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Biological noise

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https://www.readbyqxmd.com/read/28727850/hybrid-cubature-kalman-filtering-for-identifying-nonlinear-models-from-sampled-recording-estimation-of-neuronal-dynamics
#1
Mahmoud K Madi, Fadi N Karameh
Kalman filtering methods have long been regarded as efficient adaptive Bayesian techniques for estimating hidden states in models of linear dynamical systems under Gaussian uncertainty. Recent advents of the Cubature Kalman filter (CKF) have extended this efficient estimation property to nonlinear systems, and also to hybrid nonlinear problems where by the processes are continuous and the observations are discrete (continuous-discrete CD-CKF). Employing CKF techniques, therefore, carries high promise for modeling many biological phenomena where the underlying processes exhibit inherently nonlinear, continuous, and noisy dynamics and the associated measurements are uncertain and time-sampled...
2017: PloS One
https://www.readbyqxmd.com/read/28724786/emergent-cortical-circuit-dynamics-contain-dense-interwoven-ensembles-of-spike-sequences
#2
Joseph B Dechery, Jason N MacLean
Temporal codes are theoretically powerful encoding schemes, but their precise form in neocortex remains unknown in part because of the large number of possible codes and the difficulty in disambiguating informative spikes from statistical noise. A biologically plausible and computationally powerful temporal coding scheme is the Hebbian assembly phase sequence (APS), which predicts reliable propagation of spikes between functionally related assemblies of neurons. Here, we sought to measure the inherent capacity of neocortical networks to produce reliable sequences of spikes, as would be predicted by an APS code...
July 19, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28723146/generalized-noise-study-of-solid-state-nanopores-at-low-frequencies
#3
Chenyu Wen, Shuangshuang Zeng, Kai Arstila, Timo Sajavaara, Yu Zhu, Zhen Zhang, Shi-Li Zhang
Nanopore technology has been extensively investigated for analysis of biomolecules, and a success story in this field concerns DNA sequencing using a nanopore chip featuring an array of hundreds of biological nanopores (BioNs). Solid-state nanopores (SSNs) have been explored to attain longer lifetime and higher integration density than what BioNs can offer, but SSNs are generally considered to generate higher noise whose origin remains to be confirmed. Here, we systematically study low-frequency (including thermal and flicker) noise characteristics of SSNs measuring 7 to 200 nm in diameter drilled through a 20-nm-thick SiNx membrane by focused ion milling...
February 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28723112/surfen-assembled-graphene-oxide-for-fluorescence-turn-on-detection-of-sulfated-glycosaminoglycans-in-biological-matrix
#4
Yen-Ting Wang, Wei-Lung Tseng
Sulfated glycosaminoglycans (GAGs) not only serve as a biomarker for mucopolysaccharidoses disease but also participate in various biological processes, such as blood clot medication (heparin) and signal transduction (heparan sulfate). However, few fluorescent sensors, such as 1,9-dimethylmethylene blue, have been developed for the detection of sulfated GAGs in the real world. Herein, we fabricated a surfen/few-layer graphene oxide (FLGO) nanocomplex for sensing sulfated GAGs in biological fluids. Surfen molecules are self-assembled onto the surface of FLGO through electrostatic attraction, and their fluorescence was then quenched by the creation of the FLGO-surfen complex (static quenching) and partially combined with the energy transfer from surfen to FLGO (dynamic quenching)...
June 23, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28718776/coil-geometry-effects-on-scanning-single-coil-magnetic-induction-tomography
#5
Joe R Feldkamp, Stephen Quirk
Alternative coil designs for single coil MIT (magnetic induction tomography) are considered in this work, with the intention of improving upon the standard design used previously. In particular, we note that the blind spot associated with this coil type, a portion of space along its axis where eddy current generation can be very weak, has an important effect on performance. The seven designs tested here vary considerably in the size of their blind spot. To provide the most discerning test possible, we use laboratory phantoms containing feature dimensions similar to blind spot size...
July 18, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28711280/unsupervised-extraction-of-stable-expression-signatures-from-public-compendia-with-an-ensemble-of-neural-networks
#6
Jie Tan, Georgia Doing, Kimberley A Lewis, Courtney E Price, Kathleen M Chen, Kyle C Cady, Barret Perchuk, Michael T Laub, Deborah A Hogan, Casey S Greene
Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models...
July 11, 2017: Cell Systems
https://www.readbyqxmd.com/read/28709943/propagation-and-control-of-gene-expression-noise-with-non-linear-translation-kinetics
#7
J David Van Dyken
Gene expression is a stochastic process involving small numbers of molecules. As a consequence, cells in a clonal population vary randomly and sometimes substantially from one another in the concentration of mRNA and protein species, a phenomenon known as gene expression noise. Previous theoretical models of gene expression noise assumed that translation is first-order (linear) in mRNA concentration, leading to unfiltered propagation of mRNA noise to the protein level. Here I consider the biological ramifications of relaxing this assumption...
July 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28709308/temporal-disorder-as-a-mechanism-for-spatially-heterogeneous-diffusion
#8
Paul C Bressloff, Sean D Lawley
A fundamental issue in analyzing diffusion in heterogeneous media is interpreting the space dependence of the associated diffusion coefficient. This reflects the well-known Ito-Stratonovich dilemma for continuous stochastic processes with multiplicative noise. In order to resolve this dilemma it is necessary to introduce additional constraints regarding the underlying physical system. Here we introduce a mechanism for generating nonlinear Brownian motion based on a form of temporal disorder. Motivated by switching processes in molecular biology, we consider a Brownian particle that randomly switches between two distinct conformational states with different diffusivities...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28709185/fluctuation-relations-between-hierarchical-kinetically-equivalent-networks-with-arrhenius-type-transitions-and-their-roles-in-systems-and-structural-biology
#9
De-Ming Deng, Yi-Ta Lu, Cheng-Hung Chang
The legality of using simple kinetic schemes to determine the stochastic properties of a complex system depends on whether the fluctuations generated from hierarchical equivalent schemes are consistent with one another. To analyze this consistency, we perform lumping processes on the stochastic differential equations and the generalized fluctuation-dissipation theorem and apply them to networks with the frequently encountered Arrhenius-type transition rates. The explicit Langevin force derived from those networks enables us to calculate the state fluctuations caused by the intrinsic and extrinsic noises on the free energy surface and deduce their relations between kinetically equivalent networks...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28704589/novel-chemiluminescent-western-blot-blocking-and-antibody-incubation-solution-for-enhanced-antibody-antigen-interaction-and-increased-specificity
#10
Kimberly Schwartz, Dmitry Bochkariov
Western blotting is a ubiquitous tool used in protein and molecular biology research, providing information about the presence, size, relative abundance and state of a protein in a mixture. First, the proteins in a sample are separated by size using SDS-PAGE then transferred onto a membrane for detection with a set of primary and secondary antibodies. High-quality Western data requires high signal-to-noise ratios, which depend upon reduction of nonspecific antibody interactions. Blocking is a critical step in the Western blot method as it prevents the antibodies from binding nonspecifically to the membrane and irrelevant proteins...
July 13, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28701799/a-robust-method-for-inferring-network-structures
#11
Yang Yang, Tingjin Luo, Zhoujun Li, Xiaoming Zhang, Philip S Yu
Inferring the network structure from limited observable data is significant in molecular biology, communication and many other areas. It is challenging, primarily because the observable data are sparse, finite and noisy. The development of machine learning and network structure study provides a great chance to solve the problem. In this paper, we propose an iterative smoothing algorithm with structure sparsity (ISSS) method. The elastic penalty in the model is introduced for the sparse solution, identifying group features and avoiding over-fitting, and the total variation (TV) penalty in the model can effectively utilize the structure information to identify the neighborhood of the vertices...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28698108/imaging-at-ultrahigh-magnetic-fields-history-challenges-and-solutions
#12
Kamil Uğurbil
Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and spectroscopy studies of humans at 4 T and animal models at 9.4 T, leading to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has provided numerous technological solutions to challenges posed at these ultrahigh fields, and demonstrated the existence of significant advantages in signal-to-noise ratio and biological information content...
July 8, 2017: NeuroImage
https://www.readbyqxmd.com/read/28695665/analysis-of-large-16s-rrna-illumina-datasets-impact-of-singleton-read-filtering-on-microbial-community-description
#13
Lucas Auer, Mahendra Mariadassou, Michael O'Donohue, Christophe Klopp, Guillermina Hernandez-Raquet
Next generation sequencing technologies give access to large sets of data which are extremely useful in the study of microbial diversity based on 16S rRNA gene. However, the production of such large datasets is not only marred by technical biases and sequencing noise but also increases computation time and disk space use. To improve the accuracy of OTUs predictions and overcome both computations, storage and noise issues, recent studies and tools suggested removing all single reads and low abundant OTUs, considering them as noise...
July 11, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28694303/single-molecule-fluorescence-microscopy-review-shedding-new-light-on-old-problems
#14
Sviatlana Shashkova, Mark C Leake
Fluorescence microscopy is an invaluable tool in the biosciences, a genuine workhorse technique offering exceptional contrast in conjunction with high specificity of labelling with relatively minimal perturbation to biological samples compared to many competing biophysical techniques. Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilise light microscopy tools to enable the faithful detection and analysis of single fluorescent molecules used as reporter tags in biological samples...
July 10, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28692644/correction-accuracy-maximization-analysis-for-sensory-perceptual-tasks-computational-improvements-filter-robustness-and-coding-advantages-for-scaled-additive-noise
#15
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1005281.].
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28692303/searching-for-biosignatures-in-exoplanetary-impact-ejecta
#16
Gianni Cataldi, Alexis Brandeker, Philippe Thébault, Kelsi Singer, Engy Ahmed, Bernard L de Vries, Anna Neubeck, Göran Olofsson
With the number of confirmed rocky exoplanets increasing steadily, their characterization and the search for exoplanetary biospheres are becoming increasingly urgent issues in astrobiology. To date, most efforts have concentrated on the study of exoplanetary atmospheres. Instead, we aim to investigate the possibility of characterizing an exoplanet (in terms of habitability, geology, presence of life, etc.) by studying material ejected from the surface during an impact event. For a number of impact scenarios, we estimate the escaping mass and assess its subsequent collisional evolution in a circumstellar orbit, assuming a Sun-like host star...
July 10, 2017: Astrobiology
https://www.readbyqxmd.com/read/28692129/distortion-free-diffusion-mri-using-an-mri-guided-tri-cobalt-60-radiotherapy-system-sequence-verification-and-preliminary-clinical-experience
#17
Yu Gao, Fei Han, Ziwu Zhou, Minsong Cao, Tania Kaprealian, Mitchell Kamrava, Chenyang Wang, John Neylon, Daniel A Low, Yingli Yang, Peng Hu
PURPOSE: Monitoring tumor response during the course of treatment and adaptively modifying treatment plan based on tumor biological feedback may represent a new paradigm for radiotherapy. Diffusion MRI has shown great promises in assessing and predicting tumor response to radiotherapy. However, the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) technique suffers from limited resolution, severe distortion and possibly inaccurate ADC at low field strength. The purpose of this work is to develop a reliable, accurate and distortion-free diffusion MRI technique that is practicable for longitudinal tumor response evaluation and adaptive radiotherapy on a 0...
July 10, 2017: Medical Physics
https://www.readbyqxmd.com/read/28691925/design-and-analysis-of-aerodynamic-force-platforms-for-free-flight-studies
#18
Ben Hightower, Rivers Ingersoll, Diana Chin, Carl Lawhon, Andreas Haselsteiner, David Lentink
We describe and explain new advancements in the design of the aerodynamic force platform, a novel instrument that can directly measure the aerodynamic forces generated by freely flying animals and robots. Such <i>in vivo</i> recordings are essential to better understand the precise aerodynamic function of flapping wings in nature, which can critically inform the design of new bioinspired robots. By designing the aerodynamic force platform to be stiff yet lightweight, the natural frequencies of all structural components can be made over five times greater than the frequencies of interest...
July 10, 2017: Bioinspiration & Biomimetics
https://www.readbyqxmd.com/read/28689721/studying-the-evolutionary-significance-of-thermal-adaptation-in-ectotherms-the-diversification-of-amphibians-energetics
#19
Roberto F Nespolo, Julio Figueroa, Jaiber J Solano-Iguaran
A fundamental problem in evolutionary biology is the understanding of the factors that promote or constrain adaptive evolution, and assessing the role of natural selection in this process. Here, comparative phylogenetics, that is, using phylogenetic information and traits to infer evolutionary processes has been a major paradigm . In this study, we discuss Ornstein-Uhlenbeck models (OU) in the context of thermal adaptation in ectotherms. We specifically applied this approach to study amphibians's evolution and energy metabolism...
August 2017: Journal of Thermal Biology
https://www.readbyqxmd.com/read/28685463/in-vivo-epr-resolution-enhancement-using-techniques-known-from-quantum-computing-spin-technology
#20
Robabeh Rahimi, Howard J Halpern, Takeji Takui
A crucial issue with in vivo biological/medical EPR is its low signal-to-noise ratio, giving rise to the low spectroscopic resolution. We propose quantum hyperpolarization techniques based on 'Heat Bath Algorithmic Cooling', allowing possible approaches for improving the resolution in magnetic resonance spectroscopy and imaging.
2017: Advances in Experimental Medicine and Biology
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