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https://www.readbyqxmd.com/read/28735414/bone-mechanobiology-in-mice-toward-single-cell-in-vivo-mechanomics
#1
Ariane Scheuren, Esther Wehrle, Felicitas Flohr, Ralph Müller
Mechanically driven bone (re)modeling is a multiscale process mediated through complex interactions between multiple cell types and their microenvironments. However, the underlying mechanisms of how cells respond to mechanical signals are still unclear and are at the focus of the field of bone mechanobiology. Traditionally, this complex process has been addressed by reducing the system to single scales and cell types. It is only recently that more integrative approaches have been established to study bone mechanobiology across multiple scales in which mechanical load at the organ level is related to molecular responses at the cellular level...
July 22, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28735000/application-of-pharmacometrics-and-quantitative-systems-pharmacology-to-cancer-therapy-the-example-of-luminal-a-breast-cancer
#2
REVIEW
Brett Fleisher, Kayla Andrews, Ashley A Brown, Sihem Ait-Oudhia
Breast cancer (BC) is the most common cancer in women, and the second most frequent cause of cancer-related deaths in women worldwide. It is a heterogeneous disease composed of multiple subtypes with distinct morphologies and clinical implications. Quantitative systems pharmacology (QSP) is an emerging discipline bridging systems biology with pharmacokinetics (PK) and pharmacodynamics (PD) leveraging the systematic understanding of drugs' efficacy and toxicity. Despite numerous challenges in applying computational methodologies for QSP and mechanism-based PK/PD models to biological, physiological, and pharmacological data, bridging these disciplines has the potential to enhance our understanding of complex disease systems such as BC...
July 19, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28734644/postmastectomy-radiation-therapy-technique-and-cardiopulmonary-sparing-a-dosimetric-comparative-analysis-between-photons-and-protons-with-free-breathing-versus-deep-inspiration-breath-hold
#3
Sagar A Patel, Hsiao-Ming Lu, Jacqueline A Nyamwanda, Rachel B Jimenez, Alphonse G Taghian, Shannon M MacDonald, Nicolas Depauw
PURPOSE: Dosimetric studies have suggested greater cardiopulmonary sparing with protons over photons for left-sided postmastectomy radiation therapy (PMRT). Modern techniques such as deep inspiration breath hold (DIBH) can help spare the heart. This analysis compares photon and proton delivery with and without DIBH. METHODS AND MATERIALS: Ten women with left breast cancer referred for PMRT on a prospective clinical trial with unfavorable cardiac anatomy underwent free breathing (FB) and DIBH computed tomography simulation...
June 21, 2017: Practical Radiation Oncology
https://www.readbyqxmd.com/read/28733924/cellular-mechanosensitivity-to-substrate-stiffness-decreases-with-increasing-dissimilarity-to-cell-stiffness
#4
Tamer Abdalrahman, Laura Dubuis, Jason Green, Neil Davies, Thomas Franz
Computational modelling has received increasing attention to investigate multi-scale coupled problems in micro-heterogeneous biological structures such as cells. In the current study, we investigated for a single cell the effects of (1) different cell-substrate attachment (2) and different substrate modulus [Formula: see text] on intracellular deformations. A fibroblast was geometrically reconstructed from confocal micrographs. Finite element models of the cell on a planar substrate were developed. Intracellular deformations due to substrate stretch of [Formula: see text], were assessed for: (1) cell-substrate attachment implemented as full basal contact (FC) and 124 focal adhesions (FA), respectively, and [Formula: see text]140 KPa and (2) [Formula: see text], 140, 1000, and 10,000 KPa, respectively, and FA attachment...
July 21, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28733179/nurse-in-patients-health-status-assessment-data-from-a-pilot-study-assessing-agreement-among-nurse-and-gastroenterologist-in-computing-ibd-clinical-scores
#5
Filippo Mocciaro, Giulia Maria Pecoraro, Roberto Di Mitri, Daniela Scimeca, Fabrizio Bossa, Giuseppina Russo, Giuseppina Martino, Vincenzo Costanza, Maria Antonella Profita, Concetta Orlando, Gianfranco Profeta, Fabio Tinè
INTRODUCTION: Crohn's Disease (CD) and Ulcerative Colitis (UC) are chronic, systemic Inflammatory Bowel Diseases (IBDs) that need a multidisciplinary approach involving not only different medical specialists but also qualified nurses. AIM: We evaluated the concordance between IBD-nurse and physician in computing Clinical Activity Scores in IBD-patients treated with biologics. METHODS: We enrolled all consecutive IBD-patients treated with biologics in two referral centers for IBD-care...
June 23, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28732234/computational-modelling-of-genome-scale-metabolic-networks-and-its-application-to-cho-cell-cultures
#6
REVIEW
Živa Rejc, Lidija Magdevska, Tilen Tršelič, Timotej Osolin, Rok Vodopivec, Jakob Mraz, Eva Pavliha, Nikolaj Zimic, Tanja Cvitanović, Damjana Rozman, Miha Moškon, Miha Mraz
Genome-scale metabolic models (GEMs) have become increasingly important in recent years. Currently, GEMs are the most accurate in silico representation of the genotype-phenotype link. They allow us to study complex networks from the systems perspective. Their application may drastically reduce the amount of experimental and clinical work, improve diagnostic tools and increase our understanding of complex biological phenomena. GEMs have also demonstrated high potential for the optimisation of bio-based production of recombinant proteins...
July 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28731857/cytomcs-a-multiple-maximum-common-subgraph-detection-tool-for-cytoscape
#7
Simon J Larsen, Jan Baumbach
Comparative analysis of biological networks is a major problem in computational integrative systems biology. By computing the maximum common edge subgraph between a set of networks, one is able to detect conserved substructures between them and quantify their topological similarity. To aid such analyses we have developed CytoMCS, a Cytoscape app for computing inexact solutions to the maximum common edge subgraph problem for two or more graphs. Our algorithm uses an iterative local search heuristic for computing conserved subgraphs, optimizing a squared edge conservation score that is able to detect not only fully conserved edges but also partially conserved edges...
July 21, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28731476/exact-sequence-variants-should-replace-operational-taxonomic-units-in-marker-gene-data-analysis
#8
Benjamin J Callahan, Paul J McMurdie, Susan P Holmes
Recent advances have made it possible to analyze high-throughput marker-gene sequencing data without resorting to the customary construction of molecular operational taxonomic units (OTUs): clusters of sequencing reads that differ by less than a fixed dissimilarity threshold. New methods control errors sufficiently such that amplicon sequence variants (ASVs) can be resolved exactly, down to the level of single-nucleotide differences over the sequenced gene region. The benefits of finer resolution are immediately apparent, and arguments for ASV methods have focused on their improved resolution...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28731324/using-infrared-spectroscopy-and-multivariate-analysis-to-detect-antibiotics-resistant-escherichia-coli-bacteria
#9
Uraib Sharaha, Eladio Rodriguez-Diaz, Klaris Riesenberg, Irving J Bigio, Mahmoud Huleihel, Ahmad Salman
Bacterial pathogens are one of the primary causes of human morbidity worldwide. Historically, antibiotics have been highly effective against most bacterial pathogens; however, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global health-care problem. Early and rapid determination of bacterial susceptibility to antibiotics has become essential in many clinical settings, and, sometimes, can save lives. Currently classical procedures require at least 48 hours for determining bacterial susceptibility, which can constitute a life-threatening delay for effective treatment...
July 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28730495/modeling-of-receptor-tyrosine-kinase-signaling-computational-and-experimental-protocols
#10
Dirk Fey, Edita Aksamitiene, Anatoly Kiyatkin, Boris N Kholodenko
The advent of systems biology has convincingly demonstrated that the integration of experiments and dynamic modelling is a powerful approach to understand the cellular network biology. Here we present experimental and computational protocols that are necessary for applying this integrative approach to the quantitative studies of receptor tyrosine kinase (RTK) signaling networks. Signaling by RTKs controls multiple cellular processes, including the regulation of cell survival, motility, proliferation, differentiation, glucose metabolism, and apoptosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#11
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#12
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730284/a-novel-interplay-between-hotair-and-dna-methylation-in-osteosarcoma-cells-indicates-a-new-therapeutic-strategy
#13
Xingang Li, Hongming Lu, Guilian Fan, Miao He, Yu Sun, Kai Xu, Fengjun Shi
PURPOSE: Osteosarcoma (OS) is one of the most prevalent primary malignant bone tumors in adolescent. HOTAIR is highly expressed and associated with the epigenetic modifications, especially DNA methylation, in cancer. However, the regulation mechanism between HOTAIR and DNA methylation and the biological effects of them in the pathogenesis of osteosarcoma remains elusive. METHOD: Through RNA-sequencing and computational analysis, followed by a variety of experimental validations, we report a novel interplay between HOTAIR, miR-126, and DNA methylation in OS...
July 20, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28729544/remarkable-hexafunctional-anion-receptor-with-operational-urea-based-inner-cleft-and-thiourea-based-outer-cleft-novel-design-with-high-efficiency-for-sulfate-binding
#14
Maryam Emami Khansari, Ali Mirchi, Avijit Pramanik, Corey R Johnson, Jerzy Leszczynski, Md Alamgir Hossain
The recognition of anions by designed receptors has attracted much attention in recent days. In particular, the selective binding of sulfate with artificial receptors is important because of its relevance to many biological and environmental applications. However, the development of organized molecular receptors with high-efficiency for sulfate binding still remains a significant challenge. We report a novel para-phenylene-bridged hexafunctional tripodal receptor that contains a urea-based inner cleft and a thiourea-based outer cleft, providing perfect sites for step-wise binding of two anions within a single cavity...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729343/flowtrace-simple-visualization-of-coherent-structures-in-biological-fluid-flows
#15
William Gilpin, Vivek N Prakash, Manu Prakash
We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results to more experimentally-difficult and mathematically-sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential "middle ground" allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques...
July 20, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28728979/ploc-mvirus-predict-subcellular-localization-of-multi-location-virus-proteins-via-incorporating-the-optimal-go-information-into-general-pseaac
#16
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only...
July 17, 2017: Gene
https://www.readbyqxmd.com/read/28728020/neuroscience-inspired-artificial-intelligence
#17
REVIEW
Demis Hassabis, Dharshan Kumaran, Christopher Summerfield, Matthew Botvinick
The fields of neuroscience and artificial intelligence (AI) have a long and intertwined history. In more recent times, however, communication and collaboration between the two fields has become less commonplace. In this article, we argue that better understanding biological brains could play a vital role in building intelligent machines. We survey historical interactions between the AI and neuroscience fields and emphasize current advances in AI that have been inspired by the study of neural computation in humans and other animals...
July 19, 2017: Neuron
https://www.readbyqxmd.com/read/28727915/improving-accuracy-diversity-and-speed-with-prime-macrocycle-conformational-sampling
#18
Dan Sindhikara, Steven A Spronk, Tyler Day, Ken Borrelli, Daniel L Cheney, Shana L Posy
A novel method for exploring macrocycle conformational space, Prime Macrocycle Conformational Sampling (Prime-MCS), is introduced and evaluated in the context of other available algorithms (Molecular Dynamics, LowModeMD in MOE, and MacroModel Baseline Search). The algorithms were benchmarked on a dataset of 208 macrocycles which was curated for diversity from the Cambridge Structural Database, the Protein Databank, and the Biologically Interesting Molecule Reference Dictionary. The algorithms were evaluated in terms of accuracy (ability to reproduce the crystal structure), diversity (coverage of conformational space), and computational speed...
July 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28727865/proton-beam-radiotherapy-and-concurrent-chemotherapy-for-unresectable-stage-iii-non-small-cell-lung-cancer-final-results-of-a-phase-2-study
#19
Joe Y Chang, Vivek Verma, Ming Li, Wencheng Zhang, Ritsuko Komaki, Charles Lu, Pamela K Allen, Zhongxing Liao, James Welsh, Steven H Lin, Daniel Gomez, Melenda Jeter, Michael O'Reilly, Ronald X Zhu, Xiaodong Zhang, Heng Li, Radhe Mohan, John V Heymach, Ara A Vaporciyan, Stephen Hahn, James D Cox
Importance: Proton beam radiotherapy (PBT) has the potential to reduce toxic effects in the definitive management of locally advanced non-small-cell lung cancer (NSCLC), but long-term prospective data are lacking. Objective: To report the final (5-year) results of a prospective study evaluating concurrent chemotherapy and high-dose PBT to treat unresectable stage III NSCLC. Design, Setting, and Participants: In this open-label, single-group assignment study, with median follow-up of 27...
July 20, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28727554/a-human-humanoid-interaction-through-the-use-of-bci-for-locked-in-als-patients-using-neuro-biological-feedback-fusion
#20
Rosario Sorbello, Salvatore Tramonte, Marcello Giardina, Vincenzo La Bella, Rossella Spataro, Brendan Allison, Christoph Guger, Antonio Chella
This paper illustrates a new architecture for a human-humanoid interaction based on EEG-Brain Computer Interface (EEG-BCI) for patients affected by locked-in syndrome caused by Amyotrophic Lateral Sclerosis (ALS). The proposed architecture is able to recognise users' mental state accordingly to the biofeedback factor Bf , based on users' Attention, Intention and Focus, that is used to elicit a robot to perform customised behaviours. Experiments have been conducted with a population of 8 subjects: 4 ALS patients in a near Locked-in status with normal ocular movement and 4 healthy control subjects enrolled for age, education and computer expertise...
July 18, 2017: IEEE Transactions on Neural Systems and Rehabilitation Engineering
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