Search

Spatial transcriptomics measures in situ gene expression at millions of locations within a tissue 1 , hitherto with some trade-off between transcriptome depth, spatial resolution and sample size 2 . Although integration of image-based segmentation has enabled impactful work in this context, it is limited by imaging quality and tissue heterogeneity. By contrast, recent array-based technologies offer the ability to measure the entire transcriptome at subcellular resolution across large samples 3-6 . Presently, there exist no approaches for cell type identification that directly leverage this information to annotate individual cells. Here we propose a multiscale approach to automatically classify cell types at this subcellular level, using both transcriptomic information and spatial context. We showcase this on both targeted and whole-transcriptome spatial platforms, improving cell classification and morphology for human kidney tissue and pinpointing individual sparsely distributed renal mouse immune cells without reliance on image data. By integrating these predictions into a topological pipeline based on multiparameter persistent homology 7-9 , we identify cell spatial relationships characteristic of a mouse model of lupus nephritis, which we validate experimentally by immunofluorescence. The proposed framework readily generalizes to new platforms, providing a comprehensive pipeline bridging different levels of biological organization from genes through to tissues., (© 2024. The Author(s).)

Simple Summary: The paper describes the statistical analysis of the response of gastric cancer cells and normal cells to broadband terahertz radiation up to 4 THz, both with and without the use of nanostructured contrast agents. A statistical analysis was conducted towards multiple pairwise comparisons in order to identify the narrow THz frequency ranges where the contrast is enhanced and allows a clear identification of tumor cells in the presence of contrast agents. The paper describes the statistical analysis of the response of gastric cancer cells and normal cells to broadband terahertz radiation up to 4 THz, both with and without the use of nanostructured contrast agents. The THz spectroscopy analysis was comparatively performed under the ATR procedure and transmission measurement procedure. The statistical analysis was conducted towards multiple pairwise comparisons, including a support medium (without cells) versus a support medium with nanoparticles, normal cells versus normal cells with nanoparticles, and, respectively, tumor cells versus tumor cells with nanoparticles. When generally comparing the ATR procedure and transmission measurement procedure for a broader frequency domain, the differentiation between normal and tumor cells in the presence of contrast agents is superior when using the ATR procedure. THz contrast enhancement by using contrast agents derived from MRI-related contrast agents leads to only limited benefits and only for narrow THz frequency ranges, a disadvantage for THz medical imaging. [ABSTRACT FROM AUTHOR]

This paper explores a formal model of autopoiesis as presented by Maturana, Uribe and Varela, and analyzes this model and its implications through the lens of the notions of eigenforms (fixed points) and the intricacies of Goedelian coding. The paper discusses the connection between autopoiesis and eigenforms and a variety of different perspectives and examples. The paper puts forward original philosophical reflections and generalizations about its various conclusions concerning specific examples, with the aim of contributing to a unified way of understanding (formal models of) living systems within the context of natural sciences, and to see the role of such systems and the formation of information from the point of view of analogs of biological construction. To this end, we pay attention to models for fixed points, self-reference and self-replication in formal systems and in the description of biological systems. [ABSTRACT FROM AUTHOR]

Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage., (© 2024. The Author(s).)

The blood-brain barrier (BBB) protects the brain by actively allowing the entry of ions and nutrients while limiting the passage of from toxins and pathogens. A healthy BBB has low permeability and high selectivity to maintain normal brain functions. Increased BBB permeability can result from neurological diseases and traumatic injuries. Modern engineering technologies such as microfluidics and fabrication techniques have advanced the development of BBB models to simulate the basic functions of BBB. However, the intrinsic BBB properties are difficult to replicate. Existing in vitro BBB models demonstrate inconsistent BBB permeability and selectivity due to variations in microfluidic design, cell types and arrangement, expression of tight junction (TJ) proteins, and use of shear stress. Specifically, microfluidic designs have flow channels of different sizes, complexity, topology, and modular structure. Different cell types are selected to mimic various physiological conditions. These factors make it challenging to compare results obtained using different experimental setups. This paper highlights key factors that play important roles in influencing microfluidic models and discusses how these factors contribute to permeability and selectivity of the BBB models. [ABSTRACT FROM AUTHOR]

The properties of organs, tissues, organoids, and other systems of cells, are influenced by the spatial localization and distribution of their elements. Here, we used networks to describe distributions of cells on a surface where the small-world coefficient (SW) of the networks was varied between SW~1 (random uniform distributions) and SW~10 (clustered distributions). The small-world coefficient is a topological measure of graphs: networks with SW>1 are topologically biased to transmit information. For each system configuration, we then determined the total energy U as the sum of the energies that describe cell-cell interactions - approximated by a harmonic potential. The graph of energy (U) across the configuration space of the networks (SW) is the energy landscape: it indicates which configuration a system of cells will likely assume over time. We found that, depending on the model parameters, the energy landscapes of 2D distributions of cells may be of different types: from type I to type IV. Type I and type II systems have high probability to evolve into random distributions. Type III and type IV systems have a higher probability to form clustered architectures. A great many of simulations indicated that cultures of cells with high initial density and limited sensing range could evolve into clustered configurations with enhanced topological characteristics. Moreover, the strongest the binding between cells, the greater the likelihood that they will assume configurations characterized by finite values of SW. Results of the work are relevant for those working the field of tissue engineering, regenerative medicine, the formation of in-vitro-models, the analysis of neuro-degenerative diseases., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

This review is intended to contribute to the evidence of the effects of static magnetic field on cells and tissue, as well as to present research results that will elucidate the complex matters involved in the formation and remodeling of cells. The cell characteristics studied in the papers that are reviewed include cell viability and proliferation, aggregation and their differentiation, structure and membrane potential. A moderate static magnetic field in the most commonly used range of 2-80 mT has potential application in the formation and remodeling of plant and human cells. However, in the case of cancer cells, the range of fields commonly used was 0.2-9 T. Magnetism promotes changes in plant cell growth, which prompts the cell to proliferate, thereby ensuring an increased rate of biomass production. Some researches presented the enhancement of the differentiation of plant cells and skeletal muscle tissue by over 30% at 80 mT static magnetic field. Changes in the cell cycle and growth reflect directly on the cell number and viability and provide useful information to detect modifications in the cell machinery. Static magnetic field, depending on its intensity, enhances cell proliferation and thus may improve, among other processes, tissue regeneration, wound healing and the inhibition of cancer cell proliferation. Researchers showed, among other things, that cells under the influence of static magnetic field changed their shape, had a larger chloroplast, stiffer cell wall, density of the cytoskeleton and cytoplasm contained several mitochondria. Numerous studies also discussed the behavior of the cell membrane of plant and animal organisms, including humans, under the influence of an static magnetic field. The effects of static magnetic field on the cell membrane of plant and human cells were similar. The research results indicate that static magnetic fields can significantly change membrane depolarization and its potential that regulates ion movement and thus can have a significant impact on the properties and biological functionality of the cell. Studies have shown that continuous application of static magnetic field caused deformation and damage of cell membrane. Based on the theoretical analyses presented also in this review, it can be concluded that static magnetic field affects cells and tissue, giving them changes in properties and behaviors and modulates, e.g. in the activity of ion channels. Thus it may produce effects leading to changes in the functioning of the cell. It is possible to formulate directions for further research aimed at using static magnetic fields for the non-invasive remodeling and formation of plant and human cells. [ABSTRACT FROM AUTHOR]

Many people find the manipulation of the human germline—editing the DNA of sperm or egg cells such that these genetic changes are passed to the resulting offspring—to be morally impermissible. In this paper, I argue for the claim that editing the human germline is morally permissible. My argument starts with the claim that outcome uncertainty regarding the effects of germline editing shows that the duty to not harm cannot ground the prohibition of germline editing. Instead, if germline editing is wrong, it is wrong because it violates a duty to protect. However, we also have an epistemic duty to gather evidence regarding the effects of editing the human germline which overrides any moral duty to protect future generations. Thus, we have a duty to gather evidence regarding the effects of editing the human germline, which is to say that we have a duty to edit the human germline. [ABSTRACT FROM AUTHOR]

The Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts who develop standard terminologies that they link to 3D reference objects, describing anatomical structures. The third HRA release (v1.2) covers spatial reference data and ontology annotations for 26 organs. Experts access the HRA annotations via spreadsheets and view reference object models in 3D editing tools. This paper introduces the Common Coordinate Framework (CCF) Ontology v2.0.1 that interlinks specimen, biological structure, and spatial data, together with the CCF API that makes the HRA programmatically accessible and interoperable with Linked Open Data (LOD). We detail how real-world user needs and experimental data guide CCF Ontology design and implementation, present CCF Ontology classes and properties together with exemplary usage, and report on validation methods. The CCF Ontology graph database and API are used in the HuBMAP portal, HRA Organ Gallery, and other applications that support data queries across multiple, heterogeneous sources., (© 2023. The Author(s).)

Simple Summary: This scoping review of systematic reviews aims to accurately assess the degree of existing scientific evidence on the cancer hallmarks proposed in 2011 by Hanahan and Weinberg, in the form of systematic reviews and meta-analyses, applied to oral potentially malignant disorders, oral cavity and oropharyngeal squamous cell carcinomas, in order to point out gaps in evidence and lines of research that should be implemented in the future to improve the malignant transformation prediction, diagnosis and/or prognosis of these diseases. In 2000 and 2011, Hanahan and Weinberg published two papers in which they defined the characteristics that cells must fulfil in order to be considered neoplastic cells in all types of tumours that affect humans, which the authors called "hallmarks of cancer". These papers have represented a milestone in our understanding of the biology of many types of cancers and have made it possible to reach high levels of scientific evidence in relation to the prognostic impact that these hallmarks have on different tumour types. However, to date, there is no study that globally analyses evidence-based knowledge on the importance of these hallmarks in oral and oropharyngeal squamous cell carcinomas. For this reason, we set out to conduct this scoping review of systematic reviews with the aim of detecting evidence gaps in relation to the relevance of the cancer hallmarks proposed by Hanahan and Weinberg in oral and oropharyngeal cancer, and oral potentially malignant disorders, and to point out future lines of research in this field. [ABSTRACT FROM AUTHOR]

In this paper were analyzed the scientific bibliographic sources regarding the physiological and biochemical role of zinc on the tissues and organs of the organism of breeding roosters. In addition, in laboratory conditions, our researchers studied hematological, biochemical indices as well as glycine, glutamate and cysteine content in blood serum, seminal plasma and reproductive cells of breeding roosters. It is established that this element has a beneficial action on the organism of breeding roosters, maintaining and stabilizing the indices listed above at the level of physiological norms, compared to the roosters from the control group, and at the same time participating in the antioxidant protection of cells and maintaining cell homeostasis by balancing transmembrane metabolism. [ABSTRACT FROM AUTHOR]

Introduction: Alzheimer’s disease (AD) and Type 2 diabetes (T2D) are both ageassociated diseases. Identification of shared genes could help develop early diagnosis and preventive strategies. Although genetic background plays a crucial role in these diseases, we noticed an underrepresentation tendency of North African populations in omics studies. Materials and methods: First, we conducted a comprehensive review of genes and pathways shared between T2D and AD through PubMed. Then, the function of the identified genes and variants was investigated using annotation tools including PolyPhen2, RegulomeDB, and miRdSNP. Pathways enrichment analyses were performed with g:Profiler and EnrichmentMap. Next, we analyzed variant distributions in 16 worldwide populations using PLINK2, R, and STRUCTURE software. Finally, we performed an inter-ethnic comparison based on the minor allele frequency of T2D-AD common variants. Results: A total of 59 eligible papers were included in our study. We found 231 variants and 363 genes shared between T2D and AD. Variant annotation revealed six single nucleotide polymorphisms (SNP) with a high pathogenic score, three SNPs with regulatory effects on the brain, and six SNPs with potential effects on miRNA-binding sites. The miRNAs affected were implicated in T2D, insulin signaling pathways, and AD. Moreover, replicated genes were significantly enriched in pathways related to plasma protein binding, positive regulation of amyloid fibril deposition, microglia activation, and cholesterol metabolism. Multidimensional screening performed based on the 363 shared genes showed that main North African populations are clustered together and are divergent from other worldwide populations. Interestingly, our results showed that 49 SNP associated with T2D and AD were present in North African populations. Among them, 11 variants located in DNM3, CFH, PPARG, ROHA, AGER, CLU, BDNF1, CST9, and PLCG1 genes display significant differences in risk allele frequencies between North African and other populations. Conclusion: Our study highlighted the complexity and the unique molecular architecture of North African populations regarding T2D-AD shared genes. In conclusion, we emphasize the importance of T2D-AD shared genes and ethnicity-specific investigation studies for a better understanding of the link behind these diseases and to develop accurate diagnoses using personalized genetic biomarkers. [ABSTRACT FROM AUTHOR]

This paper details the content and structure of the folk concept of life, and discusses its relevance for scientific research on life. In four empirical studies, we investigate which features of life are considered salient, universal, central, and necessary. Functionings, such as nutrition and reproduction, but not material composition, turn out to be salient features commonly associated with living beings (Study 1). By contrast, being made of cells is considered a universal feature of living species (Study 2), a central aspect of life (Study 3), and our best candidate for being necessary for life (Study 4). These results are best explained by the hypothesis that people take life to be a natural kind subject to scientific scrutiny. [ABSTRACT FROM AUTHOR]

Background: The effects of laser therapy on normal cells are well known and accepted, but the impact of this therapy on malignant cells are not yet fully understood. This review aims to map and outline what the scientific literature addresses on the effects of laser therapy on malignant cells. Methods: This review article followed the guidelines of the PRISMA‐ScR protocol, being all the search, analysis, and selection of articles based on it. Results: After all application of the predetermined criteria, five studies were included, dated between the years 2013 and 2021. With the complete reading of the selected studies, 100% of the articles were classified as category III of the Agency for Healthcare as Research and Quality classification. Similar themes among the papers included were investigated and compared. In these five studies, the visible red and near infrared wavelengths were used, and energy densities varied between 1 and 5 J/cm2. It was observed that low‐level laser could alter the expression of cell proliferation and migration proteins, such as cyclin D1, E‐cadherin, and β‐catenin. In addition, changes related to increased cell viability and metabolism were also identified. Conclusion: The low‐level laser seems to positively regulate the proliferative, migratory, and viability capacity of neoplastic cells, depending on the protocol used. All these studies included in the review are equivalent to in vitro studies; the cells are not in such a complex environment as is an organized tissue, making it necessary to carry out more complex tests, such as in vivo research. [ABSTRACT FROM AUTHOR]

Cell regulatory networks are the determinants of cellular homeostasis. Any alteration to these networks results in the disturbance of cellular homeostasis and induces cells towards different fates. Myocyte enhancer factor 2A (MEF2A) is one of four members of the MEF2 family of transcription factors (MEF2A-D). MEF2A is highly expressed in all tissues and is involved in many cell regulatory networks including growth, differentiation, survival and death. It is also necessary for heart development, myogenesis, neuronal development and differentiation. In addition, many other important functions of MEF2A have been reported. Recent studies have shown that MEF2A can regulate different, and sometimes even mutually exclusive cellular events. How MEF2A regulates opposing cellular life processes is an interesting topic and worthy of further exploration. Here, we reviewed almost all MEF2A research papers published in English and summarized them into three main sections: 1) the association of genetic variants in MEF2A with cardiovascular disease, 2) the physiopathological functions of MEF2A, and 3) the regulation of MEF2A activity and its regulatory targets. In summary, multiple regulatory patterns for MEF2A activity and a variety of co-factors cause its transcriptional activity to switch to different target genes, thereby regulating opposing cell life processes. The association of MEF2A with numerous signaling molecules establishes a central role for MEF2A in the regulatory network of cellular physiopathology. [ABSTRACT FROM AUTHOR]

Stimulated Raman scattering (SRS) microscopy is a label-free chemical imaging technology. Live-cell imaging with SRS has been demonstrated for many biological and biomedical applications. However, long-term time-lapse SRS imaging of live cells has not been widely adopted. SRS microscopy often uses a high numerical aperture (NA) water-immersion objective and a high NA oil-immersion condenser to achieve high-resolution imaging. In this case, the gap between the objective and the condenser is only a few millimeters. Therefore, most commercial stage-top environmental chambers cannot be used for SRS imaging because of their large thickness with a rigid glass cover. This paper describes the design and fabrication of a flexible chamber that can be used for time-lapse live-cell imaging with transmitted SRS signal detection on an upright microscope frame. The flexibility of the chamber is achieved by using a soft material - a thin natural rubber film. The new enclosure and chamber design can be easily added to an existing SRS imaging setup. The testing and preliminary results demonstrate that the flexible chamber system enables stable, long-term, time-lapse SRS imaging of live cells, which can be used for various bioimaging applications in the future.

Electrogenetics, the combination of electronics and genetics, is an emerging field of mammalian synthetic biology in which electrostimulation is used to remotely program user-designed genetic elements within designer cells to generate desired outputs. Here, we describe recent advances in electro-induced therapeutic gene expression and therapeutic protein secretion in engineered mammalian cells. We also review available tools and strategies to engineer electro-sensitive therapeutic designer cells that are able to sense electrical pulses and produce appropriate clinically relevant outputs in response. We highlight current limitations facing mammalian electrogenetics and suggest potential future directions for research., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Atomic Force Microscopy (AFM) is a powerful tool enabling the mechanical characterization of biological materials at the nanoscale. Since biological materials are highly heterogeneous, their mechanical characterization is still considered to be a challenging procedure. In this paper, a new approach that leads to a 3-dimensional (3D) nanomechanical characterization is presented based on the average Young's modulus and the AFM indentation method. The proposed method can contribute to the clarification of the variability of the mechanical properties of biological samples in the 3-dimensional space (variability at the x–y plane and depth-dependent behavior). The method was applied to agarose gels, fibroblasts, and breast cancer cells. Moreover, new mathematical methods towards a quantitative mechanical characterization are also proposed. The presented approach is a step forward to a more accurate and complete characterization of biological materials and could contribute to an accurate user-independent diagnosis of various diseases such as cancer in the future. [ABSTRACT FROM AUTHOR]

Copyright of Biology Teaching is the property of East China Normal University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This paper presents a review of the space exploration for life signature search with a special focus on the fluorescence microscope we developed for the life signature search on Mars and in other sites. Considering where, what, and how to search for life signature is essential. Life signature search exploration can be performed on the Mars surface and underground, on Venus' cloud, moon, asteroids, icy bodies (e.g., moons of Jupiter and Saturn), and so on. It is a useful strategy to consider the targeted characteristics that may be similar to those of terrestrial microorganisms, which are microorganisms with uniform spherical or rod structures with approximately 1 μm diameter surrounded by a membrane having a metabolic activity and mainly made of carbon-based molecules. These characteristics can be analyzed by using a fluorescence microscope and a combination of fluorescence pigments with specific staining characteristics to distinguish the microorganism characteristics. Section 1 introduces the space exploration for life signature search. Section 2 reviews the scientific instruments and achievements of past and ongoing Mars exploration missions closely related to astrobiology. Section 3 presents the search targets and analysis of astrobiology. Section 4 discusses the extraterrestrial life exploration methods that use a microscope together with other methods (based on mass spectrometry, morphology, detection of growth, movement, and death, etc. for microscopic and macroscopic organism). Section 5 expounds on the life signature detection fluorescence microscope, for which we have manufactured a bread board model and tested for extraterrestrial life exploration. [ABSTRACT FROM AUTHOR]

Hydrogen peroxide (H 2 O 2) is a reactive oxygen species (ROS) that can be used as a marker for the occurrence of oxidative stress in the organism. Lysosomes serve as intracellular digestive sites, and when the concentration of H 2 O 2 in them is abnormal, lysosomal function is often impaired, leading to the development of diseases. Hydrogen sulfide (H 2 S) acts as a gaseous signaling molecule that scavenges H 2 O 2 from cells and tissues, thereby maintaining the redox environment of the body. However, most of the reported hydrogen peroxide fluorescent probes so far can only detect H 2 O 2 , but cannot maintain the intracellular redox environment. In this paper, an H 2 O 2 fluorescent probe LN-HOD with lysosomal targeting properties was designed and synthesized by combining the H 2 O 2 recognition site with a naphthylamine fluorophore via a thiocarbamate moiety. The probe has the advantages of large Stokes shift (110 nm), high sensitivity and good H 2 S release capability. The probe LN-HOD can be used to detect H 2 O 2 in cells, zebrafish and plant roots. In addition, LN-HOD detects changes in the concentration of H 2 O 2 in plant roots when Arabidopsis is stressed by cadmium ion (Cd2+). And through its ability to release H 2 S, it can help to remove excess H 2 O 2 and maintain the redox environment in cells, zebrafish and plant roots. The present work provides new ideas for the detection and assisted removal of H 2 O 2 , which contributes to the in-depth study of the cellular microenvironment in organisms. In this paper, we designed and synthesized LN-HOD , a fluorescent probe targeting the detection of H 2 O 2 in lysosomes, by combining the H 2 O 2 recognition site with a naphthalimide fluorophore via a thiocarbamate moiety. The probe has the advantages of large Stokes displacement, high sensitivity and good H 2 S release capability. The probe LN-HOD can be used to detect H 2 O 2 in cells, zebrafish and plant roots. In addition, LN-HOD detects changes in the concentration of H 2 O 2 in plant roots when Arabidopsis is stressed by cadmium ion (Cd2+). And through its ability to release H 2 S, it can help to remove excess H 2 O 2 and maintain the redox environment in cells, zebrafish and plant roots. The present work provides new ideas for the detection and assisted removal of H 2 O 2 , which contributes to the in-depth study of the cellular microenvironment in organisms. [Display omitted] • The probe LN-HOD not only detects H 2 O 2 but also releases H 2 S. • LN-HOD has the ability to release H 2 S in cells, zebrafish and Arabidopsis. • LN-HOD has a good ability to maintain the redox environment in cells. • LN-HOD can detect changes in H 2 O 2 concentration in plants induced by Cd2+ ion stress effects. [ABSTRACT FROM AUTHOR]

This is a broad overview and critical review of a particular group of closely related ex vivo and in vitro metabolic NMR spectroscopic methods. The scope of interest comprises studies of cultured cells and excised tissue, either intact or after physicochemical extraction of metabolites. Our detailed discussion includes pitfalls that have led to erroneous statements in the published literature, some of which may cause serious problems in metabolic and biological interpretation of results. To cover a wide range of work from relevant research areas, we consider not only the most recent achievements in the field, but also techniques that proved to be valid and successful in the past, although they may not have generated a very significant number of papers more recently. Thus, this comparative review also aims at providing background information useful for judiciously choosing between the metabolic ex vivo/in vitro NMR methods presented. Finally, the methods of interest are discussed in the context of, and in relation to, other metabolic analysis protocols such as HR-MAS and cell perfusion NMR, as well as the mass spectrometry approach. [ABSTRACT FROM AUTHOR]

Cardiac remodelling refers to changes in left ventricular structure and function over time, with a progressive deterioration that may lead to heart failure (HF) development (adverse remodelling) or vice versa a recovery (reverse remodelling) in response to HF treatment. Adverse remodelling predicts a worse outcome, whilst reverse remodelling predicts a better prognosis. The geometry, systolic and diastolic function and electric activity of the left ventricle are affected, as well as the left atrium and on the long term even right heart chambers. At a cellular and molecular level, remodelling involves all components of cardiac tissue: cardiomyocytes, fibroblasts, endothelial cells and leucocytes. The molecular, cellular and histological signatures of remodelling may differ according to the cause and severity of cardiac damage, and clearly to the global trend toward worsening or recovery. These processes cannot be routinely evaluated through endomyocardial biopsies, but may be reflected by circulating levels of several biomarkers. Different classes of biomarkers (e.g. proteins, non‐coding RNAs, metabolites and/or epigenetic modifications) and several biomarkers of each class might inform on some aspects on HF development, progression and long‐term outcomes, but most have failed to enter clinical practice. This may be due to the biological complexity of remodelling, so that no single biomarker could provide great insight on remodelling when assessed alone. Another possible reason is a still incomplete understanding of the role of biomarkers in the pathophysiology of cardiac remodelling. Such role will be investigated in the first part of this review paper on biomarkers of cardiac remodelling. [ABSTRACT FROM AUTHOR]

The osmotic pressure of dilute electrolyte solutions containing charged macro-ions as well as counterions can be computed directly from the particle distribution via the well-known cell model. Originally derived within the Poisson-Boltzmann mean-field approximation, the cell model considers a single macro-ion centered into a cell, together with counterions needed to neutralize the total cell charge, while it neglects the phenomena due to macro-ion correlations. While extensively applied in coarse-grained Monte Carlo (MC) simulations of continuum solvent systems, the cell model, in its original formulation, neglects the macro-ion shape anisotropy and details of the surface charge distribution. In this paper, by comparing one-body and two-body coarse-grained MC simulations, we first establish an upper limit for the assumption of neglecting correlations between macro-ions, and second, we validate the approximation of using a non-spherical macro-ion. Next, we extend the cell model to all-atom molecular dynamics simulations and show that protein concentration-dependent osmotic pressures can be obtained by confining counterions in a virtual, spherical subspace defining the protein number density. Finally, we show the possibility of using specific interaction parameters for the protein-ion and ion-ion interactions, enabling studies of protein concentration-dependent ion-specific effects using merely a single protein molecule.

MCL, Mincle and Dectin‐2 are C‐type lectin receptors expressed by subsets of myeloid cells, and their genes cluster together in the APLEC/Dectin‐2 gene complex. We have previously shown that MCL and Mincle form a heterodimer in the rat, and others have shown that MCL and Dectin‐2 form a heterodimer in the mouse. In the rat, Dectin‐2 is a pseudogene, but here, we examine the association of the three receptors in human. In co‐transfection experiments analyzed with flow cytometry and immunoprecipitation, we here show that human MCL and Mincle form a disulphide‐linked heterodimer that associates with the signalling adaptor molecule FcεRIγ, in accordance with our previous findings in the rat. In contrast to previous findings in the rat, data in this paper indicate a direct association of MCL with FcεRIγ, as previously shown for mouse MCL. We were unable to demonstrate the formation of a heterodimer between human MCL and Dectin‐2. Thus, despite similarities, there may be important differences in the conformation of these receptors between rat, mouse and human, and this may have functional consequences. [ABSTRACT FROM AUTHOR]

The error‐correcting performance of multi‐level‐cell (MLC) NAND flash memory is closely related to the block length of error‐correcting codes (ECCs) and log‐likelihood‐ratios of the read‐voltage thresholds. Driven by this issue, this paper optimizes the read‐voltage thresholds for MLC flash memory to improve the decoding performance of ECCs with finite block length. First, through the analysis of channel coding rate and decoding error probability under finite block length, the optimization problem of read‐voltage thresholds to minimize the maximum decoding error probability is formulated. Second, a cross‐iterative search algorithm to optimize read‐voltage thresholds under the perfect knowledge of flash memory channel is developed. However, it is challenging to analytically characterize the voltage distribution under the effect of data retention noise. To address this problem, a deep neural network (DNN)‐aided optimization strategy to optimize the read‐voltage thresholds is developed, where a multi‐layer perception network is employed to learn the relationship between voltage distribution and read‐voltage thresholds. Simulation results show that, compared with the existing schemes, the proposed DNN‐aided read‐voltage threshold optimization strategy with a well‐designed Low Density Parity Check (LDPC) code can not only improve the program‐and‐erase endurance but also reduce the read latency. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Tissue Engineering Research / Zhongguo Zuzhi Gongcheng Yanjiu is the property of Chinese Journal of Tissue Engineering Research and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This paper explores a formal model of autopoiesis as presented by Maturana, Uribe and Varela, and analyzes this model and its implications through the lens of the notions of eigenforms (fixed points) and the intricacies of Goedelian coding. The paper discusses the connection between autopoiesis and eigenforms and a variety of different perspectives and examples. The paper puts forward original philosophical reflections and generalizations about its various conclusions concerning specific examples, with the aim of contributing to a unified way of understanding (formal models of) living systems within the context of natural sciences, and to see the role of such systems and the formation of information from the point of view of analogs of biological construction. To this end, we pay attention to models for fixed points, self-reference and self-replication in formal systems and in the description of biological systems.

Hydrazine (N 2 H 4) plays an important role in industrial production, but it is highly toxic, leaking or exposing it will pollute the environment and cause serious harm to human beings. Therefore, it is necessary to use a simple and effective method to detect N 2 H 4 in environmental systems and organisms. Herein, a novel water-soluble fluorescent probe based on coumarin fluorophore, 2-(7-(diethylamino)-2-oxo-2H-chromen-3-yl)isoindoline-1,3-dione (C-Z1), is reported. The fluorescence intensity of the probe at 530 nm was enhanced gradually with the addition of N 2 H 4 , and the maximum enhancement was about 28 times. The probe has good selectivity and sensitivity, the detection limit of hydrazine hydrate is 1.48 × 10−7 M, and the response mechanism of the probe is proved by theoretical calculation and experiment. C-Z1 has been shown to detect N 2 H 4 in a variety of environmental samples, including water, soil, air, cells, zebrafish and plants. In addition, C-Z1 can be made into test strips for easy portability and used for rapid quantitative detection of N 2 H 4 in the field by its distinct change in fluorescence color. Thus, C-Z1 has great potential for the analysis and detection of environmental contaminants. In this paper, the deprotection of phthalimide is used as a strategy for the detection of hydrazine. We designed and synthesized a water-soluble probe C-Z1 for the detection of N 2 H 4. its absorption and emission spectra vary regularly with the concentration of the N 2 H 4 solution. C-Z1 can detect N 2 H 4 in environmental water samples, soil, and air. Portable paper test strips based on C-Z1 can be easily prepared and are well used for in situ detection of N 2 H 4. Most importantly, the successful application of the probe in cell imaging, zebrafish imaging, and Arabidopsis imaging demonstrates the potential application of the probe in biological and environmental aspects. [Display omitted] • C-Z1 is a novel probe for the detection of N 2 H 4 , which has not been reported in other literature. • The probe is a water-soluble fluorescent probe and has a maximum fluorescence intensity of 28-fold. • The probe possesses low toxicity and can be used for fluorescence imaging of cells, zebrafish and arabidopsis. • Accurate determination of hydrazine is realized in real environmental samples. • The probes are simple to prepare and can be made into test strips for physical environmental testing. [ABSTRACT FROM AUTHOR]

Simple Summary: Oral lichen planus (OLP) is a chronic inflammatory disease of autoimmune nature and unknown etiology which affects approximately 1% of the world's population. The most important feature of OLP is its behavior as an oral potentially malignant disorder (OPMD). The current study is the first systematic review and meta-analysis designed to evaluate the degree of existing scientific evidence on the cancer hallmarks proposed in 2011 by Hanahan and Weinberg, defined as the characteristics that cells must fulfill in order to be considered neoplastic cells in all types of tumors that affect humans. This systematic review and meta-analysis includes 110 studies which recruited 7064 cases of OLP, in which the expression of 104 molecular biomarkers were analyzed through an immunohistochemical technique. The earliest oncogenic molecular mechanisms that could justify the malignant transformation of this disease are analyzed in depth and critically discussed on the basis of evidence. We aimed to qualitatively and quantitatively analyze, through a systematic review and meta-analysis, the current evidence on the differential expression of the hallmarks of cancer in oral lichen planus (OLP) samples, in order to know the earliest molecular mechanisms that could be involved in the malignant transformation of this oral potentially malignant disorder. We searched MEDLINE/PubMed, Embase, Web of Science, and Scopus for studies published before November 2023. We evaluated the methodological quality of studies and carried out meta-analyses to fulfill our objectives. Inclusion criteria were met by 110 primary-level studies, with 7065 OLP samples, in which the expression of 104 biomarkers were analyzed through immunohistochemistry. Most OLP samples showed sustained cell proliferation signaling (65.48%, 95%CI = 51.87–78.02), anti-apoptotic pathways (55.93%, 95%CI = 35.99–75.0), genome instability (48.44%, 95%CI = 13.54–84.19), and tumor-promoting inflammation events (83.10%, 95%CI = 73.93–90.74). Concurrently, OLP samples also harbored tumor growth suppressor mechanisms (64.00%, 95%CI = 53.27–74.12). In conclusion, current evidence indicates that molecular mechanisms promoting hyperproliferative signaling, an antiapoptotic state with genomic instability, and an escape of epithelial cells from immune destruction, are developed in LP-affected oral mucosa. It is plausible that these events are due to the actions exerted by the chronic inflammatory infiltrate. Malignant transformation appears to be prevented by tumor suppressor genes, which showed consistent upregulation in OLP samples. [ABSTRACT FROM AUTHOR]