Latest in q-bio

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Where did the tumor start? An inverse solver with sparse localization for tumor growth modelsJul 15 2019We present a numerical scheme for solving an inverse problem for parameter estimation in tumor growth models for glioblastomas, a form of aggressive primary brain tumor. The growth model is a reaction-diffusion partial differential equation (PDE) for ... More
Markovian approach to tackle the interaction of simultaneous diseasesJul 15 2019The simultaneous emergence of several abrupt disease outbreaks or the extinction of some serotypes of multi-strain diseases are fingerprints of the interaction between pathogens spreading within the same population. Here, we propose a general and versatile ... More
What does it mean to understand a neural network?Jul 15 2019We can define a neural network that can learn to recognize objects in less than 100 lines of code. However, after training, it is characterized by millions of weights that contain the knowledge about many object types across visual scenes. Such networks ... More
MOD-Finder: Identify multi-omics data sets related to defined chemical exposureJul 15 2019Summary: Integration of multi-omics data on chemical exposure of cells or organisms promises a more complete representation of the responding pathways than single omics data. Data of different omics layers, like transcriptome or proteome is deposited ... More
Cytoskeletal filament length controlled dynamic sequestering of intracellular cargoJul 15 2019The spatial localization or sequestering of motile cargo and their dispersal within cells is an important process in a number of physiological contexts. The morphology of the cytoskeletal network, along which active, motor-driven intracellular transport ... More
Caching in or falling back at the SevilletaJul 15 2019Foraging in uncertain environments requires balancing the risks associated with finding alternative resources against potential gains. In aridland environments characterized by extreme variation in the amount and seasonal timing of primary production, ... More
Autoencoding sensory substitutionJul 14 2019Tens of millions of people live blind, and their number is ever increasing. Visual-to-auditory sensory substitution (SS) encompasses a family of cheap, generic solutions to assist the visually impaired by conveying visual information through sound. The ... More
Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysisJul 14 2019It has long been observed that trimethylamin N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work of the two osmolytes, various aspects of ... More
Complexity of Brain TumorsJul 13 2019Tumor growth is a complex process characterized by uncontrolled cell proliferation and invasion of neighboring tissues. The understanding of these phenomena is of vital importance to establish appropriate diagnosis and therapeutic strategy and starts ... More
Large and Small Data Blow-Up Solutions in the Trojan Y Chromosome ModelJul 13 2019The Trojan Y Chromosome Strategy (TYC) is an extremely well investigated biological control method for controlling invasive populations with an XX-XY sex determinism. In \cite{GP12, WP14} various dynamical properties of the system are analyzed, including ... More
Properties for the Frechet Mean in Billera-Holmes-Vogtmann TreespaceJul 12 2019The Billera-Holmes-Vogtmann (BHV) space of weighted trees can be embedded in Euclidean space, but the extrinsic Euclidean mean often lies outside of treespace. Sturm showed that the intrinsic Frechet mean exists and is unique in treespace. This Frechet ... More
How range residency and long-range perception change encounter ratesJul 12 2019Encounter rates link movement strategies to intra- and inter-specific interactions, and therefore translate individual movement behavior into higher-level ecological processes. Indeed, a large body of interacting population theory rests on the law of ... More
Signal Conditioning for Learning in the WildJul 12 2019The mammalian olfactory system learns rapidly from very few examples, presented in unpredictable online sequences, and then recognizes these learned odors under conditions of substantial interference without exhibiting catastrophic forgetting. We have ... More
The possibility of blocking the process of DNA base pairs opening by hydrogen peroxideJul 12 2019One of the most progressive methods of cancer treatment is ion beam therapy. The simulations of water radiolysis show that in the cell medium the most long-living species are hydrogen peroxide (H$_2$O$_2$) molecules. But up to the present time the role ... More
Single-cell micro- and nano-photonic technologiesJul 12 2019Since the advent of optogenetics, technology development has focused on new methods to optically interact with single nervous cells. This gave rise to the field of photonic neural interfaces, intended as the set of technologies that can modify light radiation ... More
A Model-Theoretic Approach to Modular Implementation, with Application to Biological SystemsJul 12 2019We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in the actions ... More
Evolving complexity: how tinkering shapes cells, software and ecological networksJul 12 2019A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not reducible ... More
Cortical Surface Parcellation using Spherical Convolutional Neural NetworksJul 11 2019We present cortical surface parcellation using spherical deep convolutional neural networks. Traditional multi-atlas cortical surface parcellation requires inter-subject surface registration using geometric features with high processing time on a single ... More
Method of moments for 3-D single particle ab initio modeling with non-uniform distribution of viewing anglesJul 11 2019Single-particle reconstruction in cryo-electron microscopy (cryo-EM) is an increasingly popular technique for determining the 3-D structure of a molecule from several noisy 2-D projections images taken at unknown viewing angles. Most reconstruction algorithms ... More
Warfarin dose estimation on multiple datasets with automated hyperparameter optimisation and a novel software frameworkJul 11 2019Warfarin is an effective preventative treatment for arterial and venous thromboembolism, but requires individualised dosing due to its narrow therapeutic range and high individual variation. A plethora of statistical and machine learning techniques have ... More
Theoretical Limit Of Concentration Sensing of Single Receptor Artificial BiosensorsJul 11 2019Artificially engineered biosensors are highly inefficient in accurately measuring the concentration of biomarkers, particularly, during early diagnosis of diseases. On the other hand, single cellular systems such as chemotactic bacteria can sense their ... More
Fundamental Limitations in Biomarker Based Early Disease DiagnosisJul 11 2019Clinical biosensors with low detection limit hold significant promise in the early diagnosis of debilitating diseases. Recent progress in sensor development has led to the demonstration of detection capable of detecting target molecules even down to single-molecule ... More
retina-VAE: Variationally Decoding the Spectrum of Macular DiseaseJul 11 2019In this paper, we seek a clinically-relevant latent code for representing the spectrum of macular disease. Towards this end, we construct retina-VAE, a variational autoencoder-based model that accepts a patient profile vector (pVec) as input. The pVec ... More
Fixation properties of rock-paper-scissors games in fluctuating populationsJul 11 2019Jul 12 2019Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed populations. Here, ... More
Fixation properties of rock-paper-scissors games in fluctuating populationsJul 11 2019Rock-paper-scissors games metaphorically model cyclic dominance in ecology and microbiology. In a static environment, these models are characterized by fixation probabilities obeying two different "laws" in large and small well-mixed populations. Here, ... More
Distribution of outbreak sizes for SIR disease in finite populationsJul 11 2019We consider the spread of a Susceptible-Infected-Recovered (SIR) disease through finite populations and derive an expression for the final size distribution. Our derivation allows arbitrary distributions of the number of transmissions caused by an infected ... More
On the minimum value of the Colless index and the bifurcating trees that achieve itJul 11 2019Measures of tree balance play an important role in the analysis of phylogenetic trees. One of the oldest and most popular indices in this regard is the Colless index for rooted bifurcating trees, introduced by Colless (1982). While many of its statistical ... More
From Single Neurons to Behavior in the Jellyfish Aurelia auritaJul 11 2019Jellyfish nerve nets provide insight into the origins of nervous systems, as both their taxonomic position and their evolutionary age imply that jellyfish resemble some of the earliest neuron-bearing, actively-swimming animals. Here we develop the first ... More
Extension of Sinkhorn Method: Optimal Movement Estimation of Agents Moving at Constant VelocityJul 11 2019In the field of bioimaging, an important part of analyzing the motion of objects is tracking. We propose a method that applies the Sinkhorn distance for solving the optimal transport problem to track objects. The advantage of this method is that it can ... More
A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directionsJul 11 2019Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont ... More
On the probability of strain invasion in endemic settings: accounting for individual heterogeneity and control in multi-strain dynamicsJul 11 2019The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of drug-resistant pathogens are ignited ... More
Lattice models for protein organization throughout thylakoid membrane stacksJul 11 2019Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by microscopy and ... More
FindeR: Accelerating FM-Index-based Exact Pattern Matching in Genomic Sequences through ReRAM technologyJul 11 2019Genomics is the critical key to enable the precision medicine, ensure the global food security and enforce the wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for genome ... More
Application of a pixel color- and coordinate-based K-means clustering algorithm and RGB color imaging for quantification of rice sheath blight infectionJul 10 2019Red-green-blue (RGB) digital image-based detection is a promising alternative approach to the existing subjectivity-prone and labor-intensive plant disease quantification methods. K-means clustering (KMC) is a widely used algorithm for processing plant ... More
Improving Prognostic Performance in Resectable Pancreatic Ductal Adenocarcinoma using Radiomics and Deep Learning Features Fusion in CT ImagesJul 10 2019As an analytic pipeline for quantitative imaging feature extraction and analysis, radiomics has grown rapidly in the past a few years. Recent studies in radiomics aim to investigate the relationship between tumors imaging features and clinical outcomes. ... More
Optimizing defence, counter-defence and counter-counter defence in parasitic and trophic interactions -- A modelling studyJul 10 2019In host-pathogen interactions, often the host (attacked organism) defends itself by some toxic compound and the parasite, in turn, responds by producing an enzyme that inactivates that compound. In some cases, the host can respond by producing an inhibitor ... More
Evaluating bird collision risk of a high-speed railway crossing the habitat of the crested ibis (Nipponia nippon) in Qinling Mountains, ChinaJul 10 2019Bird collisions with high-speed transport modes is a vital topic on vehicle safety and wildlife protection, especially when high-speed trains, with an average speed of 250km/h, have to run across the habitat of an endangered bird species. This paper evaluates ... More
Coarse Graining of Data via Inhomogeneous Diffusion CondensationJul 10 2019Big data often has emergent structure that exists at multiple levels of abstraction, which are useful for characterizing complex interactions and dynamics of the observations. Here, we consider multiple levels of abstraction via a multiresolution geometry ... More
Metabolite mediated modeling of microbial community dynamics captures emergent behavior more effectively than species-species modelingJul 09 2019Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We seek a modeling ... More
Modeling the relationship between regional activation and functional connectivity during wakefulness and sleepJul 09 2019Global brain activity self-organizes into discrete patterns characterized by distinct behavioral observables and modes of information processing. The human thalamocortical system is a densely connected network where local neural activation reciprocally ... More
Making Study Populations Visible through Knowledge GraphsJul 09 2019Treatment recommendations within Clinical Practice Guidelines (CPGs) are largely based on findings from clinical trials and case studies, referred to here as research studies, that are often based on highly selective clinical populations, referred to ... More
Deep Learning Techniques for Improving Digital Gait SegmentationJul 09 2019Wearable technology for the automatic detection of gait events has recently gained growing interest, enabling advanced analyses that were previously limited to specialist centres and equipment (e.g., instrumented walkway). In this study, we present a ... More
Multiscale Visual Drilldown for the Analysis of Large Ensembles of Multi-Body Protein ComplexesJul 09 2019When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of ... More
Deflation reveals dynamical structure in nondominant reaction coordinatesJul 09 2019The output of molecular dynamics simulations is high-dimensional, and the degrees of freedom among the atoms are related in intricate ways. Therefore, a variety of analysis frameworks have been introduced in order to distill complex motions into lower-dimensional ... More
Gelation impairs small molecule migration in polymer mixturesJul 09 2019Surface segregation of the low-molecular weight component in a polymeric mixture leads to degradation of industrial formulations. We report a simultaneous phase separation and surface migration phenomena in oligomer-polymer and oligomer-gel systems following ... More
On Quantitative Comparison of Chemical Reaction Network ModelsJul 09 2019Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations. Their dynamic ... More
Functional Brain Networks Discovery Using Dictionary Learning with Correlated SparsityJul 09 2019Functional Magnetic Resonance Imaging (fMRI) helps constructing functional brain networks by using brain activity information. Principal component analysis (PCA) and independent component analysis (ICA) are widely used methods to generate functional brain ... More
Applications of a Novel Knowledge Discovery and Data Mining Process Model for MetabolomicsJul 09 2019This work demonstrates the execution of a novel process model for knowledge discovery and data mining for metabolomics (MeKDDaM). It aims to illustrate MeKDDaM process model applicability using four different real-world applications and to highlight its ... More
Computer-Aided Data Mining: Automating a Novel Knowledge Discovery and Data Mining Process Model for MetabolomicsJul 09 2019This work presents MeKDDaM-SAGA, computer-aided automation software for implementing a novel knowledge discovery and data mining process model that was designed for performing justifiable, traceable and reproducible metabolomics data analysis. The process ... More
Quantitative Immunology for PhysicistsJul 08 2019The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules ... More
Optimal Control and Analysis of a Modified Trojan Y-Chromosome StrategyJul 08 2019The Trojan Y Chromosome (TYC) Strategy is a promising eradication method that attempts to manipulate the female to male ratio to promote the reduction of the population of an invasive species. The manipulation stems from an introduction of sex-reversed ... More
False Discovery Rates in Biological NetworksJul 08 2019The increasing availability of data has generated unprecedented prospects for network analyses in many biological fields, such as neuroscience (e.g., brain networks), genomics (e.g., gene-gene interaction networks), and ecology (e.g., species interaction ... More
Aggregated False Discovery Rate ControlJul 08 2019We propose an aggregation scheme for methods that control the false discovery rate (FDR). Our scheme retains the underlying methods' FDR guarantees in theory and can decrease FDR and increase power in practice.
Brain network organization as the computational architecture of cognitionJul 08 2019Understanding neurocognitive computations will require not just localizing cognitive information distributed throughout the brain but also determining how that information got there. We review recent advances in linking (empirical and simulated) brain ... More
Role of Toll-Like Receptors in the interplay between pathogen and damage associated molecular patternsJul 08 2019Various theoretical studies have been carried out to infer relevant protein-protein interactions among pathogens and their hosts. Such studies are generally based on preferential attachment of bacteria / virus to their human receptor homologs. We have ... More
Non-Invasive MGMT Status Prediction in GBM Cancer Using Magnetic Resonance Images (MRI) Radiomics Features: Univariate and Multivariate Machine Learning Radiogenomics AnalysisJul 08 2019Background and aim: This study aimed to predict methylation status of the O-6 methyl guanine-DNA methyl transferase (MGMT) gene promoter status by using MRI radiomics features, as well as univariate and multivariate analysis. Material and Methods: Eighty-two ... More
How many groups? A statistical methodology for data-driven partitioning of infectious disease incidence into age-groupsJul 08 2019Understanding age-group dynamics of infectious diseases is a fundamental issue for both scientific study and policymaking. Age-structure epidemic models were developed in order to study and improve our understanding of these dynamics. By fitting the models ... More
Network analysis of synonymous codon usageJul 07 2019Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can impact co-translational ... More
4D Liquid-phase Electron Microscopy of Ferritin by Brownian Single Particle AnalysisJul 07 2019Protein function and activity are a consequence of its three-dimensional structure. Single particle analysis of cryogenic electron micrographs has radically changed structural biology allowing atomic reconstruction of almost any type of proteins. While ... More
A family of closed-form solutions for two-dimensional correlated diffusion processesJul 07 2019Bounded diffusion processes are models of transport phenomena with wide applicability across many fields. These processes are described by their probability density functions (PDFs), which often obey Fokker-Planck equations (FPEs). While obtaining analytical ... More
Models of ConsciousnessJul 07 2019The scientific study of consciousness is a new field which has emerged as a response to groundbreaking developments in neuroscience, cognitive psychology and analytic philosophy. Its aim is to develop a scientific account, formulated in terms of formal ... More
Topological Information Data AnalysisJul 06 2019This paper presents methods that quantify the structure of statistical interactions within a given data set, and was first used in \cite{Tapia2018}. It establishes new results on the k-multivariate mutual-informations (I_k) inspired by the topological ... More
Investigating some attributes of periodicity in DNA sequences via semi-Markov modellingJul 06 2019DNA segments and sequences have been studied thoroughly during the past decades. One of the main problems in computational biology is the identification of exon-intron structures inside genes using mathematical techniques. Previous studies have used different ... More
Social inhibition maintains adaptivity and consensus of foraging honeybee swarms in dynamic environmentsJul 06 2019To effectively forage in natural environments, organisms must adapt to changes in the quality and yield of food sources across multiple timescales. Individuals foraging in groups act based on both their private observations and the opinions of their neighbors. ... More
Predicting Gene Expression Between Species with Neural NetworksJul 05 2019We train a neural network to predict human gene expression levels based on experimental data for rat cells. The network is trained with paired human/rat samples from the Open TG-GATES database, where paired samples were treated with the same compound ... More
Towards a theory of assembly of protein complexes: lessons from equilibrium statistical physicsJul 05 2019Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular functions are carried ... More
An Approximate Bayesian Approach to Surprise-Based LearningJul 05 2019Surprise-based learning allows agents to adapt quickly in non-stationary stochastic environments. Most existing approaches to surprise-based learning and change point detection assume either implicitly or explicitly a simple, hierarchical generative model ... More
A structured population model of clonal selection in acute leukemias with multiple maturation stagesJul 05 2019Recent progress in genetic techniques has shed light on the complex co-evolution of malignant cell clones in leukemias. However, several aspects of clonal selection still remain unclear. In this paper, we present a multi-compartmental continuously structured ... More
Systems biology approach to the origin of the tetrapod limbJul 05 2019It is still not understood how similar genomic sequences have generated diverse and spectacular forms during evolution. The difficulty to bridge phenotypes and genotypes stems from the complexity of multicellular systems, where thousands of genes and ... More
The Application of Information Spectrum Method on Small Molecules and Target RecognitionJul 05 2019Current methods for investigation of receptor - ligand interactions in drug discovery are based on three-dimensional complementarity of receptor and ligand surfaces, and they include pharmacophore modelling, QSAR, molecular docking etc. Those methods ... More
A Unified Framework of Online Learning Algorithms for Training Recurrent Neural NetworksJul 05 2019We present a framework for compactly summarizing many recent results in efficient and/or biologically plausible online training of recurrent neural networks (RNN). The framework organizes algorithms according to several criteria: (a) past vs. future facing, ... More
An Atomistic First-Principles Density Functional Theory Model for Single Layer Dry \textit{Stratum Corneum}Jul 04 2019Many questions concerning the biophysical and physiological properties of skin are still open. Skin aging, permeability, dermal absorption, hydration and drug transdermal delivery, are few examples of processes with its underlying mechanisms unveiled. ... More
A Cognition-Affect Integrated Model of EmotionJul 04 2019What is an emotion? an old riddle repeatedly being attempted with advance modern tools and understanding of the age. With the new advancement old theories are tested and with correction new is formed. Such is the case with defining emotion broadly shifting ... More
Evaluation of the criticality of in vitro neuronal networks: Toward an assessment of computational capacityJul 04 2019Novel computing hardwares are necessary to keep up with today's increasing demand for data storage and processing power. In this research project, we turn to the brain for inspiration to develop novel computing substrates that are self-learning, scalable, ... More
infotheory: A C++/Python package for multivariate information theoretic analysisJul 04 2019This paper introduces \texttt{infotheory}: a package that implements multivariate information theoretic measures for discrete and continuous data. This package implements widely used measures such as entropy and mutual information, as well as more recent ... More
infotheory: A C++/Python package for multivariate information theoretic analysisJul 04 2019Jul 08 2019This paper introduces \texttt{infotheory}: a package written in C++ and usable from Python and C++, for multivariate information theoretic analyses of discrete and continuous data. This package allows the user to study the relationship between components ... More
Light-Control of Localised Photo-Bio-ConvectionJul 04 2019Microorganismal motility is often characterised by complex responses to environmental physico-chemical stimuli. Although the biological basis of these responses is often not well understood, their exploitation already promises novel avenues to directly ... More
Machine learning based white matter models with permeability: An experimental study in cuprizone treated in-vivo mouse model of axonal demyelinationJul 04 2019The intra-axonal water exchange time {\tau}i, a parameter associated with axonal permeability, could be an important biomarker for understanding demyelinating pathologies such as Multiple Sclerosis. Diffusion-Weighted MRI is sensitive to changes in permeability, ... More
Dominance, Sharing, and Assessment in an Iterated Hawk--Dove GameJul 03 2019Animals use a wide variety of strategies to reduce or avoid aggression in conflicts over resources. These strategies range from sharing resources without outward signs of conflict to the development of dominance hierarchies, in which initial fighting ... More
Next Generation Radiogenomics Sequencing for Prediction of EGFR and KRAS Mutation Status in NSCLC Patients Using Multimodal Imaging and Machine Learning ApproachesJul 03 2019Aim: In the present work, we aimed to evaluate a comprehensive radiomics framework that enabled prediction of EGFR and KRAS mutation status in NSCLC cancer patients based on PET and CT multi-modalities radiomic features and machine learning (ML) algorithms. ... More
Multiplicative modulations in hue-selective cells enhance unique hue representationJul 03 2019There is still much to understand about the color processing mechanisms in the brain and the transformation from cone-opponent representations to perceptual hues. Moreover, it is unclear which areas(s) in the brain represent unique hues. We propose a ... More
One-Way Coupled Tumor Response Model for Combined-Hyperthermia-Radiotherapy Treatment with Anisotropic ScatteringJul 03 2019Therapies such as combined-hyperthermia-radiotherapy (CHR) take advantage of excellent radiosensitization properties of hyperthermia and treat of tumors with both radiation and heat. To appropriately model a CHR treatment, features like tumor heating ... More
Evolution of cooperation driven by active information spreadingJul 03 2019Cooperators forgo their interest to benefit others. Thus cooperation should not be favored by natural selection. It challenges the evolutionists, since cooperation is widespread. As one of the resolutions, information spreading has been revealed to play ... More
Model of pattern formation in marsh ecosystems with nonlocal interactionsJul 03 2019Smooth cordgrass Spartina alterniflora is a grass species commonly found in tidal marshes. It is an ecosystem engineer, capable of modifying the structure of its surrounding environment through various feedbacks. The scale-dependent feedback between marsh ... More
From voxels to pixels and back: Self-supervision in natural-image reconstruction from fMRIJul 03 2019Reconstructing observed images from fMRI brain recordings is challenging. Unfortunately, acquiring sufficient "labeled" pairs of {Image, fMRI} (i.e., images with their corresponding fMRI responses) to span the huge space of natural images is prohibitive ... More
Effect of assistive method on the sense of fulfillment with agency: Modeling with flow and attribution theoryJul 03 2019Several assistive technologies for users' operations have been recently developed. A user's sense of agency (SoA) decreases with increasing system assistance, possibly resulting in a decrease in the user's sense of fulfillment. This study aims to provide ... More
Being a leader or being the leader: The evolution of institutionalised hierarchyJul 03 2019Human social hierarchy has the unique characteristic of existing in two forms. Firstly, as an informal hierarchy where leaders and followers are implicitly defined by their personal characteristics, and secondly, as an institutional hierarchy where leaders ... More
High-Throughput Machine Learning from Electronic Health RecordsJul 03 2019The widespread digitization of patient data via electronic health records (EHRs) has created an unprecedented opportunity to use machine learning algorithms to better predict disease risk at the patient level. Although predictive models have previously ... More
Quantitative evaluation of sense of discrepancy to operation response using event-related potentialJul 03 2019This study aimed to develop a method to evaluate the sense of discrepancy to the operation response quantitatively. We examined the availability of event-related potential (P300), which is considered to reflect attention to stimulation, to evaluate the ... More
Gradient flow formulations of discrete and continuous evolutionary models: a unifying perspectiveJul 02 2019We consider three classical models of biological evolution: (i) the Moran process, an example of a reducible Markov Chain; (ii) the Kimura Equation, a particular case of a degenerated Fokker-Planck Diffusion; (iii) the Replicator Equation, a paradigm ... More
Machine Learning based Prediction of Hierarchical Classification of Transposable ElementsJul 02 2019Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a functional gene may ... More
Machine Learning based Prediction of Hierarchical Classification of Transposable ElementsJul 02 2019Jul 09 2019Transposable Elements (TEs) or jumping genes are the DNA sequences that have an intrinsic capability to move within a host genome from one genomic location to another. Studies show that the presence of a TE within or adjacent to a functional gene may ... More
Modelling the evolution of traits in a two-sex population, with an application to grandmotheringJul 02 2019We present a mathematical simplification for the evolutionary dynamics of a heritable trait within a two-sex population. This trait is assumed to control the timing of sex-specific life-history events, such as the age of sexual maturity and end of female ... More
Introducing Astrocytes on a Neuromorphic Processor: Synchronization, Local Plasticity and Edge of ChaosJul 02 2019While there is still a lot to learn about astrocytes and their neuromodulatory role associated with their spatial and temporal integration of synaptic activity, the introduction of an additional to neurons processing unit into neuromorphic hardware is ... More
Reverse engineering neural networks from many partial recordingsJul 02 2019Much of neuroscience aims at reverse engineering the brain, but we only record a small number of neurons at a time. We do not currently know if reverse engineering the brain requires us to simultaneously record most neurons or if multiple recordings from ... More
Strongly bent double-stranded DNA: reconciling theory and experimentJul 02 2019The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As the bending ... More
Cell-scale degradation of peritumoural extracellular matrix fibre network and its role within tissue-scale cancer invasionJul 02 2019Local cancer invasion of tissue is a complex, multiscale process which plays an essential role in tumour progression. Occurring over many different temporal and spatial scales, the first stage of invasion is the secretion of matrix degrading enzymes (MDEs) ... More
Cavopulmonary Support Operating Criteria for Serving the Failing Fontan Population; A Modeling InvestigatingJul 02 2019Fontan operation as the current ultimate palliation of single ventricle defects results in significant late complications eventually leading to a failing circulation. It has been suggested that introducing a cavopulmonary assist device to serve the function ... More
Mathematical Model of Emotional Habituation to Novelty: Modeling with Bayesian Update and Information TheoryJul 02 2019Novelty is an important factor of creativity in product design. Acceptance of novelty, however, depends on one's emotions. Yanagisawa, the last author, and his colleagues previously developed a mathematical model of emotional dimensions associated with ... More
Simple 1-D Convolutional Networks for Resting-State fMRI Based Classification in AutismJul 02 2019Deep learning methods are increasingly being used with neuroimaging data like structural and function magnetic resonance imaging (MRI) to predict the diagnosis of neuropsychiatric and neurological disorders. For psychiatric disorders in particular, it ... More