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Biological noise

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https://www.readbyqxmd.com/read/28805936/characterizing-hypoxia-in-human-glioma-a-simultaneous-multimodal-mri-and-pet-study
#1
Christine Preibisch, Kuangyu Shi, Anne Kluge, Mathias Lukas, Benedikt Wiestler, Jens Göttler, Jens Gempt, Florian Ringel, Mohamed Al Jaberi, Jürgen Schlegel, Bernhard Meyer, Claus Zimmer, Thomas Pyka, Stefan Förster
Hypoxia plays an important role for the prognosis and therapy response of cancer. Thus, hypoxia imaging would be a valuable tool for pre-therapeutic assessment of tumor malignancy. However, there is no standard validated technique for clinical application available yet. Therefore, we performed a study in 12 patients with high-grade glioma, where we directly compared the two currently most promising techniques, namely the MR-based relative oxygen extraction fraction (MR-rOEF) and the PET hypoxia marker H-1-(3-[(18) F]-fluoro-2-hydroxypropyl)-2-nitroimidazole ([(18) F]-FMISO)...
August 14, 2017: NMR in Biomedicine
https://www.readbyqxmd.com/read/28805306/bioprocess-scale-up-down-as-integrative-enabling-technology-from-fluid-mechanics-to-systems-biology-and-beyond
#2
Frank Delvigne, Ralf Takors, Rob Mudde, Walter van Gulik, Henk Noorman
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology...
August 14, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28802824/highly-accurate-prediction-of-protein-self-interactions-by-incorporating-the-average-block-and-pssm-information-into-the-general-pseaac
#3
Jing-Xuan Zhai, Tian-Jie Cao, Ji-Yong An, Yong-Tao Bian
It is a challenging task for fundamental research whether proteins can interact with their partners. Protein self-interaction (SIP) is a special case of PPIs, which plays a key role in the regulation of cellular functions. Due to the limitations of experimental self-interaction identification, it is very important to develop an effective biological tool for predicting SIPs based on protein sequences. In the study, we developed a novel computational method called RVM-AB that combines the Relevance Vector Machine (RVM) model and Average Blocks (AB) for detecting SIPs from protein sequences...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28802326/a-biological-inspired-fuzzy-adaptive-window-median-filter-fawmf-for-enhancing-dna-signal-processing
#4
Muneer Ahmad, Low Tan Jung, Al-Amin Bhuiyan
BACKGROUND AND OBJECTIVE: Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise...
October 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/28798694/decomposing-multifractal-crossovers
#5
Zoltan Nagy, Peter Mukli, Peter Herman, Andras Eke
Physiological processes-such as, the brain's resting-state electrical activity or hemodynamic fluctuations-exhibit scale-free temporal structuring. However, impacts common in biological systems such as, noise, multiple signal generators, or filtering by transport function, result in multimodal scaling that cannot be reliably assessed by standard analytical tools that assume unimodal scaling. Here, we present two methods to identify breakpoints or crossovers in multimodal multifractal scaling functions. These methods incorporate the robust iterative fitting approach of the focus-based multifractal formalism (FMF)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28797233/full-l1-regularized-traction-force-microscopy-over-whole-cells
#6
Alejandro Suñé-Auñón, Alvaro Jorge-Peñas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck, Arrate Muñoz-Barrutia
BACKGROUND: Traction Force Microscopy (TFM) is a widespread technique to estimate the tractions that cells exert on the surrounding substrate. To recover the tractions, it is necessary to solve an inverse problem, which is ill-posed and needs regularization to make the solution stable. The typical regularization scheme is given by the minimization of a cost functional, which is divided in two terms: the error present in the data or data fidelity term; and the regularization or penalty term...
August 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28795697/perovskite-based-photodetectors-materials-and-devices
#7
REVIEW
Huan Wang, Dong Ha Kim
While the field of perovskite-based optoelectronics has mostly been dominated by photovoltaics, light-emitting diodes, and transistors, semiconducting properties peculiar to perovskites make them interesting candidates for innovative and disruptive applications in light signal detection. Perovskites combine effective light absorption in the broadband range with good photo-generation yield and high charge carrier mobility, a combination that provides promising potential for exploiting sensitive and fast photodetectors that are targeted for image sensing, optical communication, environmental monitoring or chemical/biological detection...
August 10, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28794472/high-resolution-transport-of-intensity-quantitative-phase-microscopy-with-annular-illumination
#8
Chao Zuo, Jiasong Sun, Jiaji Li, Jialin Zhang, Anand Asundi, Qian Chen
For quantitative phase imaging (QPI) based on transport-of-intensity equation (TIE), partially coherent illumination provides speckle-free imaging, compatibility with brightfield microscopy, and transverse resolution beyond coherent diffraction limit. Unfortunately, in a conventional microscope with circular illumination aperture, partial coherence tends to diminish the phase contrast, exacerbating the inherent noise-to-resolution tradeoff in TIE imaging, resulting in strong low-frequency artifacts and compromised imaging resolution...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28792517/comparison-of-alternative-approaches-for-analysing-multi-level-rna-seq-data
#9
Irina Mohorianu, Amanda Bretman, Damian T Smith, Emily K Fowler, Tamas Dalmay, Tracey Chapman
RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D...
2017: PloS One
https://www.readbyqxmd.com/read/28791781/many-transcription-factors-contribute-to-c-%C3%A2-elegans-growth-and-fat-storage
#10
Akihiro Mori, Amy D Holdorf, Albertha J M Walhout
Reverse genetic screens by RNA interference (RNAi) in model organisms such as the nematode Caenorhabditis elegans have provided numerous insights into gene function, thereby connecting genotype to phenotype. However, genes that contribute only subtly are often missed because relatively large numbers of measurements and reliable quantification are required to overcome experimental and biological noise that may mask subtle phenotypic effects. Here, we address this challenge by focusing on two phenotypes in C...
August 8, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28789963/detection-of-prostate-cancer-risk-factor-immunosensor-based-deposition-of-graphene-layer-decorated-gold-nanoparticles
#11
Mintu Pal, Raju Khan
In this work, we report a novel electrochemical immunosensorbased on gold nanoparticles deposited on the surface of graphene layers to detect prostate-specific antigen (PSA), a valuable biomarker for early detection of prostate cancer. The biosensor was fabricated using gold nanoparticles supported graphene oxide (Au-GrO) nanocomposite on platinum electrode and was used for immobilization of monoclonal anti-PSA antibody via EDC/NHS coupling method. To confirm the functionality of the antibody, we performed immunofluorescence staining using human normal prostate epithelial cells, RWPE-1...
August 5, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28781712/trom-a-testing-based-method-for-finding-transcriptomic-similarity-of-biological-samples
#12
Wei Vivian Li, Yiling Chen, Jingyi Jessica Li
Comparative transcriptomics has gained increasing popularity in genomic research thanks to the development of high-throughput technologies including microarray and next-generation RNA sequencing that have generated numerous transcriptomic data. An important question is to understand the conservation and divergence of biological processes in different species. We propose a testing-based method TROM (Transcriptome Overlap Measure) for comparing transcriptomes within or between different species, and provide a different perspective, in contrast to traditional correlation analyses, about capturing transcriptomic similarity...
June 2017: Statistics in Biosciences
https://www.readbyqxmd.com/read/28776613/an-ultra-sensitive-colorimetric-assay-for-reliable-visual-detection-of-telomerase-activity
#13
Yaocai Wang, Luzhu Yang, Yanjun Wang, Wei Liu, Baoxin Li, Yan Jin
The visual detection of a disease biomarker is a promising strategy due to its simplicity and low cost, but the complexity of biological samples limits its application. Herein, a reliable and ultrasensitive colorimetric assay was proposed for detecting telomerase activity in crude cancer cell extracts. A telomerase substrate (TS) primer was immobilized onto magnetic beads (MBs) to form a MB/TS complex. In the presence of telomerase and deoxyribonucleotide triphosphates (dNTPs), the TS primer was elongated by adding multiple telomeric repeats (TTAGGG)n to the 3' end of the TS...
August 4, 2017: Analyst
https://www.readbyqxmd.com/read/28772563/improved-margins-detection-of-regions-enriched-with-gold-nanoparticles-inside-biological-phantom
#14
Yossef Danan, Inbar Yariv, Zeev Zalevsky, Moshe Sinvani
Utilizing the surface plasmon resonance (SPR) effect of gold nanoparticles (GNPs) enables their use as contrast agents in a variety of biomedical applications for diagnostics and treatment. These applications use both the very strong scattering and absorption properties of the GNPs due to their SPR effects. Most imaging methods use the light-scattering properties of the GNPs. However, the illumination source is in the same wavelength of the GNPs' scattering wavelength, leading to background noise caused by light scattering from the tissue...
February 20, 2017: Materials
https://www.readbyqxmd.com/read/28764976/more-than-just-noise-inter-individual-differences-in-fear-acquisition-extinction-and-return-of-fear-in-humans-biological-experiential-temperamental-factors-and-methodological-pitfalls
#15
REVIEW
Tina B Lonsdorf, Christian J Merz
Why do only some individuals develop pathological anxiety following adverse events? Fear acquisition, extinction and return of fear paradigms serve as experimental learning models for the development, treatment and relapse of anxiety. Individual differences in experimental performance were however mostly regarded as 'noise' by researchers interested in basic associative learning principles. Our work for the first time presents a comprehensive literature overview and methodological discussion on inter-individual differences in fear acquisition, extinction and return of fear...
July 29, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28764496/microcantilever-array-instrument-based-on-optical-fiber-and-performance-analysis
#16
Guangping Zhang, Lin Wu, Chao Li, Shangquan Wu, Qingchuan Zhang
We developed a microcantilever array biosensor instrument based on optical readout from a microcantilever array in fluid environment. The microcantilever signals were read out sequentially by laser beams emitted from eight optical fibers. The optical fibers were coupled to lasers, while the other ends of the fibers were embedded in eight V-grooves with 250 μm pitch microfabricated from a Si wafer. Aspherical lens was used to keep the distance between lasers. A programmable logic controller was used to make the system work stably...
July 2017: Review of Scientific Instruments
https://www.readbyqxmd.com/read/28763934/community-response-to-construction-noise-in-three-central-cities-of-zhejiang-province-china
#17
Yong Liu, Bo Xia, Caiyun Cui, Martin Skitmore
As a common source of environmental noise in China and many developing countries worldwide, construction work provokes many complaints and deterioration in acoustic climate quality. This paper describes research to obtain an improved understanding of people's community response to, and evaluation of, construction noise in three central cities of Zhejiang province, China. This involved carrying out a social survey using standard questionnaires developed by the International Commission on Biological Effects of Noise (ICBEN)...
July 25, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28756341/once-upon-a-slow-time-in-the-land-of-recurrent-neuronal-networks%C3%A2
#18
REVIEW
Chengcheng Huang, Brent Doiron
The brain must both react quickly to new inputs as well as store a memory of past activity. This requires biology that operates over a vast range of time scales. Fast time scales are determined by the kinetics of synaptic conductances and ionic channels; however, the mechanics of slow time scales are more complicated. In this opinion article we review two distinct network-based mechanisms that impart slow time scales in recurrently coupled neuronal networks. The first is in strongly coupled networks where the time scale of the internally generated fluctuations diverges at the transition between stable and chaotic firing rate activity...
July 27, 2017: Current Opinion in Neurobiology
https://www.readbyqxmd.com/read/28753631/enhancement-of-early-warning-properties-in-the-kuramoto-model-and-in-an-atrial-fibrillation-model-due-to-an-external-perturbation-of-the-system
#19
David García-Gudiño, Emmanuel Landa, Joel Mendoza-Temis, Alondra Albarado-Ibañez, Juan C Toledo-Roy, Irving O Morales, Alejandro Frank
When a complex dynamical system is externally disturbed, the statistical moments of signals associated to it can be affected in ways that depend on the nature and amplitude of the perturbation. In systems that exhibit phase transitions, the statistical moments can be used as Early Warnings (EW) of the transition. A natural question is thus to wonder what effect external disturbances have on the EWs of system. In this work we study the impact of external noise added to the system on the EWs, with particular focus on understanding the importance of the amplitude and complexity of the noise...
2017: PloS One
https://www.readbyqxmd.com/read/28749972/investigating-asymmetric-salt-profiles-for-nanopore-dna-sequencing-with-biological-porin-mspa
#20
Ian C Nova, Ian M Derrington, Jonathan M Craig, Matthew T Noakes, Benjamin I Tickman, Kenji Doering, Hugh Higinbotham, Andrew H Laszlo, Jens H Gundlach
Nanopore DNA sequencing is a promising single-molecule analysis technology. This technique relies on a DNA motor enzyme to control movement of DNA precisely through a nanopore. Specific experimental buffer conditions are required based on the preferred operating conditions of the DNA motor enzyme. While many DNA motor enzymes typically operate in salt concentrations under 100 mM, salt concentration simultaneously affects signal and noise magnitude as well as DNA capture rate in nanopore sequencing, limiting standard experimental conditions to salt concentrations greater than ~100 mM in order to maintain adequate resolution and experimental throughput...
2017: PloS One
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