Development of prospective hospital-based venous thromboembolism registry across India: a study protocol.

INTRODUCTION: Indian Council of Medical Research (ICMR), New Delhi has established a nationwide registry 'Indian Registry for Venous Thromoembolism Disorder (i-RegVeD)' for real-time analytics of sociodemographic profile of patients, disease patterns, management strategies, treatment choices and outcomes of patients with venous thromboemobolism (VTE). The purpose is to generate evidence on VTE in order to fill the gaps in the knowledge of the disease across various demographic regions. METHODS AND ANALYSIS: This prospective hospital-based registry will be a continuous data collection process on the occurrence and characteristics of VTE from the 16 hospital sites pan India. This process would include obtaining clinical profiles, risk factors, diagnostic tests, treatment and outcome information of patients collected from medical records through an active method of data abstraction and data capture mechanism guided by an online web-based tool. ETHICS AND DISSEMINATION: At centralised programme management unit, the study protocol was approved by the Institutional Ethics Committees (IEC) named ICMR-Central Ethics Committee on Human Research and similarly each of the participating site has obtained the ethical approval by their respective IECs. The results from this study will be disseminated publicly on the study website (https://iregved.icmr.org.in) as well as through scientific meetings and publications.

Strongly coupled quantum Otto cycle with single qubit bath.

We discuss a model of a closed quantum evolution of two qubits where the joint Hamiltonian is so chosen such that one of the qubits acts as a bath and thermalizes the other qubit which is acting as the system. The corresponding exact master equation for the system is derived. Interestingly, for a specific choice of parameters the master equation takes the Gorini-Kossakowski-Lindblad-Sudarshan (GKLS) form, with constant coefficients representing pumping and damping of a single qubit system. Based on this model we construct an Otto cycle connected to a single qubit bath and study its thermodynamic properties. Our analysis goes beyond the conventional weak coupling scenario and illustrates the effects of finite baths, including non-Markovianity. We find closed form expressions for efficiency (coefficient of performance), power (cooling power) for the heat engine regime (refrigerator regime), and for different modifications of the joint Hamiltonian.

Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.

Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180°-reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.

Interpolating between Positive and Completely Positive Maps: A New Hierarchy of Entangled States.

A new class of positive maps is introduced. It interpolates between positive and completely positive maps. It is shown that this class gives rise to a new characterization of entangled states. Additionally, it provides a refinement of the well-known classes of entangled states characterized in terms of the Schmidt number. The analysis is illustrated with examples of qubit maps.

Semi-quantitative and quantitative detection of ochratoxin A in agricultural by-products using a self-assembling immunochromatographic strip.

BACKGROUND: The toxicity and health risks of mycotoxins have encouraged increased awareness and strict monitoring of these contaminants in agricultural by-products. In this paper, we developed and tested a sensitive, selective, and self-assembling immunochromatographic (IC) strip for on-site detection of ochratoxin A (OTA). We were able to demonstrate semi-quantitative and quantitative detection of OTA in agricultural by-product samples. RESULTS: The optimized IC strip had a limit of detection (LOD) of 0.5 ng mL-1 OTA using the naked eye for semi-quantitative detection. When a digitized strip reader was used to achieve quantitative results, the LOD for OTA was reduced to 0.1 ng mL-1 with a linear detection range of 0.1-10 ng mL-1 . We also evaluated the specificity, stability, accuracy, and precision of the IC strip and demonstrated high performance in all of these areas. We then confirmed the ability of the IC strip to visually detect OTA contamination in authentic agricultural by-product samples from the markets in China. Furthermore, quantitative detection of OTA using the IC strip showed that the concentration of OTA ranged from 1.7 to 101.3 ng g-1 in the positive agricultural by-product samples, correlating well with the measurements obtained via liquid chromatography with tandem mass spectrometry. CONCLUSION: The results indicated that this proposed IC strip was capable of sensitive, semi-quantitative, quantitative, and on-site detection of OTA contamination in agricultural by-product samples. © 2020 Society of Chemical Industry.

Tethering-facilitated DNA 'opening' and complementary roles of ß-hairpin motifs in the Rad4/XPC DNA damage sensor protein.

XPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively 'opening' these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a 'kinetic gating' mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how 'opening' is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed 'open' undamaged DNA in solution and that such 'opening' can largely occur without one or the other of the ß-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound 'open' DNA adopts multiple conformations in solution notwithstanding the DNA's original structure or the ß-hairpins. Molecular dynamics simulations reveal compensatory roles of the ß-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA 'opening' of undamaged sites and the dynamic nature of 'open' DNA may shed light on how the protein functions within and beyond nucleotide excision repair in cells.

Cocoa-laden cadmium threatens human health and cacao economy: A critical view.

In the recent decades, Cd burden in cocoa-based products threatened global food safety, human health and the future of chocolateries. Increased Cd bioavailability is an acute problem in cacao-based horticulture. Poverty, poor maintenance, unjustified traditional farming, and paucity of knowledge on Cd-binding propensity in cacao discourage the application of risk-mitigation measures. Progressive accumulation of Cd, with a half-life of 10-30 years, in the human body even at ultra-trace levels may lead to serious health complications. If Cd accumulates in the food chain through cocoa products, consequences in children, who are the primary consumers of chocolates, include morbidity and mortality that may result in a significant demographic transition by the year 2050. Developing cacao clones with an innate capability of taking up low Cd levels from soils, and site-specific Cd-cacao research might contribute to limiting the trophic transfer of Cd. This review highlights the possible routes for Cd uptake in cacao plants and discusses the measures to rescue the chocolateries from Cd pollution to promote "healthy" cacao farming. The potential human health risks of chocolate-laden Cd and mitigation strategies to minimize Cd burden in the human body are also presented. The challenges and prospects in Cd-cacao research are discussed as well.

Author Correction: Non-Markovianity of qubit evolution under the action of spin environment.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Non-Markovianity of qubit evolution under the action of spin environment.

The question, whether an open system dynamics is Markovian or non-Markovian can be answered by studying the direction of the information flow in the dynamics. In Markovian dynamics, information must always flow from the system to the environment. If the environment is interacting with only one of the subsystems of a bipartite system, the dynamics of the entanglement in the bipartite system can be used to identify the direction of information flow. Here we study the dynamics of a two-level system interacting with an environment, which is also a heat bath, and consists of a large number of two-level quantum systems. Our model can be seen as a close approximation to the 'spin bath' model at low temperatures. We analyze the Markovian nature of the dynamics, as we change the coupling between the system and the environment. We find the Kraus operators of the dynamics for certain classes of couplings. We show that any form of time-independent or time-polynomial coupling gives rise to non-Markovianity. Also, we witness non-Markovianity for certain parameter values of time-exponential coupling. Moreover, we study the transition from non-Markovian to Markovian dynamics as we change the value of coupling strength.

Enhanced spontaneous DNA twisting/bending fluctuations unveiled by fluorescence lifetime distributions promote mismatch recognition by the Rad4 nucleotide excision repair complex.

Rad4/XPC recognizes diverse DNA lesions including ultraviolet-photolesions and carcinogen-DNA adducts, initiating nucleotide excision repair. Studies have suggested that Rad4/XPC senses lesion-induced helix-destabilization to flip out nucleotides from damaged DNA sites. However, characterizing how DNA deformability and/or distortions impact recognition has been challenging. Here, using fluorescence lifetime measurements empowered by a maximum entropy algorithm, we mapped the conformational heterogeneities of artificially destabilized mismatched DNA substrates of varying Rad4-binding specificities. The conformational distributions, as probed by FRET between a cytosine-analog pair exquisitely sensitive to DNA twisting/bending, reveal a direct connection between intrinsic DNA deformability and Rad4 recognition. High-specificity CCC/CCC mismatch, free in solution, sampled a strikingly broad range of conformations from B-DNA-like to highly distorted conformations that resembled those observed with Rad4 bound; the extent of these distortions increased with bound Rad4 and with temperature. Conversely, the non-specific TAT/TAT mismatch had a homogeneous, B-DNA-like conformation. Molecular dynamics simulations also revealed a wide distribution of conformations for CCC/CCC, complementing experimental findings. We propose that intrinsic deformability promotes Rad4 damage recognition, perhaps by stalling a diffusing protein and/or facilitating 'conformational capture' of pre-distorted damaged sites. Surprisingly, even mismatched DNA specifically bound to Rad4 remains highly dynamic, a feature that may reflect the versatility of Rad4/XPC to recognize many structurally dissimilar lesions.

Response surface optimization of a dynamic dye adsorption process: a case study of crystal violet adsorption onto NaOH-modified rice husk.

The adsorption of crystal violet from aqueous solution by NaOH-modified rice husk was investigated in a laboratory-scale fixed-bed column. A two-level three factor (2(3)) full factorial central composite design with the help of Design Expert Version 7.1.6 (Stat Ease, USA) was used for optimisation of the dynamic dye adsorption process and evaluation of interaction effects of different operating parameters: initial dye concentration (100-200 mg L(-1)), flow rate (10-30 mL min(-1)) and bed height (5-25 cm). A correlation coefficient (R (2)) value of 0.999, model F value of 1,936.59 and its low p value (<0.0001) along with lower value of coefficient of variation (1.38 %) indicated the fitness of the response surface quadratic model developed during the present study. Numerical optimisation applying desirability function was used to identify the optimum conditions for a targeted breakthrough time of 12 h. The optimum conditions were found to be initial solution pH=8.00, initial dye concentration=100 mg L(-1), flow rate=22.88 mL min(-1) and bed height=18.75 cm. A confirmatory experiment was performed to evaluate the accuracy of the optimised procedure. Under the optimised conditions, breakthrough appeared after 12.2 h and the column efficiency was determined as 99 %. The Thomas model showed excellent fit to the dynamic dye adsorption data obtained from the confirmatory experiment. Thereby, it was concluded that the current investigation gives valuable insights for designing and establishing a continuous wastewater treatment plant.

Batch and continuous (fixed-bed column) biosorption of crystal violet by Artocarpus heterophyllus (jackfruit) leaf powder.

In this study, batch and fixed-bed column experiments were performed to investigate the biosorption potential of Artocarpus heterophyllus (jackfruit) leaf powder (JLP) to remove crystal violet (CV) from aqueous solutions. Batch biosorption studies were carried out as a function of solution pH, contact time, initial dye concentration and temperature. The biosorption equilibrium data showed excellent fit to the Langmuir isotherm model with maximum monolayer biosorption capacity of 43.39 mg g(-1) at pH 7.0, initial dye concentration=50 mg L(-1), temperature=293 K and contact time=120 min. According to Dubinin-Radushkevich (D-R) isotherm model, biosorption of CV by JLP was chemisorption. The biosorption kinetics followed the pseudo-second-order kinetic model. Thermodynamic analysis revealed that biosorption of CV from aqueous solution by JLP was a spontaneous and exothermic process. In order to ascertain the practical applicability of the biosorbent, fixed-bed column studies were also performed. The breakthrough time increased with increasing bed height and decreased with increasing flow rate. The Thomas model as well as the BDST model showed good agreement with the experimental results at all the process parameters studied. It can be concluded that JLP is a promising biosorbent for removal of CV from aqueous solutions.

Biosorption of Basic Green 4 from aqueous solution by Ananas comosus (pineapple) leaf powder.

Biosorption characteristics of Ananas comosus (pineapple) leaf powder was investigated for decolorization of Basic Green 4 (BG 4), a cationic dye from its aqueous solutions employing a batch experimental set-up. Parameters that influence the sorption process such as pH, biosorbent dosage, contact time, initial dye concentration and temperature were systematically studied. The optimum conditions for removal of BG 4 were found to be pH 9.0, contact time=150 min, biosorbent dosage=5.0 g L(-1), initial dye concentration=50 mg L(-1). The temperature had a strong influence on the biosorption process. Further, the biosorbent was characterized by Fourier transform infrared (FTIR) spectroscopy, scanning electron microscopy (SEM) and Brunauer, Emmett, Teller (BET) surface area and pore size analysis. Experimental biosorption data were modeled by Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherms. The biosorption process followed the Langmuir isotherm model with high coefficients of correlation (R(2)>0.99) at different temperatures. The pseudo second order kinetic model fitted well in correlation to the experimental results. Activation energy of the biosorption process (E(a)) was found to be 45.79 kJ mol(-1) by using the Arrhenius equation, indicating chemisorption nature of BG 4 sorption onto pineapple leaf powder. Thermodynamic parameters suggest that the biosorption process is spontaneous and exothermic in nature. Overall, the present findings suggest that this environmentally friendly, efficient and low-cost biosorbent may be useful for the removal of BG 4 from aqueous media.