Robust entropy rate estimation for nonstationary neuronal calcium spike trains based on empirical probabilities.

. Temporal patterns in neuronal spiking encode stimulus uncertainty, and convey information about high-level functions such as memory and cognition. Estimating the associated information content and understanding how that evolves with time assume significance in the investigation of neuronal coding mechanisms and abnormal signaling.

Multi-component forms of the 2nd generation H1 receptor antagonist drug, Bilastine and its enhanced physicochemical characteristics.

Bilastine (BIL) is a novel 2nd generation antihistamine medication is used to treat symptoms of chronic urticaria and allergic rhinitis. However, its poor solubility limits its therapeutic efficacy. In order to enhance the physicochemical characteristics of BIL, various molecular adducts of BIL (Salt, hydrate and co-crystal) were discovered in this study using two distinct salt-formers: Terephthalic acid (TA), 2,4-Dihydroxybenzoic acid (2,4-DHBA), and three nutraceuticals (Vanillic Acid (VA), Hydroquinone (HQN) and Hippuric acid (HA)).

Nonviral Platform for Expression of Recombinant Protein in Insect Cells.

Nonviral transfection has been used to express various recombinant proteins, therapeutics, and virus-like particles (VLP) in mammalian and insect cells. Virus-free methods for protein expression require fewer steps for obtaining protein expression by eliminating virus amplification and measuring the infectivity of the virus. The nonviral method uses a nonlytic plasmid to transfect the gene of interest into the insect cells instead of using baculovirus, a lytic system.

Interaction-Based Perspective for Designing Polymer Biomaterial: A Strategic Approach to the Chitosan-Glycerophosphate System.

The conventional approach for developing any polymeric biomaterial is to follow protocols available in the literature and/or perform trial-and-error runs without a scientific basis. Here, we propose an analysis of a complex overlay of molecular interactions between drugs and polymers that provides a strategic pathway for biomaterial development. First, this work provides an innovative interaction-based method for developing an ocular formulation involving in situ gelling chitosan, gelatin, and glycerophosphate systems.

A Pipeline for Dynamic Analysis of Mitochondrial Content in Developing T Cells: Bridging the Gap Between High-Throughput Flow Cytometry and Single-Cell Microscopy Analysis.

Analyzing the dynamics of mitochondrial content in developing T cells is crucial for understanding the metabolic state during T cell development. However, monitoring mitochondrial content in real-time needs a balance of cell viability and image resolution. In this chapter, we present experimental protocols for measuring mitochondrial content in developing T cells using three modalities: bulk analysis via flow cytometry, volumetric imaging in laser scanning confocal microscopy, and dynamic live-cell monitoring in spinning disc confocal microscopy.

Mitochondrial fusion and altered beta-oxidation drive muscle wasting in a Drosophila cachexia model.

Cancer cachexia is a tumour-induced wasting syndrome, characterised by extreme loss of skeletal muscle. Defective mitochondria can contribute to muscle wasting; however, the underlying mechanisms remain unclear. Using a Drosophila larval model of cancer cachexia, we observed enlarged and dysfunctional muscle mitochondria.

A deep learning approach for automation in neurite tracing and cell size estimation from differential contrast images under healthy and hypoxic condition.

Chronic hypoxia is known to be a major cause of neurite length retraction followed be degeneration. Specifically, laser scanning confocal microscopy (LSCM) based-contrast imaging is used for monitoring neuronal morphology under hypoxic condition. Although imaging of neurons using LSCM via differential contrast imaging (DIC) is a powerful tool to identify the neuronal states under degenerative condition, fully automated quantification of neurite length and cell shape remains challenging.

In vitro laser scanning confocal microscopy and unsupervised segmentation: Quantification of cytosolic calcium and RNA distribution in hypoxic neurons.

The mimicry of neurodegenerative diseases in vitro can be observed through the induction of chronic hypoxia, and the impact of this stress is monitored using multiplexed imaging techniques. While laser scanning confocal microscopy (LSCM) is a valuable tool for observing single neurons under degenerative conditions, accurately quantifying RNA distribution and cell size by deep learning tools remains challenging due to the lack of annotated training datasets. To address this, we propose a framework that combines 3D tracking of RNA distribution and cell size identification using unsupervised image segmentation.

Identification of optimal flow rate for culture media, cell density, and oxygen toward maximization of virus production in a fed-batch baculovirus-insect cell system.

In recent times, it has been realized that novel vaccines are required to combat emerging disease outbreaks, and faster optimization is required to respond to global vaccine demands. Although, fed-batch operations offer better productivity, experiment-based optimization of a new fed-batch process remains expensive and time-consuming. In this context, we propose a novel computational framework that can be used for process optimization and control of a fed-batch baculovirus-insect cell system.

A computational model to uncover the biophysical underpinnings of neural firing heterogeneity in dissociated hippocampal cultures.

Calcium (Ca ) imaging reveals a variety of correlated firing in cultures of dissociated hippocampal neurons, pinpointing the non-synaptic paracrine release of glutamate as a possible mediator for such firing patterns, although the biophysical underpinnings remain unknown. An intriguing possibility is that extracellular glutamate could bind metabotropic receptors linked with inositol trisphosphate (IP ) mediated release of Ca from the endoplasmic reticulum of individual neurons, thereby modulating neural activity in combination with sarco/endoplasmic reticulum Ca transport ATPase (SERCA) and voltage-gated Ca channels (VGCC). However, the possibility that such release may occur in different neuronal compartments and can be inherently stochastic poses challenges in the characterization of such interplay between various Ca channels.

Three-Dimensional Tracking of Intracellular Calcium and Redox State during Real-Time Control in a Hypoxic Gradient in Microglia Culture: Comparison of the Channel Blocker and Reoxygenation under Ischemic Shock.

Real-time three-dimensional (3-D) imaging is crucial for quantifying correlations among various molecules under acute ischemic stroke. Insights into such correlations may be decisive in selecting molecules capable of providing a protective effect within a shorter period. The major bottleneck is maintaining the cultures under severely hypoxic conditions while simultaneously 3-D imaging intracellular organelles with a microscope.

Binary to ternary drug-drug molecular adducts of the antihypertensive drug ketanserin (KTS) with advanced physicochemical properties.

Focusing on a reliable supramolecular synthon approach, novel molecular salts of the antihypertensive medication ketanserin (KTS) with aromatic carboxylic acid derivatives (benzoic acid (BA), 2-hydroxybenzoic acid (2-HBA), and 2,5-dihydroxybenzoic acid (2,5-DHBA)) are reported. Binary salts of KTS with the respective salt former were obtained solvent-assisted grinding followed by solution crystallization. Salt production was confirmed through crystal structure investigations that revealed proton transfer from the carboxylic acid group of the salt former to the piperidine nitrogen atom of KTS.

Computational framework to understand the clinical stages of COVID-19 and visualization of time course for various treatment strategies.

Coronavirus disease 2019 is known to be regulated by multiple factors such as delayed immune response, impaired T cell activation, and elevated levels of proinflammatory cytokines. Clinical management of the disease remains challenging due to interplay of various factors as drug candidates may elicit different responses depending on the staging of the disease. In this context, we propose a computational framework which provides insights into the interaction between viral infection and immune response in lung epithelial cells, with an aim of predicting optimal treatment strategies based on infection severity.

Mapping of structural arrangement of cells and collective calcium transients: an integrated framework combining live cell imaging using confocal microscopy and UMAP-assisted HDBSCAN-based approach.

Live cell calcium (Ca2+) imaging is one of the important tools to record cellular activity during in vitro and in vivo preclinical studies. Specially, high-resolution microscopy can provide valuable dynamic information at the single cell level. One of the major challenges in the implementation of such imaging schemes is to extract quantitative information in the presence of significant heterogeneity in Ca2+ responses attained due to variation in structural arrangement and drug distribution.

Non-prophylactic resveratrol-mediated protection of neurite integrity under chronic hypoxia is associated with reduction of Cav1.2 channel expression and calcium overloading.

Cellular hypoxia is a major cause of oxidative stress, culminating in neuronal damage in neurodegenerative diseases. Numerous ex vivo studies have implicated that hypoxia episodes leading to disruption of Ca homeostasis and redox status contribute to the progression of various neuropathologies and cell death. Isolation and maintenance of primary cell culture being cost-intensive, the details of the time course relationship between Ca overload, L-type Ca channel function, and neurite retraction under chronic and long-term hypoxia remain undefined.

Analytics Pipeline for Visualization of Single Cell RNA Sequencing Data from Brochoaveolar Fluid in COVID-19 Patients: Assessment of Neuro Fuzzy-C-Means and HDBSCAN.

Since the mutation in SARS-COV2 poses new challenges in designing vaccines, it is imperative to develop advanced tools for visualizing the genetic information. Specially, it remains challenging to address the patient-to-patient variability and identify the signature for severe/critical conditions. In this endeavor we analyze the large-scale RNA-sequencing data collected from broncho-alveolar fluid.

Hydrogen-Bonded Organic Framework Structure: A Metal-Free Electrocatalyst for the Evolution of Hydrogen.

The hydrogen-bonded organic frameworks (HOFs) have gained significant attention due to their various alluring applications in the fascinating field of supramolecular chemistry. Herein, we report the electrocatalytic activity of HOFs toward the hydrogen evolution reaction (HER) by utilizing the molecular adduct of cyanuric and trithiocyanuric acid with various organic substrates (melamine and 4,4'-bipyridine). Both the experimental and theoretical findings provide insights and validate the electrocatalytic activity toward HER applications.

Imaging Methods for the Assessment of a Complex Hydrogel as an Ocular Drug Delivery System for Glaucoma Treatment: Opportunities and Challenges in Preclinical Evaluation.

Glaucoma is one of the leading causes of loss of vision. The problems associated with the marketed formulations of anti-glaucoma drugs are low bioavailability, unwanted side effects, and low patient compliance. Hydrogels are an important class of soft materials that play a crucial role in developing an ocular drug delivery system.

Mathematical modeling of viral infection dynamics and immune response in SARS-CoV-2: A computational framework for testing drug efficacy.

SARS-CoV-2 has emerged to cause the outbreak of COVID-19, which has expanded into a worldwide human pandemic. Although detailed experimental data on animal experiments would provide insight into drug efficacy, the scientists involved in these experiments would be exposed to severe risks. In this context, we propose a computational framework for studying infection dynamics that can be used to capture the growth rate of viral replication and lung epithelial cell in presence of SARS-CoV-2.

FDA approved L-type channel blocker Nifedipine reduces cell death in hypoxic A549 cells through modulation of mitochondrial calcium and superoxide generation.

As hypoxia is a major driver for the pathophysiology of COVID-19, it is crucial to characterize the hypoxic response at the cellular and molecular levels. In order to augment drug repurposing with the identification of appropriate molecular targets, investigations on therapeutics preventing hypoxic cell damage is required. In this work, we propose a hypoxia model based on alveolar lung epithelial cells line using chemical inducer, CoCl that can be used for testing calcium channel blockers (CCBs).

Quantitative Confocal Microscopy for Grouping of Dose-Response Data: Deciphering Calcium Sequestration and Subsequent Cell Death in the Presence of Excess Norepinephrine.

Fluorescent calcium (Ca) imaging is one of the preferred methods to record cellular activity during in vitro preclinical studies, high-content drug screening, and toxicity analysis. Visualization and analysis for dose-response data obtained using high-resolution imaging remain challenging, due to the inherent heterogeneity present in the Ca spiking. To address this challenge, we propose measurement of cytosolic Ca ions using spinning-disk confocal microscopy and machine learning-based analytics that is scalable.

Dissociation of the G protein βγ from the Gq-PLCβ complex partially attenuates PIP2 hydrolysis.

Phospholipase C β (PLCβ), which is activated by the Gq family of heterotrimeric G proteins, hydrolyzes the inner membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2), generating diacylglycerol and inositol 1,4,5-triphosphate (IP3). Because Gq and PLCβ regulate many crucial cellular processes and have been identified as major disease drivers, activation and termination of PLCβ signaling by the Gαq subunit have been extensively studied. Gq-coupled receptor activation induces intense and transient PIP2 hydrolysis, which subsequently recovers to a low-intensity steady-state equilibrium.

Microfluidic Protein Imaging Platform: Study of Tau Protein Aggregation and Alzheimer's Drug Response.

Tau protein aggregation is identified as one of the key phenomena associated with the onset and progression of Alzheimer's disease. In the present study, we performed on-chip confocal imaging of tau protein aggregation and tau-drug interactions using a spiral-shaped passive micromixing platform. Numerical simulations and experiments were performed in order to validate the performance of the micromixer design.

Detection of Specific Templates in Calcium Spiking in HeLa Cells Using Hierarchical DBSCAN: Clustering and Visualization of CellDrug Interaction at Multiple Doses.

One of the major challenges in analyzing large scale intracellular calcium spiking data obtained through fluorescent imaging is to identify various patterns present in time series data. Such an analysis identifying the distinct frequency and amplitude encoding during cell-drug interaction study is expected to provide new insights into the drug action patterns over a time course. Here, we present the HDBSCAN clustering algorithm to find a clustering pattern present in calcium spiking obtained by confocal imaging of single cells.

A detailed model and Monte Carlo simulation for predicting DIP genome length distribution in baculovirus infection of insect cells.

Baculoviruses have enormous potential for use as biopesticides to control insect pest populations without the adverse environmental effects posed by the widespread use of chemical pesticides. However, continuous baculovirus production is susceptible to DNA mutation and the subsequent production of defective interfering particles (DIPs). The amount of DIPs produced and their genome length distribution are of great interest not only for baculoviruses but for many other DNA and RNA viruses.