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Biological noise

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https://www.readbyqxmd.com/read/29150680/potential-landscape-of-high-dimensional-nonlinear-stochastic-dynamics-with-large-noise
#1
Ying Tang, Ruoshi Yuan, Gaowei Wang, Xiaomei Zhu, Ping Ao
Quantifying stochastic processes is essential to understand many natural phenomena, particularly in biology, including the cell-fate decision in developmental processes as well as the genesis and progression of cancers. While various attempts have been made to construct potential landscape in high dimensional systems and to estimate transition rates, they are practically limited to the cases where either noise is small or detailed balance condition holds. A general and practical approach to investigate real-world nonequilibrium systems, which are typically high-dimensional and subject to large multiplicative noise and the breakdown of detailed balance, remains elusive...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150629/statistically-strong-label-free-quantitative-identification-of-native-fluorophores-in-a-biological-sample
#2
Saabah B Mahbub, Martin Plöschner, Martin E Gosnell, Ayad G Anwer, Ewa M Goldys
Bioimaging using endogenous cell fluorescence, without any external biomarkers makes it possible to explore cells and tissues in their original native state, also in vivo. In order to be informative, this label-free method requires careful multispectral or hyperspectral recording of autofluorescence images followed by unsupervised extraction (unmixing) of biochemical signatures. The unmixing is difficult due to the scarcity of biochemically pure regions in cells and also because autofluorescence is weak compared with signals from labelled cells, typically leading to low signal to noise ratio...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29147512/on-the-performance-of-a-photosystem-ii-reaction-centre-based-photocell
#3
Richard Stones, Hoda Hossein-Nejad, Rienk van Grondelle, Alexandra Olaya-Castro
The photosystem II reaction centre is the photosynthetic complex responsible for oxygen production on Earth. Its water splitting function is particularly favoured by the formation of a stable charge separated state via a pathway that starts at an accessory chlorophyll. Here we envision a photovoltaic device that places one of these complexes between electrodes and investigate how the mean current and its fluctuations depend on the microscopic interactions underlying charge separation in the pathway considered...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29141554/insight-into-the-role-of-long-non-coding-rnas-during-osteogenesis-in-mesenchymal-stem-cells
#4
Sibei Huo, Yachuan Zhou, Xinyu He, Mian Wan, Wei Du, Xin Xu, Ling Ye, Xuedong Zhou, Liwei Zheng
BACKGROUND: Long non-coding RNAs (LncRNAs) are non-protein coding transcripts longer than 200 nucleotides in length. Instead of being "transcriptional noise", lncRNAs are emerging as a key modulator in various biological processes and disease development. Mesenchymal stem cells can be isolated from various adult tissues, such as bone marrow and dental tissues. The differentiation processes into multiple lineages, such as osteogenic differentiation, are precisely orchestrated by molecular signals in both genetic and epigenetic ways...
November 15, 2017: Current Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29138457/functional-annotation-of-structural-ncrnas-within-enhancer-rnas-in-the-human-genome-implications-for-human-disease
#5
Chao Ren, Feng Liu, Zhangyi Ouyang, Gaole An, Chenghui Zhao, Jun Shuai, Shuhong Cai, Xiaochen Bo, Wenjie Shu
Enhancer RNAs (eRNAs) are a novel class of non-coding RNA (ncRNA) molecules transcribed from the DNA sequences of enhancer regions. Despite extensive efforts devoted to revealing the potential functions and underlying mechanisms of eRNAs, it remains an open question whether eRNAs are mere transcriptional noise or relevant biologically functional species. Here, we identified a catalogue of eRNAs in a broad range of human cell/tissue types and extended our understanding of eRNAs by demonstrating their multi-omic signatures...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136653/drlumi-an-open-source-package-to-manage-data-calibrate-and-conduct-quality-control-of-multiplex-bead-based-immunoassays-data-analysis
#6
Hector Sanz, John J Aponte, Jaroslaw Harezlak, Yan Dong, Aintzane Ayestaran, Augusto Nhabomba, Maxmillian Mpina, Obiang Régis Maurin, Núria Díez-Padrisa, Ruth Aguilar, Gemma Moncunill, Agnandij Selidji Todagbe, Claudia Daubenberger, Carlota Dobaño, Clarissa Valim
Multiplex bead-based immunoassays are used to measure concentrations of several analytes simultaneously. These assays include control standard curves (SC) to reduce between-plate variability and normalize quantitation of analytes of biological samples. Suboptimal calibration might result in large random error and decreased number of samples with analyte concentrations within the limits of quantification. Suboptimal calibration may be a consequence of poor fitness of the functions used for the SC, the treatment of the background noise and the method used to estimate the limits of quantification...
2017: PloS One
https://www.readbyqxmd.com/read/29136588/a-facile-way-to-fabricate-manganese-phosphate-self-assembled-carbon-networks-as-efficient-electrochemical-catalysts-for-real-time-monitoring-of-superoxide-anions-released-from-hepg2-cells
#7
Xuan Cai, Libo Shi, Wenqian Sun, Hongli Zhao, Hong Li, Haiyan He, Minbo Lan
Quantification of superoxide anions (O2(•-)) is significant in the monitoring of many serious diseases and the design of enzyme-mimic catalysts plays the main role in the development of non-enzymatic O2(•-) sensors. Herein, we proposed a facile self-assembly process to synthesize manganese phosphate modified carbon networks using three kinds of widely-used carbon materials (MWCNTs, NGS and GO) as pillar connectors. Characterizations demonstrate that manganese phosphate is widely dispersed inside and on the surface of carbon networks without visible morphology...
November 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29136165/low-dose-electron-energy-loss-spectroscopy-using-electron-counting-direct-detectors
#8
Alan Maigné, Matthias Wolf
Since the development of parallel electron energy loss spectroscopy (EELS), charge-coupled devices (CCDs) have been the default detectors for EELS. With the recent development of electron-counting direct-detection cameras, micrographs can be acquired under very low electron doses at significantly improved signal-to-noise ratio. In spectroscopy, in particular in combination with a monochromator, the signal can be extremely weak and the detection limit is principally defined by noise introduced by the detector...
November 9, 2017: Microscopy
https://www.readbyqxmd.com/read/29131578/optically-detected-magnetic-resonance-for-selective-imaging-of-diamond-nanoparticles
#9
Margaret E Robinson, James D Ng, Huilong Zhang, Joseph T Buchman, Olga A Shenderova, Christy L Haynes, Zhenqiang Ma, Randall H Goldsmith, Robert J Hamers
While there is great interest in understanding the fate and transport of nanomaterials in the environment and in biological systems, the detection of nanomaterials in complex matrices by fluorescence methods is complicated by photodegradation, blinking, and by the presence of natural organic material and other fluorescent background signals that hamper detection of fluorescent nanomaterials of interest. Optically detected magnetic resonance (ODMR) of nitrogen-vacancy (NV) centers in diamond nanoparticles provides a pathway toward background-free fluorescence measurements, as the application of a resonant microwave field can selectively modulate the intensity from NV centers in the diamond in nanodiamonds of various diameters in complex materials systems using on-resonance and off-resonance microwave fields...
November 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29127572/strong-surface-enhanced-florescence-of-carbon-dot-labeled-bacteria-cells-observed-with-high-contrast-on-gold-film
#10
Rostislav Bukasov, Olena Filchakova, Kristina Gudun, Mohamed Bouhrara
Strong surface (metal) enhanced fluorescence (SEF or MEF) is observed from clusters and single E coli bacteria cells labeled with Carbon nanodots (CDs), which were synthesized from date pits. The enhancement factor (EF) for SEF of the cell clusters were close to 50 for both 533 and 633 nm laser excitation wavelength. Those EFs are ratios of emission peak areas from CD labeled cell clusters on gold film to the peak areas of the same batch cell clusters on glass substrate. SEF with 633 nm excitation performed better than SEF with 532 nm excitation, achieving higher fluorescence intensity and much higher contrast...
November 10, 2017: Journal of Fluorescence
https://www.readbyqxmd.com/read/29121044/information-theoretic-analysis-of-the-directional-influence-between-cellular-processes
#11
Sourabh Lahiri, Philippe Nghe, Sander J Tans, Martin Luc Rosinberg, David Lacoste
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying interactions. Here, we use the transfer entropy (TE), an information-theoretic quantity that quantifies the directional influence between fluctuating variables in a model-free way. We present a theoretical approach to compute the transfer entropy, even when the noise has an extrinsic component or in the presence of feedback...
2017: PloS One
https://www.readbyqxmd.com/read/29119503/inverse-problems-in-systems-biology-a-critical-review
#12
Rodolfo Guzzi, Teresa Colombo, Paola Paci
Systems Biology may be assimilated to a symbiotic cyclic interplaying between the forward and inverse problems. Computational models need to be continuously refined through experiments and in turn they help us to make limited experimental resources more efficient. Every time one does an experiment we know that there will be some noise that can disrupt our measurements. Despite the noise certainly is a problem, the inverse problems already involve the inference of missing information, even if the data is entirely reliable...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29118850/study-of-in-vitro-transcriptional-binding-effects-and-noise-using-constitutive-promoters-combined-with-up-element-sequences-in-escherichia-coli
#13
Qiang Yan, Stephen S Fong
Background: UP elements (upstream element) are DNA sequences upstream of a promoter that interact with the α-subunit of RNA polymerase (RNAP) and can affect transcription by altering the binding RNAP to DNA. However, details of UP element and binding affinity effects on transcriptional strength are unclear. Results: Here, we investigated the effects of UP element sequences on gene transcription, binding affinity, and gene expression noise. Addition of UP elements resulted in increased gene expression (maximum 95...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29118406/single-cell-co-expression-subnetwork-analysis
#14
Thomas E Bartlett, Sören Müller, Aaron Diaz
Single-cell transcriptomic data have rapidly become very popular in genomic science. Genomic science also has a long history of using network models to understand the way in which genes work together to carry out specific biological functions. However, working with single-cell data presents major challenges, such as zero inflation and technical noise. These challenges require methods to be specifically adapted to the context of single-cell data. Recently, much effort has been made to develop the theory behind statistical network models...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29116942/microfluidic-multiplexing-of-solid-state-nanopores
#15
Tarun Jain, Benjamin C Rasera, Ricardo Jose S Guerrero, Jong-Min Lim, Rohit Karnik
Although solid-state nanopores enable electronic analysis of many clinically and biologically relevant molecular structures, there are few existing device architectures that enable high-throughput measurement of solid-state nanopores. Herein, we report a method for microfluidic integration of multiple solid-state nanopores at a high density of one nanopore per (35 µm(2)). By configuring microfluidic devices with microfluidic valves, the nanopores can be rinsed from a single fluid input while retaining compatibility for multichannel electrical measurements...
November 8, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29116097/microscopy-as-a-statistical-r%C3%A3-nyi-ulam-half-lie-game-a-new-heuristic-search-strategy-to-accelerate-imaging
#16
Daniel W Drumm, Andrew D Greentree
Finding a fluorescent target in a biological environment is a common and pressing microscopy problem. This task is formally analogous to the canonical search problem. In ideal (noise-free, truthful) search problems, the well-known binary search is optimal. The case of half-lies, where one of two responses to a search query may be deceptive, introduces a richer, Rényi-Ulam problem and is particularly relevant to practical microscopy. We analyse microscopy in the contexts of Rényi-Ulam games and half-lies, developing a new family of heuristics...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29112986/simultaneous-genome-wide-gene-expression-and-transcript-isoform-profiling-in-the-human-malaria-parasite
#17
Lindsey B Turnbull, Geoffrey H Siwo, Katrina A Button-Simons, Asako Tan, Lisa A Checkley, Heather J Painter, Manuel Llinás, Michael T Ferdig
Gene expression DNA microarrays have been vital for characterizing whole-genome transcriptional profiles. Nevertheless, their effectiveness relies heavily on the accuracy of genome sequences, the annotation of gene structures, and the sequence-dependent performance of individual probes. Currently available gene expression arrays for the malaria parasite Plasmodium falciparum rely on an average of 2 probes per gene, usually positioned near the 3' end of genes; consequently, existing designs are prone to measurement bias and cannot capture complexities such as the occurrence of transcript isoforms arising from alternative splicing or alternative start/ stop sites...
2017: PloS One
https://www.readbyqxmd.com/read/29111670/non-neurotoxic-nanodiamond-probes-for-intraneuronal-temperature-mapping
#18
David A Simpson, Emma Morrisroe, Julia M McCoey, Alain H Lombard, Dulini C Mendis, François Treussart, Liam T Hall, Steven Petrou, Lloyd C L Hollenberg
Optical biomarkers have been used extensively for intracellular imaging with high spatial and temporal resolution. Extending the modality of these probes is a key driver in cell biology. In recent years, the nitrogen-vacancy (NV) center in nanodiamond has emerged as a promising candidate for bioimaging and biosensing with low cytotoxicity and stable photoluminescence. Here we study the electrophysiological effects of this quantum probe in primary cortical neurons. Multielectrode array recordings across five replicate studies showed no statistically significant difference in 25 network parameters when nanodiamonds are added at varying concentrations over various time periods, 12-36 h...
November 13, 2017: ACS Nano
https://www.readbyqxmd.com/read/29111610/the-function-and-mechanism-of-vocal-accommodation-in-humans-and-other-primates
#19
Hanna Ruch, Yvonne Zürcher, Judith M Burkart
The study of non-human animals, in particular primates, can provide essential insights into language evolution. A critical element of language is vocal production learning, i.e. learning how to produce calls. In contrast to other lineages such as songbirds, vocal production learning of completely new signals is strikingly rare in non-human primates. An increasing body of research, however, suggests that various species of non-human primates engage in vocal accommodation and adjust the structure of their calls in response to environmental noise or conspecific vocalizations...
November 7, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29111606/incubation-with-cu-ii-and-zn-ii-salts-enhances-maldi-tof-mass-spectra-of-amyloid-beta-and-%C3%AE-synuclein-toward-in-vivo-analysis
#20
Andrea R Kelley, Madeline E Colley, George Perry, Stephan B H Bach
Insoluble senile plaque aggregates are indicative of Alzheimer's disease (AD) pathology. A similar phenomenon occurs in Parkinson's disease (PD) with the build-up of Lewy bodies. The analysis of senile plaques, and other brain samples, from AD and PD patients by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has advantages but also presents obstacles due to the nature of the processes utilized in isolation procedures and storage. Salts, buffers, and detergents necessary in isolation of biological species may cause adducts and ion suppression that convolute the spectra obtained...
November 7, 2017: Journal of Mass Spectrometry: JMS
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