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https://www.readbyqxmd.com/read/28444127/hla-class-i-binding-prediction-via-convolutional-neural-networks
#1
Yeeleng S Vang, Xiaohui Xie
Motivation: Many biological processes are governed by protein-ligand interactions. One such example is the recognition of self and nonself cells by the immune system. This immune response process is regulated by the major histocompatibility complex (MHC) protein which is encoded by the human leukocyte antigen (HLA) complex. Understanding the binding potential between MHC and peptides can lead to the design of more potent, peptide-based vaccines and immunotherapies for infectious autoimmune diseases...
April 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28436837/passive-bci-in-operational-environments-insights-recent-advances-and-future-trends
#2
Pietro Arico, Gianluca Borghini, Gianluca Di Flumeri, Nicolina Sciaraffa, Alfredo Colosimo, Fabio Babiloni
OBJECTIVE: this mini-review aims to highlight recent important aspects to consider and evaluate when passive Brain-Computer Interface (pBCI) systems would be developed and used in operational environments, and remarks future directions of their applications. METHODS: Electroencephalography (EEG)-based pBCI has become an important tool for real-time analysis of brain activity, since it could potentially provide, covertly - without distracting the user from the main task - and objectively - not affected by the subjective judgement of an observer or the user itself - information about the operator cognitive state...
April 17, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28424657/magnetic-vestibular-stimulation-mvs-as-a-technique-for-understanding-the-normal-and-diseased-labyrinth
#3
REVIEW
Bryan K Ward, Jorge Otero-Millan, Prem Jareonsettasin, Michael C Schubert, Dale C Roberts, David S Zee
Humans often experience dizziness and vertigo around strong static magnetic fields such as those present in an MRI scanner. Recent evidence supports the idea that this effect is the result of inner ear vestibular stimulation and that the mechanism is a magnetohydrodynamic force (Lorentz force) that is generated by the interactions between normal ionic currents in the inner ear endolymph and the strong static magnetic field of MRI machines. While in the MRI, the Lorentz force displaces the cupula of the lateral and anterior semicircular canals, as if the head was rotating with a constant acceleration...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/28423569/accurate-prediction-of-protein-protein-interactions-by-integrating-potential-evolutionary-information-embedded-in-pssm-profile-and-discriminative-vector-machine-classifier
#4
Zheng-Wei Li, Zhu-Hong You, Xing Chen, Li-Ping Li, De-Shuang Huang, Gui-Ying Yan, Ru Nie, Yu-An Huang
Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420135/a-prosthetic-hand-body-area-controller-based-on-efficient-pattern-recognition-control-strategies
#5
Simone Benatti, Bojan Milosevic, Elisabetta Farella, Emanuele Gruppioni, Luca Benini
Poliarticulated prosthetic hands represent a powerful tool to restore functionality and improve quality of life for upper limb amputees. Such devices offer, on the same wearable node, sensing and actuation capabilities, which are not equally supported by natural interaction and control strategies. The control in state-of-the-art solutions is still performed mainly through complex encoding of gestures in bursts of contractions of the residual forearm muscles, resulting in a non-intuitive Human-Machine Interface (HMI)...
April 15, 2017: Sensors
https://www.readbyqxmd.com/read/28417600/a-bioinspired-mineral-hydrogel-as-a-self-healable-mechanically-adaptable-ionic-skin-for-highly-sensitive-pressure-sensing
#6
Zhouyue Lei, Quankang Wang, Shengtong Sun, Wencheng Zhu, Peiyi Wu
In the past two decades, artificial skin-like materials have received increasing research interests for their broad applications in artificial intelligence, wearable devices, and soft robotics. However, profound challenges remain in terms of imitating human skin because of its unique combination of mechanical and sensory properties. In this work, a bioinspired mineral hydrogel is developed to fabricate a novel type of mechanically adaptable ionic skin sensor. Due to its unique viscoelastic properties, the hydrogel-based capacitive sensor is compliant, self-healable, and can sense subtle pressure changes, such as a gentle finger touch, human motion, or even small water droplets...
April 18, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28389030/harnessing-prefrontal-cognitive-signals-for-brain-machine-interfaces
#7
REVIEW
Byoung-Kyong Min, Ricardo Chavarriaga, José Del R Millán
Brain-machine interfaces (BMIs) enable humans to interact with devices by modulating their brain signals. Despite impressive technological advancements, several obstacles remain. The most commonly used BMI control signals are derived from the brain areas involved in primary sensory- or motor-related processing. However, these signals only reflect a limited range of human intentions. Therefore, additional sources of brain activity for controlling BMIs need to be explored. In particular, higher-order cognitive brain signals, specifically those encoding goal-directed intentions, are natural candidates for enlarging the repertoire of BMI control signals and making them more efficient and intuitive...
April 4, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28386448/elasticity-improves-handgrip-performance-and-user-experience-during-visuomotor-control
#8
Michael Mace, Paul Rinne, Jean-Luc Liardon, Catherine Uhomoibhi, Paul Bentley, Etienne Burdet
Passive rehabilitation devices, providing motivation and feedback, potentially offer an automated and low-cost therapy method, and can be used as simple human-machine interfaces. Here, we ask whether there is any advantage for a hand-training device to be elastic, as opposed to rigid, in terms of performance and preference. To address this question, we have developed a highly sensitive and portable digital handgrip, promoting independent and repetitive rehabilitation of grasp function based around a novel elastic force and position sensing structure...
February 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28376782/image-analysis-driven-single-cell-analytics-for-systems-microbiology
#9
Athanasios D Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P Tampakaki, Konstantinos P Koutsoumanis, Elias S Manolakos
BACKGROUND: Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. RESULTS: BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view...
April 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28375650/emerging-frontiers-of-neuroengineering-a-network-science-of-brain-connectivity
#10
Danielle S Bassett, Ankit N Khambhati, Scott T Grafton
Neuroengineering is faced with unique challenges in repairing or replacing complex neural systems that are composed of many interacting parts. These interactions form intricate patterns over large spatiotemporal scales and produce emergent behaviors that are difficult to predict from individual elements. Network science provides a particularly appropriate framework in which to study and intervene in such systems by treating neural elements (cells, volumes) as nodes in a graph and neural interactions (synapses, white matter tracts) as edges in that graph...
March 27, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28368026/network-based-characterization-and-prediction-of-human-dna-repair-genes-and-pathways
#11
Yan-Hui Li, Gai-Gai Zhang
Network biology is a useful strategy to understand cell's functional organization. In this study, for the first time, we successfully introduced network approaches to study properties of human DNA repair genes. Compared with non-DNA repair genes, we found distinguishing features for DNA repair genes: (i) they tend to have higher degrees; (ii) they tend to be located at global network center; (iii) they tend to interact directly with each other. Based on these features, we developed the first algorithm to predict new DNA repair genes...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28336515/the-motor-activity-of-dna2-functions-as-an-ssdna-translocase-to-promote-dna-end-resection
#12
Maryna Levikova, Cosimo Pinto, Petr Cejka
DNA2 nuclease-helicase functions in DNA replication and recombination. This requires the nuclease of DNA2, while, in contrast, the role of the helicase activity has been unclear. We now show that the motor activity of both recombinant yeast and human DNA2 promotes efficient degradation of long stretches of ssDNA, particularly in the presence of the replication protein A. This degradation is further stimulated by a direct interaction with a cognate RecQ family helicase, which functions with DNA2 in DNA end resection to initiate homologous recombination...
March 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28323040/-machine-learning-based-identification-of-endogenous-cellular-microrna-sponges-against-viral-micrornas
#13
Soowon Kang, Seunghyun Park, Sungroh Yoon, Hyeyoung Min
A "miRNA sponge" is an artificial oligonucleotide-based miRNA inhibitor containing multiple binding sites for a specific miRNA. Each miRNA sponge can bind and sequester several miRNA copies, thereby decreasing the cellular levels of the target miRNA. In addition to developing artificial miRNA sponges, scientists have sought endogenous RNA transcripts and found that long non-coding RNAs, competing endogenous RNAs, pseudogenes, circular RNAs, and coding RNAs could act as miRNA sponges under precise conditions...
March 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28320651/collaborative-active-visual-recognition-from-crowds-a-distributed-ensemble-approach
#14
Gang Hua, Chengjiang Long, Ming Yang, Yan Gao
Active learning is an effective way of engaging users to interactively train models for visual recognition more efficiently. The vast majority of previous works focused on active learning with a single human oracle. The problem of active learning with multiple oracles in a collaborative setting has not been well explored. We present a collaborative computational model for active learning with multiple human oracles, the input from whom may be subject to different levels of noise. It leads to not only an ensemble kernel machine that is robust to label noise, but also a principled label quality measure to online detect irresponsible labelers...
March 15, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28318903/understanding-human-intention-by-connecting-perception-and-action-learning-in-artificial-agents
#15
Sangwook Kim, Zhibin Yu, Minho Lee
To develop an advanced human-robot interaction system, it is important to first understand how human beings learn to perceive, think, and act in an ever-changing world. In this paper, we propose an intention understanding system that uses an Object Augmented-Supervised Multiple Timescale Recurrent Neural Network (OA-SMTRNN) and demonstrate the effects of perception-action connected learning in an artificial agent, which is inspired by psychological and neurological phenomena in humans. We believe that action and perception are not isolated processes in human mental development, and argue that these psychological and neurological interactions can be replicated in a human-machine scenario...
February 11, 2017: Neural Networks: the Official Journal of the International Neural Network Society
https://www.readbyqxmd.com/read/28318277/technology-enhanced-human-interaction-in-psychotherapy
#16
Zac E Imel, Derek D Caperton, Michael Tanana, David C Atkins
Psychotherapy is on the verge of a technology-inspired revolution. The concurrent maturation of communication, signal processing, and machine learning technologies begs an earnest look at how these technologies may be used to improve the quality of psychotherapy. Here, we discuss 3 research domains where technology is likely to have a significant impact: (1) mechanism and process, (2) training and feedback, and (3) technology-mediated treatment modalities. For each domain, we describe current and forthcoming examples of how new technologies may change established applications...
March 20, 2017: Journal of Counseling Psychology
https://www.readbyqxmd.com/read/28315750/fun-cube-based-brain-gym-cognitive-function-assessment-system
#17
Tao Zhang, Chung-Chih Lin, Tsang-Chu Yu, Jing Sun, Wen-Chuin Hsu, Alice May-Kuen Wong
The aim of this study is to design and develop a fun cube (FC) based brain gym (BG) cognitive function assessment system using the wireless sensor network and multimedia technologies. The system comprised (1) interaction devices, FCs and a workstation used as interactive tools for collecting and transferring data to the server, (2) a BG information management system responsible for managing the cognitive games and storing test results, and (3) a feedback system used for conducting the analysis of cognitive functions to assist caregivers in screening high risk groups with mild cognitive impairment...
March 3, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28303256/recurring-functional-interactions-predict-network-architecture-of-interictal-and-ictal-states-in-neocortical-epilepsy
#18
Ankit N Khambhati, Danielle S Bassett, Brian S Oommen, Stephanie H Chen, Timothy H Lucas, Kathryn A Davis, Brian Litt
Human epilepsy patients suffer from spontaneous seizures, which originate in brain regions that also subserve normal function. Prior studies demonstrate focal, neocortical epilepsy is associated with dysfunction, several hours before seizures. How does the epileptic network perpetuate dysfunction during baseline periods? To address this question, we developed an unsupervised machine learning technique to disentangle patterns of functional interactions between brain regions, or subgraphs, from dynamic functional networks constructed from approximately 100 h of intracranial recordings in each of 22 neocortical epilepsy patients...
January 2017: ENeuro
https://www.readbyqxmd.com/read/28292943/molecular-details-underlying-dynamic-structures-and-regulation-of-the-human-26s-proteasome
#19
Xiaorong Wang, Peter Cimermancic, Clinton Yu, Andreas Schweitzer, Nikita Chopra, James L Engel, Charles H Greenberg, Alexander S Huszagh, Florian Beck, Eri Sakata, Yingying Yang, Eric J Novitsky, Alexander Leitner, Paolo Nanni, Abdullah Kahraman, Xing Guo, Jack E Dixon, Scott D Rychnovsky, Ruedi Aebersold, Wolfgang Baumeister, Andrej Sali, Lan Huang
The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating structural topologies of large protein assemblies, with its unique capability of studying protein complexes in cells...
March 14, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28287448/real-time-digital-signal-processing-based-on-fpgas-for-electronic-skin-implementation-%C3%A2
#20
Ali Ibrahim, Paolo Gastaldo, Hussein Chible, Maurizio Valle
Enabling touch-sensing capability would help appliances understand interaction behaviors with their surroundings. Many recent studies are focusing on the development of electronic skin because of its necessity in various application domains, namely autonomous artificial intelligence (e.g., robots), biomedical instrumentation, and replacement prosthetic devices. An essential task of the electronic skin system is to locally process the tactile data and send structured information either to mimic human skin or to respond to the application demands...
March 10, 2017: Sensors
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