Network analysis of transcriptomic data uncovers molecular signatures and the interplay of mRNAs, lncRNAs, and miRNAs in human embryonic stem cells.

Growing evidence has shown that besides the protein coding genes, the non-coding elements of the genome are indispensable for maintaining the property of self-renewal in human embryonic stem cells and in cell fate determination. However, the regulatory mechanisms and the landscape of interactions between the coding and non-coding elements is poorly understood. In this work, we used weighted gene co-expression network analysis (WGCNA) on transcriptomic data retrieved from RNA-seq and small RNA-seq experiments and reconstructed the core human pluripotency network (called PluriMLMiNet) consisting of 375 mRNA, 57 lncRNA and 207 miRNAs. Furthermore, we derived networks specific to the naïve and primed states of human pluripotency (called NaiveMLMiNet and PrimedMLMiNet respectively) that revealed a set of molecular markers (RPS6KA1, ZYG11A, ZNF695, ZNF273, and NLRP2 for naive state, and RAB34, TMEM178B, PTPRZ1, USP44, KIF1A and LRRN1 for primed state) which can be used to distinguish the pluripotent state from the non-pluripotent state and also to identify the intra-pluripotency states (i.e., naïve and primed state). The lncRNA DANT1 was found to be a crucial as it formed a bridge between the naive and primed state-specific networks. Analysis of the genes neighbouring DANT1 suggested its possible role as a competing endogenous RNA (ceRNA) for the induction and maintenance of human pluripotency. This was computationally validated by predicting the missing DANT1-miRNA interactions to complete the ceRNA circuit. Here we first report that DANT1 might harbour binding sites for miRNAs hsa-miR-30c-2-3p, hsa-miR-210-3p and hsa-let-7b-5p which may influence pluripotency.

Network approaches for modeling the effect of drugs and diseases.

The network approach is quickly becoming a fundamental building block of computational methods aiming at elucidating the mechanism of action (MoA) and therapeutic effect of drugs. By modeling the effect of drugs and diseases on different biological networks, it is possible to better explain the interplay between disease perturbations and drug targets as well as how drug compounds induce favorable biological responses and/or adverse effects. Omics technologies have been extensively used to generate the data needed to study the mechanisms of action of drugs and diseases. These data are often exploited to define condition-specific networks and to study whether drugs can reverse disease perturbations. In this review, we describe network data mining algorithms that are commonly used to study drug's MoA and to improve our understanding of the basis of chronic diseases. These methods can support fundamental stages of the drug development process, including the identification of putative drug targets, the in silico screening of drug compounds and drug combinations for the treatment of diseases. We also discuss recent studies using biological and omics-driven networks to search for possible repurposed FDA-approved drug treatments for SARS-CoV-2 infections (COVID-19).

Cholesterol-Induced Nanoscale Variations in the Thickness of Phospholipid Membranes.

Graphene-induced energy transfer (GIET) is a recently developed fluorescence-spectroscopic technique that achieves subnanometric optical localization of fluorophores along the optical axis of a microscope. GIET is based on the near-field energy transfer from an optically excited fluorescent molecule to a single sheet of graphene. It has been successfully used for estimating interleaflet distances of single lipid bilayers and for investigating the membrane organization of living mitochondria. In this study, we use GIET to measure the cholesterol-induced subtle changes of membrane thickness at the nanoscale. We quantify membrane thickness variations in supported lipid bilayers (SLBs) as a function of lipid composition and increasing cholesterol content. Our findings demonstrate that GIET is an extremely sensitive tool for investigating nanometric structural changes in biomembranes.

Effects of constant darkness on behaviour and physiology of male and female mice.

A healthy state of life suggests not only a disease-free condition but also normal psychological functioning and behaviour. To maintain a healthy life, the duration of light exposure is a crucial factor. Perturbation of the standard light-dark cycle (LD: 12 h light-12 h dark in mice) may result in brain, behavioural and physiological abnormalities. The current study determined the effects of 3 and 5 weeks of constant darkness (DD: 00 h light-24 h dark) on the behaviour, hormones, prefrontal cortex (PFC) and metabolome of male and female C57BL/6 J mice. We also studied 3 weeks of restoration in LD following 5 weeks of DD exposure. The results revealed that 3 weeks of DD affected male mice more than females, and 5 weeks of DD had a comparable impact on behaviour, hormones and the PFC of male and female mice. After restoration in LD, the DD-induced changes reverted to time-matched LD conditions in male and female mice. Furthermore, metabolome analysis corroborated male and female mice's behavioural and molecular kinetics. The present study laid the foundation for understanding how DD affects behaviour and the PFC as a function of (a) time and (b) sex and described the roles of stress and sex hormones, cytokines, neurotrophins and metabolic pathways.

EDTox: an R Shiny application to predict the endocrine disruption potential of compounds.

PURPOSE: Endocrine disruptors are a rising concern due to the wide array of health issues that it can cause. Although there are tools for mode of action (MoA)-based prediction of endocrine disruption (e.g. QSAR Toolbox and iSafeRat), none of them is based on toxicogenomics data. Here, we present EDTox, an R Shiny application enabling users to explore and use a computational method that we have recently published to identify and prioritize endocrine disrupting (ED) chemicals based on toxicogenomic data. The EDTox pipeline utilizes previously trained toxicogenomic-driven classifiers to make predictions on new untested compounds by using their molecular initiating events. Furthermore, the proposed R Shiny app allows users to extend the prediction systems by training and adding new classifiers based on new available toxicogenomic data. This functionality helps users to explore the ED potential of chemicals in new, untested exposure scenarios. AVAILABILITY AND IMPLEMENTATION: This tool is available as web application (www.edtox.fi) and stand-alone software on GitHub and Zenodo (https://doi.org/10.5281/zenodo.5817093). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Quantum Hall Interferometry in Triangular Domains of Marginally Twisted Bilayer Graphene.

Quantum Hall (QH) interferometry provides an archetypal platform for the experimental realization of braiding statistics of fractional QH states. However, the complexity of observing fractional statistics requires phase coherence over the length of the interferometer, as well as suppression of Coulomb charging energy. Here, we demonstrate a new type of QH interferometer based on marginally twisted bilayer graphene (mtBLG), with a twist angle θ ≈ 0.16°. With the device operating in the QH regime, we observe distinct signatures of electronic Fabry-Pérot and Aharonov-Bohm oscillations of the magneto-thermopower in the density-magnetic field phase space, at Landau level filling factors ν = 4, 8. We find that QH interference effects are intrinsic to the triangular AB/BA domains in mtBLG that show diminished Coulomb charging effects. Our results demonstrate phase-coherent interference of QH edge modes without any additional gate-defined complex architecture, which may be beneficial in experimental realizations of non-Abelian braiding statistics.

Pediatric Colonic Anastomosis: Can Method of Anastomosis and Wound Closure be of Help?

Background: Enhanced recovery after surgery (ERAS) protocols after colorectal surgery focused on reduced bowel preparation, standardized feeding schedule, earlier return of bowel function, and earlier resumption of normal activities. ERAS in pediatric surgical practice is not well established. The present study aims to present the results of two colonic anastomosis techniques of interrupted single-layered closure: Halsted (Horizontal Mattress) and Matheson (serosubmucosal or appositional extramucosal) along with two different methods of colostomy wound closure and their influence on the adoption of ERAS protocol of early feeding and early discharge. Materials and Methods: This single institute-based randomized control study was conducted in a tertiary care facility in Kolkata for 2.4 years. Patients were chosen randomly for serosubmucosal (Group I) and full-thickness (Group II) anastomosis. Results: Among total of 91 patients (Group I-43 and Group II-48), Return of bowel sounds and passage of bowel averaged 1.51 ± 0.51 and 1.91 ± 0.55 days in Group I and 1.91 ± 0.57 and 3.9 ± 0.66 days in Group II, respectively. Postoperative hospital stay averaged 5.88 ± 1.12 days in Group I and 8.9 ± 1.17 days in Group II. Overall 15 (16.48%) patients had complications among which SSI (Suprficial surgical site infection) and minor leaks (Group I-3 and 1 and Group II-5 and 3, respectively) which were treated conservatively (Clavien-Dindo Grade-I) and three major leaks under Group II requiring surgical intervention (Clavien-Dindo Grade-III). Conclusion: This study concludes that the technique of colostomy closure in the form serosubmucosal closure helps in the implementation of ERAS protocol by producing early bowel movement, early initiation of food, and less postoperative complications.

High-Efficiency Infrared Sensing with Optically Excited Graphene-Transition Metal Dichalcogenide Heterostructures.

Binary van der Waals heterostructures of graphene (Gr) and transition metal dichalcogenide (TMDC) have evolved as a promising candidate for photodetection with very high responsivity due to the separation of photo-excited electron-hole pairs across the interface. The spectral range of optoelectronic response in such hybrids has so far been limited by the optical bandgap of the light absorbing TMDC layer. Here, the bidirectionality of interlayer charge transfer is utilized for detecting sub-band gap photons in Gr-TMDC heterostructures. A Gr/MoSe2 heterostructure sequentially driven by visible and near infra-red (NIR) photons is employed, to demonstrate that NIR induced back transfer of charge allows fast and repeatable detection of the low energy photons (less than the optical band gap of the TMDC layer). This mechanism provides photoresponsivity as high as ≈3000 A W-1 close to the communication wavelength. The experiment provides a new strategy for achieving highly efficient photodetection over a broad range of energies beyond the spectral bandgap with the 2D semiconductor family.

Mapping Activity-Dependent Quasi-stationary States of Mitochondrial Membranes with Graphene-Induced Energy Transfer Imaging.

Graphene-induced energy transfer (GIET) was recently introduced for sub-nanometric axial localization of fluorescent molecules. GIET relies on near-field energy transfer from an optically excited fluorophore to a single sheet of graphene. Recently, we demonstrated its potential by determining the distance between two leaflets of supported lipid bilayers. Here, we use GIET imaging for mapping quasi-stationary states of the inner and outer mitochondrial membranes before and during adenosine triphosphate (ATP) synthesis. We trigger the ATP synthesis state in vitro by activating mitochondria with precursor molecules. Our results demonstrate that the inner membrane approaches the outer membrane, while the outer membrane does not show any measurable change in average axial position upon activation. The inter-membrane space is reduced by ∼2 nm. This direct experimental observation of the subtle dynamics of mitochondrial membranes and the change in intermembrane distance upon activation is relevant for our understanding of mitochondrial function.

Evidence of Lifshitz Transition in the Thermoelectric Power of Ultrahigh-Mobility Bilayer Graphene.

Resolving low-energy features in the density of states (DOS) holds the key to understanding a wide variety of rich novel phenomena in graphene-based 2D heterostructures. The Lifshitz transition in bilayer graphene (BLG) arising from trigonal warping has been established theoretically and experimentally. Nevertheless, the experimental realization of its effects on transport properties has been challenging because of its relatively low energy scale (∼1 meV). In this work, we demonstrate that the thermoelectric power (TEP) can be used as an effective probe to investigate fine changes in the DOS of BLG. We observed additional entropy features in the vicinity of the charge neutrality point (CNP) in gapped BLG. This apparent violation of the Mott formula can be explained quantitatively by considering the effects of trigonal warping, thereby serving as possible evidence of a Lifshitz transition.

Congenital Sacrococcygeal Neuroblastoma: A Report of Two Cases with Summary of Prior Published Cases.

BackgroundNeuroblastoma can arise from extra-adrenal sites in the paraspinal sympathetic chain, including the presacral region, where they must be differentiated from an immature or malignant neural lesion arising from a teratoma.Case ReportWe describe two congenital presacral neuroblastomas. The main clinical differential diagnoses were sacrococcygeal teratoma and meningomyelocele. Pathologically, they lacked teratomatous tissues, lacked germ cell serum markers, were localized without metastases, and were MYCN non-amplified. Both patients have done well without chemotherapy at 18 and 15 months of follow-up.ConclusionCongenital presacral neuroblastoma should be differentiated from teratomatous lesions, and in general have a good prognosis.

Clinico-demographic Profile and Predictors of Intensive Care Need in Children with Respiratory Syncytial Virus-associated Acute Lower Respiratory Illness during Its Recent Outbreak alongside Ongoing COVID-19 Pandemic: An Eastern Indian Perspective.

Introduction: The objective was to delineate the clinico-epidemiological characteristics of hospitalized children with respiratory syncytial virus (RSV)-associated acute lower respiratory tract infection (RSV-ALRI) during its recent outbreak and to find out the independent predictors of pediatric intensive care unit (PICU) admission. Materials and methods: Children aged between 1 month and 12 years who tested positive for RSV were included. Multivariate analysis was performed to identify the independent predictors and predictive scores were developed from the ß-coefficients. Receiver operating characteristic curve (ROC) was generated and the area under the curve (AUC) was calculated to assess the overall precision. The performance of sum scores in predicting PICU need, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and positive and negative likelihood ratios (LR+ and LR-) were calculated for each cutoff value. Results: The proportion of RSV positivity was 72.58%. A total of 127 children were included with a median [interquartile range (IQR)] age of 6 (2-12) months, of whom 61.42% were males and 33.07% had underlying comorbidity. Tachypnea, cough, rhinorrhea, and fever were predominant clinical presentations while hypoxia and extrapulmonary manifestations were present in 30.71% and 14.96% of children, respectively. About 30% required PICU admission, and 24.41% developed complications. Premature birth, age below 1 year, presence of underlying CHD, and hypoxia were independent predictors. The AUC [95% confidence interval (CI)] was 0.869 (0.843-0.935). Sum score below 4 had 97.3% sensitivity and 97.1% NPV whereas sum score above 6 had 98.9% specificity, 89.7% PPV, 81.3% NPV, 46.2 LR+, and 0.83 LR- to predict PICU needs. Conclusion: Awareness of these independent predictors and application of the novel scoring system will be beneficial for busy clinicians in planning the level of care needed, thereby optimizing PICU resource utilization. How to cite this article: Ghosh A, Annigeri S, Hemram SK, Dey PK, Mazumder S. Clinico-demographic Profile and Predictors of Intensive Care Need in Children with Respiratory Syncytial Virus-associated Acute Lower Respiratory Illness during Its Recent Outbreak alongside Ongoing COVID-19 Pandemic: An Eastern Indian Perspective. Indian J Crit Care Med 2022;26(11):1210-1217.

14-3-3 proteins protect AMPK-phosphorylated ten-eleven translocation-2 (TET2) from PP2A-mediated dephosphorylation.

Ten-eleven translocation-2 (TET2) is a member of the methylcytosine dioxygenase family of enzymes and has been implicated in cancer and aging because of its role as a global epigenetic modifier. TET2 has a large N-terminal domain and a catalytic C-terminal region. Previous reports have demonstrated that the TET2 catalytic domain remains active independently of the N-terminal domain. As such, the function of the N terminus of this large protein remains poorly characterized. Here, using yeast two-hybrid screening, co-immunoprecipitation, and several biochemical assays, we found that several isoforms of the 14-3-3 family of proteins bind TET2. 14-3-3 proteins bound TET2 when it was phosphorylated at Ser-99. In particular, we observed that AMP-activated protein kinase-mediated phosphorylation at Ser-99 promotes TET2 stability and increases global DNA 5-hydroxymethylcytosine levels. The interaction of 14-3-3 proteins with TET2 protected the Ser-99 phosphorylation, and disruption of this interaction both reduced TET2 phosphorylation and decreased TET2 stability. Furthermore, we noted that protein phosphatase 2A can interact with TET2 and dephosphorylate Ser-99. Collectively, these results provide detailed insights into the role of the TET2 N-terminal domain in TET2 regulation. Moreover, they reveal the dynamic nature of TET2 protein regulation that could have therapeutic implications for disease states resulting from reduced TET2 levels or activity.

Spontaneous Time-Reversal Symmetry Breaking at Individual Grain Boundaries in Graphene.

Graphene grain boundaries (GBs) have attracted interest for their ability to host nearly dispersionless electronic bands and magnetic instabilities. Here, we employ quantum transport and universal conductance fluctuation measurements to experimentally demonstrate a spontaneous breaking of time-reversal symmetry across individual GBs of chemical vapor deposited graphene. While quantum transport across the GBs indicate spin-scattering-induced dephasing and hence formation of local magnetic moments, below T≲4 K we observe complete lifting of time-reversal symmetry at high carrier densities (n≳5×10^{12} cm^{-2}) and low temperature (T≲2 K). An unprecedented thirtyfold reduction in the universal conductance fluctuation magnitude with increasing doping density further supports the possibility of an emergent frozen magnetic state at the GBs. Our experimental results suggest that realistic GBs of graphene can be a promising resource for new electronic phases and spin-based applications.

Defects-assisted piezoelectric response in liquid exfoliated MoS2nanosheets.

MoS2is an intrinsic piezoelectric material which offers applications such as energy harvesting, sensors, actuators, flexible electronics, energy storage and more. Surprisingly, there are not any suitable, yet economical methods that can produce quality nanosheets of MoS2in large quantities, hence limiting the possibility of commercialisation of its applications. Here, we demonstrate controlled synthesis of highly crystalline MoS2nanosheets via liquid phase exfoliation of bulk MoS2, following which we report piezoelectric response from the exfoliated nanosheets. The method of piezo force microscopy was employed to explore the piezo response in mono, bi, tri and multilayers of MoS2nanosheets. The effective piezoelectric coefficient of MoS2varies from 9.6 to 25.14 pm V-1. We attribute piezoelectric response in MoS2nanosheets to the defects formed in it during the synthesis procedure. The presence of defects is confirmed by x-ray photoelectron spectroscopy.

A simple fabrication strategy for orientationally accurate twisted heterostructures.

Van der Waals (vdW) heterostructure is a type of metamaterial where multiple layers of 2D materials are vertically aligned at controlled misorientation. The relative rotation in between the adjacent layers, or the twist angle between them plays a crucial role in changing the electronic band structure of the superlattice. The assembly of multi-layers of precisely twisted two dimensional layered materials requires knowledge of the atomic structure at the edge of the flake. It may be artificially created by the 'tear and stack' process. Otherwise, the crystallographic orientation needs to be determined through invasive processes such as transmission electron microscopy or scanning tunneling microscopy, and via second-harmonic generation (SHG). Here, we demonstrate a simple and elegant transfer protocol using only an optical microscope as a edge identifier tool through which, controlled transfer of twisted homobilayer and heterobilayer transition metal dichalcogenides is performed with close to 100% yield. The fabricated twisted vdW heterostructures have been characterized by SHG, Raman spectroscopy and photoluminiscence spectroscopy, confirming the desired twist angle within ∼0.5° accuracy. The presented method is reliable, quick and prevents the use of invasive tools which is desirable for reproducible device functionalities.

Atypical Presentation of Fulminating Subacute Sclerosing Panencephalitis: A Case Series.

Subacute sclerosing panencephalitis (SSPE) is a rare and progressive inflammatory disease of central nervous system due to aberrant measles virus with an outcome that is nearly always fatal. In acute fulminant SSPE, the disease rapidly evolves leading to death within 3 months of the diagnosis. We report here four cases of fulminant SSPE with atypical presentations, two of them presented at very early age with history of congenital measles infection in first case and gait abnormality as initial symptom in second case; acute disseminated encephalomyelitis (ADEM) with refractory seizures in third case, unilateral myoclonus with hemiparesis in fourth case at the onset of disease, respectively. The typical periodic electroencephalographic (EEG) complexes, elevated cerebrospinal fluid (CSF), and serum antimeasles antibodies in our patients led to the diagnosis of SSPE. A high index of clinical suspicion in fulminant type with awareness of atypical features, EEG, and CSF studies are of paramount importance in establishing its diagnosis.

Low-dose steroid-induced bradyarrhythmias and treatment refractory hypokalaemia: a case report.

Corticosteroid therapy has become an important modality of treatment for diseases in which rapid control of immunoinflammatory processes is required. However, one of the serious, but less known adverse effect of this therapy is cardiac arrhythmias. This includes both tachyarrhythmias and bradyarrhythmias. Corticosteroid use may also be associated with electrolyte imbalances like hypokalaemia by its mineralocorticoid activity. Those side effects are mainly seen with high-dose intravenous methyl-prednisolone or oral pulse dose prednisolone therapy. Here we report our experience in a child with warm idiopathic autoimmune haemolytic anaemia who developed sinus bradyarrhythmias and treatment refractory hypokalaemia during low-dose steroid therapy with reduction in heart rate by 60% of baseline.

Rare and Atypical Presentations of Acute Disseminated Encephalomyelitis in Children: A Case Series.

Acute disseminated encephalomyelitis (ADEM) is a monophasic demyelinating disorder of central nervous system occurring in children with a wide range of clinical manifestations after infection or vaccination. There are few case reports in literature, describing atypical presentations of ADEM with fever of unknown origin, autonomic dysfunction, complex movement disorders such as myoclonus, dystonia and chorea, acute psychosis and myocarditis. Here, we report four cases of ADEM with atypical features like uniocular blindness, myelin oligodendrocyte glycoprotein antibodies negative multiphasic disseminated encephalomyelitis, ADEM mimicking Guillain-Barre syndrome at presentation and isolated spinal ADEM. Treatment with high-dose steroids elicited an excellent neurological outcome in all patients. A high index of clinical suspicion along-with awareness of atypical features, magnetic resonance imaging and cerebrospinal fluid studies are of paramount importance in establishing ADEM diagnosis and initiation of early treatment for better outcome.

Dimerization of Human Drebrin-like Protein Governs Its Biological Activity.

Drebrin-like protein (DBNL) is a multidomain F-actin-binding protein, which also interacts with other molecules within different intracellular pathways. Here, we present quantitative measurements on the size and conformation of human DBNL. Using dual-focus fluorescence correlation spectroscopy, we determined the hydrodynamic radius of the DBNL monomer. Native gel electrophoresis and dual-color fluorescence cross-correlation spectroscopy show that both endogenous DBNL and recombinant DBNL exist as dimers under physiological conditions. We demonstrate that C-terminal truncations of DBNL downstream of the coiled-coil domain result in its oligomerization at nanomolar concentrations. In contrast, the ADF-H domain alone is a monomer, which displays a concentration-dependent self-assembly. In vivo FLIM-FRET imaging shows that the presence of only actin-binding domains is not sufficient for DBNL to localize properly at the actin filament inside the cell. In summary, our work provides detailed insight into the structure-function relationship of human drebrin-like protein.