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https://www.readbyqxmd.com/read/28641555/supervised-machine-learning-methods-applied-to-predict-ligand-binding-affinity
#1
Gabriela Sehnem Heck, Val Oliveira Pintro, Richard Rene Pereira, Mauricio Boff de Ávila, Nayara Maria Bernhardt Levin, Walter Filgueira de Azevedo
BACKGROUND: Calculation of ligand-binding affinity is an open problem in computational medicinal chemistry. The ability to computationally predict affinities has a beneficial impact in the early stages of drug development, since it allows a mathematical model to assess protein-ligand interactions. Due to the availability of structural and binding information, machine learning methods have been applied to generate scoring functions with good predictive power. OBJECTIVE: Our goal here is to review recent developments in the application of machine learning methods to predict ligand- binding affinity...
June 22, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28641529/irna-2methyl-identify-rna-2-o-methylation-sites-by-incorporating-sequence-coupled-effects-into-general-pseknc-and-ensemble-classifier
#2
Wang-Ren Qiu, Shi-Yu Jiang, Bi-Qian Sun, Xuan Xiao, Xiang Cheng, Kuo-Chen Chou
OBJECTIVE: Being a kind of post-transcriptional modification (PTCM) in RNA, the 2'-O-methylation modification occurs in the processes of life development and disease formation as well. Accordingly, from the angles of both basic research and drug development, we are facing a challenging problem: given an uncharacterized RNA sequence formed by many nucleotides of A (adenine), C (cytosine), G (guanine), and U (uracil), which one can be of 2-O-methylation modification, and which one cannot? Unfortunately, so far no computational method whatsoever has been developed to address such a problem...
June 22, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28641265/a-new-method-for-neural-spike-alignment-the-centroid-filter
#3
Benjamin Metcalfe, Chris Clarke, Nick Donaldson, John Taylor
Recordings made directly from the nervous system are a key tool in experimental electrophysiology and the development of bioelectronic medicines. Analysis of these recordings involves the identification of signals from individual neurons, a process known as spike sorting. A critical and limiting feature of spike sorting is the need to align individual spikes in time. However, electrophysiological recordings are made in extremely noisy environments that seriously limit the performance of the spike-alignment process...
June 16, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
https://www.readbyqxmd.com/read/28633990/cellular-gauge-symmetry-and-the-li-organization-principle-a-mathematical-addendum-quantifying-energetic-dynamics-in-physical-and-biological-systems-through-a-simple-geometric-tool-and-geodetic-curves
#4
REVIEW
Alexander Yurkin, Arturo Tozzi, James F Peters, Pedro C Marijuán
The present Addendum complements the accompanying paper "Cellular Gauge Symmetry and the Li Organization Principle"; it illustrates a recently-developed geometrical physical model able to assess electronic movements and energetic paths in atomic shells. The model describes a multi-level system of circular, wavy and zigzag paths which can be projected onto a horizontal tape. This model ushers in a visual interpretation of the distribution of atomic electrons' energy levels and the corresponding quantum numbers through rather simple tools, such as compasses, rulers and straightforward calculations...
June 17, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/28612293/nowhere-to-run-rabbit-the-cold-war-calculus-of-disease-ecology
#5
Warwick Anderson
During the cold war, Frank Fenner (protégé of Macfarlane Burnet and René Dubos) and Francis Ratcliffe (associate of A. J. Nicholson and student of Charles Elton) studied mathematically the coevolution of host resistance and parasite virulence when myxomatosis was unleashed on Australia's rabbit population. Later, Robert May called Fenner the "real hero" of disease ecology for his mathematical modeling of the epidemic. While Ratcliffe came from a tradition of animal ecology, Fenner developed an ecological orientation in World War II through his work on malaria control (with Ratcliffe and Ian Mackerras, among others)-that is, through studies of tropical medicine...
June 2017: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/28603726/drawing-nomograms-with-r-applications-to-categorical-outcome-and-survival-data
#6
EDITORIAL
Zhongheng Zhang, Michael W Kattan
Outcome prediction is a major task in clinical medicine. The standard approach to this work is to collect a variety of predictors and build a model of appropriate type. The model is a mathematical equation that connects the outcome of interest with the predictors. A new patient with given clinical characteristics can be predicted for outcome with this model. However, the equation describing the relationship between predictors and outcome is often complex and the computation requires software for practical use...
May 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28596936/new-bioengineering-breakthroughs-and-enabling-tools-in-regenerative-medicine
#7
REVIEW
Alvaro Mata, Helena S Azevedo, Lorenzo Botto, Nuria Gavara, Lei Su
PURPOSE OF REVIEW: In this review, we provide a general overview of recent bioengineering breakthroughs and enabling tools that are transforming the field of regenerative medicine (RM). We focus on five key areas that are evolving and increasingly interacting including mechanobiology, biomaterials and scaffolds, intracellular delivery strategies, imaging techniques, and computational and mathematical modeling. RECENT FINDINGS: Mechanobiology plays an increasingly important role in tissue regeneration and design of therapies...
2017: Current Stem Cell Reports
https://www.readbyqxmd.com/read/28582909/measuring-the-3d-motion-space-of-the-human-ankle
#8
Jinzhuang Xiao, Yunchao Zhang, Shuai Zhao, Hongrui Wang
BACKGROUND: The 3D motion space of the human ankle is an important area of study in medicine. The 3D motion space can provide significant information for establishing more reasonable rehabilitation procedures and standards of ankle injury care. OBJECTIVE: This study aims to measure the 3D motion space of the human ankle and to use mathematical methods to quantify it. METHODS: A motion capturing system was used to simultaneously capture the 3D coordinates of points marked on the foot, and convert these coordinate values into rotation angles through trigonometric functions and vectors...
May 19, 2017: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/28579895/characteristics-studies-of-molecular-structures-in-drugs
#9
Wei Gao, Yiqiao Wang, B Basavanagoud, Muhammad Kamran Jamil
In theoretical medicine, topological indices are defined to test the medicine and pharmacy characteristics, such as melting point, boiling point, toxicity and other biological activities. As basic molecular structures, hexagonal jagged-rectangle and distance-regular structure are widely appeared in medicine, pharmacy and biology engineering. In this paper, we study the chemical properties of hexagonal jagged-rectangle from the mathematical point of view. Several vertex distance-based indices are determined...
May 2017: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
https://www.readbyqxmd.com/read/28556373/high-resolution-dynamic-31-p-mrsi-using-a-low-rank-tensor-model
#10
Chao Ma, Bryan Clifford, Yuchi Liu, Yuning Gu, Fan Lam, Xin Yu, Zhi-Pei Liang
PURPOSE: To develop a rapid (31) P-MRSI method with high spatiospectral resolution using low-rank tensor-based data acquisition and image reconstruction. METHODS: The multidimensional image function of (31) P-MRSI is represented by a low-rank tensor to capture the spatial-spectral-temporal correlations of data. A hybrid data acquisition scheme is used for sparse sampling, which consists of a set of "training" data with limited k-space coverage to capture the subspace structure of the image function, and a set of sparsely sampled "imaging" data for high-resolution image reconstruction...
May 28, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28533120/evaluation-of-new-chemical-entities-as-substrates-of-liver-transporters-in-the-pharmaceutical-industry-response-to-regulatory-requirements-and-future-steps
#11
Noriko Okudaira
This article discusses the evaluation of drug candidates as hepatic transporter substrates. Recently, research on the applications of hepatic transporters in the pharmaceutical industry has improved to meet the requirements of the regulatory guidelines for the evaluation of drug interactions. To identify the risk of transporter-mediated drug-drug interactions (DDIs) at an early stage of drug development, we employed a strategy of reviewing the in vivo animal pharmacokinetics and tissue distribution data obtained in the discovery stage together with the in vitro data obtained for regulatory submission...
May 19, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28526045/standardization-of-platelet-releasate-products-for-clinical-applications-in-cell-therapy-a-mathematical-approach
#12
Francesco Agostini, Jerry Polesel, Monica Battiston, Elisabetta Lombardi, Stefania Zanolin, Alessandro Da Ponte, Giuseppe Astori, Cristina Durante, Mario Mazzucato
BACKGROUND: Standardized animal-free components are required for manufacturing cell-based medicinal products. Human platelet concentrates are sources of growth factors for cell expansion but such products are characterized by undesired variability. Pooling together single-donor products improves consistency, but the minimal pool sample size was never determined. METHODS: Supernatant rich in growth factors (SRGF) derived from n = 44 single-donor platelet-apheresis was obtained by CaCl2 addition...
May 19, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28523827/statistical-model-based-hplc-analytical-method-adjustment-strategy-to-adapt-to-different-sets-of-analytes-in-complicated-samples
#13
Binjun Yan, Xue Bai, Yunjie Sheng, Fanzhu Li
INTRODUCTION: On account of the complicated compositions of the products like traditional Chinese medicines (TCMs) and functional foods, it is a common practice to determine different sets of analytes in the same product for different purposes. OBJECTIVE: To efficiently develop the corresponding HPLC methods, a statistical model based analytical method adjustment (SMB-AMA) strategy was proposed. METHODS: In this strategy, the HPLC data acquired with design of experiments methodology were efficiently utilised to build the retention models for all the analytes and interferences shown in the chromatograms with multivariate statistical modelling methods...
May 19, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28523139/an-overview-of-the-use-of-artificial-neural-networks-in-lung-cancer-research
#14
EDITORIAL
Luca Bertolaccini, Piergiorgio Solli, Alessandro Pardolesi, Antonello Pasini
The artificial neural networks (ANNs) are statistical models where the mathematical structure reproduces the biological organisation of neural cells simulating the learning dynamics of the brain. Although definitions of the term ANN could vary, the term usually refers to a neural network used for non-linear statistical data modelling. The neural models applied today in various fields of medicine, such as oncology, do not aim to be biologically realistic in detail but just efficient models for nonlinear regression or classification...
April 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28521678/ipgk-pseaac-identify-lysine-phosphoglycerylation-sites-in-proteins-by-incorporating-four-different-tiers-of-amino-acid-pairwise-coupling-information-into-the-general-pseaac
#15
Li-Ming Liu, Yan Xu, Kuo-Chen Chou
BACKGROUND: Occurring at Lys residues, the PGK (lysine phosphoglycerylation) is a special kind of post-translational modification (PTM). It may invert the charge potential of the modified residue and change the protein structures and functions, causing various diseases in liver, brain, and kidney. OBJECTIVE: From the angles of both basic research and drug development, we are facing a critical challenging problem: for an uncharacterized protein sequence containing many Lys residues, which ones can be of phosphoglycerylation, and which ones cannot? METHOD: To address this problem, we have developed a predictor called iPGK-PseAAC by incorporating into the general PseAAC (pseudo amino acid composition) with four different tiers of amino acid pairwise coupling information, where tiers 1, 2, 3, and 4 refer to the amino acid pairwise couplings between all the 1st, 2nd, 3rd, and 4th most contiguous residues along a protein segment, respectively...
May 15, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28520403/integrated-strategy-for-unknown-ei-ms-identification-using-quality-control-calibration-curve-multivariate-analysis-ei-ms-spectral-database-and-retention-index-prediction
#16
Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900 000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a "four-step" strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions...
May 26, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28512395/keypress-based-musical-preference-is-both-individual-and-lawful
#17
Sherri L Livengood, John P Sheppard, Byoung W Kim, Edward C Malthouse, Janet E Bourne, Anne E Barlow, Myung J Lee, Veronica Marin, Kailyn P O'Connor, John G Csernansky, Martin P Block, Anne J Blood, Hans C Breiter
Musical preference is highly individualized and is an area of active study to develop methods for its quantification. Recently, preference-based behavior, associated with activity in brain reward circuitry, has been shown to follow lawful, quantifiable patterns, despite broad variation across individuals. These patterns, observed using a keypress paradigm with visual stimuli, form the basis for relative preference theory (RPT). Here, we sought to determine if such patterns extend to non-visual domains (i.e...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28507240/mathematical-methods-in-medicine-neuroscience-cardiology-and-pathology
#18
José M Amigó, Michael Small
The application of mathematics, natural sciences and engineering to medicine is gaining momentum as the mutual benefits of this collaboration become increasingly obvious. This theme issue is intended to highlight the trend in the case of mathematics. Specifically, the scope of this theme issue is to give a general view of the current research in the application of mathematical methods to medicine, as well as to show how mathematics can help in such important aspects as understanding, prediction, treatment and data processing...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28507239/pulsatile-flow-in-ventricular-catheters-for-hydrocephalus
#19
Á Giménez, M Galarza, U Thomale, M U Schuhmann, J Valero, J M Amigó
The obstruction of ventricular catheters (VCs) is a major problem in the standard treatment of hydrocephalus, the flow pattern of the cerebrospinal fluid (CSF) being one important factor thereof. As a first approach to this problem, some of the authors studied previously the CSF flow through VCs under time-independent boundary conditions by means of computational fluid dynamics in three-dimensional models. This allowed us to derive a few basic principles which led to designs with improved flow patterns regarding the obstruction problem...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28507238/clustering-how-much-bias-do-we-need
#20
Tom Lorimer, Jenny Held, Ruedi Stoop
Scientific investigations in medicine and beyond increasingly require observations to be described by more features than can be simultaneously visualized. Simply reducing the dimensionality by projections destroys essential relationships in the data. Similarly, traditional clustering algorithms introduce data bias that prevents detection of natural structures expected from generic nonlinear processes. We examine how these problems can best be addressed, where in particular we focus on two recent clustering approaches, Phenograph and Hebbian learning clustering, applied to synthetic and natural data examples...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
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