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Register a new userDrug absorption through a cell monolayer: a theoretical work on a non-linear three-compartment model
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The subject of analysis is a non-linear three-compartment model, widely used in pharmacological absorption studies. It has been transformed into a general form, thus leading automatically to an appropriate approximation. This made the absorption profile accessible and expressions for absorption times, apparent permeabilities and equilibrium values were given. These findings allowed a profound analysis of results from non-linear curve fits and delivered the dependencies on the systems parameters over a wide range of values. The results were applied to an absorption experiment with multidrug transporter-affected antibiotic CNV97100 on Caco-2 cell monolayers.
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Despite the significant advances in life science, it still takes decades to translate a basic drug discovery into a cure for human disease. To accelerate the process from bench to bedside, interdisciplinary research (especially research involving both basic research and clinical research) has been strongly recommend by many previous studies. However, the patterns and the roles of the interdisciplinary characteristics in drug research have not been deeply examined in extant studies. The purpose of this study was to characterize interdisciplinary characteristics in drug research from the perspective of translational science, and to examine the role of different kinds of interdisciplinary characteristics in translational research for drugs.
A model of genome evolution is proposed. Based on three assumptions the evolutionary theory of a genome is formulated. The general law on the direction of genome evolution is given. Both the deterministic classical equation and the stochastic quantum equation are proposed. It is proved that the classical equation can be put in a form of the least action principle and the latter can be used for obtaining the quantum generalization of the evolutionary law. The wave equation and uncertainty relation for the quantum evolution are deduced logically. It is shown that the classical trajectory is a limiting case of the general quantum evolution depicted in the coarse-grained time. The observed smooth/sudden evolution is interpreted by the alternating occurrence of the classical and quantum phases. The speciation event is explained by the quantum transition in quantum phase. Fundamental constants of time dimension, the quantization constant and the evolutionary inertia, are introduced for characterizing the genome evolution. The size of minimum genome is deduced from the quantum uncertainty lower bound. The present work shows the quantum law may be more general than thought, since it plays key roles not only in atomic physics, but also in genome evolution.
To enable personalized cancer treatment, machine learning models have been developed to predict drug response as a function of tumor and drug features. However, most algorithm development efforts have relied on cross validation within a single study to assess model accuracy. While an essential first step, cross validation within a biological data set typically provides an overly optimistic estimate of the prediction performance on independent test sets. To provide a more rigorous assessment of model generalizability between different studies, we use machine learning to analyze five publicly available cell line-based data sets: NCI60, CTRP, GDSC, CCLE and gCSI. Based on observed experimental variability across studies, we explore estimates of prediction upper bounds. We report performance results of a variety of machine learning models, with a multitasking deep neural network achieving the best cross-study generalizability. By multiple measures, models trained on CTRP yield the most accurate predictions on the remaining testing data, and gCSI is the most predictable among the cell line data sets included in this study. With these experiments and further simulations on partial data, two lessons emerge: (1) differences in viability assays can limit model generalizability across studies, and (2) drug diversity, more than tumor diversity, is crucial for raising model generalizability in preclinical screening.
The paper represents three supplements to the source paper, q-bio/0610044 [q-bio.OT], with three new series of harmonic structures of the genetic code, determined by Gauss arithmetical algorithm; by Table of Minimal Adding, as in (Rakocevic, 2011a: Table 4; 2011b: Table 4); all structures in relation to Binary-code tree (Rakocevic, 1998). The determination itself is realized through atom and nucleon number balancing and nuancing of molekular polarity. In the first supplement the word is about some additional harmonic structures in relation to a previous our paper (Rakocevic, 2004); in the second one about the relation that structures with the polarity of protein amino acids. In the third supplement we give new ideas about the genetic code by an inclusion of the notions cipher of the genetic code and the key of that cipher.
A quantum model on the chemically and physically induced pluripotency in stem cells is proposed. Based on the conformational Hamiltonian and the idea of slow variables (molecular torsions) slaving fast ones the conversion from the differentiate state to pluripotent state is defined as the quantum transition between conformational states. The transitional rate is calculated and an analytical form for the rate formulas is deduced. Then the dependence of the rate on the number of torsion angles of the gene and the magnitude of the rate can be estimated by comparison with protein folding. The reaction equations of the conformational change of the pluripotency genes in chemical reprogramming are given. The characteristic time of the chemical reprogramming is calculated and the result is consistent with experiments. The dependence of the transition rate on physical factors such as temperature, PH value and the volume and shape of the coherent domain is analyzed from the rate equation. It is suggested that by decreasing the coherence degree of some pluripotency genes a more effective approach to the physically induced pluripotency can be made.
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