ALBERT

Beschreibung: The theoretical conditions for small-angle inelastic scattering where the incident electron can effectively be treated as a particle moving in a uniform potential is examined. The motivation for this work is the recent development of a multislice method that combines plasmon energy losses with elastic scattering using Monte Carlo methods. Since plasmon excitation is delocalized, it was assumed that the Bloch wave nature of the incident electron in the crystal does not affect the scattering cross-section. It is shown here that for a delocalized excitation the mixed dynamic form factor term of the scattering cross-section is zero and the scattered intensities follow a Poisson distribution. These features are characteristic of particle-like scattering and validate the use of Monte Carlo methods to model plasmon losses in multislice simulations.

Beschreibung: This review examines methods of magnetic flux density measurements from the narrow grain boundary (GB) regions, the thickness of which is of the order of nanometers, produced in Nd–Fe–B-based sintered magnets. Despite of the complex crystallographic microstructure and the significant stray magnetic field of the sintered magnet, recent progress in electron holography allowed for the determination of the intrinsic magnetic flux density due to the GB which is embedded in the polycrystalline thin-foil. The methods appear to be useful as well for intensive studies about interface magnetism in a variety of systems.

Beschreibung: Some species of lactic acid bacteria used for the production of natural cheese produce exopolysaccharides (EPS). Electron microscopy is useful for analyzing the microstructure of EPS produced by lactic acid bacteria. However, pretreatments used to observe the microstructure of EPS by electron microscopy, such as dehydration and resin embedding, can result in EPS flowing out easily from the cell. Therefore, in this study, the Tokuyasu method was conducted on cryosection to reduce EPS outflow. Two types of observation method, namely, using lectin and ruthenium red, were conducted in an attempt to observe EPS produced by Lactobacillus helveticus SBT2171. Observation using the lectin method confirmed that colloidal gold particles conjugated with a lectin recognizing β-galactoside were present in the capsule. Structures that appeared to be β-galactoside-containing slime polysaccharides that were released from the cell wall were also observed. Observation using ruthenium red showed that capsular polysaccharides (CPS) in the capsule were present as a net-like structure. Colloidal gold conjugation with an anti-β-lactoglobulin antibody, in addition to ruthenium red staining, allowed the identification of slime polysaccharides released from the cell wall in the milk protein network derived from the culture medium. Based on these results, the Tokuyasu method was considered to be a useful pretreatment method to clarify and observe the presence of EPS. In particular, both CPS in the capsule and slime exopolysaccharides released from the cell wall were visualized.

Beschreibung: Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.

Beschreibung: Image contrast between carbon nanotubes (CNTs) and polytetrafluoroethylene (PTFE) in a CNT/PTFE composite film, which is difficult to obtain by conventional backscattered electron (BSE) imaging, was optimized to better elucidate the distribution of CNT in the film. Ultra-low landing energy condition (0.3 keV in this study) was used to prevent specimen damage due to electron beam irradiation. Signal acceptance maps, which represent the distributions of energy and take-off angle, were calculated to evaluate the features of the signal detection system used in this study. SEM images of this composite film were taken under several sets of conditions and analyzed using these acceptance maps. CNT and PTFE in the composite film can be clearly distinguished with material and topographic contrasts using the BSE signal under optimized energy and take-off angle ranges, even at ultra-low landing energy conditions.

Beschreibung: We have developed a new certified reference material (CRM) for image sharpness evaluation and magnification calibration for scanning electron microscopy (SEM). Designed to be suitable for the image sharpness evaluation by the derivative method, the CRM has nanoscale tungsten dot-array structure fabricated on silicon substrate, which gives steep contrast transition from the dot to the substrate in SEM image. The pitch of the dot-array was SI-traceably measured as a specified value with relative expanded uncertainty ($k=2$) of ~1.3%, which can be utilized for the magnification calibration of SEM. Since specimens, as one of the image formation parameters, easily affect image sharpness value, our CRM, as a ‘pinned specimen’, will play an important role to achieve robust and stable image sharpness measurement system.

Beschreibung: Here, we describe a method for tracking intracellular processing of small interfering RNA (siRNA) containing complexes using automated microscopy controls and image acquisition to minimize user effort and time. This technique uses fluorescence colocalization to monitor dual-labeled fluorescent siRNAs delivered by silica nanoparticles in different intracellular locations, including the early/late endosomes, fast/slow recycling endosomes, lysosomes and the endoplasmic reticulum. Combining the temporal association of siRNAs with each intracellular location, we reconstructed the intracellular pathways used in siRNA processing, and demonstrate how these pathways vary based on the chemical composition of the delivery vehicle.

Beschreibung: Motivation Recent technological advances produce a wealth of high-dimensional descriptions of biological processes, yet extracting meaningful insight and mechanistic understanding from these data remains challenging. For example, in developmental biology, the dynamics of differentiation can now be mapped quantitatively using single-cell RNA sequencing, yet it is difficult to infer molecular regulators of developmental transitions. Here, we show that discovering informative features in the data is crucial for statistical analysis as well as making experimental predictions. Results We identify features based on their ability to discriminate between clusters of the data points. We define a class of problems in which linear separability of clusters is hidden in a low-dimensional space. We propose an unsupervised method to identify the subset of features that define a low-dimensional subspace in which clustering can be conducted. This is achieved by averaging over discriminators trained on an ensemble of proposed cluster configurations. We then apply our method to single-cell RNA-seq data from mouse gastrulation, and identify 27 key transcription factors (out of 409 total), 18 of which are known to define cell states through their expression levels. In this inferred subspace, we find clear signatures of known cell types that eluded classification prior to discovery of the correct low-dimensional subspace. Availability and implementation https://github.com/smelton/SMD. Supplementary information Supplementary data are available at Bioinformatics online.

Beschreibung: Motivation Polymerase chain reaction (PCR) has been a revolutionary biomedical advancement. However, for PCR to be appropriately used, one must spend a significant amount of effort on PCR primer design. Carefully designed PCR primers not only increase sensitivity and specificity, but also decrease effort spent on experimental optimization. Computer software removes the human element by performing and automating the complex and rigorous calculations required in PCR primer design. Classification and review of the available software options and their capabilities should be a valuable resource for any PCR application. Results This paper focuses on currently available free PCR primer design software and their major functions (https://pcrprimerdesign.github.io/). The software are classified according to their PCR applications, such as Sanger sequencing, reverse transcription quantitative PCR, single nucleotide polymorphism detection, splicing variant detection, methylation detection, microsatellite detection, multiplex PCR and targeted next generation sequencing, and conserved/degenerate primers to clone orthologous genes from related species, new gene family members in the same species, or to detect a group of related pathogens. Each software is summarized to provide a technical review of their capabilities and utilities.

Beschreibung: Motivation Network diffusion and label propagation are fundamental tools in computational biology, with applications like gene-disease association, protein function prediction and module discovery. More recently, several publications have introduced a permutation analysis after the propagation process, due to concerns that network topology can bias diffusion scores. This opens the question of the statistical properties and the presence of bias of such diffusion processes in each of its applications. In this work, we characterised some common null models behind the permutation analysis and the statistical properties of the diffusion scores. We benchmarked seven diffusion scores on three case studies: synthetic signals on a yeast interactome, simulated differential gene expression on a protein-protein interaction network and prospective gene set prediction on another interaction network. For clarity, all the datasets were based on binary labels, but we also present theoretical results for quantitative labels. Results Diffusion scores starting from binary labels were affected by the label codification, and exhibited a problem-dependent topological bias that could be removed by the statistical normalisation. Parametric and non-parametric normalisation addressed both points by being codification-independent and by equalising the bias. We identified and quantified two sources of bias -mean value and variance- that yielded performance differences when normalising the scores. We provided closed formulae for both and showed how the null covariance is related to the spectral properties of the graph. Despite none of the proposed scores systematically outperformed the others, normalisation was preferred when the sought positive labels were not aligned with the bias. We conclude that the decision on bias removal should be problem and data-driven, i.e. based on a quantitative analysis of the bias and its relation to the positive entities. Availability The code is publicly available at https://github.com/b2slab/diffuBench Supplementary information Supplementary data are available at Bioinformatics online.