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Toward resistance‐compromised DHFR inhibitors part 1: Combined structure/ligand‐based virtual screenings and ADME‐Tox profiling

Published: Jul 27, 2016

Author(s): Prashant Gahtori, Rahul Pandey, Vinod Kumar, Surajit Kumar Ghosh, Aparoop Das, Jun Moni Kalita, Supriya Sahu, Anil Prakash, Divya Ranjan Bhattacharyya

Journal: Journal of Chemometrics

The front‐line antimalarial drugs, for example, chloroquine, mefloquine, sulfadoxine, pyrimethamine, atovaquone, and artemether, are often failing because of the worldwide spread of drug‐resistant parasites. There has been significant recent interest in virtual screening to drive innovative drug discovery and to combat resistance efforts for a wide range of diseases. In fact, virtual screening has become the “gold standard” for major...

Read More thumbnail image: Toward resistancecompromised DHFR inhibitors part 1 Combined structureligandbased virtual screenings and ADMETox profiling

A heuristic and parallel simulated annealing algorithm for variable selection in near‐infrared spectroscopy analysis

Published: Jul 27, 2016

Author(s): Jiyong Shi, Xuetao Hu, Xiaobo Zou, Jiewen Zhao, Wen Zhang, Xiaowei Huang, Yaodi Zhu, Zhihua Li, Yiwei Xu

Journal: Journal of Chemometrics

A new heuristic and parallel simulated annealing algorithm was proposed for variable selection in near‐infrared spectroscopy analysis. The algorithm employs a parallel mechanism to enhance the search efficiency, a heuristic mechanism to generate high‐quality candidate solutions, and the concept of Metropolis criterion to estimate accuracy of the candidate solutions. Several near‐infrared datasets have been evaluated under the proposed new...

Read More thumbnail image: A heuristic and parallel simulated annealing algorithm for variable selection in nearinfrared spectroscopy analysis

A new insight into polyurethane foam deterioration – the use of Raman microscopy for the evaluation of long‐term storage conditions

Published: Jul 27, 2016

Author(s): Susana França de Sá, Joana Lia Ferreira, Ana Sofia Matos, Rita Macedo, Ana Maria Ramos

Journal: Journal of Raman Spectroscopy

This research aims at bringing new contributions for lowering the polyether‐based polyurethane (PUR) flexible foam high deterioration rate by studying selected storage conditions. With a life expectancy of 20–50 years, many PUR objects show severe deterioration signs that, so far, cannot be prevented. To establish a preservation strategy, a natural ageing experiment in the dark (12 months, 45–55% relative humidity) has been carried out...

Read More thumbnail image: A new insight into polyurethane foam deterioration  the use of Raman microscopy for the evaluation of longterm storage conditions

Thermoelectric properties of bilayer phosphorene under tensile strain

Published: Jul 27, 2016

Author(s): Satoru Konabe, Shiro Kawabata, Takahiro Yamamoto

Journal: Surface and Interface Analysis

The thermoelectric power factor of bilayer phosphorene is investigated by performing first‐principle calculations based on density functional theory combined with semiclassical Boltzmann transport theory. Our simulations show that the thermoelectric performance of phosphorene strongly depends on the interlayer coupling, the direction of the temperature gradient, and the direction of strain. We find that the interlayer coupling oppositely...

Read More thumbnail image: Thermoelectric properties of bilayer phosphorene under tensile strain

Spin‐polarized electron energy loss spectroscopy at high momentum resolution

Published: Jul 27, 2016

Author(s): D. Vasilyev, J. Kirschner

Journal: Surface and Interface Analysis

An improved spin‐polarized electron energy loss spectroscopy apparatus with high momentum resolution was developed during the last few years. It is equipped with a multichannel energy analyzer and multichannel spin imaging detector. This technique allows to see features on the energy loss spectra, angular dependence of asymmetry and intensity and pronounced sensitivity on the primary energy. In this work, we studied dipolar scattering...

Read More thumbnail image: Spinpolarized electron energy loss spectroscopy at high momentum resolution

Abundance of field‐ionized ion species and current stability of ion beam emitted in He–Ne gas mixture

Published: Jul 27, 2016

Author(s): Keisuke Komaki, Shigekazu Nagai, Tatsuo Iwata, Kazuo Kajiwara, Koichi Hata

Journal: Surface and Interface Analysis

An attempt to increase the He ion current of a gas field ion source is made using a He–Ne mixture. The abundance of each ion in the produced ion beam is examined as a function of the applied field, along with the composition of the supplied gas mixture, using a field ion microscope equipped with a time‐of‐flight mass spectrometer. The operating conditions under which the He ion current is enhanced and no Ne ions are detected are...

Read More thumbnail image: Abundance of fieldionized ion species and current stability of ion beam emitted in HeNe gas mixture

Effect of Cu in electroless Ni–Cu–P coating on passivation process

Published: Jul 27, 2016

Author(s): Yiwei Gan, Tingting Zhao, Zhixin Kang, Jing Sang

Journal: Surface and Interface Analysis

Electroless Ni–P and Ni–Cu–P coatings were passivated by chromate conversion treatment respectively. The anticorrosive performances of passivated coatings were investigated by potentiodynamic polarization and electrochemical impedance spectroscopy measurements. The passivated Ni–Cu–P coating exhibited a high corrosion resistance with the icorr of 0.236 μA/cm,2 while the value of passivated Ni–P coating was only 1.030 μA/cm,2 indicating the passive...

Read More thumbnail image: Effect of Cu in electroless NiCuP coating on passivation process

Hydrogen desorption kinetics from H‐Si (111) surfaces studied by optical sum frequency generation and second harmonic generation

Published: Jul 27, 2016

Author(s): Md. Abdus Sattar, Khuat Thi Thu Hien, Yoshihiro Miyauchi, Goro Mizutani, Harvey N. Rutt

Journal: Surface and Interface Analysis

We have studied hydrogen desorption from a flat H‐Si (111)1 × 1 surface at 711 K by observing sum frequency generation (SFG) and second harmonic generation (SHG) spectra. Flat H‐Si (111) surfaces were prepared by dosing hydrogen molecules in an ultra‐high vacuum chamber with a base pressure of 〜10−8 Pa. Combining the SFG and SHG methods, the desorption order has been clarified over the whole hydrogen coverage range from 1 monolayer (ML)...

Read More thumbnail image: Hydrogen desorption kinetics from HSi 111 surfaces studied by optical sum frequency generation and second harmonic generation

Mechanisms of hydrophobization of polymeric composites etched in CF 4 plasma

Published: Jul 27, 2016

Author(s): Harinarayanan Puliyalil, Nina Recek, Gregor Filipič, Miha Čekada, Ivan Jerman, Miran Mozetič, Sabu Thomas, Uroš Cvelbar

Journal: Surface and Interface Analysis

Achieving optimal hydrophobicity of polymer materials especially polymer–matrix composites is important for many material applications. Herein the interplay of factors determining hydrophobic surface is presented during CF4 plasma treatments which lead to functionalization as well as selective polymer–matrix etching. The continuous exposure to plasma reactive species induces functionalization and etching on the surface, which decides the surface...

Read More thumbnail image: Mechanisms of hydrophobization of polymeric composites etched in CF 4 plasma

An advanced ionizing radiation monitoring network based on using SrI 2 (Eu)/MPPC module

Published: Jul 27, 2016

Author(s): Shigekazu Nagai, Ken Kawamura, Yoshihide Kimura, Junji Yoshii, Renzo Ikeda, Ryuichi Shimizu

Journal: Surface and Interface Analysis

An advanced ionizing radiation monitoring network (AIRMN) system using a single‐crystal SrI2(Eu) scintillator has been developed. The SrI2(Eu)‐scintillator (25 mmφ × 25 mm) has excellent material properties, including a high light yield (>80 000 photons/MeV), a high photoelectric cross section, and high energy resolution (<4%). The system has a multi‐pixel photon counter as a light detector. The resolution and sensitivity of the new AIRMN allow...

Read More thumbnail image: An advanced ionizing radiation monitoring network based on using SrI 2 EuMPPC module

REELS study of a LiNi 1/3 Mn 1/3 Co 1/3 O 2 positive electrode

Published: Jul 27, 2016

Author(s): N. Taguchi, M. Kitta, H. Sakaebe, T. Akita

Journal: Surface and Interface Analysis

Li K‐edge analysis obtained by scanning reflection energy loss spectroscopy (REELS) has been used to investigate the positive electrode of a Li‐ion battery. Using spectral imaging data, Li mapping of a LiNi1/3Mn1/3Co1/3O2 electrode has been constructed. Inhomogeneous Li distributions are observed in LiNi1/3Mn1/3Co1/3O2 particles after cyclic electrode charging and discharging. The REELS results agree well with those obtained by scanning transmission ...

Read More thumbnail image: REELS study of a LiNi 13 Mn 13 Co 13 O 2 positive electrode

Linewidth analysis of image potential states on noble metal surfaces with high‐energy resolved two‐photon photoemission spectroscopy

Published: Jul 27, 2016

Author(s): Takeo Nakazawa, Ryuichi Arafune, Noriaki Takagi, Maki Kawai

Journal: Surface and Interface Analysis

Electron dynamics in the excited states are governed by inelastic and quasielastic scattering processes. It is required to determine both scattering rates for complete understanding of the electron dynamics. Although time‐resolved two‐photon photoemission (2PPE) spectroscopy is a unique and powerful tool to measure the scattering rates directly, it is not easy to evaluate the quasielastic scattering rate. Precise measurement of spectral...

Read More thumbnail image: Linewidth analysis of image potential states on noble metal surfaces with highenergy resolved twophoton photoemission spectroscopy

Systematic approach to optimize a pretreatment method for ultrasensitive liquid chromatography with tandem mass spectrometry analysis of multiple target compounds in biological samples

Published: Jul 27, 2016

Author(s): Kazutaka Togashi, Kuninori Mutaguchi, Setsuko Komuro, Makoto Kataoka, Hiroshi Yamazaki, Shinji Yamashita

Journal: Journal of Separation Science

In current approaches for new drug development, highly sensitive and robust analytical methods for the determination of test compounds in biological samples are essential. These analytical methods should be optimized for every target compound. However, for biological samples that contain multiple compounds as new drug candidates obtained by cassette dosing tests, it would be preferable to develop a single method that allows the...

Read More thumbnail image: Systematic approach to optimize a pretreatment method for ultrasensitive liquid chromatography with tandem mass spectrometry analysis of multiple target compounds in biological samples

Meet the neighbors: Mapping local protein interactomes by proximity‐dependent labeling with BioID

Published: Jul 27, 2016

Author(s): Renata Varnaitė, Stuart A. MacNeill

Journal: PROTEOMICS

Proximity‐dependent biotin identification (BioID) is a recently developed method that allows the identification of proteins in the close vicinity of a protein of interest in living cells. BioID relies on fusion of the protein of interest with a mutant form of the biotin ligase enzyme BirA (BirA*) that is capable of promiscuously biotinylating proximal proteins irrespective of whether these interact directly or indirectly with the fusion...

Read More thumbnail image: Meet the neighbors Mapping local protein interactomes by proximitydependent labeling with BioID

Chemical exchange saturation transfer of the cervical spinal cord at 7 T

Published: Jul 26, 2016

Author(s): Adrienne N. Dula, Siddharama Pawate, Lindsey M. Dethrage, Benjamin N. Conrad, Blake E. Dewey, Robert L. Barry, Seth A. Smith

Journal: NMR in Biomedicine

High‐magnetic‐field (7 T) chemical exchange saturation transfer (CEST) MRI provides information on the tissue biochemical environment. Multiple sclerosis (MS) affects the entire central nervous system, including the spinal cord. Optimal CEST saturation parameters found via simulation were implemented for CEST MRI in 10 healthy controls and 10 patients with MS, and the results were examined using traditional asymmetry analysis and a...

Read More thumbnail image: Chemical exchange saturation transfer of the cervical spinal cord at 7 T

Molecular modeling studies of human immunodeficiency virus type 1 protease inhibitors using three‐dimensional quantitative structure‐activity relationship, virtual screening, and docking simulations

Published: Jul 26, 2016

Author(s): Jianbo Tong, Pei Zhan, Min Bai, Tuanli Yao

Journal: Journal of Chemometrics

In this paper, two 3‐dimensional quantitative structure‐activity relationship models for 60 human immunodeficiency virus (HIV)‐1 protease inhibitors were established using random sampling analysis on molecular surface and translocation comparative molecular field vector analysis (Topomer CoMFA). The non–cross‐validation (r2), cross‐validation (q2), correlation coefficient of external validation (Q2ext), and F of 2 models were 0.94, 0.80, 0.79, and...

Read More thumbnail image: Molecular modeling studies of human immunodeficiency virus type 1 protease inhibitors using threedimensional quantitative structureactivity relationship virtual screening and docking simulations

Gambir, “Gambir Sarawak” and toad venom

Published: Jul 26, 2016

Author(s): Wendy J.L. Lim, Angeline T.W. Yap, Merula Mangudi, Charmaine Y. Hu, Cheryl Y.Y. Yeo, Z.W. Eyo, Sarah X.W. Chia, K.B. Chan

Journal: Drug Testing and Analysis

Read More thumbnail image: Gambir Gambir Sarawak and toad venom

Analysis of multiblock datasets using ComDim: Overview and extension to the analysis of ( K + 1) datasets

Published: Jul 26, 2016

Author(s): Angélina El Ghaziri, Véronique Cariou, Douglas N. Rutledge, El Mostafa Qannari

Journal: Journal of Chemometrics

ComDim analysis was designed to assess the relationships between individuals and variables within a multiblock setting where several variables, organized in blocks, are measured on the same individuals. An overview of this method is presented together with some of its properties. Furthermore, we discuss a new extension of the method of analysis to the case of (K+1) datasets. More precisely, the aim is to explore the relationships between a response...

Read More thumbnail image: Analysis of multiblock datasets using ComDim Overview and extension to the analysis of  K  1 datasets

A rapid inversion technique for the measurement of longitudinal relaxation times of brain metabolites: application to lactate in high‐grade gliomas at 3 T

Published: Jul 25, 2016

Author(s): Karl Landheer, Arjun Sahgal, Sten Myrehaug, Albert P. Chen, Charles H. Cunningham, Simon J. Graham

Journal: NMR in Biomedicine

The aim of this study was to develop a time‐efficient inversion technique to measure the T1 relaxation time of the methyl group of lactate (Lac) in the presence of contaminating lipids and to measure T1 at 3 T in a cohort of primary high‐grade gliomas. Three numerically optimized inversion times (TIs) were chosen to minimize the expected error in T1 estimates for a given input total scan duration (set to be 30 min). A two‐cycle spectral editing scheme was used...

Read More thumbnail image: A rapid inversion technique for the measurement of longitudinal relaxation times of brain metabolites application to lactate in highgrade gliomas at 3 T

Ultra‐high performance supercritical fluid chromatography of lignin‐derived phenols from alkaline cupric oxide oxidation

Published: Jul 25, 2016

Author(s): Mingzhe Sun, Gunnar Lidén, Margareta Sandahl, Charlotta Turner

Journal: Journal of Separation Science

Traditional chromatographic methods for the analysis of lignin‐derived phenolic compounds in environmental samples are generally time consuming. In this work, an ultra‐high performance supercritical fluid chromatography method with a diode array detector for the analysis of major lignin‐derived phenolic compounds produced by alkaline cupric oxide oxidation was developed. In an analysis of a collection of 11 representative monomeric lignin...

Read More thumbnail image: Ultrahigh performance supercritical fluid chromatography of ligninderived phenols from alkaline cupric oxide oxidation
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