Split (1)

train · 127k rows

text large_stringlengths 7 3.02k
To extract accurate speaker information for text-independent speaker verification, temporal dynamic CNNs (TDY-CNNs) adapting kernels to each time bin was proposed. However, model size of TDY-CNN is too large and the adaptive kernel's degree of freedom is limited.
We present a fully on-device streaming Speech2Speech conversion model that normalizes a given input speech directly to synthesized output speech. Deploying such a model on mobile devices pose significant challenges in terms of memory footprint and computation requirements.
Congenital heart disease (CHD) is a critical condition that demands early detection, particularly in infancy and childhood. This study presents a deep learning model designed to detect CHD using phonocardiogram (PCG) signals, with a focus on its application in global health.
In this study, we present recent developments of models trained with the RNN-T loss in ESPnet. It involves the use of various architectures such as recently proposed Conformer, multi-task learning with different auxiliary criteria and multiple decoding strategies, including our own proposition.
Recent advances in flexible keyword spotting (KWS) with text enrollment allow users to personalize keywords without uttering them during enrollment. However, there is still room for improvement in target keyword performance.
The aim of the Detection and Classification of Acoustic Scenes and Events Challenge Task 4 is to evaluate systems for the detection of sound events in domestic environments using an heterogeneous dataset. The systems need to be able to correctly detect the sound events present in a recorded audio clip, as well as loca...
Room geometry inference algorithms rely on the localization of acoustic reflectors to identify boundary surfaces of an enclosure. Rooms with highly absorptive walls or walls at large distances from the measurement setup pose challenges for such algorithms.
Local changes in pH are known to significantly alter the state and activity of proteins and in particular enzymes. pH variations induced by pulses propagating along soft interfaces (e.g. the lipid bilayer) would therefore constitute an important pillar towards a new physical mechanism of biochemical regulation and bio...
Thermophoresis moves molecules along temperature gradients, typically from hot to cold. We superpose fluid flow with thermophoretic molecule flow under well defined microfluidic conditions, imaged by fluorescence microscopy.
Movement behavior of an indicator species, zebrafish (Danio rerio), was analyzed with one- and two-individual groups before and after treatment with a toxic chemical, formaldehyde, at a low concentration (1 ppm). After the boundary area had been determined based on experimental data, intermittency was defined as the p...
Intrinsically disordered proteins and regions are increasingly appreciated for their abundance in the proteome and the many functional roles they play in the cell. In this short review, we describe a variety of approaches used to obtain biological insight from the structural ensembles of disordered proteins, regions, ...
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and replicate DNA.
The bioprotective nature of disaccharides is hypothesized to derive from the modification of the hydrogen bonding network of water which protects biomolecules through lowered water activity at the protein interface. Using ultrafast fluorescence spectroscopy we measured the relaxation of bulk water dynamics around the ...
The Electron Paramagnetic Spectroscopy (EPR) is the most direct and powerful method for the detection and identification of free radicals and other species with unpaired electrons. Statistics disorders are a common gynaecological disorder occurring in women.
We generalize a model of Haeussler and von der Malsburg which describes the self-organized generation of retinotopic projections between two one-dimensional discrete cell arrays on the basis of cooperative and competitive interactions of the individual synaptic contacts. Our generalized model is independent of the spe...
Antibody drugs are usually formulated as highly-concentrated solutions, which would easily generate oligomer and aggregation, resulting in loss of efficacy. Although low pH increases the colloidal dispersion of antibodies, acid denaturation can be an issue.
Accurate assessment of the antibacterial activity of graphene requires consideration of both the graphene fabrication method and, for supported films, the properties of the substrate. Large-area graphene films produced by chemical vapor deposition were grown directly on copper substrates or transferred on a gold subst...
In this work, we look at the symmetry of normal modes in symmetric structures, particularly structures with cyclic symmetry. We show that normal modes of symmetric structures have different levels of symmetry, or symmetricity.
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the model successfully reproduces some of the observed properties of real syste...
Enormous progress have been made in the last 20 years since the publication of our review \cite{csk05polrev} in this journal on transport and traffic phenomena in biology. In this brief article we present a glimpse of the major advances during this period.
The integration of motile cells into biohybrid microrobots offers unique properties such as sensitive responses to external stimuli, resilience, and intrinsic energy supply. Here we study biohybrid microtransporters that are driven by amoeboid Dictyostelium discoideum cells and explore how the speed of transport and t...
Phylogenetic studies show that horizontal gene transfer (HGT) is a significant contributor to genetic variability of prokaryotes, and was perhaps even more abundant during early evolution. Hitherto, research of natural HGT has mainly focused on three mechanisms: conjugation, natural competence, and viral transduction....
Muscle cells with sarcomeric structure exhibit highly nontrivial passive mechanical response. The difficulty of its continuum modeling is due to the presence of long-range interactions transmitted by extended protein skeleton.
Organic molecules are widely present in the dense interstellar medium, and many have been synthesized in the laboratory on Earth under the conditions typical for an interstellar environment. Until now, however, only relatively small molecules of biological interest have been demonstrated to form experimentally under t...
Temperature sensing is a ubiquitous cell behavior, but the fundamental limits to the precision of temperature sensing are poorly understood. Unlike in chemical concentration sensing, the precision of temperature sensing is not limited by extrinsic fluctuations in the temperature field itself.
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours.
Evolving systems, be it an antibody repertoire in the face of mutating pathogens or a microbial population exposed to varied antibiotics, constantly search for adaptive solutions in time-varying fitness landscapes. Generalists correspond to genotypes that remain fit across diverse selective pressures; cross-reactive a...
Artificial analogues of the natural nucleic acids have attracted recent interest as a diverse class of information storage molecules capable of self-replication. In the present study, we use the computational potential energy landscape framework to investigate the structural and dynamical properties of xylo- and deoxy...
Globular proteins undergo thermal fluctuations in solution, while maintaining an overall well-defined folded structure. In particular, studies have shown that the core structure of globular proteins differs in small, but significant ways when they are solved by x-ray crystallography versus solution-based NMR spectrosc...
In this letter, we point out the inaccurate figures in a letter by Peyrard and Bishop, who investigated the statistical mechanics of a nonlinear model for DNA denaturation. We give the correct figures.
The collective motion of groups of animals emerges from the net effect of the interactions between individual members of the group. In many cases, such as birds, fish, or ungulates, these interactions are mediated by sensory stimuli that predominantly arise from nearby neighbors.
We study the evolution of asexual microorganisms with small mutation rate in fluctuating environments, and develop techniques that allow us to expand the formal solution of the evolution equations to first order in the mutation rate. Our method can be applied to both discrete time and continuous time systems.
Some dividing cells sense their shape by becoming polarized along their long axis. Cell polarity is controlled in part by polarity proteins like Rho GTPases cycling between active membrane-bound forms and inactive cytosolic forms, modeled as a "wave-pinning" reaction-diffusion process.
Electronic circuits are useful tools for studying potential dynamical behaviors of synthetic genetic networks. The circuit models are complementary to numerical simulations of the networks, especially providing a framework for verification of dynamical behaviors in the presence of intrinsic and extrinsic noise of the ...
Biological functions in each animal cell depend on coordinated operations of a wide variety of molecular motors. Some of the these motors transport cargo to their respective destinations whereas some others are mobile workshops which synthesize macromolecules while moving on their tracks.
Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species:
Refractive index of tubulin is an important parameter underlying fundamental electromagnetic and biophysical properties of microtubules - protein fibers essential for several cell functions including cell division. Yet, the only experimental data available in the current literature show values of tubulin refractive in...
The protein dynamical transition is investigated as a function of protein structure using terahertz time domain spectroscopy (THz-TDS). Measurements performed for native state and denatured hen egg white lysozyme (HEWL) show that protein structure is not necessary for the dynamical transition.
Cells are modeled with spherical grains connected each other. Each cell can shrink and swell by transporting its fluid content to other connected neighbor while still maintaining its density at constant value.
Atrial fibrillation is one of the most frequent cardiac arrhythmias in the industrialized world and ablation therapy is the method of choice for many patients. However, ablation scars alter the electrophysiological activation and the mechanical behavior of the affected atria.
Photosynthetic algae play a significant role in oceanic carbon capture. Their performance, however, is constantly challenged by fluctuations in environmental light conditions.
The high internal quantum efficiency observed in higher plants remains an outstanding problem in understanding photosynthesis. Several approaches such as quantum entanglement and quantum coherence have been explored.
The ability of many living systems to actively self-propel underlies critical biomedical, environmental, and industrial processes. While such active transport is well-studied in uniform settings, environmental complexities such as geometric constraints, mechanical cues, and external stimuli such as chemical gradients ...
A model of coupled molecular oscillators is proposed to study nonequilibrium thermodynamics of synchronization. We find that synchronization of nonequilibrium oscillators costs energy even when the oscillator-oscillator coupling is conservative.
Stochastic resonance (SR) is a well known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic noise.
Associative polymers with sticker-and-spacer architectures undergo phase transitions that combine phase separation and bond percolation. Here, we generalize mean-field models for bond percolation and extract effective sticker interaction strengths from experimental data for specific proteins.
We generated a computational approach to analyze the biomechanics of epithelial cell aggregates, either island or stripes or entire monolayers, that combines both vertex and contact-inhibition-of-locomotion models to include both cell-cell and cell-substrate adhesion. Examination of the distribution of cell protrusion...
The alarming growth of the antibiotic-resistant superbugs methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) is driving the development of new technologies to investigate antibiotics and their modes of action. We report the label-free detection of vancomycin binding to bacte...
Anomalously slow passive diffusion, $\langle \delta x^2(t)\rangle\simeq t^{\alpha}$, with $0<\alpha<1$, of larger tracers such as messenger RNA and endogenous submicron granules in the cytoplasm of living biological cells has been demonstrated in a number of experiments and has been attributed to the viscoelastic...
Molecular adhesion plays a central role in many biological systems, yet existing methods to quantify adhesive strength often struggle to bridge the gap between single-molecule resolution and biologically relevant environments. Here, we present a scalable micromagnetic bead-based adhesion assay capable of quantifying d...
Photosystem I is a protein-pigment complex that performs photosynthesis in plants, green algae, and cyanobacteria. It contains an aggregate of chlorophylls that absorbs light and delivers the resulting electronic excitation to the special pair of chlorophylls where the excitation energy is used for producing charge se...
Interruptions in nonlinear wave propagation, commonly referred to as wave breaks, are typical of many complex excitable systems. In the heart they lead to fatal rhythm disorders, the so-called arrhythmias, which are one of the main causes of sudden death in the industrialized world.
Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Fluid dynamics predicts this circular motion to be clockwise (CW) above a rigid surface (when viewed from inside the fluid) and counter-clockwise (CCW) below a free surface.
As two-dimensional fluid shells, lipid bilayer membranes resist bending and stretching but are unable to sustain shear stresses. This property gives membranes the ability to adopt dramatic shape changes.
We studied the effect of additive and multiplicative noises on the growth of a tumor based on a logistic growth model. The steady-state probability distribution and the average population of the tumor cells were given to explain the important roles of correlated noises in the tumor growth.
Sperm are propelled by bending waves travelling along the flagellum. During steering in gradients of sensory cues, sperm adjust the flagellar beat waveform.
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between open and closed regions of the DNA chain.
Synthetic lipid membranes can display channel-like ion conduction events even in the absence of proteins. We show here that these events are voltage-gated with a quadratic voltage dependence as expected from electrostatic theory of capacitors.
Male reproductive health in both humans and animals is an important research field in biological study. In order to characterize the morphology, the motility and the concentration of the sperm cells, which are the most important parameters to feature them, digital holography demonstrated to be an attractive technique....
We introduce a model for the global optimization problem of nectar harvesting by flower visitors, e.g., nectar-feeding bats, as a generalization of the (multiple) traveling-salesperson problem (TSP). The model includes multiple independent animals and many flowers with time-dependent content.
The $\beta$-relaxation associated with the sub-glass transition temperature ($T_{\text{g},\beta}$) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature ($T_{g\alpha}$). Despite $T_{\text{g},\beta}$ being observed well-below storage temperatures, the $\beta$-...
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in protein devices. By studying two different model protein machines, with different bi...
Dynamic patterning of specific proteins is essential for the spatiotemporal regulation of many important intracellular processes in procaryotes, eucaryotes, and multicellular organisms. The emergence of patterns generated by interactions of diffusing proteins is a paradigmatic example for self-organization.
Methods for time series prediction and classification of gene regulatory networks (GRNs) from gene expression data have been treated separately so far. The recent emergence of attention-based recurrent neural networks (RNN) models boosted the interpretability of RNN parameters, making them appealing for the understand...
Complex systems with global interactions tend to be stable if interactions between components are sufficiently homogeneous. In biological systems, which often have small copy numbers and interactions mediated by diffusing agents, noise and non-locality may affect stability.
Single strand breaks are induced in DNA plasmids, pBR322 and pUC19, in aqueous media exposed to strong fields generated using ultrashort laser pulses (820 nm wavelength, 45 fs pulse duration, 1 kHz repetition rate) at intensities of 1-12 TW cm$^{-2}$. The strong fields generate, {\it in situ}, electrons and radicals t...
A technology for recording electrical activity of large neuron populations at arbitrary depth in brain tissues with less than cell spatial and millisecond temporal resolutions was the most craving dream of neuroscientists and a long pursued goal of engineers for decades. Even though many imaging techniques have been d...
Collective behavior in cellular populations is coordinated by biochemical signaling networks within individual cells. Connecting the dynamics of these intracellular networks to the population phenomena they control poses a considerable challenge because of network complexity and our limited knowledge of kinetic parame...
The bodies of snakes, such as king cobras, are very soft so that it is nearly impossible for them to raise their heads higher than around one meter. By direct measurement, we were only possible to hold the body of a freshly killed cobra vertically at around 0.05 m.
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, $\Delta G$ (phosphorylation potential), ...
We present two methods to reveal protein-ligand unbinding mechanisms in biased unbinding simulations by clustering trajectories into ensembles representing unbinding paths. The first approach is based on a contact principal component analysis for reducing the dimensionality of the input data, followed by identificatio...
The iron stress-induced protein A (IsiA) is a source of interest and debate in biological research. The IsiA super-complex, binding over 200 chlorophylls, assembles in multimeric rings around photosystem I (PSI).
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyse for which types of sequences a particularly simple landscape st...
The hydrodynamic drag at a lipid bilayer surface determines in part the flow properties of suspensions of cells and liposomes. Given the fluidity of lipid bilayers, it is not obvious a priori whether solid-like no-slip, liquid-like no-stress, or intermediate boundary conditions apply at the water-bilayer interface.
Silicon nanowires have been surface functionalized with the enzyme urease for biosensor applications to detect and quantify urea concentration. The device is nanofabricated from a silicon on insulator (SOI) wafer with a top down lithography approach.
I use a mean-field approximation to show the rapid collapse of heteropolymers from random walk size to a much smaller, molten globule state due to hydrophobic interactions, to be followed by a slower annealing process in which there is little change in overall size.
Biological mixtures, such as the cellular cytoplasm, are composed of a large number of different components. From this heterogeneity, ordered mesoscopic structures emerge, such as liquid phases with controlled composition.
Cell proliferation, apoptosis, and myosin-dependent contraction can generate elastic stress and strain in living tissues, which may be dissipated by internal rearrangement through cell topological transition and cytoskeletal reorganization. Moreover, cells and tissues can change their sizes in response to mechanical c...
The chromosomal DNA of bacteria is folded into a compact body called the nucleoid, which is composed essentially of DNA (80%), RNA (10%), and a number of different proteins (10%). These nucleoid proteins act as regulators of gene expression and influence the organization of the nucleoid by bridging, bending, or wrappi...
In contexts ranging from embryonic development to bacterial ecology, cell populations migrate chemotactically along self-generated chemical gradients, often forming a propagating front. Here, we theoretically show that the stability of such chemotactic fronts to morphological perturbations is determined by limitations...
Surface molecules, distributed in diverse patterns and clusters on cell membranes, influence vital functions of living cells. It is therefore important to understand their molecular surface organisation under different physiological and pathological conditions.
One of the most impressive features of moving animal groups is their ability to perform sudden coherent changes in travel direction. While this collective decision can be a response to an external perturbation, such as the presence of a predator, recent studies show that such directional switching can also emerge from...
Self-replicability is the unique attribute observed in all the living organisms and the question how the life was physically initiated could be equivalent to the question how self-replicating informative polymers were formed in the abiotic material world. It has been suggested that the present DNA and proteins world w...
The study of microorganisms, or microbiology, has demonstrated significant development since its inception and is currently a key field of biological sciences that has a huge impact on modern society and scientific research. Over the centuries, this discipline has undergone significant changes, shaping our understandi...
We present a new theory for modeling forced indentation spectral lineshapes of biological particles, which considers non-linear Hertzian deformation due to an indenter-particle physical contact and bending deformations of curved beams modeling the particle structure. The bending of beams beyond the critical point trig...
Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property of the network, regardless of complexity.
A classification in universality classes of broad categories of phenomenologies, belonging to different disciplines, may be very useful for a crossfertilization among them and for the purpose of pattern recognition. We present here a simple scheme for the classification of nonlinear growth problems.
Chaperone-assisted translocation through a nanopore embedded in membrane holds a prominent role in the transport of biopolymers. Inspired by classical Brownian ratchet, we develop a theoretical framework characterizing such translocation process through a master equation approach.
A spiking neuron ``computes'' by transforming a complex dynamical input into a train of action potentials, or spikes. The computation performed by the neuron can be formulated as dimensional reduction, or feature detection, followed by a nonlinear decision function over the low dimensional space.
Motivated by recent experimental developments in functional genomics, we construct and test a numerical technique for inferring it process pathways, in which one process calls another process, from time series data. We validate using a case in which data are readily available and formulate an extension, appropriate fo...
We present a novel machine learning architecture for classification suggested by experiments on olfactory systems. The network separates input stimuli, represented as spatially distinct currents, via winnerless competition---a process based on the intrinsic sequential dynamics of the neural system---then uses a suppor...
It is shown that at low temperatures and moderate electron dephasing the electron transmission function reveales a structure containing information about donor/acceptor sites effectively participating in the electron transfer (ET) processes and primary pathways of electrons tunneling through molecular bridges in macrom...
The primary and metastatic stages of BC consider different cancerous cell lines (MDAs), meaning the highest number of cells in this research (300,000) represents the metastatic stages of BC, and 50,000 represents the primary level of BC developments have been studied based on fluorescence-enhanced photodynamic characte...
A network of propagating nonlinear oscillatory modes (waves) in the human brain is shown to generate collectively synchronized spiking activity (hypersynchronous spiking) when both amplitude and phase coupling between modes are taken into account. The nonlinear behavior of the modes participating in the network are th...
Eukarya and Bacteria are the most evolutionarily distant domains of life, which is reflected by differences in their cellular structure and physiology. For example, Eukarya feature membrane-bound organelles such as nuclei and mitochondria, whereas Bacteria have none.
We present a local spread model of disease transmission on a regular network and compare different control options ranging from treating the whole population to local control in a well-defined neighborhood of an infectious individual. Comparison is based on a total cost of epidemic, including cost of palliative treatm...
Confluent populations of elongated cells give rise to ordered patterns seen in nematic phase liquid crystals. We correlate cell elongation and intercellular distance with intercellular alignment using an amorphous spin glass model.
Significant variations of delays among connecting neurons cause an inevitable disadvantage of asynchronous brain dynamics compared to synchronous deep learning. However, this study demonstrates that this disadvantage can be converted into a computational advantage using a network with a single output and M multiple de...
A very high rate for cyclic electron flow (CEF) around PSI (~180 s-1 or 210 s-1 in minimum medium or in the presence of a carbon source respectively) is measured in the presence of methyl viologen (MV) in intact cells of Chlamydomonas reinhardtii under anaerobic conditions. The observation of an efficient CEF in the p...
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt...

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.