Speciation of toxic metals in metal finishing filter cake by X-ray absorption spectroscopy.

The speciation of Cr, Zn, Cu and Pb in two metal finishing filter cakes (TX and ST) was investigated by X-ray absorption spectroscopy (XAS) complemented by X-ray fluorescence (XRF) and X-ray diffraction (XRD). XRF showed that concentrations of Cr, Zn, Cu and Pb were 1.4%, 0.19%, 0.20% and 0.01%, respectively, in TX, and 12.6%, 3.3%, 1.3% and 0.21% in ST. No crystalline phases were detected in TX by XRD whereas ST was dominated by calcite. Cr and Fe K edge XAS showed Cr to be trivalent and octahedrally coordinated, co-precipitated with Fe as CrxFe1-x-(oxy)hydroxides in both filter cakes. Zn, P and Ca K edge XAS showed that 2ZnCO3∙3Zn(OH)2 and Zn3(PO4)2 were the dominant zinc-containing phases, with combined tetrahedral and octahedral coordination; Zn phases were slightly more crystalline in TX than ST. Pb L3 edge X-ray absorption near edge spectroscopy (XANES) found that Pb was likely adsorbed on amorphous SiO2. Cu, Si and S K edge XAS showed that all Cu was divalent, and the dominant copper phases were found to be Cu2Cl(OH)3, Cu(OH)2 and CuSO4·5H2O for ST, whereas Cu appeared to adsorb to amorphous SiO2 for TX, which contained much less Pb. Cr is thus immobilized in the filter cakes in a phase with low solubility at environmentally feasible pH values, whereas Zn, Cu and Pb could be released when the pH decreases below 8 or above 11. These findings are significant for the development of waste management regulations and/or metal recovery methods (e.g., hydro/pyrometallurgy).

Solvent-Free Depolymerization of Plastic Waste Enabled by Plastic-Catalyst Interfacial Engineering.

Depolymerization of condensation polymers by chemolysis often suffers from the large usage of solvents and homogeneous catalysts such as acids, bases, and metal salts. The catalytic efficiency of heterogeneous catalysts is largely constrained by the poor interfacial contact between solid catalysts and solid plastics below melting points. We report here our discovery of autogenous heterogeneous catalyst layer on polyethylene terephthalate surfaces during the generally believed homogeneous catalytic depolymerization process. Inspired by the "contact mass" concept in industrial chlorosilane production, we further demonstrate that the construction of plastic-catalyst solid-solid interfaces enables solvent-free depolymerization of polyethylene terephthalate by vapor phase methanolysis at relatively low temperatures. Trace amounts of earth-abundant element (zinc) introduced by electrostatic adsorption is sufficient for catalyzing the depolymerization. The concept of plastic-catalyst contact mass interfacial catalysis might inspire new pathways for tackling plastic waste problems.

A comparative study for phosphate adsorption on amorphous FeOOH and goethite (α-FeOOH): An investigation of relationship between the surface chemistry and structure.

Eutrophication is generally caused by excess nitrogen and phosphorus being released into surface waters by runoff. Developing adsorbents for adsorbing phosphate within soil buffer zones and/or water treatment columns may be effective methods to mitigate this problem. In this study, an amorphous FeOOH (AF) and a well-crystallized α-FeOOH (CF) was formulated to compare phosphate adsorption behavior. The physicochemical properties between these species showed significant differences in morphology, crystallization, zeta potential, and specific surface area. The AF exhibited higher phosphate uptake than CF. X-ray photoelectron spectroscopy (XPS) verified that the hydroxyl groups within AF were 13.28% higher than that in CF. The triply coordinated hydroxyl groups (µ3-OH) associated with AF and CF appeared at different positions as shown in the diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) analyses, confirming that AF contains more adsorption reactive sites (µ3-OH). Mechanisms for monodentate formations and a stable six-member ring structure were proposed. The X-ray absorption near the edge structure (XANES) and XPS results suggested that the iron valence in AF was dominated by Fe (III). XANES also demonstrated that the amorphous structure found in the AF was caused by the disordered tetrahedron and octahedron alignments, leading to a higher phosphate adsorption.

Modeling the assembly order of multimeric heteroprotein complexes.

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.

Modeling disordered protein interactions from biophysical principles.

Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs.

Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.

We report the performance of protein-protein docking predictions by our group for recent rounds of the Critical Assessment of Prediction of Interactions (CAPRI), a community-wide assessment of state-of-the-art docking methods. Our prediction procedure uses a protein-protein docking program named LZerD developed in our group. LZerD represents a protein surface with 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. The appropriate soft representation of protein surface with 3DZD makes the method more tolerant to conformational change of proteins upon docking, which adds an advantage for unbound docking. Docking was guided by interface residue prediction performed with BindML and cons-PPISP as well as literature information when available. The generated docking models were ranked by a combination of scoring functions, including PRESCO, which evaluates the native-likeness of residues' spatial environments in structure models. First, we discuss the overall performance of our group in the CAPRI prediction rounds and investigate the reasons for unsuccessful cases. Then, we examine the performance of several knowledge-based scoring functions and their combinations for ranking docking models. It was found that the quality of a pool of docking models generated by LZerD, that is whether or not the pool includes near-native models, can be predicted by the correlation of multiple scores. Although the current analysis used docking models generated by LZerD, findings on scoring functions are expected to be universally applicable to other docking methods. Proteins 2017; 85:513-527. © 2016 Wiley Periodicals, Inc.

Long-distance correlations of rhinovirus capsid dynamics contribute to uncoating and antiviral activity.

Human rhinovirus (HRV) and other members of the enterovirus genus bind small-molecule antiviral compounds in a cavity buried within the viral capsid protein VP1. These compounds block the release of the viral protein VP4 and RNA from inside the capsid during the uncoating process. In addition, the antiviral compounds prevent "breathing" motions, the transient externalization of the N-terminal regions of VP1 and VP4 from the inside of intact viral capsid. The site for externalization of VP1/VP4 or release of RNA is likely between protomers, distant to the binding cavity for antiviral compounds. Molecular dynamics simulations were conducted to explore how the antiviral compound, WIN 52084, alters properties of the HRV 14 capsid through long-distance effect. We developed an approach to analyze capsid dynamics in terms of correlated radial motion and the shortest paths of correlated motions. In the absence of WIN, correlated radial motion is observed between residues separated by as much as 85 Å, a remarkably long distance. The most frequently populated path segments of the network were localized near the fivefold symmetry axis and included those connecting the N termini of VP1 and VP4 with other regions, in particular near twofold symmetry axes, of the capsid. The results provide evidence that the virus capsid exhibits concerted long-range dynamics, which have not been previously recognized. Moreover, the presence of WIN destroys this radial correlation network, suggesting that the underlying motions contribute to a mechanistic basis for the initial steps of VP1 and VP4 externalization and uncoating.

Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective.

Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

Baseline Demographic Profile and General Health Influencing the Post-Radiotherapy Health Related Quality-of-Life in Women with Gynaecological Malignancy Treated with Pelvic Irradiation.

BACKGROUND: Cancer specific survival and quality-of-life (QOL) assessment are important in evaluating cancer treatment outcomes. Baseline demographic profiles have significant effects on follow-up health related QOL (HRQOL) and affect the outcome of treatments. MATERIALS AND METHODS: Post-operative gynaecological cancer patients required adjuvant pelvic radiation enrolled longitudinal assessment study. Patients had completed the short form-36 (SF-36) questionnaire before the adjuvant radiotherapy and functional assessments of cancer therapy-general module at 6(th) month's follow-up period to assess the HRQOL. Baseline variables were race, age, body mass index (BMI), education, marital status, type of surgery, physical composite scores (PCS) and mental composite scores (MCS) summary scores of the SF-36. Univariate and multivariate regression analysis used to determine the influence of these variables on post-radiotherapy HRQOL domains. RESULTS: Baseline PCS, MCS, age, education and marital status had positively correlation with post-radiotherapy HRQOL while higher BMI had a negative impact in univariate analysis. In multivariate regression analysis, education and MCS had a positive correlation while higher BMI had a negative correlation with HRQOL domains. CONCLUSION: Enhance our ability to detect demographic variables and modify those factors and develops new treatment aimed at improving all aspect of gynaecological cancer including good QOL.

Speciation of toxic pollutants in Pb/Zn smelter slags by X-ray Absorption Spectroscopy in the context of the literature.

Pb/Zn smelter slag is a hazardous industrial waste from the Imperial Smelting Process (ISP). The speciation of zinc, lead, copper and arsenic in the slag controls their recovery or fate in the environment but has been little investigated. X-ray Absorption Spectroscopy (XAS) was applied to this complex poorly crystalline material for the first time to gain new insights about speciation of elements at low concentration. Zn, Cu, As K-edge and Pb L3-edge XAS was carried out for a Pb/Zn slag from a closed ISP facility in England, supported by Fe, S and P K-edge XAS. Results are presented in the context of a full review of the literature. X-ray fluorescence showed that concentrations of Zn, Pb, Cu and As were 8.4, 1.6, 0.48 and 0.45 wt%, respectively. Wüstite (FeO) was the only crystalline phase identified by X-ray diffraction, but XAS provided a more complete understanding of the matrix. Zn was found to be mainly present in glass, ZnS, and possibly solid solutions with Fe oxides; Pb was mainly present in glass and apatite minerals (e.g., Pb5(PO4)3OH); Cu was mainly speciated as Cu2S, with some metallic Cu and a weathering product, Cu(OH)2; As speciation was likely dominated by arsenic (III) and (V) oxides and sulfides.

Homogeneous versus MOF-supported catalysis: a direct comparison of catalytic hydroboration with Ni tripodal P3E (E = Si, Ge) complexes.

The MOF material NU-1000 was employed to host Ni tripodal complexes prepared from new organometallic precursors [HNi(κ4(E,P,P,P)-E(o-C6H4CH2PPh2)3], E = Si (Ni-1), Ge (Ni-2). The new heterogeneous catalytic materials, Ni-1@NU-1000 and Ni-2@NU-1000, show the advantages of both homogeneous and heterogeneous catalysts. They catalyze the hydroboration of aldehydes and ketones more efficiently than the homogeneous Ni-1 and Ni-2, under aerobic conditions and show recyclability.

Local Structure of ZnO micro flowers and nanoparticles obtained by micro-segmented flow synthesis.

The micro-segmented flow technique was applied for continuous synthesis of ZnO micro- and nanoparticles with short residence times of 9.4 s and 21.4 s, respectively. The obtained particles were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Small angle X-ray scattering (SAXS) and photoluminescence spectroscopy were used to determine the size and optical properties of ZnO nanoparticles. In addition, extended X-ray absorption fine structure (EXAFS) spectroscopy was employed to investigate local structural properties. The EXAFS measurements reveal a larger degree of structural disorder in the nanoparticles than the microparticles. These structural changes should be taken into consideration while evaluating the size-dependent visible emission of ZnO nanoparticles.

Design, simulation, and development of bipolar pulse forming network based Marx generator for S band backward wave oscillator.

Pulse power systems have a wide range of applications, one of which is microwave generation. Microwave emission is associated with a certain time delay between the application of a high voltage pulse and the generation of the microwave signal. This time delay is known as microwave delay time, and it depends on the time period of the microwave signal being generated. As the time period of the microwave signal increases, the required input electrical pulse duration also goes up. To achieve this, a pulse forming network (PFN) based Marx generator is proposed. The Bipolar Marx generator is preferred over the uni-polar Marx generator to obtain the high voltage high current pulse. This also helps in maintaining the impedance requirement for Backward Wave Oscillator (BWO) devices that generate the microwave pulse. To the best of our knowledge, PFN based Marx generators have been developed up to 400 kV. Here, a bipolar Marx generator has been designed with ratings of 800 kV peak voltage, 10 kA peak current, and 150 ns flattop pulse duration. The design includes analytical calculations and numerical analysis by electromagnetic simulation. The triggering method to get a wide triggering range has also been discussed. The design values have also been experimentally verified, and the resulting parameters were applied to a BWO to simulate the microwave power that it can produce. A peak microwave power of ∼1 GW has been observed in the particle-in-cell simulation.

A 500 kV, 10 kA, 40 ns coaxial Marx generator pulser for cable fed flash x-ray system.

Flash x-ray (FXR) systems are used for dynamic radiography. Depending on the speed of the object, these systems typically require a very short pulse duration (∼25 ns) for image acquisition without motion blur. The conventional Marx generators with zigzag discharge paths result in higher inductance; hence, they do not meet the requirement of shorter pulse duration (30-40 ns) and low impedance (40-60 Ω) simultaneously. A coaxial Marx generator has been designed and developed, which is capable of generating 500 kV peak voltages and 10 kA peak current within a 40 ns pulse duration. The CST simulation of the coaxial Marx generator has been carried out to validate the design parameters. The FXR electron beam diode is powered by this Marx generator. Experiments were carried out to measure the x-ray parameters like pulse width, source size, x-ray energy spectrum, penetration depth, and cone angle. The maximum measured x-ray dose was 62 mR at 1 m distance from the source window. The x-ray radiograph demonstrates a penetration depth of 32 mm in steel kept at 2.5 m distance from the source for 500 kV diode voltages.

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets.

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ∼40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ∼3.7 billion candidate molecules.

CoCrFeNi High-Entropy Alloy as an Enhanced Hydrogen Evolution Catalyst in an Acidic Solution.

High-entropy alloys (HEAs) have intriguing material properties, but their potential as catalysts has not been widely explored. Based on a concise theoretical model, we predict that the surface of a quaternary HEA of base metals, CoCrFeNi, should go from being nearly fully oxidized except for pure Ni sites when exposed to O2 to being partially oxidized in an acidic solution under cathodic bias, and that such a partially oxidized surface should be more active for the electrochemical hydrogen evolution reaction (HER) in acidic solutions than all the component metals. These predictions are confirmed by electrochemical and surface science experiments: the Ni in the HEA is found to be most resistant to oxidation, and when deployed in 0.5 M H2SO4, the HEA exhibits an overpotential of only 60 mV relative to Pt for the HER at a current density of 1 mA/cm2.

Accommodation of In-Register N-Linked Glycans on Prion Protein Amyloid Cores.

Although prion protein fibrils can have either parallel-in-register intermolecular ß-sheet (PIRIBS) or, probably, ß-solenoid architectures, the plausibility of PIRIBS architectures for the usually glycosylated natural prion strains has been questioned based the expectation that such glycans would not fit if stacked in-register on each monomer within a fibril. To directly assess this issue, we have added N-linked glycans to a recently reported cryo-electron microscopy-based human prion protein amyloid model with a PIRIBS architecture and performed in silico molecular dynamics studies to determine if the glycans can fit. Our results show that triantennary glycans can be sterically accommodated in-register on both N-linked glycosylation sites of each monomer. Additional simulations with an artificially mutated ß-solenoid model confirmed that glycans can be accommodated when aligned with ∼4.8 Å spacing on every rung of a fibril. Altogether, we conclude that steric intermolecular clashes between glycans do not, in themselves, preclude PIRIBS architectures for prions.

Uniform Mesoporous Amorphous Cobalt-Inherent Silicon Oxide as a Highly Active Heterogeneous Catalyst in the Activation of Peroxymonosulfate for Rapid Oxidation of 2,4-Dichlorophenol: The Important Role of Inherent Cobalt in the Catalytic Mechanism.

Amorphous cobalt-inherent silicon oxide (Co-SiOx) was synthesized for the first time and employed as a highly active catalyst in the activation of peroxymonosulfate (PMS) for the rapid oxidation of 2,4-dichlorophenol (2,4-DCP). The characterization results revealed that the 0.15Co-SiOx possessed a high specific surface area of 607.95 m2/g with a uniform mesoporous structure (24.33 nm). The X-ray diffraction patterns indicate that the substituted cobalt atoms enlarge the unit cell parameter of the original SiO2, and the selected area electron diffraction pattern confirmed the amorphous nature of Co-SiOx. More bulk oxygen vacancies (Ov) existing in the Co-SiOx were identified to be one of the primary contributors to the significantly enhanced catalytic activation of PMS. The cobalt substitution both creates and stabilizes the surficial Ov and forms the adequately active Co(II)-Ov pairs which engine the electron transfer process during the catalytic activities. The active Co(II)-Ov pairs weaken the average electronegativity of Co/Si and Co/O sites, resulting in the prevalent changes in final state energy, which is the main driving cause of the binding energy shifts in the X-ray photoelectron spectroscopy (XPS) spectra of Si and O among all samples. The increase of the relative proportion of Co(III) in the spent Co-SiOx probably causes the binding energy shifts of the Co XPS spectrum compared to that of the Co-SiOx. The amorphous Co-SiOx outperforms stable and quick 2,4-DCP degradation, achieving a much higher kinetic rate of 0.7139 min-1 at pH = 7.02 than others via sulfate radical advanced oxidation processes (AOPs), photo-Fenton AOPs, H2O2 reagent AOPs, and other AOP approaches. The efficient degradation performance makes the amorphous Co-SiOx as a promising catalyst in removing 2,4-DCP or organic-rich pollutants.

Effects of plasticizers and surfactants on the film forming properties of hydroxypropyl methylcellulose for the coating of diclofenac sodium tablets.

Hydroxy propyl methyl cellulose (HPMC) 5cPs, an aqueous soluble polymer was employed for coating diclofenac sodium (DFS) tablets 25 mg for protecting the integrity of the drug yet rendering the drug to release at a faster rate on contact with the gastric environment. Proper optimization for the aqueous based film coating formulation was undertaken primarily employing plasticizers like polyethylene glycol (PEG) 400 and propylene glycol (PG). The defect free selected formulations were further subjected for studying the effects of surfactants like sodium lauryl sulphate (SLS) and Tween-80 along with the plasticizers. The quality of the aqueous film coats or the plasticizer efficiency in case of PEG-400 is in the order 1.5 > 0.5 > 1.0% and for PG 1 > 4 > 3% which can be stated on the basis of less incidence of major coat defects like chipping, cracking, orange peel, roughness, blistering, blooming, picking. The quality of aqueous film coat or the surfactant efficiency in case of SLS + PEG-400 is in the order 0.3 < 0.5 < 0.1% and SLS + PG is in the order 0.5 < 0.1 < 0.3%. In case of Tween-80 + PEG-400 the order is 0.3 < 0.5 < 0.1% and Tween-80 + PG is in the order 0.3 < 0.1 < 0.5%. Elegant film formation can be stated from fewer incidences of coat defects. The obtained coated tablets eventually satisfied all the normal physical parameters like thickness, weights, and weight gain, drug content, crushing strength, percent friability, disintegration time, dissolution profile and possible drug-polymer interactions. ANOVA was undertaken followed by Dunnet multiple comparison for the dissolution profile considering uncoated as the standard. The difference was considered significant at p â©½ 0.01.