Search

Background: This study utilized quantitative susceptibility mapping (QSM) to evaluate magnetic susceptibility of brain nuclei in Parkinson's disease (PD). Purpose: To explore iron deposition patterns in PD and ascertain if these patterns can distinguish between motor subtypes. Material and Methods: This study enrolled 30 healthy controls and 34 patients with PD categorized mainly into postural instability and gait disorder (PIGD) (n = 12) and tremor dominance (TD) (n = 16). A total of 18 regions of interest were delineated, and a comprehensive classification of nuclei was conducted, including the differentiation of globus pallidus (GP) into its external (GPe) and internal (GPi) segments. All participants underwent brain magnetic resonance imaging. Results: Notable differences in magnetic susceptibility were identified in bilateral substantia nigra pars reticulate (SNr) and substantia nigra pars compacta (SNc) between PD and HC. Significant differences in QSM values of bilateral GPe, SNr, and SNc-R were found between TD and PIGD. The susceptibility values of bilateral putamen (PUT) were positively correlated with MDS-UPDRSIII score and Hoehn–Yahr scale in PD. QSM values of bilateral PUT and SNc-L showed associations with MDS-UPDRSIII score in TD. QSM values showed associations with MDS-UPDRSIII in bilateral PUT and Hoehn–Yahr scale in PUT-L and TH-L in PIGD. Conclusion: Pathologic iron deposition exhibits variability across nuclei of PD, with age also influencing this distribution. SN may be meaningful in identifying different subtypes of PD, such as differentiating PD from HC in the future. [ABSTRACT FROM AUTHOR]

We consider the nuclear shadowing in deep inelastic scattering (DIS) corresponding to kinematic regions accessible by future experiments at electron–ion colliders. The gluon distribution at small x is obtained using an improved dipole model which depends on the impact parameter for the atomic nucleus and is compared with nCETQ15 parametrisation group. The nuclear shadowing at small x is defined within the colour dipole formalism with respect to the mass number A. Its behaviour is predicted for light nuclei in a wide range of the impact parameter b and the transverse dipole size r. The nuclear saturation can be observed at large-r (small μ 2 ). The behaviour of the nuclear ratio σ dip A / σ 0 using our model is similar to the Golec–Biernat–W u ¨ sthoff (GBW) model in a wide range of r for light and heavy nuclei at small x. [ABSTRACT FROM AUTHOR]

Accurately identifying and analyzing nuclei is pivotal for both the diagnosis and examination of cancer. However, the complexity of this task arises due to the presence of overlapping and cluttered nuclei with blurred boundaries, variations in nuclei sizes and shapes, and an imbalance in the available datasets. Although current methods utilize region proposal techniques and feature encoding frameworks, but they often fail to precisely identify occluded nuclei instances. We propose a model named AFINITI, which is both simple, efficient, achieves high accuracy, recognizes instance boundaries cluttered and overlapping nuclei, and addresses class imbalance issues. Our approach utilizes nuclei pixel positional information and a novel loss function to yield accurate class information for each nuclei. Our network features a lightweight, attention-aware feature fusion architecture with separate instance probability, shape radial estimator, and classification heads. We use a compound classification loss function to assign a weighted loss to each class according to its occurrence frequency, thereby addressing the class imbalance issues. The AFINITI model outperforms current leading networks across eight major publicly available nuclei segmentation datasets achieving up to an 8% increase in Dice Similarity Coefficient (DSc) and a 17% increase in Panoptic Quality (PQ) compared to existing techniques demonstrating its effectiveness and potential for clinical applications. The source code and the weights of the trained model have been released to the public and can be accessed at: https://github.com/Vision-At-SEECS/AF-Net. [ABSTRACT FROM AUTHOR]

In this study, we introduced a novel dual‐laser multi‐color imaging system. Integrated with a multi‐channel filter wheel, this system compared three spectral decontamination algorithms (nonnegative matrix factorization [NMF], RCAN, and PICASSO) showcasing its efficacy in achieving four‐color imaging with only two laser sources. Combined with a reliable image reconstruction algorithm, the spatial resolution of four channels super‐resolution four‐color images reached 130, 125, 133, and 132 nm, respectively. Lipid droplets, mitochondria, lysosomes, and nuclei from the mouse hepatocytes (AML12), human neuroblastoma cells (SH‐SY5Y), mouse hippocampal neuronal cells (HT‐22), and immortalized murine bone marrow‐derived macrophages were imaged. At the same time, the chromatin condensation, nuclear contraction, DNA fragmentation, apoptotic body formation, as well as the fusion of Mito and Lyso involved in mitochondrial autophagy were observed in HT‐22 and SH‐SY5Y cells suffering oxidative stress. Our multi‐color SIM imaging system establishes a powerful platform for dynamic organelle studies and other high‐resolution investigations in live cells. [ABSTRACT FROM AUTHOR]

The microspectrophotometer/microspectrofluorimeter was used to find the azulenes on the intact surface of 30 allelopathic and medicinal plant species growing in moderate or drought climatic conditions. Here in the maxima range of 580-620 nm, peculiar to blue pigments (azulenes), were clearly observed. The pigments were found in blue or silver leaves (needles) or plant parts (petioles, flowers and pollen). The peaks 590-610 nm, characteristic to azulenes were also observed in the absorbance spectra of ethanolic 10 min -extracts from the leaf surface, and 24 h - extracts from whole leaves. Among plants studied, the pigments were first observed in 14 terrestrial species (Anthriscus sylvestris, Lolium perenne, Petasites spurius, Phlomis tuberosa, Crambe maritima, Seseli gummiferum, Filipendula ulmaria, Echinocystis lobata, Colutea cilica, Rhus coriaria, Quercus pubescens, Pinus brutia and 2 algae (Chara vulgaris and Spirogyra sp.) use of spectral methods is recommended to search new azulene-containing species for pharmacy, agriculture and ecology. [ABSTRACT FROM AUTHOR]

Stilbonematinae are nematodes commonly found in shallow marine sands. They are overgrown by a genus- and species-specific coat of chemoautotrophic sulphur-oxidizing ectosymbiotic bacteria which profit from the vertical migration of their hosts through the chemocline by alternately gaining access to oxidizing and reducing chemical species, while in return, the host feeds on its symbionts. The subfamily exhibits a large morphological variability; e.g. the anterior pharynx is cylindrical in genera possessing a voluminous coat, but species with a bacterial monolayer possess a distinctly swollen corpus and therefore a tripartite pharynx. Since 18S-based phylogenetic analyses do not show close relationships between corpus-bearing species, we investigated the pharynx morphology using phalloidin staining in combination with confocal laser scanning microscopy, transmission electron microscopy and light microscopy in order to assess an independent evolution. The class-wide stable position of the subventral pharynx ampullae was used as a morphological marker. Ampullae are positioned at the anterior-most end of the isthmus in Cyathorobbea, further posterior in Catanema and Robbea and inside the corpus in Laxus oneistus. We therefore conclude an independent evolution of corpus enlargements within Stilbonematinae. This further suggests that pharynx morphology is driven by the volume of the symbiotic bacterial coat rather than phylogeny. Based on an existing mathematical model, an enlarged corpus should enable its bearer to ingest food in smaller quantities, in gourmet style, whereas a cylindrical pharynx would restrict its bearer to ancestral gourmand feeding. A review of pharynx types of Nematoda showed that the Stilbonematinae pharynx is substantially different compared to other tripartite pharynges. The lack of pharyngeal tubes and valves, the undivided corpus and evenly distributed nuclei in the isthmus warrant the definition of the "stilbonematoid" three-part pharynx. [ABSTRACT FROM AUTHOR]

Saccharomyces cerevisiae is a genetically tractable, affordable, and extensively documented eukaryotic single-cell model organism. This budding yeast is amenable for the development of genetic and biochemical experiments and is frequently used to investigate the function, activity, and mechanism of mammalian proteins. However, yeast contains a cell wall that hinders select assays including organelle isolation. Lytic enzymes, with Zymolyase as the most effective and frequently used tool, are utilized to weaken the yeast cell wall resulting in yeast spheroplasts. Spheroplasts are easily lysed by, for example, osmotic-shock conditions to isolate yeast nuclei or mitochondria. However, during our studies of the DNA repair enzyme tyrosyl-DNA phosphodiesterase I (Tdp1), we encountered a negative effect of Zymolyase. We observed that Zymolyase treatment affected the steady-state protein levels of Tdp1. This was revealed by inconsistencies in technical and biological replicate lysates of plasmid-born galactose-induced expression of Tdp1. This off-target effect of Zymolyase is rarely discussed in articles and affects a select number of intracellular proteins, including transcription factors and assays such as chromatin immunoprecipitations. Following extensive troubleshooting, we concluded that the culprit is the Ser-protease, Zymolyase B, component of the Zymolyase enzyme mixture that causes the degradation of Tdp1. In this study, we report the protocols we have used, and our final protocol with an easy, affordable adaptation to any assay/protocol involving Zymolyase. [ABSTRACT FROM AUTHOR]

Recent research on algebraic models of quasi-Nelson logic has brought new attention to a number of classes of algebras which result from enriching (subreducts of) Heyting algebras with a special modal operator, known in the literature as a nucleus. Among these various algebraic structures, for which we employ the umbrella term intuitionistic modal algebras, some have been studied since at least the 1970s, usually within the framework of topology and sheaf theory. Others may seem more exotic, for their primitive operations arise from algebraic terms of the intuitionistic modal language which have not been previously considered. We shall for instance investigate the variety of weak implicative semilattices, whose members are (non-necessarily distributive) meet semilattices endowed with a nucleus and an implication operation which is not a relative pseudo-complement but satisfies the postulates of Celani and Jansana's strict implication. For each of these new classes of algebras we establish a representation and a topological duality which generalize the known ones for Heyting algebras enriched with a nucleus. [ABSTRACT FROM AUTHOR]

Background: Neuroanatomy is considered one of the most challenging parts of anatomy curriculum and the complexity in understanding neuroanatomy generates from the lack of a 3-dimensional view of the structures. Since everything appears grey and white and is difficult to differentiate the various structures in a cross section of brain, staining aids in the visual interpretation and retention. There are various staining methods employed such as Mulligan's method, Alston's method, Prussian blue reaction method, however the results obtained by Alston's method was the best as gathered from previous literature. Material and methods: The study was conducted in the department of Anatomy, formalin fixed brain slices measuring 10 mm thickness were stained using Alston's method. 250 medical students of the first professional year were demonstrated features such as the internal capsule, caudate nucleus, lentiform and thalamus in the stained and unstained transverse sections of cerebrum during their neuroanatomy practical sessions. Following which a feedback was collected regarding both the specimens using Microsoft Forms. Results: There was a positive feedback from the students with 83 % of them preferring the stained over the unstained section. Excerpts from the open ended question where all in favour of the stained sections -“much easier to see and identify the parts in the stained section because of the clear distinction between white and grey matter”. Conclusions: Macroscopic staining of sections of the brain using Alston's method could be implemented as a valuable method for effective teaching of neuroanatomy since students appreciated the structures better in the stained sections which enhanced their retention of neuroanatomy. Since Alston stain produces the least shrinkage, these stained sections could be utilized for research studies and such specimens could also be plastinated.

Abstract Changes in myonuclear architecture and positioning are associated with exercise adaptations and ageing. However, data on the positioning and number of myonuclei following exercise are inconsistent. Additionally, whether myonuclear domains (MNDs; i.e., the theoretical volume of cytoplasm within which a myonucleus is responsible for transcribing DNA) and myonuclear positioning are altered with age remains unclear. The aim of this investigation was to investigate relationships between age and activity status and myonuclear domains and positioning. Vastus lateralis muscle biopsies from younger endurance‐trained (YT) and older endurance‐trained (OT) individuals were compared with age‐matched untrained counterparts (YU and OU; OU samples were acquired during surgical operation). Serial, optical z‐slices were acquired throughout isolated muscle fibres and analysed to give three‐dimensional coordinates for myonuclei and muscle fibre dimensions. The mean cross‐sectional area (CSA) of muscle fibres from OU individuals was 33%–53% smaller compared with the other groups. The number of nuclei relative to fibre CSA was 90% greater in OU compared with YU muscle fibres. Additionally, scaling of MND volume with fibre size was altered in older untrained individuals. The myonuclear arrangement, in contrast, was similar across groups. Fibre CSA and most myonuclear parameters were significantly associated with age in untrained individuals, but not in trained individuals. These data indicate that regular endurance exercise throughout the lifespan might better preserve the size of muscle fibres in older age and maintain the relationship between fibre size and MND volumes. Inactivity, however, might result in reduced muscle fibre size and altered myonuclear parameters.

The microRNAs are endogenous, regulating gene expression either at the DNA or RNA level. Despite the availability of extensive studies on microRNA generation in plants, reports on their abundance, biogenesis, and consequent gene regulation in plant organelles remain naïve. Building on previous studies involving pre-miRNA sequencing in Abelmoschus esculentus , we demonstrated that three putative microRNAs were raised from the chloroplast genome. In the current study, we have characterized the genesis of these three microRNAs through a combination of bioinformatics and experimental approaches. The gene sequence for a miRNA, designated as AecpmiRNA1 ( A. esculentus chloroplast miRNA), is potentially located in both the genomic DNA, i.e., nuclear and chloroplast genome. In contrast, the gene sequences for the other two miRNAs (AecpmiRNA2 and AecpmiRNA3) are exclusively present in the chloroplast genome. Target prediction revealed many potential mRNAs as targets for AecpmiRNAs. Further analysis using 5ʹ RACE-PCR determined the AecpmiRNA3 binding and cleavage site at the photosystem II protein N (psbN). These results indicate that AecpmiRNAs are generated from the chloroplast genome, possessing the potential to regulate mRNAs arising from chloroplast gene(s). On the other side, the possibility of nuclear genome-derived mRNA regulation by AecpmiRNAs cannot be ruled out.

Ni–Al films produced by resistive thermal evaporation using a VUP-5 vacuum station are studied. The basic stages in film synthesis are described. The wavefront velocity in synthesis is determined, along with the radial growth rate of the nuclei (islands) formed. The grain size in the surface is investigated. Fourier analysis provides information regarding the structural properties of the surface. The electrical conductivity of the thin metallic film is determined. [ABSTRACT FROM AUTHOR]

Changes in myonuclear architecture and positioning are associated with exercise adaptations and ageing. However, data on the positioning and number of myonuclei following exercise are inconsistent. Additionally, whether myonuclear domains (MNDs; i.e., the theoretical volume of cytoplasm within which a myonucleus is responsible for transcribing DNA) and myonuclear positioning are altered with age remains unclear. The aim of this investigation was to investigate relationships between age and activity status and myonuclear domains and positioning. Vastus lateralis muscle biopsies from younger endurance‐trained (YT) and older endurance‐trained (OT) individuals were compared with age‐matched untrained counterparts (YU and OU; OU samples were acquired during surgical operation). Serial, optical z‐slices were acquired throughout isolated muscle fibres and analysed to give three‐dimensional coordinates for myonuclei and muscle fibre dimensions. The mean cross‐sectional area (CSA) of muscle fibres from OU individuals was 33%–53% smaller compared with the other groups. The number of nuclei relative to fibre CSA was 90% greater in OU compared with YU muscle fibres. Additionally, scaling of MND volume with fibre size was altered in older untrained individuals. The myonuclear arrangement, in contrast, was similar across groups. Fibre CSA and most myonuclear parameters were significantly associated with age in untrained individuals, but not in trained individuals. These data indicate that regular endurance exercise throughout the lifespan might better preserve the size of muscle fibres in older age and maintain the relationship between fibre size and MND volumes. Inactivity, however, might result in reduced muscle fibre size and altered myonuclear parameters. What is the central question of the study?How do endurance exercise and the ageing process affect the positioning and number of myonuclei within muscle fibres?What are the main findings and their importance?There was reduced muscle fibre size, with smaller myonuclear domains and altered myonuclear domain scaling in older, untrained individuals. However, older trained individuals maintained similar muscle and myonuclear characteristics to younger trained individuals. This suggests that inactivity, rather than ageing, influences muscle fibre and myonuclear characteristics. These observations suggest that consistent endurance exercise over one's lifetime might help to preserve muscle fibre size and quality and myonuclear arrangement into old age. [ABSTRACT FROM AUTHOR]

In the United States, 1 in 10 infants are born preterm. The majority of neonatal deaths and nearly a third of infant deaths are linked to preterm birth. Preterm birth is initiated when the quiescent state of the uterus ends prematurely, leading to contractions and parturition beginning as early as 32 weeks, though the origins are not well understood. To enable research and discovery of therapeutics with potential to better address preterm birth, the capability to study isolated cell processes of pregnant uterine tissue in vitro is needed. Our development of an in vitro model of the myometrium utilizing human uterine smooth muscle cells (uSMCs) responsible for contractions provides a methodology to examine cellular mechanisms of late-stage pregnancy potentially involved in preterm birth. We discuss culture of uSMCs on a flexible polydimethylsiloxane (PDMS) substrate functionalized with cationic poly-l-lysine (PLL), followed by extracellular matrix (ECM) protein coating. Previous work exploring uSMC behavior on PDMS substrates have utilized collagen-I coatings, however, we demonstrated the first exploration of human uSMC response to strain on fibronectin-coated flexible membranes, importantly reflecting the significant increase of fibronectin content found in the myometrial ECM during late-stage pregnancy. Using the model we developed, we conducted proof-of-concept studies to investigate the impact of substrate strain on uSMC cell morphology and gene expression. It was found that PLL and varied ECM protein coatings (collagen I, collagen III, and fibronectin) altered cell nuclei morphology and density on PDMS substrates. Additionally, varied strain rates applied to uSMC substrates significantly impacted uSMC gene expression of IL-6, a cytokine associated with instances of preterm labor. These results suggest that both surface and mechanical properties of in vitro systems impact primary human uSMC phenotype and offer uSMC culture methodologies that can be utilized to further the understanding of cellular pathways involved in the uterus under mechanical load.

A comparison has been made between theoretical results and the experimental data for different nuclei (even-even) that possess the same mass number A = 44 and which have close values of the experimental deformation parameter such as 16S44, 18Ar44, 20Ca44 and 22Ti44. The core-polarization effects and model space were adopted through the inclusion of effective charges. Transition probability B(E2), theoretical deformation parameters, and theoretical intrinsic quadruple moments were calculated using two different interactions for each case, the first case the hasp interaction for nuclei in the sd shell, and the fpd6 interaction for nuclei in the fp shell, the second case the vpnp interaction for nuclei in the sd shell, and the kb3 interaction for nuclei in the fp shell, as well as adopted to different effective charges, such as Bohr and Mottelson effective charges, standard effective charges, and the effective charges from program NuShellX. The theoretical results of the transition probability B(E2), deformations parameters, and intrinsic quadruple moments were compared and found to be close to the experimental values for these nuclei.

The present study explores the symmetries associated with the cluster structure of light nuclei and draws the connection between solutions of the Schrödinger equation for the harmonic oscillator and the quasi-crystalline arrangements of α-particles, which gives rise to a series of collective behaviors. The double-center harmonic oscillator is used to formulate the collisions of two nuclei described by harmonic oscillator solutions and traces out the evolution of the cluster structure in the dynamics of the collision process and demonstrates that the symmetries are preserved in this process. The connection between this study and stellar nucleosynthesis is described. [ABSTRACT FROM AUTHOR]

The microRNAs are endogenous, regulating gene expression either at the DNA or RNA level. Despite the availability of extensive studies on microRNA generation in plants, reports on their abundance, biogenesis, and consequent gene regulation in plant organelles remain naVve. Building on previous studies involving pre-miRNA sequencing in Abelmoschus esculentus, we demonstrated that three putative microRNAs were raised from the chloroplast genome. In the current study, we have characterized the genesis of these three microRNAs through a combination of bioinformatics and experimental approaches. The gene sequence for a miRNA, designated as AecpmiRNA1 (A. esculentus chloroplast miRNA), is potentially located in both the genomic DNA, i.e., nuclear and chloroplast genome. In contrast, the gene sequences for the other two miRNAs (AecpmiRNA2 and AecpmiRNA3) are exclusively present in the chloroplast genome. Target prediction revealed many potential mRNAs as targets for AecpmiRNAs. Further analysis using 5N RACE-PCR determined the AecpmiRNA3 binding and cleavage site at the photosystem II protein N (psbN). These results indicate that AecpmiRNAs are generated from the chloroplast genome, possessing the potential to regulate mRNAs arising from chloroplast gene(s). On the other side, the possibility of nuclear genome-derived mRNA regulation by AecpmiRNAs cannot be ruled out. [ABSTRACT FROM AUTHOR]

In Ukraine, among other industries, beekeeping occupies an important place. This fact is facilitated by the developed agricultural direction of the country and the high percentage of cultivation of entomophilic crops. However, despite the broad prospects for development and transition to an industrial basis, the beekeeping industry of Ukraine is represented, in the vast majority, by relatively small farms. One of the reasons for the low development of industrial honey production in Ukraine is the high costs of organizing an industrial apiary, which include the purchase of modern equipment for quick and efficient opening of frames, special equipment for pumping honey, the construction of separate premises for the honey pumping workshop, as well as the constant updating of equipment, such as new hives and frames, and the purchase of breeding queens. Another significant problem is the death of bee colonies due to a variety of diseases, including Varroa mite infestation. The use of pesticides to combat diseases and pests of agricultural plants and forest lands contributes to its negative share. An effective and cost-effective way to expand and increase the productivity of the apiary is the formation of bee packages using high-quality breeding queens. The use of early fertile queens makes it possible to form a strong full-fledged family and make full use of the honey collection this year. The effectiveness of the use of different types of nuclei and methods of replanting fertile queen bees in the formation of bee packages was checked. The study was carried out on bees of the Ukrainian steppe breed. The best results in terms of the percentage of fertile queens and the cost of queens per fertile were obtained using a full-size nucleus for 3 standard frames in a 16-frame bed. However, the same method required a larger number (10 times) of worker bees compared to the micronucleus. With traditional replanting using the Titov cage, the share of accepted queen bees is 90 %, and the maximum rate of reception of queen bees in packages is recorded when using the fourth method of transplantation. So, when transferring a queen with a frame of printed brood and young worker bees, the relative proportion of accepted queen bees was 98 %. Therefore, the traditional method can be considered optimal in terms of indicators: reception, manufacturability, costs. [ABSTRACT FROM AUTHOR]

The work presented in this paper represents a preliminary study on the performance of the new Silicon tracker layer, Layer 0 (L0), that will be installed on top of the Alpha Magnetic Spectrometer (AMS-02), at the end of 2024. AMS-02 is a cosmic ray (CR) detector that has been operating on the International Space Station (ISS) since May 2011. Thanks to its nine-layer Silicon tracker, this apparatus can perform high-energy CR measurements with an unprecedented level of statistics and precision. However, high-Z (Z ≥ 15) CR nuclei statistics is strongly affected by fragmentation along the detector: with the installation of the new Silicon layer, it will be possible to achieve new unique high-energy (TeV region) measurements of those nuclei along with increased statistics for all nuclei up to Zinc. To achieve this, a Silicon ladder prototype, which will be part of the final Silicon layer, was exposed to an ion test beam at the super-proton synchrotron (SPS) of CERN to characterize its charge resolution and the readout electronics. Preliminary results have shown a charge resolution of 10 % for nuclei up to Z = 7. [ABSTRACT FROM AUTHOR]

DiamondTM Nucleic Acid Dye (DD) has been evaluated for visualizing DNA material on various evidence types, including nuclei in plucked hair roots. While plucked hair roots exhibit a rapid DNA visualization process, shed hairs, even when stained with DD, pose challenges due to the lack of cell nuclei. In the absence of clear cell nuclei, the sole indicator of DNA presence is the fluorescent signal from DD bound to DNA. This study aimed to assess the stability of the fluorescent signal in shed hairs, revealing a rapid decline within 2–3 min post-staining, likely attributed to the cell-free nature of the DNA present on the hair root. Consequently, immediate microscopic visualization and imaging post-staining are crucial during shed hair examination. [ABSTRACT FROM AUTHOR]

The hippocampus is a brain region associated with memory, learning and spatial navigation, its aging-related dysfunction is a common sign of Alzheimer's disease. Pig is a good model for human neurodegenerative disease, but our understanding of the regulatory program of the pig hippocampus and its cross-species conservation in humans remains limited. Here, we profiled chromatin accessibility in 33,409 high-quality nuclei and gene expression in 8,122 high-quality nuclei of the pig hippocampus at four postnatal stages. We identified 510,908 accessible chromatin regions (ACRs) in 12 major cell types, among which progenitor cells such as neuroblasts and oligodendrocyte progenitor cells showed a dynamic decrease from early to later developmental stages. We revealed significant enrichment of transposable elements in cell type-specific ACRs, particularly in neuroblasts. We identified oligodendrocytes as the most prominent cell type with the greatest number of genes that showed significant changes during the development. We identified ACRs and key transcription factors underlying the trajectory of neurogenesis (such as POU3F3 and EGR1) and oligodendrocyte differentiation (RXRA and FOXO6). We examined 27 Alzheimer's disease-related genes in our data and found that 15 showed cell type-specific activity (TREM2, RIN3 and CLU), and 15 genes displayed age-associated dynamic activity (BIN1, RABEP1 and APOE). We intersected our data with human genome-wide association study results to detect neurological disease-associated cell types. The present study provides a single nucleus-accessible chromatin landscape of the pig hippocampus at different developmental stages and is helpful for the exploration of pigs as a biomedical model in human neurodegenerative diseases. [ABSTRACT FROM AUTHOR]

A comparison has been made between theoretical results and the experimental data for different nuclei (even-even) that possess the same mass number A = 44 and which have close values of the experimental deformation parameter such as 16S 44, 18Ar44, 20Ca44 and 22Ti44. The core-polarization effects and model space were adopted through the inclusion of effective charges. Transition probability B(E2), theoretical deformation parameters, and theoretical intrinsic quadrupole moments were calculated using two different interactions for each case, the first case the hasp interaction for nuclei in the sd shell, and the fpd6 interaction for nuclei in the fp shell, the second case the vpnp interaction for nuclei in the sd shell, and the kb3 interaction for nuclei in the fp shell, as well as adopted to different effective charges, such as Bohr and Mottelson effective charges, standard effective charges, and the effective charges from program NuShellX. The theoretical results of the transition probability B(E2), deformations parameters, and intrinsic quadrupole moments were compared and found to be close to the experimental values for these nuclei. [ABSTRACT FROM AUTHOR]

The brainstem is a site of early pathology in several neurodegenerative diseases. The overall goal of this project was (a) To develop a method to segment internal brainstem structures from MP2RAGE derived images. (b) To compare the segmentations at 3 and 7 T. (c) To investigate age effects on intensities and segmentations. MP2RAGE derived T1 weighted images (UNI) and T1 relaxation maps (T1map) were obtained from two public data sets (LEMON: 50 3 T data sets, ATAG: 46 7 T data sets). The UNI and T1map images were rescaled using a linear scaling procedure and a ratio (RATIO) image calculated. The brainstem was extracted and k-mean clustering used to identify six intensity clusters from the UNI, T1map and RATIO at 3 and 7 T. Nonlinear diffeomorphic mapping was used to warp the six intensity clusters in subject space into a common space to generate probabilistic group averages/priors that were used to inform the final probabilistic segmentations at the single subject level for each field strength. The six clusters corresponded to six brainstem tissue types (three gray matter clusters and two white matter clusters and one csf/tissue boundary cluster). The quantitative comparison of the 3 and 7 T probabilistic averages showed subtle differences that affected the localization of age-associated brainstem volume losses. The segmentation approach presented here identified the same brainstem gray and white matter structures at both field strengths. Further studies are necessary to investigate how resolution and field strength contribute to the subtle differences observed at the two field strengths.

The production of nuclei and hypernuclei is of interest for experimental and theoretical studies: it is a big question how such weakly bound objects survive in a hot, dense environment and which new insights on the heavy-ion collisions dynamics they can bring us. We present the results on the hypernuclei feasibility study for the flagship Nuclotron-based Ion Collider fAcility (NICA)/Multi-Purpose Detector (MPD) experiment at the Joint Institute for Nuclear Research (JINR) in Dubna using the Parton-Hadron-Quantum-Molecular Dynamics (PHQMD) transport approach and a realistic reconstruction chain.

The elimination of organelles to create the lens organelle-free zone (OFZ) is a macroautophagy/autophagy-dependent mechanism that occurs without causing cell death. This process is essential to the ability of the lens to focus incoming images on the retina, as the presence of these organelles would interfere with lens refraction of light and impair vision. Therefore, organelles are removed from differentiating lens fiber cells during development, their elimination beginning with the non-nuclear organelles in the central lens fiber cells, and expanding over time to the neighboring fiber cells in the lens cortex. The removal of fiber cell nuclei lags behind that of non-nuclear organelles, following the same spatiotemporal patterning. We find that removal of organelles to form the OFZ depends on the induction of autophagy through the inhibition of phosphoinositide 3-kinase (PI3K) signaling. Abbreviation OFZ– organelle-free zone

Examination of tissue biopsy and quantification of the various characteristics of cellular processes are clinical benchmarks in cancer diagnosis. Nuclei and glands instance segmentation greatly assists the high-throughput quantification of cellular process and accurate appraisal of tissue biopsy. It subsequently makes a significant improvement to the computational pathology process for cancer diagnosis, treatment planning, and survival analysis. Recent advancements in the field of computer vision have automated the manual, laborious, and time-consuming histopathological analysis process. Automated image analysis of histopathological images for cells and tissues to trace the entirety of the ultrastructures, has been an active area of research in medical informatics for decades. The developments in computers, microscopy hardware, and the availability of large-scale public datasets have further fastened the development in this field. And the realization that scientific and diagnostic pathology calls for fresh ways to undertake, automated image analysis of histopathological images has captivated contemporary attention. In this survey, 126 papers illustrating the AI-based methods for nuclei and glands instance segmentation published in the last five years (2017–2022) are deeply analyzed, and the limitations of current approaches and the open challenges are discussed. Moreover, the potential future research direction is presented, and the contribution of state-of-the-art methods is summarized. Further, a generalized summary of publicly available datasets and detailed insights on the grand challenges illustrating the top-performing methods specific to each challenge is also provided. Besides, we intended to give the reader the current state of existing research and pointers to the future directions in developing methods that can be used in clinical practice enabling improved diagnosis, grading, prognosis, and treatment planning of cancer. To the best of our knowledge, no previous work has reviewed the instance segmentation in histology images focusing on nuclei and glands instance segmentation. [ABSTRACT FROM AUTHOR]

In order to establish a system for extracting nuclei and constructing library of assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) in gramineous plants, the leaves and roots of rice, wheat, and zoysia were used as the research materials. The best method to extract nuclei was determined by designing control variable experiments: grinding samples with liquid nitrogen, selecting 1200 x g centrifugal stress for extracting initial nuclei, using ORB buffer twice and SCB buffer to purify nuclei. It was suggested that the extracted nuclei were suitable for the sequencing of transposase accessible chromatin and high-quality sequencing data could be obtained by testing. In summary, an integrated system suitable for gramineous plants to extract nuclei had been established. This method will lay a foundation for obtaining the information of chromatin accessible regions and the regulation of gene expression in gramineous plants. [ABSTRACT FROM AUTHOR]

Single-nucleus RNA sequencing (sNucRNA-seq) is an emerging technology that has been rapidly adopted and demonstrated to be a powerful tool for detailed characterization of each cell- and sub cell-types in complex tissues of higher eukaryotes. sNucRNA-seq has also been used to dissect cell-type-specific transcriptional responses to environmental or developmental signals. In plants, this technology is being utilized to identify cell-type-specific trajectories for the study of several tissue types and important traits, including the single-cell dissection of the genetic determinants regulating plant–microbe interactions. The isolation of high-quality nuclei is one of the prerequisite steps to obtain high-quality sNucRNA-seq results. Although nuclei isolation from several plant tissues is well established, this process is highly troublesome when plant tissues are associated with beneficial or pathogenic microbes. For example, root tissues colonized with rhizobium bacteria (nodules), leaf tissue infected with bacterial or fungal pathogens, or roots infected with nematodes pose critical challenges to the isolation of high-quality nuclei and use for downstream application. Therefore, isolation of microbe-free, high-quality nuclei from plant tissues are necessary to avoid clogging or interference with the microfluidic channel (e.g., 10× Genomics) or particle-templated emulsion that are used in sNucRNA-seq platforms. Here, we developed a simple, effective, and efficient method to isolate high-quality nuclei from soybean roots and root nodules, followed by washing out bacterial contamination. This protocol has been designed to be easily implemented into any lab environment, and it can also be scaled up for use with multiple samples and applicable to a variety of samples with the presence of microbes. We validated this protocol by successfully generating a barcoded library using the 10× Genomics microfluidic platform from tissue subjected to this procedure. This workflow was developed to provide an accessible alternative to instrument-based approaches (e.g., fluorescent cell sorting) and will expand the ability of researchers to perform experiments such as sNucRNA-seq and sNucATAC-seq on inherently heterogeneous plant tissue samples. [ABSTRACT FROM AUTHOR]

The nuclei segmentation of microscopic images is a key pre-requisite for cancerous pathological image analysis. However, an accurate nuclei cell segmentation is a long running major challenge due to the enormous color variability of staining, nuclei shapes, sizes, and clustering of overlapping cells. To address this challenges, we proposed a deep learning model, namely, AlexSegNet which is based upon AlexNet model Encoder-Decoder framework. In Encoder part, it stitches feature maps in the channel dimension to achieve feature fusion and uses a skip structure in Decoder part to combine low- and high-level features to ensure the segmentation effect of the nucleus. At final stage, we have also introduced a stacked network where feature maps are stacks on top of each other. We have used a publically available 2018 Data Science Bowl and Triple Negative Breast Cancer (TNBC) datasets of microscopic nuclei images for this study which comprises of several sample types such as small and large fluorescent, pink, purple, and grayscale tissue samples. Experimental results show that our proposed AlexSegNet achieved a segmentation maximum performance of 91.66% for Data Science Bowl dataset and 66.88% for TNBC dataset. The results are competitive compared to the results of other state-of-the-art models. This model is expected to be useful clinically for technician experts to succeed the analysis of cancer diagnosis into the survival chances of patients. [ABSTRACT FROM AUTHOR]

Confocal microscopy study of musculature and other anatomical structures in whole‐mount preparations of arthropods and some other cuticle‐bearing animals often presents a significant difficulty because the cuticle poses a barrier to fluorescent dyes and their pigmented tissues can cause attenuation of fluorescent signal. This paper describes a simple and inexpensive procedure based on the use of clove oil as a tissue‐clearing, staining, and mounting medium that helps overcome the problem of slow dye penetration and tissue opaqueness and allows muscles and several other organ systems to be visualized by confocal or epifluorescent microscopy. This clove oil‐induced fluorescence (COIF) method relies on the ability of clove oil to accumulate in muscles and some other tissues and become steadily fluorescent if irradiated at 488 nm. For this method, animals were fixed in 70% ethanol or 4% formaldehyde, then dehydrated and mounted in clove oil. Heavily pigmented animals were additionally bleached in hydrogen peroxide prior to the dehydration step. The COIF method showed excellent results in all major groups of arthropods and some mollusks and annelids revealing the three‐dimensional arrangement of muscles, gonads, glands, cellular nuclei and some parts of the nervous and digestive systems. In the other animal groups tested, clove oil stained all tissues making it difficult to observe the anatomical details. The COIF method is advantageous in some respects over other methods such as phalloidin staining because of its tissue penetration and clearing abilities, low cost of the reagents, resistance to photodamage and the possibility of staining museum specimens. [ABSTRACT FROM AUTHOR]

The production of nuclei and hypernuclei is of interest for experimental and theoretical studies: it is a big question how such weakly bound objects survive in a hot, dense environment and which new insights on the heavy-ion collisions dynamics they can bring us. We present the results on the hypernuclei feasibility study for the flagship Nuclotron-based Ion Collider fAcility (NICA)/Multi-Purpose Detector (MPD) experiment at the Joint Institute for Nuclear Research (JINR) in Dubna using the Parton-Hadron-Quantum-Molecular Dynamics (PHQMD) transport approach and a realistic reconstruction chain. [ABSTRACT FROM AUTHOR]