Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

Determination of C-13 Chemical Shift Anisotropy Tensors and Molecular Order of 4-Hexyloxybenzoic Acid

4-Alkoxy benzoic acids belong to an important class of thermotropic liquid crystals that are structurally simple and often used as starting materials for many novel mesogens. 4-Hexyloxybenzoic acid (HBA) is a homologue of the same series and exhibits an enantiotropic nematic phase. As this molecule could serve as an ideal model compound, high resolution C-13 NMR studies of HEA in solution, solid, and liquid crystalline phases have been undertaken. In the solid state, two-dimensional separation of undistorted powder patterns by effortless recoupling (2D SUPER) experiments have been carried out to estimate the magnitude of the components of the chemical shift anisotropy (GSA) tensor of all the aromatic carbons. These values have been used subsequently for calculating the orientational order parameters in the liquid crystalline phase. The GSA values computed by density functional theory (DFT) calculations showed good agreement with the 2D SUPER values. Additionally, C-13-H-1 dipolar couplings in the nematic phase have been determined by separated local field (SLF) spectroscopy at various temperatures and were used for computing the order parameters, which compared well with those calculated by using the chemical shifts. It is anticipated that the CSA values determined for MBA would be useful for the assignment of carbon chemical shifts and for the study of order and dynamics of structurally similar novel mesogens in their nematic phases.

Methods for Detecting Early Warnings of Critical Transitions in Time Series Illustrated Using Simulated Ecological Data

Many dynamical systems, including lakes, organisms, ocean circulation patterns, or financial markets, are now thought to have tipping points where critical transitions to a contrasting state can happen. Because critical transitions can occur unexpectedly and are difficult to manage, there is a need for methods that can be used to identify when a critical transition is approaching. Recent theory shows that we can identify the proximity of a system to a critical transition using a variety of so-called `early warning signals', and successful empirical examples suggest a potential for practical applicability. However, while the range of proposed methods for predicting critical transitions is rapidly expanding, opinions on their practical use differ widely, and there is no comparative study that tests the limitations of the different methods to identify approaching critical transitions using time-series data. Here, we summarize a range of currently available early warning methods and apply them to two simulated time series that are typical of systems undergoing a critical transition. In addition to a methodological guide, our work offers a practical toolbox that may be used in a wide range of fields to help detect early warning signals of critical transitions in time series data.

A Series of Trifacial Pd6 Molecular Barrels with Porphyrin Walls

Three new nanoscopic trigonal prisms, (tmen)6Pd6(H2L)3](NO3)12 (1), (Meen)6Pd6(H2L)3](NO3)12 (2), and (2,2'-bipy)6Pd6(H2L)3](NO3)12 (3), have been synthesized in excellent yields through single-step metalligand-coordination-driven self-assembly using 5,10,15,20-tetrakis(3-pyridyl)porphyrin (H2L) as a donor and cis-blocked PdII 90 degrees acceptors. These complexes were fully characterized by spectroscopic studies and single-crystal X-ray diffraction. All of these barrels quantitatively bind ZnII ions in the N4 pockets of the porphyrin walls at room temperature. Their corresponding zinc-embedded complexes, (tmen)6Pd6(ZnL)3](NO3)12 (1?a), (Meen)6Pd6(ZnL)3](NO3)12 (2?a), and (2,2'-bipy)6Pd6(ZnL)3](NO3)12 (3?a), were synthesized under ambient conditions by the post-synthetic binding of ZnII ions into the H2N4 pockets of the porphyrin walls of these complexes. These zinc-embedded complexes were characterized by electronic absorption, fluorescence emission, 1H NMR spectroscopy, as well as elemental analysis. Complexes 13 exhibited considerable microporosity in their solid state. Complex 1 was an efficient adsorbent for nitrogen gas and EtOH, MeOH, and water vapors.

LOCAL TWO-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS OF THE COLLISIONLESS MAGNETOROTATIONAL INSTABILITY

The magnetorotational instability (MRI) is a crucial mechanism of angular momentum transport in a variety of astrophysical accretion disks. In systems accreting at well below the Eddington rate, such as the central black hole in the Milky Way (Sgr A*), the plasma in the disk is essentially collisionless. We present a nonlinear study of the collisionless MRI using first-principles particle-in-cell plasma simulations. We focus on local two-dimensional (axisymmetric) simulations, deferring more realistic three-dimensional simulations to future work. For simulations with net vertical magnetic flux, the MRI continuously amplifies the magnetic field, B, until the Alfven velocity, v(A), is comparable to the speed of light, c (independent of the initial value of v(A)/c). This is consistent with the lack of saturation of MRI channel modes in analogous axisymmetric MHD simulations. The amplification of the magnetic field by the MRI generates a significant pressure anisotropy in the plasma (with the pressure perpendicular to B being larger than the parallel pressure). We find that this pressure anisotropy in turn excites mirror modes and that the volume-averaged pressure anisotropy remains near the threshold for mirror mode excitation. Particle energization is due to both reconnection and viscous heating associated with the pressure anisotropy. Reconnection produces a distinctive power-law component in the energy distribution function of the particles, indicating the likelihood of non-thermal ion and electron acceleration in collisionless accretion disks. This has important implications for interpreting the observed emission-from the radio to the gamma-rays-of systems such as Sgr A*.

A Rare Phenoxido/Acetato/Azido Bridged Trinuclear and an Unprecedented Phenoxido/Azido Bridged One-Dimensional Polynuclear Nickel(II) Complexes: Synthesis, Crystal Structure, and Magnetic Properties with Theoretical Investigations on the Exchange Mechanism

The reaction of a tridentate Schiff base ligand HL (2-(3-dimethylaminopropylimino)-methyl]-phenol) with Ni(II) acetate or perchlorate salts in the presence of azide as coligand has led to two new Ni(II) complexes of formulas Ni3L2(OAc)(2)(mu(1,1)-N-3)(2)(H2O)(2)]center dot 2H(2)O (1) and Ni2L2(mu(1,1)-N-3) (mu(1,3)-N-3)](n)(2). Single crystal X-ray structures show that complex 1 is a linear trinuclear Ni(II) compound containing a mu(2)-phenwddo, an end-on (EO) azido and a syn-syn acetato bridge between the terminal and the central Ni(II) ions. Complex 2 can be viewed as a one-dimensional (1D) chain in which the triply bridged (di-mu(2)-phenoxido and EO azido) dimeric Ni-2 units are linked to each other in a zigzag pattern by a single end-to-end (EE) azido bridge. Variable-temperature magnetic susceptibility studies indicate the presence of moderate ferromagnetic exchange coupling in complex 1 with J value of 16.51(6) cm(-1). The magnetic behavior of 2 can be fitted in an alternating ferro- and antiferromagnetic model J(FM) = +34.2(2.8) cm(-1) and J(AF) = -21.6(1.1) cm(-1)] corresponding to the triple bridged dinuclear core and EE azido bridge respectively. Density functional theory (DFT) calculations were performed to corroborate the magnetic results of 1 and 2. The contributions of the different bridges toward magnetic interactions in both compounds have also been calculated.

Colossal nonsaturating linear magnetoresistance in two-dimensional electron systems at a GaAs/(Al,Ga)As heterointerface

Engineering devices with a large electrical response to magnetic field is of fundamental importance for a range of applications such as magnetic field sensing and magnetic read heads. We show that a colossal nonsaturating linear magnetoresistance (NLMR) arises in two-dimensional electron systems hosted in a GaAs/AlGaAs heterostructure in the strongly insulating regime. When operated at high source-drain bias, the magnetoresistance of our devices increases almost linearly with magnetic field, reaching nearly 10 000% at 8 T, thus surpassing many known nonmagnetic materials that exhibit giant NLMR. The temperature dependence and mobility analysis indicate that the NLMR has a purely classical origin, driven by nanoscale inhomogeneities. A large NLMR combined with small device dimensions makes these systems an attractive candidate for on-chip magnetic field sensing.

VAM applied to dimensional reduction of non-linear hyperelastic plates

This work aims at dimensional reduction of non-linear isotropic hyperelastic plates in an asymptotically accurate manner. The problem is both geometrically and materially non-linear. The geometric non-linearity is handled by allowing for finite deformations and generalized warping while the material non-linearity is incorporated through hyperelastic material model. The development, based on the Variational Asymptotic Method (VAM) with moderate strains and very small thickness to shortest wavelength of the deformation along the plate reference surface as small parameters, begins with three-dimensional (3-D) non-linear elasticity and mathematically splits the analysis into a one-dimensional (1-D) through-the-thickness analysis and a two-dimensional (2-D) plate analysis. Major contributions of this paper are derivation of closed-form analytical expressions for warping functions and stiffness coefficients and a set of recovery relations to express approximately the 3-D displacement, strain and stress fields. Consistent with the 2-D non-linear constitutive laws, 2-D plate theory and corresponding finite element program have been developed. Validation of present theory is carried out with a standard test case and the results match well. Distributions of 3-D results are provided for another test case. (c) 2012 Elsevier Ltd. All rights reserved.

Porous Three Dimensional Arrays of Plasmonic Nanoparticles

Plasmonic interactions in a well-defined array of metallic nanoparticles can lead to interesting optical effects, such as local electric field enhancement and shifts in the extinction spectra, which are of interest in diverse technological applications, including those pertaining to biochemical sensing and photonic circuitry. Here, we report on a single-step wafer scale fabrication of a three-dimensional array of metallic nanoparticles whose sizes and separations can be easily controlled to be anywhere between fifty to a few hundred nanometers, allowing the optical response of the system to be tailored with great control in the visible region of the spectrum. The substrates, apart from having a large surface area, are inherently porous and therefore suitable for optical sensing applications, such as surface enhanced Raman scattering, containing a high density of spots with enhanced local electric fields arising from plasmonic couplings.

Unconventional metallicity and giant thermopower in a strongly interacting two-dimensional electron system

We present thermal and electrical transport measurements of low-density (10(14) m(-2)), mesoscopic two-dimensional electron systems (2DESs) in GaAs/AlGaAs heterostructures at sub-Kelvin temperatures. We find that even in the supposedly strongly localized regime, where the electrical resistivity of the system is two orders of magnitude greater than the quantum of resistance h/e(2), the thermopower decreases linearly with temperature indicating metallicity. Remarkably, the magnitude of the thermopower exceeds the predicted value in noninteracting metallic 2DESs at similar carrier densities by over two orders of magnitude. Our results indicate a new quantum state and possibly a novel class of itinerant quasiparticles in dilute 2DESs at low temperatures where the Coulomb interaction plays a pivotal role.

Natural convection in a series of thermally interacting cavities with wall mounted heaters

Laminar natural convection in a series of thermally interacting cavities is numerically studied. Each cavity consists of a conducting bottom wall with a surface mounted heater. The side walls of the cavities are isothermally cooled. Each cavity thermally interacts with its adjacent cavities through the conducting walls. Flow and heat transfer characteristics are studied in detail for various Rayleigh numbers. The convection characteristics in multiple cavities are compared with those in single independent cavity. The thermal interaction between the cavities results in lower temperatures compared with those in independent cavities. While heat is rejected into the adjacent upper cavity through some portion of the conducting wall, heat is received from the adjacent cavity through the remaining portion of the wall. The influence of substrate conductivity on heat exchange between adjacent cavities are examined. Substrate conductivity shows strong effect on temperature distribution. When cooling at both vertical sides is changed to one side cooling, the heat transfer characteristics are changed drastically and many interesting flow features are observed. Effects of cavity aspect ratio is studied and higher heat transfer rates are observed at higher aspect ratios. Correlations for dimensionless temperature maximum and average Nusselt number are presented in terms of Rayleigh number.

Recapitulating tumour microenvironment in chitosan-gelatin three-dimensional scaffolds: an improved in vitro tumour model

Owing to the reduced co-relationship between conventional flat Petri dish culture (two-dimensional) and the tumour microenvironment, there has been a shift towards three-dimensional culture systems that show an improved analogy to the same. In this work, an extracellular matrix (ECM)-mimicking three-dimensional scaffold based on chitosan and gelatin was fabricated and explored for its potential as a tumour model for lung cancer. It was demonstrated that the chitosan-gelatin (CG) scaffolds supported the formation of tumoroids that were similar to tumours grown in vivo for factors involved in tumour-cell-ECM interaction, invasion and metastasis, and response to anti-cancer drugs. On the other hand, the two-dimensional Petri dish surfaces did not demonstrate gene-expression profiles similar to tumours grown in vivo. Further, the three-dimensional CG scaffolds supported the formation of tumoroids, using other types of cancer cells such as breast, cervix and bone, indicating a possible wider potential for in vitro tumoroid generation. Overall, the results demonstrated that CG scaffolds can be an improved in vitro tool to study cancer progression and drug screening for solid tumours.

Projecting low-dimensional chaos from spatiotemporal dynamics in a model for plastic instability

We investigate the possibility of projecting low-dimensional chaos from spatiotemporal dynamics of a model for a kind of plastic instability observed under constant strain rate deformation conditions. We first discuss the relationship between the spatiotemporal patterns of the model reflected in the nature of dislocation bands and the nature of stress serrations. We show that at low applied strain rates, there is a one-to-one correspondence with the randomly nucleated isolated bursts of mobile dislocation density and the stress drops. We then show that the model equations are spatiotemporally chaotic by demonstrating the number of positive Lyapunov exponents and Lyapunov dimension scale with the system size at low and high strain rates. Using a modified algorithm for calculating correlation dimension density, we show that the stress-strain signals at low applied strain rates corresponding to spatially uncorrelated dislocation bands exhibit features of low-dimensional chaos. This is made quantitative by demonstrating that the model equations can be approximately reduced to space-independent model equations for the average dislocation densities, which is known to be low-dimensionally chaotic. However, the scaling regime for the correlation dimension shrinks with increasing applied strain rate due to increasing propensity for propagation of the dislocation bands.

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.

Low dimensional fabrication of giant dielectric CaCu3Ti4O12 through soft e-beam lithography

We report low-dimensional fabrication of technologically important giant dielectric material CaCu3Ti4O12 (CCTO) using soft electron beam lithographic technique. Sol-gel precursor solution of CCTO was prepared using inorganic metal nitrates and Ti-isopropoxide. Employing the prepared precursor solution and e-beam lithographically fabricated resist mask CCTO dots with similar to 200 nm characteristic dimension were fabricated on platinized Si (111) substrate. Phase formation, chemical purity and crystalline nature of fabricated low dimensional structures were investigated with X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDS) and selected area electron diffraction (SAED), respectively. Morphological investigations were carried out with the help of scanning electron microscopy (SEM) and transmission electron microscopy (TEM). This kind of solution based fabrication of patterned low-dimensional high dielectric architectures might get potential significance for cost-effective technological applications. (C) 2012 Elsevier B.V. All rights reserved.