Two-way Bayesian hierarchical phylogenetic models: An application to the co-evolution of gp120 and gp41 during and after enfuvirtide treatment

Enfuvirtide (ENF) is a fusion inhibitor that prevents the entry of HIV virions into target cells. Studying the characteristics of viral evolution during treatment and after a treatment interruption can lend insight into the mechanisms of viral evolution and fitness. Although interruption of anti-HIV therapy often results in rapid emergence of an archived “wild-type” virus population, previous work from our group indicates that when only ENF is interrupted, viral gp41 continues to evolve forward and resistance mutations are lost due to back-mutation and remodeling of the envelope protein. To examine the co-evolution of gp120 and gp41 during ENF interruption we extend the Bayesian Hierarchical Phylogenetic model (HPM). Current HPMs enforce conditional independence across all outcomes while biologically all gene regions within a patient should return the same tree unless recombination confers an evolutionary selective advantage. A two-way-interaction HPM is proposed that provides middle ground between these two extremes and allows us to test for differences in evolutionary pressures across gene regions in multiple patients simultaneously. When the model is applied to a well-characterized cohort of HIV-infected patients interrupting ENF we find that across patients, the virus continued to evolve forward in both gene regions. Overall, the hypothesis of independence over dependence between the gene regions is supported. Models that allow for the examination of co-evolution over time will be increasingly important as more therapeutic classes are developed, each of which may impact other through novel and complex mechanisms.     

Halogen bonding: Recent advances

Halogen bonding (XB), as a directional interaction between covalently bound halogen atoms (XB donor) and Lewis bases (A, XB acceptor), has been recently intensively investigated as a powerful tool in crystal engineering. After a short review on the origin and general features of halogen bonding, current developments towards (i) the elaboration of three-dimensional networks, (ii) the interaction with anionic XB acceptors, (iii) its identification in biological systems and (iv) the formation of liquid crystal phases will be described. Theoretical analyses, statistical studies and experimental electron density determinations converge to describe halogen bonding as a relatively weak structure directing tool, when compared with hydrogen bonding. However, when the halogen atom is strongly activated as in iodoperfluorinated molecules or cationic aromatic systems can halogen bonding act as an efficient and reliable structure directing tool.     

Megasonic agitation for enhanced electrodeposition of copper

In this paper we propose an agitation method based on megasonic acoustic streaming to overcome the limitations in plating rate and uniformity of the metal deposits during the electroplating process. Megasonic agitation at a frequency of 1 MHz allows the reduction of the thickness of the Nernst diffusion layer to less than 600 nm. Two applications that demonstrate the benefits of megasonic acoustic streaming are presented: the formation of uniform ultra-fine pitch flip-chip bumps and the metallisation of high aspect ratio microvias. For the latter application, a multi-physics based numerical simulation is implemented to describe the hydrodynamics introduced by the acoustic waves as they travel inside the deep microvias.     

Impact of the Cd2+ treatment on the electrical properties of Cu2ZnSnSe4 and Cu(In,Ga)Se2 solar cells

The present contribution aims at determining the impact of modifying the properties of the absorber/buffer layer interface on the electrical performance of Cu₂ZnSnSe₄ (CZTSe) thin‐film solar cells, by using a Cd²⁺ partial electrolyte (Cd PE) treatment of the absorber before the buffer layer deposition. In this work, CZTSe/CdS solar cells with and without Cd PE treatment were compared with their respective Cu(In,Ga)Se₂ (CIGSe)/CdS references. The Cd PE treatment was performed in a chemical bath for 7 min at 70 °C using a basic solution of cadmium acetate. X‐ray photoemission spectroscopy measurements have revealed the presence of Cd at the absorber surface after the treatment. The solar cells were characterized using current density–voltage (J–V), external quantum efficiency, and drive‐level capacitance profiling measurements. For the CZTSe‐based devices, the fill factor increased from 57.7% to 64.0% when using the Cd PE treatment, leading to the improvement of the efficiency (η) from 8.3% to 9.0% for the best solar cells. Similar observations were made on the CIGSe solar cell reference. This effect comes from a considerable reduction of the series resistance (R_S) of the dark and light J–V, as determined using the one‐diode model. The crossover effect between dark and light J–V curves is also significantly reduced by Cd PE treatment. Copyright © 2015 John Wiley & Sons, Ltd.     

Inversion of the Neugebauer equations

The Neugebauer equations are considered as the basic physical model for printing systems and, hence, they have often been used either in their original form or in any adapted version to model color printers. The main problem with printer models is that they relate color as a function of colorant values. In practice, however, the inverse relation is needed and, hence, the printer model needs to be inverted. This is done by making use of iterative techniques and, as a result, only one colorant combination will be obtained to achieve a given color. However, in this publication it is shown that, in the case of the Neugebauer model for three colorants, there are up to six solutions with which a given color can be reached. Between these solutions there may be a number of pairs that are complex conjugated. Mathematical formulas to find all these solutions are given. The extension of this inversion technique for more than three inks and for the localized Neugebauer equations is presented. © 1996 John Wiley & Sons, Inc.     

Effect of processing conditions on wood and glass fiber length attrition during twin screw composite compounding

In this study, we compare the effect of twin-screw extrusion processing on the attrition of wood fibers (WFs) with glass fiber. The effects of process variables and screw design on fiber length were investigated by performing a range of dead-stop experiments where the extruder was stopped, opened-up, and compound removed from the screw elements. Fibers, chemically extracted from the polypropylene matrix, were analyzed for length and width using a commercial fiber analyzer. It was found that WF length attrition and composite properties were less affected by screw design and twin-screw processing conditions (feed rate and screw speed) than glass fiber. Length weighted fiber length and X50 length (a measure used in particle size analysis) were equally correlated with process conditions and composite performance for both fiber types. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020 , 137, 48551.     

Structural and Functional Characterization of 4-Hydroxyphenylacetate 3-Hydroxylase from Escherichia coli

The hydroxylation of phenols into polyphenols, which are valuable chemicals and pharmaceutical products, is a challenging reaction. The search for green synthetic processes has led to considering microorganisms and pure hydroxylases as catalysts for phenol hydroxylation. Herein, we report the structural and functional characterization of the flavin adenine dinucleotide (FAD)-dependent 4-hydroxyphenylacetate 3-monooxygenase from Escherichia coli, named HpaB. It is shown that this enzyme enjoys a relatively broad substrate specificity, which allows the conversion of a number of non-natural phenolic compounds, such as tyrosol, hydroxymandelic acid, coumaric acid, hydroxybenzoic acid and its methyl ester, and phenol, into the corresponding catechols. The reaction can be performed by using a simple chemical assay based on formate as the electron donor and the organometallic complex [Rh(bpy)Cp*(H₂O)]²⁺ (Cp*: 1,2,3,4,5-pentamethylcyclopentadiene, bpy: 2,2′-bipyridyl) as the catalyst for FAD reduction. The availability of a crystal structure of HpaB in complex with FAD at 1.8 Å resolution opens up the possibility of the rational tuning of the substrate specificity and activity of this interesting class of phenol hydroxylases.     

Metazoans and Intrinsic Apoptosis: An Evolutionary Analysis of the Bcl-2 Family

The B-cell lymphoma-2 (Bcl-2) family is a group of genes regulating intrinsic apoptosis, a process controlling events such as development, homeostasis and the innate and adaptive immune responses in metazoans. In higher organisms, Bcl-2 proteins coordinate intrinsic apoptosis through their regulation of the integrity of the mitochondrial outer membrane; this function appears to have originated in the basal metazoans. Bcl-2 genes predate the cnidarian-bilaterian split and have been identified in porifera, placozoans and cnidarians but not ctenophores and some nematodes. The Bcl-2 family is composed of two groups of proteins, one with an α-helical Bcl-2 fold that has been identified in porifera, placozoans, cnidarians, and almost all higher bilaterians. The second group of proteins, the BH3-only group, has little sequence conservation and less well-defined structures and is found in cnidarians and most bilaterians, but not porifera or placozoans. Here we examine the evolutionary relationships between Bcl-2 proteins. We show that the structures of the Bcl-2-fold proteins are highly conserved over evolutionary time. Some metazoans such as the urochordate Oikopleura dioica have lost all Bcl-2 family members. This gene loss indicates that Bcl-2 regulated apoptosis is not an absolute requirement in metazoans, a finding mirrored in recent gene deletion studies in mice. Sequence analysis suggests that at least some Bcl-2 proteins lack the ability to bind BH3-only antagonists and therefore potentially have other non-apoptotic functions. By examining the foundations of the Bcl-2 regulated apoptosis, functional relationships may be clarified that allow us to understand the role of specific Bcl-2 proteins in evolution and disease.