bluuebunny/crossref_metadata_2025 huggingface dataset:
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations
Authors: Xu Zhijun , Lazim Raudah , Sun Tiedong , Mei Ye , Zhang Dawei
Published: April 2012

Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents from AHBC simulations and experimental results, we observed based on the presented simulations that the two ends of the peptide may simultaneously take part in the formation of the helical structure at the early stage of folding and finally merge to form a helix with lowest backbone RMSD of about 0.9 Å in 40% 2,2,2-trifluoroethanol solution. However, in pure water, the folding may start at the center of the peptide sequence instead of at the two opposite ends. The analysis of the free energy landscape indicates that the solvent may determine the folding clusters of E6ap, which subsequently leads to the different final folded structure. The current study demonstrates new insight to the role of solvent in the determination of protein structure and folding dynamics.
Active control of the lifetime of excited resonance states by means of laser pulses
Authors: García-Vela A.
Published: April 2012

Quantum control of the lifetime of a system in an excited resonance state is investigated theoretically by creating coherent superpositions of overlapping resonances. This control scheme exploits the quantum interference occurring between the overlapping resonances, which can be controlled by varying the width of the laser pulse that creates the superposition state. The scheme is applied to a realistic model of the Br2(B)-Ne predissociation decay dynamics through a three-dimensional wave packet method. It is shown that extensive control of the system lifetime is achievable, both enhancing and damping it remarkably. An experimental realization of the control scheme is suggested.
Epitaxial growth of thin films and nanodots of ZnO on Si(111) by pulsed laser deposition
Authors: Kyun Lee Sung , Yeog Son Jong
Published: April 2012

Epitaxial (0001) ZnO thin films were grown on (111) Si substrates buffered with intermediate epitaxial (111) yttria-stabilized zirconia (YSZ) layers by pulsed laser deposition (PLD). X-ray diffraction and transmission electron microscopy characterizations revealed that the YSZ buffer layers enabled the epitaxial growth of structurally high quality ZnO films and an atomically sharp ZnO/YSZ interface, proving to be an effective epitaxial template. The epitaxial orientation relationships were revealed as follows: (0001) ZnO||(111) YSZ||(111) Si and [1¯21¯0] ZnO||[1¯10] YSZ||[1¯10] Si. Room temperature photoluminescence spectrum of the ZnO films showed the excitonic ultraviolet emission with few green emissions relevant to oxygen vacancies in the film. Furthermore, we fabricated ZnO nanostructures on the same (111) YSZ||(111) Si substrates by simply manipulating PLD conditions for the epitaxial film growth. The size control of the ZnO nanodots was realized by varying the number of laser pulses. A blueshift behavior induced by quantum confinement was observed, as the nanodot size decreases.
Water density and polarizability deduced from the refractive index determined by interferometric measurements up to 250 MPa
Authors: Weiss L. , Tazibt A. , Tidu A. , Aillerie M.
Published: April 2012

The refractive index of water is precisely determined in the visible light range as a function of the pressure until 250 MPa by means of a new measurement device that uses a special pipe tee included in an interferometer set. This technique allows revisiting the Bradley-Tait and Sellmeier equations to make them dependent on the wavelength and the pressure, respectively. The Bradley-Tait equation for the pressure dependence of the water refractive index is completed by a wavelength-dependent factor. Also, in the considered pressure and wavelength ranges, it is shown that the Sellmeier coefficients can be straightforwardly linked to the pressure, allowing the determination of the refractive index of water for either any wavelength or pressure. A new simple model allows the determination of the density of water as a function of the measured refractive index. Finally, the polarizability of water as function of pressure and wavelength is calculated by means of the Lorentz-Lorenz equation.
Do we have to explicitly model the ions in Brownian dynamics simulations of proteins?
Authors: Zimmer Melanie J. , Geyer Tihamér
Published: April 2012

Brownian dynamics (BD) is a very efficient coarse-grained simulation technique which is based on Einstein's explanation of the diffusion of colloidal particles. On these length scales well beyond the solvent granularity, a treatment of the electrostatic interactions on a Debye-Hückel (DH) level with its continuous ion densities is consistent with the implicit solvent of BD. On the other hand, since many years BD is being used as a workhorse simulation technique for the much smaller biological proteins. Here, the assumption of a continuous ion density, and therefore the validity of the DH electrostatics, becomes questionable. We therefore investigated for a few simple cases how far the efficient DH electrostatics with point charges can be used and when the ions should be included explicitly in the BD simulation. We find that for large many-protein scenarios or for binary association rates, the conventional continuum methods work well and that the ions should be included explicitly when detailed association trajectories or protein folding are investigated.
Geometrically induced electric polarization in conical topological insulators
Authors: Fonseca Jakson M. , Moura-Melo Winder A. , Pereira Afranio R.
Published: April 2012

Topological magnetoelectric and gravitation-like Aharonov-Bohm effects yield electric polarization of conical topological insulators that depends only on the cone aperture angle, δ. Concretely, under the same external conditions, wider (δ > 30°) and narrower (δ < 30°) cones appear to polarize in opposite directions. Observation of such a phenomenon could be faced as a microscopic physical realization of (2 + 1)-dimensional Einstein gravity.
Coupled systems of fractional equations related to sound propagation: Analysis and discussion
Authors: Garra Roberto , Polito Federico
Published: April 2012

In this paper, we analyse the propagation of a small density perturbation in a one-dimensional compressible fluid by means of fractional calculus modelling, replacing thus the ordinary time derivative with the Caputo fractional derivative in the constitutive equations. By doing so, we embrace a vast phenomenology, including subdiffusive, superdiffusive, and also memoryless processes such as classical diffusions. From a mathematical point of view, we study systems of coupled fractional equations, leading to fractional diffusion equations or to equations with sequential fractional derivatives. In this framework, we also propose a method to solve partial differential equations with sequential fractional derivatives by analysing the corresponding coupled system of equations.
Attenuation of propagating spin wave induced by layered nanostructures
Authors: Sekiguchi K. , Vader T. N. , Yamada K. , Fukami S. , Ishiwata N. , Seo S. M. , Lee S. W. , Lee K. J. , Ono T.
Published: April 2012

Spin wave attenuation in the layered [FeNi/Pt]6/FeNi thin films was investigated by the time-domain electrical measurement. The spin-wave waveform was detected with an asymmetric coplanar strip transmission line, as an induced voltage flowing into a fast oscilloscope. We report that the amplitude of a spin-wave packet was systematically changed by controlling the thickness of a platinum layer, up to a maximum change of 50%. The virtues of spin wave, ultrafast propagation velocity and non-reciprocal emission, are preserved in this manner. This means that the Pt layer can manipulate an arbitral power-level of spin-wave input signal (reliable attenuator).
Design of strain-engineered quantum tunneling devices for topological surface states
Authors: Zhao L. , Liu Junwei , Tang Peizhe , Duan Wenhui
Published: April 2012

Strain-dependent charge and spin transport on a topological insulator (TI) surface are investigated by combining first-principles calculations with quantum tunneling theory. It is shown that the Dirac point of helical surface states can be significantly shifted by applying compressive uniaxial strain. As an example of strain engineering applications based on this effect, a strain-induced quantum tunneling nanostructure is designed, where the tunneling conductance and the spin texture of surface states can be sensitively modulated by strain. Our work suggests that various local strain patterns can be integrated to manipulate surface states in all-TI-based spintronic nanodevices.
Transmission and temperature sensing characteristics of a selectively liquid-filled photonic-bandgap-fiber-based Sagnac interferometer
Authors: Zheng Xibao , Liu Yan-ge , Wang Zhi , Han Tingting , Wei Chengli , Chen Jinjie
Published: April 2012

A selectively liquid-filled photonic-bandgap-fiber-based Sagnac interferometer is proposed and demonstrated. Extraordinary transmission and sensing characteristics of the interferometer are observed and investigated theoretically and experimentally. Due to the unique modal and group birefringence characteristics of the material-infiltrated photonic bandgap fiber, the temperature sensitivity of the interference peaks strongly depends on the wavelength. Furthermore, the interference peaks at the two edges of the bandgap appear to shift in the opposite direction alongside changes in the temperature, providing a method of achieving two- or multi-parameter simultaneous sensing measurement with a compact structure.
In-situ nanoscale mapping of surface potential in all-solid-state thin film Li-ion battery using Kelvin probe force microscopy
Authors: Zhu Jing , Zeng Kaiyang , Lu Li
Published: April 2012

This paper presents an in-situ study by combining contact dc-writing in biased scanning probe microscopy and non-contact Kelvin probe force microscopy to characterize the effect of bias-induced Li+ insertion/extraction on the changes of surface potential of TiO2 anode in an all-solid-state thin film Li-ion battery at nanoscale. With single layer TiO2 film as the reference, the factors affecting the changes of the surface potential, including the Fermi energy level shift and charge screening related to TiO2 semiconductor behavior, and bias-induced Li+ intercalation/ de-intercalation related to battery behavior are investigated. Surface potential hysteresis loop can be formed for TiO2 anode film, in which the potential value increases under the positive polarization and decreases under the negative polarization. In addition, TiO2 anode film after Li+ insertion/extraction cycles has a lower surface potential, indicating the decrease of charge sustaining capacity and the surface electrical degradation. In addition, surface potential barriers (pits) after the positive (negative) polarization have been also observed, which is mainly attributed to the different electrical properties and charge accumulation at grain boundaries.
Operation mechanism of Schottky barrier nonvolatile memory with high conductivity InGaZnO active layer
Authors: Thuy Trinh Thanh , Duy Nguyen Van , Hanh Nguyen Hong , Raja Jayapal , Jang Juyeon , Jang Kyungsoo , Baek Kyunghyun , Ai Dao Vinh , Yi Junsin
Published: April 2012

Influence of Schottky contact between source/drain electrodes and high conductivity a-InGaZnO active layer to the performance of nonvolatile memory devices was first proposed. The Schottky barrier devices faced to the difficulty on electrical discharging process due to the energy barrier forming at the interface, which can be resolved by using Ohmic devices. A memory window of 2.83 V at programming/erasing voltage of ±13 V for Ohmic and 5.58 V at programming voltage of 13 V and light assisted erasing at −7 V for Schottky devices was obtained. Both memory devices using SiO2/SiOx/SiOxNy stacks showed a retention exceeding 70% of trapped charges 10 yr with operation voltages of ±13 V at an only programming duration of 1 ms.
Structure of Si-capped Ge/SiC/Si (001) epitaxial nanodots: Implications for quantum dot patterning
Authors: Petz C. W. , Yang D. , Levy J. , Floro J. A.
Published: April 2012

Artificially ordered quantum dot (QD) arrays, where confined carriers can interact via direct exchange coupling, may create unique functionalities such as cluster qubits and spintronic bandgap systems. Development of such arrays for quantum computing requires fine control over QD size and spatial arrangement on the sub-35 nm length scale. We employ electron-beam irradiation to locally decompose ambient hydrocarbons onto a bare Si (001) surface. These carbonaceous patterns are annealed in ultra-high vacuum (UHV), forming ordered arrays of nanoscale SiC precipitates that have been suggested to template subsequent epitaxial Ge growth to form ordered QD arrays. We show that 3C-SiC nanodots form, in cube-on-cube epitaxial registry with the Si substrate. The SiC nanodots are fully relaxed by misfit dislocations and exhibit small lattice rotations with respect to the substrate. Ge overgrowth at elevated deposition temperatures, followed by Si capping, results in expulsion of the Ge from SiC template sites due to the large chemical and lattice mismatch between Ge and C. Maintaining an epitaxial, low-defectivity Si matrix around the quantum dots is important for creating reproducible electronic and spintronic coupling of states localized at the QDs.
Integrability of nonlinear wave equations and solvability of their initial value problem
Authors: Borgna Juan Pablo , Degasperis Antonio , De Leo Mariano Fernando , Rial Diego
Published: April 2012

We investigate one particular prototypical system of evolution equations in 1+1 dimensions, which models the (nonlocal) interaction of two waves in quadratic nonlinear media. These equations are integrable as they possess a Lax pair. We consider the spectral method of solving the associated initial value problem and, as recently pointed out, we show that generically the associated initial value problem cannot be linearized. We further elaborate on the integrability issue for this model by displaying the corresponding conservation laws and the motion of a particular soliton.
Fast programming metal-gate Si quantum dot nonvolatile memory using green nanosecond laser spike annealing
Authors: Lien Yu-Chung , Shieh Jia-Min , Huang Wen-Hsien , Tu Cheng-Hui , Wang Chieh , Shen Chang-Hong , Dai Bau-Tong , Pan Ci-Ling , Hu Chenming , Yang Fu-Liang
Published: April 2012

The ultrafast metal-gate silicon quantum-dot (Si-QD) nonvolatile memory (NVM) with program/erase speed of 1 μs under low operating voltages of ± 7 V is achieved by thin tunneling oxide, in situ Si-QD-embedded dielectrics, and metal gate. Selective source/drain activation by green nanosecond laser spike annealing, due to metal-gate as light-blocking layer, responds to low thermal damage on gate structures and, therefore, suppresses re-crystallization/deformation/diffusion of embedded Si-QDs. Accordingly, it greatly sustains efficient charge trapping/de-trapping in numerous deep charge-trapping sites in discrete Si-QDs. Such a gate nanostructure also ensures excellent endurance and retention in the microsecond-operation Si-QD NVM.
Use of aquatic plants to create fluctuating hypoxia in an experimental environment
Authors: Flint Nicole , Pearson Richard G. , Crossland Michael R.
Published: April 2012

In freshwater systems, dissolved oxygen (DO) saturation frequently fluctuates, falling at night and rising during the day in response to respiration and photosynthesis, respectively, of aquatic biota. Low DO (hypoxia) is a common cause of fish kills in freshwater systems around the world. Laboratory studies on responses of fish to fluctuating DO are currently limited, and require techniques that produce a realistic cycle of DO depletion and replacement. Artificial DO-depletion mechanisms frequently used for hypoxia studies may underestimate the field effects of hypoxia on fish because of the lack of the naturally occurring synergistic effect of lower pH, and seldom allow fish to employ behavioural adaptations to hypoxia, such as aquatic surface respiration. We demonstrate proof-of-principle for an alternative method of creating fluctuating hypoxia in an experimental environment, using the natural rhythms of photosynthesis and respiration of aquatic plants to create realistic conditions. A range of volumes of aquatic macrophytes were used alone and in combination with fish to lower DO saturation in sealed freshwater aquaria, and achieved DO saturations as low as 1.3%. This cost-effective method can be deployed over long periods with minimal effort in comparison to traditional methods of DO reduction.
Breaking the ties that bind: New advances in centrosome biology
Authors: Mardin Balca R. , Schiebel Elmar
Published: April 2012

The centrosome, which consists of two centrioles and the surrounding pericentriolar material, is the primary microtubule-organizing center (MTOC) in animal cells. Like chromosomes, centrosomes duplicate once per cell cycle and defects that lead to abnormalities in the number of centrosomes result in genomic instability, a hallmark of most cancer cells. Increasing evidence suggests that the separation of the two centrioles (disengagement) is required for centrosome duplication. After centriole disengagement, a proteinaceous linker is established that still connects the two centrioles. In G2, this linker is resolved (centrosome separation), thereby allowing the centrosomes to separate and form the poles of the bipolar spindle. Recent work has identified new players that regulate these two processes and revealed unexpected mechanisms controlling the centrosome cycle.
Metal-diffusion-induced ITO nanoparticles at the organic/ITO interface
Authors: Li Yun , Liu Chuan , Tong Shengfu , Pan Lijia , Pu Lin , Minari Takeo , Tsukagoshi Kazuhito , Shi Yi
Published: April 2012

Metal-diffusion-induced indium tin oxide (ITO) nanoparticles have been observed at the 2-amino-4,5-dicyanoimidazole (AIDCN)/ITO interface. X-ray photoelectron spectroscopy depth profiles reveal that the indium (In) and tin (Sn) elements of the nanoparticles are diffused from the ITO film into the organic layer. And the bonding states of In and Sn in the nanoparticles are identified to be In2O3 and SnO2, respectively. Furthermore, it is found that the ITO nanoparticles have an influence on the electrical property, causing electrical switching behaviour in the Al/AIDCN/ITO sandwich structure.
Emerging roles for specific fatty acids in developmental processes
Authors: Vrablik Tracy L. , Watts Jennifer L.
Published: April 2012

Animals synthesize a vast range of fatty acids serving diverse cellular functions. The roles of specific fatty acids in early development are just beginning to be characterized. In the March 15, 2012, issue of Genes & Development, Kniazeva and colleagues (pp. 554–566) describe how the particular combination of a branched chain fatty acid and an acyl-CoA synthetase is required for critical cellular processes during early embryogenesis in Caenorhabditis elegans.
In Vitro Transfection with Plasmid DNA Using Polylysine Copolymers
Authors: Kim Sung Wan
Published: April 2012

The terplex system for delivering DNA to targeted cells comprises three components—stearyl polylysine (PLL), low-density lipoprotein (LDL), and DNA. This article describes a method for optimizing the relative amounts of these components and determining the transfection parameters for a given cell line.
Alignment and Calibration of Total Internal Reflection Fluorescence Microscopy Systems
Authors: Toomre Derek
Published: April 2012

Live cell fluorescent microscopy is important in elucidating dynamic cellular processes such as cell signaling, membrane trafficking, and cytoskeleton remodeling. Often, transient intermediate states are revealed only when imaged and quantitated at the single-molecule, vesicle, or organelle level. Such insight depends on the spatiotemporal resolution and sensitivity of a given microscopy method. Confocal microscopes optically section the cell and improve image contrast and axial resolution (>600 nm) compared with conventional epifluorescence microscopes. Another approach, which can selectively excite fluorophores in an even thinner optical plane (<100 nm) is total internal reflection fluorescence microscopy (TIRFM). The key principle of TIRFM is that a thin, exponentially decaying, evanescent field of excitation can be generated at the interface of two mediums of different refractive index (RI) (e.g., the glass coverslip and the biological specimen); as such, TIRFM is ill-suited to deep imaging of cells or tissue. However, for processes near the lower cell cortex, the sensitivity of TIRFM is exquisite. The recent availability of a very high numerical-aperture (NA) objective lens (>1.45) and turnkey TIRFM systems by all the major microscopy manufacturers has made TIRFM increasingly accessible and attractive to biologists, especially when performed in a quantitative manner and complemented with orthogonal genetic and molecular manipulations. This protocol describes the procedure for alignment and calibration of TIRFM systems using standard cellular samples. The goal is to correctly collimate and align the TIRF illuminator vis-à-vis the downstream optics. For illustration, a 488-nm laser and green fluorescent protein (GFP) filter cube are used.
Statistical approaches to assess intraspecific variations of morphological continuous characters: the case study of the family Phytoseiidae (Acari: Mesostigmata)
Authors: Tixier Marie‐Stephane
Published: April 2012

Statistical methods for delimiting species with morphological data remain woefully understudied. The present study presents statistical approaches to study the intraspecific variations of continuous characters used in species diagnosis. For this, the data set comprised 14 species of the mite family Phytoseiidae (Acari: Mesostigmata) and 23 continuous characters (seta lengths). The statistical approaches aim to determine (i) how intraspecific variations differ depending on the characters and species considered, and (ii) how to choose the number of specimens to be considered for characterizing intraspecific boundaries. The means of the related confident limits at 95% (rCL95) of the 14 species and the 23 setae are around 20%, suggesting that 95% of the specimens of a same species are included in the interval μ ± 0.2μ. No relationship was found between seta variations and the number of specimens considered for each species, nor for seta variations and their position on the mite body. However, a correlation between seta lengths and rCL95 means was observed. An abacus was proposed to determine the coefficient that must be applied to mean seta length to calculate the lower and upper limits of the interval that will include 95% of the specimens of a same species. The higher the precision around the mean, the higher the number of specimens considered. Furthermore, this number varies considerably depending on the characters and species considered for high precisions. However, for a priori error around the mean of 15%, the number of specimens needed to characterize the intraspecific variation is quite homogeneous and ten specimens would be required. I discuss the utility of such results to resolve some persistent problems in the alpha‐taxonomy of the family Phytoseiidae but also of other taxa.

© The Willi Hennig Society 2012.
Job discrimination against childhood cancer survivors in Japan: A cross‐sectional survey
Authors: Asami Keiko , Ishida Yasushi , Sakamoto Naoko
Published: April 2012

Background:  The aim of this study was to investigate the policies to identify job discrimination by company recruiters against childhood cancer survivors in Japan.

Methods:  We conducted a cross‐sectional study using a mailed questionnaire for the Japanese companies that were divided into three groups: companies listed on the stock market, companies not listed on the stock market, and public offices. We randomly selected 2000 of the 4000 listed companies and 2500 of the 4300 unlisted companies. We selected 47 public offices from prefectures and 17 from government ordinance‐designated cities. Outcomes were health certificate requirements, how to treat past medical history and present illness, childhood cancer survivors' employment experience, and company's policy for evaluating applicants based on past medical history and present illness.

Results:  Response rates were 17.7% for listed companies, 28.9% for unlisted companies, and 56.3% for public offices. A health certificate was required by 86% of listed companies, 77% of unlisted companies, and 75% of public offices. However, 33% of listed companies and 36% of unlisted companies, and none of the public offices demanded it at the time of application. Small numbers of private companies (0.7% of listed companies and 1.0% of unlisted companies) and public offices (4%) reject applicants outright if they have a disease in their past medical history. Using multivariate analysis, we found that large companies and company policies were significantly associated with the demand for a health certificate at the time of job applications.

Conclusions:  In Japan, employment‐related discrimination still occurs in a small number of companies and public offices.
Home mechanical ventilation in children is feasible in developing countries
Authors: Sovtic Aleksandar , Minic Predrag , Vukcevic Miodrag , Markovic‐Sovtic Gordana , Rodic Milan , Gajic Milan
Published: April 2012

Background:  The results of many national surveys on pediatric home mechanical ventilation (HMV) in developed countries have been presented elsewhere, but data from developing countries with low national incomes are scarce.

Methods:  Twenty‐nine pediatric patients, treated in the Mother and Child Institute of Serbia, who had been receiving long‐term ventilatory support at home, were surveyed. The major criterion for initiating HMV was hypercapnia, diagnosed by blood gas analysis, performed in the morning, after awakening. Other criteria were either symptoms of hypoventilation during the night associated with an apnea index of >5, or apnoea–hypopnoea index of >15, or nocturnal hypoxemia, defined as an oxygen saturation rate of <90% for >5% of total sleep time.

Results:  The mean age at initiation of HMV was 9.3 years (range 0.5–17.8 years). Patients waited for HMV initiation either in hospital or at home; the mean period was 6.3 months (range 1–18 months). The subjects received HMV for a mean of 25.06 months (range 3–119 months). There was a significant difference in the duration of HMV for different underlying diseases (P= 0.046), and mechanical malfunction was strongly dependent on the duration of HMV (P= 0.011). Eleven patients underwent invasive HMV via a tracheostomy, and 18 others received non‐invasive ventilation, via nasal and full‐face masks.

Conclusion:  HMV is feasible in developing countries. Valuable reimbursement policies as well as an organized and functional network are essential for its implementation, as a standard of care in leading national pediatric hospitals.
Effect of hydrocortisone therapy on severe leaky lung syndrome in ventilated preterm infants
Authors: Mizobuchi Masami , Iwatani Sota , Sakai Hitomi , Yoshimoto Seiji , Nakao Hideto
Published: April 2012

Background:  The aim of this study was (i) to determine the incidence and risk factors of severe leaky lung syndrome (sLLS), persistent pulmonary edema characterized by massive tracheal secretions and resistance to surfactant therapy, in extremely low gestational age newborns requiring ventilatory support; and (ii) to evaluate the effects of hydrocortisone (HC) therapy for sLLS on tracheal aspirate fluid (TAF) volume and β2‐microglobulin levels in TAF.

Methods:  Infants born at <28 weeks gestation requiring ventilation beyond day of life (DOL) 7 were included. Daily TAF volume changes were assessed using a TAF scoring system. Levels of TAF β2‐microglobulin, an indicator of capillary leakage, were measured at DOL0, 7, before, and 4 days after starting HC therapy (started at 4 mg/kg/day; tapered for 1–3 weeks).

Results:  Of the 54 infants enrolled, 24 (44%) were diagnosed with sLLS. Lower gestational age, lower birthweight, and higher TAF β2‐microglobulin levels at DOL7 were independent risk factors for sLLS. Seventeen infants with sLLS received HC therapy starting at DOL17 (median), with subsequent decreases in TAF volume and β2‐microglobulin levels.

Conclusions:  The incidence of sLLS, as defined in this study, was 44% in extremely low gestational age newborns requiring ventilator support beyond a week. HC therapy effectively reduced TAF volume and β2‐microglobulin levels, suggesting suppression of increased permeability of pulmonary capillaries in infants with sLLS.
Integrative Study of Brazilian Anurans: Geographic Distribution, Size, Environment, Taxonomy, and Conservation
Authors: Toledo Luís Felipe , Batista Rômulo Fernandes
Published: April 2012

Most megadiversity regions lack basic wild animal diversity information such as species lists. This absence of basic knowledge restricts the development and effectiveness of conservation action plans, which are urgently needed for animal groups such as amphibians, the most threatened vertebrate group in the world. In this study, we estimated Brazilian anuran diversity based on species range distribution shapes and evaluated factors that likely affect species lists, such as current taxonomy knowledge, current number of specimens collected in each region, biome characteristics, and anuran size (snout–vent length). We were able to demonstrate differences among the distributional patterns of species within each biome and each Brazilian federative state and among certain factors that influence their diversity, such as latitudinal variation. In this integrative study, we provide zoogeographic information about the richest (in terms of anuran biodiversity) country in the world (at least 849 described species, about 60% of which are endemic), which may be fundamental to future conservation actions in Brazil.
Casting a net: fibres produced by Microcystis sp. in field and laboratory populations
Authors: Harel Moshe , Weiss Gad , Daniel Einat , Wilenz Avraham , Hadas Ora , Sukenik Assaf , Sedmak Bojan , Dittmann Elke , Braun Sergei , Kaplan Aaron
Published: April 2012

The reasons for the apparent dominance of the toxic cyanobacterium Microcystis sp., reflected by its massive blooms in many fresh water bodies, are poorly understood. We show that in addition to a large array of secondary metabolites, some of which are toxic to eukaryotes, Microcystis sp. secretes large amounts of fibrous exopolysaccharides that form extremely long fibres several millimetres in length. This phenomenon was detected in field and laboratory cultures of various Microcystis strains. In addition, we have identified and characterized three of the proteins associated with the fibres and the genes encoding them in Microcystis sp. PCC 7806 but were unable to completely delete them from its genome. Phylogenetic analysis of the most abundant one, designated IPF‐469, showed its presence only in cyanobacteria. Its closest relatives were detected in Synechocystis sp. PCC 6803 and in Cyanothece sp. strains; in the latter the genomic organization of the IPF‐469 was highly conserved. IPF‐469 and the other two proteins identified here, a haloperoxidase and a haemolysin‐type calcium‐binding protein, may be part of the fibres secretion pathway. The biological role of the fibres in Microcystis sp. is discussed.
A Micromechanically Based Anisotropic Constitutive Model for the Microtubule Wall
Authors: Arslan Melis , Boyce Mary C.
Published: April 2012

Microtubules serve as one of the structural components of the cell and govern several important cellular functions including mitosis and vesicular transport. Microtubules are comprised of tubulin subunits formed by α and β tubulin dimers arranged in a cylindrical hollow tube with diameter ∼20 nm. The tube is typically comprised of 13 or 14 protofilaments extending axially and staggered to give a spiral configuration. The longitudinal bonds between the tubulin dimers are much stiffer and stronger than the lateral bonds. This gives a highly anisotropic structure and mechanical properties of the microtubule. In this work, the aim is to define a complete set of effective anisotropic elastic properties of the tube wall that capture the atomistic interactions. A seamless microtubule wall is represented as a two dimensional triangulated lattice of dimers from which a representative volume element is defined. A harmonic potential is adapted for the dimer–dimer interactions. Estimating the lattice elastic constants and following the methodology from the analysis of the mechanical behavior of the triangulated spectrin network of the red blood cell membrane (Arslan and Boyce, 2006, “Constitutive Modeling of the Finite Deformation Behavior of Membranes Possessing a Triangulated Network Microstructure,” ASME J. Appl. Mech., 73, pp. 536–543), a general anisotropic hyperelastic strain energy function is formulated and used to define the effective anisotropic continuum level constitutive model of the mechanical behavior of the microtubule wall. In particular, the role of the anisotropic microstructure resulting from the different lattice bond lengths and bond stiffnesses is examined to explain nature’s optimization of microstructural orientation in providing a high axial stiffness combined with low shear stiffness.
Perturbation Finite Element Transfer Matrix Method for Random Eigenvalue Problems of Uncertain Structures
Authors: Rong Bao , Rui Xiaoting , Tao Ling
Published: April 2012

The rapid computation of random eigenvalue problems of uncertain structures is the key point in structural dynamics, and it is prerequisite to the efficient dynamic analysis and optimal design of structures. In this paper, by combining finite element-transfer matrix method (FE-TMM) with perturbation method, a new method named as perturbation FE-TMM is presented for random eigenvalue problems of uncertain structures. By using the proposed method, the rapid computation of random eigenvalue problems of uncertain structures with complicated shapes and boundaries can be achieved, and the repeated eignvalues and characteristic vectors can be solved conveniently. Compared with stochastic finite element method, this method has the low memory requirement, high computational efficiency and high computational stability. It has more advantages for dynamic design of uncertain structures. Formulations as well as some numerical examples are given to validate the method.
Multiterm Extended Kantorovich Method for Three-Dimensional Elasticity Solution of Laminated Plates
Authors: Kapuria Santosh , Kumari Poonam
Published: April 2012

In an article recently published in this journal, the powerful single-term extended Kantorovich method (EKM) originally proposed by Kerr in 1968 for two-dimensional (2D) elasticity problems was further extended by the authors to the three-dimensional (3D) elasticity solution for laminated plates. The single-term solution, however, failed to predict accurately the stress field near the boundaries; thus limiting its applicability. In this work, the method is generalized to the multiterm solution. The solution is developed using the Reissner-type mixed variational principle that ensures the same order of accuracy for displacements and stresses. An n-term solution generates a set of 8n algebraic-ordinary differential equations in the in-plane direction and a similar set in the thickness direction for each lamina, which are solved in close form. The problem of large eigenvalues associated with higher order terms is addressed. In addition to the composite laminates considered in the previous article, results are also presented for sandwich laminates, for which the inaccuracy in the single-term solution is even more prominent. It is shown that considering just one or two additional terms in the solution (n = 2 or 3) leads to a very accurate prediction and drastic improvement over the single-term solution (n = 1) for all entities including the stress field near the boundaries. This work will facilitate development of near-exact solutions of many important unresolved problems involving 3D elasticity, such as the free edge stresses in laminated structures under bending, tension and torsion.
A genetic linkage map of crested wheatgrass based on AFLP and RAPD markers
Authors: Yu Xiaoxia , Li Xiaolei , Ma Yanhong , Yu Zhuo , Li Zaozhe
Published: April 2012

Using a population of 105 interspecific F2 hybrids derived from a cross between Agropyron mongolicum Keng and Agropyron cristatum (L.) Gaertn. ‘Fairway’ as a mapping population, a genetic linkage map of crested wheatgrass was constructed based on AFLP and RAPD molecular markers. A total of 175 markers, including 152 AFLP and 23 RAPD markers, were ordered in seven linkage groups. The map distance was 416 cM, with a mean distance of 2.47 cM between markers. The number of markers ranged from 13 to 46 in each linkage group and the length of groups ranged from 18 to 104 cM. The research found that 30 out of 175 molecular markers showed segregation distortion, accounting for 17% of all markers. This is the first genetic linkage map of crested wheatgrass. This map will facilitate gene localization, cloning, and molecular marker-assisted selection in the future.
Error Modeling and Analysis for InSAR Spatial Baseline Determination of Satellite Formation Flying
Authors: Tu Jia , Gu Defeng , Wu Yi , Yi Dongyun
Published: April 2012

Spatial baseline determination is a key technology for interferometric synthetic aperture radar (InSAR) missions. Based on the intersatellite baseline measurement using dual‐frequency GPS, errors induced by InSAR spatial baseline measurement are studied in detail. The classifications and characters of errors are analyzed, and models for errors are set up. The simulations of single factor and total error sources are selected to evaluate the impacts of errors on spatial baseline measurement. Single factor simulations are used to analyze the impact of the error of a single type, while total error sources simulations are used to analyze the impacts of error sources induced by GPS measurement, baseline transformation, and the entire spatial baseline measurement, respectively. Simulation results show that errors related to GPS measurement are the main error sources for the spatial baseline determination, and carrier phase noise of GPS observation and fixing error of GPS receiver antenna are main factors of errors related to GPS measurement. In addition, according to the error values listed in this paper, 1 mm level InSAR spatial baseline determination should be realized.
PEDF and VEGF-A Output from Human Retinal Pigment Epithelial Cells Grown on Novel Microcarriers
Authors: Falk Torsten , Congrove Nicole R. , Zhang Shiling , McCourt Alexander D. , Sherman Scott J. , McKay Brian S.
Published: April 2012

Human retinal pigment epithelial (hRPE) cells have been tested as a cell-based therapy for Parkinson’s disease but will require additional study before further clinical trials can be planned. We now show that the long-term survival and neurotrophic potential of hRPE cells can be enhanced by the use of FDA-approved plastic-based microcarriers compared to a gelatin-based microcarrier as used in failed clinical trials. The hRPE cells grown on these plastic-based microcarriers display several important characteristics of hRPE foundin vivo: (1) characteristic morphological features, (2) accumulation of melanin pigment, and (3) high levels of production of the neurotrophic factors pigment epithelium-derived factor (PEDF) and vascular endothelial growth factor-A (VEGF-A). Growth of hRPE cells on plastic-based microcarriers led to sustained levels (>1 ng/ml) of PEDF and VEGF-A in conditioned media for two months. We also show that the expression of VEGF-A and PEDF is reciprocally regulated by activation of the GPR143 pathway. GPR143 is activated by L-DOPA (1 μM) which decreased VEGF-A secretion as opposed to the previously reported increase in PEDF secretion. The hRPE microcarriers are therefore novel candidate delivery systems for achieving long-term delivery of the neuroprotective factors PEDF and VEGF-A, which could have a value in neurodegenerative conditions such as Parkinson’s disease.
A Model for Selecting Technologies in New Product Development
Authors: Kang He-Yau , Lee Amy H. I. , Chang Chao-Cheng , Kang Mei-Sung
Published: April 2012

Due to fast changing technologies, shortening product lifecycles, and increased global competition, companies today often need to develop new products continuously and faster. Successful introduction and acceleration of new product development (NPD) is important to obtain competitive advantage for companies. Since technology selection for NPD involves complex decision makings that are critical to the profitability and growth of a company, the selection of the most appropriate technology for a new product requires the use of a robust decision‐making framework capable of evaluating several technology candidates based on multiple criteria. This paper presents an integrated model that adopts interpretive structural modeling (ISM) and fuzzy analytic network process (FANP) to evaluate various different available technologies for NPD. The ISM is used to understand the interrelationships among the factors, and the FANP is to facilitate the evaluation process of decision makers under an uncertain environment with interrelated factors. A case study of a flat panel manufacturer is performed to examine the practicality of the proposed model. The results show that the model can be applied for group decision making on the available technology evaluation and selection in new product development.
Using a Geographical-Information-System-Based Decision Support to Enhance Malaria Vector Control in Zambia
Authors: Chanda Emmanuel , Mukonka Victor Munyongwe , Mthembu David , Kamuliwo Mulakwa , Coetzer Sarel , Shinondo Cecilia Jill
Published: April 2012

Geographic information systems (GISs) with emerging technologies are being harnessed for studying spatial patterns in vector-borne diseases to reduce transmission. To implement effective vector control, increased knowledge on interactions of epidemiological and entomological malaria transmission determinants in the assessment of impact of interventions is critical. This requires availability of relevant spatial and attribute data to support malaria surveillance, monitoring, and evaluation. Monitoring the impact of vector control through a GIS-based decision support (DSS) has revealed spatial relative change in prevalence of infection and vector susceptibility to insecticides and has enabled measurement of spatial heterogeneity of trend or impact. The revealed trends and interrelationships have allowed the identification of areas with reduced parasitaemia and increased insecticide resistance thus demonstrating the impact of resistance on vector control. The GIS-based DSS provides opportunity for rational policy formulation and cost-effective utilization of limited resources for enhanced malaria vector control.
Differentiating between Hemorrhagic Infarct and Parenchymal Intracerebral Hemorrhage
Authors: Choi P. M. C. , Ly J. V. , Srikanth V. , Ma H. , Chong W. , Holt M. , Phan T. G.
Published: April 2012

Differentiating hemorrhagic infarct from parenchymal intracerebral hemorrhage can be difficult. The immediate and long-term management of the two conditions are different and hence the importance of accurate diagnosis. Using a series of intracerebral hemorrhage cases presented to our stroke unit, we aim to highlight the clues that may be helpful in distinguishing the two entities. The main clue to the presence of hemorrhagic infarct on computed tomography scan is the topographic distribution of the stroke. Additional imaging modalities such as computed tomography angiogram, perfusion, and magnetic resonance imaging may provide additional information in differentiating hemorrhagic infarct from primary hemorrhages.
Resistance of Subtype C HIV-1 Strains to Anti-V3 Loop Antibodies
Authors: Almond David , Krachmarov Chavdar , Swetnam James , Zolla-Pazner Susan , Cardozo Timothy
Published: April 2012

HIV-1’s subtype C V3 loop consensus sequence exhibits increased resistance to anti-V3 antibody-mediated neutralization as compared to the subtype B consensus sequence. The dynamic 3D structure of the consensus C V3 loop crown, visualized byab initiofolding, suggested that the resistance derives from structural rigidity and non-β-strand secondary protein structure in the N-terminal strand of theβ-hairpin of the V3 loop crown, which is where most known anti-V3 loop antibodies bind. The observation of either rigidity or non-β-strand structure in this region correlated with observed resistance to antibody-mediated neutralization in a series of chimeric pseudovirus (psV) mutants. The results suggest the presence of an epitope-independent, neutralization-relevant structural difference in the antibody-targeted region of the V3 loop crown between subtype C and subtype B, a difference that we hypothesize may contribute to the divergent pattern of global spread between these subtypes. As antibodies to a variable loop were recently identified as an inverse correlate of risk for HIV infection, the structure-function relationships discussed in this study may have relevance to HIV vaccine research.
The Modulation of PPARγ1 and PPARγ2 mRNA Expression by Ciglitazone in CD3/CD28-Activated Naïve and Memory CD4+ T Cells
Authors: Norazmi Mohd Nor , Mohamed Rafeezul , Nurul Asma Abdullah , Yaacob Nik Soriani
Published: April 2012

Given their roles in immune regulation, the expression of the nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) 1 and 2 isoforms was investigated in human naïve (CD45RA+) and memory (CD45RO+) CD4+ T cells. Stimulation of both types of cells via the CD3/CD28 pathway resulted in high expression of both PPARγ receptors as measured by real-time PCR. Treatment with the PPARγ agonist, ciglitazone, increased PPARγ1 expression but decreased PPARγ2 expression in stimulated naïve and memory cells. Furthermore, when present, the magnitude of both PPARγ receptors expression was lower in naïve cells, perhaps suggesting a lower regulatory control of these cells. Similar profiles of selected proinflammatory cytokines were expressed by the two cell types following stimulation. The induction of PPARγ1 and suppression of PPARγ2 expressions in naïve and memory CD4+ T cells in the presence of ciglitazone suggest that the PPARγ subtypes may have different roles in the regulation of T-cell function.
Pathogenetic and Prognostic Significance of Inactivation of RASSF Proteins in Human Hepatocellular Carcinoma
Authors: Calvisi Diego F. , Evert Matthias , Dombrowski Frank
Published: April 2012

Hepatocellular carcinoma (HCC) is one of the most frequent solid tumors worldwide, with limited treatment options and a dismal prognosis. Thus, there is a strong need to expand the basic and translational research on this deadly disease in order to improve the prognosis of HCC patients. Although the etiologic factors responsible for HCC development have been identified, the molecular pathogenesis of liver cancer remains poorly understood. Recent evidence has shown the frequent downregulation of Ras association domain family (RASSF) proteins both in the early and late stages of hepatocarcinogenesis. Here, we summarize the data available on the pathogenetic role of inactivation of RASSF proteins in liver cancer, the molecular mechanisms responsible for suppression of RASSF proteins in HCC, and the possible clinical implications arising from these discoveries. Altogether, the data indicate that inactivation of the RASSF1A tumor suppressor is ubiquitous in human liver cancer, while downregulation of RASSF2 and RASSF5 proteins is limited to specific HCC subsets. Also, the present findings speak in favour of therapeutic strategies aimed at reexpressingRASSF1A,RASSF2, andRASSF5genes and/or inactivating the RASSF cellular inhibitors for the treatment of human liver cancer.