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.

Effect of frequency on seismic response of reinforced soil slopes in shaking table tests

This paper studies the effect of frequency of base shaking on the dynamic response of unreinforced and reinforced soil slopes through a series of shaking table tests. Slopes were constructed using clayey sand and geogrids were used for reinforcing the slopes. Two different slope angles 45 degrees and 60 degrees were used in tests and the quantity and location of reinforcement is varied in different tests. Acceleration of shaking is kept constant as 0.3 g in all the tests to maximize the response and the frequency of shaking was 2 Hz, 5 Hz and 7 Hz in different tests. The slope is instrumented with ultrasonic displacement sensors and accelerometers at different elevations. The response of different slopes is compared in terms of the deformation of the slope and acceleration amplifications measured at different elevations. It is observed that the displacements at all elevations increased with increase in frequency for all slopes, whereas the effect of frequency on acceleration amplifications is not significant for reinforced slopes. Results showed that the acceleration and displacement response is not increasing proportionately with the increase in the frequency, suggesting that the role of frequency in the seismic response is very important. Reinforced slopes showed lesser displacements compared to unreinforced slopes at all frequency levels. (C) 2012 Elsevier Ltd. All rights reserved.

Biochemical characterization of C4 protein of cotton leaf curl Kokhran virus-Dabawali

Background: Cotton leaf curl Kokhran Virus-Dabawali (CLCuKV-Dab) is a monopartite begomovirus encoding two proteins V1 and V2 in the virion sense and four proteins Cl, C2, C3 and C4 in the complementary sense. The C4 protein of monopartite begomoviruses has been implicated to play a role in symptom determination and virus movement. The present work aims at the biochemical characterization of this protein. Methods: The C4 protein of CLCuKV-Dab was purified in fusion with GST and tested for the ability to hydrolyze ATP and other phosphate containing compounds. ATPase activity was assayed by using radiolabeled gamma-32P]-ATP and separating the product of reaction by thin layer chromatography. The hydrolysis of other compounds was monitored by the formation of a blue colored phosphomolybdate complex which was estimated by measuring the absorbance at 655 nm. Results: The purified GST-C4 protein exhibited metal ion dependent ATPase and inorganic pyrophosphatase activities. Deletion of a sequence resembling the catalytic motif present in phosphotyrosine phosphatases resulted in 70% reduction in both the activities. Mutational analysis suggested arginine 13 to be catalytically important for the ATPase and cysteine 8 for the pyrophosphatase activity of GST-C4. Interaction of V2 with GST-C4 resulted in an increase in both the enzymatic activities of GST-C4. Conclusions: The residues important for the enzymatic activities of GST-C4 are present in a motif different from the classical Walker motifs and the non-classical ATP binding motifs reported so far. General significance: The C4 protein of CLCuKV-Dab, a putative natively unfolded protein, exhibits enzymatic activities.

A POSTERIORI ERROR CONTROL OF DISCONTINUOUS GALERKIN METHODS FOR ELLIPTIC OBSTACLE PROBLEMS

In this article, we derive an a posteriori error estimator for various discontinuous Galerkin (DG) methods that are proposed in (Wang, Han and Cheng, SIAM J. Numer. Anal., 48: 708-733, 2010) for an elliptic obstacle problem. Using a key property of DG methods, we perform the analysis in a general framework. The error estimator we have obtained for DG methods is comparable with the estimator for the conforming Galerkin (CG) finite element method. In the analysis, we construct a non-linear smoothing function mapping DG finite element space to CG finite element space and use it as a key tool. The error estimator consists of a discrete Lagrange multiplier associated with the obstacle constraint. It is shown for non-over-penalized DG methods that the discrete Lagrange multiplier is uniformly stable on non-uniform meshes. Finally, numerical results demonstrating the performance of the error estimator are presented.

De novo inference of protein function from coarse-grained dynamics

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 mu s coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. (C) 2014 Wiley Periodicals, Inc.

Local Structural and Environmental Factors Define the Efficiency of an RNA Pseudoknot Involved in Programmed Ribosomal Frameshift Process

In programmed -1 ribosomal frameshift, an RNA pseudoknot stalls the ribosome at specific sequence and restarts translation in a new reading frame. A precise understanding of structural characteristics of these pseudoknots and their PRF inducing ability has not been clear to date. To investigate this phenomenon, we have studied various structural aspects of a -1 PRF inducing RNA pseudoknot from BWYV using extensive molecular dynamics simulations. A set of functional and poorly functional forms, for which previous mutational data were available, were chosen for analysis. These structures differ from each other by either single base substitutions or base-pair replacements from the native structure. We have rationalized how certain mutations in RNA pseudoknot affect its function; e.g., a specific base substitution in loop 2 stabilizes the junction geometry by forming multiple noncanonical hydrogen bonds, leading to a highly rigid structure that could effectively resist ribosome-induced unfolding, thereby increasing efficiency. While, a CG to AU pair substitution in stem 1 leads to loss of noncanonical hydrogen bonds between stems and loop, resulting in a less stable structure and reduced PRF inducing ability, inversion of a pair in stem 2 alters specific base-pair geometry that might be required in ribosomal recognition of nucleobase groups, negatively affecting pseudoknot functioning. These observations illustrate that the ability of an RNA pseudoknot to induce -1 PRF with an optimal rate depends on several independent factors that contribute to either the local conformational variability or geometry

FEM Simulations and Optimization about Residual Stresses in Coating Structures with Functionally Graded Materials Layer

An elasto-plastic finite element method is developed to predict the residual stresses of thermal spraying coatings with functionally graded material layer. In numerical simulations, temperature sensitivity of various material constants is included and mix

An Analytical Solution for Three-Dimensional Diffraction of Plane P-Waves by a Hemispherical Alluvial Valley with Saturated Soil Deposits

An analytical solution for the three-dimensional scattering and diffraction of plane P-waves by a hemispherical alluvial valley with saturated soil deposits is developed by employing Fourier-Bessel series expansion technique. Unlike previous studies, in which the saturated soil deposits were simulated with the single-phase elastic theory, in this paper, they are simulated with Biot's dynamic theory for saturated porous media, and the half space is assumed as a single-phase elastic medium. The effects of the dimensionless frequency, the incidence angle of P-wave and the porosity of soil deposits on the surface displacement magnifications of the hemispherical alluvial valley are investigated. Numerical results show that the existence of a saturated hemispherical alluvial valley has much influence on the surface displacement magnifications. It is more reasonable to simulate soil deposits with Biot's dynamic theory when evaluating the displacement responses of a hemispherical alluvial valley with an incidence of P-waves.

Dynamic properties and asymmetry of tension and compression of metal matrix composites under impact loading

The mechanical behaviors of 2124, Al-5Cu, Al-Li and 6061 alloys reinforced by silicon carbide particulates, together with 15%SiCw/6061 alloy, were studied under the quasi-static and impact loading conditions, using the split Hopkinson tension/compression bars and Instron universal testing machine. The effect of strain rate on the ultra tensile strength (UTS), the hardening modulus and the failure strain was investigated. At the same time, the SEM observations of dynamic fracture surfaces of various MMC materials showed some distinguished microstructures and patterns. Some new characteristics of asymmetry of mechanical behaviors of MMCs under tension and compression loading were also presented and explained in details, and they could be considered as marks to indicate, to some degree, the mechanism of controlling damage and failure of MMCs under impact loading. The development of new constitutive laws about MMCs under impact loading should benefit from these experimental results and theoretical analysis.

Influential Factors of Loess Liquefaction and Pore Pressure Development

The liquefaction of loess under dynamic loading is studied experimentally with a dynamic triaxial test system. The effects of over-consolidation ratio (OCR), saturation degree and the frequency of dynamic loading upon loess liquefaction are investigated. The development of pore pressure within loess samples is also discussed. Based on the experimental results, the empirical relationship between pore pressure ratio and loading cycle number ratio is established for normal consolidated saturated loess.

Real-Time Measurement on Deformation Fields of Hole-Excavated Samples under Impact Tension

In this paper, the real-time deformation fields are observed in two different kinds of hole-excavated dog-bone samples loaded by an SHTB, including single hole sample and dual holes sample with the aperture size of 0.8mm. The testing system consists of a high-speed camera, a He-Ne laser, a frame grabber and a synchronization device with the controlling accuracy of I microsecond. Both the single hole expanding process and the interaction of the two holes are recorded with the time interval of 10 mu s. The observed images on the sample surface are analyzed by newly developed software based on digital correlation theory and a modified image processing method. The 2-D displacement fields in plane are obtained with a resolution of 50 mu m and an accuracy of 0.5 mu m. Experimental results obtained in this paper are proofed, by compared with FEM numerical simulations.

Estudio descriptivo de la carcasa de cerdos alimentados con diferentes niveles de inclusión de marango (Moringa oleifera L.)

El presente estudio se realizo en la granja porcina de la Universidad Nacional Agraria (UNA), ubicada en el kilometro 13 carretera Norte desvío a Sabana Grande, Managua, Nicaragua. Este estudio duró 28 semanas comprendidas entre el 15 de Agosto del año 2000 al 8 de Marzo del año 2001. El objetivo general de estudio fue: contribuir a definir la calidad de la canal de cerdos a través de procesos de engorda utilizando dietas no convencionales para establecer las potencialidades o viabilidad de éstas en producción, utilizando diferentes raciones: (T1) Concentrado 100%, (T2) Marango 30% + 70% Concentrado, (T3) Marango 48% + 52% de Concentrado. Se utilizaron 36 cerdos híbridos, formándose grupos de 12 cerdos por tratamiento. los cerdos se pesaron al inicio y luego cada 15 días hasta el momento de su sacrificio: 1er sacrificio y 2do sacrificio. En el primer sacrificio el T1 presento el mayor rendimiento en canal con un 71.28%, superando en un 9.32% al T2 y en un 17.53% al T3. En el segundo sacrificio el T2 presento el mayor rendimiento en canal con un 75.79%, superando en un 4.19% al T3 y en un 4.51% al T1. En el primer sacrificio se obtuvo una distribución similar entre los puntos de grasa dorsal de cada tratamiento, sin embargo el T1 alcanzo el mayor espesor de grasa dorsal con un promedio de 32.6 mm con una diferencia respecto al T2 de 10 mm y de 17 mm respecto al T3. En el segundo sacrificio se obtuvo una distribución variada entre los diferentes puntos de grasa dorsal de cada tratamiento, aquí el T1 siempre mantuvo el mayor espesor de grasa dorsal con promedio entre puntos de 32,6 mm con una diferencia respecto al T2 de 9.4 mm y de 12.2 mm respecto al T3. Se utilizó un análisis descriptivo, siendo las variables principales: rendimiento en canal (RC), peso vivo (PV), peso canal (PC), composición de la canal (CC), composición de la grasa (CG) y espesor de la grasa dorsal (EGD). los cerdos del T2 en el 1er sacrificio obtuvieron un mayor porcentaje de carne en comparación con los otros tratamientos, mientras que los cerdos del T3 obtuvieron el mayor porcentaje de costilla y hueso en comparación con los otros tratamientos. los cerdos del 2do sacrificio del T3 obtuvieron el mayor porcentaje de carne en comparación con los otros tratamientos, mientras que los cerdos del T1 obtuvieron el mayor porcentaje de costilla y el T2 obtuvo el mayor porcentaje de hueso y el menor porcentaje de grasa. El análisis estadístico demostró que para el primer sacrificio existieron diferencias altamente significativas con respecto al peso final, peso canal, rendimiento y significativo en el hueso. En el segundo sacrificio existieron diferencias significativas en grasa, costilla y en el porcentaje de carne. Se realizo un análisis de separación de medias según Tukey al 5% para los casos en que se encontraron diferencias significativas. Esta prueba se realizó con el fin de categorízar los tratamientos.

Integrating vertically aligned carbon nanotubes on micromechanical structures

The integration of high yield, uniform and preferential growth of vertically aligned carbon nanotubes (VACNT) on low stress micromechanical structures was analyzed. A combination of electron-beam crosslinked surface micromachining and direct current plasma enhanced chemical vapor deposition of electric field aligned carbon nanotubes was used for the analysis. The selective placement of high yield and uniform VACNTs on a partially suspended Ni/SiO2/Ti microstructure was also demonstrated.