Bayesian approaches to include real-world data in clinical studies.

Randomized clinical trials have been the mainstay of clinical research, but are prohibitively expensive and subject to increasingly difficult patient recruitment. Recently, there is a movement to use real-world data (RWD) from electronic health records, patient registries, claims data and other sources in lieu of or supplementing controlled clinical trials. This process of combining information from diverse sources calls for inference under a Bayesian paradigm. We review some of the currently used methods and a novel non-parametric Bayesian (BNP) method. Carrying out the desired adjustment for differences in patient populations is naturally done with BNP priors that facilitate understanding of and adjustment for population heterogeneities across different data sources. We discuss the particular problem of using RWD to create a synthetic control arm to supplement single-arm treatment only studies. At the core of the proposed approach is the model-based adjustment to achieve equivalent patient populations in the current study and the (adjusted) RWD. This is implemented using common atoms mixture models. The structure of such models greatly simplifies inference. The adjustment for differences in the populations can be reduced to ratios of weights in such mixtures. This article is part of the theme issue 'Bayesian inference: challenges, perspectives, and prospects'.

Drynaria quercifolia suppresses paracetamol­induced hepatotoxicity in mice by inducing Nrf-2.

Paracetamol is a popular and safe drug preferred by victims of pain or pyrexia; however, its overdose or abuse is a growing concern worldwide. Here the hepatoprotective effect of an ethnomedicinal plant Drynaria quercifolia against paracetamol­induced toxicity in murine model is demonstrated. This fern, native to tropical countries including the Northeast India, is used by local tribes to treat inflammatory conditions. Paracetamol 500 mg/kg body weight was orally administered on alternate days for a period of 21days to mimic a chronic overdose. Drynaria quercifolia acetone extract (DQA) treatment interspaced with paracetamol significantly decreased serum biomarkers of hepatotoxicity (ALT, AST and ALP) renal toxicity (urea, creatinine), lipid peroxidation level, histological damage in liver and kidney. The protein and mRNA expressions of the transcription factor, Nrf2, and its target antioxidant genes (SOD1, CAT and GST) as well as activities of these antioxidant enzymes were downregulated by paracetamol administration but significantly recovered following the DQA treatment (Tab. 3, Fig. 5, Ref. 31). Keywords: acetaminophen/paracetamol, Drynaria quercifolia, renal toxicity, hepatotoxicity, Nrf-2.

Peptidoglycan-treated tumor antigen-pulsed dendritic cells impart complete resistance against tumor rechallenge.

Solid tumors elicit suppressive T cell responses which impair antigen-presenting cell (APC) functions. Such immune suppression results in uncontrolled tumor growth and mortality. Addressing APC dysfunction, dendritic cell (DC)-mediated anti-tumor vaccination was extensively investigated in both mice and humans. These studies never achieved full resistance to tumor relapse. Herein, we describe a repetitive RM-1 murine tumor rechallenge model for recurrence in humans. Using this newly developed model, we show that priming with tumor antigen-pulsed, Toll-like receptor (TLR)2 ligand-activated DCs elicits a host-protective anti-tumor immune response in C57BL/6 mice. Upon stimulation with the TLR2 ligand peptidoglycan (PGN), the tumor antigen-pulsed DCs induce complete resistance to repetitive tumor challenges. Intra-tumoral injection of PGN reduces tumor growth. The tumor resistance is accompanied by increased expression of interleukin (IL)-27, T-box transcription factor TBX21 (T-bet), IL-12, tumor necrosis factor (TNF)-α and interferon (IFN)-γ, along with heightened cytotoxic T lymphocyte (CTL) functions. Mice primed four times with PGN-stimulated tumor antigen-pulsed DCs remain entirely resistant to repeat challenges with RM-1 tumor cells, suggesting complete prevention of relapse and recurrence of tumor. Adoptive transfer of T cells from these mice, which were fully protected from RM-1 rechallenge, confers anti-tumor immunity to syngeneic naive recipient mice upon RM-1 challenge. These observations indicate that PGN-activated DCs induce robust host-protective anti-tumor T cells that completely resist tumor growth and recurrence.

An alkaliphilic bacterium BKH4 of Bakreshwar hot spring pertinent to bioconcrete technology.

AIMS: Hot springs have always drawn attention due to their unique chemical richness and the presence of different microbial communities. The use of hot spring bacteria in concrete technology is our primary focus; isolation of an alkaliphilic bacterium from the Bakreshwar hot springs having longer survival and better efficacy towards cementitious environment was the basis of our study's design. METHODS AND RESULTS: A novel facultative anaerobic and highly alkaliphilic bacterial strain (BKH4; GenBank accession no. KX622782) belonging to the family 'Bacillaceae' and homologous (99%) with Lysinibacillus fusiformis was isolated from Bakreshwar hot springs. The isolated coccoid-type Gram-positive bacterium grows well in a defined semi-synthetic medium (pH 12·0 and 65°C). This bacterium survives for more than a month and shows better efficacy in enhancing compressive strengths (>50%), ultrasonic pulse velocity (>25%) and durability of the cementitious mortar when incorporated at a concentration of 104  cells per ml of water used. CONCLUSION: The novel bacterium BKH4 is more effective for the enhancement of the bioconcrete properties. SIGNIFICANCE AND IMPACT OF THE STUDY: BKH4 bacterium will add a new dimension to future concrete technology for its usefulness in strength enhancement and durability due to its alkaliphilic nature and longer survival within a cementitious environment.

DNA damage in marine rock oyster (Saccostrea Cucullata) exposed to environmentally available PAHs and heavy metals along the Arabian Sea coast.

Molecular biomarkers are used world wide for quick assessment of the immediate effect of environmental pollution on marine ecosystems. Recently, we evaluated oxidative stress responses of marine rock oyster, Saccostrea cucullata impacted due to polycyclic aromatic hydrocarbons (PAHs) accumulated in their tissues at a few sampling sites along the coast of Goa around the region of the Arabian sea coast, India (Sarkar et al., 2017). Using a combination of partial alkaline unwinding and comet assays, we now report a comprehensive study on the impairment of DNA integrity (DI) in S. cucullata due to exposure to environmentally available PAHs and also heavy metals (Pb, Cd, Cu, Fe and Mn) along the Arabian Sea coast, Goa, India exclusively around the entire coast of Goa. First, we determined significant correlation between DI in S. cucullata and the extent of exposure to and bioaccumulation of different PAH compounds including 2-3 aromatic ring PAHs (R2, 0.95), 4-6 aromatic ring PAHs (R2, 0.85), oxygenated-PAHs (oxy-PAHs, R2, 0.84) and total PAHs (t-PAHs, R2, 0.98). Second, we observed dose-dependent decrease in DI in S. cucullata with increasing concentrations of different PAH components in oyster tissues. We substantiated our field observations with appropriate laboratory controls using benzo[a]pyrene (BaP). Third, we performed stepwise multiple regression analyses of different water quality parameters including pH, salinity, temperature, dissolved oxygen (DO), biochemical oxygen demand (BOD), nitrite (NO2), nitrate (NO3), phosphate (PO4), turbidity and also t-PAH-biota, t-PAH-water with DI as the dependent variable. Among all these parameters, only four parameters such as t-PAH-biota in combination with DO, BOD and NO2 showed significant correlation (R¯2 = 0.95) with loss in DI in S. cucullata. Based on these results, we created a map indicating the percentage of DNA damage in S. cucullata exposed to PAHs and heavy metals at each sampling location along the west coast of India around Goa, India.

Potentiation of antibiotic against Pseudomonas aeruginosa biofilm: a study with plumbagin and gentamicin.

AIMS: Pseudomonas aeruginosa is one of the fatal biofilm-forming pathogens which pose to be a problem in clinical infections, contamination of food and marine ecosystems. In this report, a naphthoquinone-plumbagin has been explored for its antimicrobial (antibacterial and antibiofilm) activity against P. aeruginosa biofilm. The ability of plumbagin to enhance the bioactivity of a known broad-spectrum antibiotic was further assayed by combining the sub-MIC doses of plumbagin with sub-MIC doses of gentamicin against P. aeruginosa biofilm. METHODS AND RESULTS: This combinatorial approach was used for a series of experiments for understanding the mechanism of action for antibiofilm activity against P. aeruginosa (MTCC 424, MTCC 2488). Antibiofilm activity was studied by safranin staining, estimating total protein, visualization of biofilms and extra polymeric substances quantification. Antivirulent activity of these doses was studied by azocasein degradation, expression of virulent factors and molecular docking. Expression of quorum sensing (QS) phenotypes was studied by motility assessment and mRNA expression pattern of virulence genes. It was observed that plumbagin alone and the combinatorial doses of plumbagin and gentamicin exhibit significant antibiofilm and antivirulent activity coupled with the reduction in the expression of QS phenotypes and virulence genes. Molecular docking study revealed that plumbagin had variable affinity for different QS proteins. CONCLUSION: Low doses of plumbagin and gentamicin exhibit synergistic activity against P. aeruginosa biofilm while maintaining their effectiveness. SIGNIFICANCE AND IMPACT OF THE STUDY: As the P. aeruginosa biofilms are reservoir of persister bacteria, thus, the increasing concern of antibiotic tolerance has to be dealt with combinatorial approaches. In this report, plumbagin has been explored in potentiating the antibiofilm effect of a broad-spectrum antibiotic gentamicin for better therapeutic efficacy.

Evaluation of the impact of bioaccumulation of PAH from the marine environment on DNA integrity and oxidative stress in marine rock oyster (Saccostrea cucullata) along the Arabian sea coast.

Marine pollution due to oil spills is of great concern globally for their impact on the health of marine ecosystems. We assessed the genotoxic effects and oxidative stress due to genotoxic pollutants accumulated from the ambient marine environment in the tissues of marine rock oyster, Saccostrea cucullata along the Arabian Sea coast around Goa, India. The extent of DNA damage in S. cucullata was determined by comet assay as variation of comet parameter: mean % tail DNA along the coast with respect to that at the reference site (Tiracol, Goa, India). In addition, the oxidative stress responses of rock oysters exposed to marine pollutants such as polycyclic aromatic hydrocarbons (PAHs) were assessed as a function of variation in antioxidant enzyme activities such as glutathione-s-transferase (GST), catalase (CAT) and superoxide dismutase (SOD) along the coast. Spearman correlation analysis showed significant correlation between different components of PAHs (viz., 2-3-PAH, 4-6-PAH and oxy-PAH) in the tissues of the rock oysters and the antioxidant enzyme activities. The antioxidant enzyme activities in S. cucullata increased with increasing concentrations of PAHs in tissues in the following order of sampling sites: Tiracol < Arambol < Betul < Velsao. Among the PAHs, oxy-PAH was found to be most predominant in causing DNA damage in S. cucullata. These results provide an insight into environmental genotoxicity and oxidative stress induced by PAHs along the Arabian Sea coast, India.

Determination of Insulin Secretory Defect and Insulin Sensitivity in Type 2 Diabetic Subjects in Bangladesh.

Diabetes mellitus (DM) is defined as a group of metabolic diseases characterized by hyperglycemia resulting from defects in insulin secretion, insulin action, or both. This study was undertaken to explore the basic defect in type 2 diabetes patients in Bangladesh. This was an observational study with case control design, was conducted in the Biomedical Research Group, Research Division, Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine Metabolic Disorders (BIRDEM), Dhaka, Bangladesh, during the period of July 2008 to June 2009. A total of 153 subjects were included in study of which 63 belonged to type 2 diabetes mellitus group and 90 were healthy controls. Fasting and 2 hours postprandial blood glucose, serum insulin, HOMA%B, HOMA%S, QuickI, Glucose /insulin ratio, TG were measured and age, BMI, WHR were recorded. Waist-hip ratio (WHR), was significantly higher in T2DM as compared to control subjects [WHR, mean±SD, 0.94±0.12 vs. 0.88±0.06, p<0.001]; Glucose and insulin ratio of T2DM was significantly higher as compared to control subject [Glu: Ins, Median (range) of 0.54 (0.17-2.33) vs. 0.37(0.06-1.52)]. Insulin secretion (HOMA%B) was significantly lower in diabetic as compared to control subjects [HOMA%B, median (range), 71(4.90-391) vs. 180(59-634) p<0.001]; The quantitative insulin sensitivity check Index (QUICKI) of diabetic subjects were significantly higher as compared to control [QUICKI median (range) 39.90(4.80-138.10) vs. 0.55(0.36-0.85), <0.001]. Triglyceride (TG) and cholesterol (Chol) were significantly higher [(mg/dl), (mean±SD), TG (142±80.14) vs. (142±80.14); Chol (189±50.76) vs. (172±45), p=0.029] in T2DM as compared to control subjects. Those with diabetes showed significant association with insulin secretory defect (HOMA%B, p=0.006) and insulin resistance as assessed by GINR (p<0.001) and QuickI (p<0.001) but not by HOMA%S (p=0.127). The present data suggest that both insulin secretory defect and insulin sensitivity are present in T2 diabetic subjects of Bangladesh.

Automated nonparametric method for detection of step-like features in biological data sets.

Experimental data from single-molecule DNA-protein experiments, such as experiments using optical traps or magnetic tweezers, typically contain steps, plateaus, or dwell regions that are obscured by thermal and other noise sources. We present a nonparametric method for detecting step-like features in noisy biological data sets. Our algorithm does not assume that the steps can be modeled as Heaviside functions or any particular parametric form. No assumptions about the noise source, such as whether the noise is Gaussian or colored, are made either. Instead, for detection of plateaus, the algorithm uses the novel method of analyzing a probability distribution function of the data values. The vast majority of previously published methods for step detection rely on statistical fitting of step functions with the flat segments linked by vertical segments. Our approach is intended for use on data which cannot be modelled as a series of step functions but applies to step functions as a special case. These type of data traces have, so far, been difficult to characterize effectively. We examine the performance of the algorithm through systematic simulation studies and illustrate the use of our algorithm to analyze single molecule DNA-protein micromanipulation experiments carried out by our laboratory. The simulation results and experimental validation suggest that our method is very robust, avoids overfitting, and functions effectively in the presence of noise sources characteristic of single molecule experiments.

Evaluation of impairment of DNA in marine gastropod, Morula granulata as a biomarker of marine pollution.

The impairment of DNA in marine gastropod Morula granulata was evaluated in terms of the loss of DNA integrity in the species as a measure of the impact of genotoxic contaminants prevalent in the marine environment along the coast of Goa, India. The extent of DNA damage occurred in the marine gastropods collected from different sampling sites such as Arambol, Anjuna, Sinquerim, Dona Paula, Bogmalo, Hollant, Velsao, Betul and Palolem along the coast of Goa was measured following the technique of partial alkaline unwinding as well as comet assays. The highest DNA integrity was observed at Arambol (F, 0.75), identified as the reference site, whereas the lowest DNA integrity at Hollant (F, 0.33) situated between the two most contaminated sites at Bogmalo and Velsao. The impact of genotoxic contaminants on marine gastropods was pronounced by their low DNA integrity at Sinquerim (F, 0.40) followed by Betul (F, 0.47), Velsao (F, 0.51), Anjuna (F, 0.54), Bogmalo (F, 0.55), Dona Paula (F, 0.67) and Palolem (F, 0.70). The extent of DNA damage occurred in M. granulata due to ecotoxicological impact of the prevailing marine pollutants along the coast of Goa was further substantiated by comet assay and expressed in terms of %head-DNA, %tail DNA, tail length and Olive tail moment. The single cell gel electrophoresis of M. granulata clearly showed relatively higher olive tail moment in the marine gastropod from the contaminated sites, Anjuna, Hollant, Velsao and Betul. The variation in the mean %head DNA at different sampling sites clearly indicated that the extent of DNA damage in marine gastropod increases with the increase in the levels of contamination at different sampling sites along the coast. The stepwise multiple regression analysis of the water quality parameters showed significant correlation between the variation in DNA integrity and PAH in combination with NO3, salinity and PO4 (R¯(2), 0.90). The measurement of DNA integrity in M. granulata thus provides an early warning signal of contamination of the coastal ecosystem of Goa by genotoxic contaminants.

7q11.23 Microduplication: a recognizable phenotype.

Williams-Beuren syndrome is a well-known microdeletion syndrome with a recognizable clinical phenotype. The subtle phenotype of the reciprocal microduplication of the Williams-Beuren critical region has been described recently. We report seven further patients, and a transmitting parent, with 7q11.23 microduplication. All our patients had speech delay, autistic features and facial dysmorphism consistent with the published literature. We conclude that the presence of specific dysmorphic features, including straight, neat eyebrows, thin lips and a short philtrum, in our patients with speech delay and autistic features provides further evidence that the children with 7q11.23 microduplication have a recognizable phenotype.

Electrochemical oxygen reduction behavior of selectively deposited platinum atoms on gold nanoparticles.

Carbon-supported Pt@Au "core-shell" nanoparticles with varying surface concentration of platinum atoms have been synthesized using a novel redox-mediated synthesis approach. The synthesis technique allows for a selective deposition of platinum atoms on the surface of prefabricated gold nanoparticles. Energy dispersive spectroscopic analyses in a scanning electron microscope reveal that the platinum to gold atomic ratios are close to the nominal values, validating the synthesis scheme. X-ray diffraction data indicate an un-alloyed structure. The platinum to gold surface atomic ratio determined from cyclic voltammetry and copper under-potential deposition experiments reveal good agreement with the calculated values at low platinum concentration. However, there is an increase in non-uniformity in the deposition process upon increasing the platinum concentration. Koutecky-Levich analysis of the samples indicates a transition of the total number of electrons transferred (n) in the electrochemical oxygen reduction reaction from two to four electrons upon increasing the surface concentration of platinum atoms. Furthermore, the data indicate that isolated platinum atoms can reduce molecular oxygen but via a two-electron route. Moreover, successful four-electron reduction of molecular oxygen requires clusters of platinum atoms.

Dissolved methane in Indian freshwater reservoirs.

Emission of methane (CH4), a potent greenhouse gas, from tropical reservoirs is of interest because such reservoirs experience conducive conditions for CH4 production through anaerobic microbial activities. It has been suggested that Indian reservoirs have the potential to emit as much as 33.5 MT of CH4 per annum to the atmosphere. However, this estimate is based on assumptions rather than actual measurements. We present here the first data on dissolved CH4 concentrations from eight freshwater reservoirs in India, most of which experience seasonal anaerobic conditions and CH4 buildup in the hypolimnia. However, strong stratification prevents the CH4-rich subsurface layers to ventilate CH4 directly to the atmosphere, and surface water CH4 concentrations in these reservoirs are generally quite low (0.0028-0.305 µM). Moreover, only in two small reservoirs substantial CH4 accumulation occurred at depths shallower than the level where water is used for power generation and irrigation, and in the only case where measurements were made in the outflowing water, CH4 concentrations were quite low. In conjunction with short periods of CH4 accumulation and generally lower concentrations than previously assumed, our study implies that CH4 emission from Indian reservoirs has been greatly overestimated.

Static in vitro digestion model adapted to the general older adult population: an INFOGEST international consensus.

Understanding the mechanisms of food digestion is of paramount importance to determine the effect foods have on human health. Significant knowledge on the fate of food during digestion has been generated in healthy adults due to the development of physiologically-relevant in vitro digestion models. However, it appears that the performance of the oro-gastrointestinal tract is affected by ageing and that a model simulating the digestive conditions found in a younger adult (<65 years) is not relevant for an older adult (>65 years). The objectives of the present paper were: (1) to conduct an exhaustive literature search to find data on the physiological parameters of the older adult oro-gastrointestinal tract, (2) to define the parameters of an in vitro digestion model adapted to the older adult. International experts have discussed all the parameters during a dedicated workshop organized within the INFOGEST network. Data on food bolus properties collected in the older adult were gathered, including food particle size found in older adult boluses. In the stomach and small intestine, data suggest that significant physiological changes are observed between younger and older adults. In the latter, the rate of gastric emptying is slowed down, the pH of the stomach content is higher, the amount of secretions and thus the hydrolytic activities of gastric and intestinal digestive enzymes are reduced and the concentration of bile salts lower. The consensus in vitro digestion model of the older adult proposed here will allow significant progress to be made in understanding the fate of food in this specific population, facilitating the development of foods adapted to their nutritional needs. Nevertheless, better foundational data when available and further refinement of the parameters will be needed to implement the proposed model in the future.

Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis.

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.

A framework for supervising lifestyle diseases using long-term activity monitoring.

Activity monitoring of a person for a long-term would be helpful for controlling lifestyle associated diseases. Such diseases are often linked with the way a person lives. An unhealthy and irregular standard of living influences the risk of such diseases in the later part of one's life. The symptoms and the initial signs of these diseases are common to the people with irregular lifestyle. In this paper, we propose a novel healthcare framework to manage lifestyle diseases using long-term activity monitoring. The framework recognizes the user's activities with the help of the sensed data in runtime and reports the irregular and unhealthy activity patterns to a doctor and a caregiver. The proposed framework is a hierarchical structure that consists of three modules: activity recognition, activity pattern generation and lifestyle disease prediction. We show that it is possible to assess the possibility of lifestyle diseases from the sensor data. We also show the viability of the proposed framework.

CURRENT THERAPEUTIC STRATEGIES AND CHALLENGES IN NSCLC TREATMENT: A COMPREHENSIVE REVIEW.

Non-small cell lung cancer (NSCLC) is one of the most lethal malignancies accountings for nearly 80% of all lung cancer cases diagnosed and causing over one million deaths annually worldwide. The discovery of molecular alterations including driver mutations and gene fusions has led to innovation of numerous targeted therapies, which certainly provided an edge over the classical chemotherapeutic treatment regimens and improved survival of the patients. Despite all the breakthrough innovations, the five-year survival statistics has not improved the way it was expected, pointing the challenges and limitations of currently approved diagnostic methods and therapies. This review summarizes various innovative therapies, treatment regimens developed over the last two decades for NSCLC treatment and the current challenges and limitations in the NSCLC treatment landscape.

Investigation of the interaction mechanism of 3-allyl-2-hydantoin anti-cancer on the pristine and functionalized BC2N nanotubes as an effective drug delivery nanocarriers.

One of the exciting aspects of different nanomaterials in biomedical applications is the delivery of a wide range of anti-cancer drugs to mitigate their negative side effects via precise targeting of the tumor cells. In the present study, the DFT B3LYP/6-31G (d, p) level of theory was used to evaluate the capabilities of raw BC2N nanotubes (BC2NNTs) and functionalized BC2NNTs nanostructures as a carrier for an anti-cancer drug (i.e., 3-allyl-2-hydantoin (3-ASH)). It was specified that the existing interaction between 3-ASH and BC2N nanotubes is weak (-10.97 kcal mol-1). Therefore, the functionalized BC2NNTs were investigated for 3-ASH interaction. According to our computations, compared with raw BC2NNTs, the role of hydrogen bonds between 3-ASH molecules' active sites and carboxyl-functionalized BC2NNTs in the complexes' fixation, adsorption, and thermodynamic energy is of great importance. A considerable transfer of charge between 3-ASH molecule to the functionalized BC2NNTs was detected via MEP, NBO, and fractional charge transfer analysis. Also, it was found that these nanostructures have high stability on the water medium while their solvation energies have negative values. This negative value is beneficial for the applications of 3-ASH drug delivery. The present work proposes a new method to load 3-ASH drugs with a high density on BC2NNTs' surfaces.