scholarly journals Spike2Vec: An Efficient and Scalable Embedding Approach for COVID-19 Spike Sequences

2021 ◽  
Author(s):  
Sarwan Ali ◽  
Murray Patterson
Keyword(s):  
Spike Sequences

scholarly journals Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human

2020 ◽  
Vol 2020 (1) ◽  
pp. 290-303
Author(s):  
Kuan Cheok Lei ◽  
Xiaohua Douglas Zhang
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Mutation Analysis ◽  
Evolutionary History ◽  
Sequence Similarity ◽  
Similarity Analysis ◽  
Current Form ◽  
Conservation Analysis ◽  
Spike Sequences ◽  
History Of ◽  
Spike Sequence

Abstract Background The current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome (SARS)-CoV-2, has become the most devastating public health emergency in the 21st century and one of the most influential plagues in history. Studies on the origin of SARS-CoV-2 have generally agreed that the virus probably comes from bat, closely related to a bat CoV named BCoV-RaTG13 taken from horseshoe bat (Rhinolophus affinis), with Malayan pangolin (Manis javanica) being a plausible intermediate host. However, due to the relatively low number of SARS-CoV-2-related strains available in public domain, the evolutionary history remains unclear. Methodology Nine hundred ninety-five coronavirus sequences from NCBI Genbank and GISAID were obtained and multiple sequence alignment was carried out to categorize SARS-CoV-2 related groups. Spike sequences were analyzed using similarity analysis and conservation analyses. Mutation analysis was used to identify variations within receptor-binding domain (RBD) in spike for SARS-CoV-2-related strains. Results We identified a family of SARS-CoV-2-related strains, including the closest relatives, bat CoV RaTG13 and pangolin CoV strains. Sequence similarity analysis and conservation analysis on spike sequence identified that N-terminal domain, RBD and S2 subunit display different degrees of conservation with several coronavirus strains. Mutation analysis on contact sites in SARS-CoV-2 RBD reveals that human-susceptibility probably emerges in pangolin. Conclusion and implication We conclude that the spike sequence of SARS-CoV-2 is the result of multiple recombination events during its transmission from bat to human, and we propose a framework of evolutionary history that resolve the relationship of BCoV-RaTG13 and pangolin coronaviruses with SARS-CoV-2. Lay Summary This study analyses whole-genome and spike sequences of coronavirus from NCBI using phylogenetic and conservation analyses to reconstruct the evolutionary history of severe acute respiratory syndrome (SARS)-CoV-2 and proposes an evolutionary history of spike in the progenitors of SARS-CoV-2 from bat to human through mammal hosts before they recombine into the current form.

scholarly journals Neural mechanisms of context-dependent segmentation tested on large-scale recording data

2021 ◽  
Author(s):  
Toshitake Asabuki ◽  
Tomoki Fukai
Keyword(s):  
Cortical Neurons ◽  
Large Scale ◽  
Neural Mechanism ◽  
Imaging Data ◽  
Unsupervised Segmentation ◽  
Spike Sequences ◽  
Multiple Cell ◽  
Context Dependent ◽  
Current Flows ◽  
The Given

The brain performs various cognitive functions by learning the spatiotemporal salient features of the environment. This learning likely requires unsupervised segmentation of hierarchically organized spike sequences, but the underlying neural mechanism is only poorly understood. Here, we show that a recurrent gated network of neurons with dendrites can context-dependently solve difficult segmentation tasks. Dendrites in this model learn to predict somatic responses in a self-supervising manner while recurrent connections learn a context-dependent gating of dendro-somatic current flows to minimize a prediction error. These connections select particular information suitable for the given context from input features redundantly learned by the dendrites. The model selectively learned salient segments in complex synthetic sequences. Furthermore, the model was also effective for detecting multiple cell assemblies repeating in large-scale calcium imaging data of more than 6,500 cortical neurons. Our results suggest that recurrent gating and dendrites are crucial for cortical learning of context-dependent segmentation tasks.

scholarly journals Flexible theta sequence compression mediated via phase precessing interneurons

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Angus Chadwick ◽  
Mark CW van Rossum ◽  
Matthew F Nolan
Keyword(s):  
Action Potentials ◽  
High Capacity ◽  
Theta Oscillations ◽  
Sequence Generation ◽  
Spike Sequences ◽  
Theta Frequency ◽  
Neural Substrate ◽  
Hippocampal Theta ◽  
Novel Model ◽  
Sequence Compression

Encoding of behavioral episodes as spike sequences during hippocampal theta oscillations provides a neural substrate for computations on events extended across time and space. However, the mechanisms underlying the numerous and diverse experimentally observed properties of theta sequences remain poorly understood. Here we account for theta sequences using a novel model constrained by the septo-hippocampal circuitry. We show that when spontaneously active interneurons integrate spatial signals and theta frequency pacemaker inputs, they generate phase precessing action potentials that can coordinate theta sequences in place cell populations. We reveal novel constraints on sequence generation, predict cellular properties and neural dynamics that characterize sequence compression, identify circuit organization principles for high capacity sequential representation, and show that theta sequences can be used as substrates for association of conditioned stimuli with recent and upcoming events. Our results suggest mechanisms for flexible sequence compression that are suited to associative learning across an animal’s lifespan.

scholarly journals Independent theta phase coding accounts for CA1 population sequences and enables flexible remapping

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Angus Chadwick ◽  
Mark CW van Rossum ◽  
Matthew F Nolan
Keyword(s):  
Traveling Wave ◽  
Action Potentials ◽  
Theta Rhythm ◽  
Place Cells ◽  
Population Activity ◽  
Phase Coding ◽  
Synaptic Interactions ◽  
Spike Sequences ◽  
Rate Coding ◽  
Theta Phase

Hippocampal place cells encode an animal's past, current, and future location through sequences of action potentials generated within each cycle of the network theta rhythm. These sequential representations have been suggested to result from temporally coordinated synaptic interactions within and between cell assemblies. Instead, we find through simulations and analysis of experimental data that rate and phase coding in independent neurons is sufficient to explain the organization of CA1 population activity during theta states. We show that CA1 population activity can be described as an evolving traveling wave that exhibits phase coding, rate coding, spike sequences and that generates an emergent population theta rhythm. We identify measures of global remapping and intracellular theta dynamics as critical for distinguishing mechanisms for pacemaking and coordination of sequential population activity. Our analysis suggests that, unlike synaptically coupled assemblies, independent neurons flexibly generate sequential population activity within the duration of a single theta cycle.

scholarly journals Machine learning methods accurately predict host specificity of coronaviruses based on spike sequences alone

2020 ◽  
Vol 533 (3) ◽  
pp. 553-558
Author(s):  
Kiril Kuzmin ◽  
Ayotomiwa Ezekiel Adeniyi ◽  
Arthur Kevin DaSouza ◽  
Deuk Lim ◽  
Huyen Nguyen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Host Specificity ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Spike Sequences

Non-uniform quantization of neural spike sequences through an information distortion measure

2001 ◽  
Vol 38-40 ◽  
pp. 175-181 ◽  
Author(s):  
Alexander G. Dimitrov ◽  
John P. Miller ◽  
Zane Aldworth ◽  
Tomáš Gedeon
Keyword(s):  
Information Distortion ◽  
Neural Spike ◽  
Spike Sequences ◽  
Uniform Quantization ◽  
Distortion Measure

DECONVOLUTION OF REFRACTION SEISMOGRAMS FROM LARGE UNDERWATER EXPLOSIONS

Geophysics ◽  
1972 ◽  
Vol 37 (3) ◽  
pp. 431-444 ◽  
Author(s):  
R. E. White ◽  
R. F. Mereu
Keyword(s):  
Source Parameters ◽  
Nonlinear Effects ◽  
Synthetic Seismograms ◽  
Phase Changes ◽  
P Wave ◽  
Source Spectrum ◽  
Underwater Explosions ◽  
Basic Wavelet ◽  
Spike Sequences ◽  
Short Time

The P-wave spectra of seismograms from large underwater explosions are frequently dominated by reverberations. When this is so, a simple reverberation model similar to that of Backus (1959) gives a good approximation to the source spectrum. The basic wavelet determined by this method is not necessarily minimum‐delay. A few promising deconvolutions have been carried out, revealing a sequence of arrivals of comparable amplitudes separated by short time intervals. Synthetic seismograms which have been constructed from these spike sequences differ very little from the field records. However, the technique often yields output seismograms which are not easily interpreted. A study using synthetic seismograms suggests five reasons for this: 1) low signal‐to‐noise ratios, which result in too narrow a frequency band in which signal is predominant; 2) pulses arriving at the recorder having undergone phase changes during transmission, especially in combination with 3) very close spacing of the sequence of arrivals, causing overlap of the deconvolved output pulses; 4) the presence of arrivals which are not propagated along simple ray‐theory paths, and 5) poor estimation of the source parameters. Nonlinear effects and complex geology at the source are other possible causes of complications in the deconvolved records.

scholarly journals Multineuronal spike sequences repeat with millisecond precision

2013 ◽  
Vol 7 ◽  
Author(s):  
Koki Matsumoto ◽  
Tomoe Ishikawa ◽  
Norio Matsuki ◽  
Yuji Ikegaya
Keyword(s):  
Spike Sequences
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