accounts for soft-masked alignments and overlapping paired-end reads. MethylCoder outputs data in text and binary formats in addition to the final alignment in SAM format, so that common high-throughput sequencing tools can be used on the resulting output. It is more flexible than existing software and competitive in terms of speed and memory use.

Availability: MethylCoder requires only a python interpreter and a C compiler to run. Extensive documentation and the full source code are available under the MIT license at: https://github.com/brentp/methylcode.

Contact:  bpederse@gmail.com
Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
Authors: Goncearenco Alexander , Berezovsky Igor N.
Published: July 2011

Motivation: Enzymes are complex catalytic machines, which perform sequences of elementary chemical transformations resulting in biochemical function. The building blocks of enzymes, elementary functional loops (EFLs), possess distinct functional signatures and provide catalytic and binding amino acids to the enzyme's active sites. The goal of this work is to obtain primordial prototypes of EFLs that existed before the formation of enzymatic domains and served as their building blocks.

Results: We developed a computational strategy for reconstructing ancient prototypes of EFLs based on the comparison of sequence segments on the proteomic scale, which goes beyond detection of conserved functional motifs in homologous proteins. We illustrate the procedure by a CxxC-containing prototype with a very basic and ancient elementary function of metal/metal-containing cofactor binding and redox activity. Acquiring the prototypes of EFLs is necessary for revealing how the original set of protein folds with enzymatic functions emerged in predomain evolution.

Supplementary Information:  Supplementary data are available at Bioinformatics online.

Contact:  igor.berezovsky@uni.no
Current-induced spin–orbit torques
Authors: Gambardella Pietro , Miron Ioan Mihai
Published: July 2011

The ability to reverse the magnetization of nanomagnets by current injection has attracted increased attention ever since the spin-transfer torque mechanism was predicted in 1996. In this paper, we review the basic theoretical and experimental arguments supporting a novel current-induced spin torque mechanism taking place in ferromagnetic (FM) materials. This effect, hereafter named spin–orbit (SO) torque, is produced by the flow of an electric current in a crystalline structure lacking inversion symmetry, which transfers orbital angular momentum from the lattice to the spin system owing to the combined action of SO and exchange coupling. SO torques are found to be prominent in both FM metal and semiconducting systems, allowing for great flexibility in adjusting their orientation and magnitude by proper material engineering. Further directions of research in this field are briefly outlined.
Multi-ferroic and magnetoelectric materials and interfaces
Authors: Velev J. P. , Jaswal S. S. , Tsymbal E. Y.
Published: July 2011

The existence of multiple ferroic orders in the same material and the coupling between them have been known for decades. However, these phenomena have mostly remained the theoretical domain owing to the fact that in single-phase materials such couplings are rare and weak. This situation has changed dramatically recently for at least two reasons: first, advances in materials fabrication have made it possible to manufacture these materials in structures of lower dimensionality, such as thin films or wires, or in compound structures such as laminates and epitaxial-layered heterostructures. In these designed materials, new degrees of freedom are accessible in which the coupling between ferroic orders can be greatly enhanced. Second, the miniaturization trend in conventional electronics is approaching the limits beyond which the reduction of the electronic element is becoming more and more difficult. One way to continue the current trends in computer power and storage increase, without further size reduction, is to use multi-functional materials that would enable new device capabilities. Here, we review the field of multi-ferroic (MF) and magnetoelectric (ME) materials, putting the emphasis on electronic effects at ME interfaces and MF tunnel junctions.
Single electron spintronics
Authors: Dempsey Kari J. , Ciudad David , Marrows Christopher H.
Published: July 2011

Single electron electronics is now well developed, and allows the manipulation of electrons one-by-one as they tunnel on and off a nanoscale conducting island. In the past decade or so, there have been concerted efforts in several laboratories to construct single electron devices incorporating ferromagnetic components in order to introduce spin functionality. The use of ferromagnetic electrodes with a non-magnetic island can lead to spin accumulation on the island. On the other hand, making the dot also ferromagnetic introduces new physics such as tunnelling magnetoresistance enhancement in the cotunnelling regime and manifestations of the Kondo effect. Such nanoscale islands are also found to have long spin lifetimes. Conventional spintronics makes use of the average spin-polarization of a large ensemble of electrons: this new approach offers the prospect of accessing the quantum properties of the electron, and is a candidate approach to the construction of solid-state spin-based qubits.
Nanowire spintronics for storage class memories and logic
Authors: Hrkac G. , Dean J. , Allwood D. A.
Published: July 2011

Patterned magnetic nanowires are extremely well suited for data storage and logic devices. They offer non-volatile storage, fast switching times, efficient operation and a bistable magnetic configuration that are convenient for representing digital information. Key to this is the high level of control that is possible over the position and behaviour of domain walls (DWs) in magnetic nanowires. Magnetic random access memory based on the propagation of DWs in nanowires has been released commercially, while more dynamic shift register memory and logic circuits have been demonstrated. Here, we discuss the present standing of this technology as well as reviewing some of the basic DW effects that have been observed and the underlying physics of DW motion. We also discuss the future direction of magnetic nanowire technology to look at possible developments, hurdles to overcome and what nanowire devices may appear in the future, both in classical information technology and beyond into quantum computation and biology.
Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways
Authors: Huang Sui
Published: July 2011

Stem cell behaviours, such as stabilization of the undecided state of pluripotency or multipotency, the priming towards a prospective fate, binary fate decisions and irreversible commitment, must all somehow emerge from a genome-wide gene-regulatory network. Its unfathomable complexity defies the standard mode of explanation that is deeply rooted in molecular biology thinking: the reduction of observables to linear deterministic molecular pathways that are tacitly taken as chains of causation. Such culture of proximate explanation that uses qualitative arguments, simple arrow–arrow schemes or metaphors persists despite the ceaseless accumulation of ‘omics’ data and the rise of systems biology that now offers precise conceptual tools to explain emergent cell behaviours from gene networks. To facilitate the embrace of the principles of physics and mathematics that underlie such systems and help to bridge the gap between the formal description of theorists and the intuition of experimental biologists, we discuss in qualitative terms three perspectives outside the realm of their familiar linear-deterministic view: (i) state space (ii), high-dimensionality and (iii) heterogeneity. These concepts jointly offer a new vista on stem cell regulation that naturally explains many novel, counterintuitive observations and their inherent inevitability, obviating the need for ad hoc explanations of their existence based on natural selection. Hopefully, this expanded view will stimulate novel experimental designs.
Induced pluripotent stem cells: opportunities and challenges
Authors: Okita Keisuke , Yamanaka Shinya
Published: July 2011

Somatic cells have been reprogrammed into pluripotent stem cells by introducing a combination of several transcription factors, such as
Oct3/4
,
Sox2
,
Klf4
and
c-Myc
. Induced pluripotent stem (iPS) cells from a patient's somatic cells could be a useful source for drug discovery and cell transplantation therapies. However, most human iPS cells are made by viral vectors, such as retrovirus and lentivirus, which integrate the reprogramming factors into the host genomes and may increase the risk of tumour formation. Several non-integration methods have been reported to overcome the safety concern associated with the generation of iPS cells, such as transient expression of the reprogramming factors using adenovirus vectors or plasmids, and direct delivery of reprogramming proteins. Although these transient expression methods could avoid genomic alteration of iPS cells, they are inefficient. Several studies of gene expression, epigenetic modification and differentiation revealed the insufficient reprogramming of iPS cells, thus suggesting the need for improvement of the reprogramming procedure not only in quantity but also in quality. This report will summarize the current knowledge of iPS generation and discuss future reprogramming methods for medical application.