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Biological noise

Yangxiaolu Cao, Allison Lopatkin, Lingchong You
Oscillations in time and space are ubiquitous in nature and play critical roles in dynamic cellular processes. Although the molecular mechanisms underlying the generation of the dynamics are diverse, several distinct regulatory elements have been recognized as being critical in producing and modulating oscillatory dynamics. These include negative and positive feedback, time delay, nonlinearity in regulation, and random fluctuations ('noise'). Here we discuss the specific roles of these five elements in promoting or attenuating oscillatory dynamics, by drawing on insights from quantitative analyses of natural or synthetic biological networks...
December 6, 2016: Nature Structural & Molecular Biology
Yitan Zhu, Niya Wang, David J Miller, Yue Wang
Blind Source Separation (BSS) is a powerful tool for analyzing composite data patterns in many areas, such as computational biology. We introduce a novel BSS method, Convex Analysis of Mixtures (CAM), for separating non-negative well-grounded sources, which learns the mixing matrix by identifying the lateral edges of the convex data scatter plot. We propose and prove a sufficient and necessary condition for identifying the mixing matrix through edge detection in the noise-free case, which enables CAM to identify the mixing matrix not only in the exact-determined and over-determined scenarios, but also in the under-determined scenario...
December 6, 2016: Scientific Reports
Jeroen J A van Boxtel, Yujia Peng, Junzhu Su, Hongjing Lu
Human actions are rich in social cues and play an essential role in interacting with the social environment. Hence, the perception of biological motion (i.e., movement elicited by humans and other animals) is considered to be an important gauge of a person's social cognition capacities. It has been well-documented that Autism Spectrum Disorder (ASD) is associated with difficulties in social interactions. In the present study, we examined whether individual differences in biological motion perception relate to the degree of autistic traits among people in the typically-developing population...
December 2, 2016: Vision Research
Ross H Johnstone, Rémi Bardenet, David J Gavaghan, Gary R Mirams
Dose-response (or 'concentration-effect') relationships commonly occur in biological and pharmacological systems and are well characterised by Hill curves. These curves are described by an equation with two parameters: the inhibitory concentration 50% (IC50); and the Hill coefficient. Typically just the 'best fit' parameter values are reported in the literature. Here we introduce a Python-based software tool, PyHillFit , and describe the underlying Bayesian inference methods that it uses, to infer probability distributions for these parameters as well as the level of experimental observation noise...
2016: Wellcome Open Res
Tsung-Chih Wu, Chi-Hsiang Chen, Nai-Wen Yi, Pei-Chen Lu, Shan-Chi Yu, Chien-Peng Wang
Identifying, evaluating, and controlling workplace hazards are important functions of safety professionals (SPs). The purpose of this study was to investigate the content and frequency of hazard management dealt by safety professionals in colleges. The authors also explored the effects of organizational factors/individual factors on SPs' perception of frequency of hazard management. The researchers conducted survey research to achieve the objective of this study. The researchers mailed questionnaires to 200 SPs in colleges after simple random sampling, then received a total of 144 valid responses (response rate = 72%)...
December 3, 2016: International Journal of Environmental Research and Public Health
Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo
The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end...
2016: PloS One
Ahmad Haider, Daniel Potter, Todd A Sulchek
Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
Xue Yang, Yajia Hu, Gang Li, Ling Lin
There exist lots of difficulties in optical transillumination of biological tissues, especially, low-level-light detection and low gray-scale resolution could reduce recognition accuracy of differences in tissue. Aiming at the problems, this paper proposes a method for optical transillumination using sawtooth-shaped-function optical signal and frame accumulation technology to explore the spatial information of heterogeneity in the tissue. Sawtooth-shaped-function optical signal combined with frame accumulation technology is applied to realize the low-level-light image detection, where frame accumulation technology improves the signal-to-noise ratio and detection sensitivity, and sawtooth-shaped-function signal improves gray-scale resolution...
November 2016: Review of Scientific Instruments
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
Meltem Isik, T Keith Blackwell, Eugene Berezikov
Diverse stresses and aging alter expression levels of microRNAs, suggesting a role for these posttranscriptional regulators of gene expression in stress modulation and longevity. Earlier studies demonstrated a central role for the miR-34 family in promoting cell cycle arrest and cell death following stress in human cells. However, the biological significance of this response was unclear. Here we show that in C. elegans mir-34 upregulation is necessary for developmental arrest, correct morphogenesis, and adaptation to a lower metabolic state to protect animals against stress-related damage...
December 1, 2016: Scientific Reports
Hannah Lee, Jejoong Kim
It has been reported that visual perception can be influenced not only by the physical features of a stimulus but also by the emotional valence of the stimulus, even without explicit emotion recognition. Some previous studies reported an anger superiority effect while others found a happiness superiority effect during visual perception. It thus remains unclear as to which emotion is more influential. In the present study, we conducted two experiments using biological motion (BM) stimuli to examine whether emotional valence of the stimuli would affect BM perception; and if so, whether a specific type of emotion is associated with a superiority effect...
November 29, 2016: Perception
Julian Sorrensen, Lukasz Wiklendt, Tim James Hibberd, Marcello C Costa, Nick J Spencer
Calcium imaging is commonly used to record dynamic changes in excitability from axons or cell bodies in the nervous system of vertebrates. These recordings often reveal discrete calcium transients which have variable amplitudes, durations, and rates-of-rise and decay, all of which can arise from an unstable, or "noisy" baseline. This often leads to considerable ambiguity about how to discriminate and quantify calcium transients. We describe an analytical methodology that objectively identifies multiple calcium transients from multiple recording sites and quantifies the degree of temporal synchrony between each event...
November 30, 2016: Journal of Neurophysiology
Kazunari Iwamoto, Yuki Shindo, Koichi Takahashi
Cellular heterogeneity, which plays an essential role in biological phenomena, such as drug resistance and migration, is considered to arise from intrinsic (i.e., reaction kinetics) and extrinsic (i.e., protein variability) noise in the cell. However, the mechanistic effects of these types of noise to determine the heterogeneity of signal responses have not been elucidated. Here, we report that the output of epidermal growth factor (EGF) signaling activity is modulated by cellular noise, particularly by extrinsic noise of particular signaling components in the pathway...
November 2016: PLoS Computational Biology
Tuan Trieu, Jianlin Cheng
The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data...
November 29, 2016: Nucleic Acids Research
Pablo Cordero, Joshua M Stuart
The availability of gene expression data at the single cell level makes it possible to probe the molecular underpinnings of complex biological processes such as differentiation and oncogenesis. Promising new methods have emerged for reconstructing a progression 'trajectory' from static single-cell transcriptome measurements. However, it remains unclear how to adequately model the appreciable level of noise in these data to elucidate gene regulatory network rewiring. Here, we present a framework called Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR) that infers progressions from static single-cell transcriptomes by employing a continuous parametrization of Gaussian mixtures in high-dimensional curves...
2016: Pacific Symposium on Biocomputing
Yulong Sun, Dijie Li, Ru Zhang, Shang Peng, Ge Zhang, Tuanming Yang, Airong Qian
Natural antisense transcripts, originally considered as transcriptional noises arising from so-called "junk DNA", are recently recognized as important modulators for gene regulation. They are prevalent in nearly all realms of life and have been found to modulate gene expression positively or negatively. By affecting almost all stages of gene expression range from pre-transcriptional, transcriptional and post-transcriptional to translation, NATs are fundamentally involved in various biological processes. However, compared to increasing huge data from transcriptional analysis especially high-throughput sequencing technologies (such as RNA-seq), limited functional NATs (around 70) are so far reported, which hinder our advanced comprehensive understanding for this field...
November 25, 2016: Biochimie
Viktor Jonsson, Tobias Österlund, Olle Nerman, Erik Kristiansson
Metagenomics is the study of microorganisms in environmental and clinical samples using high-throughput sequencing of random fragments of their DNA. Since metagenomics does not require any prior culturing of isolates, entire microbial communities can be studied directly in their natural state. In metagenomics, the abundance of genes is quantified by sorting and counting the DNA fragments. The resulting count data are high-dimensional and affected by high levels of technical and biological noise that make the statistical analysis challenging...
November 28, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Silvia Viciani, Stefano Gherardini, Manuela Lima, Marco Bellini, Filippo Caruso
Transport phenomena represent a very interdisciplinary topic with applications in many fields of science, such as physics, chemistry, and biology. In this context, the possibility to design a perfectly controllable experimental setup, where to tune and optimize its dynamics parameters, is a challenging but very relevant task to emulate, for instance, the transmission of energy in light harvesting processes. Here, we experimentally build a scalable and controllable transport emulator based on optical fiber cavity networks where the system noise parameters can be finely tuned while maximizing the transfer efficiency...
November 25, 2016: Scientific Reports
Mark Brink, Dirk Schreckenberg, Danielle Vienneau, Christian Cajochen, Jean-Marc Wunderli, Nicole Probst-Hensch, Martin Röösli
The type of noise annoyance scale and aspects of its presentation such as response format or location within a questionnaire and other contextual factors may affect self-reported noise annoyance. By means of a balanced experimental design, the effect of type of annoyance question and corresponding scale (5-point verbal vs. 11-point numerical ICBEN (International Commission on Biological Effects of Noise) scale), presentation order of scale points (ascending vs. descending), question location (early vs. late within the questionnaire), and survey season (autumn vs...
November 23, 2016: International Journal of Environmental Research and Public Health
Robert W Smith, Britta Helwig, Adrie H Westphal, Eran Pel, Maximilian Hörner, Hannes M Beyer, Sophia L Samodelov, Wilfried Weber, Matias D Zurbriggen, Jan Willem Borst, Christian Fleck
BACKGROUND: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states...
November 25, 2016: BMC Systems Biology
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