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https://www.readbyqxmd.com/read/29149186/cell-cycle-time-series-gene-expression-data-encoded-as-cyclic-attractors-in-hopfield-systems
#1
Anthony Szedlak, Spencer Sims, Nicholas Smith, Giovanni Paternostro, Carlo Piermarocchi
Modern time series gene expression and other omics data sets have enabled unprecedented resolution of the dynamics of cellular processes such as cell cycle and response to pharmaceutical compounds. In anticipation of the proliferation of time series data sets in the near future, we use the Hopfield model, a recurrent neural network based on spin glasses, to model the dynamics of cell cycle in HeLa (human cervical cancer) and S. cerevisiae cells. We study some of the rich dynamical properties of these cyclic Hopfield systems, including the ability of populations of simulated cells to recreate experimental expression data and the effects of noise on the dynamics...
November 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29145933/quantitative-structure-pharmacokinetics-relationships-for-plasma-protein-binding-of-basic-drugs
#2
Zvetanka Dobreva Zhivkova
PURPOSE: Binding of drugs to plasma proteins is a common physiological occurrence which may have a profound effect on both pharmacokinetics and pharmacodynamics. The early prediction of plasma protein binding (PPB) of new drug candidates is an important step in drug development process. The present study is focused on the development of quantitative structure - pharmacokinetics relationship (QSPkR) for the negative logarithm of the free fraction of the drug in plasma (pfu) of basic drugs...
2017: Journal of Pharmacy & Pharmaceutical Sciences: a Publication of the Canadian Society for Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29145487/defining-external-factors-that-determine-neuronal-survival-apoptosis-and-necrosis-during-excitotoxic-injury-using-a-high-content-screening-imaging-platform
#3
Ujval Anilkumar, Petronela Weisova, Jasmin Schmid, Tytus Bernas, Heinrich J Huber, Heiko Düssmann, Niamh M C Connolly, Jochen H M Prehn
Cell death induced by excessive glutamate receptor overactivation, excitotoxicity, has been implicated in several acute and chronic neurological disorders. While numerous studies have demonstrated the contribution of biochemically and genetically activated cell death pathways in excitotoxic injury, the factors mediating passive, excitotoxic necrosis are less thoroughly investigated. To address this question, we developed a high content screening (HCS) based assay to collect high volumes of quantitative cellular imaging data and elucidated the effects of intrinsic and external factors on excitotoxic necrosis and apoptosis...
2017: PloS One
https://www.readbyqxmd.com/read/29144791/is-there-a-role-for-programmed-death-ligand-1-testing-and-immunotherapy-in-colorectal-cancer-with-microsatellite-instability-part-i-colorectal-cancer-microsatellite-instability-testing-and-clinical-implications
#4
Esmeralda Celia Marginean, Barbara Melosky
CONTEXT: - Colorectal cancer (CRC) represents the third most-common cancer in developed countries and is a leading cause of cancer deaths worldwide. Two recognized pathways contribute to CRC development: a more-common chromosomal instability pathway and, in 15% of cases, a deficient mismatch repair or microsatellite instability-high (MSI-H) pathway. The MSI-H CRC can be associated with somatic or germline mutations. Microsatellite status has been recognized as a prognostic and predictive biomarker...
November 16, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/29143909/design-of-an-optimum-poincar%C3%A3-plane-for-extracting-meaningful-samples-from-eeg-signals
#5
Babak Sharif, Amir Homayoun Jafari
Biosignals are considered as important sources of data for diagnosing and detecting abnormalities, and modeling dynamics in the body. These signals are usually analyzed using features taken from time and frequency domain. In theory' these dynamics can also be analyzed utilizing Poincaré plane that intersects system's trajectory. However' selecting an appropriate Poincaré plane is a crucial part of extracting best Poincaré samples. There is no unique way to choose a Poincaré plane' because it is highly dependent to the system dynamics...
November 16, 2017: Australasian Physical & Engineering Sciences in Medicine
https://www.readbyqxmd.com/read/29143652/genetic-profiles-of-ten-dirofilaria-immitis-isolates-susceptible-or-resistant-to-macrocyclic-lactone-heartworm-preventives
#6
Catherine Bourguinat, Kathy Keller, Jianguo Xia, Pierre Lepage, Tom L McTier, Debra J Woods, Roger K Prichard
BACKGROUND: For dogs and cats, chemoprophylaxis with macrocyclic lactone (ML) preventives for heartworm disease is widely used in the United States and other countries. Since 2005, cases of loss of efficacy (LOE) of heartworm preventives have been reported in the U.S. More recently, ML-resistant D. immitis isolates were confirmed. Previous work identified 42 genetic markers that could predict ML response in individual samples. For field surveillance, it would be more appropriate to work on microfilarial pools from individual dogs with a smaller subset of genetic markers...
November 9, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29142438/molecular-simulation-based-combinatorial-modeling-and-antioxidant-activities-of-zingiberaceae-family-rhizomes
#7
Talambedu Usha, Sushen Pradhan, Arvind Kumar Goyal, Shanmugarajan Dhivya, H P Prashanth Kumar, Manoj Kumar Singh, Neelu Joshi, Bharat Chandra Basistha, K R Siddalinga Murthy, Saravanakumar Selvaraj, Sushil Kumar Middha
Objective: The main aim of this scientific report was to investigate a series of phytochemicals in silico and the pharmacology of four plants found at higher altitude in the ginger family, Zingiberaceae (incl. Costaceae) from North-East India, particularly Sikkim. First, the goal was to determine the biological activities of the four herbs (used under Zingiberaceae family) using antioxidant assays to identify the best species. Second, previously reported compounds in litero were subsequently screened for their anticancerous activities using in silico methods...
October 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/29141776/evaluation-of-a-new-ensemble-learning-framework-for-mass-classification-in-mammograms
#8
Omid Rahmani Seryasat, Javad Haddadnia
BACKGROUND: Mammography is the most common screening method for diagnosis of breast cancer. MATERIALS AND METHODS: In this study, a computer-aided system for diagnosis of benignity and malignity of the masses was implemented in mammogram images. In the computer aided diagnosis system, we first reduce the noise in the mammograms using an effective noise removal technique. After the noise removal, the mass in the region of interest must be segmented and this segmentation is done using a deformable model...
May 22, 2017: Clinical Breast Cancer
https://www.readbyqxmd.com/read/29140792/a-bayesian-hierarchical-model-for-identifying-significant-polygenic-effects-while-controlling-for-confounding-and-repeated-measures
#9
Christopher McMahan, James Baurley, William Bridges, Chase Joyner, Muhamad Fitra Kacamarga, Robert Lund, Carissa Pardamean, Bens Pardamean
Genomic studies of plants often seek to identify genetic factors associated with desirable traits. The process of evaluating genetic markers one by one (i.e. a marginal analysis) may not identify important polygenic and environmental effects. Further, confounding due to growing conditions/factors and genetic similarities among plant varieties may influence conclusions. When developing new plant varieties to optimize yield or thrive in future adverse conditions (e.g. flood, drought), scientists seek a complete understanding of how the factors influence desirable traits...
November 15, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29136028/path-oriented-test-cases-generation-based-adaptive-genetic-algorithm
#10
Xiaoan Bao, Zijian Xiong, Na Zhang, Junyan Qian, Biao Wu, Wei Zhang
The automatic generation of test cases oriented paths in an effective manner is a challenging problem for structural testing of software. The use of search-based optimization methods, such as genetic algorithms (GAs), has been proposed to handle this problem. This paper proposes an improved adaptive genetic algorithm (IAGA) for test cases generation by maintaining population diversity. It uses adaptive crossover rate and mutation rate in dynamic adjustment according to the differences between individual similarity and fitness values, which enhances the exploitation of searching global optimum...
2017: PloS One
https://www.readbyqxmd.com/read/29132927/whole-exome-sequencing-identified-a-pathogenic-mutation-in-ryr2-in-a-chinese-family-with-unexplained-sudden-death
#11
Yubi Lin, Siqi He, Zili Liao, Ruiling Feng, Ruilin Liu, Yongzheng Peng, Nan Yu, Hang Qi, Jia Chen, Zifeng Huang, Heping Lei, Yang Liu, Fang Rao, Chunyu Deng, Yumei Xue, Guolin Zhang, Bin Zhang, Hua Yao, Shulin Wu
OBJECTIVE: This study aimed to identify the pathogenic mutation in a Chinese family with unexplained sudden death (USD) or occasional syncope. MATERIALS AND METHODS: Whole exome sequencing and target capture sequencing were respectively conducted for two related patients. The genetic data was screened using the 1000 genomes project and SNP database (PubMed), and the identified mutations were assessed for predicted pathogenicity using the SIFT and Polyphen-2 algorithms...
October 10, 2017: Journal of Electrocardiology
https://www.readbyqxmd.com/read/29132014/a-genetic-algorithm-for-simulating-correlated-binary-data-from-biomedical-research
#12
Jochen Kruppa, Bernd Lepenies, Klaus Jung
Correlated binary data arise in a large variety of biomedical research. In order to evaluate methods for their analysis, computer simulations of such data are often required. Existing methods can often not cover the full range of possible correlations between the variables or are not available as implemented software. We propose a genetic algorithm that approaches the desired correlation structure under a given marginal distribution. The procedure generates a large representative matrix from which the probabilities of individual observations can be derived or from which samples can be drawn directly...
October 31, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29131940/fe-cluster-compounds-of-chalcogenides-candidates-for-rare-earth-free-permanent-magnet-and-magnetic-nodal-line-topological-material
#13
Xin Zhao, Cai-Zhuang Wang, Minsung Kim, Kai-Ming Ho
Fe-cluster-based crystal structures are predicted for chalcogenides Fe3X4 (X = S, Se, Te) using an adaptive genetic algorithm. Topologically different from the well-studied layered structures of iron chalcogenides, the newly predicted structures consist of Fe clusters that are either separated by the chalcogen atoms or connected via sharing of the vertex Fe atoms. Using first-principles calculations, we demonstrate that these structures have competitive or even lower formation energies than the experimentally synthesized Fe3X4 compounds and exhibit interesting magnetic and electronic properties...
November 13, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/29131868/design-of-the-smart-home-system-based-on-the-optimal-routing-algorithm-and-zigbee-network
#14
Dengying Jiang, Ling Yu, Fei Wang, Xiaoxia Xie, Yongsheng Yu
To improve the traditional smart home system, its electric wiring, networking technology, information transmission and facility control are studied. In this paper, we study the electric wiring, networking technology, information transmission and facility control to improve the traditional smart home system. First, ZigBee is used to replace the traditional electric wiring. Second, a network is built to connect lots of wireless sensors and facilities, thanks to the capability of ZigBee self-organized network and Genetic Algorithm-Particle Swarm Optimization Algorithm (GA-PSOA) to search for the optimal route...
2017: PloS One
https://www.readbyqxmd.com/read/29131699/genotype-specific-minimal-residual-disease-interpretation-improves-stratification-in-pediatric-acute-lymphoblastic-leukemia
#15
David O'Connor, Amir Enshaei, Jack Bartram, Jeremy Hancock, Christine J Harrison, Rachael Hough, Sujith Samarasinghe, Claire Schwab, Ajay Vora, Rachel Wade, John Moppett, Anthony V Moorman, Nick Goulden
Purpose Minimal residual disease (MRD) and genetic abnormalities are important risk factors for outcome in acute lymphoblastic leukemia. Current risk algorithms dichotomize MRD data and do not assimilate genetics when assigning MRD risk, which reduces predictive accuracy. The aim of our study was to exploit the full power of MRD by examining it as a continuous variable and to integrate it with genetics. Patients and Methods We used a population-based cohort of 3,113 patients who were treated in UKALL2003, with a median follow-up of 7 years...
November 13, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/29129922/statistical-and-integrative-system-level-analysis-of-dna-methylation-data
#16
REVIEW
Andrew E Teschendorff, Caroline L Relton
Epigenetics plays a key role in cellular development and function. Alterations to the epigenome are thought to capture and mediate the effects of genetic and environmental risk factors on complex disease. Currently, DNA methylation is the only epigenetic mark that can be measured reliably and genome-wide in large numbers of samples. This Review discusses some of the key statistical challenges and algorithms associated with drawing inferences from DNA methylation data, including cell-type heterogeneity, feature selection, reverse causation and system-level analyses that require integration with other data types such as gene expression, genotype, transcription factor binding and other epigenetic information...
November 13, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/29127892/estimation-of-the-late-postmortem-interval-using-ftir-spectroscopy-and-chemometrics-in-human-skeletal-remains
#17
Qi Wang, Yinming Zhang, Hancheng Lin, Shuai Zha, Ruoxi Fang, Xin Wei, Shuanliang Fan, Zhenyuan Wang
Due to a lack of reliable and accurate methods, determining the postmortem interval (PMI) of human skeletal remains is one of the most important and challenging tasks in forensic medicine. In this paper, we studied the changes to bone chemistry with increasing PMI in two different experimental conditions using Fourier transform infrared (FTIR) spectroscopy in conjunction with chemometrics methods Paired bone samples collected from 56 human corpses were buried (placed in soil) and unburied (exposed to the air) for intervals between 76 and 552 days...
November 8, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29126456/virological-response-hiv-1-drug-resistance-mutations-and-genetic-diversity-among-patients-on-first-line-antiretroviral-therapy-in-n-djamena-chad-findings-from-a-cross-sectional-study
#18
Chatté Adawaye, Joseph Fokam, Erick Kamangu, Hamit Mahamat Alio, Aoudalkarim Moussa Chahad, Fabrice Susin, Ali Mahamat Moussa, Tchombou Hig-Zounet Bertin, Abdelsalam Tidjani, Dolores Vaira, Michel Moutschen
BACKGROUND: The national antiretroviral therapy in the Republic of Chad provides free of charge antiretroviral regimens and therapeutic monitoring for patients receiving antiretroviral therapy nationwide. For a successful programmatic uptake, these efforts merit to be supported by thorough assessments of antiretroviral therapy response and HIV-1 drug resistance surveillance, especially with risks of cross-resistance due to the gradual stavudine phasing out in such national settings. We therefore evaluated the virological response to antiretroviral therapy, HIV-1 drug resistance emergence and circulating HIV-1 clades in a Chad context...
November 10, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29125742/heterogeneous-oh-oxidation-shielding-effects-and-implications-for-the-atmospheric-fate-of-terbuthylazine-and-other-pesticides
#19
Joanna Socorro, Pascale S J Lakey, Lei Han, Thomas Berkemeier, Gerhard Lammel, Cornelius Zetzsch, Ulrich Pöschl, Manabu Shiraiwa
Terbuthylazine (TBA) is a widely used herbicide, and its heterogeneous reaction with OH radicals is important for assessing its potential to undergo atmospheric long-range transport and to affect the environment and public health. The apparent reaction rate coefficients obtained in different experimental investigations, however, vary by orders of magnitude depending on the applied experimental techniques and conditions. In this study, we used a kinetic multilayer model of aerosol chemistry with reversible surface adsorption and bulk diffusion (KM-SUB) in combination with a Monte Carlo genetic algorithm to simulate the measured decay rates of TBA...
November 17, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/29124304/modeling-coverage-gaps-in-haplotype-frequencies-via-bayesian-inference-to-improve-stem-cell-donor-selection
#20
Yoram Louzoun, Idan Alter, Loren Gragert, Mark Albrecht, Martin Maiers
Regardless of sampling depth, accurate genotype imputation is limited in regions of high polymorphism which often have a heavy-tailed haplotype frequency distribution. Many rare haplotypes are thus unobserved. Statistical methods to improve imputation by extending reference haplotype distributions using linkage disequilibrium patterns that relate allele and haplotype frequencies have not yet been explored. In the field of unrelated stem cell transplantation, imputation of highly polymorphic human leukocyte antigen (HLA) genes has an important application in identifying the best-matched stem cell donor when searching large registries totaling over 28,000,000 donors worldwide...
November 9, 2017: Immunogenetics
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