Spatial Distribution Of Nuclei Research Articles

Automated Layer Analysis (ALAn): An Image Analysis Tool for the Unbiased Characterization of Mammalian Epithelial Architecture in Culture.

Cultured mammalian cells are a common model system for the study of epithelial biology and mechanics. Epithelia are often considered as pseudo-two dimensional and thus imaged and analyzed with respect to the apical tissue surface. We found that the three-dimensional architecture of epithelial monolayers can vary widely even within small culture wells, and that layers that appear organized in the plane of the tissue can show gross disorganization in the apical-basal plane. Epithelial cell shapes should be analyzed in 3D to understand the architecture and maturity of the cultured tissue to accurately compare between experiments. Here, we present a detailed protocol for the use of our image analysis pipeline, Automated Layer Analysis (ALAn), developed to quantitatively characterize the architecture of cultured epithelial layers. ALAn is based on a set of rules that are applied to the spatial distributions of DNA and actin signals in the apical-basal (depth) dimension of cultured layers obtained from imaging cultured cell layers using a confocal microscope. ALAn facilitates reproducibility across experiments, investigations, and labs, providing users with quantitative, unbiased characterization of epithelial architecture and maturity. Key features • This protocol was developed to spatially analyze epithelial monolayers in an automated and unbiased fashion. • ALAn requires two inputs: the spatial distributions of nuclei and actin in cultured cells obtained using confocal fluorescence microscopy. • ALAn code is written in Python3 using the Jupyter Notebook interactive format. • Optimized for use in Marbin-Darby Canine Kidney (MDCK) cells and successfully applied to characterize human MCF-7 mammary gland-derived and Caco-2 colon carcinoma cells. • This protocol utilizes Imaris software to segment nuclei but may be adapted for an alternative method. ALAn requires the centroid coordinates and volume of nuclei.

Enrichment Effects Induced by Non-uniform Wettability Surfaces in the Presence of Non-condensable Gas: A Molecular Dynamics Simulation.

For vapor condensation, the control of heterogeneous nucleation and spatial distribution of nuclei are crucial for regulating droplet dynamics and improving condensation efficiency. However, due to the complex characteristics of multicomponent, multiphase, and multiscale, the underlying mechanism of mixed vapor condensation remains unclear, especially at the nucleation stage. In this paper, we focus on the enrichment effects of non-uniform wettability surfaces by molecular dynamics simulation, which could intensify the droplet nucleation and growth processes in a water-air mixed system. The results clarify the inhibitory effect of non-condensable gas on droplet nucleation and prove that only 1% of non-condensable gas could reduce one half of the condensation performance from a molecular perspective. Furthermore, non-uniform surfaces are designed to promote the efficient enrichment of vapor molecules on nucleation sites, and the synergistic effect of hydrophilic and hydrophobic regions is proposed. In addition, the non-uniform wettability surfaces are characterized by varying the proportion and dispersion of hydrophilic regions. The results reveal that an optimal proportion of hydrophilic region (R = 5/6) could furnish the non-uniform surface with the best transfer performance. Moreover, the enhancement of condensation performance can also be achieved through the dispersed arrangement of hydrophilic regions. The results provide guidance for the optimized design of functionalized surfaces with enhanced mixed vapor condensation.

Abstract 1721: Spatial distribution of immune cells as quantitative prognosis indicator in hepatocellular carcinoma

Abstract Background: We previously demonstrated that the analysis of the tumor microenvironment (TME) in histopathology images via tissue segmentation [1] and cell density in lymphocyte-rich area [2] impacts prognosis and treatment in hepatocellular carcinoma (HCC). Few biomarker models exist to prognosticate patients with HCC via the automated analysis of TME at the cellular level. Methods: Clinical outcomes data and histopathology images of 351 patients with HCC were obtained from TCGA. We advanced a deep learning-based algorithm to analyze the tumor volume and spatial distribution of nuclei in TME. This was based on combination of two models: the PAIP2019 dataset was used for DenseNet-based HCC segmentation, which showed the performance of 0.8582 on the F1-score metric [3]; HoverNet-based cell detection model, which showed the performance of 0.654 on the binary PQ metric, annotated lymphocytes, macrophages, and neutrophils on the MonuSac dataset [4]. Results: The HCC segmentation model divided the TME into tumoral, marginal, and peritumoral areas by image processing. The marginal and peritumoral areas were defined as inner 50 um area and outer 100 um area from the estimated tumoral boundary, respectively. The ratios of neutrophils, lymphocytes, macrophages to the total cell count on marginal and peritumoral areas were calculated through integration of HCC segmentation and cell detection models. The proportions of leukocytes were subjected into Cox proportional hazard analysis. The results of Cox proportional hazard analysis calculated the proportions of macrophages and lymphocytes to other cells in the TME. The macrophage proportion on the peritumoral area was a significant prognostic indicator showing Log(hazard ratio) (-2.42 ± 2.14, p=0.026). The lymphocyte proportion on both areas of the peritumor and margins showed significant Log(hazard ratio) (-1.70 ± 1.61, p=0.042). Conclusions: The retrospective analysis of the TME using deep learning-assisted algorithm combining tissue segmentation and cell detection models reveals that the ratio of lymphocytes and macrophages in the peri-tumoral areas of HCC TME significantly impact prognosis. Further analyses in the prospective studies may provide more information about cellular biomarkers. [1] Kim et al. Cancer Res 2020 (80) (16 Supp) 2631 [2] Park et al. Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021) 4107-4107 [3] Kim, Yoo Jung, Jang, Hyungjoon, Lee, Kyoungbun et al. Medical Image Analysis 67 (2021): 101854. [4] Verma, Ruchika. IEEE Transactions on Medical Imaging 39 (2020): 1380-1391. [5] Graham, Simon. Medical Image Analysis 58 (2019): 101563. Citation Format: Hongseok Lee, Kyungdoc Kim, Guhyun Kang, Kyu-Hwan Jung, Sunyoung S. Lee. Spatial distribution of immune cells as quantitative prognosis indicator in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1721.

Karbonátos konkréciók az alsó-miocén Pétervásárai Homokkő Formációban (Pétervásárai-dombság, Leleszi-völgy): genetikai megfontolások morfológiai és petrográfiai vizsgálatok eredményei alapján

Rocks of the shallow marine Lower Miocene Pétervására Sandstone Formation outcrop in spectacular forms in Northern Hungary. Origin of the typical carbonate concretions together with the mechanism of sandstone cementation is, however, still under debate. In this paper, selected outcrops of the Pétervására Sandstone (Pétervására Hills, Lelesz Valley) are studied using field observations and petrographic investigations. Based on our results, isolated (spherical and ellipsoidal) and stratabound concretions as well as continuously cemented layers were equally developed. In the isolated concretions grown in very coarse grained sandstones, bioclasts (e.g. mollusk fragments, benthic foraminifers) of different sizes and shapes were observed. Consequently, the primary source of the calcite cement could be the large amount of the detrital bioclast material (aragonite/calcite) in the studied formation. Related to the cementation processes, early crystallization of the calcite cement started around a nucleus concentrically and the diagenetic redistribution of carbonate phases could take place during burial by diffusion. Cementation and growth mechanisms of the concretions could be significantly affected by petrological characteristics of the sediments (e.g. sorting, grain-size distribution, permeability) and by the spatial distribution of nuclei. Additionally, based on the microtextural features, the significant amount of glauconite-like grains in the Pétervására Sandstone are dominantly detrital in origin and could form earlier in the intragranular pores of the redeposited bioclast.

GPU-enabled design of an adaptable pattern recognition system for discriminating squamous intraepithelial lesions of the cervix.

The aim of the present study was to design an adaptable pattern recognition (PR) system to discriminate low- from high-grade squamous intraepithelial lesions (LSIL and HSIL, respectively) of the cervix using microscopy images of hematoxylin and eosin (H&E)-stained biopsy material from two different medical centers. Clinical material comprised H&E-stained biopsies of 66 patients diagnosed with LSIL (34 cases) or HSIL (32 cases). Regions of interest were selected from each patient's digitized microscopy images. Seventy-seven features were generated, regarding the texture, morphology and spatial distribution of nuclei. The probabilistic neural network (PNN) classifier, the exhaustive search feature selection method, the leave-one-out (LOO) and the bootstrap validation methods were used to design the PR system and to assess its precision. Optimal PR system design and evaluation were made feasible by the employment of graphics processing unit (GPU) and Compute Unified Device Architecture (CUDA) technologies. The accuracy of the PR-system was 93% and 88.6% when using the LOO and bootstrap validation methods, respectively. The proposed PR system for discriminating LSIL from HSIL of the cervix was designed to operate in a clinical environment, having the capability of being redesigned when new verified cases are added to its repository and when data from other medical centers are included, following similar biopsy material preparation procedures.

2D Voronoi tessellation generated by lines and belts of dots

The application of the Voronoi tessellation for studying the nucleation process at the basis of thin film formation dates back to the end of nineties. In particular, Poissonian and spatial correlated nuclei distributions were investigated. The growth of stressed interfaces, however, has evidenced that elastic strain can modify the spatial distribution of nuclei giving rise to new challenges at the level of stochastic geometry. Here we report a study of a 2D nucleation of dots randomly arranged in lines and/or belts on the surface. The results are compared to the experimental case of multilayer structures of InAs quantum dots grown on GaAs(001).

X-ray scattering on charge-density-wave superconductor 2H-NbSe2

A direct evidence of X-ray scattering by electron modulation in a charge-density wave metal dominating over the periodic lattice distortion (PLD) is presented for hexagonal modification of niobium diselenide (2H-NbSe2). Namely, new pronounced features appear in X-ray diffraction below TCDW indexed in the space group D3h1 with a doubled in-plane parameter a and the inversion symmetry axis instead of screw one. Above TCDW transition, the space group D6h4 with lattice parameters a0=3.44Å, c=12.8Å is revealed in agreement with published data. The observed difference is due in particular to different mechanisms of neutron and X-rays scattering by spatial distribution of nuclei or electron density, respectively. A CDW formation in 2H-NbSe2 is then accompanied by spatial modulation of electron density with periodicity 2a, manifested in X-ray scattering with a nuclei shift insufficient for neutron scattering. Indeed, numerous studies show enigmatic absence of Fermi-surface nesting in 2H-NbSe2 and, eventually, long coherence length. Within McMillan's consideration it means that in this case, electron modulation should dominate the distortion of periodic crystal potential rather than commonly observed periodic lattice distortion, e.g. in TaSe2.

3D Spatial Distribution of Nuclei in 90% Cold Rolled Aluminium

The distribution of nucleation sites in 90% cold rolled aluminium (AA1050) annealed for 1h at 280°C has been determined by serial sectioning the sample and characterizing each section using the electron back scattering pattern (EBSP) method in the SEM. In total 1844 nuclei are identified. It was found that the nuclei are not randomly distributed but clustered preferentially along TD-RD planes in the sample. The results are presented and implications of clustered nucleation on recrystallization kinetics are discussed.

Number and spatial distribution of nuclei in the muscle fibres of normal mice studied in vivo.

We present here a new technique with which to visualize nuclei in living muscle fibres in the intact animal, involving injection of labelled DNA into single cells. This approach allowed us to determine the position of all of nuclei within a sarcolemma without labelling satellite cells. In contrast to what has been reported in tissue culture, we found that the nuclei were immobile, even when observed over several days. Nucleic density was uniform along the fibre except for the endplate and some myotendinous junctions, where the density was higher. The perijunctional region had the same number of nuclei as the rest of the fibre. In the extensor digitorum longus (EDL) muscle, the extrajunctional nuclei were elongated and precisely aligned to the long axis of the fibre. In the soleus, the nuclei were rounder and not well aligned. When comparing small and large fibres in the soleus, the number of nuclei varied approximately in proportion to cytoplasmic volume, while in the EDL the number was proportional to surface area. Statistical analysis revealed that the nuclei were not randomly distributed in either the EDL or the soleus. For each fibre, actual distributions were compared with computer simulations in which nuclei were assumed to repel each other, which optimizes the distribution of nuclei with respect to minimizing transport distances. The simulated patterns were regular, with clear row-like structures when the density of nuclei was low. The non-random and often row-like distribution of nuclei observed in muscle fibres may thus reflect regulatory mechanisms whereby nuclei repel each other in order to minimize transport distances.

Structure Evolution of Spherulitic Crystallization in Semicrystalline Polymer Films

Isothermal nucleation-growth phenomena in 2D semicrystalline polymer films have been investigated by the time-resolved two-dimensional fast Fourier transform (2DFFT) as a quasi-scattering method via real-time in situ observation and measurements. The dynamic evolution of the structure function has been used to interpret the observed scattering intensity connected with crystallization kinetics. The important dynamic quantities, such as the intradomain scattering (domain-size distribution) and spatial distribution of nuclei, have been distinguished by the analysis of the power spectra for different crystallization conditions. The interdomain interference (spatial correlations) was interpreted by the aid of a pair correlation function. Experimental data confirm Porod's law, that is, the q-4 dependence of the tails. A scaling relation of the structure function is found experimentally for the free growth of domains during the postnucleation stage; however, it is not valid after impingement occurs.

A computer simulation model for the diffusion controlled nucleation and growth processes on electrode surfaces—a two-dimensional study

A computer simulation model is presented to study the monolayer formation under conditions of diffusion controlled nucleation and growth in a linear electrode in contact with a bidimensional solution. The diffusion of the electroactive particles in the solution and on the electrode surface is described explicitly. This fact allows the study of the nucleation and growth phenomena without the need to impose analytical laws that would condition the behaviour of the system. The model is focused on the role of the diffusion process in the kinetics of the electrode surface coverage and in the spatial distribution of nuclei. Thus, no restrictions are imposed on the position where a nucleus may appear and on the overlap among growing nuclei. The temporal evolution of the number of nuclei and the rate of nuclear growth is analysed. The electrode surface coverage values yielded by the computer simulations differ by 5–20% from the Avrami theorem predictions due to a non-random distribution of nuclei on the electrode surface as the g ( r ) internuclear pair correlation functions indicate. The electrode coverage follows a non-poissonian probability distribution which has been characterized. The correlation found among the g ( r ) curves, the rate of nuclear growth and the nucleation probability values permit the non-Avrami behaviour to be interpreted in terms of the depletion of electroactive particles and the appearance of zones of reduced nucleation around every growing nucleus. A nuclear deficiency parameter is defined to quantify the reduced nucleation zones. Finally, the influence of the surface diffusion on the coverage properties is also studied.

Modeling the kinetics and microstructural evolution during static recrystallization—Monte Carlo simulation of recrystallization

The kinetics of microstructure and texture evolution during static recrystallization of a cold-rolled and annealed f.c.c. material is simulated by coupling a finite element model of microstructural deformation with a Monte Carlo simulation of recrystallization. The salient features of the simulations include a nucleation model for recrystallization based on subgrain growth and the modeling of simultaneous recovery during recrystallization. The simulation results quantify the effects of non-uniform stored energy distribution and orientation gradients present in the cold-worked microstructure on recovery by subgrain growth, and hence on the spatial distribution of nuclei and their orientations. The growth of these recrystallized nuclei in the presence of continued recovery of the substructure has been simulated for initial cold-work levels of ε=0.7 and 1.1 obtained by plane strain compression. The simulations are shown to be potentially capable of capturing the formation and evolution of cube texture commonly observed in cold-rolled and annealed f.c.c. materials.

Spatial distribution of nuclei inhibition of local nucleation rates by the most influential neighbours

The effects of nearest neighbours on the local nucleation rates and on the spatial distribution of electrodeposited nuclei growing under diffusion control have been analysed. Based upon the Dirichlet tessellation procedure, a systematic criterion is developed for selecting for each site on the surface its natural neighbours, i.e. those nuclei whose diffusional fields are not screened by other nuclei. Through computer simulations, the combined effect of the natural neighbours on the local nucleation rate at a site, or that of only the most influential neighbour, as well as the resulting spatial distributions of nuclei, are analysed. Comparison with experimental results shows that the effect of the most influential neighbour determines the spatial distribution of nuclei. It is also shown that the spatial distribution of nuclei does not depend on the detailed dependence of the local nucleation rate on the radial distance to its most influential or natural neighbours, as long as their propagation occurs with the same time-dependence.

Silver electrocrystallization from a nonpolluting aqueous leaching solution containing ammonia and chloride

Silver electrocrystallization from aqueous solutions at pH 11, pC10 and pNH3 - 0.2, where Ag(NH3) + is the dominant Ag(i) species, has been studied. In spite of the complexities of this medium, the experimental results can be satisfactorily described in terms of multiple nucleation and diffusioncontrolled growth of hemispherical nuclei. Nucleation rates, A, and number densities of active sites on the electrode surface, No, were determined from potentiostatic current transients as a function of overpotential. Saturation number densities of silver nuclei on the electrode surface obtained from the A and No values were found to be in excellent agreement with those obtained from the direct, microscopic observation of the electrode surface. Spatial distributions of nuclei were also analysed for silver electrodeposited at different potentials. It was found that nuclei were uniformly distributed when electrodeposited at low overpotentiats, whereas inhibition of nucleation close to already established nuclei occurred at higher overpotentials. From the change of the true nucleation rate with overpotential, it was found that the critical nucleus is formed by a single atom within the - 100 to -300 mV overpotential range.

Formation and Spatial Statistics of Spherulitic Grain Pattern in Solidified Films of Isotactic Polypropylene

AbstractImage analysis and measurements on forimation and spatial statistics of spherulitic grain pattern in solidified films of a model polymer, isotactic polypropylene (iPP), have been carried out during in-situ observation experiments under isothermnl conditions. Topological correlations and geometrical distribution fuinctions of polymer grain sides and area are reported. Some topologically unstable configurations, such as multi-vertices, “T” type vertices and two sided grain (lens), have been found. Analysis by spatial tessellations shows that the tenWal evolution and spatial distributions of nuclei point patterns play a role in all of these microstructural properties.

Sources and Nature of Variation in DNA Analysis of Follicular Thyroid Adenoma

We investigated the sources and nature of variation that may occur in the DNA analysis of thyroid adenomas from cytological and histological samples. Imprints and smears gave identical results. However, the nuclear area was higher in smears where the optical density of the nuclei was lower. In measuring imprints, the interactive selection of nuclei was preferred to the automatic, because the risk of measuring nuclear fragments or undesired objects was thus avoided. The reproducibility and the variation of the DNA measurements depended on the degree of observer training in quantitative pathology, the method of field selection, and the type of instrumentation. Biological variation in the spatial distribution of nuclei with different ploidy values in some adenomas seemed to hide the influence of section thickness on measurements. Our data seem to suggest that it is best to apply a constant section thickness and 5 micron sections seem acceptable.