A refined circular template matching method for classification of human cytomegalovirus capsids in TEM images

An automatic image analysis method for describing, segmenting, and classifying human cytomegalovirus capsids in transmission electron micrograph (TEM) images of host cell nuclei has been developed. Three stages of the capsid assembly process in the host cell nucleus have been investigated. Each class is described by a radial density profile, which is the average grey-level at each radial distance from the center. A template, constructed from the profile, is used to find possible capsid locations by correlation based matching. The matching results are further refined by size and distortion analysis of each possible capsid, resulting in a final segmentation and classification.     

DCE-MRI of hepatocellular carcinoma: perfusion quantification with Tofts model versus shutter-speed model—initial experience

Objective

To quantify hepatocellular carcinoma (HCC) perfusion and flow with the fast exchange regime-allowed Shutter-Speed model (SSM) compared to the Tofts model (TM).

Materials and methods

In this prospective study, 25 patients with HCC underwent DCE-MRI. ROIs were placed in liver parenchyma, portal vein, aorta and HCC lesions. Signal intensities were analyzed employing dual-input TM and SSM models. ART (arterial fraction), K ^trans (contrast agent transfer rate constant from plasma to extravascular extracellular space), v _e (extravascular extracellular volume fraction), k _ep (contrast agent intravasation rate constant), and τ _i (mean intracellular water molecule lifetime) were compared between liver parenchyma and HCC, and ART, K ^trans, v _e and k _ep were compared between models using Wilcoxon tests and limits of agreement. Test–retest reproducibility was assessed in 10 patients.

Results

ART and v _e obtained with TM; ART, v _e , k _e and τ _i obtained with SSM were significantly different between liver parenchyma and HCC (p < 0.04). Parameters showed variable reproducibility (CV range 14.7–66.5 % for both models). Liver K ^trans and v _e ; HCC v _e and k _ep were significantly different when estimated with the two models (p < 0.03).

Conclusion

Our results show differences when computed between the TM and the SSM. However, these differences are smaller than parameter reproducibilities and may be of limited clinical significance.

     

Colistin Resistance in Aeromonas spp.

The increase in the use of antimicrobials such as colistin for the treatment of infectious diseases has led to the appearance of Aeromonas strains resistant to this drug. However, resistance to colistin not only occurs in the clinical area but has also been determined in Aeromonas isolates from the environment or animals, which has been determined by the detection of mcr genes that confer a resistance mechanism to colistin. The variants mcr-1, mcr-3, and mcr-5 have been detected in the genus Aeromonas in animal, environmental, and human fluids samples. In this article, an overview of the resistance to colistin in Aeromonas is shown, as well as the generalities of this molecule and the recommended methods to determine colistin resistance to be used in some of the genus Aeromonas.     

Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding

Although the main features of the protein folding problem are coming into clearer focus, the microscopic viewpoint of nucleic acid folding mechanisms is only just beginning to be addressed. Experiments, theory, and simulations are pointing to complex thermodynamic and kinetic mechanisms. As is the case for proteins, molecular dynamics (MD) simulations continue to be indispensable tools for providing a molecular basis for nucleic acid folding mechanisms. In this review, we provide an overview of biomolecular folding mechanisms focusing on nucleic acids. We outline the important interactions that are likely to be the main determinants of nucleic acid folding energy landscapes. We discuss recent MD simulation studies of empirical force field and Go-type MD simulations of RNA and DNA folding mechanisms to outline recent successes and the theoretical and computational challenges that lie ahead.     

Ni supported on sepiolite catalysts for the hydrogenation of furfural to value-added chemicals: influence of the synthesis method on the catalytic performance

Topics in Catalysis - Nickel-based catalysts supported on sepiolite catalysts, with a nickel loading between 1 and 10 wt%, have been synthesized by several synthetic strategies...     

Tunable temperature‐ and shear‐responsive hydrogels based on poly(alkyl glycidyl ether)s

We describe the synthesis, characterization and direct‐write 3D printing of triblock copolymer hydrogels that have a tunable response to temperature and shear stress. In aqueous solutions, these polymers utilize the temperature‐dependent self‐association of poly(alkyl glycidyl ether) ‘A’ blocks and a central poly(ethylene oxide) segment to create a physically crosslinked three‐dimensional network. The temperature response of these hydrogels was dependent upon composition, chain length and concentration of the ‘A’ block in the copolymer. Rheological experiments confirmed the existence of sol–gel transitions and the shear‐thinning behavior of the hydrogels. The temperature‐ and shear‐responsive properties enabled direct‐write 3D printing of complex objects with high fidelity. Hydrogel cytocompatibility was also confirmed by incorporating HeLa cells into select hydrogels resulting in high viabilities over 24 h. The tunable temperature response and innate shear‐thinning properties of these hydrogels, coupled with encouraging cell viability results, present an attractive opportunity for additive manufacturing and tissue engineering applications. © 2018 Society of Chemical Industry     

Polar Lipids Reduce In Vitro Duodenal Lipolysis Rate of Oat Oil and Liquid Oat Base Products

Alternative ways for increased appetite control are today widely sought for due to the growing global health issues connected to obesity. In in vivo studies, oat has been proven an attractive candidate for inducing satiety. Oat is rich in polar lipids, of which the galactolipids are especially interesting, and a hypothesis is that these lipids play an important role for the ileal brake mechanism. In this study, the aim is to investigate the role of polar oat lipids on pancreatic lipolysis rate, using a pH-stat based in vitro digestion model of the duodenum. Lipolysis of oat oil, a mix of oat oil/rapeseed oil (RSO), as well as a liquid oat base (OB) simulating an oat drink with different polar lipid content are investigated, and compared with RSO as control. Increasing the polar lipid content of the product digested leads to a significantly decreased lipolysis rate, and this effect is even observed when mixing RSO with a low amount of oat oil (10%). The results support the hypothesis that polar lipids can delay lipolysis also in a complex, natural system like the liquid OB, and even a minor amount of oat lipids can have large effect on lipolysis rates. Practical applications: The number of studies connecting galactolipids with a decreasing effect on duodenal lipolysis is growing; however, the mechanism behind this phenomenon is still not clarified. Here, the same effect is seen in a complex, natural food system. These findings open up for interesting future food products, where inclusion of oat oil, even at low concentrations, can have a prolonging effect on satiety. Oat for human consumption is an increasing market, thanks to the positive health benefits oat has been connected to, in combination with the current trend toward climate-friendly plant-based options for meat and dairy products. It is believed that oat oil can be attractive as an ingredient in various food products, for example, protein bars and spreads. More studies are needed to confirm the results in vivo. However, a great potential is seen for the use of oat oil to enhance appetite control.     

Metals in ALS TDP-43 Pathology

Amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease and similar neurodegenerative disorders take their toll on patients, caregivers and society. A common denominator for these disorders is the accumulation of aggregated proteins in nerve cells, yet the triggers for these aggregation processes are currently unknown. In ALS, protein aggregation has been described for the SOD1, C9orf72, FUS and TDP-43 proteins. The latter is a nuclear protein normally binding to both DNA and RNA, contributing to gene expression and mRNA life cycle regulation. TDP-43 seems to have a specific role in ALS pathogenesis, and ubiquitinated and hyperphosphorylated cytoplasmic inclusions of aggregated TDP-43 are present in nerve cells in almost all sporadic ALS cases. ALS pathology appears to include metal imbalances, and environmental metal exposure is a known risk factor in ALS. However, studies on metal-to-TDP-43 interactions are scarce, even though this protein seems to have the capacity to bind to metals. This review discusses the possible role of metals in TDP-43 aggregation, with respect to ALS pathology.