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https://www.readbyqxmd.com/read/28720701/de-novo-peptide-sequencing-by-deep-learning
#1
Ngoc Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan, Ming Li
De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28719406/toward-a-biopsychosocial-ecology-of-the-human-microbiome-brain-gut-axis-and-health
#2
Karl J Maier, Mustafa al'Absi
OBJECTIVE: Rapidly expanding insights to the human microbiome and health suggest that Western medicine is poised for significant evolution, or perhaps revolution - this while the field continues on a trajectory from reductionism to a biopsychosocial (BPS) paradigm recognizing biological, psychological, and social influences on health. The apparent sensitivity of the microbiota to perturbations across BPS domains suggests that a broad and inclusive framework is needed to develop applicable knowledge in this area...
July 18, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28716962/gamma-oscillations-in-the-rat-ventral-striatum-originate-in-the-piriform-cortex
#3
James E Carmichael, Jimmie M Gmaz, Matthijs A A van der Meer
Local field potentials (LFPs) recorded from the human and rodent ventral striatum (vStr) exhibit prominent, behaviorally relevant gamma-band oscillations. These oscillations are related to local spiking activity and transiently synchronize with anatomically related areas, suggesting a possible role in organizing vStr activity. However, the origin of vStr gamma is unknown. We recorded vStr gamma oscillations across a 1.4mm(2) grid spanned by 64 recording electrodes as male rats rested and foraged for rewards, revealing a highly consistent power gradient originating in the adjacent piriform cortex...
July 17, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28708000/reactive-oxygen-species-and-mitochondrial-homeostasis-as-regulators-of-stem-cell-fate-and-function
#4
Darren Qiancheng Tan, Toshio Suda
SIGNIFICANCE: The precise role and impact of reactive oxygen species (ROS) in stem cells, which are essential for lifelong tissue homeostasis and regeneration, remains of significant interest to the field. The long-term regenerative potential of a stem cell compartment is determined by the delicate balance between quiescence, self-renewal and differentiation; all of which can be influenced by ROS levels. Recent advances: The past decade has seen a growing appreciation for the importance of ROS and redox homeostasis in various stem cell compartments; particularly those of hematopoietic, neural and muscle tissues...
July 14, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28700611/in-vivo-calcium-imaging-from-dentate-granule-cells-with-wide-field-fluorescence-microscopy
#5
Yuichiro Hayashi, Satoshi Yawata, Kazuo Funabiki, Takatoshi Hikida
A combination of genetically-encoded calcium indicators and micro-optics has enabled monitoring of large-scale dynamics of neuronal activity from behaving animals. In these studies, wide-field microscopy is often used to visualize neural activity. However, this method lacks optical sectioning capability, and therefore its axial resolution is generally poor. At present, it is unclear whether wide-field microscopy can visualize activity of densely packed small neurons at cellular resolution. To examine the applicability of wide-field microscopy for small-sized neurons, we recorded calcium activity of dentate granule cells having a small soma diameter of approximately 10 micrometers...
2017: PloS One
https://www.readbyqxmd.com/read/28698464/leaf-area-index-estimation-using-chinese-gf-1-wide-field-view-data-in-an-agriculture-region
#6
Xiangqin Wei, Xingfa Gu, Qingyan Meng, Tao Yu, Xiang Zhou, Zheng Wei, Kun Jia, Chunmei Wang
Leaf area index (LAI) is an important vegetation parameter that characterizes leaf density and canopy structure, and plays an important role in global change study, land surface process simulation and agriculture monitoring. The wide field view (WFV) sensor on board the Chinese GF-1 satellite can acquire multi-spectral data with decametric spatial resolution, high temporal resolution and wide coverage, which are valuable data sources for dynamic monitoring of LAI. Therefore, an automatic LAI estimation algorithm for GF-1 WFV data was developed based on the radiative transfer model and LAI estimation accuracy of the developed algorithm was assessed in an agriculture region with maize as the dominated crop type...
July 8, 2017: Sensors
https://www.readbyqxmd.com/read/28696758/local-dynamics-in-trained-recurrent-neural-networks
#7
Alexander Rivkind, Omri Barak
Learning a task induces connectivity changes in neural circuits, thereby changing their dynamics. To elucidate task-related neural dynamics, we study trained recurrent neural networks. We develop a mean field theory for reservoir computing networks trained to have multiple fixed point attractors. Our main result is that the dynamics of the network's output in the vicinity of attractors is governed by a low-order linear ordinary differential equation. The stability of the resulting equation can be assessed, predicting training success or failure...
June 23, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28694229/motor-expertise-modulates-neural-oscillations-and-temporal-dynamics-of-cognitive-control
#8
Chun-Hao Wang, Cheng-Ta Yang, David Moreau, Neil G Muggleton
The field of motor expertise in athletes has recently been receiving increasing levels of investigation. However, there has been less investigation of how dynamic changes in behavior and in neural activity as a result of sporting participation might result in superiority for athletes in domain-general cognition. We used a flanker task to investigate conflict-related behavioral measures, such as mean reaction time (RT) and RT variability, in conjunction with electroencephalographic (EEG) measures, including N2d, theta activity power, and inter-trial phase coherence (ITPC)...
July 8, 2017: NeuroImage
https://www.readbyqxmd.com/read/28681390/a-deep-feature-fusion-methodology-for-breast-cancer-diagnosis-demonstrated-on-three-imaging-modality-datasets
#9
Natalia Antropova, Benjamin Q Huynh, Maryellen L Giger
Deep learning methods for radiomics/computer-aided diagnosis (CADx) are often prohibited by small datasets, long computation time, and the need for extensive image preprocessing. We present a methodology that extracts and pools low- to mid-level features using a pre-trained convolutional neural network and fuses them with handcrafted radiomic features computed using conventional CADx methods. Our fusion-based method demonstrates significant improvements to previous breast cancer CADx methods across three clinical imaging modalities (dynamic contrast-enhanced MRI, full-field digital mammography, and ultrasound) in terms of predictive performance in the task of estimating lesion malignancy...
July 6, 2017: Medical Physics
https://www.readbyqxmd.com/read/28680506/an-investigation-of-the-dynamical-transitions-in-harmonically-driven-random-networks-of-firing-rate-neurons
#10
Kyriacos Nikiforou, Pedro A M Mediano, Murray Shanahan
Continuous-time recurrent neural networks are widely used as models of neural dynamics and also have applications in machine learning. But their dynamics are not yet well understood, especially when they are driven by external stimuli. In this article, we study the response of stable and unstable networks to different harmonically oscillating stimuli by varying a parameter ρ, the ratio between the timescale of the network and the stimulus, and use the dimensionality of the network's attractor as an estimate of the complexity of this response...
2017: Cognitive Computation
https://www.readbyqxmd.com/read/28676297/inferring-synaptic-excitation-inhibition-balance-from-field-potentials
#11
Richard Gao, Erik J Peterson, Bradley Voytek
Neural circuits sit in a dynamic balance between excitation (E) and inhibition (I). Fluctuations in E:I balance have been shown to influence neural computation, working memory, and information flow, while more drastic shifts and aberrant E:I patterns are implicated in numerous neurological and psychiatric disorders. Current methods for measuring E:I dynamics require invasive procedures that are difficult to perform in behaving animals, and nearly impossible in humans. This has limited the ability to examine the full impact that E:I shifts have in cognition and disease...
July 1, 2017: NeuroImage
https://www.readbyqxmd.com/read/28674500/dynamic-skin-patterns-in-cephalopods
#12
Martin J How, Mark D Norman, Julian Finn, Wen-Sung Chung, N Justin Marshall
Cephalopods are unrivaled in the natural world in their ability to alter their visual appearance. These mollusks have evolved a complex system of dermal units under neural, hormonal, and muscular control to produce an astonishing variety of body patterns. With parallels to the pixels on a television screen, cephalopod chromatophores can be coordinated to produce dramatic, dynamic, and rhythmic displays, defined collectively here as "dynamic patterns." This study examines the nature, context, and potential functions of dynamic patterns across diverse cephalopod taxa...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28661136/insertable-no-co-microsensors-recording-gaseous-vasomodulators-reflecting-differential-neuronal-activation-level-with-respect-to-seizure-focus
#13
Yejin Ha, Youngmi Lee, Minah Suh
Nitric oxide (NO) and carbon monoxide (CO) are important signaling molecules shaping vasomodulation. This paper reports simultaneous in vivo monitoring of NO, CO and dendritic summation of action potential at three different cortical regions: seizure focus and two additional places, vertically and horizontally separated by 1.2 mm from the seizure focus, during epileptic seizure induced by 4-aminopyrindine injection. An amperometric dual microsensor having a high spatiotemporal resolution monitored fast and dynamic changes of NO and CO, and neural changes were recorded with a glass pipette electrode for local field potential (LFP)...
June 29, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28660418/basal-forebrain-activation-enhances-between-trial-reliability-of-low-frequency-local-field-potentials-lfp-and-spiking-activity-in-tree-shrew-primary-visual-cortex-v1
#14
Paolo De Luna, Julia Veit, Gregor Rainer
Brain state has profound effects on neural processing and stimulus encoding in sensory cortices. While the synchronized state is dominated by low-frequency local field potential (LFP) activity, low-frequency LFP power is suppressed in the desynchronized state, where a concurrent enhancement in gamma power is observed. Recently, it has been shown that cortical desynchronization co-occurs with enhanced between-trial reliability of spiking activity in sensory neurons, but it is currently unclear whether this effect is also evident in LFP signals...
June 28, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/28659842/functional-synchronization-the-emergence-of-coordinated-activity-in-human-systems
#15
Andrzej Nowak, Robin R Vallacher, Michal Zochowski, Agnieszka Rychwalska
The topical landscape of psychology is highly compartmentalized, with distinct phenomena explained and investigated with recourse to theories and methods that have little in common. Our aim in this article is to identify a basic set of principles that underlie otherwise diverse aspects of human experience at all levels of psychological reality, from neural processes to group dynamics. The core idea is that neural, behavioral, mental, and social structures emerge through the synchronization of lower-level elements (e...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28658617/reliable-and-elastic-propagation-of-cortical-seizures-in%C3%A2-vivo
#16
Michael Wenzel, Jordan P Hamm, Darcy S Peterka, Rafael Yuste
Mapping the fine-scale neural activity that underlies epilepsy is key to identifying potential control targets of this frequently intractable disease. Yet, the detailed in vivo dynamics of seizure progression in cortical microcircuits remain poorly understood. We combine fast (30-Hz) two-photon calcium imaging with local field potential (LFP) recordings to map, cell by cell, the spread of locally induced (4-AP or picrotoxin) seizures in anesthetized and awake mice. Using single-layer and microprism-assisted multilayer imaging in different cortical areas, we uncover reliable recruitment of local neural populations within and across cortical layers, and we find layer-specific temporal delays, suggesting an initial supra-granular invasion followed by deep-layer recruitment during lateral seizure spread...
June 27, 2017: Cell Reports
https://www.readbyqxmd.com/read/28656774/emulating-bilingual-synaptic-response-using-a-junction-based-artificial-synaptic-device
#17
He Tian, Xi Cao, Yujun Xie, Xiaodong Yan, Andrew Kostelec, Don DiMarzio, Cheng Chang, Li-Dong Zhao, Wei Wu, Jesse Tice, Judy J Cha, Jing Guo, Han Wang
Excitatory and inhibitory postsynaptic potentials are the two fundamental categories of synaptic responses underlying the diverse functionalities of the mammalian nervous system. Recent advances in neuroscience have revealed the co-release of both glutamate and GABA neurotransmitters from a single axon terminal in neurons at the ventral tegmental area that can result in the reconfiguration of the postsynaptic potentials between excitatory and inhibitory effects. The ability to mimic such features of the biological synapses in semiconductor devices, which is lacking in the conventional field effect transistor-type and memristor-type artificial synaptic devices, can enhance the functionalities and versatility of neuromorphic electronic systems in performing tasks such as image recognition, learning, and cognition...
June 28, 2017: ACS Nano
https://www.readbyqxmd.com/read/28656608/flexible-ionic-electronic-hybrid-oxide-synaptic-tfts-with-programmable-dynamic-plasticity-for-brain-inspired-neuromorphic-computing
#18
Rohit Abraham John, Jieun Ko, Mohit R Kulkarni, Naveen Tiwari, Nguyen Anh Chien, Ng Geok Ing, Wei Lin Leong, Nripan Mathews
Emulation of biological synapses is necessary for future brain-inspired neuromorphic computational systems that could look beyond the standard von Neuman architecture. Here, artificial synapses based on ionic-electronic hybrid oxide-based transistors on rigid and flexible substrates are demonstrated. The flexible transistors reported here depict a high field-effect mobility of ≈9 cm(2) V(-1) s(-1) with good mechanical performance. Comprehensive learning abilities/synaptic rules like paired-pulse facilitation, excitatory and inhibitory postsynaptic currents, spike-time-dependent plasticity, consolidation, superlinear amplification, and dynamic logic are successfully established depicting concurrent processing and memory functionalities with spatiotemporal correlation...
June 28, 2017: Small
https://www.readbyqxmd.com/read/28651813/magnetic-oculomotor-prosthetics-for-acquired-nystagmus
#19
Parashkev Nachev, Geoff E Rose, David H Verity, Sanjay G Manohar, Kelly MacKenzie, Gill Adams, Maria Theodorou, Quentin A Pankhurst, Christopher Kennard
PURPOSE: Acquired nystagmus, a highly symptomatic consequence of damage to the substrates of oculomotor control, often is resistant to pharmacotherapy. Although heterogeneous in its neural cause, its expression is unified at the effector-the eye muscles themselves-where physical damping of the oscillation offers an alternative approach. Because direct surgical fixation would immobilize the globe, action at a distance is required to damp the oscillation at the point of fixation, allowing unhindered gaze shifts at other times...
June 23, 2017: Ophthalmology
https://www.readbyqxmd.com/read/28644841/low-dimensional-spike-rate-models-derived-from-networks-of-adaptive-integrate-and-fire-neurons-comparison-and-implementation
#20
Moritz Augustin, Josef Ladenbauer, Fabian Baumann, Klaus Obermayer
The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation. When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the Fokker-Planck equation. This approach, however, leads to a model with an infinite-dimensional state space and non-standard boundary conditions. Here we derive from that description four simple models for the spike rate dynamics in terms of low-dimensional ordinary differential equations using two different reduction techniques: one uses the spectral decomposition of the Fokker-Planck operator, the other is based on a cascade of two linear filters and a nonlinearity, which are determined from the Fokker-Planck equation and semi-analytically approximated...
June 2017: PLoS Computational Biology
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