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Biological noise

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https://www.readbyqxmd.com/read/28528232/a-mathematical-and-biological-plausible-model-of-decision-execution-regulation-in-go-no-go-tasks-focusing-on-the-fronto-striatal-thalamic-pathway
#1
Golnaz Baghdadi, Farzad Towhidkhah, Reza Rostami
Discovering factors influencing the speed and accuracy of responses in tasks such as "Go/No-Go" is one of issues which have been raised in neurocognitive studies. Mathematical models are considered as tools to identify and to study decision making procedure from different aspects. In this paper, a mathematical model has been presented to show several factors can alter the output of decision making procedure before execution in a "Go/No-Go" task. The dynamic of this model has two stable fixed points, each of them corresponds to the "Press" and "Not-press" responses...
May 13, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28524926/a-980-nm-laser-activated-upconverted-persistent-probe-for-nir-to-nir-rechargeable-in-vivo-bioimaging
#2
Zhenluan Xue, Xiaolong Li, Youbin Li, Mingyang Jiang, Guozhong Ren, Hongrong Liu, Songjun Zeng, Jianhua Hao
Long-lasting persistent luminescent nanoparticles (PLNPs) with efficient near-infrared (NIR) emission have emerged as a new generation of probes for in vivo optical bioimaging owing to their advantages of zero-autofluorescence benefited from the self-sustained emission after excitation, deep penetration depth, and a high signal-to-noise ratio. However, most of the PLNPs are charged by ultraviolet (UV) or visible light, remarkably limiting their applications for in vivo long-term bioimaging. Here we demonstrate 980 nm laser activated upconversion-PLNPs (UC-PLNPs) with efficient NIR emission...
May 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28521011/translation-initiation-events-on-structured-eukaryotic-mrnas-generate-gene-expression-noise
#3
Estelle Dacheux, Naglis Malys, Xiang Meng, Vinoy Ramachandran, Pedro Mendes, John Eg McCarthy
Gene expression stochasticity plays a major role in biology, creating non-genetic cellular individuality and influencing multiple processes, including differentiation and stress responses. We have addressed the lack of knowledge about posttranscriptional contributions to noise by determining cell-to-cell variations in the abundance of mRNA and reporter protein in yeast. Two types of structural element, a stem-loop and a poly(G) motif, not only inhibit translation initiation when inserted into an mRNA 5΄ untranslated region, but also generate noise...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520403/integrated-strategy-for-unknown-ei-ms-identification-using-quality-control-calibration-curve-multivariate-analysis-ei-ms-spectral-database-and-retention-index-prediction
#4
Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900,000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a 'four-step' strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) Quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28518097/light-sheet-based-fluorescence-microscopy-of-living-or-fixed-and-stained-tribolium-castaneum-embryos
#5
Frederic Strobl, Selina Klees, Ernst H K Stelzer
The red flour beetle Tribolium castaneum has become an important insect model organism in developmental genetics and evolutionary developmental biology. The observation of Tribolium embryos with light sheet-based fluorescence microscopy has multiple advantages over conventional widefield and confocal fluorescence microscopy. Due to the unique properties of a light sheet-based microscope, three dimensional images of living specimens can be recorded with high signal-to-noise ratios and significantly reduced photo-bleaching as well as photo-toxicity along multiple directions over periods that last several days...
April 28, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28509528/synthesis-of-water-soluble-ag2s-quantum-dots-with-fluorescence-in-the-second-near-infrared-window-for-turn-on-detection-of-zn-ii-and-cd-ii
#6
Qian Wu, Ming Zhou, Jing Shi, Qijun Li, Mingyang Yang, Zhixun Zhang
The second near-infrared window emission (1.0-1.7 μm, NIR-II) has received extensive attention with the advantages of negligible tissue scattering, reduced auto-fluorescence and less background noise. Here a novel analysis platform based on quantum dots (QDs) for highly selective detection of Zn(2+) and Cd(2+) with an enhanced NIR-II fluorescence is reported for the first time. We have developed a facile two-step route to synthesize the water-soluble Ag2S QDs, constituting of a green hydrothermal process and followed surface ligands exchange...
May 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28507154/information-socialtaxis-and-efficient-collective-behavior-emerging-in-groups-of-information-seeking-agents
#7
Ehud D Karpas, Adi Shklarsh, Elad Schneidman
Individual behavior, in biology, economics, and computer science, is often described in terms of balancing exploration and exploitation. Foraging has been a canonical setting for studying reward seeking and information gathering, from bacteria to humans, mostly focusing on individual behavior. Inspired by the gradient-climbing nature of chemotaxis, the infotaxis algorithm showed that locally maximizing the expected information gain leads to efficient and ethological individual foraging. In nature, as well as in theoretical settings, conspecifics can be a valuable source of information about the environment...
May 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28505824/classification-framework-for-partially-observed-dynamical-systems
#8
Yuan Shen, Peter Tino, Krasimira Tsaneva-Atanasova
We present a general framework for classifying partially observed dynamical systems based on the idea of learning in the model space. In contrast to the existing approaches using point estimates of model parameters to represent individual data items, we employ posterior distributions over model parameters, thus taking into account in a principled manner the uncertainty due to both the generative (observational and/or dynamic noise) and observation (sampling in time) processes. We evaluate the framework on two test beds: a biological pathway model and a stochastic double-well system...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28505785/noise-induced-polarization-switching-in-complex-networks
#9
Jan O Haerter, Albert Díaz-Guilera, M Ángeles Serrano
The combination of bistability and noise is ubiquitous in complex systems, from biology to social interactions, and has important implications for their functioning and resilience. Here we use a simple three-state dynamical process, in which nodes go from one pole to another through an intermediate state, to show that noise can induce polarization switching in bistable systems if dynamical correlations are significant. In large, fully connected networks, where dynamical correlations can be neglected, increasing noise yields a collapse of bistability to an unpolarized configuration where the three possible states of the nodes are equally likely...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28499413/ranking-metrics-in-gene-set-enrichment-analysis-do-they-matter
#10
Joanna Zyla, Michal Marczyk, January Weiner, Joanna Polanska
BACKGROUND: There exist many methods for describing the complex relation between changes of gene expression in molecular pathways or gene ontologies under different experimental conditions. Among them, Gene Set Enrichment Analysis seems to be one of the most commonly used (over 10,000 citations). An important parameter, which could affect the final result, is the choice of a metric for the ranking of genes. Applying a default ranking metric may lead to poor results. METHODS AND RESULTS: In this work 28 benchmark data sets were used to evaluate the sensitivity and false positive rate of gene set analysis for 16 different ranking metrics including new proposals...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28497559/macromolecular-structures-quality-assessment-and-biological-interpretation
#11
REVIEW
Dinakar M Salunke, Deepak T Nair
Structure determination using X-ray crystallography involves collection of diffraction data, determination of initial phases followed by iterative rounds of model building and crystallographic refinement to improve the phases and minimize the differences between calculated and observed structure factors. At each of these stages, a variety of statistical filters exist to ensure appropriate validation. Biologically important observations often come from interpretations of signals that need to be carefully deciphered from noise, and therefore human intervention is as important as the automated methods and filters...
May 11, 2017: IUBMB Life
https://www.readbyqxmd.com/read/28494372/separation-and-preconcentration-of-riboflavin-from-human-plasma-using-polythionine-coated-magnetite-hydroxyapatite-nanocomposite-prior-to-analysis-by-surfactant-enhanced-fluorimetry
#12
Leila Farzin, Mojtaba Shamsipur
The exploration of novel adsorption properties of conductive polymers based on hybridization with biocompatible nanomaterials receives an increasing interest. In this regard, hydroxyapatite (HA) bioceramic is of critical importance mainly owing to its facile synthesis, high surface area, economic and low toxicity in biological environments. In this work, we first prepared and characterized a magnetite/hydroxyapatite (Fe3O4/HA) nanocomposite using the bio-waste chicken eggshell via an attractive green way that involved low cost and irrespective of toxicity...
May 2, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28494367/enhanced-detection-sensitivity-of-carcinoembryonic-antigen-on-a-plasmonic-nanoimmunosensor-by-transmission-grating-based-total-internal-reflection-scattering-microscopy
#13
Sujin Ahn, Hyunung Yu, Seong Ho Kang
Carcinoembryonic antigen (CEA) is a glycoprotein associated with colorectal carcinomas and is commonly used as a clinical tumor marker. Enhanced detection sensitivity for the assay of CEA molecules was achieved on a plasmonic nanoimmunosensor by wavelength-dependent transmission grating (TG)-based total internal reflection scattering microscopy (TIRSM). The plasmonic nanoparticles were placed in an evanescent field layer on a glass nanoimmunosensor that produced evanescent wave scattering by the total internal reflection of light from two lasers...
May 4, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28488803/promises-and-challenges-in-continuous-tracking-utilizing-amino-acids-in-skin-secretions-for-active-multi-factor-biometric-authentication-for-cybersecurity
#14
Juliana Agudelo, Vladimir Privman, Jan Halámek
We consider a new concept of biometric-based cybersecurity systems for active authentication by continuous tracking, which utilizes biochemical processing of metabolites present in skin secretions. Skin secretions contain a large number of metabolites and small molecules that can be targeted for analysis. Here we argue that amino acids found in sweat can be exploited for the establishment of an amino acid profile capable of identifying an individual user of a mobile or wearable device. Individual and combinations of amino acids processed by biocatalytic cascades yield physical (optical or electronic) signals, providing a time-series of several outputs that, in their entirety, should suffice to authenticate a specific user based on standard statistical criteria...
May 10, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28486051/characterization-of-differences-in-functional-connectivity-associated-with-close-range-blast-exposure
#15
Meghan Robinson, Dustin Clark, William Milberg, Regina McGlinchey, David Salat
Despite the prevalence of blast injuries in recent overseas conflicts, our knowledge of their impact on neural health is lacking. We have recently published work demonstrating differences in functional magnetic resonance imaging (fMRI) connectivity that were specific to close-range blast exposure (CBE), as opposed to other prevalent military-related factors. Here, we replicate this finding in an independent sample of 135 Veterans, again finding that CBE, regardless of concussion, is predictive of persistent changes in brain physiology...
May 9, 2017: Journal of Neurotrauma
https://www.readbyqxmd.com/read/28485132/robust-numerical-phase-stabilization-for-long-range-swept-source-optical-coherence-tomography
#16
Shaozhen Song, Jingjiang Xu, Shaojie Men, Tueng T Shen, Ruikang K Wang
A novel phase stabilization technique is demonstrated with significant improvement in the phase stability of a micro-electromechanical (MEMS) vertical cavity surface-emitting laser (VCSEL) based swept-source optical coherence tomography (SS-OCT) system. Without any requirements of hardware modifications, the new fully numerical phase stabilization technique features high tolerance to acquisition jitter, and significantly reduced budget in computational effort. We demonstrate that when measured with biological tissue, this technique enables a phase sensitivity of 89 mrad in highly scattering tissue, with image ranging distance of up to 12...
May 9, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28484032/heritability-analysis-with-repeat-measurements-and-its-application-to-resting-state-functional-connectivity
#17
Tian Ge, Avram J Holmes, Randy L Buckner, Jordan W Smoller, Mert R Sabuncu
Heritability, defined as the proportion of phenotypic variation attributable to genetic variation, provides important information about the genetic basis of a trait. Existing heritability analysis methods do not discriminate between stable effects (e.g., due to the subject's unique environment) and transient effects, such as measurement error. This can lead to misleading assessments, particularly when comparing the heritability of traits that exhibit different levels of reliability. Here, we present a linear mixed effects model to conduct heritability analyses that explicitly accounts for intrasubject fluctuations (e...
May 8, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28482571/optimization-and-development-of-maghemite-%C3%AE-fe2o3-filled-poly-l-lactic-acid-plla-thermoplastic-polyurethane-tpu-electrospun-nanofibers-using-taguchi-orthogonal-array-for-tissue-engineering-heart-valve
#18
Ehsan Fallahiarezoudar, Mohaddeseh Ahmadipourroudposht, Ani Idris, Noordin Mohd Yusof
Tissue engineering (TE) is an advanced principle to develop a neotissue that can resemble the original tissue characteristics with the capacity to grow, to repair and to remodel in vivo. This research proposed the optimization and development of nanofiber based scaffold using the new mixture of maghemite (γ-Fe2O3) filled poly-l-lactic acid (PLLA)/thermoplastic polyurethane (TPU) for tissue engineering heart valve (TEHV). The chemical, structural, biological and mechanical properties of nanofiber based scaffold were characterized in terms of morphology, porosity, biocompatibility and mechanical behaviour...
July 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28474674/tradict-enables-accurate-prediction-of-eukaryotic-transcriptional-states-from-100-marker-genes
#19
Surojit Biswas, Konstantin Kerner, Paulo José Pereira Lima Teixeira, Jeffery L Dangl, Vladimir Jojic, Philip A Wigge
Transcript levels are a critical determinant of the proteome and hence cellular function. Because the transcriptome is an outcome of the interactions between genes and their products, it may be accurately represented by a subset of transcript abundances. We develop a method, Tradict (transcriptome predict), capable of learning and using the expression measurements of a small subset of 100 marker genes to predict transcriptome-wide gene abundances and the expression of a comprehensive, but interpretable list of transcriptional programs that represent the major biological processes and pathways of the cell...
May 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28463291/high-brightness-low-coherence-digital-holographic-microscopy-for-3d-visualization-of-an-in-vitro-sandwiched-biological-sample
#20
D G Abdelsalam, Takeshi Yasui
We achieve practically a bright-field digital holographic microscopy (DHM) configuration free from coherent noise for three-dimensional (3D) visualization of an in-vitro sandwiched sarcomere sample. Visualization of such sandwiched samples by conventional atomic force microscope (AFM) is impossible, while visualization using DHM with long coherent lengths is challenging. The proposed configuration is comprised of an ultrashort pulse laser source and a Mach-Zehnder interferometer in transmission. Periodically poled lithium niobate (PPLN) crystal was used to convert the fundamental beam by second harmonic generation (SHG) to the generated beam fit to the CCD camera used...
May 1, 2017: Applied Optics
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