DroplIT, an improved image analysis method for droplet identification in high-throughput crystallization trials

The application of robotics to protein crystallization trials has resulted in the production of millions of images. Manual inspection of these images to find crystals and other interesting outcomes is a major rate-limiting step. As a result there has been intense activity in developing automated algorithms to analyse these images. The very first step for most systems that have been described in the literature is to delineate each droplet. Here, a novel approach that reaches over 97% success rate and subsecond processing times is presented. This will form the seed of a new high-throughput system to scrutinize massive crystallization campaigns automatically. © 2010 International Union of Crystallography Printed in Singapore-all rights reserved.

A micro-level investigation of the solid displacement method for porosity determination of dried food

Porosity is one of the key parameters of the macroscopic structure of porous media, generally defined as the ratio of the free spaces occupied (by the volume of air) within the material to the total volume of the material. Porosity is determined by measuring skeletal volume and the envelope volume. Solid displacement method is one of the inexpensive and easy methods to determine the envelope volume of a sample with an irregular shape. In this method, generally glass beads are used as a solid due to their uniform size, compactness and fluidity properties. The smaller size of the glass beads means that they enter into the open pores which have a larger diameter than the glass beads. Although extensive research has been carried out on porosity determination using displacement method, no study exists which adequately reports micro-level observation of the sample during measurement. This study set out with the aim of assessing the accuracy of solid displacement method of bulk density measurement of dried foods by micro-level observation. Solid displacement method of porosity determination was conducted using a cylindrical vial (cylindrical plastic container) and 57 µm glass beads in order to measure the bulk density of apple slices at different moisture contents. A scanning electron microscope (SEM), a profilometer and ImageJ software were used to investigate the penetration of glass beads into the surface pores during the determination of the porosity of dried food. A helium pycnometer was used to measure the particle density of the sample. Results show that a significant number of pores were large enough to allow the glass beads to enter into the pores, thereby causing some erroneous results. It was also found that coating the dried sample with appropriate coating material prior to measurement can resolve this problem.

A finite element modelling method for thin layer mortared masonry systems

This paper deals with a finite element modelling method for thin layer mortared masonry systems. In this method, the mortar layers including the interfaces are represented using a zero thickness interface element and the masonry units are modelled using an elasto-plastic, damaging solid element. The interface element is formulated using two regimes; i) shear-tension and ii) shearcompression. In the shear-tension regime, the failure of joint is consiedered through an eliptical failure criteria and in shear-compression it is considered through Mohr Coulomb type failure criterion. An explicit integration scheme is used in an implicit finite element framework for the formulation of the interface element. The model is calibrated with an experimental dataset from thin layer mortared masonry prism subjected to uniaxial compression, a triplet subjected to shear loads a beam subjected to flexural loads and used to predict the response of thin layer mortared masonry wallettes under orthotropic loading. The model is found to simulate the behaviour of a thin layer mortated masonry shear wall tested under pre-compression and inplane shear quite adequately. The model is shown to reproduce the failure of masonry panels under uniform biaxial state of stresses.

Active learning: A step towards automating medical concept extraction

Objective This paper presents an automatic active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort, and (2) the robustness of incremental active learning framework across different selection criteria and datasets is determined. Materials and methods The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional Random Fields as the supervised method, and least confidence and information density as two selection criteria for active learning framework were used. The effect of incremental learning vs. standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. Two clinical datasets were used for evaluation: the i2b2/VA 2010 NLP challenge and the ShARe/CLEF 2013 eHealth Evaluation Lab. Results The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared to the Random sampling baseline, the saving is at least doubled. Discussion Incremental active learning guarantees robustness across all selection criteria and datasets. The reduction of annotation effort is always above random sampling and longest sequence baselines. Conclusion Incremental active learning is a promising approach for building effective and robust medical concept extraction models, while significantly reducing the burden of manual annotation.

A new registration method based on Log-Euclidean tensor metrics and its application to genetic studies

In structural brain MRI, group differences or changes in brain structures can be detected using Tensor-Based Morphometry (TBM). This method consists of two steps: (1) a non-linear registration step, that aligns all of the images to a common template, and (2) a subsequent statistical analysis. The numerous registration methods that have recently been developed differ in their detection sensitivity when used for TBM, and detection power is paramount in epidemological studies or drug trials. We therefore developed a new fluid registration method that computes the mappings and performs statistics on them in a consistent way, providing a bridge between TBM registration and statistics. We used the Log-Euclidean framework to define a new regularizer that is a fluid extension of the Riemannian elasticity, which assures diffeomorphic transformations. This regularizer constrains the symmetrized Jacobian matrix, also called the deformation tensor. We applied our method to an MRI dataset from 40 fraternal and identical twins, to revealed voxelwise measures of average volumetric differences in brain structure for subjects with different degrees of genetic resemblance.

The rapid manufacture of uniform composite multicellular-biomaterial micropellets, their assembly into macroscopic organized tissues, and potential applications in cartilage tissue engineering

We and others have published on the rapid manufacture of micropellet tissues, typically formed from 100-500 cells each. The micropellet geometry enhances cellular biological properties, and in many cases the micropellets can subsequently be utilized as building blocks to assemble complex macrotissues. Generally, micropellets are formed from cells alone, however when replicating matrix-rich tissues such as cartilage it would be ideal if matrix or biomaterials supplements could be incorporated directly into the micropellet during the manufacturing process. Herein we describe a method to efficiently incorporate donor cartilage matrix into tissue engineered cartilage micropellets. We lyophilized bovine cartilage matrix, and then shattered it into microscopic pieces having average dimensions < 10 μm diameter; we termed this microscopic donor matrix "cartilage dust (CD)". Using a microwell platform, we show that ~0.83 μg CD can be rapidly and efficiently incorporated into single multicellular aggregates formed from 180 bone marrow mesenchymal stem/stromal cells (MSC) each. The microwell platform enabled the rapid manufacture of thousands of replica composite micropellets, with each micropellet having a material/CD core and a cellular surface. This micropellet organization enabled the rapid bulking up of the micropellet core matrix content, and left an adhesive cellular outer surface. This morphological organization enabled the ready assembly of the composite micropellets into macroscopic tissues. Generically, this is a versatile method that enables the rapid and uniform integration of biomaterials into multicellular micropellets that can then be used as tissue building blocks. In this study, the addition of CD resulted in an approximate 8-fold volume increase in the micropellets, with the donor matrix functioning to contribute to an increase in total cartilage matrix content. Composite micropellets were readily assembled into macroscopic cartilage tissues; the incorporation of CD enhanced tissue size and matrix content, but did not enhance chondrogenic gene expression.

Phase-selective hydrothermal synthesis of Cu2ZnSnS4nanocrystals: The effect of the sulphur precursor

High quality Cu2ZnSnS4 (CZTS) films with uniform thickness and smooth surface were prepared using nanocrystals synthesized by a one-step hydrothermal method. It is found that the nature of the sulphur precursor used in the hydrothermal reaction influences both the compositional purity and the crystal structure of the synthesized hydrothermal product significantly. The CZTS material consisting of both wurtzite and kesterite crystal structures was obtained when using an organic sulfur precursor such as thioacetamide and thiourea in the precursor solution of the hydrothermal reaction while the pure kesterite phase CZTS nanocrystals were made when Na2S was employed as the sulphur precursor. CZTS thin films deposited on a Mo–soda lime glass substrate with uniform thickness (1.7 μm) were made by a simple doctor-blading method. The investigation of the effect of thermal treatment on the film has indicated that the wurtzite CZTS material was completely transformed to the kesterite phase when the material was annealed at 550 °C. Large grains (around 2 μm in size) were found on the surface of the CZTS film which was annealed at 600 °C. The evaluation of the photoresponse of the CZTS thin films has showed that a higher and very stable photocurrent was generated by the film annealed at 600 °C compared to the film annealed at 550 °C.

One-step synthesis of high quality kesterite Cu2ZnSnS4nanocrystals: A hydrothermal approach

The present work demonstrates a systematic approach for the synthesis of pure kesterite-phase Cu2ZnSnS4 (CZTS) nanocrystals with a uniform size distribution by a one-step, thioglycolic acid (TGA)-assisted hydrothermal route. The formation mechanism and the role of TGA in the formation of CZTS compound were thoroughly studied. It has been found that TGA interacted with Cu2+ to form Cu+ at the initial reaction stage and controlled the crystal-growth of CZTS nanocrystals during the hydrothermal reaction. The consequence of the reduction of Cu2+ to Cu+ led to the formation Cu2−xS nuclei, which acted as the crystal framework for the formation of CZTS compound. CZTS was formed by the diffusion of Zn2+ and Sn4+ cations to the lattice of Cu2−xS during the hydrothermal reaction. The as-synthesized CZTS nanocrystals exhibited strong light absorption over the range of wavelength beyond 1000 nm. The band gap of the material was determined to be 1.51 eV, which is optimal for application in photoelectric energy conversion device.

A new method of detecting changes in corneal health in response to toxic insults

The size and arrangement of stromal collagen fibrils (CFs) influence the optical properties of the cornea and hence its function. The spatial arrangement of the collagen is still questionable in relation to the diameter of collagen fibril. In the present study, we introduce a new parameter, edge-fibrillar distance (EFD) to measure how two collagen fibrils are spaced with respect to their closest edges and their spatial distribution through normalized standard deviation of EFD (NSDEFD) accessed through the application of two commercially available multipurpose solutions (MPS): ReNu and Hippia. The corneal buttons were soaked separately in ReNu and Hippia MPS for five hours, fixed overnight in 2.5% glutaraldehyde containing cuprolinic blue and processed for transmission electron microscopy. The electron micrographs were processed using ImageJ user-coded plugin. Statistical analysis was performed to compare the image processed equivalent diameter (ED), inter-fibrillar distance (IFD), and EFD of the CFs of treated versus normal corneas. The ReNu-soaked cornea resulted in partly degenerated epithelium with loose hemidesmosomes and Bowman’s collagen. In contrast, the epithelium of the cornea soaked in Hippia was degenerated or lost but showed closely packed Bowman’s collagen. Soaking the corneas in both MPS caused a statistically significant decrease in the anterior collagen fibril, ED and a significant change in IFD, and EFD than those of the untreated corneas (p < 0.05, for all comparisons). The introduction of EFD measurement in the study directly provided a sense of gap between periphery of the collagen bundles, their spatial distribution; and in combination with ED, they showed how the corneal collagen bundles are spaced in relation to their diameters. The spatial distribution parameter NSDEFD indicated that ReNu treated cornea fibrils were uniformly distributed spatially, followed by normal and Hippia. The EFD measurement with relatively lower standard deviation and NSDEFD, a characteristic of uniform CFs distribution, can be an additional parameter used in evaluating collagen organization and accessing the effects of various treatments on corneal health and transparency.

A two-stage SVM method to predict membrane protein types by incorporating amino acid classifications and physicochemical properties into a general form of Chou's PseAAC

Membrane proteins play important roles in many biochemical processes and are also attractive targets of drug discovery for various diseases. The elucidation of membrane protein types provides clues for understanding the structure and function of proteins. Recently we developed a novel system for predicting protein subnuclear localizations. In this paper, we propose a simplified version of our system for predicting membrane protein types directly from primary protein structures, which incorporates amino acid classifications and physicochemical properties into a general form of pseudo-amino acid composition. In this simplified system, we will design a two-stage multi-class support vector machine combined with a two-step optimal feature selection process, which proves very effective in our experiments. The performance of the present method is evaluated on two benchmark datasets consisting of five types of membrane proteins. The overall accuracies of prediction for five types are 93.25% and 96.61% via the jackknife test and independent dataset test, respectively. These results indicate that our method is effective and valuable for predicting membrane protein types. A web server for the proposed method is available at http://www.juemengt.com/jcc/memty_page.php

Non-Newtonian mixed convection flow from a horizontal circular cylinder with uniform surface heat flux

Mixed convection laminar two-dimensional boundary-layer flow of non-Newtonian pseudo-plastic fluids is investigated from a horizontal circular cylinder with uniform surface heat flux using a modified power-law viscosity model, that contains no unrealistic limits of zero or infinite viscosity; consequently, no irremovable singularities are introduced into boundary-layer formulations for such fluids. The governing boundary layer equations are transformed into a non-dimensional form and the resulting nonlinear systems of partial differential equations are solved numerically applying marching order implicit finite difference method with double sweep technique. Numerical results are presented for the case of shear-thinning fluids in terms of the fluid temperature distributions, rate of heat transfer in terms of the local Nusselt number.

Step based physical activity guidelines for preschool-aged children

OBJECTIVE Public health organizations recommend that preschool-aged children accumulate at least 3h of physical activity (PA) daily. Objective monitoring using pedometers offers an opportunity to measure preschooler's PA and assess compliance with this recommendation. The purpose of this study was to derive step-based recommendations consistent with the 3h PA recommendation for preschool-aged children. METHOD The study sample comprised 916 preschool-aged children, aged 3 to 6years (mean age=5.0+/-0.8years). Children were recruited from kindergartens located in Portugal, between 2009 and 2013. Children wore an ActiGraph GT1M accelerometer that measured PA intensity and steps per day simultaneously over a 7-day monitoring period. Receiver operating characteristic (ROC) curve analysis was used to identify the daily step count threshold associated with meeting the daily 3hour PA recommendation. RESULTS A significant correlation was observed between minutes of total PA and steps per day (r=0.76, p<0.001). The optimal step count for >/=3h of total PA was 9099 steps per day (sensitivity (90%) and specificity (66%)) with area under the ROC curve=0.86 (95% CI: 0.84 to 0.88). CONCLUSION Preschool-aged children who accumulate less than 9000 steps per day may be considered Insufficiently Active.

In-situ one-step hydrothermal synthesis of a lead germanate-graphene composite as a novel anode material for lithium-ion batteries

Lead germanate-graphene nanosheets (PbGeO3-GNS) composites have been prepared by an efficient one-step, in-situ hydrothermal method and were used as anode materials for Li-ion batteries (LIBs). The PbGeO3 nanowires, around 100–200 nm in diameter, are highly encapsulated in a graphene matrix. The lithiation and de-lithiation reaction mechanisms of the PbGeO3 anode during the charge-discharge processes have been investigated by X-ray diffraction and electrochemical characterization. Compared with pure PbGeO3 anode, dramatic improvements in the electrochemical performance of the composite anodes have been obtained. In the voltage window of 0.01–1.50 V, the composite anode with 20 wt.% GNS delivers a discharge capacity of 607 mAh g−1 at 100 mA g−1 after 50 cycles. Even at a high current density of 1600 mA g−1, a capacity of 406 mAh g−1 can be achieved. Therefore, the PbGeO3-GNS composite can be considered as a potential anode material for lithium ion batteries.

An approximate method for the solution of an influence function foil rolling model

Fleck and Johnson (Int. J. Mech. Sci. 29 (1987) 507) and Fleck et al. (Proc. Inst. Mech. Eng. 206 (1992) 119) have developed foil rolling models which allow for large deformations in the roll profile, including the possibility that the rolls flatten completely. However, these models require computationally expensive iterative solution techniques. A new approach to the approximate solution of the Fleck et al. (1992) Influence Function Model has been developed using both analytic and approximation techniques. The numerical difficulties arising from solving an integral equation in the flattened region have been reduced by applying an Inverse Hilbert Transform to get an analytic expression for the pressure. The method described in this paper is applicable to cases where there is or there is not a flat region.