Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes.

Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana. A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.

Development of TaqMan Probe-Based One-Step RT-qPCR Assay Targeting 2B-NSP Coding Region for Diagnosis of Foot-and-Mouth Disease in India.

A one-step TaqMan probe-based RT-qPCR assay in the duplex format simultaneously targeting FMD Virus (FMDV) 2B NSP-coding region and 18S rRNA housekeeping gene was developed and evaluated. The duplex RT-qPCR assay specifically detected FMDV genome in both infected cell culture suspensions and a variety of clinical samples such as FMD-affected tongue/feet epithelium, oral/nasal swabs, milk and oro-pharyngeal fluids. The RT-qPCR assay was found to be highly sensitive, since the assay was 105-fold more sensitive than the traditional FMDV detecting antigen-ELISA (Ag-ELISA) and 102-fold better sensitive than both virus isolation and agarose gel-based RT-multiplex PCR. In addition, the assay could detect up to 100 copies of FMDV genome per reaction. In the epithelial samples (n = 582) collected from the FMD-affected animals, the diagnostic sensitivity was 100% (95% CI 99-100%). Similarly, all the FMDV-negative samples (n = 65) tested were confirmed negative by the new RT-qPCR assay, corresponding to 100% diagnostic specificity (95% CI = 94-100%). Further, the duplex RT-qPCR assay proved to be robust, showing an inter-assay co-efficient of variations ranging from 1.4 to 3.56% for FMDV-2B gene target, and from 2 to 4.12% for 18S rRNA gene target. While analyzing FMDV-infected cell culture suspension, a fairly strong positive correlation (correlation coefficient = 0.85) was observed between 2B-based RT-qPCR and WOAH-approved 5'UTR RT-qPCR assays. Therefore, the one-step RT-qPCR assay developed here with an internal control could be used for rapid, effective, and reliable detection of FMDV in pan-serotypic manner, and has the potential for routine diagnosis of FMDV in high throughput manner.

Implication of storage conditions on luminescence response from Photobacterium phosphoreum in free and immobilized form.

Bioluminescent bacteria in the form of a cell suspension for on-site hazard analysis are not suitable as in vivo luminescence in free cells fluctuates and may lead to erroneous results. Furthermore, the culture broth cannot be stored for long durations to continue sensing analytes as the luminescence ceases over time. Factors that affect luminescence response include growth dynamism, and ambient environmental conditions. The present study investigated the effect of storage conditions such as temperature (25 ± 2°C, room temperature; 4°C; and -20°C) and ambient aqueous environment (M1: sucrose, 1.02 M; M2, bioluminescent media [tryptone, 10 g L-1 ; NaCl, 28.5 g L-1 ; MgCl2 .7H2 O, 4.5 g L-1 ; CaCl2 , 0.5 g L-1 ; KCl 0.5 g L-1 ; yeast extract, 1 g L-1 ; H2 O, 1 L]; M3, bioluminescent media and 95% glycerol, 1:1 ratio) on the luminescence emission from the calcium alginate-immobilized Photobacterium phosphoreum (Sb ) against the cells in free suspension for an extended period. The results indicated that both the parameters that were undertaken markedly affected the luminescence. In the study, Sb showed an enhanced luminescence emission than the control up to 18.5-fold and for a prolonged period which can be efficiently utilized for rapid biosensing of hazardous materials.

Electronically Tunable Memristor Emulator Implemented Using a Single Active Element and Its Application in Adaptive Learning.

In recent times, much-coveted memristor emulators have found their use in a variety of applications such as neuromorphic computing, analog computations, signal processing, etc. Thus, a 100 MHz flux-controlled memristor emulator is proposed in this research brief. The proposed memristor emulator is designed using a single differential voltage current conveyor (DVCC), three PMOS transistors, and one capacitor. Among three PMOS transistors, two transistors are used to implement an active resistor, and one transistor is used as the multiplier required for the necessary memristive behaviors. Through simple adjustment of the switch, the proposed emulator can be operated in incremental as well as decremental configurations. The simulations are performed using a 180 nm technology node to validate the proposed design and are experimentally verified using AD844AN and CD4007 ICs. The memristor states of the proposed emulator are perfectly retained even in the absence of external stimuli, thereby ascertaining the non-volatility behavior. The robustness of the design is further analyzed using the PVT and Monte Carlo simulations, which suggest that the circuit operation is not hindered by the mismatch and process variations. A simple neuromorphic adaptive learning circuit based on the proposed memristor is also designed as an application.

PROBLEMATIC USE OF SMARTPHONE AND NOMOPHOBIA AMONG MEDICAL AND NURSING UNDERGRADUATE STUDENTS OF A TERTIARY CARE REFERRAL HOSPITAL IN INDIA AND ITS ASSOCIATION WITH QUALITY OF LIFE: A CROSS-SECTIONAL OBSERVATIONAL STUDY.

BACKGROUND: Overuse of smartphone amongst today's young generation has assumed an epidemic proportion. Assessment of severity of Nomophobia and Smartphone use related problems is important as it can help to ascertain the current adverse consequences of Smartphone problematic use. The study aims to assess the association between smartphone dependence, nomophobia and quality of life in undergraduate medical and nursing students in a tertiary care referral hospital cum medical institution in India. SUBJECTS AND METHODS: This cross-sectional study involved 437 medical and nursing undergraduate students, which involved assessing their dependence for smartphone and nomophobia using the Test for Mobile Phone dependence (TMD) questionnaire brief version and Nomophobia Questionnaire (NMP-Q) respectively. RESULTS: The average hours spent on smartphone per day for the study population was 3.2 hours. Smartphone dependence was found in 12% of study participants. Nearly 50% in each batch had moderate degree of nomophobia and around 13-15% had severe nomophobia. Both smartphone dependence and nomophobia were significantly associated with each other and had significant associations with poorer quality of life in the medical and nursing students. Preclinical medical students scored higher in all the domains of Smartphone dependence and nomophobia questionnaire and were associated with poor quality of life compared to other batches. CONCLUSION: Excessive smartphone use is associated with poorer quality of life in medical and nursing students. More studies in future are required that will involve various age groups and other educational streams which willadd up to the existing knowledge on technology addiction.

EFFECT OF PSYCHOLOGICAL FIRST AID ON MENTAL HEALTH IN HOSPITALIZED STABLE COVID-19 PATIENTS: A PRE-POST RESEARCH DESIGN.

BACKGROUND: The COVID-19 pandemic is known to affect mental health of sufferers. Psychological First Aid (PFA) is a mental health service for individuals in crisis, which can be provided to anyone regardless of age and it does not require mental health expertise. Its effect on mental health issues of COVID-19 patients has not been studied effectively. The present study aimed to assess the psychological impact and effect of PFA on mental health in stable COVID-19 hospitalized patients. SUBJECTS AND METHODS: This was an interventional study with a pre-post research design in a tertiary government teaching hospital in eastern India. 93 stable patients who were admitted in a period of a month with COVID-19 were included in the study after obtaining appropriate consent. They were provided PFA (both structured individual and group sessions) by trained nurses. The Depression, Anxiety, and Stress scale (DASS-21) was used to assess depression, anxiety, and stress in the patients before and after intervention. RESULTS: The mean age of study population which comprised of 68.8% males was 56.2 ± 13.7 years. Median scores for depression, anxiety and stress were 4, 6 and 6 on admission and 0, 2 and 2 respectively before discharge after intervention (P<0.001). 13%, 25.9% and 8.6% were the combined percentages scores of patients with varying levels of depression, anxiety and stress at the time of admission which were reduced to 4.3% (P=0.046), 5.4% (P=0.001), 2.2% (P=0.03) respectively before discharge after intervention within one week. CONCLUSION: PFA may be a cost-effective intervention in stable COVID-19 admitted patients who had depression, anxiety, and stress.

Optical temperature sensing by tuning photoluminescence in a wide (visible to near infrared) wavelength range in a Eu3+-doped Bi-based relaxor ferroelectric.

The prevalent material design principles for optical thermometry primarily rely on thermally driven changes in the relative intensities of the thermally coupled levels (TCLs) of rare-earth-doped phosphor materials, where the maximum achievable sensitivity is limited by the energy gap between the TCLs. In this work, a new, to the best of our knowledge, approach to thermometric material design is proposed, which is based on temperature tuning of PL emission from the visible to the NIR region. We demonstrate a model ferroelectric phosphor, Eu3+-doped 0.94(Na1/2Bi1/2TiO3)-0.06(BaTiO3) (NBT-6BT), which, by virtue of the contrasting effects of temperature on PL signals from the host and Eu3+ intraband transitions, can achieve a relative thermal sensitivity as high as 3.05% K-1. This model system provides a promising alternative route for developing self-referencing optical thermometers with high thermal sensitivity and good signal discriminability.

One-step SYBR green-based real-time RT-PCR assay for detection of foot-and-mouth disease virus circulating in India.

Rapid, sensitive, and reliable laboratory detection of foot-and-mouth disease virus (FMDV) infection is essential for containing and controlling virus infection in any geographical area. In this report a SYBR green-based 3Dpol-specific one-step real-time RT-PCR (rRT-PCR) assay was developed for the pan-serotype detection of FMDV in India. The detection limit of the SYBR green-based rRT-PCR was 10-2 TCID50/50 µl, which is 10 times more sensitive than the traditional agarose gel electrophoresis-based RT-multiplex PCR (RT-mPCR). The standard curve exhibited a linear range across 8-log10 units of viral RNA dilution. The reproducibility and specificity of this assay were reasonably high suggesting that the 3Dpol-specific SYBR green rRT-PCR could detect FMDV genome specifically and with little run-to-run variation. The new 3Dpol-specific SYBR green rRT-PCR assay was evaluated alongside the established RT-mPCR using the archived FMDV isolates and clinical field samples from suspected FMD outbreaks. A perfect concordance was observed between the new rRT-PCR and the traditional RT-mPCR on viral RNA in the archived FMDV cell culture isolates tested. Furthermore, 73% of FMDV-suspected clinical samples were detected positive through the 3Dpol-specific SYBR green rRT-PCR, while the detection rate through the traditional RT-mPCR was 57%. Therefore, the SYBR green-based 3Dpol-specific one-step rRT-PCR could be considered as a valuable assay with higher diagnostic sensitivity to complement the routine assays that are being used for FMD virus diagnosis in India.

Leptin signaling impairs macrophage defenses against Salmonella Typhimurium.

The dynamic interplay between metabolism and immune responses in health and disease, by which different immune cells impact on metabolic processes, are being increasingly appreciated. However, the potential of master regulators of metabolism to control innate immunity are less understood. Here, we studied the cross-talk between leptin signaling and macrophage function in the context of bacterial infections. We found that upon infection with Gram-negative pathogens, such as Salmonella Typhimurium, leptin receptor (Lepr) expression increased in both mouse and human macrophages. Unexpectedly, both genetic Lepr ablation in macrophages and global pharmacologic leptin antagonization augmented lysosomal functions, reduced S Typhimurium burden, and diminished inflammation in vitro and in vivo. Mechanistically, we show that leptin induction activates the mTORC2/Akt pathway and subsequently down-regulates Phlpp1 phosphatase, allowing for phosphorylated Akt to impair lysosomal-mediated pathogen clearance. These data highlight a link between leptin signaling, the mTORC2/Phlpp1/Akt axis, and lysosomal activity in macrophages and have important therapeutic implications for modulating innate immunity to combat Gram-negative bacterial infections.

Mediator subunit OsMED14_1 plays an important role in rice development.

Mediator, a multisubunit co-activator complex, regulates transcription in eukaryotes and is involved in diverse processes in Arabidopsis through its different subunits. Here, we have explored developmental aspects of one of the rice Mediator subunit gene OsMED14_1. We analyzed its expression pattern through RNA in situ hybridization and pOsMED14_1:GUS transgenics that showed its expression in roots, leaves, anthers and seeds prominently at younger stages, indicating possible involvement of this subunit in multiple aspects of rice development. To understand the developmental roles of OsMED14_1 in rice, we generated and studied RNAi-based knockdown rice plants that showed multiple effects including less height, narrower leaves and culms with reduced vasculature, lesser lateral root branching, defective microspore development, reduced panicle branching and seed set, and smaller seeds. Histological analyses showed that slender organs were caused by reduction in both cell number and cell size in OsMED14_1 knockdown plants. Flow cytometric analyses and expression analyses of cell cycle-related genes revealed that defective cell-cycle progression led to these defects. Expression analyses of auxin-related genes and indole-3-acetic acid (IAA) immunolocalization study indicated altered auxin level in these knockdown plants. Reduction of lateral root branching in knockdown plants was corrected by exogenous IAA supplement. OsMED14_1 physically interacts with transcription factors YABBY5, TAPETUM DEGENERATION RETARDATION (TDR) and MADS29, possibly regulating auxin homeostasis and ultimately leading to lateral organ/leaf, microspore and seed development.

Regenerated silica-based RNA purification columns to address the short supply of RNA purification kits for COVID-19 diagnosis.

BACKGROUND: RT-qPCR technique is the current world-wide method used for the early detection of SARS-CoV2 RNA in the suspected clinical samples. Viral RNA extraction is the key pre-analytical step for SARS-CoV2 detection which often achieved using commercial RNA-extraction kits. However, due to the COVID-19 pandemic, bulk production and the supply chains for the commercial RNA-extraction kit have been seriously compromised. The shortage of commercial RNA-extraction kit is even more acute in developing country. Furthermore, use of one-off design RNA-columns can generate plastic wastes that have an environmental pollution effect. METHODS AND RESULTS: To address these issues, in this study, we used warm alkaline solution containing Triton X-100 for the complete removal of the residual SARS-CoV2 RNA from the used RNA-binding silica column. Columns regenerated using the alkaline solution have the viral RNA purification capability that is comparable to the fresh silica columns. We also demonstrated that RNA-binding silica columns can be regenerated and reused for a minimum of five-times. CONCLUSIONS: Therefore, the use of the RNA-column regeneration method may benefits several SARS-CoV2 diagnostic laboratories throughout the world by cutting down the requirement of commercial RNA-purification column.

ß-Lactam Resistance Gene NDM-1 in the Aquatic Environment: A Review.

New Delhi Metallo-ß-lactamase-1 (NDM-1) offers carbapenem antibiotics resistance that creates an evolving challenge in treating bacterial infections. NDM-1-bearing strains were observed in surface waters around New Delhi in 2010 and after then identified globally. The usage of antibiotics may hasten the growth of the NDM-1-producing bacteria, which pose severe hazards to human and animal health. The emergence of the NDM-1 in the aquatic environment is turning out to be a growing concern worldwide. NDM-1 gene conferring resistance to a widespread class of antibiotics has been observed in bacteria disseminated in animal production wastewaters, hospital sewage, domestic sewage, industrial effluents, wastewater treatment plants, drinking water, surface water, and even in groundwater. This review recapitulates the currently published research studies on the prevalence and geographical distribution of the NDM-1 gene in the aquatic environment, its habitats, and healthcare risk associated with NDM-1-producing bacteria, in addition to molecular techniques employed to reveal the occurrence of the NDM-1 in the aquatic environment, including conventional polymerase chain reaction, real-time qPCR, DNA hybridization, and microarray-based methods.

Face recognition accuracy of forensic examiners, superrecognizers, and face recognition algorithms.

Achieving the upper limits of face identification accuracy in forensic applications can minimize errors that have profound social and personal consequences. Although forensic examiners identify faces in these applications, systematic tests of their accuracy are rare. How can we achieve the most accurate face identification: using people and/or machines working alone or in collaboration? In a comprehensive comparison of face identification by humans and computers, we found that forensic facial examiners, facial reviewers, and superrecognizers were more accurate than fingerprint examiners and students on a challenging face identification test. Individual performance on the test varied widely. On the same test, four deep convolutional neural networks (DCNNs), developed between 2015 and 2017, identified faces within the range of human accuracy. Accuracy of the algorithms increased steadily over time, with the most recent DCNN scoring above the median of the forensic facial examiners. Using crowd-sourcing methods, we fused the judgments of multiple forensic facial examiners by averaging their rating-based identity judgments. Accuracy was substantially better for fused judgments than for individuals working alone. Fusion also served to stabilize performance, boosting the scores of lower-performing individuals and decreasing variability. Single forensic facial examiners fused with the best algorithm were more accurate than the combination of two examiners. Therefore, collaboration among humans and between humans and machines offers tangible benefits to face identification accuracy in important applications. These results offer an evidence-based roadmap for achieving the most accurate face identification possible.

A noninvasive and qualitative bioluminescent assay for express diagnostics of athletes' responses to physical exertion.

Upcoming professional sports authorities seek rapid noninvasive biosensing tools for regular monitoring of athletes' physiological states. The analysis of saliva through luminescence-based biosensors has been perceived as a suitable candidate for such purposes. The present study reports a qualitative bioluminescence assay based on a coupled enzyme system that consists of bacterial luciferase (BLuc) and nicotinamide adenine dinucleotide (NADH):flavin mononucleotide (FMN) oxidoreductase (Red), BLuc-Red, for the express diagnostics of athletes' stress levels before and after physical exertion. The volunteers who participated in the study were grouped as freestyle wrestlers and students who adapted to different levels of physical activities. Under physical exertion modelling conditions, the influence of participant saliva on BLuc-Red catalyzed light emission was investigated. Results showed a significant increase in residual luminescence (Iexp , mean maximum bioluminescence intensity of the experimental measurement (Iexp ); Ic , luminescence intensity in control; Iexp /Ic , %) values for participants in the wrestler group while a decrease in the student group (P < 0.05). Such contrasting residual luminescence values in both groups were found to be dependent on the catalase activity of saliva. The proposed bioluminescence assay can be utilized as a potential nonspecific biosensing tool for determining the physical state of athletes under high loads.

Short communication: preliminary observations on the serum levels of HSP70 and its correlation with serum cortisol, thyroid hormones, and acute-phase protein concentration in cattle naturally infected with foot-and-mouth disease virus.

The study aimed to explore the serum levels of HSP70 and identify its possible association with serum cortisol, thyroid hormones, and acute-phase protein concentrations in cattle naturally infected with foot-and-mouth disease (FMD) virus. After the FMD outbreak in an organized dairy cattle farm in India, blood samples were obtained from clinically infected (n = 40) and apparently healthy (n = 30) animals. Samples were processed and tested by an in-house DIVA assay for confirmation of FMD infection. Serum was analyzed for HSP70, cortisol, T4, T3, haptoglobin, and serum amyloid A by enzyme-linked immunosorbent assay (ELISA). HSP70 concentrations were significantly higher in the serum of clinically infected cattle (p < 0.01) than the healthy group. To the best of our knowledge, this is the first report describing the elevated serum levels of HSP70 under infectious diseases of bovines. Cortisol (p < 0.05), haptoglobin (p < 0.001), and serum amyloid A (p < 0.05) concentrations also markedly increased in the diseased animals; however, no differences (p > 0.05) were found in T4 and T3 levels between healthy and infected cattle. Elevated HSP70 concentration correlated positively with high cortisol (p < 0.05) and haptoglobin (p < 0.001) levels suggesting an essential link between these acute events during clinical infectious phase of FMD.

Effect on Mental Health among Undergraduate College Students of India during the COVID-19 Pandemic: A Cross-Sectional Multicentric Study.

BACKGROUND: College students show higher prevalence of mental health issues as compared to the general population. Unfortunately, this year, students all over the world have to face, added pressure due to COVID-19. This study aimed to estimate the effect of COVID-19 pandemic and lockdown on the mental health of Medical and Engineering Students. SUBJECTS AND METHODS: The study was carried out at different medical and engineering colleges in Bihar, Delhi and Maharashtra, and Tamil Nadu. 699 responses were collected and analyzed during the study period. Data was collected by email/ online platform through Google form via non- probability Sampling Technique. Mental health status was determined by using Corona virus anxiety screening (CAS), GHQ (General Health Questionnaire)-12, GAD (General Anxiety Disorder)-7 scale and PHQ (Patient Health Questionnaire)-9 scales.369 (53%) MBBS and 330 (47%) Engineering students participated in the study. RESULTS: Maximum participants in both groups did not have anxiety related to COVID-19 (MBBS (96.8%) and Engineering (95.2%). About two-third participants secured above cut off score i.e., MBBS (62.3%) and Engineering (64.8%) in GHQ-12. Approximately comparable proportion in both groups were found to have severe anxiety and depression (16% vs 20%), when applied GAD-7 and PHQ-9. Uncertainty in the timing of the exams/ Academic delay was found to be the most worrying factor (MBBS, 41.19% vs Engineering 31.82%). CONCLUSIONS: About two-thirds of medical and engineering students psychologically equally affected by current pandemic in our study. A student wellness clinic is the need of hour in current scenario, which is supported by mental health experts (Psychiatrists, Clinical Psychologists) and residents on rotation basiswhere all psychological problem including Stress, Anxiety, Interpersonal crisis, Relationship issues and Personality problems of the students are dealt effectively in institute campus near to student residential area.

Preclinical Development of Inhalable d-Cycloserine and Ethionamide To Overcome Pharmacokinetic Interaction and Enhance Efficacy against Mycobacterium tuberculosis.

We compared the pharmacokinetics and efficacy of a combination of d-cycloserine (DCS) and ethionamide (ETO) via oral and inhalation routes in mice. The plasma half-life (t1/2) of oral ETO at a human-equivalent dose decreased from 4.63 ± 0.61 h to 1.64 ± 0.40 h when DCS was coadministered. The area under the concentration-time curve from 0 h to time t (AUC0-t ) was reduced to one-third. Inhalation overcame the interaction. Inhalation, but not oral doses, reduced the lung CFU/g of Mycobacterium tuberculosis H37Rv from 6 to 3 log10 in 4 weeks, indicating bactericidal activity.

Electrostrain in excess of 1% in polycrystalline piezoelectrics.

Piezoelectric actuators transform electrical energy into mechanical energy, and because of their compactness, quick response time and accurate displacement, they are sought after in many applications. Polycrystalline piezoelectric ceramics are technologically more appealing than single crystals due to their simpler and less expensive processing, but have yet to display electrostrain values that exceed 1%. Here we report a material design strategy wherein the efficient switching of ferroelectric-ferroelastic domains by an electric field is exploited to achieve a high electrostrain value of 1.3% in a pseudo-ternary ferroelectric alloy system, BiFeO3-PbTiO3-LaFeO3. Detailed structural investigations reveal that this electrostrain is associated with a combination of several factors: a large spontaneous lattice strain of the piezoelectric phase, domain miniaturization, a low-symmetry ferroelectric phase and a very large reverse switching of the non-180° domains. This insight for the design of a new class of polycrystalline piezoceramics with high electrostrains may be useful to develop alternatives to costly single-crystal actuators.

Integration of stimulated Raman gain and stimulated Raman losses detection modes in a single nonlinear microscope.

This work addresses some key challenges in the fields of bio and nanophotonics by stimulated Raman microscopy. We present the design and the implementation of a femtosecond stimulated Raman scattering microscope, equipped with three femtosecond laser sources, which allows the coexistence of stimulated Raman gain (SRG) and stimulate Raman losses (SRL) detection modes in a single microscopy setup and to generate images of the same region in succession, without adding or removing components. In order to demonstrate the switching between the two detection modes, SRL and SRG images of polystyrene beads are acquired and the images quality are evaluated and compared.