Due to the intrinsic evaporation properties of the material studied, insufficient mass-resolving power and lack of knowledge of the kinetic energy of incident ions, peaks in the atom probe mass-to-charge spectrum can overlap and result in incorrect composition measurements. Contributions to these peak overlaps can be deconvoluted globally, by simply examining adjacent peaks combined with knowledge of natural isotopic abundances. However, this strategy does not account for the fact that the relative contributions to this convoluted signal can often vary significantly in different regions of the analysis volume; e.g., across interfaces and within clusters. Some progress has been made with spatially localized deconvolution in cases where the discrete microstructural regions can be easily identified within the reconstruction, but this means no further point cloud analyses are possible. Hence, we present an ion-by-ion methodology where the identity of each ion, normally obscured by peak overlap, is resolved by examining the isotopic abundance of their immediate surroundings. The resulting peak-deconvoluted data are a point cloud and can be analyzed with any existing tools. We present two detailed case studies and discussion of the limitations of this new technique.

By using an experimental model of dexamethasone-induced osteoporosis we investigated the effects of different therapeutic schemes combining sodium alendronate (SA) and simvastatin on bone mineral and protein composition, microstructural and mechanical remodeling. Wistar rats were randomized into eight groups: G1: non-osteoporotic; G2: osteoporotic; G3, G4, and G5: osteoporotic+SA (0.2, 0.4, and 0.8 mg/kg, respectively); G6, G7, and G8: osteoporotic+SA (0.2, 0.4, and 0.8 mg/kg, respectively)+simvastatin (0.4, 0.6, and 1 mg/kg, respectively). Osteoporosis was induced by dexamethasone (7 mg/kg, i.m.) once a week for 5 weeks. All treatments were administered for 8 weeks. Dexamethasone increased serum levels of alkaline phosphatase, calcium, phosphorus, and urea, especially in non-treated animals, which showed severe osteoporosis. Dexamethasone also induced bone microstructural fragility and reduced mechanical resistance, which were associated with a marked depletion in mineral mass, collagenous and non-collagenous protein levels in cortical and cancellous bone. Although SA has attenuated osteoporosis severity, the effectiveness of drug therapy was enhanced combining alendronate and simvastatin. The restoration in serum parameters, organic and inorganic bone mass, and mechanical behavior showed a dose-dependent effect that was potentially related to the complementary mechanisms by which each drug acts to induce bone anabolism, accelerating tissue repair.

Beam damage is a major limitation in electron microscopy that becomes increasingly severe at higher resolution. One possible route to circumvent radiation damage, which forms the basis for single-particle electron microscopy and related techniques, is to distribute the dose over many identical copies of an object. For the acquisition of low-dose data, ideally no dose should be applied to the region of interest before the acquisition of data. We present an automated approach that can collect large amounts of data efficiently by acquiring images in a user-defined area-of-interest with atomic resolution. We demonstrate that the stage mechanics of the Nion UltraSTEM, combined with an intelligent algorithm to move the sample, allow the automated acquisition of atomically resolved images from micron-sized areas of a graphene substrate. Moving the sample stage automatically in a regular pattern over the area-of-interest enables the collection of data from pristine sample regions without exposing them to the electron beam before recording an image. Therefore, it is possible to obtain data with minimal dose (no prior exposure during focusing), which is only limited by the minimum signal needed for data processing. This enables us to minimize beam-induced damage in the sample and to acquire large data sets within a reasonable amount of time.

Lithotripsy methods show relatively low efficiency in the fragmentation of sialoliths compared with the success rates achieved in the destruction of renal calculi. However, the information available on the mechanical behavior of sialoliths is limited and their apparently tougher response is not fully understood. This work evaluates the hardness and Young’s modulus of sialoliths at different scales and analyzes specific damage patterns induced in these calcified structures by ultrasonic vibrations, pneumoballistic impacts, shock waves, and laser ablation. A clear correlation between local mechanical properties and ultrastructure/chemistry has been established: sialoliths are composite materials consisting of hard and soft components of mineralized and organic nature, respectively. Ultrasonic and pneumoballistic reverberations damage preferentially highly mineralized regions, leaving relatively unaffected the surrounding organic matter. In contrast, shock waves leach the organic component and lead to erosion of the overall structure. Laser ablation destroys homogeneously the irradiated zones regardless of the mineralized/organic nature of the underlying ultrastructure; however, damage is less extensive than with mechanical methods. Overall, the present results show that composition and internal structure are key features behind sialoliths’ comminution behavior and that the organic matter contributes to reduce the therapeutic efficiency of lithotripsy methods.

In this work, we report on the atom probe tomography analysis of two metallic hydrides formed by pressurized charging using an ex situ hydrogen charging cell, in the pressure range of 200–500 kPa (2–5 bar). Specifically we report on the deuterium charging of Pd/Rh and V systems. Using this ex situ system, we demonstrate the successful loading and subsequent atom probe analysis of deuterium within a Pd/Rh alloy, and demonstrate that deuterium is likely present within the oxide–metal interface of a native oxide formed on vanadium. Through these experiments, we demonstrate the feasibility of ex situ hydrogen analysis for hydrides via atom probe tomography, and thus a practical route to three-dimensional imaging of hydrogen in hydrides at the atomic scale.

Trefoil factor family 3 (Tff3) peptide is present during intrauterine endochondral ossification in mice, and its deficiency affects cancellous bone quality in secondary ossification centers of mouse tibiae. The aim of this study was to quantitatively analyze parameters describing the growth plate and primary ossification centers in tibiae of 1-month-old wild-type and Tff3 knock-out mice (n=5 per genotype) by using free and open-source software. Digital photographs of the growth plates and trabecular bone were processed by open-source computer programs GIMP and FIJI. Histomorphometric parameters were calculated using measurements made with FIJI. Tff3 knock-out mice had significantly smaller trabecular number and significantly larger trabecular separation. Trabecular bone volume, trabecular bone surface, and trabecular thickness showed no significant difference between the two groups. Although such histomorphological differences were found in the cancellous bone structure, no significant differences were found in the epiphyseal plate histomorphology. Tff3 peptide probably has an effect on the formation and quality of the cancellous bone in the primary ossification centers, but not through disrupting the epiphyseal plate morphology. This work emphasizes the benefits of using free and open-source programs for morphological studies in life sciences.

The aim of this study was to investigate if load cycling affects interfacial integrity of glass ionomer cements bonded to sound- or caries-affected dentin. A conventional glass ionomer, Ketac Bond, and a resin-modified glass ionomer (Vitrebond Plus), were applied to dentin. Half of the specimens were load cycled. The interfaces were submitted to dye-assisted confocal microscopy evaluation. The unloaded specimens of sound and carious dentin were deficiently hybridized when Ketac Bond was used. Ketac Bond samples showed an absorption layer and an adhesive layer that were scarcely affected by fluorescein penetration (nanoleakage), in sound dentin. Nevertheless, a higher degree of micropermeability was found in carious dentin. In Ketac Bond specimens, load cycling improves the sealing capability and remineralization at the cement–dentin interface as porosity and nanoleakage was reduced. In contrast, samples treated with Vitrebond Plus exhibited a Rhodamine B-labeled absorption layer with scarce nanoleakage in both sound and carious unloaded dentin. The adhesive layer was affected by dye sorption throughout the porous cement–dentin interface. Samples treated with Vitrebond Plus had significant increases in nanoleakage and cement–dye sorption after load cycling. Within the limitations of an in vitro study, it is expected that conventional glass ionomers will provide major clinical efficacy when applied to carious-affected or sound dentin.

Endogenous melatonin is a hormone secreted by pineal gland; it has several roles in metabolism, reproduction, and remarkable antioxidant properties. Studies on the melatonin effect on the adrenal glands which are important endocrine organs, controlling essential physiological functions, are still deficient. In this study, we attempted to investigate the effect of exogenous melatonin treatment on the adrenal cortex and medulla using several approaches. Adrenal glands of 15 Soay ram were examined to detect the effect of melatonin treatment. Our results revealed that the cells of adrenal cortex of the treated animals were separated by wide and numerous blood sinusoids and showed signs of increase steroidogenic activity, which are evidenced by functional hypertrophy with increase profiles of mitochondria, smooth endoplasmic reticulum, and lipid droplets. The most striking ultrastructural features in the medulla of the treated group were the engorgement of chromaffin cells with enlarged secretory granules enclosed within a significantly increased diameter of these cells. The cytoplasm of these cells showed numerous mitochondria, rough endoplasmic reticulum (rER), Golgi apparatus, lysosomes, and glycogen granules. Exocytosis of secretory granules to the lumen of blood vessels was evident in the treated group. Piecemeal degranulation mode of secretion was recorded after melatonin treatment. Chromaffin cells in the control group expressed moderate immunoreactivity to Synaptophysin and tyrosine hydroxylase, compared with intensified expression after melatonin treatment. The ganglion cells of the melatonin-treated group showed a significant increase in diameter with numerous rER. The most interesting feature in this study is the presence of small granule chromaffin cells (SGC) and telocytes (TCs) for the first time in the adrenal glands of sheep. Moreover, these SGC cells, Schwann cells, fibroblasts, and progenitor stem cells showed a stimulatory response. The TCs were small branched cells scattered in the adrenal glands around cortical cells, chromaffin cells, nerve fibers, and blood vessels. These cells increased significantly in number, length of their telopodes, and secretory activity after melatonin treatment. In addition, multiple profiles of unmyelinated nerve fibers were demonstrated in all treated specimens. These results indicated that melatonin treatment caused a stimulatory action on all cellular and neuronal elements of the adrenal gland. This study may act as a new direction for treatment of adrenal insufficiency.

High-resolution atomic force microscopy (AFM) was used for the in situ evaluation of the anti-inflammatory effects of triptolide on rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) to understand the anti-RA effects of triptolide, based on the morphological and biophysical changes observed in RA-FLS. RA-FLS have been reported to play a primary role in inflammatory bone destruction during the development of RA and thus are regarded as an important target for RA treatment. Triptolide pretreatment significantly inhibited tumor necrosis factor-α-induced expression of the interleukin (IL)-1β, IL-6, and IL-8 genes in MH7A cells. Using AFM, we showed that triptolide-induced morphological damage in MH7A cells by inducing significant ultrastructure changes in the membrane, which were closely related to triptolide-induced apoptosis in MH7A cells. Using force measurements determined with AFM, triptolide was shown to increase the stiffness of MH7A cells. These findings not only revealed the strong anti-inflammatory effects of triptolide on RA-FLS, highlighting triptolide as a potential anti-RA agent, but also revealed the possible use of AFM for studying anti-inflammatory responses in RA-FLS, which we expect to be developed into a potential tool for anti-RA drug studies in RA-FLS.

Atom probe tomography is routinely used for the characterization of materials microstructures, usually assuming that the microstructure is unaltered by the analysis. When analyzing ionic conductors, however, gradients in the chemical potential and the electric field penetrating dielectric atom probe specimens can cause significant ionic mobility. Although ionic mobility is undesirable when aiming for materials characterization, it offers a strategy to manipulate materials directly in situ in the atom probe. Here, we present experimental results on the analysis of the ionic conductor lithium-manganese-oxide with different atom probe techniques. We demonstrate that, at a temperature of 30 K, characterization of the materials microstructure is possible without measurable Li mobility. Also, we show that at 298 K the material can be deintercalated, in situ in the atom probe, without changing the manganese-oxide host structure. Combining in situ atom probe deintercalation and subsequent conventional characterization, we demonstrate a new methodological approach to study ionic conductors even in early stages of deintercalation.

Elemental mapping at the atomic-scale by scanning transmission electron microscopy (STEM) using energy-dispersive X-ray spectroscopy (EDS) provides a powerful real-space approach to chemical characterization of crystal structures. However, applications of this powerful technique have been limited by inefficient X-ray emission and collection, which require long acquisition times. Recently, using a lattice-vector translation method, we have shown that rapid atomic-scale elemental mapping using STEM-EDS can be achieved. This method provides atomic-scale elemental maps averaged over crystal areas of ~few 10 nm2 with the acquisition time of ~2 s or less. Here we report the details of this method, and, in particular, investigate the experimental conditions necessary for achieving it. It shows, that in addition to usual conditions required for atomic-scale imaging, a thin specimen is essential for the technique to be successful. Phenomenological modeling shows that the localization of X-ray signals to atomic columns is a key reason. The effect of specimen thickness on the signal delocalization is studied by multislice image simulations. The results show that the X-ray localization can be achieved by choosing a thin specimen, and the thickness of less than about 22 nm is preferred for SrTiO3 in [001] projection for 200 keV electrons.

Calcite spherulites have been observed in many laboratory experiments with different bacteria, and spherulitic growth has received much interest in mineralogy research. However, the nucleation and growth mechanism, as well as geological significance of calcite spherulites in solution with bacteria is still unclear. Herein, spherulites composed of an amorphous core, a Mg-calcite body and an organic film were precipitated by the Curvibacter lanceolatus HJ-1 bacterial strain in a solution with a molar Mg/Ca ratio of 3. Based on the results, we provide a possible mechanism for the biomineralization of Mg-calcite spherulites. First, amorphous calcium carbonate particles are deposited and aggregated into a stable sphere-like core in combination with organic molecules. The core then acts as the nucleus of spherulitic radial growth. Finally, the organic film grows on the surface of Mg-calcite spherulites as a result of bacterial metabolism and calcification. These findings provide insight into the growth mode and crystallization of biogenic spherulites during biomineralization, and are of significance in the application of novel biological materials.

As erythrocyte and estrogens interact so closely and erythrocytes can indicate the healthiness of an individual, it is essential to investigate the effects of natural estrogens as well as synthetic estrogens on these cells. Whole blood samples were used for thromboelastography (TEG), light microscopy (LM), and scanning electron microscopy (SEM) investigation. Viscoelastic investigation with TEG revealed that estrogens affected the rate of clot formation without any significant effect on the strength or stability of the clot. Axial ratio analysis with LM showed a statistically significant increase in number of erythrocytes with decreased roundness. Morphological analysis with SEM confirmed the change in erythrocyte shape and revealed both ultrastructural membrane changes and erythrocyte interactions. As erythrocyte shape and membrane flexibility correlates to physiological functioning of these cells in circulation, these changes, indicative of possible eryptosis brought on by estrogens, when experienced by individuals with an underlying inflammatory or hematological illness, could impair erythrocyte functioning and even result in obstructions in circulation. In conclusion, we suggest that whole blood analysis with viscoelastic and morphological techniques could be used as assessment of the hematological healthiness of individuals using estrogens.

Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

Both fibronectin (FN) and filamentous actin (F-actin) fibers play a critical role for endothelial cells (ECs) in responding to shear stress and modulating cell alignment and functions. FN is dynamically coupled to the F-actin cytoskeleton via focal adhesions. However, it is unclear how ECs cooperatively remodel their subcellular FN matrix and intracellular F-actin cytoskeleton in response to shear stress. Current studies are hampered by the lack of a reliable and sensitive quantification method of FN orientation. In this study, we developed a MATLAB-based feature enhancement method to quantify FN and F-actin orientation. The role of F-actin in FN remodeling was also studied by treating ECs with cytochalasin D. We have demonstrated that FN and F-actin codistributed and coaligned parallel to the flow direction, and that F-actin alignment played an essential role in regulating FN alignment in response to shear stress. Our findings offer insight into how ECs cooperatively remodel their subcellular ECM and intracellular F-actin cytoskeleton in response to mechanical stimuli, and are valuable for vascular tissue engineering.

Six precursors were evaluated for use as in situ electron beam-induced deposition capping layers in the preparation of atom probe tomography specimens with a focus on near-surface features where some of the deposition is retained at the specimen apex. Specimens were prepared by deposition of each precursor onto silicon posts and shaped into sub-70-nm radii needles using a focused ion beam. The utility of the depositions was assessed using several criteria including composition and uniformity, evaporation behavior and evaporation fields, and depth of Ga+ ion penetration. Atom probe analyses through depositions of methyl cyclopentadienyl platinum trimethyl, palladium hexafluoroacetylacetonate, and dimethyl-gold-acetylacetonate [Me2Au(acac)] were all found to result in tip fracture at voltages exceeding 3 kV. Examination of the deposition using Me2Au(acac) plus flowing O2 was inconclusive due to evaporation of surface silicon from below the deposition under all analysis conditions. Dicobalt octacarbonyl [Co2(CO)8] and diiron nonacarbonyl [Fe2(CO)9] depositions were found to be effective as in situ capping materials for the silicon specimens. Their very different evaporation fields [36 V/nm for Co2(CO)8 and 21 V/nm for Fe2(CO)9] provide options for achieving reasonably close matching of the evaporation field between the capping material and many materials of interest.

Although there are numerous recent works focusing on fractal properties of DNA and chromatin, many issues regarding changes in chromatin fractality during physiological aging remain unclear. In this study, we present results indicating that in mice, there is an age-related reduction of chromatin fractal complexity in a population of spleen follicular cells (SFCs). Spleen tissue was obtained from 16 mice and fixated in Carnoy solution. The youngest animal was newborn, and each animal was exactly 1 month older than the previous. We performed fractal analysis of SFC chromatin structure, stained using Giemsa technique. Fractal analysis was done in a plugin algorithm of ImageJ software. We also performed gray-level co-occurrence matrix (GLCM) analysis of all chromatin structures with the calculation of parameters such as angular second moment and inverse difference moment. Giemsa-stained SFC chromatin exhibited an age-dependent reduction of fractal dimension with statistically significant (p<0.01) linear trend. Moreover, there was a statistically significant increase of SFC chromatin lacunarity. The chromatin GLCM parameters did not significantly change. To our knowledge, this is the first study to perform fractal and GLCM analyses of SFC chromatin and to investigate potential changes of fractal parameters during postnatal development.