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https://www.readbyqxmd.com/read/29788413/eztag-tagging-biomedical-concepts-via-interactive-learning
#1
Dongseop Kwon, Sun Kim, Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu
Recently, advanced text-mining techniques have been shown to speed up manual data curation by providing human annotators with automated pre-annotations generated by rules or machine learning models. Due to the limited training data available, however, current annotation systems primarily focus only on common concept types such as genes or diseases. To support annotating a wide variety of biological concepts with or without pre-existing training data, we developed ezTag, a web-based annotation tool that allows curators to perform annotation and provide training data with humans in the loop...
May 18, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29785723/decreased-e-cadherin-in-mcf7-human-breast-cancer-cells-forming-multicellular-spheroids-exposed-to-simulated-microgravity
#2
Jayashree Sahana, Mohamed Zakaria Nassef, Markus Wehland, Sascha Kopp, Marcus Krüger, Thomas J Corydon, Manfred Infanger, Johann Bauer, Daniela Grimm
MCF7 human breast cancer cells were cultured under normal gravity (1g) and on a random positioning machine (RPM) preventing sedimentation. After two weeks, adherent 1g-control and adherent RPM cells (AD) as well as multicellular spheroids (MCS) were harvested. AD and MCS had been exposed to the RPM in the same culture flask. In a subsequent proteome analysis, the majority of the proteins detected showed similar label-free quantification scores (LFQ) in each of the respective subpopulations, but in both AD or MCS cultures, proteins were also found whose LFQs deviated at least twofold from their counterparts in the 1g-control cells...
May 21, 2018: Proteomics
https://www.readbyqxmd.com/read/29775322/prediction-of-human-cytochrome-p450-inhibition-using-a-multi-task-deep-autoencoder-neural-network
#3
Xiang Li, Youjun Xu, Luhua Lai, Jianfeng Pei
Adverse side effects of drug-drug interactions induced by human cytochrome P450 (CYP450) inhibition is an important consideration in drug discovery. It is highly desirable to develop computational models that can predict the inhibitive effect of a compound against a specific CYP450 isoform. In this study, we developed a multi-task model for concurrent inhibition prediction of five major CYP450 isoforms, namely 1A2, 2C9, 2C19, 2D6, and 3A4. The model was built by training multi-task autoencoder deep neural network (DNN) on a large dataset containing more than 13000 compounds, extracted from PubChem BioAssay Database...
May 18, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29771674/multisource-transfer-double-dqn-based-on-actor-learning
#4
Jie Pan, Xuesong Wang, Yuhu Cheng, Qiang Yu
Deep reinforcement learning (RL) comprehensively uses the psychological mechanisms of "trial and error" and "reward and punishment" in RL as well as powerful feature expression and nonlinear mapping in deep learning. Currently, it plays an essential role in the fields of artificial intelligence and machine learning. Since an RL agent needs to constantly interact with its surroundings, the deep Q network (DQN) is inevitably faced with the need to learn numerous network parameters, which results in low learning efficiency...
June 2018: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/29771494/screen-printed-washable-electronic-textiles-as-self-powered-touch-gesture-tribo-sensor-for-intelligent-human-machine-interaction
#5
Ran Cao, Xianjie Pu, Xinyu Du, Wei Yang, Jiaona Wang, Hengyu Guo, Shuyu Zhao, Zuqing Yuan, Chi Zhang, Congju Li, Zhong Lin Wang
Electronic textile (E-textile) with designable electric circuit and multi-functionalities holds great application prospect for future wearable electronics. However, most of the E-textiles still have critical challenges, including air permeability, satisfactory washability and massive fabrication. In this work, we fabricate a washable E-textile that addresses all of the concerns and show its application as a self-powered triboelectric gesture textile for intelligent human-machine interface. Utilizing conductive carbon nanotubes (CNTs) and screen-printing technology, this kind of E-textile embraces high conductivity (0...
May 17, 2018: ACS Nano
https://www.readbyqxmd.com/read/29737567/impact-of-a-non-synonymous-q281r-polymorphism-on-structure-of-human-lipoprotein-associated-phospholipase-a-2-lp-pla-2
#6
Arun B Gurung, Atanu Bhattacharjee
Non-synonymous single nucleotide polymorphisms (nsSNPs) are genetic variations at single base resulting in an amino acid change which have been associated with various complex human diseases. The human Lipoprotein-associated phospholipase A2 (Lp-PLA2 ) gene harbours a rare Q281R polymorphism which was previously reported to cause loss of enzymatic function. Lp-PLA2 is an important enzyme which catalyzes the hydrolysis of polar phospholipids releasing pro-atherogenic and pro-inflammatory mediators involved in the pathogenesis of atherosclerosis...
May 8, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29735743/the-substrate-specificity-of-eukaryotic-cytosolic-chaperonin-cct
#7
REVIEW
Keith R Willison
The cytosolic chaperonin CCT (chaperonin containing TCP-1) is an ATP-dependent double-ring protein machine mediating the folding of members of the eukaryotic cytoskeletal protein families. The actins and tubulins are obligate substrates of CCT because they are completely dependent on CCT activity to reach their native states. Genetic and proteomic analysis of the CCT interactome in the yeast Saccharomyces cerevisiae revealed a CCT network of approximately 300 genes and proteins involved in many fundamental biological processes...
June 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29735729/ensemble-allosteric-model-energetic-frustration-within-the-intrinsically-disordered-glucocorticoid-receptor
#8
REVIEW
Jordan T White, Jing Li, Emily Grasso, James O Wrabl, Vincent J Hilser
Allostery is an important regulatory phenomenon enabling precise control of biological function. Initial understanding of allostery was gained from seminal work on conformational changes exhibited by structured proteins. Within the last decade, protein allostery has also been demonstrated to occur within intrinsically disordered proteins. This emerging concept of disorder-mediated allostery can be usefully understood in the context of a thermodynamic ensemble. The advantage of this ensemble allosteric model is that it unifies the explanations of allostery occurring within both structured and disordered proteins...
June 19, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29713270/eye-movements-during-everyday-behavior-predict-personality-traits
#9
Sabrina Hoppe, Tobias Loetscher, Stephanie A Morey, Andreas Bulling
Besides allowing us to perceive our surroundings, eye movements are also a window into our mind and a rich source of information on who we are, how we feel, and what we do. Here we show that eye movements during an everyday task predict aspects of our personality. We tracked eye movements of 42 participants while they ran an errand on a university campus and subsequently assessed their personality traits using well-established questionnaires. Using a state-of-the-art machine learning method and a rich set of features encoding different eye movement characteristics, we were able to reliably predict four of the Big Five personality traits (neuroticism, extraversion, agreeableness, conscientiousness) as well as perceptual curiosity only from eye movements...
2018: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/29706071/ultrahigh-sensitive-and-flexible-magnetoelectronics-with-magnetic-nanocomposites-toward-an-additional-perception-of-artificial-intelligence
#10
Shu-Yi Cai, Cheng-Han Chang, Hung-I Lin, Yuan-Fu Huang, Wei-Ju Lin, Shih-Yao Lin, Yi-Rou Liou, Tien Lin Shen, Yen-Hsiang Huang, Po-Wei Tsao, Chen-Yang Tzou, Yu-Ming Liao, Yang-Fang Chen
In recent years, flexible magnetoelectronics has attracted a great attention for their intriguing functionalities and potential applications, such as healthcare, memory, soft robots, navigation and touchless human-machine interaction systems. Here, we provide the first attempt to demonstrate a new type of magneto-piezoresistance device, which possesses an ultrahigh sensitivity with several orders of resistance change under an external magnetic field (100 mT). In our device, the Fe-Ni alloy powders are embedded in the AgNWs-coated micro-pyramid PDMS films...
April 30, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29693379/skin-inspired-electronics-an-emerging-paradigm
#11
Sihong Wang, Jin Young Oh, Jie Xu, Helen Tran, Zhenan Bao
Future electronics will take on more important roles in people's lives. They need to allow more intimate contact with human beings to enable advanced health monitoring, disease detection, medical therapies, and human-machine interfacing. However, current electronics are rigid, nondegradable and cannot self-repair, while the human body is soft, dynamic, stretchable, biodegradable, and self-healing. Therefore, it is critical to develop a new class of electronic materials that incorporate skinlike properties, including stretchability for conformable integration, minimal discomfort and suppressed invasive reactions; self-healing for long-term durability under harsh mechanical conditions; and biodegradability for reducing environmental impact and obviating the need for secondary device removal for medical implants...
April 25, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29693084/spider-web-inspired-multi-resolution-graphene-tactile-sensor
#12
Lu Liu, Yu Huang, Fengyu Li, Ying Ma, Wenbo Li, Meng Su, Xin Qian, Wanjie Ren, Kanglai Tang, Yanlin Song
Multi-dimensional accurate response and smooth signal transmission are critical challenges in the advancement of multi-resolution recognition and complex environment analysis. Inspired by the structure-activity relationship between discrepant microstructures of the spiral and radial threads in a spider web, we designed and printed graphene with porous and densely-packed microstructures to integrate into a multi-resolution graphene tactile sensor. The three-dimensional (3D) porous graphene structure performs multi-dimensional deformation responses...
April 25, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29683404/agency-modulates-interactions-with-automation-technologies
#13
Kevin Le Goff, Arnaud Rey, Patrick Haggard, Olivier Oullier, Bruno Berberian
The increasing presence of automation between operators and automated systems tends to disrupt operators from action outcomes, leading them to leave the control loop. The theoretical framework of agency suggests that priming the operator about the system's upcoming behaviour could help restore an appropriate sense of control and increase user acceptance of what the system is doing. In a series of two experiments, we test whether providing information about what the system is about to do next leads to an increase in the level of user acceptance, concomitant with an increase in control and performance...
April 23, 2018: Ergonomics
https://www.readbyqxmd.com/read/29683373/gesture-segmentation-and-classification-using-affine-speed-and-energy
#14
Jenny Cifuentes, Minh Tu Pham, Pierre Boulanger, Richard Moreau, Flavio Prieto
The characterization and analysis of hand gestures are challenging tasks with an important number of applications in human-computer interaction, machine vision and control, and medical gesture recognition. Specifically, several researchers have tried to develop objective evaluation methods of surgical skills for medical training. As a result, the adequate selection and extraction of similarities and differences between experts and novices have become an important challenge in this area. In particular, some of these works have shown that human movements performed during surgery can be described as a sequence of constant affine-speed trajectories...
April 1, 2018: Proceedings of the Institution of Mechanical Engineers. Part H, Journal of Engineering in Medicine
https://www.readbyqxmd.com/read/29678073/a-decision-support-tool-for-healthcare-professionals-in-the-management-of-hyperphosphatemia-in-hemodialysis
#15
Sisse H Laursen, Amanda A Buus, Lisbet Brandi, Peter Vestergaard, Ole K Hejlesen
Hyperphosphatemia is known as one of the more challenging conditions in end-stage renal disease patients. This study set out to present and evaluate a healthcare-oriented decision support tool in the management of hyperphosphatemia within hemodialysis therapy. A prototype module was designed to fit into the interface of a modern dialysis machine (Fresenius 5008). The prototype included three main functions: 1) immediate bedside blood sample access, 2) a model based prognosis tool with estimates of P-phosphate and 3) an overview of the user's phosphate related activities during dialysis treatments...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29676519/development-of-machine-learning-models-to-predict-inhibition-of-3-dehydroquinate-dehydratase
#16
Maurício Boff de Ávila, Walter Filgueira de Azevedo
In the present study, we describe the development of new machine learning models to predict inhibition of the enzyme 3-dehydroquinate dehydratase (DHQD). This enzyme is the third step of the shikimate pathway and is responsible for the synthesis of chorismate, which is a natural precursor of aromatic amino acids The enzymes of shikimate pathway are absent in humans, which make them protein targets for the design of antimicrobial drugs. We focus our study on the crystallographic structures of DHQD in complex with competitive inhibitors, for which experimental inhibition constant data is available...
April 20, 2018: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29668682/biogeography-and-environmental-conditions-shape-bacteriophage-bacteria-networks-across-the-human-microbiome
#17
Geoffrey D Hannigan, Melissa B Duhaime, Danai Koutra, Patrick D Schloss
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease. Most previous work has relied on studying bacteria and viruses independently, thereby reducing them to two separate communities. Such approaches are unable to capture how these microbial communities interact, such as through processes that maintain community robustness or allow phage-host populations to co-evolve. We implemented a network-based analytical approach to describe phage-bacteria network diversity throughout the human body...
April 18, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29659916/human-gut-microbiota-predicts-susceptibility-to-vibrio-cholerae-infection
#18
Firas S Midani, Ana A Weil, Fahima Chowdhury, Yasmin A Begum, Ashraful I Khan, Meti D Debela, Heather K Durand, Aspen T Reese, Sai N Nimmagadda, Justin D Silverman, Crystal N Ellis, Edward T Ryan, Stephen B Calderwood, Jason B Harris, Firdausi Qadri, Lawrence A David, Regina C LaRocque
Background: Cholera is a public health problem worldwide and the risk factors for infection are only partially understood. Methods: We prospectively studied household contacts of cholera patients to compare those who were infected with those who were not. We constructed predictive machine learning models of susceptibility using baseline gut microbiota data. We identified bacterial taxa associated with susceptibility to Vibrio cholerae infection and tested these taxa for interactions with V...
April 12, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29652486/biochemistry-and-molecular-biology-of-flaviviruses
#19
Nicholas J Barrows, Rafael K Campos, Kuo-Chieh Liao, K Reddisiva Prasanth, Ruben Soto-Acosta, Shih-Chia Yeh, Geraldine Schott-Lerner, Julien Pompon, October M Sessions, Shelton S Bradrick, Mariano A Garcia-Blanco
Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA-protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes...
April 13, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29650030/harnessing-qatar-biobank-to-understand-type-2-diabetes-and-obesity-in-adult-qataris-from-the-first-qatar-biobank-project
#20
Ehsan Ullah, Raghvendra Mall, Reda Rawi, Naima M Moustaid, Adeel A Butt, Halima Bensmail
BACKGROUND: Human tissues are invaluable resources for researchers worldwide. Biobanks are repositories of such human tissues and can have a strategic importance for genetic research, clinical care, and future discoveries and treatments. One of the aims of Qatar Biobank is to improve the understanding and treatment of common diseases afflicting Qatari population such as obesity and diabetes. METHODS: In this study we apply a panorama of state-of-the-art statistical methods and machine learning algorithms to investigate associations and risk factors for diabetes and obesity on a sample of 1000 Qatari population...
April 12, 2018: Journal of Translational Medicine
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