Wavepacket Approach to the Cumulative Reaction Probability within the Flux Operator Formalism

Expressions for the singular flux operator eigenfunctions and eigenvalues are given in terms of the Dirac δ-function representable as a localized Gaussian wavepacket. This functional form enables computation of the cumulative reaction probability N(E) from the wavepacket time-correlation functions. The Gaussian based form of the flux eigenfunctions, which is not tied to a finite basis of a quantum-mechanical calculation, is particularly useful for approximate calculation of N(E) with the trajectory based wavepacket propagation techniques. Numerical illustration is given for the Eckart barrier using the conventional quantum-mechanical propagation and the quantum trajectory dynamics with the approximate quantum potential. N(E) converges with respect to the Gaussian width parameter, and the convergence is faster at low energy. The approximate trajectory calculation overestimates tunneling in the low energy regime, but gives a significant improvement over the parabolic estimate of the tunneling probability

Efficient Quantum Trajectory Representation of Wavefunctions Evolving in Imaginary Time

The Boltzmann evolution of a wavefunction can be recast as imaginary-time dynamics of the quantum trajectory ensemble. The quantum effects arise from the momentum-dependent quantum potential – computed approximately to be practical in high-dimensional systems – influencing the trajectories in addition to the external classical potential [S. Garashchuk, J. Chem. Phys.132, 014112 (2010)]. For a nodelesswavefunction represented as ψ(x, t) = exp ( − S(x, t)/ℏ) with the trajectory momenta defined by ∇S(x, t), analysis of the Lagrangian and Eulerian evolution shows that for bound potentials the former is more accurate while the latter is more practical because the Lagrangian quantum trajectories diverge with time. Introduction of stationary and time-dependent components into the wavefunction representation generates new Lagrangian-type dynamics where the trajectory spreading is controlled improving efficiency of the trajectory description. As an illustration, different types of dynamics are used to compute zero-point energy of a strongly anharmonic well and low-lying eigenstates of a high-dimensional coupled harmonic system

Apple Flavonoids Suppress Carcinogen-Induced DNA Damage in Normal Human Bronchial Epithelial Cells

Scope. Human neoplastic transformation due to DNA damage poses an increasing global healthcare concern. Maintaining genomic integrity is crucial for avoiding tumor initiation and progression. The present study aimed to investigate the efficacy of an apple flavonoid fraction (AF4) against various carcinogen-induced toxicity in normal human bronchial epithelial cells and its mechanism of DNA damage response and repair processes. Methods and Results. AF4-pretreated cells were exposed to nicotine-derived nitrosamine ketones (NNK), NNK acetate (NNK-Ae), methotrexate (MTX), and cisplatin to validate cytotoxicity, total reactive oxygen species, intracellular antioxidants, DNA fragmentation, and DNA tail damage. Furthermore, phosphorylated histone (γ-H2AX) and proteins involved in DNA damage (ATM/ATR, Chk1, Chk2, and p53) and repair (DNA-PKcs and Ku80) mechanisms were evaluated by immunofluorescence and western blotting, respectively. The results revealed that AF4-pretreated cells showed lower cytotoxicity, total ROS generation, and DNA fragmentation along with consequent inhibition of DNA tail moment. An increased level of γ-H2AX and DNA damage proteins was observed in carcinogen-treated cells and that was significantly (p≤0.05) inhibited in AF4-pretreated cells, in an ATR-dependent manner. AF4 pretreatment also facilitated the phosphorylation of DNA-PKcs and thus initiation of repair mechanisms. Conclusion. Apple flavonoids can protect in vitro oxidative DNA damage and facilitate repair mechanisms

Study of Mitral Annular Calcification in Chronic Kidney Disease

A case control study was conducted on prevalence of MAC in chronic kidney disease patients compared to subjects with normal kidney function. After obtaining ethical committee clearance, 102 CKD patients and 100 non CKD subjects comparable in age and sex distribution were selected randomly. After recording clinical data, blood investigations and ultrasonographic study, echocardiogram was done in all to look for MAC Results on analysis showed significantly high MAC in CKD patients. Among 102 CKD patients 10 (9.8%) had MAC while only one(1%) had MAC in non CKD group. Among 10 who had MAC in CKD group, 6 (60%) were in 40 to 60 age group and 4 (40%) were in above 60 age group. In non CKD group MAC was present only in an elderly female. In CKD patients MAC occurs even in younger age group. Significant association of high levels of calcium, phosphorus and calcium x phosphorus product with MAC was also noticed in the study. Increased MAC in CKD patients may be due to altered calcium and phosphorus metabolism in them. CAD was significantly high in those with MAC which may be due to the burden of shared risk factors for atherosclerosis in both groups

Examination of the Community Multiscale Air Quality (CMAQ) model performance over the North American and European domains

Copyright 2011 Elsevier B.V., All rights reserved.The CMAQ modeling system has been used to simulate the air quality for North America and Europe for the entire year of 2006 as part of the Air Quality Model Evaluation International Initiative (AQMEII). The operational model performance of tropospheric ozone (O), fine particulate matter (PM) and total particulate matter (PM) for the two continents has been assessed. The model underestimates daytime (8am-8pm LST) O mixing ratios by 13% in the winter for North America, primarily due to an underestimation of daytime O mixing ratios in the middle and lower troposphere from the lateral boundary conditions. The model overestimates winter daytime O mixing ratios in Europe by an average of 8.4%. The model underestimates daytime O by 4-5% in the spring for both continents, while in the summer daytime O is overestimated by 9.8% for North America and slightly underestimated by 1.6% for Europe. The model overestimates daytime O in the fall for both continents, grossly overestimating daytime O by over 30% for Europe. The performance for PM varies both seasonally and geographically for the two continents. For North American, PM is overestimated in the winter and fall, with an average Normalized Mean Bias (NMB) greater than -30%, while performance in the summer is relatively good, with an average NMB of -4.6%. For Europe, PM is underestimated throughout the entire year, with the NMB ranging from -24% in the fall to -55% in the winter. PM is underestimated throughout the year for both North America and Europe, with remarkably similar performance for both continents. The domain average NMB for PM ranges between -45% and -65% for the two continents, with the largest underestimation occurring in the summer for North American and the winter for Europe.Peer reviewedSubmitted Versio

Evaluation of the performance of four chemical transport models in predicting the aerosol chemical composition in Europe in 2005

© Author(s) 2016.Four regional chemistry transport models were applied to simulate the concentration and composition of particulate matter (PM) in Europe for 2005 with horizontal resolution 20 km. The modelled concentrations were compared with the measurements of PM chemical composition by the European Monitoring and Evaluation Programme (EMEP) monitoring network. All models systematically underestimated PM10 and PM2:5 by 10–60 %, depending on the model and the season of the year, when the calculated dry PM mass was compared with the measurements. The average water content at laboratory conditions was estimated between 5 and 20% for PM2:5 and between 10 and 25% for PM10. For majority of the PM chemical components, the relative underestimation was smaller than it was for total PM, exceptions being the carbonaceous particles and mineral dust. Some species, such as sea salt and NO3, were overpredicted by the models. There were notable differences between the models’ predictions of the seasonal variations of PM, mainly attributable to different treatments or omission of some source categories and aerosol processes. Benzo(a)pyrene concentrations were overestimated by all the models over the whole year. The study stresses the importance of improving the models’ skill in simulating mineral dust and carbonaceous compounds, necessity for high-quality emissions from wildland fires, as well as the need for an explicit consideration of aerosol water content in model–measurement comparison.Peer reviewedFinal Published versio

Mitochondrial DNA, a Powerful Tool to Decipher Ancient Human Civilization from Domestication to Music, and to Uncover Historical Murder Cases

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Mitochondria are unique organelles carrying their own genetic material, independent from that in the nucleus. This review will discuss the nature of mitochondrial DNA (mtDNA) and its levels in the cell, which are the key elements to consider when trying to achieve molecular identification in ancient and degraded samples. mtDNA sequence analysis has been appropriately validated and is a consistent molecular target for the examination of biological evidence encountered in forensic cases-and profiling, in certain conditions-especially for burnt bodies and degraded samples of all types. Exceptional cases and samples will be discussed in this review, such as mtDNA from leather in Beethoven's grand piano, mtDNA in mummies, and solving famous historical criminal cases. In addition, this review will be discussing the use of ancient mtDNA to understand past human diet, to trace historical civilizations and ancient trade routes, and to uncover geographical domestication origins and lineage relationships. In each topic, we will present the power of mtDNA and how, in many cases, no nuclear DNA was left, leaving mitochondrial DNA analysis as a powerful alternative. Exploring this powerful tool further will be extremely useful to modern science and researchers, due to its capabilities in providing us with previously unattainable knowledge.Peer reviewedFinal Published versio

Plant Flavonoids on Oxidative Stress-Mediated Kidney Inflammation

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Simple Summary: Increased stress is often observed in patients with kidney diseases, contributing to renal injury progression. Flavonoids are naturally occurring plant compounds with known health benefits, including antiapoptotic, anti-inflammatory, and antioxidant properties. Flavonoids can protect the kidney by improving antioxidant status, ameliorating excess reactive oxygen species levels, and acting as Nrf2-mediators in generating antioxidant responses in the body. Flavonoids also modulate inflammatory markers, exert anti-inflammatory effects, and protect the cells from apoptotic cell death in the kidney. Interestingly, few clinical trials have reported a direct correlation between a flavonoid-rich diet and better kidney disease prognosis. However, flavonoids have a low bioavailability in the body, making it essential to understand better their molecular mechanism of action. We suggest that a flavonoid-rich diet could have promising nephroprotective effects and beneficial outcomes in treating patients with kidney diseases. Abstract: The kidney is susceptible to reactive oxygen species-mediated cellular injury resulting in glomerulosclerosis, tubulointerstitial fibrosis, tubular cell apoptosis, and senescence, leading to renal failure, and is a significant cause of death worldwide. Oxidative stress-mediated inflammation is a key player in the pathophysiology of various renal injuries and diseases. Recently, flavonoids’ role in alleviating kidney diseases has been reported with an inverse correlation between dietary flavonoids and kidney injuries. Flavonoids are plant polyphenols possessing several health benefits and are distributed in plants from roots to leaves, flowers, and fruits. Dietary flavonoids have potent antioxidant and free-radical scavenging properties and play essential roles in disease prevention. Flavonoids exert a nephroprotective effect by improving antioxidant status, ameliorating excessive reactive oxygen species (ROS) levels, and reducing oxidative stress, by acting as Nrf2 antioxidant response mediators. Moreover, flavonoids play essential roles in reducing chemical toxicity. Several studies have demonstrated the effects of flavonoids in reducing oxidative stress, preventing DNA damage, reducing inflammatory cytokines, and inhibiting apoptosis-mediated cell death, thereby preventing or improving kidney injuries/diseases. This review covers the recent nephroprotective effects of flavonoids against oxidative stress-mediated inflammation in the kidney and their clinical advancements in renal therapy.Peer reviewe

DNA-dependent protein kinase: Epigenetic alterations and the role in genomic stability of cancer

DNA-dependent protein kinase (DNA-PK), a member of phosphatidylinositol-kinase family, is a key protein in mammalian DNA double-strand break (DSB) repair that helps to maintain genomic integrity. DNA-PK also plays a central role in immune cell development and protects telomerase during cellular aging. Epigenetic deregulation due to endogenous and exogenous factors may affect the normal function of DNA-PK, which in turn could impair DNA repair and contribute to genomic instability. Recent studies implicate a role for epigenetics in the regulation of DNA-PK expression in normal and cancer cells, which may impact cancer progression and metastasis as well as provide opportunities for treatment and use of DNA-PK as a novel cancer biomarker. In addition, several small molecules and biological agents have been recently identified that can inhibit DNA-PK function or expression, and thus hold promise for cancer treatments. This review discusses the impact of epigenetic alterations and the expression of DNA-PK in relation to the DNA repair mechanisms with a focus on its differential levels in normal and cancer cells

Microplate assay for quantitation of neutral lipids in extracts from microalgae

Lipid quantitation is widespread in the algae literature, but popular methods such as gravimetry, gas chromatography and mass spectrometry (GC-MS), and Nile red cell staining suffer drawbacks, including poor quantitation of neutral lipids, expensive equipment, and variable results among algae species, respectively. A high-throughput microplate assay was developed that uses Nile red dye to quantify neutral lipids that have been extracted from algae cells. Because the algal extracts contained pigments that quenched Nile red fluorescence, a mild bleach solution was used to destroy pigments, resulting in a nearly linear response for lipid quantities in the range of 0.75 to 40 μg. Corn oil was used as a standard for quantitation, although other vegetable oils displayed a similar response. The assay was tested on lipids extracted from three species of Chlorella and resulted in close agreement with triacylglycerol (TAG) levels determined by thin layer chromatography. The assay was found to more accurately measure algal lipids conducive to biodiesel production and nutrition applications than the widely used gravimetric assay. Assay response was also consistent among different species, in contrast to Nile red cell staining procedures