Single particle analysis with cryogenic electron microscopy (cryo-EM) can determine high resolution structures of macromolecular assemblies. To reconstruct final three-dimension(3D) density map, a reliable initial model is essential and ab-initio reconstruction usually can avoid model bias. The grand challenge for ab-initio reconstruction is to alignment two-dimension(2D) low signal-to-noise ratio(SNR) of particle images with random and unknown parameters. Here we formulate a fast ab initio reconstruction method(named AlignFM) based on Fourier Mellin transform and particle-swarm intelligence optimization(PSO) algorithm. It enables simultaneous 2D alignment and 3D refinement, which can fast generate a reliable 3D map. After experiments on several real datasets. AlignFM shows high performance on fast ab initio reconstruction with a small amount of data.

Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in the last years, it was observed a huge increase in the number of MPs solved by cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB). However, sample preparation remains a significant challenge in the field. Here, we evaluated in the MPs solved by cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å the most critical parameters for sample preparation: i) the surfactant used for protein extraction from the membrane, ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, iii) the vitrification method employed, and iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs, but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.

The up-to-date challenge towards clean road transport are non-exhaust emissions. Important advances regarding measurement systems, including well defined characterisation techniques, as well as regulation, will happen in the next few years. In this work we present detailed results of particle emissions from a test bed for wheel suspension and brakes, consisting of aerosol (size distribution, particle number (PN) and mass (PM)) and electron microscopy measurements (EM) under different load conditions. Standard tyres and brakes from series production were tested with a high-load driving cycle while particle measurements were conducted by gravimetric measurements and with a TSI SMPS, a TSI APS and a GRIMM OPS. Furthermore, samples were analyzed by electron microscopy. A bimodal particle size distribution (PSD) was obtained with the SMPS, with peaks at 20nm and around 400nm. EM analysis of >1400 single particles from the electrostatic sampler matches the PSD results. EM analysis also showed ultrafine particles, mainly from O, Fe, Si, Ba, Mg and S and also fractal particles with high C fractions. Our results suggest, in agreement with previously published literature, that particulate emissions are related to brake disc temperature and occur in significant amounts above a threshold temperature.

Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common one has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.

With forty years of developments, bio-macromolecule cryo-electron microscopy has met its revolution of resolution and is playing a very important role in structural biology study. According to different specimen states, cryo-electron microscopy (cryo-EM) involves three specific techniques, single particle analysis (SPA), electron tomography and sub-tomogram averaging, and electron diffraction. All these three techniques have not realized their full potentials of solving structures of bio-macromolecules and therefore need to be developed in the future. In this review, the current existing bottlenecks of cryo-EM SPA are discussed with theoretical analysis, which includes air-water interface during specimen cryo-vitrification, bio-macromolecular conformational heterogeneity, focus gradient within thick specimen, and electron radiation damage. Besides, potential solutions of these bottlenecks are proposed and discussed, which are worthy of further investigations in the future.

Friction and wear take place on two solid surfaces in sliding contact as a result of the mechanical, thermal and chemical interactions with the participation of environmental species. Electron microscopy and the associated spectroscopic analyses are powerful in probing these mechanisms in spatial resolutions from micro to atomic scale. This article provides a review of the author’s work in the wear and friction mechanisms of PVD hard coatings in which various SEM- and TEM-based microscopic and spectroscopic techniques were employed. Understanding on the failure mechanisms and the origin of self-adaptive friction has been improved to nano-scale. Other related issues are also discussed, such as sample preparation techniques for cross-sectional electron microscopy, energy dispersive X-ray spectroscopy and electron energy loss spectroscopy.

Although good field emission from graphene has been demonstrated from a wide variety of different microfabricated structures, very few of them can be used to improve the design of cold field emitters for electron microscopy applications. Most of them consist of densely packed nano-emitters, which produce a large array of defocused overlapping electron beams, and therefore cannot be subsequently focused down to a single nanometer electron probe. This paper reviews the kind of single-tip cathode structures suitable in cold field emission guns for instruments such as scanning electron microscopy, transmission electron microscope or scanning transmission electron microscopy, and reviews progress in fabricating them from graphene-based materials.

Metal-organic frameworks (MOFs), composed of metal nodes and inorganic linkers are promising for a wide range of applications due to their unique periodic frameworks that can be flexibly tuned. Understanding of the structure-activity relationships can facilitate the development and application of MOFs nanomaterials. Transmission electron microscopy (TEM) is a one-of-a-kind technique capable of characterizing MOFs microstructures at the atomic scale. Besides, in-situ TEM set-ups make it possible to direct visualize the microstructural evolution of MOFs in real time, which enables monitoring transitions of MOFs during growth as well as under working conditions. However, MOFs are so sensitive to the high-energy electron beam which makes TEM-based characterizing methods challenging. In this review, we first introduce the main damage mechanisms for MOFs under electron beam irradiation and two strategies to minimize the damages: low-dose TEM and cryo-TEM. Then, we discuss the techniques combined with the two strategies to analyze the MOFs’ microstructure, including three-dimensional electron diffraction, direct detection electron counting camera, and iDPC-STEM. Groundbreaking milestones and research advances with respect to static characterization of MOFs structures are highlighted. In-situ TEM studies are exemplary reviewed to provide insights into MOFs dynamics induced by various stimuli. Additionally, perspectives on promising techniques that may further facilitate the MOFs study using TEM are analyzed.

This article develops a multi-perspective view on motivations and methods for tobamovirus purification through the ages, and presents a novel efficient, easy-to-use approach that can be well-adapted to different species of native and functionalized virions. We survey the various driving forces prompting researchers to enrich tobamoviruses: from the search for the causative agents of mosaic diseases in plants to their increasing recognition as versatile nanocarriers in biomedical and engineering applications. Best practice and also rarely applied options for the serial processing steps required for successful isolation of tobamoviruses are then reviewed. Adaptations for distinct particle species, pitfalls and 'forgotten' or underrepresented technologies are considered as well. The article is topped off with our own development of a method for virion preparation, rooted in historical protocols. It combines selective re-solubilization of polyethylene glycol (PEG) virion raw precipitates with density step gradient centrifugation in biocompatible iodixanol formulations, yielding ready-to-use particle suspensions. This newly established protocol and some considerations for perhaps worthwile further developments could serve as putative stepping stones towards preparation procedures appropriate for routine practical uses of the multivalent soft-matter nanorods.

Much has been learned about the interaction between myosin and actin through biochemistry, in vitro motility assays and cryo-electron microscopy of F-actin decorated with myosin heads. Comparatively less is known about actin-myosin interactions within the filament lattice of muscle, where myosin heads function as independent force generators and thus most measurements report an average signal from multiple biochemical and mechanical states. All of the 3-D imaging by electron microscopy that has revealed the interplay of the regular array of actin subunits and myosin heads within the filament lattice has been accomplished using the flight muscle of the large waterbug Lethocerus sp. Lethocerus flight muscle possesses a particularly favorable filament arrangement that enables all the myosin cross-bridges contacting the actin filament to be visualized in a thin section. This review covers the history of this effort and the progress toward visualizing the complex set of conformational changes that myosin heads make when binding to actin in several static states as well as fast frozen actively contracting muscle. The efforts have revealed a consistent pattern of changes to the myosin head structures determined by X-ray crystallography needed to explain the structure of the different acto-myosin interactions observed in situ.

Under inflammatory conditions including lymphatic disorders, bone marrow-derived myeloid cells often express lymphatic endothelial cell (LEC) markers called LEC progenitor cells, which extend lymphatic vessels by fusing with existing lymphatic vessels. However, studies on the mechanism of lymphatic regeneration using three-dimensional images of lymphatic structures are limited. In this study, scanning electron microscopy (SEM) was used to observe the three-dimensional structure of lymphangiogenesis in a mouse model of secondary lymphedema. The model was established in C57BL/6J mice via circumferential incision in the inguinal region of the left hind limb. Skin samples were obtained from the lymphedema region on days 2, 5, and 8 after surgery. To determine lymphatic vessel positions using SEM analysis, we detected anti-lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) immunoreactivity in serial sections and overlaid them during SEM observation. On days 2 and 5, spherical cells, probably myeloid cells, were attached and fused to the LYVE-1-positive lymphatic vessel walls. On day 8, spherical cells were converted to string-shaped cells, forming a new lymphatic vessel wall resembling an intraluminal pillar. Our results show the three-dimensional lymphatic structures formed during lymphatic regeneration.

The present work investigates primarily the morphology evolution of the body-centered-cubic (BCC)/B2 phases in AlxNiCoFeCr high-entropy alloys (HEAs) with increasing Al content, which has been neglected so far. There exist two types of microscopic morphologies of BCC and B2 phases in this HEA series: one is the weave-like morphology induced by the spinodal decomposition, and the other is the microstructure of a spherical disordered BCC precipitation on the ordered B2 matrix that appears in HEAs with a much higher Al content. The shape of coherent precipitates is found to be closely related to the lattice misfit between BCC and B2 phases, which is sensitive to Al. The mechanical properties, including the compressive yielding strength and microhardness of the AlxNiCoFeCr HEAs, are also discussed in light of the concept of the valence electron concentration (VEC).

Scanning electron microscopy (SEM) is a powerful tool in the domain of material science, mining, and geology, owing to its enormous potential to provide unique insights into the micro and nanoscale worlds. This comprehensive review discusses the background development of SEM, basic SEM operation including the specimen preparation and imaging process, and fundamental theoretical calculations underlying the SEM operation. It provides foundational understanding to the engineers and scientists, who never got a chance to dig in-depth into the SEM, to understand the working and development of this robust analytical technique. The present review covers how SEM has been serving as a crucial tool in mineral characterization, with specific discussions on the working and research fronts of SEM-EDX, SEM-AM, SEM-MLA, and QEMSCAN. With automation gaining pace in the development of all spheres of technology, the understanding of uncertainties in SEM measurements is very important. The constraints in mineral phase identification by EDS spectra and sample preparation are conferred. In the end, future research directions for SEM are analyzed with the possible incorporation of machine learning, deep learning, and artificial intelligence tools, for automating the process of mineral identification, quantification, and efficient communication with the researchers, so that the analytical process robustness and objectivity can be improved, and the analysis time and the involved costs can be brought down. This review also discusses the idea of integrating robotics with SEM, to make the equipment portable, so that further mineral characterization insights can be gained not only on earth but also on other terrestrial grounds.

One in four adults in the US suffer from cartilage degeneration of the Intervertebral Disc (DDD) or load bearing joints (DJD). Combined DDD and DJD leads to billions of dollars in surgical health care costs annually. Since cartilage is avascular, it has a limited regenerative capacity. Conventional non-surgical treatment modalities provide brief symptomatic relief, have sided effects, and do not address the actual structural tissue defect in the cartilage itself. As such, new alternatives are needed. Perinatal tissue allografts have emerged as a novel frontier for bio-mechanical cartilage engineering research. Birth product-specific therapeutic roles and clinical outcomes are actively being investigated. The tissues of interest include umbilical cord-derived Wharton’s Jelly (WJ). This study assessed WJ tissue samples via ZEISS Supra 55VP Field-Emission Scanning Electron Microscope (SEM) at 100 and 300nm resolution scales. The captured images of pre and post-processed structural tissue matrices in WJ allografts were analyzed against themselves and peer-reviewed SEM images of articular cartilage, intervertebral disc cartilage, and muscle fascia. SEM images of post-processed WJ structural tissue matrices were analogous to structural tissue matrices in human articular cartilage, intervertebral disc cartilage, and muscle fascia. Relevant characteristics of pre- and post-processed structural tissue matrices in WJ allografts were comparable. This is the first study, that we are aware of, to utilize SEM to compare the pre-and post-processing relevant structural characteristics of WJ allografts and additionally demonstrate that structural collagen matrices in post-processed WJ allografts are analogous in structure to the cartilage in articular joints, intervertebral discs, and muscle fascia.

Mitochondrial dysregulation is implicated in numerous neurological disorders. Mitochondrial dynamics, including biogenesis, fusion and fission, are essential components of mitostasis which is modulated by complex regulatory mechanisms. Although expression studies are often used to investigate mitochondrial dynamics, these studies may be limited by the interdependent and temporal nature of mitostasis. Transmission electron microscopy (TEM) and cryogenic preparation methods provide a direct approach to examine mitochondrial ultrastructure in neurons. We investigated the utility of TEM to visualize mitochondrial morphological changes in SH-SY5Y cells treated with propionic acid (PPA). We examined whether morphological alterations were associated with differences in membrane potential or expression of biogenesis, fusion and fission genes. PPA induced a significant decrease in mitochondrial area (p<0.01 5mM), Feret's diameter and perimeter (p<0.05 5mM), and in area2 (p<0.05 3mM, p<0.01 5mM) – consistent with a shift towards fission. Morphological changes were not associated with significant differences in mitochondrial membrane potential. However, we observed decreased gene expression of NRF1 (p<0.01), TFAM (p<0.05), and STOML2 (p<0.0001). These data support a disruption of the balance in dynamics to preserve function under stress. This demonstrates the utility of TEM to provide insight into mitochondrial dynamics and function which can inform targeted mechanistic investigations into neuropathology.

Waste biogenic materials from seafood exploitation are valuable resources of new compounds exploitation within the blue bioeconomy concept. Here, we describe the effectiveness of Raman technology implementation as an in-line tool for demineralization process control of crustaceans or gastropods. We produced transparent chitin polymer foils from three waste crustacean shells (C. sapidus, S. mantis and M. squinado) using a slow, green chemical approach employing acetic acid, and showed the progressive process of biogenic carbonate dissolution and increasing the Raman characteristic signal of chitin, in a time dependence manner. It turned that chitin foils obtaining is species-specific, and the demineralization bath of waste shell mixture can be effectively tracked by Raman spectroscopy, for solvent control and the recovery of the calcium acetate as valuable by-product. Comparatively, calcium acetate drug, a compound widely used in kidney failure diseases, or as additive in nutraceuticals and food industry, has been obtained here, following a green demineralization path of the sea snail Rapana venosa intact shell, assisted by Raman tech-nology, using 9% acetic acid (vinegar) solution for 14 days. To validate the final products identity and quality, The process of waste shells demineralization and the final products of the treatment were investigated using various Raman techniques and technologies, cross-validating the results with FT-IR, XRD and SEM-EDX techniques. NIR Raman spectroscopy revealed chitin bands in a time-dependent manner, while Resonance Raman spectroscopy showed the preservation of ca-rotenoids after two weeks of acetic acid treatment. A hand-held flexible TacticID Raman system with a 1064 nm excitation demonstrated its effectiveness as a rapid, in-line decision making tool during process control and revealed excellent reproducibility of the lab-based instrument signal, suitable for in situ evaluation of the demineralization status and solvent saturation control. The calcium acetate recovered from residual treatment solutions was assessed regarding its hydration status, purity, and suitability as recrystallized material for further use as pharmaceutical product or ingredient in complex formulations.

A homogenization of billets from Al-Cu-Li-Mg-Sc-Zr alloys should be accomplished at high annealing temperatures exceeding 500 °C. This type of aluminum alloy is susceptible to the depletion of surface layers from Li. Therefore, choosing a suitable homogenization temperature and duration is a crucial step in assuring a homogeneous distribution of alloying elements and optimal exploitation of the potential of the alloy. In-situ heating in an electron microscope was performed on a twin-roll cast Al-Cu-Li-Mg-Sc-Zr alloy to understand the peculiarities of the homogenization process. Four types of primary phase particles rich in Cu, Li, Mg, and Fe were identified in the as-cast material. They appear as coarse particles at the boundaries of eutectic cells. Their partial dissolution occurs at temperatures above 450 °C. They are almost fully dissolved at 550 °C, except for complex phases containing Fe and Cu. Small dimensions of eutectic cells in the range of 10 µm assure a homogeneous distribution of main alloying elements within the matrix after 20 min of annealing. Direct comparison with the same material prepared by mold-casting indicates that such short annealing times result in the dissolution of main primary phase particles but do not assure a homogeneous distribution of alloying elements in the whole volume of the specimen.

In the current industrial revolution, advanced technologies and methods can be effectively utilized for the detection and verification of defects in high-speed steel filament production. This paper introduces an innovative methodology for the precise detection and verification of micro surface defects found in steel filaments through the application of the Eddy current principle. Permanent magnets are employed to generates a magnetic field with high frequency surrounding a coil of sensor positioned at the filament's output end. The sensor's capacity to detect defects is validated through a meticulous rewinding process, followed by a thorough analysis involving scanning electron microscopy (SEM) and energy-dispersive spectroscopy (EDS). Artificial defects were intentionally introduced into a sample, and their amplitudes were monitored to establish a threshold value. The amplitude signal of these created defect was identified at approximately 10% FSH, which corresponds to a crack depth of about 20 µm. In the experimental production of 182 samples covering 38 km, the defect ratio was notably high, standing at 26.37%. These defects appeared randomly along the length of the samples. The verification results underscore the exceptional precision achieved in the detection of micro surface defects within steel filaments. These defects were primarily characterized by longitudinal scratches and inclusions containing physical tungsten carbide.

Background: Microscopic examination of acid-fast stained sputum smears for detecting mycobacterial acid-fast bacilli (AFB) remains the most economical and readily available method for laboratory diagnosis of tuberculosis (TB). However, this conventional approach has limitations, including low sensitivity and labor-intensive procedures. Methods: An automated microscopy system incorporating artificial intelligence (AI) and machine learning for AFB identification was evaluated. The study was conducted at an Infectious Disease Hospital in Jiangsu Province, China, utilizing an intelligent microscope system (TB-Scan, Wellgen Medical, Kaohsiung). A total of 1,000 sputum smears were included in the analysis, with the system capturing digital microscopic images and employing an image recognition model to automatically identify and classify AFB. Referee technicians provided the gold standard for discrepant results. Results: The automated system demonstrated an overall accuracy of 95.00% (950/1,000), sensitivity of 91.24% (177/194), and specificity of 95.91% (773/806). Notably, the system identified 21 smears as positive that were previously reported as negative, with referee technicians confirming 17 of these as true positive and retracting the test results accordingly. Recalculating the performance, the accuracy increased to 96.70% (967/1,000), sensitivity to 91.94% (194/211), and specificity to 97.97% (773/789), with a false negative rate of 8.06% (17/211) and a false positive rate of 2.03% (16/789). Conclusions: The incorporation of AI and machine learning into an automated microscopy system demonstrated the potential to enhance the sensitivity and efficiency of AFB detection in sputum smears compared to conventional manual microscopy. This approach holds promise for widespread application in TB diagnostics and potentially other fields requiring labor-intensive microscopic examination.

The study concentrates on researching possibilities of using computer image analysis and neural modeling in order to assess selected quality discriminants of spray-dried chokeberry powder. The aim of the paper is quality identification of chokeberry powders on account of their highest dying power, the highest bioactivity as well as technologically satisfying looseness of powder. The article presents neural models with vision technique backed up by devices such as digital camera as well as electron microscope. Reduction in size of input variables with PCA has influence on improving the processes of learning data sets, thus increasing effectiveness of identifying chokeberry fruit powders included in digital pictures, which is shown in the results of the conducted research. The effectiveness of image recognition are presented by classifying abilities as well as low Root Mean Square Error (RMSE), for which the best results are achieved with typology of network type Multi-Layer Perceptron (MLP). The selected networks type MLP are characterized by the highest degree of classification at 0.99 and RMSE at 0.11 at most at the same time.

High-quality and large-size single crystals of lead-free Na0.5Bi0.5TiO3 were grown using the Czo-chralski technique. The crystals had pure perovskite structure with rhombohedral symmetry and were translucent in the visible and near infrared spectral ranges recorded in the interval 350-1050 nm. The energy gaps determined from the X-ray photoelectron spectroscopy (XPS) and optical measurements were approximately 2.92 eV. The current-voltage characteristics, depolarization current, dc (σdc) and ac (σac) electrical conductivity, and Seebeck coefficient of the crystals were investigated. The frequency/temperature-dependent electrical properties were also measured and analyzed through complex impedance spectroscopy. An overlapping reversible insulator-metal transition (resistive switching) on nanoscales, caused by the electric field, was detected. This was the first time that most of these investigations were performed for this material. The following conductivity mechanisms of NBT single crystals were identified: (i) quasi-free electron and hole conduction and hopping-charges mechanism at low temperatures, (ii) small polaron conductivity in the middle temperature range, and (iii) a significant contribution of the oxygen vacancies to conductivity in the high temperature range. The activation energy values determined from the conductivity data, the imaginary part of the electric impedance and the modulus indicate that the relaxation process in the high-temperature range is attributable to both single and double ionized oxygen vacancies, in combination with the hopping of electrons between Ti4+ and Ti3+. P-type electrical conductivity was also found. These discoveries create new possibilities of reducing the electrical conductivity of NBT and improving the process of effectively poling this material. The density of the electronic states was investigated using an ab initio method. The energy gap cal-culated for NBT (R3c) was 2.8 eV, and is well comparable to those determined from XPS and optical measurements. Our results indicate the possibility of tuning material properties by inten-tionally creating non-stoichiometry/structural defects (oxygen vacancies, cation excess and cation deficiency).

Primary ciliary dyskinesia (PCD) is an inherited disorder that impairs motile cilia, essential for respiratory health, with a reported prevalence of 1 in 16,309 within Hispanic populations. Despite having the RSPH4A [c.921+3_921+6del (intronic)] founder mutation in 70% of Puerto Rican patients, the characterization of the ciliary dysfunction remains unidentified due to the unavailability of advanced diagnostic modalities like High-Speed Video Microscopy Analysis (HSVA). Our study implemented HSVA for the first time on the island as a tool to better diagnose and characterize the RSPH4A [c.921+3_921+6del (intronic)] founder mutation in Puerto Rican patients. By applying HSVA, we analyzed the ciliary beat frequency (CBF) and pattern (CBP) in native Puerto Rican patients with PCD. Our results showed decreased CBF and a rotational CBP linked to the RSPH4A founder mutation in Puerto Ricans, presenting a novel diagnostic marker that could be implemented as an axillary test into the PCD diagnosis algorithm in Puerto Rico. The integration of HSVA technology in Puerto Rico substantially enhances the framework for PCD evaluation and diagnosis, facilitating prompt detection and early intervention for improved disease management. This initiative, demonstrating the potential of HSVA as an adjunctive test within the PCD diagnostic algorithm, could serve as a blueprint for analogous developments throughout Latin America.

In this work, we designed a MEMS device which allows simultaneous direct measurement of mechanical properties during deformation under external stress and characterization of the evolution of microstructure of nanomaterials within a transmission electron microscope. This MEMS device makes it easy to establish the correlation between microstructure and mechanical properties of nanomaterials. The device uses piezoresistive sensors to qualitatively measure the force and displacement of nanomaterials, e.g., in wire and thin plate forms. The device has a theoretical displacement resolution of 0.19 nm and a force resolution of 2.1 μN. The device has a theoretical displacement range limit of 2.74 μm and a load range limit of 27.75 mN.

Biohydrogen is a versatile energy carrier for the generation of electric energy from renewable sources. Hydrogenases can be used in enzymatic fuel cells to oxidize dihydrogen. The rate of electron transfer (ET) at the anodic side between the [NiFe]-hydrogenase enzyme distal iron-sulfur cluster and the electrode surface can be described by the Marcus equation. All parameters for the Marcus equation are accessible from DFT calculations. The distal cubane FeS-cluster has a three cysteine and one histidine coordination [Fe₄S₄](His)(Cys)₃ first ligation sphere. The reorganization energy (inner- and outer-sphere) is almost unchanged upon a histidine-to-cysteine substitution. Differences in rates of electron transfer between the wild-type enzyme and the all-cysteine mutant can be rationalized by a diminished electronic coupling between the donor and acceptor molecules in the [Fe₄S₄](Cys)₄ case. The fast and efficient electron transfer from the distal iron-sulfur cluster is realized by a fine-tuned protein environment which facilitates the flow of electrons. This study enables the design and control of electron transfer rates and pathways by protein engineering.

Kininogens are multidomain glycoproteins found in the blood of most vertebrates. They are important in the blood coagulation cascade pathways - in intrinsic pathway activation leading to thrombin generation partially independently from tissue factor dependent extrinsic pathway, connecting blood coagulation with the kallikrein-kinin system. Nothing is known about the shape on atomic level therefore the endeavor to obtain the good-quality spatial structure of kininogens is important for a better understanding of their role in disease and treatment. Application of cryo-EM is important for solving the spatial structure of kininogens, drawing new frontiers in understanding the function and opening new pathways for drug development.

The quiet-time solar wind electrons feature non-thermal characteristics when viewed from the perspective of their velocity distribution functions. They typically have an appearance of being composed of a denser thermal “core” population plus a tenuous energetic “halo” population. At first, such a feature was empirically fitted with the Kappa velocity space distribution function, but ever since the ground-breaking work by Tsallis, the space physics community has embraced the potential implication of the Kappa distribution as reflecting the non-extensive nature of the space plasma. From the viewpoint of microscopic plasma theory, the formation of non-thermal electron velocity distribution function can be interpreted in terms of the plasma being in a state of turbulent quasi equilibrium. Such a finding brings forth the possible existence of a profound inter-relationship between the non-extensive statistical state and the turbulent quasi-equilibrium state. The present paper further develops the idea of solar wind electrons being in the turbulent equilibrium, but unlike the previous model, which involves the electrostatic turbulence near the plasma oscillation frequency (i.e., Langmuir turbulence), the present paper considers the impact of transverse electromagnetic turbulence, particularly, the turbulence in the whistler-mode frequency range. It is found that the coupling of spontaneously-emitted thermal fluctuations and the background turbulence leads to the formation of non-thermal electron velocity distribution function of the type observed in the solar wind during quiet times. This demonstrates that the whistler-range turbulence represents an alternative mechanism for producing the Kappa-like non-thermal distribution, especially close to the Sun and in the near-Earth space environment.

The unicellular eukaryote S. cerevisiae is an invaluable resource for the study of basic eukaryotic cellular and molecular processes. However, due to its small size compared to other eukaryotic organisms the study of subcellular structures is challenging. Expansion microscopy (ExM) holds great potential to study the intracellular architecture of yeast, especially when paired with pan-labelling techniques visualising the full protein content inside cells. ExM allows to increase imaging resolution by physically enlarging a fixed sample that is embedded and cross- linked to a swellable gel followed by isotropic expansion in water. The cell wall present in fungi – including yeast – and Gram-positive bacteria is a resilient structure that resists denaturation and conventional digestion processes usually used in ExM protocols, resulting in uneven expansion. Thus, the digestion of the cell wall while maintaining the structure of the resulting protoplasts are crucial steps to ensure isotropic expansion. For this reason, specific experimental strategies are needed, and only a few protocols are currently available. We have developed a modified ExM protocol for S. cerevisiae, with 4x expansion factor, which allows the visualisation of the ultrastructure of the cells. Here, we describe the experimental procedure in detail, focusing on the most critical steps required to achieve isotropic expansion for ExM of S. cerevisiae.

We report a very frugal microscope building method from easily realizable parts. We show a highly portable field ready compound type microscope with bright field, dark field and projection microscopy capabilities. It has good resolution and magnification for multiple aspects of education and diagnosis. We demonstrate that such a system can be built from simple lenses in laser pointers and camera modules with no specific 3d printed parts or costly lenses. We show all the parts of the system like stage, coarse and fine focussing system, microscope body, even slides can be built from commonly available materials like soda bottle and DVD disks. We list alternate, safer and easily available staining methods and chemicals. The microscope is developed with a target that it can be self-developed even in rural areas of the world with only resources at one’s disposal with very little education. This features a stable focussing and panning system for comfortable viewing through eyes and also easy imaging with a smartphone. We show its utility for microorganism analysis and potential for clinical diagnosis.

A time-sequential working, spatially multiplexed autostereoscopic 3D display design consisting of a fast switchable RGB-color filter array is presented. The wavelength-selective filter barrier emits the light from a display over a larger active area than common autostereoscopic barrier displays. An optical modelling of wavelength-selective barriers has been used for instance to calculate the light ray distribution properties of that arrangement. To find well working display designs, automated searches by simulation and computational evaluation has been proceeded. Wavelength-selective filter barrier arrangements exhibit characteristics different from common barrier displays with similar barrier pitch and ascent. In particular, these constructions show strong angular luminance dependency under barrier inclination specified by correspondent slant angle. In time-sequential implementation it is important to avoid that quick eye or eyelid movement lead to visible color artifacts. In the millisecond regime tunable liquid crystal Fabry-Pérot color filters for the colors red, green and blue are presented. They consist of a sub-micrometer thick nematic layer sandwiched between dielectric mirrors and ITO-electrodes. These cells shall switch narrow-banding light of red, green or blue. An array for a glasses-free 3D display has to be equipped with several thousand switchable filter elements having different color apertures. The newly introduced design is usable as a multi user display as well as a single user system with user adaptive control.

Alnus glutinosa is important woody plant in Lithuanian forest ecosystems. Knowledge of fluorescence properties of black alder pollen is necessary for scientific and practical purposes. By the results of the study we aimed to evaluate possibilities of identifying Alnus glutinosa pollen fluorescence properties by modeling ozone effect and applying two different fluorescence-based devices. To implement experiments, black alder pollen was collected in a typical habitat during the annual flowering period in 2018-2019. There were three groups of experimental variants, which differed in the duration of exposure to ozone, conditions of pollen storage before the start of the experiment, and the experiment start time. Data for pollen fluorescence analysis were collected using two methods. The microscopy method was used in order to evaluate the possibility of employing image analysis systems for investigation of pollen fluorescence. The second data collection method is related to the automatic device identifying pollen in real-time, which uses the fluorescence method in the pollen recognition process. Data were assessed employing image analysis and principal component analysis (PCA) methods. Digital images of ozone-exposed pollen observed under the fluorescence microscope showed the change of the dominant green colour towards the blue spectrum. Meanwhile, the automatic detector detects more pollen whose fluorescence is at the blue light spectrum. It must be noted that assessing pollen fluorescence several months after exposure to ozone, no effect of ozone on fluorescence remains.

The rationalization and modeling of an electric discharge in a fluid require the knowledge of electron swarm parameters. In this work, transport coefficients of alcohols, including methanol, ethanol, propanol, and butanol are reported. The electron energy distribution function, mean energy, reduced mobility, and diffusion coefficient, are calculated using the two-term expansion of the electron Boltzmann equation in the frame of BOLSIG+ and the Monte Carlo collision code METHES. For such, experimental and theoretical values of the electron-alcohol collision cross-section, covering a range of electron impact energy from 1 eV to 1000 eV, are employed. A temperature of 300K, reduced fields E/N between $1-10^4$ Td (1Td = $10^{-21}~\rm Vm^2$), and Plasma density of $10^{19}~\rm m^{-3}$ were used in simulations. The calculated coefficients are compared with data available from previous studies.

This article presents answers to the questions on superresolution and structured illumination microscopy as raised in the editorial of a recent publication [K. Prakash et al. arXiv, 2102.13649, 2021]. The answers are based on my personal views on superresolution in light microscopy, supported by reasoning. Discussed are the definition of superresolution, Abbe’s resolution limit and the classification of superresolution methods into non-linear-, prior-knowledge- and near-field-based superresolution. A further focus is put on capabilities and technical aspects of present and future structured illumination microscopy (SIM) methods.

Quantitative phase microscopy (QPM), a technique combining phase imaging and microscopy, enables visualization of the 3-D topography in reflective samples as well as the inner structure or refractive index distribution of transparent and translucent samples. However, as in conventional optical microscopy, QPM provides either a large field of view (FOV) or a high resolution but not both. Many approaches such as oblique illumination, structured illumination and speckle illumination have been proposed to improve the spatial resolution of phase microscopy by restricting other degrees of freedom (mostly time). Therefore, the space bandwidth product (SBP) of QPM becomes enlarged. This paper aims to provide an up-to-date review on the resolution enhancement approaches of QPM, discussing the pros and cons of each technique as well as the confusion on resolution definition claim on QPM and other coherent microscopy.

Super-Resolution Microscopy enables non-invasive, molecule-specific imaging of the internal structure and dynamics of cells with sub-diffraction limit spatial resolution. One of its major limitations is the requirement for high-intensity illumination, generating considerable cellular phototoxicity. This factor considerably limits the capacity for live-cell observations, particularly for extended periods of time. Here, we overview new developments in hardware, software and probe chemistry aiming to reduce phototoxicity. Additionally, we discuss how the choice of biological model and sample environment impacts the capacity for live-cell observations.

In order to study the effects of irradiation on the physicochemical properties and digestion behavior of chickpea protein, chickpea protein concentrate (CPC) was treated with electron beam irradiation (EBI) at doses of 5, 10, 15 and 20 kGy, respectively. After irradiation, protein solubility first increased at 10 kGy and 15 kGy, and then decreased at higher dose of 20 kGy. This was supported by SDS-PAGE where the intensity of major protein bands first increased and then decreased. Increased does of EBI generally led to greater oxidative modification of proteins in CPC, indicated by reduced sulfhydryls and increased carbonyls. In addition, protein structure was modified by EBI shown by Fourier transform infrared spectroscopy analysis where α-helix generally decreased and β-sheet increased. Although the protein digestibility was not significantly affected by EBI, the peptidomic analysis of the digests revealed significant difference among CPC irradiated with varying doses. A total of 337 peptides were identified from CPC irradiated with 0 kGy, 10 kGy and 20 kGy, respectively, with 18 overlapping peptides and 60, 29 and 40 peptides specific to the groups of 0, 10 and 20 kGy respectively. Theoretical calculation showed that the distribution of peptide length, hydrophobicity, net charge, and C-terminal residues were affected by irradiation. The 2, 2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activity showed a marginal decrease with increasing dose of irradiation. In conclusion, EBI led to oxidative modification and structural changes of the chickpea protein, which subsequently affected the physicochemical properties of peptides obtained from in-vitro digestion of CPC despite of similar digestibility.

Unwanted proteins and metabolic waste in cerebral spinal fluid are cleared from the brain by meningeal and nasal lymphatics, and perineural sheath of cranial nerves; however, the distribution and clearance of CSF along the subarachnoid space of the entire spinal cord is not fully understood. It was hypothesized that the anatomical resolution of Cryo-Fluorescence Tomography (CFT) could provide the visual evidence of clearance across the spinal cord at each level of the vertebral column. To that end, isoflurane anesthetized mice were infused into the lateral cerebroventricle with 5.0 µl of quantum dots [QdotR 605 ITKTM amino (PEG)] over two mins. Mice were allowed to recover (ca 2-3 min) and remained awake and ambulatory for 5, 15, 30, 60 and 120 minutes after which they were euthanized, and the entire intact body frozen at -800. The entire mouse was sectioned and imaged to produce an isotropic voxel resolution of 35 µm. Both white light and fluorescent images were captured after each slice to produce high resolution three-dimensional volumes for each mouse. CFT highlighted the circulation of tracer throughout the ventricular system and central canal of the spinal cord and the entire subarachnoid space of the CNS. Signal could be visualized in the nasal cavity, deep cervical lymph nodes, thoracic lymph nodes and more superficial submandibular lymph nodes as early as 15 min post infusion. Fluorescent signal could be visualized along the dorsal root ganglia and down the proximal extension of the spinal nerves of the thoracic and lumbar segments at 30 min. There was significant accumulation of tracer in the lumbar and sacral lymph nodes between 15- 60 min. The dense fluorescent signal in the thoracic vertebrae noted at 5- and 15-mins post infusion was significantly reduced by 30 min. Indeed, all signal in the spinal cord was ostensibly absent by 120 min except for trace amounts in the coccyx. The brain still had some residual signal at 120 min. These data show that Qdots with a hydrodynamic diameter of 16-20 nm rapidly clear from the brain of awake mice. These data also clearly demonstrate the rapid distribution and efflux of trace along a major length of the vertebral column and the potential contribution of the spinal cord in the clearance of brain waste.

We have repeated the experiment performed recently by Krasznahorkay et al., (Phys. Rev. Lett. 116, 042501 (2016)), which may indicate a new particle called X17 in the literature. In order to get a reliable, and independent result, we used a different type of electron-positron pair spectrometer which have a more simple acceptance/efficiency as a function of the correlation angle, but the other conditions of the experiment were very similar to the published ones. We could confirm the presence of the anomaly measured at the Ex=18.15 MeV resonance, and also confirm their absence at the Ex=17.6 MeV resonance, and at Ep= 800 keV off resonance energies.

For many disciplines of science, all conceivable collisional cross sections and reactions must be precisely known. Although the recent decades were a trial of large-scale research to give these data, many essential atomic and molecular cross section data still missing, and the reliability of the existing cross sections has to be validated. In this paper, we present electron stripping, electron capture, and system breakdown cross sections in carbon (C5+) ions and lithium (Li2+) ions collisions with atomic hydrogen based on the Monte Carlo models of classical and quasi-classical trajectories. According to our expectation, the QCTMC results show higher results in comparison to standard CTMC data, emphasizing the role of Heisenberg correction constraint, especially in the low energy regime. On the Other hand, at high energy, the Heisenberg correction term has less influence as a projectile momentum increase. We present the total cross sections of electron stripping, electron capture, and system breakdown in C5+ ions and Li2+ ions collisions with atomic hydrogen in the impact energy range from 10 keV to 160 keV, which is of interest in astrophysical plasmas, atmospheric sciences, plasma laboratories, and fusion research.

In this paper, we propose an assumption of which the relation between electron and phonon is discussed and investigated based on the experiment of γ photon and electric interconverting with each other. We calculated the charge of a particular standing wave topology with Maxwell’s equation rotated in accordance space with the SO3 transformation. The derived charge value is 1.6035 × 10E−19C around 0.0826% different from the experimental data, indicating the proposal is a promising theory to explain the origin of charge and spin of electron particle. Electron spin angular momentum comes from the orbital angular momentum of photon rotation (electromagnetic field rotation), and electron charge comes from photon, that is, the space-time rotation effect of electromagnetic wave.

The maker movement has reached the optics labs, empowering researchers to actively create and modify microscope designs and imaging accessories. 3D printing has especially had a disruptive impact on the field, as it entails an accessible new approach in fabrication technologies, namely additive manufacturing, making prototyping in the lab available at low cost. Examples of this trend are taking advantage of the easy availability of 3D printing technology. For example, inexpensive microscopes for education have been designed, such as the FlyPi. Also, the highly complex robotic microscope OpenFlexure represents a clear desire for the democratisation of this technology. 3D printing facilitates new and powerful approaches to science and promotes collaboration between researchers, as 3D designs are easily shared. This holds the unique possibility to extend the open-access concept from knowledge to technology, allowing researchers from everywhere to use and extend model structures. Here we present a review of additive manufacturing applications in microscopy, guiding the user through this new and exciting technology and providing a starting point to anyone willing to employ this versatile and powerful new tool.

Artificial Intelligence based on Deep Learning is opening new horizons in Biomedical research and promises to revolutionize the Microscopy field. Slowly, it now transitions from the hands of experts in Computer Sciences to researchers in Cell Biology. Here, we introduce recent developments in Deep Learning applied to Microscopy, in a manner accessible to non-experts. We overview its concepts, capabilities and limitations, presenting applications in image segmentation, classification and restoration. We discuss how Deep Learning shows an outstanding potential to push the limits of Microscopy, enhancing resolution, signal and information content in acquired data. Its pitfalls are carefully discussed, as well as the future directions expected in this field.

The mechanisms of formation of induced intrinsic and impurity radiative states, which consist of intrinsic and impurity electron-hole trapping centers in irradiated Ca2P2O7-Mn and Ca2P2O7 phosphates, were investigated using thermoactivation and vacuum-ultraviolet spectroscopy methods. These centers are excited at photon energies of 4.0 eV and 4.5 eV, which are within the matrix's transparency region. New radiative induced states at 3.06 eV and 2.92 eV are demonstrated to be generated upon the excitation of anions by photons with energies of 5.0 and 5.64 eV. This process is due to charge transfer from the ion to the impurities, specifically Mn^2+ O^2- Mn^2+ and the neighboring ion O^2- (P2O7)^4-. Furthermore, upon the excitation of matrix anions with photon energies exceeding the band gap (8.0 - 8.25 eV), electron trapping by impurities such as Mn^2+ and (P2O7)^4- ions results.

We have investigated the canine of olive flounder in terms of the nonlinear optical signals of two-photon excitation autofluorescence (2PEF) and second harmonic generation (SHG), whereby two kinds of nonlinear microscope images of the canine were obtained using ~140 femtosecond pulses. For increasing excitation power of laser pulses, a photobleaching effect was found to be significant in the red and green ranges of autofluorescence, where a double-exponential decay of the intensity occurs within hundreds of second due to collagen fluorophores in the canine. In the blue range of autofluorescence, the photobleaching is suppressed due to an energy conversion of the incident laser pulse to SHG signal. As a result, the signal in blue range remains constant for long term exposure to laser. We have also found that the SHG intensity depends on the orienta-tion of linearly polarized excitation, and the optical anisotropy of SHG can be attributed to the collagen alignment of canines.

Embryoid bodies (EBs) are multicellular three-dimensional (3D) aggregates generated from induced pluripotent stem cells (iPSCs) in suspension and serve as useful biological sources for many downstream applications. Imaging of live EBs has been hampered mainly due to the inherent limitations of the imaging techniques applied to date. This study aimed to image human iPSC (hiPSC) derived EBs to obtain their 3D volume, determining size, morphology, and cell viability from day 7 to 14 using Light Sheet Fluorescence Microscopy (LSFM). Furthermore, chromosomal stability was assessed using Multicolor fluorescence in situ hybridization (M-FISH) from day 8 to 14. EB volume increased from day 7 to 13 which, decreased at day 14. From day 7 to 11, the EBs mainly appeared spherical and morphed into an ellipsoidal shape by day 13. All EBs showed varied external morphologies and larger cavities at day 14. The EB karyotype was diploid 46XY at day 8 and exhibited a low level of aneuploidy from day 10 to 14. This study shows that an increase in cell death affects the morphology and chromosomal stability in EBs derived from hiPSC. We demonstrate that the combination of LSFM and M-FISH helps characterize EBs that will assist future stem cell therapies.

Microscopes based on dielectric mesoscale particles, using the effect of a photonic jet or terajet in the terahertz range, are a promising tool for overcoming the diffraction limit. However, the image they generate has limited contrast, which limits the application of this method. In this letter, we demonstrate that it is possible to increase the contrast of an image based on dielectric mesoscale particles that provide the formation of photonic hooks. In this case, the illumination of the object is carried out by an oblique incidence of subwavelength terajet, which significantly (more than 2 times) increases the contrast of the image.

Pollen analysis as a part of palynology deals with the morphological determination of pollen and spores. Different technologies with different resolutions varying from simple light microscopy to highly elaborate electron microscopy are used for the examination, depending on the area of application (e.g. sedimentology, melissopalynology, forensic palynology, etc.). To answer the question of whether laser scanning microscopy (LSM) can replace scanning electron microscopy (SEM) for the determination of pollen species, 168 species were examined using LSM. It was concluded that LSM is both efficient and easy to handle. After preparing the fresh pollen, a 3D laser scan takes 5-10 minutes and unlike using SEM, the pollen does not have to be sputtered or processed. The 3D scans can be measured quickly and easily with the integrated software and there were no observable artifacts. At magnifications up to 8545x, the image quality is comparable to that of a sputtered SEM sample whereas at higher magnifications, the SEM method is superior. Overall, pollen display by LSM is much less time consuming and more cost effective than with the SEM method.

Our knowledge of electricity is based on two parallel lines of research: one focusing on ‘charge’, the other on ‘electron’. The distinction is blurred. The difficulty is that the fundamental nature of elementary charge is unknown. Here I present evidence that charge is a resting electron and electron is a moving charge – one physical entity two behavioural identities. That is, charge is nonrelativistic electron and electron is relativistic charge. Charges obey the laws of static electricity (electrostatics); electrons obey the laws of moving electricity (electrodynamics). Whether positive or negative, a charge is ejected from the atom at tremendous speed, losing the characteristics of ‘a charge’ and gaining those of ‘an electron’. I conclude that an atom, hence nature in general, contains an equal number of positive and negative electrons, recognised at rest as opposite charges. This solves the mystery of the electron-positron numerical asymmetry. It means that static positions and negatrons (charges) play equivalent roles as subatomic building blocks of matter, revealing a new atomic structure.

We investigate the shear quasinormal modes (QNMs) in the context of electron stars, focusing on the Lifshitz geometry and exploring the behavior in the small star limit. The study begins by analyzing the shear sector modes in the infrared (IR) Lifshitz limit, where the geometry approaches that of a pure Lifshitz space. We derive and solve the differential equations governing the shear modes, revealing the asymptotic behavior in terms of the Lifshitz exponent. In the special case of integer values of the exponent, we obtain analytic corrections to the solutions to extract hydrodynamical QNMs. We then explore the cases with a Lifshitz exponent equal to or greater than three, providing analytical corrections to the Lifshitz IR solutions. A special case with an exponent of two is also considered, leading to modified solutions. The study extends to finding hydrodynamical QNMs, emphasizing the role of the Lifshitz geometry. Further investigations involve the flux with real and complex frequencies, considering the off-shell Lagrangian and deriving conserved flux expressions. Our analysis focuses on the exterior of the star, modeled by the Reissner-Nordström-AdS geometry. The small star limit is examined, revealing interesting features in the behavior of fermionic excitations. In summary, we provide a detailed exploration of shear quasinormal modes in electron stars, shedding light on their behavior in Lifshitz geometry, small star limits, and the interplay between real and complex frequencies. Our findings contribute to our understanding of the dynamics of electron stars and their gravitational properties.

The energies of spin singlet and triplet bound electron pairs are reckoned for electrons interacting through the Coulomb interaction, while sitting on neigbouring lattice sites. It is concluded that triplet pairs are unlikely to be observed due to screening. The interplay of inter-electron couplings of different spatial range is investigated. High-pressure induced superconductivity is analysed and qualitative agreement is achieved with observed results by working out the dependence of the critical temperature on the microscopic parameters, characterising the electron motion. This approach can be applied to other kinds of inter-electron interactions.

The impact of the cell community on its individual components in the prokaryotic realm is often overlooked. However, in the case of intracellular pathogens, where each infected cell can be considered as a single community, understanding how a population adapts to its environment to evolve and successfully propagate is key. Chlamydia infections are characterised by a silent propagation of the bacteria within individual hosts and the wider population. Chlamydia are strict intracellular pathogens residing within a specialised membrane-bound compartment called the inclusion. The life cycle of Chlamydia involves altering between the invasive elementary bodies (EBs) and replicative reticulate bodies (RBs). We have used cryo-soft X-ray tomography to observe individual inclusions, combining excellent resolution (40 nm) and large volume imaging (up to 16 µm). Combined with a semi-automated segmentation pipeline, we were able to consider each inclusion as an individual bacterial niche. Within the inclusion, we identified and classified different forms of the bacteria and confirmed the recent finding that RBs have a variety of volumes (small, large and abnormal). Moreover, we demonstrate that the proportions of these different RB forms depend on the bacterial concentration in the cell demonstrating the impact of the group on its individual component. We conclude that each inclusion operates as an autonomous community which regulates the characteristics of individual bacteria within the inclusion

Spatial biology is a rapidly growing research field which focuses on the transcriptomic or proteomic profiling of single cells within tissues with preserved spatial information. Imaging-based spatial transcriptomics uses epifluorescence microscopy, which has shown remarkable results for identification of multiple targets in situ. Nonetheless, the number of genes that can be reliably visualized is limited by the diffraction of light. Here, we investigate the effect of structured illumination (SIM), a super-resolution microscopy approach, over the performance of single gene transcript detection in spatial transcriptomics experiments. We performed direct mRNA-targeted hybridization in situ sequencing for multiple genes in mouse coronal brain tissue sections. We evaluated spot detection performance in widefield and confocal images versus those with SIM in combination with 20X, 25X and 60X objectives. In general, SIM increases the detection efficiency of gene transcripts spots compared to widefield and confocal modes. For each case, the specific fold increase in localizations is dependent on gene transcripts density and the numerical aperture of the objective used, which showed to play an important role especially for densely clustered spots. Taken together, our results suggest that SIM has the capacity to improve spot detection and overall data quality in spatial transcriptomics.

Modern imaging strategies are paramount to studying living systems such as cells, bacteria, and fungi and their response to pathogens, toxicants, and nanomaterials as modulated by exposure and environmental factors. The need to understand the processes and mechanisms of damage, healing and cell survivability of living systems continues to motivate the development of alternative imaging strategies. Of particular interest is the use of label-free techniques that minimize interference of biological processes by foreign marking substances and reduce intense light exposure and potential photo-toxicity effects. This review focus on the potential synergic capabilities of atomic force microscopy (AFM) as a well-developed and robust imaging strategy with demonstrated applications to unravel intimate details in biomedical applications, with the label-free, fast, and enduring Holotomographic Microscopy (HT) strategy. We first review the operating principles that form the basis for the complementary details provided by these techniques regarding the surface and internal information provided by HT and AFM is essential and complimentary for the development of several biomedical areas studying the interaction mechanisms of nanomaterials with living organisms. First, AFM can provide superb resolution on surface morphology and biomechanical characterization. Second, the quantitative phase capabilities of HT enable superb modeling and quantification of the volume, surface area, protein content, and mass density of the main components of cells and microorganisms, including morphology of cells in microbiological systems. These capabilities result from directly quantifying refractive index changes without requiring fluorescent markers or chemicals. As such, HT is ideally suited for long-term monitoring of living organisms in conditions close to their natural settings. We present a case-based review of the principal uses of both techniques and their essential contributions to nanomedicine and nanotoxicology, emphasizing cancer and infectious disease control. The synergic impact of the sequential use of these complementary strategies provides a clear drive for adopting these techniques as interdependent fundamental tools.

The interaction between single or a fixed number of photons with a single absorber is of fundamental interest in quantum technology. The harnessing of light matter interactions at the single particle limit has several potential applications ranging from quantum communication and quantum metrology to quantum imaging. In this letter, a setup for heralded two-photon absorption at the single absorber level is proposed. The setup is based on a heralded two-photon source utilizing spontaneous parametric down-conversion, entanglement swapping and sum frequency generation for joint detection. The feasibility of the scheme is discussed by reviewing recent achievements in utilizing entangled and correlated photons for two-photon absorption as well as single photon absorption experiments at the limit of single absorbers in the context of applications in imaging (here mainly microscopy) and spectroscopy.

This article explores the transformative role of neural networks in the realm of biology, particularly within microscopy image processing and illustrations. Neural networks have revolutionized cell segmentation and analysis, enabling precise delineation of cell boundaries and tracking of cellular behaviours. They excel in detecting subcellular structures, unravelling intricate organelle interactions. In 3D image reconstruction, neural networks navigate volumetric datasets, enhancing our understanding of spatial cellular architecture. These networks enhance disease diagnosis by identifying anomalies and irregularities, potentially revolutionizing early detection and classification. Moreover, neural networks restore and enhance microscopy images, unveiling hidden details. Lastly, they bridge art and science, fostering captivating biological art and enriching science communication. As neural networks evolve, they promise a future of limitless possibilities, weaving together technology, science, and art to illuminate the microscopic realm in unprecedented ways.

Cells receive external stimuli to incur structural and functional damages. On scanning acoustic microscopy (SAM), speed-of-sound (SOS), attenuation-of-sound (AOS), and thickness values are plotted on the screen to create cellular images, which are related to stiffness, viscosity, and cell size, respectively. The obtained digital data compared using statistical analysis. We aimed to investigate the effects of anticancer drugs, acidic fluids, and heat effects on the cells by using SAM. Anticancer drug cisplatin induced cancer cell apoptosis/necrosis and regeneration in culture, causing elevated SOS, reduced AOS, and thickness. During a more prolonged incubation, the SAM values fluctuated differently between the cisplatin-treated and untreated cells. The tannic and acetic acid and microwave stimuli induced SOS and AOS elevations. These stimuli altered the cell size, number, differentiation, viscosity, and stiffness, which corresponded well to the fluctuation of the SOS and AOS values after incubation. Different anticancer drugs interacted with cancer cells to induce the characteristic alterations of the SAM values. These structural and mechanical alterations induced in cells was difficult to observe on light microscopy. Cellular damages were statistically compared between different stimuli and time-lapse cellular changes were observed using a SAM analysis. SAM is a useful modality to evaluate cellular damage.

The analysis of microscopy images has always been an important yet time consuming process in in materials science. Convolutional Neural Networks (CNNs) have been very successfully used for a number of tasks, such as image segmentation. However, training a CNN requires a large amount of hand annotated data, which can be a problem for material science data. We present a procedure to generate synthetic data based on ad-hoc parametric data modelling for enhancing generalization of trained neural network models. Especially for situations where it is not possible to gather a lot of data, such an approach is beneficial and may enable to train a neural network reasonably. Furthermore, we show that targeted data generation by adaptively sampling the parameter space of the generative models gives superior results compared to generating random data points.

HIV-1 assembly is a complex mechanism taking place at the plasma membrane of the host cell. It requires nice spatial and temporal coordination to end up with a full immature virus. Researchers have extensively studied HIV-1 assembly molecular mechanism during the past decades, in order to dissect the respective roles of viral proteins, viral genome and host cell factors. Nevertheless, the time course of the process has been observed in living cells only a decade ago. The very recent revolution of optical microscopy, combining high speed and high spatial resolution now permit to study assemblies and their consequences at the single molecule level within (living) cells. In this review, after a short description of these new approaches, we will show how HIV-1 assembly in cells has been revisited using these advanced super resolution microscopy techniques and how much it could make a bridge in studying assembly from the single molecule to the host cell.

The nuclear lamina consists of a dense fibrous meshwork made of nuclear lamins, Type V intermediate filaments, and is ~14 nm thick according to recent cryo-electron tomography studies. Recent advances in light microscopy have extended the resolution to a scale allowing for the fine structure of the lamina to be imaged in the context of the whole nucleus. We review quantitative approaches to analyze the imaging data of the nuclear lamina as acquired by structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM), as well as the requisite cell preparation techniques. In particular, we discuss the application of steerable filters and graph based methods to segment the structure of the four mammalian lamin isoforms (A, C, B1, and B2) and extract quantitative information.

Electrons moving at slow speeds much lower that the speed of light are described by a wave function which is a solution of Pauli’s equation. This is a low velocity limit of the relativistic Dirac equation. Here we compare two approaches, one which is the more conservative Copenhagen’s interpretation denying a trajectory of the electron but allowing a trajectory to the electron expectation value through Ehrenfest theorem. The said expectation value is of course calculated using a solution of Pauli’s equation. A less orthodox approach is championed by Bohm, and attributes a velocity field to the electron also derived from the Pauli wave function. It is thus interesting to compare the trajectory followed by the electron according to Bohm and its expectation value according to Ehrenfest. Both similarities and differences will be considered.

We report the electronic, magnetic and transport properties of a prototypical antiferromagnetic (AFM) spintronic device. We chose Cr as the active layer because it is the only room-temperature AFM elemental metal. We sandwiched Cr between two non-magnetic metals (Pt or Au) with large spin-orbit coupling. We also inserted a buffer layer of insulating MgO to mimic the structure and finite resistivity of a real device. We found that, while spin-orbit has a negligible effect on the current flowing through the device, the MgO layer plays a crucial role. Its effect is to decouple the Cr magnetic moment from Pt (or Au) and to develop an overall spin magnetization. We have also calculated the spin-polarized ballistic conductance of the device within the Büttiker-Landauer framework, and we have found that for small applied bias our Pt/Cr/MgO/Pt device presents a spin polarization of the current amounting to ~25%.

High-content fluorescence microscopy combines the efficiency of high-throughput techniques with the ability to extract quantitative information from biological systems. The planarian community has developed sensitive and robust assays for whole animals, yet cell based assays, despite their practical aspects, have not been explored to the same extent. Here we describe a modular collection of detailed protocols adapted for fixed planarian cells that enable multiplexed measurements of biomarkers in microwell plates. Methods include the detection of RNA transcripts by RNA fluorescent in situ hybridization combined with tyramide signal amplification using hapten-labeled riboprobes. In addition, immunocytochemical protocols for quantifying proliferating cells by the detection of phosphorylated histone H3 as well as 5-bromo-2'-deoxyuridine incorporation into the nuclear genome are described. The assays are compatible with planarians of virtually any size, as the tissue is disaggregated into a single cell suspension before fixation and staining. By sharing many reagents with established planarian whole mount staining protocols, preparation of samples for high-content microscopy adoption requires little additional investment. Recommendations for successful experimental workflows and common sources of errors are discussed.

It is shown that structuring at the microlevel is the intrinsic property of water and aqueous solutions. At room conditions water (including "ultrapure" one) and aqueous solutions are dispersed systems in which microcrystals of NaCl, surrounded by a layer of hydrated water (average diameter - 10-15 microns), are "elementary microparticles", which form the basis of the dispersed phase. Possible ways of formation of these microparticles and their evolution in the process of evaporation of unstructured part of water - dispersion medium - are considered. It is shown, in particular, that they are present in the air as aerosol contaminants. When the ionic strength of the solution increases, the water-salt particles coagulate, forming a new phase - coacervates, remaining on the substrate after evaporation of the liquid part of the water. The aggregates of coacervate structures, formed in a liquid medium, are disordered during heating, which can cause a change in a number of physicochemical properties of water at the temperatures of 50°-60°C range that have not been correctly explained in the framework of atomic-molecular concepts.

Label-free confocal photothermal (CPT) microscopy was utilized for the first time to investigate malignancy in mouse skin cells. A laser diode (LD) with 405nm or 488nm was used as a pump and 638nm LD as a probe for the CPT microscope. The Grey Level Cooccurrence Matrix (GLCM) for texture analysis was applied to the CPT images. Nine parameters of GLCM were calculated for the intracellular super-resolved CPT images, and the parameters Entropy and Prominence were found to be most suited among the nine parameters to discriminate between healthy cells and MM cells in case pump wavelength of 488nm is used.

The redefined vacuum approach, which is frequently employed in the many-body perturbation theory, proved to be a powerful tool for formula derivation. Here, we elaborate this approach within the bound-state QED perturbation theory. In addition to general formulation, we consider the particular example of a single particle (electron or vacancy) excitation with respect to the redefined vacuum. Starting with simple one-electron QED diagrams, we deduce first- and second-order many-electron contributions: screened self-energy, screened vacuum polarization, one-photon exchange, and two-photon exchange. The redefined vacuum approach provides a straightforward and streamlined derivation and facilitates its application to any electronic configuration. Moreover, based on the gauge invariance of the one-electron diagrams, we can identify various gauge-invariant subsets within derived many-electron QED contributions.

Collisions of low energy electrons with molecules are important for understanding many aspects of the environment and technologies. Understanding the processes that occur in these types of collisions can give insights into plasma etching processes, edge effects in fusion plasmas, radiation damage to biological tissues and more. A radical update of the previous expert system for computing observables relevant to these processes, Quantemol-N, is presented. The new Quantemol Electron Collision (QEC) expert system simplifyies the user experience, improving reliability and implements new features. The QEC GUI interfaces the Molpro quantum chemistry package for molecular target setups and to the sophisticated UKRmol+ codes to generate accurate and reliable cross-sections. These include elastic cross-sections, super elastic cross-sections between excited states, electron impact dissociation, scattering reaction rates, dissociative electron attachment, differential cross-sections, momentum transfer cross-sections, ionization cross sections and high energy electron scattering cross-sections. With this new interface we will be implementing dissociative recombination estimations, vibrational excitations for neutrals and ions, and effective core potentials in the near future.

Urinary tract infections are among the most frequent infectious diseases and require screening of a great amount of urine samples from patients. However, a high percentage of samples results as negative after urine culture plate test (CPT), demanding a simple and fast preliminary technique to screen out the negative samples. We propose a digital holographic microscopy (DHM) method to inspect fresh urine samples flowing in a glass capillary for 3 minutes, recording holograms at 2 frames per second. After digital reconstruction, bacteria, white and red blood cells, epithelial cells and crystals were identified and counted and the samples were classified as negative or positive according to clinical cutoff values. Taking CPT as reference, we processed 180 urine samples and compared the results with those of urine flow cytometry (UFC). Using standard evaluation metrics for our screening test, we found similar performance for DHM and UFC, indicating DHM as a suitable and fast screening technique retaining several advantages. As a benefit of DHM, the technique is label-free and does not require sample preparation. Moreover, the phase and amplitude images of the cells and other particles present in urine are digitally recorded and can serve for further investigation afterwards.

Additive manufacturing (AM) is a promising new technology that is having a very fast growth from home workshops to high-tech cutting-edge factories. As any manufacturing technique, adequate metrology services are needed to assure the quality of items manufactured by AM. One of the most widely used instruments to measure the characteristics of surfaces manufactured with AM is the confocal microscope. In this paper, authors present a whole calibration procedure for confocal microscopes designed to be implemented preferably in workshops or industrial environments rather than in research and development departments. Because of that, it is as simple as possible. The procedure is designed without forgetting any of the key aspects that need to be taken into account and based on classical reference material standards. These standards can be easily found in industrial dimensional laboratories and easily calibrated in accredited calibration laboratories.

Precipitation processes are technologies commonly used in hydrometallurgical plants to recover metals or to treat wastewaters. Moreover, solid-liquid separation technologies, such as thickening or filtering, are relevant unit operations, included in the precipitation technologies. These methods are strongly dependent on the characteristics of the solid precipitates formed during the specific precipitation reaction. One of these characteristics is the particle size distribution (PSD) of the solid precipitates which are fed into a solid-liquid separation process. Therefore, PSD determination is a typical practice for the characterization of the slurries generated in a precipitation plant. Furthermore, the precipitates generated in these processes have a colloidal or aggregation behavior, depending on the operational conditions. Nevertheless, the conventional methods used to estimate PSD (e.g., laser diffraction and/or ciclosizer) have not been designed to measure particles that tend to aggregate or disaggregate, since they include external forces (e.g., centrifugal, agitation, pumping and sonication). These forces affect the true size of the aggregates formed in a unit operation, thereby losing representativity in terms of aggregates particle size. This study presents an alternative method of measuring the size distribution of particles with aggregation behavior, particularly, by using non-invasive microscopy and image processing and analysis. The samples used have been obtained from an experimental precipitation process by applying sulfidization to treat the cyanide-copper complexes contained in a cyanidation solution. This method has been validated with statistical tools and compared with a conventional analysis based on laser diffraction. Our results show significant differences between the methods analyzed, demonstrating that image processing and analysis by microscopy is an excellent and non-invasive alternative to obtaining size distribution of aggregates in precipitation processes.

The superconductivity of CaC6 as a function of pressure and of abundant Ca isotopes is revisited using DFT calculations on a 2c – double hexagonal superlattice. The introduction of superlattices is motivated by previous synchrotron absorption and Raman spectroscopy results on other superconductors that show evidence of superlattice vibrations at low (THz) frequencies. A 2c superlattice for CaC6 is illustrative of atomic orbital symmetry and periodicity, including bonding and antibonding s-orbital character implied by cosine modulated electronic bands. Inspection of the cosine band reveals that the cosine function has a small (meV) energy difference between bonding and antibonding regions relative to a midpoint non-bonding energy. Fermi surface nesting is apparent in an appropriately folded Fermi surface using a superlattice construct. Nesting relationships identify phonon vectors for conservation of energy and for phase coherency between coupled electrons at opposite sides of the Fermi surface. Detailed analysis of this Fermi surface nesting provides accurate estimates of the superconducting gaps for CaC6 with change in applied pressure. Recognition of superlattices within a rhombohedral or hexagonal representation provides consistent mechanistic insight on superconductivity and electron−phonon coupling in CaC6.

We propose a description of the electromagnetic field in the form of a four-component complex spinor, from which a vector of electromagnetic potential with two degrees of freedom, calibrated by two conditions - zero length and zero component along the y-axis - is obtained by using Pauli matrices. A similar approach is applied to the field of a fermion, in particular, the electron. It is known that the quantum field of the electron and the electron itself is a four-component complex spinor, so, existing in the Minkowski vector space, we cannot observe it directly. But with the help of Pauli matrices a vector is formed from the electron spinor, which is known to us as an electric current vector, and this current vector describes exactly a single particle. As a vector, it is available to us for observation in our vector space. Similarly, the electromagnetic field and its photon particle is also a four-component spinor, from which the universal formula using Pauli matrices produces a vector, it is known to us as the electromagnetic potential vector, and it too describes even a single photon. All the differences in the properties of the current vector and the electromagnetic potential vector, and hence the electron and the electromagnetic field, are due only to a slight difference in the structures of their four-component spinors and inextricable linked to them momentum spinors and coordinate spinors. Expressions for the electric and magnetic fields of a photon during its interaction with an electron.Thus, a unified way to describe bosons and fermions in spinor space is proposed. Each spinor using the same formula corresponds to a vector, in the case of a fermion it is a current vector, in the case of a boson it is a vector, for example, of the electromagnetic potential. Each spinor of a field is matched with a spinor of coordinates and a spinor of momentum, which are transformed by the same Lorentz transformations and which have the same structure as their corresponding field spinor, that is, the momentum and coordinates of boson have a bosonic spinor structure, while momentum and coordinates of fermion are a spinor with a fermionic structure. Field, coordinates and momentum vectors of boson automatically have a zero length, while in the case of fermion they all have a nonzero length, so the fermion, in contrast to the boson, has a nonzero mass, nonzero charge and moves with a sub light speed.While quantum mechanics treats probability as a real number, quantum field theory deals with probability as a four-dimensional real vector. The place of the probability amplitude, which in quantum mechanics is a complex number, in quantum field theory is taken by a complex spinor.In the same way as in quantum mechanics the processes of propagation and interaction are described at the level of complex probability amplitudes, and the final result is translated into a real probability value, so in quantum field theory all processes should be described in terms of complex spinor space, and the result is translated into the form of a real vector in Minkowski space.The presented approach, at its proper development, makes it possible to carry out calculations of the interaction of particles in two-dimensional spinor space, and to interpret in terms of the Minkowski vector space only the final results.

A topological quantum interplay between the magnetic flux and the mass has been investigated, for the case of an electron, by evaluating a gauge-invariant phase factor (a Wilson loop) linked to the electromagnetic gauge field of the particle. In particular, from this phase factor and the quantization of the magnetic flux variations, a relationship between the mass at rest of the electron and its self-energy , arising from radiative corrections, has been obtained also within a QED approach. Besides, a formulation of an energy scale comparable to the energy at rest of an electron-positron pair is proposed. Remarkably, a reckoning of the Bohr energy of a W⁺ W^- pair is compatible with constants and parameters usually employed within the electroweak theory and comparable to the energy at rest of an electron-positron pair.

We explores the hydrodynamical limit of a homogeneous electron gas, considering the interplay between the infrared limit and phenomenological hydrodynamics. Our study involves interactions generated by non-linear coordinate transformations. The focus begins with an analysis of non-linear coordinate transformations and their impact on normal modes in a harmonic system. The Lagrangian for a harmonic oscillator is used as an illustrative example, highlighting the role of position-dependent effective mass in preventing certain coordinate values. Moving beyond single degrees of freedom, we extend the discussion to a system with several harmonic degrees of freedom, introducing a collective variable. The effective dynamics of this collective variable are defined through a Lagrange multiplier term, emphasizing linearity in the description. Our study extends to the Current Two-Point function (CTP) formalism, introducing matrices and their inverses, such as $\hD$ and $\hD^{-1}$. Further, we delve into the dynamics of current in a homogeneous electron gas at finite density and zero temperature. Green's functions are generated using a functional integral approach, and the effective action is constructed via functional Legendre transformation. The quadratic part of the generator functional is expanded to derive the effective action, leading to the Maxwell equation and the subsequent elimination of the photon field. The resulting effective action for current dynamics is expressed in terms of the Current Two-Point function, paving the way for further exploration of the hydrodynamical aspects of the electron gas. Our study combines theoretical developments and mathematical formalism to provide insights into the hydrodynamical behavior of homogeneous electron gases.

Electron can tunnel between cofactor molecules positioned along biological electron transport chains up to the distance of ≃20 Å on the millisecond time scale of enzymatic turnover. This tunneling range mostly determines the design of biological energy chains facilitating cross-membrane transport of electrons. Tunneling distance and cofactors’ redox potentials become main physical parameters of this design. The protein identity, flexibility, or dynamics are missing from this picture assigning universal charge-transport properties to all proteins. This paradigm is challenged by dynamical models of electron transfer showing that the hopping rate is constant within the crossover distance R*≃12 Å, followed with an exponential tunneling falloff at longer distances. In this view, energy chains for electron transport are best designed by placing redox cofactors near the crossover distance R*. Protein flexibility and dynamics affect the magnitude of the maximum hopping rate within the crossover radius. Protein charge transport is not driven by universal parameters anymore and protein identity matters.

In this review, photoinduced electron transfer processes in specifically designed assembled ar-chitectures have been investigated on the basis of recent results reported from our laboratories. A convenient and useful way to study these kinds of systems has been described in order to under-stand the rules that drive to a light induced charge separation and its subsequent decay to the ground state, also with the aim of offering a tutorial for young researchers. Assembled systems of covalent or supramolecular nature have been presented and some functional multicomponent systems for the conversion of light energy into chemical energy have been discussed.

Classical k-ratio models, e.g. ZAF and phi(rho z), used in electron probe microanalysis (EPMA) assume a homogeneous or multi-layered material structure, which essentially limits the spatial resolution of EPMA to the size of the interaction volume where characteristic x-rays are produced. We present a new model for characteristic x-ray emission that avoids assumptions on the material structure to not restrict the resolution of EPMA a-priori. Our model bases on the spherical harmonic (PN) approximation of the Boltzmann equation for electron transport in continuous slowing down approximation. PN models have a simple structure, are hierarchical in accuracy and well-suited for efficient adjoint-based gradient computation, which makes our model a promising alternative to classical models in terms of improving the resolution of EPMA in the future. We present results of various test cases including a comparison of the PN model to a minimum entropy moment model as well as Monte-Carlo (MC) trajectory sampling, a comparison of PN-based k-ratios to k-ratios obtained with MC, a comparison with experimental data of electron backscattering yields as well as a comparison of PN and Monte-Carlo based on characteristic X-ray generation in a three-dimensional material probe with fine structures.

In particle physics, spin is an intrinsic form of angular momentum carried by the elementary particles. It is believed that spin is a solely quantum-mechanical phenomenon, which does not have a counterpart in classical mechanics. We have derived the simplest equations of spin and magnetic moment of a charged elementary particle. These formulas enable us to understand the physical nature of the spin and the structure of elementary particles. It is shown that the electron and muon are in the shape of a thin ring with a circular cross section (torus), and the proton is in the form of a ring with a non-circular cross section (toroid). The connection between the photon’s spin of and the propagation of electromagnetic waves is considered.

Plankton monitoring by microscopy offers long-term ecological perspective of plankton com-munities but different detection approaches are biased uniquely. Genetic identification of marine plankton has become standard but is still not used in routine monitoring. This study assessed the diversity of plankton taxa using 18S high throughput sequencing from 2011-2012 from small-volume (~200ml) samples from the Water and Microplankton Sampler (WaMS) deployed on the Continuous Plankton Recorder platform (CPR). The 18S-HTS survey revealed a bias towards heterotrophic taxa, and phototrophs under 10µm within the photosynthetic community. In comparison with phytoplankton microscopic counts from the CPR survey and Western Channel Observatory station L4, only 8-12 taxonomic families were common to all three surveys, with a bias towards larger diatoms and dinoflagellate taxa in microscopy surveys. The WaMS survey detected a contrasting but complementary taxa set to that of microscopic surveys. Additional Quantitative PCR was carried out on the picoeukaryotic pelagophyte, Aureococcus anophagefferens, and the nanoeukaryotic potential harmful algae, Pseudo-nitzschia delicatissima, from 2011-2013. This confirmed the persistence presence of A. anophagefferens in the Western Channel and an elevated abundance of both species in 2011. Species specific seasonality were distinct from those of aggregrate phytoplankton groups.

The quality assurance of malaria microscopy unit was established by National Malaria Control Program, Ministry of Health (MoH) in 2009 to respond to the internal malaria microscopy validation process, in microscopy training for malaria diagnosis in the country, monitoring and supervision, and other relevant activities regarding laboratory diagnosis of malaria in Timor-Leste is described. Trained laboratory technicians who are working in the relevant unit. There are two ways of malaria microscopy validation process such as onsite validation and monthly validation after received malaria blood smear from senior analyst at the municipality level. The aim of this work is to describe the quality assurance of malaria microscopy system in Timor-Leste. The management of quality assurance service support, the importance of quality assurance of malaria microscopy, the role of quality assurance of malaria microscopy, challenge and opportunities encountered by quality assurance microscopy unit, National Health Laboratory are highlighted. Key words: Quality assurance of malaria microscopy, system, Timor-Leste.

Atomic force microscopy (AFM) has been extensively used for the nanoscale characterization of polymeric materials. The coupling of AFM with infrared spectroscope (AFM-IR) provides another advantage to the chemical analyses and thus helps to shed light upon the study of polymers. In this perspective paper, we review recent progress in the use of AFM-IR in polymer science. We describe first the principle of AFM-IR and the recent improvements to enhance its resolution. We discuss then the last progress in the use of AFM-IR as a super-resolution correlated scanned-probe IR spectroscopy for chemical characterization of polymer materials dealing with polymer composites, polymer blends, multilayers and biopolymers. To highlight the advantages of AFM-IR, we report here several results in studying crystallization of both miscible and immiscible blends as well as polymer aging. Then, we demonstrate how this novel technique can be used to determine phase separation, spherulitic structure and crystallization mechanisms at the nanoscale, which have never been achieved before. The review also discusses future trends in the use of AFM-IR in polymer materials, especially in polymer thin film investigation.

We discuss the implementation of a suite of virtual diagnostics at the FACET-II facility currently under commissioning at SLAC National Accelerator Laboratory. The diagnostics will be used for prediction of the longitudinal phase space along the linac, spectral reconstruction of the bunch profile and non-destructive inference of transverse beam quality (emittance) using edge radiation at the injector dogleg and bunch compressor locations. These measurements will be folded in to adaptive feedbacks and ML-based reinforcement learning controls to improve the stability and optimize the performance of the machine for different experimental configurations. In this paper we describe each of these diagnostics with expected measurement results based on simulation data and discuss progress towards implementation in regular operations.

Some contaminants of emerging concern (CECs) are known to survive conventional wastewater treatment plants, which introduce them back to the environment and can potentially cycle up in drinking water supplies. This is especially concerning because of the inherent ability of some CECs to induce physiological effects in humans at very low doses. Advanced oxidation processes (AOPs) such as TiO2 based photocatalysis are of prominent interest for addressing CECs in aqueous environments. Natural water resources often contain dissolved metal cations concentrations in excess of targeted CEC concentrations. These cations may significantly, adversely impact degradation of CECs by scavenging TiO2 surface generated electrons. Consequently, simple pseudo first order or Langmuir-Hinshelwood kinetics are not sufficient for reactor design and process analysis in some scenarios. Rhodamine B dye and dissolved copper cations were studied as reaction surrogates to demonstrate that TiO₂ catalyzed degradation for very dilute solutions is very nearly completely due to homogeneous reaction with hydroxyl radicals and that in this scenario the hole trapping pathway has negligible impact. Chemical reaction kinetic studies were then carried out to develop a robust model for RB/metal reactions that is exact in the electron pathways for hydroxyl radical production and metal scavenging.

(1) Background: Myelodysplastic syndromes (MDS) are a group of diseases that affect the morphology and function of neutrophils. Rapid diagnosis of MDS is crucial for the initiation of treatment that can vastly improve disease outcome. (2) methods: In this work, we present a new approach for detecting morphological differences between neutrophils isolated from blood samples of high risk MDS patients and that for patients and blood bank donors (BBDs). First, using fluorescent flow cytometry CD66b positive cells were stained with 2′,7′-dichlorofluorescin diacetate (DCF) and Hoechst. Secondly, we imaged the cells using interferometric phase microscopy (IPM) without utilizing cell staining. (3) Results: flow cytometry results show MDS patients present different dispersion patterns compared to BBDs. BBDs present two distinct subpopulations (one of these are the H cells constituting 16% for neutrophils) whereas MDS patients present only 4% of this subpopulation. IPM results are consistent with this pattern: ~20% of BBDs neutrophils were characterized as H cells and whereas MDS patients present only ~4% of these cells. (5) Conclusion- IPM can be utilized for diagnosis of complex hematological pathologies such as MDS.

When existing at emulsion interface and continuous phase, dispersibility of water-soluble flexible polymer chains has obvious effect on rheology and dielectric properties of whole emulsion. CNF Pickering emulsion is a good system to research these properties with respect to their microscopic phase structure, dielectric and rheological properties by using cellulose nanofibers (CNF) as water-soluble Pickering emulsifier, liquid Paraffin as oil phase and DDAB as a cationic auxiliary surfactant. The CNF- and DDAB-contents were systematically varied while the water to paraffin oil ratio remained constant to discern the influence of the Pickering emulsifiers. Polarized optical microscopic images revealed that the droplets have tendency to become smaller size for higher CNF content, but bigger size for higher DDAB content, which was proved by the fluorescent analysis for CNF dispersibility with varying DDAB content. The dielectric damping exhibits a minimum, whose value decreases with increasing DDAB- and CNF-content. Increasing the DDAB-content promotes solubilization of CNFs in the aqueous phase and will increase the overall viscosity and yield points. Similarly, a higher CNF-content leads to a higher viscosity and yield point, but at high DDAB-contents the viscosity function exhibits an S-shape at intermediate CNF-content. To evaluate the results further they were compared with CNF-dispersions (without oil-phase), which showed a surfactant effect slightly on maximum stress but strongly on yield stress τy, indicating DDAB can promote the formation of CNF network rather than the viscosity of whole system.

With an estimated 3 to 5 million human cases annually and the potential to infect domestic and wild animal populations, influenza viruses are one of the greatest health and economic burdens to our society [1] and pose an ongoing threat of large-scale pandemics. Despite our knowledge of many important aspects of influenza virus biology, there is still much to learn about how influenza viruses replicate in infected cells, for instance how they use entry receptors or exploit host cell trafficking pathways. These gaps in our knowledge are due, in part, to the difficulty of directly observing viruses in living cells. In recent years, advances in light microscopy, including super-resolution microscopy and single-molecule imaging, have enabled many viral replication steps to be visualised dynamically in living cells. In particular, the ability to track single virions and their components, in real time, now allows specific pathways to be interrogated providing new insights to various aspects of the virus-host cell interaction. In this review, we discuss how state-of-the-art imaging technologies, notably quantitative live-cell and super-resolution microscopy, are shedding new nanoscale and molecular insights into influenza virus replication and revealing new opportunities for developing antiviral strategies.

The critical role of global electron density transfer (GEDT) in increasing the reaction rate of polar organic reactions has been studied within the framework of Molecular Electron Density Theory (MEDT). To this end, the series of the polar Diels-Alder (P-DA) reactions of cyclopentadiene with cyanoethylene derivatives, for which experimental kinetic data are available, have been chosen. A complete linear correlation between the computed activation Gibbs free energies and the GEDT taking place at the polar transition state structures (TSs) is found; the higher the GEDT at the TS, the lower the activation Gibbs free energy. An interacting quantum atoms (IQA) energy partitioning analysis allows establishing a complete linear correlation between the electronic stabilization of the electrophilic ethylene frameworks and the GEDT taking place at the polar TSs. This finding supports Parr’s proposal for the definition of the electrophilicity  index (J. Am. Chem. Soc., 1999, 121, 1922). The present MEDT study allows establishing the critical role of the GEDT in the acceleration of polar reactions, since the electronic stabilization of the electrophilic framework with the electron density gain is greater than the destabilization of the nucleophilic one, making a net favorable electronic contribution to the decrease of the activation energy.

This research focuses on exploring generalized electron emissions in one-dimensional conducting materials, specifically examining field emission and thermionic emission. Additionally, the study investigates one-dimensional thermal radiation. The current density is derived for both one-dimensional thermionic emission and one-dimensional field emission. A generalized current density in one dimension is devised, taking into account arbitrary accelerating fields and temperature conditions. The formula for the one-dimensional current density is depicted with accelerating field and temperature across various work function materials. The current is also represented as a function of both temperature and electric field for various temperatures.

Over the past two decades, covalent organic frameworks (COFs) have become the most widely studied porous crystalline materials. Its specific physical and chemical properties are determined by the arrangement of atoms (crystal structure). Therefore, the determination of its structure is arguably the most important characterization step for COFs. Although single crystal X-ray diffraction (SCXRD) is the most widely used method for structure determination, the size of COF crystals is too small, or their crystal quality is so poor that confirmation of their structure is limited to lattice fringes by transmission electron microscopy (TEM). At present, many 2D-COFs have clear PXRD patterns, but not all 2D-COFs can obtain specific lattice fringes. This severely hinders the development of the COF field. Here, we discover the lattice shrinkage behavior of COFs under electron beam irradiation by comparing the lattice fringes of 2D-COFs under different conditions. By comparing the lattice fringes of TAPT-TFPT COF at room temperature and under liquid nitrogen freezing conditions, we found that the lattice fringes are in good agreement with the Powder X-ray diffraction (PXRD) and theoretical values of COF (2.213 nm) under freezing conditions, however, the lattice fringe spacing is only 1.656 nm at room temperature. The discovery not only provides new insights into the TEM characterization of COFs, but also further expands the range of crystalline COF materials.

Electroactive microorganisms have received a lot of interest in the field of environmental engineering and biotechnology because of their extracellular electron transfer (EET) capability of energy recovery and environmental remediation. However, the low efficiency of EET remains a barrier to its practical implementation. This review presents an introduction to EET, followed by addressing strategies for enhancing EET through different approaches including enhancing EET by mediator materials, external electricity, photo, and magnetism as well as integrated strategies, that is, the combination of multiple means to promote extracellular electron transport and improve the performance of microbial electrochemical systems. Finally, the challenges, perspectives, and new directions for EET enhancement will be discussed.

The generalized dual-kinetic-balance approach for axially symmetric systems is employed to solve the two-center Dirac problem. The spectra of one-electron homonuclear quasimolecules are calculated and compared with the previous calculations. The analysis of the monopole approximation with two different choices of the origin is performed. Special attention is paid to the lead and xenon dimers, Pb82+–Pb82+–e− and Xe54+–Xe54+–e−, where the energies of the ground and several excited σ-states are presented in the wide range of internuclear distances. The developed method provides the quasicomplete finite basis set and allows for construction of the perturbation theory, including within the bound-state QED.

In the Standard Model of elementary particles, the rest mass, magnetic moment and electric charge of the electron are considered to be natural constants. In this article it is proposed that these properties can be calculated in a simple way from the corresponding Planck units using the well-known period doubling phenomenon in nonlinear dynamical systems. Periods corresponding to the values of the electron and positron properties belong to a subset of stable periods. The periodic structures of the rest energy and magnetic moment consist of three internal degrees of freedom, whereas the Coulomb energy of the electric charge consists of four. The number of period doublings for the elementary charge determines the value of the fine structure constant alpha.

An analysis is presented of the possible existence of a second anomalous dipole moment of Dirac’s particle next to the angular one. It includes a discussion why, in spite of his own derivation, Dirac has doubted about its relevancy. It is shown why since then it has been overlooked and why it has vanished from leading textbooks. A critical survey is given on the reasons of its reject, including the failure of attempts to measure and the perceived violations of time reversal symmetry and chargeparity symmetry. It is emphasized that the anomalous electric dipole moment of the pointlike electron (AEDM) is fundamentally different from the quantum field type electric dipole moment of an electron (eEDM) as defined in the standard model of particle physics and that its measurement requires different instrumentation. A proposal has been described how to prove or disprove its existence by experiment. Moreover, by reference from literature, the possible impact is discussed in the nuclear domain and in the gravitational domain.

A rigorous model for the electron is presented by generalizing the Coulomb's Law or Gauss's Law of electrostatics, using a unified theory of electricity and gravity. The permittivity of the free-space is allowed to be variable, dependent on the energy density associated with the electric field at a given location, employing generalized concepts of gravity and mass/energy density. The electric field becomes a non-linear function of the source charge, where concept of the energy density needs to be properly defined. Stable solutions are derived for a spherically symmetric, surface-charge distribution of an elementary charge. This is implemented by assuming that the gravitational field and its equivalent permittivity function is proportional to the energy density, as a simple first-order approximation, with the constant of proportionality referred to as the Unifield Electro-Gravity (UEG) constant. The stable solution with the lowest mass/energy is assumed to represent a ``static'' electron without any spin. Further, assuming that the mass/energy of a static electron is half of the total mass/energy of an electron including its spin contribution, the required UEG constant is estimated. More fundamentally, the lowest stable mass of a static elementary charged particle, its associated classical radius, and the UEG constant are related to each other by a dimensionless constant, independent of any specific value of the charge or mass of the particle. This dimensionless constant is numerologically found to be closely related to the the fine structure constant. This possible origin of the fine structure constant is further strengthened by applying the proposed theory to successfully model the Casimir effect, from which approximately the same above relationship between the UEG constant, electron's mass and classical radius, and the fine structure constant, emerges.

Real-time evolution of the electron densities under excitations in La₂CuO₄ was calculated by the time-dependent density functional theory (TDDFT). The author found, for the first time, under excitations, the electron cloud of Cu²⁺ changes obviously and the characteristic frequencies are 83 meV and 36 meV, respectively, for two different modes. The results are unexpected and close to that of lattice vibrations. The results show that the electron cloud of Cu²⁺ (just like the lattice) can be the electron-pairing medium in high temperature copper oxide superconductors.

This work communicates results from optical emission spectroscopy following laser-induced optical breakdown at or near nanomaterial. Selected atomic lines of silver are evaluated for consistent determination of electron density. Comparisons are presented with Balmer series hydrogen results. Of particular interest are measurements free of self-absorption effects. For several silver lines, asymmetries are observed in the recorded line profiles. Electron densities of interest range from 0.5 to 3 × 10¹⁷ cm^-3, for 5 nanosecond Q-switched Nd:YAG radiation at wavelengths of 1064, 532, and 355 nm, and for selected silver emission lines including 328.0, 338.2, 768.7, and 827.3 nm, and the hydrogen alpha Balmer series line at 656.3 nm. Line asymmetries are presented for the 328.0 nm Ag I line that is measured following generation of the plasma due to multiple photon absorption. This work explores electron density variations for different irradiance levels, and reports spectral line asymmetry of resonance lines for different laser fluence levels.

Nanoparticles -- regularly patterned or randomly dispersed -- are a key ingredient for emerging technologies in photonics. Of particular interest are scattering and field enhancement effects of metal nanoparticles for energy harvesting and converting systems. An often neglected aspect in the modeling of nanoparticles are light interaction effects beyond classical electrodynamics stemming from electron dynamics in confined and accelerated systems. We give a detailed account on free electron phenomena in metal nanoparticles and discuss analytic expressions, stemming from microscopic and semi-classical theories. These can improve standard computational schemes to produce more reliable results on the optical properties of metal nanoparticles. We combine these solutions into a single framework and study their joint impact on isolated Au, Ag, and Al nanoparticles as well as dimer structures.

Despite their relatively low incidence globally, CNS tumors remain amongst the most lethal cancers, with only a few other malignancies surpassing them in 5-year mortality rates. Treatment decisions for brain tumors heavily rely on histopathological analysis, particularly intraoperatively, to guide surgical interventions and optimize patient outcomes. Frozen sectioning has emerged as a vital intraoperative technique, allowing for highly accurate, rapid analysis of tissue samples, although it poses challenges regarding interpretive errors and tissue distortion. Raman histology, based on Raman spectroscopy, has shown great promise in providing label-free, molecular information for accurate intraoperative diagnosis, aiding in tumor resection and identification of neurodegenerative disease. Techniques including Stimulated Raman Scattering (SRS), Coherent Anti-Stokes Raman Scattering (CARS), Surface-Enhanced Raman Scattering (SERS), and Tip-Enhanced Raman Scattering (TERS) have profoundly enhanced the speed and resolution of Raman imaging. Similarly, Confocal Laser Endomicroscopy (CLE) allows for real-time imaging and rapid intraoperative histologic evaluation of specimens. While CLE is primarily utilized in gastrointestinal procedures, its application in neurosurgery is promising, particularly in the context of gliomas and meningiomas. This review focuses on discussing the immense progress in intraoperative histology within neurosurgery and provides insight into the impact of these advancements on enhancing patient outcomes..

Classical models of gene expression were built using genetics and biochemistry. Although these approaches are powerful, they have very limited consideration of the spatial and temporal organization of gene expression. Although the spatial organization and dynamics of RNA polymerase II (RNAPII) transcription machinery has fundamental functional consequences for gene expression, its detailed studies have been for long time abrogated by the limits of classical light microscopy. The advent of super-resolution microscopy (SRM) techniques allowed for the visualization of the RNAPII transcription machinery with nanometer resolution and millisecond precision. In this review, we summarize the recent methodological advances in SRM, focus on its application for studies of the nanoscale organization in space and time of RNAPII transcription, and discuss its consequences for the mechanistic understanding of gene expression.

Magnetic force microscopy (MFM) is a widespread technique for imaging magnetic structures with a resolution of some 10 nanometers. MFM can be calibrated to obtain quantitative (qMFM) spatially resolved magnetization data in units of A/m by determining the calibrated point spread function of the instrument, its instrument calibration function (ICF), from a measurement of a well-known reference sample. Beyond quantifying the MFM data, a deconvolution of the MFM image data with the ICF also corrects the smearing caused by the finite width of the MFM tip stray field distribution. However, the quality of the calibration depends critically on the calculability of the magnetization distribution of the reference sample. Here, we discuss a Ti/Pt/Co multilayer stack which shows a stripe domain pattern as a suitable reference material. A precise control of the fabrication process combined with a characterization of the sample micromagnetic parameters allows to reliably calculate the sample’s magnetic stray field, proven by a very good agreement between micromagnetic simulations and qMFM measurements. A calibrated qMFM measurement using the Ti/Pt/Co stack as a reference sample is shown and validated and the application area for quantitative MFM measurements calibrated with the Ti/Pt/Co stack is discussed.

Microbial-mediated biogeochemical cycling of iron is widespread in anaerobic environments such as sediments and deep Earth aquifers, and is one of the major pathways for metabolising iron in nature. Organic matter containing quinone groups can act as electron shuttles to transfer electrons between microorganisms and Fe(III) oxides, facilitating the biotransformation of iron; this process also influences the transport transformation of pollutants. In this paper, the reduction of Fe(III) oxides by aniline in the heterogeneous iron-reducing bacterium Shewanella oneidensis MR-1 mediated by the electron shuttle AQS was investigated. The results showed that aniline significantly promoted the reduction of Fe(III) by MR-1 in the AQS-mediated reaction, and the best Fe(III) reduction was achieved in the reaction group of "GT+MR-1+0.5mM AQS+3μM aniline", in which the Fe(II) production was significantly higher than that in the reaction groups of only microorganisms and no aniline reaction. The amount of Fe(II) produced was significantly higher than that of the microorganism-only and aniline-free reaction groups, and the addition of aniline also significantly increased the consumption of sodium lactate by MR-1 in the reaction system. The solid mineral Fe(II)-O content increased to 41.32% after the reaction. However, the structure of needle ferrite is relatively stable, and the surface morphology did not change significantly by SEM, and the generation of other secondary minerals was not observed in the XRD results. The results of this experimental study can help to understand the biogeochemical cycle of iron in multicomponent reactions and are of great significance for environmental management.

The main aspects of material research: material synthesis, material structure, and material properties, are interrelated. Acquiring atomic structure information of electron beam sensitive materials by electron microscope, such as porous zeolites, organic-inorganic hybrid perovskites, metal-organic frameworks, is an important and challenging task. The difficulties in characterization of the structures will inevitably limit the optimization of their synthesis methods and further improve their performance. The emergence of integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM), a STEM characterization technique capable of obtaining images with high signal-to-noise ratio under lower doses, has made great breakthroughs in the atomic structure characterization of these materials. This article reviews the developments and applications of iDPC-STEM in electron beam sensitive materials, and provides an outlook on its capabilities and development.