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https://www.readbyqxmd.com/read/28643328/drug-repurposing-by-simulating-flow-through-protein-protein-interaction-networks
#1
M Manczinger, V Bodnár, B T Papp, B Sz Bolla, K Szabó, B Balázs, E Csányi, E Szél, G Erős, L Kemény
As drug development is extremely expensive, the identification of novel indications for in-market drugs is financially attractive. Multiple algorithms are used to support such drug repurposing, but highly reliable methods combining simulation of intracellular networks and machine learning are currently not available. We developed an algorithm that simulates drug effects on the flow of information through protein-protein interaction networks, and uses Support Vector Machine to identify potentially effective drugs in our model disease, psoriasis...
June 23, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/28640448/overview-of-the-muscle-cytoskeleton
#2
Christine A Henderson, Christopher G Gomez, Stefanie M Novak, Lei Mi-Mi, Carol C Gregorio
Cardiac and skeletal striated muscles are intricately designed machines responsible for muscle contraction. Coordination of the basic contractile unit, the sarcomere, and the complex cytoskeletal networks are critical for contractile activity. The sarcomere is comprised of precisely organized individual filament systems that include thin (actin), thick (myosin), titin, and nebulin. Connecting the sarcomere to other organelles (e.g., mitochondria and nucleus) and serving as the scaffold to maintain cellular integrity are the intermediate filaments...
June 18, 2017: Comprehensive Physiology
https://www.readbyqxmd.com/read/28623339/machine-learning-and-network-analysis-of-molecular-dynamics-trajectories-reveal-two-chains-of-red-ox-specific-residue-interactions-in-human%C3%A2-protein-disulfide-isomerase
#3
Razieh Karamzadeh, Mohammad Hossein Karimi-Jafari, Ali Sharifi-Zarchi, Hamidreza Chitsaz, Ghasem Hosseini Salekdeh, Ali Akbar Moosavi-Movahedi
The human protein disulfide isomerase (hPDI), is an essential four-domain multifunctional enzyme. As a result of disulfide shuffling in its terminal domains, hPDI exists in two oxidation states with different conformational preferences which are important for substrate binding and functional activities. Here, we address the redox-dependent conformational dynamics of hPDI through molecular dynamics (MD) simulations. Collective domain motions are identified by the principal component analysis of MD trajectories and redox-dependent opening-closing structure variations are highlighted on projected free energy landscapes...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28617227/in-silico-re-identification-of-properties-of-drug-target-proteins
#4
Baeksoo Kim, Jihoon Jo, Jonghyun Han, Chungoo Park, Hyunju Lee
BACKGROUND: Computational approaches in the identification of drug targets are expected to reduce time and effort in drug development. Advances in genomics and proteomics provide the opportunity to uncover properties of druggable genomes. Although several studies have been conducted for distinguishing drug targets from non-drug targets, they mainly focus on the sequences and functional roles of proteins. Many other properties of proteins have not been fully investigated. METHODS: Using the DrugBank (version 3...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28613808/sensitivity-enhanced-wearable-active-voiceprint-sensor-based-on-cellular-polypropylene-piezoelectret
#5
Wenbo Li, Sheng Zhao, Nan Wu, Junwen Zhong, Bo Wang, Shizhe Lin, Shuwen Chen, Fang Yuan, Hulin Jiang, Yongjun Xiao, Bin Hu, Jun Zhou
Wearable active sensors have extensive applications in mobile biosensing and human-machine interaction but require good flexibility, high sensitivity, excellent stability and self-powered feature. In this work, cellular polypropylene (PP) piezoelectret was chosen as the core material of a sensitivity-enhanced wearable active voiceprint sensor (SWAVS) to realize voiceprint recognition. By virtue of dipole orientation control method, the air layers in piezoelectret were efficiently utilized and the current sensitivity was enhanced (from 1...
June 14, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28611621/whole-body-awareness-for-controlling-a-robotic-transfemoral-prosthesis
#6
Andrea Parri, Elena Martini, Joost Geeroms, Louis Flynn, Guido Pasquini, Simona Crea, Raffaele Molino Lova, Dirk Lefeber, Roman Kamnik, Marko Munih, Nicola Vitiello
Restoring locomotion functionality of transfemoral amputees is essential for early rehabilitation treatment and for preserving mobility and independence in daily life. Research in wearable robotics fostered the development of innovative active mechatronic lower-limb prostheses designed with the goal to reduce the cognitive and physical effort of lower-limb amputees in rehabilitation and daily life activities. To ensure benefits to the users, active mechatronic prostheses are expected to be aware of the user intention and properly interact in a closed human-in-the-loop paradigm...
2017: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/28611573/simultaneous-and-continuous-estimation-of-shoulder-and-elbow-kinematics-from-surface-emg-signals
#7
Qin Zhang, Runfeng Liu, Wenbin Chen, Caihua Xiong
In this paper, we present a simultaneous and continuous kinematics estimation method for multiple DoFs across shoulder and elbow joint. Although simultaneous and continuous kinematics estimation from surface electromyography (EMG) is a feasible way to achieve natural and intuitive human-machine interaction, few works investigated multi-DoF estimation across the significant joints of upper limb, shoulder and elbow joints. This paper evaluates the feasibility to estimate 4-DoF kinematics at shoulder and elbow during coordinated arm movements...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28602352/cryo-em-reveals-how-human-cytoplasmic-dynein-is-auto-inhibited-and-activated
#8
Kai Zhang, Helen E Foster, Arnaud Rondelet, Samuel E Lacey, Nadia Bahi-Buisson, Alexander W Bird, Andrew P Carter
Cytoplasmic dynein-1 binds dynactin and cargo adaptor proteins to form a transport machine capable of long-distance processive movement along microtubules. However, it is unclear why dynein-1 moves poorly on its own or how it is activated by dynactin. Here, we present a cryoelectron microscopy structure of the complete 1.4-megadalton human dynein-1 complex in an inhibited state known as the phi-particle. We reveal the 3D structure of the cargo binding dynein tail and show how self-dimerization of the motor domains locks them in a conformation with low microtubule affinity...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28588473/a-human-robot-interaction-perspective-on-assistive-and-rehabilitation-robotics
#9
Philipp Beckerle, Gionata Salvietti, Ramazan Unal, Domenico Prattichizzo, Simone Rossi, Claudio Castellini, Sandra Hirche, Satoshi Endo, Heni Ben Amor, Matei Ciocarlie, Fulvio Mastrogiovanni, Brenna D Argall, Matteo Bianchi
Assistive and rehabilitation devices are a promising and challenging field of recent robotics research. Motivated by societal needs such as aging populations, such devices can support motor functionality and subject training. The design, control, sensing, and assessment of the devices become more sophisticated due to a human in the loop. This paper gives a human-robot interaction perspective on current issues and opportunities in the field. On the topic of control and machine learning, approaches that support but do not distract subjects are reviewed...
2017: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/28583429/towards-the-virtual-human-patient-quantitative-systems-pharmacology-in-alzheimer-s-disease
#10
Hugo Geerts, Athan Spiros, Patrick Roberts, Robert Carr
Development of successful therapeutic interventions in Central Nervous Systems (CNS) disorders is a daunting challenge with a low success rate. Probable reasons include the lack of translation from preclinical animal models, the individual variability of many pathological processes converging upon the same clinical phenotype, the pharmacodynamical interaction of various comedications and last but not least the complexity of the human brain. This paper argues for a re-engineering of the pharmaceutical CNS Research & Development strategy using ideas focused on advanced computer modeling and simulation from adjacent engineering-based industries...
June 2, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28580033/dynamics-of-blood-flow-and-thrombus-formation-in-a-multi-bypass-microfluidic-ladder-network
#11
Jevgenia Zilberman-Rudenko, Joanna L Sylman, Hari H S Lakshmanan, Owen J T McCarty, Jeevan Maddala
The reaction dynamics of a complex mixture of cells and proteins, such as blood, in branched circulatory networks within the human microvasculature or extravascular therapeutic devices such as extracorporeal oxygenation machine (ECMO) remains ill-defined. In this report we utilize a multi-bypass microfluidics ladder network design with dimensions mimicking venules to study patterns of blood platelet aggregation and fibrin formation under complex shear. Complex blood fluid dynamics within multi-bypass networks under flow were modeled using COMSOL...
February 2017: Cellular and Molecular Bioengineering
https://www.readbyqxmd.com/read/28572842/grid-based-stochastic-search-for-hierarchical-gene-gene-interactions-in-population-based-genetic-studies-of-common-human-diseases
#12
Jason H Moore, Peter C Andrews, Randal S Olson, Sarah E Carlson, Curt R Larock, Mario J Bulhoes, James P O'Connor, Ellen M Greytak, Steven L Armentrout
BACKGROUND: Large-scale genetic studies of common human diseases have focused almost exclusively on the independent main effects of single-nucleotide polymorphisms (SNPs) on disease susceptibility. These studies have had some success, but much of the genetic architecture of common disease remains unexplained. Attention is now turning to detecting SNPs that impact disease susceptibility in the context of other genetic factors and environmental exposures. These context-dependent genetic effects can manifest themselves as non-additive interactions, which are more challenging to model using parametric statistical approaches...
2017: BioData Mining
https://www.readbyqxmd.com/read/28570104/detection-of-complexes-in-biological-networks-through-diversified-dense-subgraph-mining
#13
Xiuli Ma, Guangyu Zhou, Jingbo Shang, Jingjing Wang, Jian Peng, Jiawei Han
Protein-protein interaction (PPI) networks, providing a comprehensive landscape of protein interaction patterns, enable us to explore biological processes and cellular components at multiple resolutions. For a biological process, a number of proteins need to work together to perform a job. Proteins densely interact with each other, forming large molecular machines or cellular building blocks. Identification of such densely interconnected clusters or protein complexes from PPI networks enables us to obtain a better understanding of the hierarchy and organization of biological processes and cellular components...
June 1, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28544880/systems-wide-studies-uncover-commander-a-multiprotein-complex-essential-to-human-development
#14
REVIEW
Anna L Mallam, Edward M Marcotte
Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to other ubiquitous machines involved in expression, proteostasis, and trafficking. Experiments on individual subunits support roles in endosomal protein sorting, including the trafficking of Notch proteins, copper transporters, and lipoprotein receptors...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544097/multiple-hydrogen-bonding-enables-the-self-healing-of-sensors-for-human-machine-interaction
#15
Jie Cao, Canhui Lu, Jian Zhuang, Manxiao Liu, Xinxing Zhang, Yanmei Yu, Qingchuan Tao
Despite its widespread use in signal collection, flexible sensor has been rarely used in human-machine interaction due to its indistinguishable signal, poor reliability and stability when suffered from unavoidable scratches and/or mechanical cuts. Here, we demonstrate a highly sensitive and self-healing sensor enabled by multiple hydrogen bonding network and nanostructured conductive network. The nanostructured supramolecular sensor displays extremely fast (~15 s) and repeatable self-healing ability with high healing efficiency (93% after the 3rd healing process)...
May 23, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28540682/the-limitations-of-existing-approaches-in-improving-microrna-target-prediction-accuracy
#16
Rasiah Loganantharaj, Thomas A Randall
MicroRNAs (miRNAs) are small (18-24 nt) endogenous RNAs found across diverse phyla involved in posttranscriptional regulation, primarily downregulation of mRNAs. Experimentally determining miRNA-mRNA interactions can be expensive and time-consuming, making the accurate computational prediction of miRNA targets a high priority. Since miRNA-mRNA base pairing in mammals is not perfectly complementary and only a fraction of the identified motifs are real binding sites, accurately predicting miRNA targets remains challenging...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540465/technology-induced-errors-associated-with-computerized-provider-order-entry-software-for-older-patients
#17
Manuel Vélez-Díaz-Pallarés, Ana María Álvarez Díaz, Teresa Gramage Caro, Noelia Vicente Oliveros, Eva Delgado-Silveira, María Muñoz García, Alfonso José Cruz-Jentoft, Teresa Bermejo-Vicedo
Background The introduction of new technologies in the prescribing process has seen the emergence of new types of medication errors. Objective To determine the prevalence and consequences of technology-induced prescription errors associated with a computerized provider order entry (CPOE) system in hospitalized older patients. Setting Patients 65 years or older admitted to the Departments of Internal Medicine, General Surgery, and Vascular Surgery of a tertiary hospital. Method Prospective observational 6-month study...
May 24, 2017: International Journal of Clinical Pharmacy
https://www.readbyqxmd.com/read/28514151/deepppi-boosting-prediction-of-protein-protein-interactions-with-deep-neural-networks
#18
Xiuquan Du, Shiwei Sun, Changlin Hu, Yu Yao, Yuanting Yan, Yanping Zhang
The complex language of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many proteins variants statistically associated with human disease, nearly all such variants have unknown mechanisms, for example, protein-protein interactions (PPIs). In this study, we address this challenge using a recent machine learning advance-deep neural networks (DNNs). We aim at improving the performance of PPIs prediction and propose a method called DeepPPI (Deep neural networks for Protein-Protein Interactions prediction), which employs deep neural networks to learn effectively the representations of proteins from common protein descriptors...
May 26, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28509865/detecting-and-classifying-human-touches-in-a-social-robot-through-acoustic-sensing-and-machine-learning
#19
Fernando Alonso-Martín, Juan José Gamboa-Montero, José Carlos Castillo, Álvaro Castro-González, Miguel Ángel Salichs
An important aspect in Human-Robot Interaction is responding to different kinds of touch stimuli. To date, several technologies have been explored to determine how a touch is perceived by a social robot, usually placing a large number of sensors throughout the robot's shell. In this work, we introduce a novel approach, where the audio acquired from contact microphones located in the robot's shell is processed using machine learning techniques to distinguish between different types of touches. The system is able to determine when the robot is touched (touch detection), and to ascertain the kind of touch performed among a set of possibilities: stroke, tap, slap, and tickle (touch classification)...
May 16, 2017: Sensors
https://www.readbyqxmd.com/read/28500008/wearable-haptic-systems-for-the-fingertip-and-the-hand-taxonomy-review-and-perspectives
#20
Claudio Pacchierotti, Stephen Sinclair, Massimiliano Solazzi, Antonio Frisoli, Vincent Hayward, Domenico Prattichizzo
In the last decade, we have witnessed a drastic change in the form factor of audio and vision technologies, from heavy and grounded machines to lightweight devices that naturally fit our bodies. However, only recently, haptic systems have started to be designed with wearability in mind. The wearability of haptic systems enables novel forms of communication, cooperation, and integration between humans and machines. Wearable haptic interfaces are capable of communicating with the human wearers during their interaction with the environment they share, in a natural and yet private way...
May 9, 2017: IEEE Transactions on Haptics
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