Nucleus Size Research Articles

The relative sizes of nuclei in the oculomotor complex vary by order and behaviour in birds.

Eye movements are a critical component of visually guided behaviours, allowing organisms to scan the environment and bring stimuli of interest to regions of acuity in the retina. Although the control and modulation of eye movements by cranial nerve nuclei are highly conserved across vertebrates, species variation in visually guided behaviour and eye morphology could lead to variation in the size of oculomotor nuclei. Here, we test for differences in the size and neuron numbers of the oculomotor nuclei among birds that vary in behaviour and eye morphology. Using unbiased stereology, we measured the volumes and numbers of neurons of the oculomotor (nIII), trochlear (nIV), abducens (nVI), and Edinger-Westphal (EW) nuclei across 71 bird species and analysed these with phylogeny-informed statistics. Owls had relatively smaller nIII, nIV, nVI and EW nuclei than other birds, which reflects their limited degrees of eye movements. In contrast, nVI was relatively larger in falcons and hawks, likely reflecting how these predatory species must shift focus between the central and temporal foveae during foraging and prey capture. Unexpectedly, songbirds had an enlarged EW and relatively more nVI neurons, which might reflect accommodation and horizontal eye movements. Finally, the one merganser we measured also has an enlarged EW, which is associated with the high accommodative power needed for pursuit diving. Overall, these differences reflect species and clade level variation in behaviour, but more data are needed on eye movements in birds across species to better understand the relationships among behaviour, retinal anatomy, and brain anatomy.

Breast Tumor Tissue Image Classification Using DIU-Net.

Inspired by the observation that pathologists pay more attention to the nuclei regions when analyzing pathological images, this study utilized soft segmentation to imitate the visual focus mechanism and proposed a new segmentation-classification joint model to achieve superior classification performance for breast cancer pathology images. Aiming at the characteristics of different sizes of nuclei in pathological images, this study developed a new segmentation network with excellent cross-scale description ability called DIU-Net. To enhance the generalization ability of the segmentation network, that is, to avoid the segmentation network from learning low-level features, we proposed the Complementary Color Conversion Scheme in the training phase. In addition, due to the disparity between the area of the nucleus and the background in the pathology image, there is an inherent data imbalance phenomenon, dice loss and focal loss were used to overcome this problem. In order to further strengthen the classification performance of the model, this study adopted a joint training scheme, so that the output of the classification network can not only be used to optimize the classification network itself, but also optimize the segmentation network. In addition, this model can also provide the pathologist model's attention area, increasing the model's interpretability. The classification performance verification of the proposed method was carried out with the BreaKHis dataset. Our method obtains binary/multi-class classification accuracy 97.24/93.75 and 98.19/94.43 for 200× and 400× images, outperforming existing methods.

Probing the Critical Nucleus Size in the Metal-Insulator Phase Transition of VO_{2}.

In a first-order phase transition, critical nucleus size governs nucleation kinetics, but the direct experimental test of the theory and determination of the critical nucleation size have been achieved only recently in the case of ice formation in supercooled water. The widely known metal-insulator phase transition (MIT) in strongly correlated VO_{2} is a first-order electronic phase transition coupled with a solid-solid structural transformation. It is unclear whether classical nucleation theory applies in such a complex case. In this Letter, we directly measure the critical nucleus size of the MIT by introducing size-controlled nanoscale nucleation seeds with focused ion irradiation at the surface of a deeply supercooled metal phase of VO_{2}. The results compare favorably with classical nucleation theory and are further explained by phase-field modeling. This Letter validates the application of classical nucleation theory as a parametrizable model to describe phase transitions of strongly correlated electron materials.

Efficient Staining-Invariant Nuclei Segmentation Approach Using Self-Supervised Deep Contrastive Network.

Existing nuclei segmentation methods face challenges with hematoxylin and eosin (H&E) whole slide imaging (WSI) due to the variations in staining methods and nuclei shapes and sizes. Most existing approaches require a stain normalization step that may cause losing source information and fail to handle the inter-scanner feature instability problem. To mitigate these issues, this article proposes an efficient staining-invariant nuclei segmentation method based on self-supervised contrastive learning and an effective weighted hybrid dilated convolution (WHDC) block. In particular, we propose a staining-invariant encoder (SIE) that includes convolution and transformers blocks. We also propose the WHDC block allowing the network to learn multi-scale nuclei-relevant features to handle the variation in the sizes and shapes of nuclei. The SIE network is trained on five unlabeled WSIs datasets using self-supervised contrastive learning and then used as a backbone for the downstream nuclei segmentation network. Our method outperforms existing approaches in challenging multiple WSI datasets without stain color normalization.

Induction of polyploids in acid lime (Citrus aurantifolia) through colchicine treatment of in vitro derived shoot tip explants

AbstractPolyploid breeding is an effective tool to induce variability in the existing population, specifically in the crops having very narrow genetic base such as acid lime. Hence, an experiment was conducted to induce polyploidy in acid lime through colchicine treatment. Higher frequency of triploids were obtained in 250 μM colchicine treatment (27.27%), whereas combination of 3× (21.42%), 4× (13.33%) and aneuploid (6.67%) were induced at 500 μM colchicine treatment. Measurement of stomatal density and guard cell size of colchiploids revealed that the former one has negative relation with ploidy level and a positive relation was observed between guard cell size and ploidy level. Further, area and size of nuclei also had a positive relation with ploidy level. Hence, stomatal density, guard cell and nuclei size can be used effectively as morphological marker for preliminary polyploid screening. From the experiment, it can be concluded that 500 μM colchicine treatment of in vitro derived shoot tip explants of acid lime is optimum for creating maximum possible variability through polyploidization in the existing acid lime population.

Neutron star inner crust: reduction of shear modulus by nuclei finite size effect

ABSTRACT The elasticity of neutron star crust is important for adequate interpretation of observations. To describe elastic properties one should rely on theoretical models. The most widely used is Coulomb crystal model (system of point-like charges on neutralizing uniform background), in some works it is corrected for electron screening. These models neglect finite size of nuclei. This approximation is well justified except for the innermost crustal layers, where nuclei size becomes comparable with the inter-nuclear spacing. Still, even in those dense layers it seems reasonable to apply the Coulomb crystal result, if one assumes that nuclei are spherically symmetric: Coulomb interaction between them should be the same as interaction between point-like charges. This argument is indeed correct; however, as we point here, shear of crustal lattice generates (microscopic) quadrupole electrostatic potential in a vicinity of lattice cites, which induces deformation on the nuclei. We analyse this problem analytically within compressible liquid drop model. In particular, for ground state crust composition the effective shear modulus is reduced for a factor of $1-u^{5/3}/(2+3\, u-4\, u^{1/3})$, where u is the ratio of the nuclei volume to the volume of the cell. This result is universal, i.e. it does not depend on the applied nucleon interaction model within applied approach. For the innermost layers of inner crust u ∼ 0.2 leading to reduction of the shear modulus by $\sim 25{{\ \rm per\ cent}}$, which can be important for correct interpretation of quasi-periodic oscillations in the tails of magnetar flares.

Melting temperature, critical nucleus size, and interfacial free energy in single FCC metals — A Molecular Dynamics study of liquid–solid phase equilibria

Molecular dynamics simulations in the isobaric–isenthalpic ensemble are used to derive various important parameters related to nucleation from the melt. In particular, by using results from liquid–solid phase equilibria, we present a simple, yet reliable, approach to extract melting temperature, critical nucleus size, and liquid–solid interfacial free energy for six different embedded atom FCC systems. Our approach is based on the fundamental thermodynamic relation given by the Gibbs–Thomson equation that uses the heat released during solidification to drive growth of the solid phase until thermodynamic equilibrium is achieved. Equilibrium between the liquid and solid phases is identified by a steady-state evolution in the temperature of the two-phase system.

A general relation between the largest nucleus and all nuclei distributions for free energy calculations.

Prediction of nucleation rates in first order phase transitions requires the knowledge of the barrier associated with the free energy profile W. Molecular simulations offer a direct route through W = -kT ln pa, where k is Boltzmann's constant, T is temperature, and pa is the probability distribution of the size of any nucleus. However, in practice, the extremely scarce spontaneous occurrence of large nuclei impedes the full determination of pa, and a numerical bias must be introduced, which is generally done on the size of the largest nucleus in the system, leading to the probability size distribution of the largest nucleus pl. Although pl is known to be system size dependent, unlike pa, it has extensively been used as an approximation for pa. This communication demonstrates an improved relation between pa and pl, which cures this approximation and allows an accurate calculation of free energy barriers from biased simulations.

Ligancy effects on nucleation kinetics.

Nucleation of particles into crystalline structures can be observed in a wide range of systems from metallic and metal-organic compounds to colloidal and polymeric patch particles. Here, we perform kinetic Monte Carlo simulations to study the nucleation kinetics of particles with different ligancies z at constant supersaturation s. This approach allows one to determine several physico-chemical quantities as a function of s, including the growth probability P(n), the critical nucleus size n*, and the stationary nucleation rate Js. Our numerical results are rationalized in terms of a self-consistent nucleation theory where both n* and Js present a non-trivial dependence on s, but which can be determined from the values of effective z-dependent parameters.

Chromosome Conformation Capture for Large Genomes.

The gigantic 32Gb Axolotl genome inspires fascinating questions such as: how such a big genome is organized and packed in nuclei and how regulation of gene transcription can happen over such large genomic distances. Currently, there are many technical challenges when we investigate chromatin architecture in axolotl. For example, probing promoter-enhancer interactions in such a large genome. Chromatin capture methods (e.g., Chromatin Conformation Capture) have been used in a variety of species. The large size of the axolotl nuclei and its genome requires the adaptation of such methods. Here, we describe a detailed protocol for high-throughput genome-wide conformation capture (Hi-C) using axolotl limb cells. This Hi-C library preparation protocol can also be used to prepare libraries from other nonmodel organisms such as Lungfish and Cephalopods. We believe that our protocol could be useful for a variety of animal systems including other salamanders.

Physical properties of aqueous solutions of 1-propanol near its pequliar point

The work is devoted do the investigation of ultrasound absorption in aqueous solutions of 1- and 2-propanols near their peculiar points. It is assumed that the anomalous ultrasound absorption is caused by the formation of unstable nuclei of a new phase. It is noted, that the concentrations xp(MLS) and xp(US), where the intensities of molecular light scattering and ultrasound absorption take their maxima respectively as well as the point where the concentration curves for differ temperatures intersect are close to each other. A theoretical model for the ultrasound absorption by a nucleus is constructed. The characteristic size of nucleus and the typical time decay for its radial vibrations are estimated. The behavior of the ultrasound absorption coefficient is analyzed on resonance frequencies (f∼10 MHz) and ones removed from them (f≫10MHz). All characteristic experimental peculiarities of the resonance and classic absorption are reproduced with satisfactory accuracy in the framework of the model proposed.

Cage recognition algorithms of clathrate hydrate and their applications

Clathrate hydrates have diverse significant applications in many research areas including natural energy source, carbon dioxide sequestration, gas storage, oil development and so on. However, many fundamental questions concerning clathrate hydrate formation and deformation still remain. Due to the time and space scales involved in these processes, it is challenging to study these questions by experiments but can be accessible by molecular dynamic simulations. Therefore, the cage recognition algorithm of clathrate hydrate is essentially important. In this review, we summarize the existing hydrate cage structure identification algorithms and specifically describe their recognition principal and specialty. Then we present the application of these algorithms, which extracted various dynamic and thermal dynamic information from the molecular dynamic simulation trajectories of clathrate hydrate, including nucleation mechanism, nucleation pathways, hydrate nucleation rates, critical nucleus size and micro/nano-mechanical property. It’s hoped that this review can provide a unified picture and guidance for future work on clathrate hydrate systems and their structure recognition algorithms.

Effects of finite sizes of atomic nuclei on shear modulus and torsional oscillations in neutron stars

ABSTRACT The shear modulus of neutron star matter is one of the important properties used for determining torsional oscillations in neutron stars. We take into account the effects of finite sizes of spherical nuclei on the shear modulus and examine the frequencies of crustal torsional oscillations. The shear modulus decreases owing to the finite-size effect, which in turn decreases the frequencies of torsional oscillations. In particular, the finite-size effect becomes more crucial for oscillations with a larger azimuthal quantum number and for neutron star models with a weaker density dependence of nuclear symmetry energy. In practice, when one identifies quasi-periodic oscillations from a neutron star, where magnetic effects are negligible, with crustal torsional oscillations, the finite-size effect can be more significant at frequencies higher than ∼100 Hz.

Cynara Scolymus (Artichoke) Improves Liver Regeneration after Partial Liver Resection in Rats

Objective: Liver regeneration is necessary to restore hepatic mass and functional capacity after partial hepatectomy (PH). Cynara scolymus (CS) is a pharmacologically important plant that contains phenolic acids and flavonoids, and experimental studies have indicated that it has antioxidant and hepatoprotective effects. The aim of this study was to investigate the role of CS in liver regeneration after PH in rats. 
 Methods: A total of 36 Wistar albino rats weighing 280.5 ± 18.6 g were used. CS leaf extract was administered after partial hepatectomy. The rats were sacrificed at postoperative day 14, and the histological changes were assessed. The mitotic index (MI), nucleus size, hepatocyte size, and binucleation rate (BR) of hepatocytes were assessed using hematoxylin-eosin (H&E) staining. 
 Results: The rats that received CS extract had significant differences in liver regeneration markers, including the hepatocyte size, mitotic index, and Ki-67 proliferation index (p

H&E-like staining of OCT images of human skin via generative adversarial network

Noninvasive and high-speed optical coherence tomography (OCT) systems have been widely deployed for daily clinical uses. High-resolution OCTs are advancing rapidly; however, grey-level OCT images are not easy to read for pathologists due to the lack of diagnosis specificity compared with hematoxylin and eosin (H&E) stained images. This work presents an OCT to H&E image translation model to convert the OCT images to H&E-like stained images using unpaired OCT and H&E datasets. “H&E like” means the stratum corneum (SC) boundary and the dermal-epidermal junction (DEJ) of the OCT and the translated images are consistent. Pre-trained segmentation models for the DEJ and the SC are exploited to enhance the performance of anatomical image translation and reduce the DEJ and SC lower boundary errors to ±2.3 and ±1.7 μm, respectively. A pre-trained VGG16 network extracts the features of the nuclei. Pearson's correlation coefficient of the nuclei location and size consistency is 84% ± 1%. As a result, in vivo medical image translation accuracy with cellular resolution was achieved.

Sleep duration is associated with Caudate volume and executive function.

The ineligible role of the caudate nucleus in sleep has been implicated. Previous literature showed that the caudate volume is associated with longer habitual sleep duration in older adults. However, the association between sleep duration and caudate volume remains unknown in the younger population. In this study, we examined the caudate volume in youth to older adults (10 to 85 years old) with a greater sample size (N = 464). The volumetric size of the caudate nucleus showed significantly positive association with habitual sleep duration, especially in younger population. Sleep duration showed a significant association with executive function performance. However, caudate volume did not significantly predict executive function. Our results suggested that sleep duration is associated with the caudate volume and executive function. It is also suggested that there are some external mechanisms that modulate executive function which prevent the caudate-sleep relation's effect on executive function.

Nucleus size and its effect on nucleosome stability in living cells

DNA architectural proteins play a major role in organization of chromosomal DNA in living cells by packaging it into chromatin, whose spatial conformation is determined by an intricate interplay between the DNA-binding properties of architectural proteins and physical constraints applied to the DNA by a tight nuclear space. Yet, the exact effects of the nucleus size on DNA-protein interactions and chromatin structure currently remain obscure. Furthermore, there is even no clear understanding of molecular mechanisms responsible for the nucleus size regulation in living cells. To find answers to these questions, we developed a general theoretical framework based on a combination of polymer field theory and transfer-matrix calculations, which showed that the nucleus size is mainly determined by the difference between the surface tensions of the nuclear envelope and the endoplasmic reticulum membrane as well as the osmotic pressure exerted by cytosolic macromolecules on the nucleus. In addition, the model demonstrated that the cell nucleus functions as a piezoelectric element, changing its electrostatic potential in a size-dependent manner. This effect has been found to have a profound impact on stability of nucleosomes, revealing a previously unknown link between the nucleus size and chromatin structure. Overall, our study provides new insights into the molecular mechanisms responsible for regulation of the nucleus size, as well as the potential role of nuclear organization in shaping the cell response to environmental cues.

First record of nucleus migration in premeiotic antherial cells of Saccharum spontaneum L. (Poaceae)

The occurrence of nucleus migration is reported for the first time in a clone (2n = 64) of ‘Thatch’ grass (Saccharum spontaneum L.) of the family Poaceae. Usually, its premeiotic antherial cells are thin walled, uninucleate and without any trace of chromosome individuality. However, the cells of those anthers that had been affected from flood water stress conditions were anucleated to hexanucleated in varying frequencies. Out of 2567 cells analyzed, two and three cells were noticed to be connected to each other through a well-defined cytoplasmic channel. The nuclei were observed at various stages of their migration in interconnected cells. The remaining cells exhibited a mosaic of anucleate to hexanucleate cells in varying frequencies with a dominance of binucleated condition (43.75%). The anucleate ‘ghost’ cells were much smaller in size than the uninucleate, binucleate and multinucleate cells showing insignificant variation among themselves. The anucleate, binucleate and multinucleate cells appeared to be resulted due to nucleus migration through cytoplasmic channels between two cells. The presence of a nucleus in donor cell united with recipient cell having four nuclei of different sizes, diminutive anucleate cell in the neighbourhood of uninucleate/trinucleate cell or connected with cytoplasmic channel/pentanucleate cell, and disorganizing cytoplasmic channel attached with binucleate/ tetranucleate cell witnessed the accomplishment of nucleus migration. This rare phenomenon of nucleus migration seemed to be triggered by flood water induced stress and facilitated by feeble cell wall. The variation in sizes of nuclei in multinucleate cells might be due to the transfer of nucleus/nuclei of different size(s). The prominent features of nucleus migration distinguishing it from the cytomixis have been discussed in detail. The syncytes resulted due to nucleus migration might have generated the pollen grains with different genetic constitution resulting into the origin of new intraspecific aneuploids/ polyploids for better adaptability.

Thermal behavior of Li electrode in all-solid-state batteries and improved performance by temperature modulation

All-solid-state lithium metal batteries (ASSLMBs) hold tremendous promise in electric vehicles and portable electronic devices owing to the remarkably improved safety and energy density. However, the uncontrollable Li dendrites seriously hinder the cycling performance of ASSLMBs, and the fickle environment urgently requires a reliable energy supply over a wide temperature range. Understanding the temperature-dependent behavior of Li metal electrode holds great significance for breaking the bottleneck. Herein, we experimentally and theoretically investigate the temperature-dependent morphological evolution of electrodeposited Li in solid electrolyte from -20 °C to 90 °C. It is found that as temperature increases, nuclei size, nuclei density, structural compactness and growth direction of electrodeposited Li are significantly altered. The thermal effect on Li nucleation and growth is further revealed by molecular dynamics simulations. Based on this, we propose a temperature modulation strategy to improve the cyclability of Li metal electrode. By charging at the optimal temperature, the cycling life and Coulomb efficiency of Li electrode can be simultaneously improved. Our investigation gives valuable insights towards temperature-dependent Li deposition in solid electrolyte and will provide rational guidance for the thermal management of ASSLMBs operated in extreme environments.

Optimization of alternative breeding schemes for the genetic improvement of common Tigray highland sheep in northern Ethiopia

BackgroundGenetic improvement is one of the major means to enhance the productivity of livestock, and well-designed animal genetic improvement schemes are necessary to achieve genetic gains. The objective of the current study was to design an alternative breeding program to improve the productivity of common Tigray highland sheep. Two village- and two central nucleus-based breeding schemes were simulated and evaluated in terms of genetic gain, bio-economic efficiency and operational feasibility.MethodsFour breeding schemes were simulated: scheme 1, a one-tier cooperative village-based breeding scheme, scheme 2, a two-tier cooperative village breeding scheme (dispersed village-based nuclei scheme), scheme 3, a central open nucleus-based scheme with 5% nucleus size; and scheme 4, a three-tier breeding schemes (central open nucleus-based linked with multiplier units). Simulation analyses were performed using the ZPLAN computer program, which is based on a deterministic approach to estimate genetic and economic gains in the breeding programs.ResultsBetween the two village-based breeding schemes, scheme 2 showed higher genetic gain and economic efficiency in the breeding traits analysed than scheme 1. The central nuclei schemes were more efficient than the village breeding schemes. Scheme 3 was the most efficient with a genetic gain in the breeding objective of US $ 1.03 and a profit of US $ 2.73/ewe/year, but operationally it is also the most difficult to implement as it requires a big central nucleus. A central nucleus linked with the village-based nuclei would be a feasible option to overcome the operational difficulties of the conventional central nucleus schemes. If a village-based breeding program is considered it should be the first step in most low-input systems. In this case, scheme 2 is the most efficient.ConclusionsWith some support from the public sector at the outset and a strong collaboration among the stakeholders including smallholders, scheme 4 could lead to substantial genetic gains in the common Tigray highland sheep breed within its habitat that covers large areas of the Tigray region. Therefore, we recommend a long-term breeding program which should include cross-breeding, genomic selection, updated estimates of genetic and economic values for the common Tigray highland sheep breed.