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Biological noise

Hyun Jik Kim, Young Hun Seo, Sujin An, Ara Jo, Ick Chan Kwon, Sehoon Kim
Rationale: Hydrogen peroxide (H2 O2 ) provides an important mechanism for resisting infectious pathogens within the respiratory tract, and accordingly, the in situ analysis of H2 O2 generation in real time provides a valuable tool for assessing immune response. Methods: In this study, we applied a chemiluminescent nanoparticle-based real-time imaging approach to noninvasive evaluation of the Duox2-mediated H2 O2 generation after viral infection, and assessed its usefulness for analytical purposes in mouse nasal mucosa...
2018: Theranostics
Vandana Padala, Arindam Basu, Garrick Orchard
Asynchronous event-based sensors, or "silicon retinae," are a new class of vision sensors inspired by biological vision systems. The output of these sensors often contains a significant number of noise events along with the signal. Filtering these noise events is a common preprocessing step before using the data for tasks such as tracking and classification. This paper presents a novel spiking neural network-based approach to filtering noise events from data captured by an Asynchronous Time-based Image Sensor on a neuromorphic processor, the IBM TrueNorth Neurosynaptic System...
2018: Frontiers in Neuroscience
Oana Ursu, Nathan Boley, Maryna Taranova, Y X Rachel Wang, Galip Gurkan Yardimci, William Stafford Noble, Anshul Kundaje
Motivation: The three-dimensional organization of chromatin plays a critical role in gene regulation and disease. High-throughput chromosome conformation capture experiments such as Hi-C are used to obtain genome-wide maps of 3D chromatin contacts. However, robust estimation of data quality and systematic comparison of these contact maps is challenging due to the multi-scale, hierarchical structure of chromatin contacts and the resulting properties of experimental noise in the data. Measuring concordance of contact maps is important for assessing reproducibility of replicate experiments and for modeling variation between different cellular contexts...
March 15, 2018: Bioinformatics
Karl A Hujsak, Eric W Roth, William Kellogg, Yue Li, Vinayak P Dravid
Technological advances in electron microscopy, particularly improved detectors and aberration correctors, have led to higher throughput and less invasive imaging of materials and biological structures by enhancing signal-to-noise ratios at lower electron exposures. Analytical methods, such as electron energy loss spectroscopy (EELS) and energy dispersive x-ray spectrometry (EDS), have also benefitted and offer a rich set of local elemental and bonding information with nano-or atomic resolution. However, spatially resolved spectrum imaging with EELS and EDS continue to be difficult to scale due to limited detector collection angles or high signal background, requiring hours or even days for full maps...
March 10, 2018: Micron: the International Research and Review Journal for Microscopy
Roland Opfer, Ann-Christin Ostwaldt, Christine Walker-Egger, Praveena Manogaran, Maria Pia Sormani, Nicola De Stefano, Sven Schippling
BACKGROUND: Measurements of brain volume loss (BVL) in individual patients are currently discussed controversially. One concern is the impact of short-term biological noise, like hydration status. METHODS: Three publicly available reliability MRI datasets with scan intervals of days to weeks were used. An additional cohort of 60 early relapsing multiple sclerosis (MS) patients with MRI follow-ups was analyzed to test whether after 1 year pathological BVL is detectable in a relevant fraction of MS patients...
March 16, 2018: Journal of Neurology
Andrea Crisanti, Andrea De Martino, Jonathan Fiorentino
Genetic regulatory circuits universally cope with different sources of noise that limit their ability to coordinate input and output signals. In many cases, optimal regulatory performance can be thought to correspond to configurations of variables and parameters that maximize the mutual information between inputs and outputs. Since the mid-2000s, such optima have been well characterized in several biologically relevant cases. Here we use methods of statistical field theory to calculate the statistics of the maximal mutual information (the "capacity") achievable by tuning the input variable only in an ensemble of regulatory motifs, such that a single controller regulates N targets...
February 2018: Physical Review. E
Leland J Dunwoodie, William L Poehlman, Stephen P Ficklin, Frank Alexander Feltus
Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors...
February 16, 2018: Oncotarget
Jonathan M Grimes, David R Hall, Alun W Ashton, Gwyndaf Evans, Robin L Owen, Armin Wagner, Katherine E McAuley, Frank von Delft, Allen M Orville, Thomas Sorensen, Martin A Walsh, Helen M Ginn, David I Stuart
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments...
February 1, 2018: Acta Crystallographica. Section D, Structural Biology
Béatrice Milon, Sunayana Mitra, Yang Song, Zachary Margulies, Ryan Casserly, Virginia Drake, Jessica A Mong, Didier A Depireux, Ronna Hertzano
BACKGROUND: Noise-induced hearing loss (NIHL) is the most prevalent form of acquired hearing loss and affects about 40 million US adults. Among the suggested therapeutics tested in rodents, suberoylanilide hydroxamic acid (SAHA) has been shown to be otoprotective from NIHL; however, these results were limited to male mice. METHODS: Here we tested the effect of SAHA on the hearing of 10-week-old B6CBAF1/J mice of both sexes, which were exposed to 2 h of octave-band noise (101 dB SPL centered at 11...
March 12, 2018: Biology of Sex Differences
Isabelle Niedhammer, Thomas Lesuffleur, Géraldine Labarthe, Jean-François Chastang
BACKGROUND: Social inequalities in work injury have been observed but explanations are still missing. The objectives of this study were to evaluate the contribution of working conditions in the explanation of social inequalities in work injury in a national representative sample of employees. METHODS: The study was based on the cross-sectional sample of the national French survey SUMER 2010 including 46,962 employees, 26,883 men and 20,079 women. The number of work injuries within the last 12 months was studied as the outcome...
March 12, 2018: BMC Public Health
Rick P F Wolthusen, Garth Coombs, Emily A Boeke, Stefan Ehrlich, Stephanie N DeCross, Shahin Nasr, Daphne J Holt
BACKGROUND: Delusions are a defining and common symptom of psychotic disorders. Recent evidence suggests that subclinical and clinical delusions may represent distinct stages on a phenomenological and biological continuum. However, few studies have tested whether subclinical psychotic experiences are associated with neural changes that are similar to those observed in clinical psychosis. For example, it is unclear if overactivity of the hippocampus, a replicated finding of neuroimaging studies of schizophrenia, is also present in individuals with subclinical psychotic symptoms...
February 2018: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
James A Roberts, Karl J Friston, Michael Breakspear
Brain activity derives from intrinsic dynamics (due to neurophysiology and anatomical connectivity) in concert with stochastic effects that arise from sensory fluctuations, brainstem discharges, and random microscopic states such as thermal noise. The dynamic evolution of systems composed of both dynamic and random fluctuations can be studied with stochastic dynamic models (SDMs). This article, Part II of a two-part series, reviews applications of SDMs to large-scale neural systems in health and disease. Stochastic models have already elucidated a number of pathophysiological phenomena, such as epilepsy and hypoxic ischemic encephalopathy, although their use in biological psychiatry remains rather nascent...
April 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
James A Roberts, Karl J Friston, Michael Breakspear
Biological phenomena arise through interactions between an organism's intrinsic dynamics and stochastic forces-random fluctuations due to external inputs, thermal energy, or other exogenous influences. Dynamic processes in the brain derive from neurophysiology and anatomical connectivity; stochastic effects arise through sensory fluctuations, brainstem discharges, and random microscopic states such as thermal noise. The dynamic evolution of systems composed of both dynamic and random effects can be studied with stochastic dynamic models (SDMs)...
April 2017: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
Ariel Amir, Nathalie Q Balaban
For many decades, the wedding of quantitative data with mathematical modeling has been fruitful, leading to important biological insights. Here, we review some of the ongoing efforts to gain insights into problems in microbiology - and, in particular, cell-cycle progression and its regulation - through observation and quantitative analysis of the natural fluctuations in the system. We first illustrate this idea by reviewing a classic example in microbiology - the Luria-Delbrück experiment - and discussing how, in that case, useful information was obtained by looking beyond the mean outcome of the experiment, but instead paying attention to the variability between replicates of the experiment...
March 8, 2018: Trends in Microbiology
Kelley M Swanberg, Hetty Prinsen, Daniel Coman, Robin A de Graaf, Christoph Juchem
Glutathione (GSH) is an endogenous antioxidant implicated in numerous biological processes, including those associated with multiple sclerosis, aging, and cancer. Spectral editing techniques have greatly facilitated the acquisition of glutathione signal in living humans via proton magnetic resonance spectroscopy, but signal quantification at 7 Tesla is still hampered by uncertainty about the glutathione transverse decay rate T2 relative to those of commonly employed quantitative references like N-acetyl aspartate (NAA), total creatine, or water...
March 1, 2018: Journal of Magnetic Resonance
Nadav Yayon, Amir Dudai, Nora Vrieler, Oren Amsalem, Michael London, Hermona Soreq
Three-dimensional structures in biological systems are routinely evaluated using large image stacks acquired from fluorescence microscopy; however, analysis of such data is muddled by variability in the signal across and between samples. Here, we present Intensify3D: a user-guided normalization algorithm tailored for overcoming common heterogeneities in large image stacks. We demonstrate the use of Intensify3D for analyzing cholinergic interneurons of adult murine brains in 2-Photon and Light-Sheet fluorescence microscopy, as well as of mammary gland and heart tissues...
March 9, 2018: Scientific Reports
Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas Fitzgerald, Jan Ellenberg, Ewan Birney
The 3D structure of chromatin plays a key role in genome function, including gene expression, DNA replication, chromosome segregation, and DNA repair. Furthermore the location of genomic loci within the nucleus, especially relative to each other and nuclear structures such as the nuclear envelope and nuclear bodies strongly correlates with aspects of function such as gene expression. Therefore, determining the 3D position of the 6 billion DNA base pairs in each of the 23 chromosomes inside the nucleus of a human cell is a central challenge of biology...
March 9, 2018: PLoS Computational Biology
Matthew Sonnett, Eyan Yeung, Martin Wühr
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitations...
March 9, 2018: Analytical Chemistry
Hongxin Wang, Stephan Friedrich, Lei Li, Ziliang Mao, Pinghua Ge, Mahalingam Balasubramanian, Daulat S Patil
According to L-edge sum rules, the number of 3d vacancies at a transition metal site is directly proportional to the integrated intensity of the L-edge X-ray absorption spectrum (XAS) for the corresponding metal complex. In this study, the numbers of 3d holes are characterized quantitatively or semi-quantitatively for a series of manganese (Mn) and nickel (Ni) complexes, including the electron configurations 3d10 → 3d0 . In addition, extremely dilute (<0.1% wt/wt) Ni enzymes were examined by two different approaches: (1) by using a high resolution superconducting tunnel junction X-ray detector to obtain XAS spectra with a very high signal-to-noise ratio, especially in the non-variant edge jump region; and (2) by adding an inert tracer to the sample that provides a prominent spectral feature to replace the weak edge jump for intensity normalization...
March 9, 2018: Physical Chemistry Chemical Physics: PCCP
Xiaonan Gao, Lulu Jiang, Bo Hu, Fanpeng Kong, Xiaojun Liu, Kehua Xu, Bo Tang
The gold nanosensors based on Au-S bond have been widely applied to biochemical detections. However, the signal distortion caused by biothiols has been seldom mentioned and urgently needed to be solved. Herein, we designed a novel but easily assembled gold nanoprobe by coupling selenol-modified peptide with FITC onto the gold nanoparti-cle's surface via Au-Se bond for florescence imaging of a tumor marker matrix metalloproteinases 2 (MMP-2). The Au-Se probes display a higher signal-noise ratio (SNR, 10.1) and a lower detection limit (LOD, 1...
March 9, 2018: Analytical Chemistry
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