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Biological noise

Marco Grisi, Franck Vincent, Beatrice Volpe, Roberto Guidetti, Nicola Harris, Armin Beck, Giovanni Boero
Nuclear magnetic resonance (NMR) spectroscopy enables non-invasive chemical studies of intact living matter. However, the use of NMR at the volume scale typical of microorganisms is hindered by sensitivity limitations, and experiments on single intact organisms have so far been limited to entities having volumes larger than 5 nL. Here we show NMR spectroscopy experiments conducted on single intact ova of 0.1 and 0.5 nL (i.e. 10 to 50 times smaller than previously achieved), thereby reaching the relevant volume scale where life development begins for a broad variety of organisms, humans included...
March 20, 2017: Scientific Reports
Markus F Weber, Erwin Frey
This review provides a pedagogic and self-contained introduction to master equations and to their representation by path integrals. Since the 1930s, master equations have served as a fundamental tool to understand the role of fluctuations in complex biological, chemical, and physical systems. Despite their simple appearance, analyses of master equations most often rely on low-noise approximations such as the Kramers-Moyal or the system size expansion, or require ad-hoc closure schemes for the derivation of low-order moment equations...
April 2017: Reports on Progress in Physics
Jeffrey K Aronson, Robin E Ferner
A biomarker is a biological observation that substitutes for and ideally predicts a clinically relevant endpoint or intermediate outcome that is more difficult to observe. The use of clinical biomarkers is easier and less expensive than direct measurement of the final clinical endpoint, and biomarkers are usually measured over a shorter time span. They can be used in disease screening, diagnosis, characterization, and monitoring; as prognostic indicators; for developing individualized therapeutic interventions; for predicting and treating adverse drug reactions; for identifying cell types; and for pharmacodynamic and dose-response studies...
March 17, 2017: Current Protocols in Pharmacology
Wojciech Labaj, Anna Papiez, Andrzej Polanski, Joanna Polanska
Large collections of data in studies on cancer such as leukaemia provoke the necessity of applying tailored analysis algorithms to ensure supreme information extraction. In this work, a custom-fit pipeline is demonstrated for thorough investigation of the voluminous MILE gene expression data set. Three analyses are accomplished, each for gaining a deeper understanding of the processes underlying leukaemia types and subtypes. First, the main disease groups are tested for differential expression against the healthy control as in a standard case-control study...
March 16, 2017: Interdisciplinary Sciences, Computational Life Sciences
Terrie M Williams, Traci L Kendall, Beau P Richter, Courtney R Ribeiro-French, Jason S John, Kim L Odell, Barbara A Losch, David A Feuerbach, M Andrew Stamper
Exponential increases in hydrodynamic drag and physical exertion occur when swimmers move quickly through water, and underlie the preference for relatively slow routine speeds by marine mammals regardless of body size. Because of this and the need to balance limited oxygen stores when submerged, flight (escape) responses may be especially challenging for this group. To examine this, we used open-flow respirometry to measure the energetic cost of producing a swimming stroke during different levels of exercise in bottlenose dolphins (Tursiops truncatus)...
March 15, 2017: Journal of Experimental Biology
Soudeh Jahanshahi, Hartmut Löwen, Borge Ten Hagen
We study the dynamics of a Brownian circle swimmer with a time-dependent self-propulsion velocity in an external temporally varying harmonic potential. For several situations, the noise-free swimming paths, the noise-averaged mean trajectories, and the mean-square displacements are calculated analytically or by computer simulation. Based on our results, we discuss optimal swimming strategies in order to explore a maximum spatial range around the trap center. In particular, we find a resonance situation for the maximum escape distance as a function of the various frequencies in the system...
February 2017: Physical Review. E
Oliva Saldanha, Rita Graceffa, Clement Hemonnot, Christiane Ranke, Gerrit Brehm, Marianne Liebi, Benedetta Marmiroli, Britta Weinhausen, Manfred Burghammer, Sarah Koester
Encapsulating reacting biological or chemical samples in microfluidic droplets has the great advantage over phase flows of providing separate reaction compartments. These compartments can be filled in a combinatoric way and prevent the sample from adsorbing to the channel walls. In recent years, small angle x-ray scattering (SAXS) in combination with microfluidics has evolved as a nanoscale method of such systems. Here, we approach two major challenges associated with combining droplet microfluidics and SAXS...
March 10, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Amelia A Green, Kishore R Mosaliganti, Ian A Swinburne, Nikolaus D Obholzer, Sean G Megason
BACKGROUND Paired organs in animals are largely bilaterally symmetric despite inherent noise in most biological processes. How is precise organ shape and size achieved during development despite this noise? Examining paired organ development is a challenge because it requires repeated quantification of two structures in parallel within living embryos. Here we combine bilateral quantification of morphology through time with asymmetric perturbations to study regulation of organ shape, size and symmetry in developing organ pairs...
March 13, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
Doaa Altarawy, Fatma-Elzahraa Eid, Lenwood S Heath
With abundance of biological data, computational prediction of gene regulatory networks (GRNs) from gene expression data has become more feasible. Although incorporating other prior knowledge (PK), along with gene expression data, greatly improves prediction accuracy, the overall accuracy is still low. PK in GRN inference can be categorized into noisy and curated. In noisy PK, relations between genes do not necessarily correspond to regulatory relations and are thus considered inaccurate by inference algorithms such as transcription factor binding and protein-protein interactions...
March 15, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Tomoyuki Mano, Jean-Baptiste Delfau, Junichiro Iwasawa, Masaki Sano
Although making artificial micrometric swimmers has been made possible by using various propulsion mechanisms, guiding their motion in the presence of thermal fluctuations still remains a great challenge. Such a task is essential in biological systems, which present a number of intriguing solutions that are robust against noisy environmental conditions as well as variability in individual genetic makeup. Using synthetic Janus particles driven by an electric field, we present a feedback-based particle-guiding method quite analogous to the "run-and-tumbling" behavior of Escherichia coli but with a deterministic steering in the tumbling phase: the particle is set to the run state when its orientation vector aligns with the target, whereas the transition to the "steering" state is triggered when it exceeds a tolerance angle [Formula: see text] The active and deterministic reorientation of the particle is achieved by a characteristic rotational motion that can be switched on and off by modulating the ac frequency of the electric field, which is reported in this work...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
Marie D Harton, Eric Batchelor
Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaustive review of the growing literature in this field, in this review we focus on single cell studies based on quantitative microscopy that have generated a deeper understanding of the sources, characteristics, limitations, and benefits of biological noise...
March 10, 2017: Journal of Molecular Biology
Thomas Atta-Fosu, Weihong Guo, Dana Jeter, Claudia M Mizutani, Nathan Stopczynski, Rui Sousa-Neves
Image segmentation is an important process that separates objects from the background and also from each other. Applied to cells, the results can be used for cell counting which is very important in medical diagnosis and treatment, and biological research that is often used by scientists and medical practitioners. Segmenting 3D confocal microscopy images containing cells of different shapes and sizes is still challenging as the nuclei are closely packed. The watershed transform provides an efficient tool in segmenting such nuclei provided a reasonable set of markers can be found in the image...
December 2016: J Imaging
Bin Wang, Yingjie Xie, Shihua Zhou, Changjun Zhou, Xuedong Zheng
Biocomputing, especially DNA, computing has got great development. It is widely used in information security. In this paper, a novel algorithm of reversible data hiding based on DNA computing is proposed. Inspired by the algorithm of histogram modification, which is a classical algorithm for reversible data hiding, we combine it with DNA computing to realize this algorithm based on biological technology. Compared with previous results, our experimental results have significantly improved the ER (Embedding Rate)...
2017: Computational Intelligence and Neuroscience
Tenta Sasaya, Naoki Sunaguchi, Thet- Thet-Lwin, Kazuyuki Hyodo, Tsutomu Zeniya, Tohoru Takeda, Tetsuya Yuasa
We propose a pinhole-based fluorescent x-ray computed tomography (p-FXCT) system with a 2-D detector and volumetric beam that can suppress the quality deterioration caused by scatter components. In the corresponding p-FXCT technique, projections are acquired at individual incident energies just above and below the K-edge of the imaged trace element; then, reconstruction is performed based on the two sets of projections using a maximum likelihood expectation maximization algorithm that incorporates the scatter components...
March 8, 2017: Scientific Reports
Erdenetogtokh Jamsranjav, Kenichi Kuge, Atsushi Ito, Yasuhito Kinjo, Tatsuo Shiina
Soft X-ray microscopy has been developed for high resolution imaging of hydrated biological specimens due to the availability of water window region. In particular, a projection type microscopy has advantages in wide viewing area, easy zooming function and easy extensibility to computed tomography (CT). The blur of projection image due to the Fresnel diffraction of X-rays, which eventually reduces spatial resolution, could be corrected by an iteration procedure, i.e., repetition of Fresnel and inverse Fresnel transformations...
March 3, 2017: Journal of X-ray Science and Technology
Li Shen, Eric Todd Quinto, Shiqiang Wang, Ming Jiang
Electron micrography (EM) is an important method for determining the three-dimensional (3D) structure of macromolecular complexes and biological specimens. But there are several limitations such as poor signal-to-noise, limitation on range of tilt angles and sub-region subject to electron exposure, unintentional movements of the specimen, with EM systems that make the reconstruction procedure a severely ill-posed problem. A different choice of reconstruction method may lead to different results and create different additional artifacts in reconstructed images...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Michael R Nowak, Yoonsuck Choe
We introduce a simple, yet effective, procedure for accurate classification of connected components embedded in biological images. In our method, a training set is generated from user-delineated features of manually-labeled examples; we subsequently train a classifier using the resultant training set. The overall process is described using imaging data acquired from an India-ink perfused C57BL/6J mouse brain using Knife Edge Scanning Microscopy. We illustrate the procedure through segmentation of cerebral vasculature structures from mechanical noise using trained classifiers...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Maritza Leon-Bejarano, Guadalupe Dorantes-Mendez, Miguel Ramirez-Elias, Martin O Mendez, Alfonso Alba, Ildefonso Rodriguez-Leyva, M Jimenez
Raman spectroscopy of biological tissue presents fluorescence background, an undesirable effect that generates false Raman intensities. This paper proposes the application of the Empirical Mode Decomposition (EMD) method to baseline correction. EMD is a suitable approach since it is an adaptive signal processing method for nonlinear and non-stationary signal analysis that does not require parameters selection such as polynomial methods. EMD performance was assessed through synthetic Raman spectra with different signal to noise ratio (SNR)...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Rupin Dalvi, Adrian Suszko, Vijay S Chauhan
Biological signals, such as intracardiac electrograms during atrial fibrillation (AF), can contain multiple periodic components or peaks. We propose a method for identifying individual periodic peak trains in signals containing multiple such periodic sequences. We use dominant frequency-based periodicity detection along with a graph search algorithm to identify the most dominant periodic activation set or peaks of interest. We then remove these peaks and iterate until all periodic sequences are identified. The proposed method is tested on simulated AF intra-cardiac electrograms with periodic activation trains of three distinct frequencies corrupted by noise and complex aperiodic signal features...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Seyed Hadi Nasrollaholhosseini, Preston Steele, Walter G Besio
Electrodes are used to transform ionic currents to electrical currents in biological systems. Modeling the electrode-electrolyte interface could help to optimize the performance of the electrode interface to achieve higher signal to noise ratios. There are previous reports of accurate models for single-element biomedical electrodes. In this paper we develop a model for the electrode-electrolyte interface for tripolar concentric ring electrodes (TCRE) that are used to record brain signals.
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
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