A Descriptive Study on Imperiled Cochlear Implant Salvage Using Double Flap Cover-What We Learned in 6 Years.

Cochlear implant surgery is the standard of care for severe sensorineural hearing loss. Infection followed by implant extrusion is an infrequent complication of this surgery. The ideal treatment is explantation of the implant. However, implant removal and reimplantation is a challenging surgery and may have poor speech reception outcomes. The cost of a new implant especially in developing countries is also a deterrent. Our study dwells on the feasibility of salvaging exposed cochlear implants by a combination of pericranial flaps followed by a scalp flap cover. The study was done in a tertiary care hospital over a period of six years. Out of 303 cochlear implant surgeries, 12 patients had implant exposure and extrusion. Patients having meningitis and sepsis were excluded from the study. All patients underwent debridement and cover with double flap (Pericranial flaps and scalp rotation flap). The average operating time was 2.17 h. The surgery is technically simple with a short learning curve. It brings in rich blood supply and there is fair amount of tissue mobility. In 11 patients we were able to salvage the implant. Patients were followed for a period of 01 year post operatively. Our study suggests that salvage of infected implant should be attempted as it is feasible, durable and effective in appropriate patients.

Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase.

The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.

NK and NKT cells in the pathogenesis of Hidradenitis suppurativa: Novel therapeutic strategy through targeting of CD2.

Hidradenitis suppurativa (HS) is a chronic debilitating inflammatory skin disease with poorly understood pathogenesis. Single-cell RNAseq analysis of HS lesional and healthy individual skins revealed that NKT and NK cell populations were greatly expanded in HS, and they expressed elevated CD2, an activation receptor. Immunohistochemistry analyses confirmed significantly expanded numbers of CD2+ cells distributed throughout HS lesional tissue, and many co-expressed the NK marker, CD56. While CD4+ T cells were expanded in HS, CD8 T cells were rare. CD20+ B cells in HS were localized within tertiary follicle like structures. Immunofluorescence microscopy showed that NK cells (CD2 + CD56 dim ) expressing perforin, granzymes A and B were enriched within the hyperplastic follicular epidermis and tunnels of HS and juxtaposed with apoptotic cells. In contrast, NKT cells (CD2 + CD3 + CD56 bright ) primarily expressed granzyme A and were associated with α-SMA expressing fibroblasts within the fibrotic regions of the hypodermis. Keratinocytes and fibroblasts expressed high levels of CD58 (CD2 ligand) and they interacted with CD2 expressing NKT and NK cells. The NKT/NK maturation and activating cytokines, IL-12, IL-15 and IL-18, were significantly elevated in HS. Inhibition of cognate CD2-CD58 interaction with blocking anti-CD2 mAb in HS skin organotypic cultures resulted in a profound reduction of the inflammatory gene signature and secretion of inflammatory cytokines and chemokines in the culture supernate. In summary, we show that a cellular network of heterogenous NKT and NK cell populations drives inflammation, tunnel formation and fibrosis in the pathogenesis of HS. Furthermore, CD2 blockade is a viable immunotherapeutic approach for the management of HS.

Integrative systems biology framework discovers common gene regulatory signatures in multiple mechanistically distinct inflammatory skin diseases.

More than 20% of the population across the world is affected by non-communicable inflammatory skin diseases including psoriasis, atopic dermatitis, hidradenitis suppurativa, rosacea, etc. Many of these chronic diseases are painful and debilitating with limited effective therapeutic interventions. However, recent advances in psoriasis treatment have improved the effectiveness and provide better management of the disease. This study aims to identify common regulatory pathways and master regulators that regulate molecular pathogenesis. We designed an integrative systems biology framework to identify the significant regulators across several inflammatory skin diseases. With conventional transcriptome analysis, we identified 55 shared genes, which are enriched in several immune-associated pathways in eight inflammatory skin diseases. Next, we exploited the gene co-expression-, and protein-protein interaction-based networks to identify shared genes and protein components in different diseases with relevant functional implications. Additionally, the network analytics unravels 55 high-value proteins as significant regulators in molecular pathogenesis. We believe that these significant regulators should be explored with critical experimental approaches to identify the putative drug targets for more effective treatments. As an example, we identified IKZF1 as a shared significant master regulator in three inflammatory skin diseases, which can serve as a putative drug target with known disease-derived molecules for developing efficacious combinatorial treatments for hidradenitis suppurativa, atopic dermatitis, and rosacea. The proposed framework is very modular, which can indicate a significant path of molecular mechanism-based drug development from complex transcriptomics data and other multi-omics data.

Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis.

Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of high-priority transcription factors (TFs), dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We identified distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficient nodes. Dynamic transcriptional regulatory modeling of integrated TF targets and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs, as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that could potentially be used in future genetic crop engineering programs.

Comparative study of the efficacy of Ionic Silver Solution and Super Oxidized Solution in the management of chronic wounds.

Background: Chronic wounds are of many etiologies and difficult to treat. Many commercial products to manage such wounds are available, which claim to have good outcomes. Aim of this study was to compare the efficacy of Ionic Silver Solution and Super Oxidized Solution in the management of chronic wounds. Methods: Patients with chronic wounds were randomly placed in two groups-Group A (Ionic Silver Solution) and Group B (Super Oxidized Solution) with 30 patients each. The dressings were continued until the wound healed completely or the wound was ready for a definitive procedure. Wound parameters were recorded as per Bates Jensen Wound Assessment Tool (BJWAT) Score. Results: FIfty patients completed the study. The scores were compared at the initiation and endpoint of treatment. The pretreatment total for BJWAT was 916 and 924 in group A and group B respectively, which was not statistically significant. Post-treatment improvement was noticed in both the groups and the score decreased to 510 and 675 in group A and group B respectively (p = 0.001). Ionic Silver Solution and Super Oxidized Solution both were found to be effective in improving the overall wound condition. However, Ionic Silver Solution was found to be more effective than Super Oxidized Solution in the healing of chronic wounds. Complete healing was noticed in a small number (6%) of patients. These agents can therefore best prepare the wounds for early surgical intervention. Conclusion: Both the agents were found to be safe and useful in the management of chronic wounds. However, Ionic Silver Solution was found to be more effective than the super oxidized solution in this study.

A pipeline of integrating transcriptome and interactome to elucidate central nodes in host-pathogens interactions.

Investigating the complexity of host-pathogen interactions is challenging. Here, we outline a pipeline to identify important proteins and signaling molecules in human-viral interactomes. Firstly, we curate a comprehensive human interactome. Subsequently, we infer viral targets and transcriptome-specific human interactomes (VTTSHI) for papillomavirus and herpes viruses by integrating viral targets and transcriptome data. Finally, we reveal the common and shared nodes and pathways in viral pathogenesis following network topology and pathway enrichment analyses. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2020).

Sparking a sulfur war between plants and pathogens.

The biochemical versatility of sulfur (S) lends itself to myriad roles in plant-pathogen interactions. This review evaluates the current understanding of mechanisms by which pathogens acquire S from their plant hosts and highlights new evidence that plants can limit S availability during the immune responses. We discuss the discovery of host disease-susceptibility genes related to S that can be genetically manipulated to create new crop resistance. Finally, we summarize future research challenges and propose a research agenda that leverages systems biology approaches for a holistic understanding of this important element's diverse roles in plant disease resistance and susceptibility.

A rice protein interaction network reveals high centrality nodes and candidate pathogen effector targets.

Network science identifies key players in diverse biological systems including host-pathogen interactions. We demonstrated a scale-free network property for a comprehensive rice protein-protein interactome (RicePPInets) that exhibits nodes with increased centrality indices. While weighted k-shell decomposition was shown efficacious to predict pathogen effector targets in Arabidopsis, we improved its computational code for a broader implementation on large-scale networks including RicePPInets. We determined that nodes residing within the internal layers of RicePPInets are poised to be the most influential, central, and effective information spreaders. To identify central players and modules through network topology analyses, we integrated RicePPInets and co-expression networks representing susceptible and resistant responses to strains of the bacterial pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola (Xoc) and generated a RIce-Xanthomonas INteractome (RIXIN). This revealed that previously identified candidate targets of pathogen transcription activator-like (TAL) effectors are enriched in nodes with enhanced connectivity, bottlenecks, and information spreaders that are located in the inner layers of the network, and these nodes are involved in several important biological processes. Overall, our integrative multi-omics network-based platform provides a potentially useful approach to prioritizing candidate pathogen effector targets for functional validation, suggesting that this computational framework can be broadly translatable to other complex pathosystems.

Protective effect of Celastrus paniculatus on cognitive function in glutamate-induced brain-injured mice by reducing the intracellular influx of Ca.

Present investigation evaluates the protective effect of Celastrus paniculatus (CP) on the cognitive function in neuronal injured mice. Neuronal injury was induced by oral administration of monosodium glutamate (MSG) at a dose of 1.66 g/kg/day for 30 days. Mice in the CP-treated group receives CP 30 mg/kg ip and CP + GGA-treated group received CP 30 mg/kg ip and glutamic acid (GGA, 1.5 mg/kg, ip) 30 min prior to the administration of MSG for 30 days. Assessment of cognitive function was done using Morris water maze. Level of inflammatory cytokines and production of reactive oxygen species (ROS) was estimated in the brain tissue of brain-injured mice. Moreover, intracellular concentration of Ca+ ion was estimated in the brain tissue and expression of Bcl-2, Bax, and caspase-3 protein was estimated in the brain tissue by western blot assay. Cognitive function was attenuated in CP-treated glutamate-injured mice. Data of the study suggest that treatment with CP reduces the level of inflammatory cytokines and production of ROS in the brain tissue compared to negative control group. There was reduction in the concentration of Ca+ ion in the neuronal cells in CP-treated group than negative control group of mice. Treatment with CP ameliorates the expression of Bax, Bcl-2, and caspase-3 in the brain tissue of glutamate-induced brain-injured mice. In conclusion, data of the study suggest that treatment with CP attenuates the cognitive function and neuronal apoptosis in glutamate-induced neuronal injury by reducing the concentration of intracellular Ca+ ion.

Salvage of Infected Cardiac Implantable Electrical Devices with Subpectoral Plane Pocket Revision.

Introduction Infection of cardiac implantable electrical devices (CIEDs) may lead to serious complications. Complete CIED explantation is expensive, requires expertise, not free from complications, and may not be an option in patients with device dependence. Aim To highlight that carefully selected infected CIEDs can be salvaged by placing the device in a subpectoral pocket below the pectoralis major muscle. We conducted a retrospective descriptive observational study. Material and Methods Twelve patients (10 male and two female) with erosion, exposure or infection of infraclavicular, subcutaneously placed CIED were treated over a 30-month period between July 2018 and December 2020. The technique involved debridement and excision of a peridevice capsule, creating a subpectoral pocket beneath the pectoralis major muscle, and placing the CIED in a new pocket with total muscle coverage and closure of skin without tension. Results Twelve patients ( m = 10; f = 2) with a mean age of 65 years (range, 46-82 years) presented with infection of CIED within 9 months of implantation. None had sepsis or endocarditis. In nine patients, CIEDs were successfully salvaged with relocation to subpectoral pocket. Mean follow-up was 20 months (range, 8-30 months). Three out of 12 developed reinfection that ultimately required CIED explantation. There was no mortality. Conclusion In the absence of sepsis or endocarditis, infected CIEDs may be attempted at salvage by subpectoral pocket placement. This obviates the need for potentially risky explantation or replacement of expensive CIEDs.

Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC.

With the advent of recent next-generation sequencing (NGS) technologies in genomics, transcriptomics, and epigenomics, profiling single-cell sequencing became possible. The single-cell RNA sequencing (scRNA-seq) is widely used to characterize diverse cell populations and ascertain cell type-specific regulatory mechanisms. The gene regulatory network (GRN) mainly consists of genes and their regulators-transcription factors (TF). Here, we describe the lightning-fast Python implementation of the SCENIC (Single-Cell reEgulatory Network Inference and Clustering) pipeline called pySCENIC. Using single-cell RNA-seq data, it maps TFs onto gene regulatory networks and integrates various cell types to infer cell-specific GRNs. There are two fast and efficient GRN inference algorithms, GRNBoost2 and GENIE3, optionally available with pySCENIC. The pipeline has three steps: (1) identification of potential TF targets based on co-expression; (2) TF-motif enrichment analysis to identify the direct targets (regulons); and (3) scoring the activity of regulons (or other gene sets) on single cell types.

Dynamic Regulatory Event Mining by iDREM in Large-Scale Multi-omics Datasets During Biotic and Abiotic Stress in Plants.

The system-wide complexity of genome regulation encoding the organism phenotypic diversity is well understood. However, a major challenge persists about the appropriate method to describe the systematic dynamic genome regulation event utilizing enormous multi-omics datasets. Here, we describe Interactive Dynamic Regulatory Events Miner (iDREM) which reconstructs gene-regulatory networks from temporal transcriptome, proteome, and epigenome datasets during stress to envisage "master" regulators by simulating cascades of temporal transcription-regulatory and interactome events. The iDREM is a Java-based software that integrates static and time-series transcriptomics and proteomics datasets, transcription factor (TF)-target interactions, microRNA (miRNA)-target interaction, and protein-protein interactions to reconstruct temporal regulatory network and identify significant regulators in an unsupervised manner. The hidden Markov model detects specialized manipulated pathways as well as genes to recognize statistically significant regulators (TFs/miRNAs) that diverge in temporal activity. This method can be translated to any biotic or abiotic stress in plants and animals to predict the master regulators from condition-specific multi-omics datasets including host-pathogen interactions for comprehensive understanding of manipulated biological pathways.

Network biology to uncover functional and structural properties of the plant immune system.

In the last two decades, advances in network science have facilitated the discovery of important systems' entities in diverse biological networks. This graph-based technique has revealed numerous emergent properties of a system that enable us to understand several complex biological processes including plant immune systems. With the accumulation of multiomics data sets, the comprehensive understanding of plant-pathogen interactions can be achieved through the analyses and efficacious integration of multidimensional qualitative and quantitative relationships among the components of hosts and their microbes. This review highlights comparative network topology analyses in plant-pathogen co-expression networks and interactomes, outlines dynamic network modeling for cell-specific immune regulatory networks, and discusses the new frontiers of single-cell sequencing as well as multiomics data integration that are necessary for unraveling the intricacies of plant immune systems.

Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity.

Macrophages are ubiquitous custodians of tissues, which play decisive role in maintaining cellular homeostasis through regulatory immune responses. Within tissues, macrophage exhibit extremely heterogeneous population with varying functions orchestrated through regulatory response, which can be further exacerbated in diverse genetic backgrounds. Gene regulatory networks (GRNs) offer comprehensive understanding of cellular regulatory behavior by unfolding the transcription factors (TFs) and regulated target genes. RNA-Seq coupled with ATAC-Seq has revolutionized the regulome landscape influenced by gene expression modeling. Here, we employ an integrative multi-omics systems biology-based analysis and generated GRNs derived from the unstimulated bone marrow-derived macrophages of five inbred genetically defined murine strains, which are reported to be linked with most of the population-wide human genetic variants. Our probabilistic modeling of a basal hemostasis pan regulatory repertoire in diverse macrophages discovered 96 TFs targeting 6279 genes representing 468,291 interactions across five inbred murine strains. Subsequently, we identify core and distinctive GRN sub-networks in unstimulated macrophages to describe the system-wide conservation and dissimilarities, respectively across five murine strains. Our study concludes that discrepancies in unstimulated macrophage-specific regulatory networks not only drives the basal functional plasticity within genetic backgrounds, additionally aid in understanding the complexity of racial disparity among the human population during stress.

Dynamic Response of Angle Ply Laminates with Uncertainties Using MARS, ANN-PSO, GPR and ANFIS.

In the present work, for the first time, free vibration response of angle ply laminates with uncertainties is attempted using Multivariate Adaptive Regression Spline (MARS), Artificial Neural Network-Particle Swarm Optimization (ANN-PSO), Gaussian Process Regression (GPR), and Adaptive Network Fuzzy Inference System (ANFIS). The present approach employed 2D C 0 stochastic finite element (FE) model based on the Third Order Shear Deformation Theory (TSDT) in conjunction with MARS, ANN-PSO, GPR, and ANFIS. The TSDT model used eliminates the requirement of shear correction factor owing to the consideration of the actual parabolic distribution of transverse shear stress. Zero transverse shear stress at the top and bottom of the plate is enforced to compute higher-order unknowns. C 0 FE model makes it commercially viable. Stochastic FE analysis done with Monte Carlo Simulation (MCS) FORTRAN inhouse code, selection of design points using a random variable framework, and soft computing with MARS, ANN-PSO, GPR, and ANFIS is implemented using MATLAB in-house code. Following the random variable frame, design points were selected from the input data generated through Monte Carlo Simulation. A total of four-mode shapes are analyzed in the present study. The comparison study was done to compare present work with results in the literature and they were found in good agreement. The stochastic parameters are Young's elastic modulus, shear modulus, and the Poisson ratio. Lognormal distribution of properties is assumed in the present work. The current soft computation models shrink the number of trials and were found computationally efficient as the MCS-based FE modelling. The paper presents a comparison of MARS, ANN-PSO, GPR, and ANFIS algorithm performance with the stochastic FE model based on TSDT.

Dynamic Regulation of the Nexus Between Stress Granules, Roquin, and Regnase-1 Underlies the Molecular Pathogenesis of Warfare Vesicants.

The use of chemical warfare agents is prohibited but they have been used in recent Middle Eastern conflicts. Their accidental exposure (e.g. arsenical lewisite) is also known and causes extensive painful cutaneous injury. However, their molecular pathogenesis is not understood. Here, we demonstrate that a nexus of stress granules (SGs), integrated stress, and RNA binding proteins (RBPs) Roquin and Reganse-1 play a key role. Lewisite and its prototype phenylarsine oxide (PAO) induce SG assembly in skin keratinocytes soon after exposure, which associate with various RBPs and translation-related proteins. SG disassembly was detected several hours after exposure. The dynamics of SG assembly-disassembly associates with the chemical insult and cell damage. Enhanced Roquin and Regnase-1 expression occurs when Roquin was recruited to SGs and Regnase-1 to the ribosome while in the disassembling SGs their expression is decreased with consequent induction of inflammatory mediators. SG-targeted protein translational control is regulated by the phosphorylation-dependent activation of eukaryotic initiation factors 2α (eIF2α). Treatment with integrated stress response inhibitor (ISRIB), which blocks eIF2α phosphorylation, impacted SG assembly dynamics. Topical application of ISRIB attenuated the inflammation and tissue disruption in PAO-challenged mice. Thus, the dynamic regulation of these pathways provides underpinning to cutaneous injury and identify translational therapeutic approach for these and similar debilitating chemicals.