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Biological noise

Anne T M Konkle, Stephen E Keith, James P McNamee, David Michaud
INTRODUCTION: Epidemiological studies have suggested an association between the relative risk for developing cardiovascular disease (CVD) and long-term exposure to elevated levels of transportation noise. The contention is that this association is largely owing to an increase in stress-related biomarkers that are thought to be associated with CVD. Animal models have demonstrated that acute noise exposure is capable of triggering a stress response; however, similar studies using chronic noise models are less common...
September 2017: Noise & Health
Amanda Marie Lauer, Katrina Marie Schrode
INTRODUCTION: Sex differences in brain biochemistry, physiology, structure, and function have been gaining increasing attention in the scientific community. Males and females can have different responses to medications, diseases, and environmental variables. A small number of the approximately 7500 studies of noise-induced hearing loss (NIHL) have identified sex differences, but the mechanisms and characterization of these differences have not been thoroughly studied. The National Institutes of Health (NIH) issued a mandate in 2015 to include sex as a biological variable in all NIH-funded research beginning in January 2016...
September 2017: Noise & Health
M E Dokukin, I Sokolov
Recently developed sub-resonance tapping modes (such as Digital Pulse, Peak Force Tapping, HybriD, etc.) of atomic force microscopy (AFM) allow imaging of compositional contrast of (bio)materials and biological cells down to the nanoscale. Here we report on a powerful extension of those modes, "ringing" mode, which more than doubles the number of non-trivial physical channels that can be collected with a regular sub-resonance tapping. It can simultaneously record five new additional compositional parameters related to adhesive and viscoelastic properties of the sample surface: the restored (averaged) adhesion, adhesion height, pull-off neck height, detachment distance, and detachment energy losses...
September 19, 2017: Scientific Reports
Ren Ren, Yanjun Zhang, Binoy Paulose Nadappuram, Bernice Akpinar, David Klenerman, Aleksandar P Ivanov, Joshua B Edel, Yuri Korchev
There has been a significant drive to deliver nanotechnological solutions to biosensing, yet there remains an unmet need in the development of biosensors that are affordable, integrated, fast, capable of multiplexed detection, and offer high selectivity for trace analyte detection in biological fluids. Herein, some of these challenges are addressed by designing a new class of nanoscale sensors dubbed nanopore extended field-effect transistor (nexFET) that combine the advantages of nanopore single-molecule sensing, field-effect transistors, and recognition chemistry...
September 19, 2017: Nature Communications
Lina Meinecke
We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid...
September 18, 2017: Bulletin of Mathematical Biology
Jialin Zhang, Jiasong Sun, Qian Chen, Jiaji Li, Chao Zuo
High-resolution wide field-of-view (FOV) microscopic imaging plays an essential role in various fields of biomedicine, engineering, and physical sciences. As an alternative to conventional lens-based scanning techniques, lensfree holography provides a new way to effectively bypass the intrinsical trade-off between the spatial resolution and FOV of conventional microscopes. Unfortunately, due to the limited sensor pixel-size, unpredictable disturbance during image acquisition, and sub-optimum solution to the phase retrieval problem, typical lensfree microscopes only produce compromised imaging quality in terms of lateral resolution and signal-to-noise ratio (SNR)...
September 18, 2017: Scientific Reports
Jizhou Li, Florian Luisier, Thierry Blu
We propose a non-iterative image deconvolution algorithm for data corrupted by Poisson or mixed Poisson-Gaussian noise. Many applications involve such a problem, ranging from astronomical to biological imaging. We parametrize the deconvolution process as a linear combination of elementary functions, termed as linear expansion of thresholds (LET). This parametrization is then optimized by minimizing a robust estimate of the true mean squared error, the Poisson unbiased risk estimate (PURE). Each elementary function consists of a Wiener filtering followed by a pointwise thresholding of undecimated Haar wavelet coefficients...
September 18, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
G Sikora, E Kepten, A Weron, M Balcerek, K Burnecki
Modern live-imaging fluorescent microscopy techniques following the stochastic motion of labeled tracer particles, i.e. single particle tracking (SPT) experiments, have uncovered significant deviations from the laws of Brownian motion in a variety of biological systems. Accurately characterizing the anomalous diffusion for SPT experiments has become a central issue in biophysics. However, measurement errors raise difficulty in the analysis of single trajectories. In this paper, we introduce a novel surface calibration method based on a fractionally integrated moving average (FIMA) process as an effective tool for extracting both the magnitude of the measurement error and the anomalous exponent for autocorrelated processes of various origins...
September 18, 2017: Physical Chemistry Chemical Physics: PCCP
Elena Fimmel, Lutz Strüngmann
Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept...
September 13, 2017: Bio Systems
Xinggui Gu, Ryan T K Kwok, Jacky W Y Lam, Ben Zhong Tang
Biological processes are of great significance for the normal physiological functions of living organisms and closely related to the health. Monitoring of biological processes and diagnosis of diseases based on fluorescent techniques would provide comprehensive insight into mechanism of life and pathogenesis of diseases, precisely guiding therapeutic effect in theranostics. It largely relied on fluorophores with the properties of excellent photostability, large Stokes shift, high signal-to-noise ratio and free of aggregation-caused quenching (ACQ) effect...
September 4, 2017: Biomaterials
Nayeli Huidobro, Abraham Mendez-Fernandez, Ignacio Mendez-Balbuena, Ranier Gutierrez, Rumyana Kristeva, Elias Manjarrez
Stochastic resonance (SR) is an inherent and counter-intuitive mechanism of signal-to-noise ratio (SNR) facilitation in biological systems associated with the application of an intermediate level of noise. As a first step to investigate in detail this phenomenon in the somatosensory system, here we examined whether the direct application of noisy light on pyramidal neurons from the mouse-barrel cortex expressing a light-gated channel channelrhodopsin-2 (ChR2) can produce facilitation in somatosensory evoked field potentials...
2017: Frontiers in Neuroscience
Cornel Zachiu, Mario G Ries, Pascal Ramaekers, Jean-Luc Guey, Chrit T W Moonen, Baudouin Denis de Senneville
Biological motion is a problem for non- or mini-invasive interventions when conducted in mobile/deformable organs due to the targeted pathology moving/deforming with the organ. This may lead to high miss rates and/or incomplete treatment of the pathology. Therefore, real-time tracking of the target anatomy during the intervention would be beneficial for such applications. Since the aforementioned interventions are often conducted under B-mode ultrasound (US) guidance, target tracking can be achieved via image registration, by comparing the acquired US images to a separate image established as positional reference...
September 13, 2017: Physics in Medicine and Biology
Jan Walther Perthold, Chris Oostenbrink
Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein-protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task...
September 12, 2017: Journal of Chemical Theory and Computation
Ning Yuan, Hong-Xue Sun, Dan-Dan Ju, Da-Yu Liu, Zi-Bo Zhang, Wing-Han Wong, Feng Song, Dao-Yin Yu, Edwin Yue-Bun Pun, De-Long Zhang
We developed a highly efficient optical thermometer based on intensity ratio of upconversion green fluorescence of Er(3+)/Yb(3+)-codoped NaYF4 microcrystals. The sensor consists simply of a 980nm laser diode, one narrow-band interference filter, two lenses, one Si-photocell and one multimeter, while being without use of spectrometer and additional electronics. The device not only has a simple, compact structure (hence a low cost), but also displays highly efficient sensing performance, characterized by large signal-to-noise ratio due to strong fluorescence intensity, high thermal resolution and sensitivity, which have the values 1...
December 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
Linh T Tran, Lachlan Chartier, David Bolst, Alex Pogossov, Susanna Guatelli, Marco Petasecca, Michael L F Lerch, Dale A Prokopovich, Mark I Reinhard, Benjamin Clasie, Nicolas Depauw, Hanne Kooy, Jacob B Flanz, Aimee McNamara, Harald Paganetti, Chris Beltran, Keith Furutani, Vladimir L Perevertaylo, Michael Jackson, Anatoly B Rosenfeld
PURPOSE: This work aims to characterise a proton pencil-beam scanning (PBS) and passive double scattering (DS) systems as well as to measure parameters relevant to the relative biological effectiveness (RBE) of the beam using a silicon-on-insulator (SOI) microdosimeter with well-defined 3D sensitive volumes (SV). The dose equivalent downstream and laterally outside of a clinical PBS treatment field was assessed and compared to that of a DS beam. METHODS: A novel silicon microdosimeter with well-defined 3D SVs was used in this study...
September 8, 2017: Medical Physics
Dennis Pischel, Kai Sundmacher, Robert J Flassig
Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples...
July 15, 2017: Bioinformatics
Pang Wei Koh, Emma Pierson, Anshul Kundaje
Motivation: Chromatin immune-precipitation sequencing (ChIP-seq) experiments are commonly used to obtain genome-wide profiles of histone modifications associated with different types of functional genomic elements. However, the quality of histone ChIP-seq data is affected by many experimental parameters such as the amount of input DNA, antibody specificity, ChIP enrichment and sequencing depth. Making accurate inferences from chromatin profiling experiments that involve diverse experimental parameters is challenging...
July 15, 2017: Bioinformatics
Alexander Schriewer, Cristina Cadenas, Heiko Hayen
Cofactors such as coenzyme A and its derivatives acetyl-coenzyme A and malonyl-coenzyme A are involved in many metabolic pathways. Due to trace level concentrations in biological samples and the high reactivity of cofactors, a fast, sensitive and selective method for quantification is mandatory. In this study, online solid-phase extraction was coupled successfully to hydrophilic interaction liquid chromatography with tandem mass spectrometry for analytes' isolation in complex matrix and quantification by external calibration...
September 6, 2017: Journal of Separation Science
Martin Christner, Dirk Dressler, Mark Andrian, Claudia Reule, Orlando Petrini
The fast and reliable characterization of bacterial and fungal pathogens plays an important role in infectious disease control and tracking of outbreak agents. DNA based methods are the gold standard for epidemiological investigations, but they are still comparatively expensive and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a fast, reliable and cost-effective technique now routinely used to identify clinically relevant human pathogens. It has been used for subspecies differentiation and typing, but its use for epidemiological tasks, e...
2017: PloS One
Macarena Parra, Jimmy Jung, Travis D Boone, Luan Tran, Elizabeth A Blaber, Mark Brown, Matthew Chin, Tori Chinn, Jacob Cohen, Robert Doebler, Dzung Hoang, Elizabeth Hyde, Matthew Lera, Louie T Luzod, Mark Mallinson, Oana Marcu, Youssef Mohamedaly, Antonio J Ricco, Kathleen Rubins, Gregory D Sgarlato, Rafael O Talavera, Peter Tong, Eddie Uribe, Jeffrey Williams, Diana Wu, Rukhsana Yousuf, Charles S Richey, Julie Schonfeld, Eduardo A C Almeida
The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit...
2017: PloS One
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