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https://www.readbyqxmd.com/read/28525957/determining-dominant-driving-forces-affecting-controlled-protein-release-from-polymeric-nanoparticles
#1
Josh Smith, Kayla G Sprenger, Rick Liao, Andrea Joseph, Elizabeth Nance, Jim Pfaendtner
Enzymes play a critical role in many applications in biology and medicine as potential therapeutics. One specific area of interest is enzyme encapsulation in polymer nanostructures, which have applications in drug delivery and catalysis. A detailed understanding of the mechanisms governing protein/polymer interactions is crucial for optimizing the performance of these complex systems for different applications. Using a combined computational and experimental approach, this study aims to quantify the relative importance of molecular and mesoscale driving forces to protein release from polymeric nanoparticles...
May 19, 2017: Biointerphases
https://www.readbyqxmd.com/read/28524769/machine-learning-for-epigenetics-and-future-medical-applications
#2
Lawrence B Holder, M Muksitul Haque, Michael K Skinner
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets...
May 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
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
#3
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 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28520105/large-scale-computational-models-of-liver-metabolism-how-far-from-the-clinics
#4
REVIEW
Tanja Cvitanović, Matthias C Reichert, Miha Moškon, Miha Mraz, Frank Lammert, Damjana Rozman
Understanding the dynamics of human liver metabolism is fundamental for effective diagnosis and treatment of liver diseases in general and the metabolism of drugs in particular. This knowledge can be obtained with systems biology/medicine approaches that account for the complexity of hepatic responses and their systemic consequences in other organs. Computational modelling can reveal hidden principles of the system by classification of individual components, analysing their interactions and simulating the effects that are difficult to investigate experimentally...
May 18, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28507237/multiscale-ordinal-network-analysis-of-human-cardiac-dynamics
#5
M McCullough, M Small, H H C Iu, T Stemler
In this study, we propose a new information theoretic measure to quantify the complexity of biological systems based on time-series data. We demonstrate the potential of our method using two distinct applications to human cardiac dynamics. Firstly, we show that the method clearly discriminates between segments of electrocardiogram records characterized by normal sinus rhythm, ventricular tachycardia and ventricular fibrillation. Secondly, we investigate the multiscale complexity of cardiac dynamics with respect to age in healthy individuals using interbeat interval time series and compare our findings with a previous study which established a link between age and fractal-like long-range correlations...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28507231/biological-modelling-of-a-computational-spiking-neural-network-with-neuronal-avalanches
#6
Xiumin Li, Qing Chen, Fangzheng Xue
In recent years, an increasing number of studies have demonstrated that networks in the brain can self-organize into a critical state where dynamics exhibit a mixture of ordered and disordered patterns. This critical branching phenomenon is termed neuronal avalanches. It has been hypothesized that the homeostatic level balanced between stability and plasticity of this critical state may be the optimal state for performing diverse neural computational tasks. However, the critical region for high performance is narrow and sensitive for spiking neural networks (SNNs)...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28497135/unscrambling-micro-solvation-of-cooh-and-nh-groups-in-neat-dimethyl-sulfoxide-insights-from-1-h-nmr-spectroscopy-and-computational-studies
#7
Panteleimon G Takis, Konstantinos D Papavasileiou, Loukas D Peristeras, Georgios C Boulougouris, Vasilios S Melissas, Anastassios N Troganis
Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via(1)H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i...
May 12, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28473853/3d-evaluation-of-maxillary-sinus-using-computed-tomography-a-sexual-dimorphic-study
#8
Balaji Babu Bangi, Uday Ginjupally, Lakshmi Kavitha Nadendla, Bhavana Vadla
Purpose. Gender determination is considered to be an important step in the reconstruction of the biological profile in forensic medicine. Maxillary sinus can be used for identification of sex when other methods are indecisive. Computed tomography (CT) provides an excellent method for examining maxillary sinuses. Hence the aim of the study was to determine the accuracy of gender determination using maxillary sinus with CT. Materials and Methods. CT images were used to measure the mediolateral, superoinferior, and anteroposterior dimensions and the volume of the maxillary sinuses in 100 patients (50 males and 50 females) to determine the gender of an individual for forensic identification...
2017: International Journal of Dentistry
https://www.readbyqxmd.com/read/28465021/morphology-based-non-invasive-quantitative-prediction-of-the-differentiation-status-of-neural-stem-cells
#9
Masaya Fujitani, Noor Safika Huddin, Shun Kawai, Kei Kanie, Yasujiro Kiyota, Kazunori Shimizu, Hiroyuki Honda, Ryuji Kato
Neural stem cells (NSCs) are multipotent and are considered ideal source for regenerating damaged neural cells for neurological disorders. During culture of NSCs, both the measurement and the evaluation of their differentiation potential are important to maintain stable quality-assured NSCs for regenerative treatments since the rate of differentiation into certain lineages from NSCs is still not fully controllable. However, conventional cell evaluation techniques using biological molecular are still invasive, costly, and time-consuming...
April 29, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28456033/an-overview-of-azoles-targeting-sterol-14%C3%AE-demethylase-for-antileishmanial-therapy
#10
REVIEW
Saeed Emami, Pegah Tavangar, Masoud Keighobadi
The azole antifungal drugs are an important class of chemotherapeutic agents with broad-spectrum of activity against yeasts and filamentous fungi, act in the ergosterol biosynthetic pathway through inhibition of the cytochrome P450-dependent enzyme sterol 14α-demethylase. Azole antifungals have also been repurposed for treatment of tropical protozoan infections including human leishmaniasis. Recent advances in molecular biology and computational chemistry areas have increased our knowledge about sterol biochemical pathway in Leishmania parasites...
April 21, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28453775/deconvoluting-kinase-inhibitor-induced-cardiotoxicity
#11
Sarah D Lamore, Ernst Ahlberg, Scott Boyer, Michelle L Lamb, Maria P Hortigon-Vinagre, Victor Rodriguez, Godfrey L Smith, Johanna Sagemark, Lars Carlsson, Stephanie M Bates, Allison L Choy, Jonna Stålring, Clay W Scott, Matthew F Peters
Many drugs designed to inhibit kinases have their clinical utility limited by cardiotoxicity-related label warnings or prescribing restrictions. While this liability is widely recognized, designing safer kinase inhibitors (KI) requires knowledge of the causative kinase(s). Efforts to unravel the kinases have encountered pharmacology with nearly prohibitive complexity. At therapeutically relevant concentrations, KIs show promiscuity distributed across the kinome. Here, to overcome this complexity, 65 KIs with known kinome-scale polypharmacology profiles were assessed for effects on cardiomyocyte beating...
April 26, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#12
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28426839/medical-history-in-the-hellenic-journal-of-nuclear-medicine
#13
EDITORIAL
Andreas Otte
The Hellenic Journal of Nuclear Medicine is about to celebrate its 20th anniversary end of 2017. On board of the editorial team since 2003, this journal has influenced me like a good friend over the many past years. From time to time, the journal has published interesting and valuable historical notes. They show that nuclear medicine has a history and that medicine is its basis. They also teach us today, and some of the ancient perspectives and approaches are still valid. The reader of HJNM may be interested in these historical contributions, as they are timeless...
January 2017: Hellenic Journal of Nuclear Medicine
https://www.readbyqxmd.com/read/28426095/models-of-global-gene-expression-define-major-domains-of-cell-type-and-tissue-identity
#14
Andrew P Hutchins, Zhongzhou Yang, Yuhao Li, Fangfang He, Xiuling Fu, Xiaoshan Wang, Dongwei Li, Kairong Liu, Jiangping He, Yong Wang, Jiekai Chen, Miguel A Esteban, Duanqing Pei
The current classification of cells in an organism is largely based on their anatomic and developmental origin. Cells types and tissues are traditionally classified into those that arise from the three embryonic germ layers, the ectoderm, mesoderm and endoderm, but this model does not take into account the organization of cell type-specific patterns of gene expression. Here, we present computational models for cell type and tissue specification derived from a collection of 921 RNA-sequencing samples from 272 distinct mouse cell types or tissues...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28405621/lipidfinder-a-computational-workflow-for-discovery-of-lipids-identifies-eicosanoid-phosphoinositides-in-platelets
#15
Anne O'Connor, Christopher J Brasher, David A Slatter, Sven W Meckelmann, Jade I Hawksworth, Stuart M Allen, Valerie B O'Donnell
Accurate and high-quality curation of lipidomic datasets generated from plasma, cells, or tissues is becoming essential for cell biology investigations and biomarker discovery for personalized medicine. However, a major challenge lies in removing artifacts otherwise mistakenly interpreted as real lipids from large mass spectrometry files (>60 K features), while retaining genuine ions in the dataset. This requires powerful informatics tools; however, available workflows have not been tailored specifically for lipidomics, particularly discovery research...
April 6, 2017: JCI Insight
https://www.readbyqxmd.com/read/28398502/pygold-a-python-based-api-for-docking-based-virtual-screening-workflow-generation
#16
Hitesh Patel, Tobias Brinkjost, Oliver Koch
Motivation: Molecular docking is one of the successful approaches in structure based discovery and development of bioactive molecules in chemical biology and medicinal chemistry. Due to the huge amount of computational time that is still required, docking is often the last step in a virtual screening approach. Such screenings are set as workflows spanned over many steps, each aiming at different filtering task. These workflows can be automatized in large parts using python based toolkits except for docking using the docking software GOLD...
April 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28387809/the-anatomy-of-phenotype-ontologies-principles-properties-and-applications
#17
Georgios V Gkoutos, Paul N Schofield, Robert Hoehndorf
The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies...
April 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28381613/direct-determination-of-diploid-genome-sequences
#18
Neil I Weisenfeld, Vijay Kumar, Preyas Shah, Deanna M Church, David B Jaffe
Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses, and in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been constructed free of reference bias, but nearly all were constructed by merging homologous loci into single "consensus" sequences, generally absent from nature...
May 2017: Genome Research
https://www.readbyqxmd.com/read/28361683/comparative-network-stratification-analysis-for-identifying-functional-interpretable-network-biomarkers
#19
Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
BACKGROUND: A major challenge of bioinformatics in the era of precision medicine is to identify the molecular biomarkers for complex diseases. It is a general expectation that these biomarkers or signatures have not only strong discrimination ability, but also readable interpretations in a biological sense. Generally, the conventional expression-based or network-based methods mainly capture differential genes or differential networks as biomarkers, however, such biomarkers only focus on phenotypic discrimination and usually have less biological or functional interpretation...
March 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28359959/designing-new-surfactant-peptides-for-binding-to-carbon-nanotubes-via-computational-approaches
#20
Alireza Mansouri, Karim Mahnam
The non-covalent interaction between single-walled carbon nanotube and surfactant peptides makes them soluble in biological media to be used in nano-medicine, drug delivery and gene therapy. Pervious study has shown that two important parameters in binding peptides into nanotubes are hydrophobic effect and the number of aromatic amino acids. Ten surfactant peptides with the length of eight residue, including Lys, Trp, Tyr, Phe and Val, were designed to investigate the important parameters in binding peptides to a (6, 6) carbon nanotube...
March 14, 2017: Journal of Molecular Graphics & Modelling
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