OmniSpect: An Open MATLAB-Based Tool for Visualization and Analysis of Matrix-Assisted Laser Desorption/Ionization and Desorption Electrospray Ionization Mass Spectrometry Images

We present omniSpect, an open source web- and MATLAB-based software tool for both desorption electrospray ionization (DESI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) that performs computationally intensive functions on a remote server. These functions include converting data from a variety of file formats into a common format easily manipulated in MATLAB, transforming time-series mass spectra into mass spectrometry images based on a probe spatial raster path, and multivariate analysis. OmniSpect provides an extensible suite of tools to meet the computational requirements needed for visualizing open and proprietary format MSI data.      

Coexistence of two kinds of fluorinated hydrogenated micelles as building blocks for the design of bimodal mesoporous silica with two ordered mesopore networks

A simple and effective route has been developed for the synthesis of bimodal (3.6 and 9.4 nm) mesoporous silica materials that have two ordered interconnected pore networks. Mesostructures have been prepared through the self-assembly mechanism by using a mixture of polyoxyethylene fluoroalkyl ether and triblock copolymer as building blocks. The investigation of the R(F)(8)(EO)(9)/P123/water phase diagram shows that in the considered surfactant range of concentrations the system is micellar (L(1)). DLS measurements indicate that this micellar phase is composed of two types of micelles; the size of the first one at around 7.6 nm corresponds unambiguously to the pure fluorinated micelles. The second type of micelles at higher diameter consists of fluorinated micelles that have accommodated a weak fraction of P123 molecules. Thus, in this study the bimodal mesoporous silica is really templated by two kinds of micelles.     

Solvent-exfoliated graphene at extremely high concentration

We describe three related methods to disperse graphene in solvents with concentrations from 2 to 63 mg/mL. Simply sonicating graphite in N-methyl-2-pyrrolidinone, followed by centrifugation, gives dispersed graphene at concentrations of up to 2 mg/mL. Filtration of a sonicated but uncentrifuged dispersion gives a partially exfoliated powder that can be redispersed at concentrations of up to 20 mg/mL. However, this process can be significantly improved by removing any unexfolaited graphite from the starting dispersion by centrifugation. The centrifuged dispersion can be filtered to give a powder of exfoliated few-layer graphene. This powder can be redispersed at concentrations of at least 63 mg/mL. The dispersed flakes are ~1 μm long and ~3 to 4 layers thick on average. Although some sedimentation occurs, ~26-28 mg/mL of the dispersed graphene appears to be indefinitely stable.     

An improved method for the preparations of nanostructured lipid carriers containing heat-sensitive bioactives

Heat-sensitive bioactive compounds such as β-carotene and tocols, are widely used in the pharmaceutical and cosmetic fields. Their chemical stability in delivery systems is one of the major concerns in the production of nanostructured lipid carriers (NLCs). A previously established high-temperature high-pressure homogenisation technique involved in the preparation of NLCs can cause degradation of heat-sensitive compounds. Therefore, a novel preparation process needs to be developed to minimise the degradation of heat-sensitive active compounds during the preparation of NLCs. In this work, modified methods A and B were designed to minimise the degradation of β-carotene and tocols during the production of NLCs. These methods improved the chemical stability of heat-sensitive bioactive compounds (β-carotene and tocols) significantly compared to the previously established method. The physical stability of the formulation was maintained throughout study duration.     

Bi-functional gold-coated magnetite composites with improved biocompatibility

The effect of gold attachment on the physical characteristics, cellular uptake, gene expression efficiency, and biocompatibility of magnetic iron oxide (MNP) vector was investigated in vitro in BHK21 cells. The surface modification of magnetite with gold was shown to alter the morphology and surface charge of the vector. Nonetheless, despite the differences in the surface charge with and without gold attachment, the surface charge of all vectors were positive when conjugated with PEI/DNA complex, and switched from positive to negative when suspended in cell media containing serum, indicating the adsorption of serum components onto the composite. The cellular uptake of all MNP vectors under the influence of a magnetic field increased when the composite loadings increased, and was higher for the MNP vector that was modified with gold. Both bare magnetite and gold-coated magnetite vectors gave similar optimal gene expression efficiency, however, the gold-coated magnetite vector required a 25-fold higher overall loading to achieve a comparable efficiency as the attachment of gold increased the particle size, thus reducing the surface area for PEI/DNA complex conjugation. The MNP vector without gold showed optimal gene expression efficiency at a specific magnetite loading, however further increases beyond the optimum loading decreased the efficiency of gene expression. The drop in efficiency at high magnetite loadings was attributed to the significant reduction in cellular viability, indicating the bare magnetite became toxic at high intracellular levels. The gene expression efficiency of the gold-modified vector, on the other hand, did not diminish with increasing magnetite loadings. Intracellular examination of both bare magnetite and gold-coated magnetite vectors at 48h post-magnetofection using transmission electron microscopy provided evidence of the localization of both vectors in the cell nucleus for gene expression and elucidated the nuclear uptake mechanism of both vectors. The results of this work demonstrate the efficacy of gold-modified vectors to be used in cellular therapy research that can function both as a magnetically-driven gene delivery vehicle and an intracellular imaging agent with negligible impact on cell viability.     

Preparation and optical properties of silver nanowires and silver-nanowire thin films

Silver nanowires and silver-nanowire thin films have attracted much attention due to their extensive applications in Surface-Enhanced Raman Scattering (SERS) and Surface-Enhanced Fluorescence (SEF). Thin films of silver nanowires within polyelectrolyte layers of poly(allylamine hydrochloride) (PAH) and poly(sodium 4-styrenesulfonate) (PSS) were fabricated by the Spin-Assisted Layer-by-Layer (SA-LbL) method. The surface coverage, thickness, and absorbance properties of the silver-nanowire films were controlled by the number of layers deposited. Both transverse and longitudinal surface plasmon (SP) modes of the silver-nanowires were observed in the absorbance spectra, as was evidence for nanowire interaction. Two-dimensional finite difference time-domain (2D FDTD) simulations predict that the maximum field enhancement occurs at the ends and cross-sectional edges of the wires for the longitudinal and transverse modes, respectively. Silver nanowires were synthesized by a facile, high-yield solvothermal approach, which can be easily manipulated to control the aspect ratio of the nanowires. The effects of polyvinylpyrrolidone (PVP) concentration and molecular weight on the growth of the silver nanowires, which are not documented in the original procedure, are discussed. It is shown that the growth mechanism for silver nanowires in the solvothermal synthesis is similar to that reported for the polyol synthesis.     

The Poisson-Helmholtz-Boltzmann model

We present a mean-field model of a one-component electrolyte solution where the mobile ions interact not only via Coulomb interactions but also through a repulsive non-electrostatic Yukawa potential. Our choice of the Yukawa potential represents a simple model for solvent-mediated interactions between ions. We employ a local formulation of the mean-field free energy through the use of two auxiliary potentials, an electrostatic and a non-electrostatic potential. Functional minimization of the mean-field free energy leads to two coupled local differential equations, the Poisson-Boltzmann equation and the Helmholtz-Boltzmann equation. Their boundary conditions account for the sources of both the electrostatic and non-electrostatic interactions on the surface of all macroions that reside in the solution. We analyze a specific example, two like-charged planar surfaces with their mobile counterions forming the electrolyte solution. For this system we calculate the pressure between the two surfaces, and we analyze its dependence on the strength of the Yukawa potential and on the non-electrostatic interactions of the mobile ions with the planar macroion surfaces. In addition, we demonstrate that our mean-field model is consistent with the contact theorem, and we outline its generalization to arbitrary interaction potentials through the use of a Laplace transformation.     

Photoinduced dynamics to photoluminescence in Ln3+ (Ln = Ce,Pr) doped β-NaYF4 nanocrystals computed in basis of non-collinear spin DFT with spin-orbit coupling

ABSTRACT

In this work, non-collinear spin DFT + U approaches with spin-orbit coupling (SOC) are applied to Ln³⁺ doped β-NaYF₄ (Ln = Ce, Pr) nanocrystals in Vienna ab initio Simulation Package taking into account unpaired spin configurations using the Perdew–Burke–Ernzerhof functional in a plane wave basis set. The calculated absorption spectra from non-collinear spin DFT + U approaches are compared with that from spin-polarised DFT + U approaches. The spectral difference indicates the importance of spin–flip transitions of Ln³⁺ ions. Suite of codes for nonadiabatic dynamics has been developed for 2-component spinor orbitals. On-the-fly nonadiabatic coupling calculations provide transition probabilities facilitated by nuclear motion. Relaxation rates of electrons and holes are calculated using Redfield theory in the reduced density matrix formalism cast in the basis of non-collinear spin DFT + U with SOC. The emission spectra are calculated using the time-integrated method along the excited state trajectories based on nonadiabatic couplings.     

A convenient synthesis of the novel 5H-thieno[2,3-e]-4,1,2-oxathiazepine ring system via an alkoxycarbenium ion intermediate

3-(Methoxymethoxymethyl)-2-thiophenesulfonamides and 3-hydroxymethyl-N-methoxymethyl-2-thiophenesulfonamides have been shown to undergo cyclization when treated under anhydrous acidic conditions to provide the novel 2,3-dihydro-5H-thieno[2,3-e]-4,1,2-oxathiazepine ring system. Incorporation of a primary sulfonamide group into position seven of the molecule provided compounds which inhibit human carbonic anhydrase II.     

Instance Segmentation of Multiple Myeloma Cells Using Deep-Wise Data Augmentation and Mask R-CNN

Multiple myeloma is a condition of cancer in the bone marrow that can lead to dysfunction of the body and fatal expression in the patient. Manual microscopic analysis of abnormal plasma cells, also known as multiple myeloma cells, is one of the most commonly used diagnostic methods for multiple myeloma. However, as it is a manual process, it consumes too much effort and time. Besides, it has a higher chance of human errors. This paper presents a computer-aided detection and segmentation of myeloma cells from microscopic images of the bone marrow aspiration. Two major contributions are presented in this paper. First, different Mask R-CNN models using different images, including original microscopic images, contrast-enhanced images and stained cell images, are developed to perform instance segmentation of multiple myeloma cells. As a second contribution, a deep-wise augmentation, a deep learning-based data augmentation method, is applied to increase the performance of Mask R-CNN models. Based on the experimental findings, the Mask R-CNN model using contrast-enhanced images combined with the proposed deep-wise data augmentation provides a superior performance compared to other models. It achieves a mean precision of 0.9973, mean recall of 0.8631, and mean intersection over union (IOU) of 0.9062.