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Biological noise

A V Kargovsky, A Yu Chikishev, O A Chichigina
An open system that can be analyzed using the Langevin equation with multiplicative noise is considered. The stationary state of the system results from a balance of deterministic damping and random pumping simulated as noise with controlled periodicity. The dependence of statistical moments of the variable that characterizes the system on parameters of the problem is studied. A nontrivial decrease in the mean value of the main variable with an increase in noise stochasticity is revealed. Applications of the results in several physical, chemical, biological, and technical problems of natural and humanitarian sciences are discussed...
March 2018: Physical Review. E
Amit Singh Vishen, J-F Rupprecht, G V Shivashankar, J Prost, Madan Rao
We study stochastic dynamics of a point and extended inclusion within a one-dimensional confined active viscoelastic gel. We show that the dynamics of a point inclusion can be described by a Langevin equation with a confining potential and multiplicative noise. Using a systematic adiabatic elimination over the fast variables, we arrive at an overdamped equation with a proper definition of the multiplicative noise. To highlight various features and to appeal to different biological contexts, we treat the inclusion in turn as a rigid extended element, an elastic element, and a viscoelastic (Kelvin-Voigt) element...
March 2018: Physical Review. E
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
Imtiaz Awan, Wajid Aziz, Imran Hussain Shah, Nazneen Habib, Jalal S Alowibdi, Sharjil Saeed, Malik Sajjad Ahmed Nadeem, Syed Ahsin Ali Shah
Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects...
2018: PloS One
C Caranica, A Al-Omari, Z Deng, J Griffith, R Nilsen, L Mao, J Arnold, H-B Schüttler
A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data...
2018: PloS One
Sevdenur Keskin, Gnanapackiam S Devakanmalai, Soo Bin Kwon, Ha T Vu, Qiyuan Hong, Yin Yeng Lee, Mohammad Soltani, Abhyudai Singh, Ahmet Ay, Ertuğrul M Özbudak
Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of expression variability, we studied a biological clock, the vertebrate segmentation clock, controlling the precise spatiotemporal patterning of the vertebral column. By counting single transcripts of segmentation clock genes in zebrafish, we show that clock genes have low RNA amplitudes and expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling...
May 15, 2018: Cell Reports
Brian K Taylor
Diverse taxa use Earth's magnetic field in conjunction with other sensory modalities to accomplish navigation tasks ranging from local homing to long-distance migration across continents and ocean basins. However, despite extensive research, the mechanisms that underlie animal magnetoreception are not clearly understood, and how animals use Earth's magnetic field to navigate is an active area of investigation. Concurrently, Earth's magnetic field offers a signal that engineered systems can leverage for navigation in environments where man-made systems such as GPS are unavailable or unreliable...
May 15, 2018: Bioinspiration & Biomimetics
Suresh K Vasa, Petra Rovó, Rasmus Linser
Solid-state nuclear magnetic resonance (ssNMR) is a spectroscopic technique that is used for characterization of molecular properties in the solid phase at atomic resolution. In particular, using the approach of magic-angle spinning (MAS), ssNMR has seen widespread applications for topics ranging from material sciences to catalysis, metabolomics, and structural biology, where both isotropic and anisotropic parameters can be exploited for a detailed assessment of molecular properties. High-resolution detection of protons long represented the holy grail of the field...
May 15, 2018: Accounts of Chemical Research
Shunqi Zhang, Tao Yin, Zhipeng Liu
Detecting and imaging method of biological electrical characteristics based on magneto-acoustic coupling effect gives valuable information of tissue in early tumor diagnosis and bioelectrical current monitoring. Normal exciting and receiving method is to use single pulse. In this method the signal to noise ratio (SNR) is limited, so the imaging quality and imaging speed are low. In this study, we propose a processing method based on coded excitation to improve SNR and shorten the processing time. The processing method using 13 bit Barker coded excitation and 16 bit Golay code excitation are studied by simulation and experiments...
October 1, 2017: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
Xiaomei Kang, Qingqun Kong, Yi Zeng, Bo Xu
Compared to computer vision systems, the human visual system is more fast and accurate. It is well accepted that V1 neurons can well encode contour information. There are plenty of computational models about contour detection based on the mechanism of the V1 neurons. Multiple-cue inhibition operator is one well-known model, which is based on the mechanism of V1 neurons' non-classical receptive fields. However, this model is time-consuming and noisy. To solve these two problems, we propose an improved model which integrates some additional other mechanisms of the primary vision system...
2018: Frontiers in Computational Neuroscience
Jennifer N Phillips, Elizabeth P Derryberry
Animals modify acoustic communication signals in response to noise pollution, but consequences of these modifications are unknown. Vocalizations that transmit best in noise may not be those that best signal male quality, leading to potential conflict between selection pressures. For example, slow paced, narrow bandwidth songs transmit better in noise but are less effective in mate choice and competition than fast paced, wide bandwidth songs. We test the hypothesis that noise affects response to song pace and bandwidth in the context of competition using white-crowned sparrows (Zonotrichia leucophrys)...
May 14, 2018: Scientific Reports
Chan-Il Kim, Jong-Ha Lee
In these days, wearable devices have been developed for effectively measuring biological data. However, these devices have tissue allege and noise problem. To solve these problems, biometric measurement based on a non-contact method, such as face image sequencing is developed. This makes it possible to measure biometric data without any operation and side effects. However, it is impossible for a remote center to identify the person whose data are measured by the novel methods. In this paper, we propose the novel non-contact heart rate and blood pressure imaging system, Deep Health Eye...
April 25, 2018: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
Dirk Schreckenberg, Christin Belke, Jan Spilski
In 2001, Team#6 of the International Commission on Biological Effects of Noise (ICBEN) recommended the use of two single international standardised questions and response scales. This recommendation has been widely accepted in the scientific community. Nevertheless, annoyance can be regarded as a multidimensional construct comprising the three elements: (1) experience of an often repeated noise-related disturbance and the behavioural response to cope with it, (2) an emotional/attitudinal response to the sound and its disturbing impact, and (3) the perceived control or coping capacity with regard to the noise situation...
May 12, 2018: International Journal of Environmental Research and Public Health
Maike M K Hansen, Winnie Y Wen, Elena Ingerman, Brandon S Razooky, Cassandra E Thompson, Roy D Dar, Charles W Chin, Michael L Simpson, Leor S Weinberger
Diverse biological systems utilize fluctuations ("noise") in gene expression to drive lineage-commitment decisions. However, once a commitment is made, noise becomes detrimental to reliable function, and the mechanisms enabling post-commitment noise suppression are unclear. Here, we find that architectural constraints on noise suppression are overcome to stabilize fate commitment. Using single-molecule and time-lapse imaging, we find that-after a noise-driven event-human immunodeficiency virus (HIV) strongly attenuates expression noise through a non-transcriptional negative-feedback circuit...
May 4, 2018: Cell
Nicole De March, Sandra Denise Prado, Leon G Brunnet
Assuming the selectivity filter of KcsA potassium ion channel may exhibit quantum coherence, we extend a previous model by Vaziri \& Plenio to take into account Coulomb repulsion between potassium ions. We show that typical ion transit timescales are determined by this interaction, which imposes optimal input/output parameter ranges. Also, as observed in other examples of quantum tunneling in biological systems, addition of moderate noise helps coherent ion transport.
May 11, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Mahmoud K Madi, Fadi N Karameh
Many physical models of biological processes including neural systems are characterized by parametric nonlinear dynamical relations between driving inputs, internal states, and measured outputs of the process. Fitting such models using experimental data (data assimilation) is a challenging task since the physical process often operates in a noisy, possibly non-stationary environment; moreover, conducting multiple experiments under controlled and repeatable conditions can be impractical, time consuming or costly...
May 11, 2018: Journal of Neural Engineering
Chao Zhang, Maryam Rabiee, Erfan Sayyari, Siavash Mirarab
BACKGROUND: Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees from gene trees while accounting for gene tree discordance. ASTRAL uses dynamic programming to search for the tree that shares the maximum number of quartet topologies with input gene trees, restricting itself to a predefined set of bipartitions. RESULTS: We introduce ASTRAL-III, which substantially improves the running time of ASTRAL-II and guarantees polynomial running time as a function of both the number of species (n) and the number of genes (k)...
May 8, 2018: BMC Bioinformatics
Huaiming Li, Dandan Yan, Hai Liu
Through magnetic resonance electrical properties tomography (MR-EPT), electrical conductivity and permittivity of biological tissues could be reconstructed based on radio frequency field of magnetic resonance imaging (MRI) system. High precision and high resolution image could be obtained without current injection. In this study, XFDTD software was used to establish a finite element model of the human breast. Simulation was delivered at the Larmor frequency of 128 MHz by a 16-channel radio frequency coil. Conductivity and permittivity of the mammary tissue was reconstructed according to the B 1 + field's amplitude and phase of forward problem...
August 1, 2017: Sheng Wu Yi Xue Gong Cheng Xue za Zhi, Journal of Biomedical Engineering, Shengwu Yixue Gongchengxue Zazhi
Alberto Sosa-Costa, Izabela K Piechocka, Lucia Gardini, Francesco S Pavone, Marco Capitanio, Maria F Garcia-Parajo, Carlo Manzo
Time traces obtained from a variety of biophysical experiments contain valuable information on underlying processes occurring at the molecular level. Accurate quantification of these data can help explain the details of the complex dynamics of biological systems. Here, we describe PLANT (Piecewise Linear Approximation of Noisy Trajectories), a segmentation algorithm that allows the reconstruction of time-trace data with constant noise as consecutive straight lines, from which changes of slopes and their respective durations can be extracted...
May 8, 2018: Biophysical Journal
Rui Chen, Shuhao Shen, Nanguang Chen
A spatiotemporal phase modulator (STPM) is theoretically investigated using the vectorial diffraction theory. The STPM is equivalent to a time-dependent phase-only pupil filter that alternates between a homogeneous filter and a stripe-shaped filter with a sinusoidal phase distribution. It is found that two-photon focal modulation microscopy (TPFMM) using this STPM can significantly suppress the background contribution from out-of-focus ballistic excitation and achieve almost the same resolution as two-photon microscopy...
May 2018: Journal of Biomedical Optics
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