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Biological noise

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https://www.readbyqxmd.com/read/28105915/spectral-consensus-strategy-for-accurate-reconstruction-of-large-biological-networks
#1
Séverine Affeldt, Nataliya Sokolovska, Edi Prifti, Jean-Daniel Zucker
BACKGROUND: The last decades witnessed an explosion of large-scale biological datasets whose analyses require the continuous development of innovative algorithms. Many of these high-dimensional datasets are related to large biological networks with few or no experimentally proven interactions. A striking example lies in the recent gut bacterial studies that provided researchers with a plethora of information sources. Despite a deeper knowledge of microbiome composition, inferring bacterial interactions remains a critical step that encounters significant issues, due in particular to high-dimensional settings, unknown gut bacterial taxa and unavoidable noise in sparse datasets...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#2
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103789/nonlinear-dimensionality-reduction-methods-for-synthetic-biology-biobricks-visualization
#3
Jiaoyun Yang, Haipeng Wang, Huitong Ding, Ning An, Gil Alterovitz
BACKGROUND: Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103008/quantitative-tracking-of-combinatorially-engineered-populations-with-multiplexed-binary-assemblies
#4
Ramsey Zeitoun, Gur Pines, William C Grau, Ryan T Gill
Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory timescales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28099482/a-new-statistical-approach-to-characterize-chemical-elicited-behavioral-effects-in-high-throughput-studies-using-zebrafish
#5
Guozhu Zhang, Lisa Truong, Robert L Tanguay, David M Reif
Zebrafish have become an important alternative model for characterizing chemical bioactivity, partly due to the efficiency at which systematic, high-dimensional data can be generated. However, these new data present analytical challenges associated with scale and diversity. We developed a novel, robust statistical approach to characterize chemical-elicited effects in behavioral data from high-throughput screening (HTS) of all 1,060 Toxicity Forecaster (ToxCast™) chemicals across 5 concentrations at 120 hours post-fertilization (hpf)...
2017: PloS One
https://www.readbyqxmd.com/read/28095198/effects-of-small-world-rewiring-probability-and-noisy-synaptic-conductivity-on-slow-waves-cortical-network
#6
Ramazan Tekin, Mehmet Emin Tagluk
Physiological rhythms play a critical role in the functional development of living beings. Many biological functions are executed with an interaction of rhythms produced by internal characteristics of scores of cells. While synchronized oscillations may be associated with normal brain functions, anomalies in these oscillations may cause or relate the emergence of some neurological or neuropsychological pathologies. This study was designed to investigate the effects of topological structure and synaptic conductivity noise on the spatial synchronization and temporal rhythmicity of the waves generated by cells in the network...
January 17, 2017: Neural Computation
https://www.readbyqxmd.com/read/28092691/effective-detection-of-variation-in-single-cell-transcriptomes-using-matq-seq
#7
Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng, Chenghang Zong
The quantification of transcriptional variation in single cells, particularly within the same cell population, is currently limited by the low sensitivity and high technical noise of single-cell RNA-seq assays. We report multiple annealing and dC-tailing-based quantitative single-cell RNA-seq (MATQ-seq), a highly sensitive and quantitative method for single-cell sequencing of total RNA. By systematically determining technical noise, we show that MATQ-seq captures genuine biological variation between whole transcriptomes of single cells...
January 16, 2017: Nature Methods
https://www.readbyqxmd.com/read/28092361/designed-cell-consortia-as-fragrance-programmable-analog-to-digital-converters
#8
Marius Müller, Simon Ausländer, Andrea Spinnler, David Ausländer, Julian Sikorski, Marc Folcher, Martin Fussenegger
Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28092029/an-efficient-semi-supervised-learning-approach-to-predict-sh2-domain-mediated-interactions
#9
Kousik Kundu, Rolf Backofen
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28089543/optimal-regulatory-circuit-topologies-for-fold-change-detection
#10
Miri Adler, Pablo Szekely, Avi Mayo, Uri Alon
Evolution repeatedly converges on only a few regulatory circuit designs that achieve a given function. This simplicity helps us understand biological networks. However, why so few circuits are rediscovered by evolution is unclear. We address this question for the case of fold-change detection (FCD): a response to relative changes of input rather than absolute changes. Two types of FCD circuits recur in biological systems-the incoherent feedforward and non-linear integral-feedback loops. We performed an analytical screen of all three-node circuits in a class comprising ∼500,000 topologies...
January 10, 2017: Cell Systems
https://www.readbyqxmd.com/read/28088482/combined-spatiotemporal-ica-stica-for-continuous-and-dynamic-lag-structure-analysis-of-mreg-data
#11
Ville Raatikainen, Niko Huotari, Vesa Korhonen, Aleksi Rasila, Janne Kananen, Lauri Raitamaa, Tuija Keinänen, Jussi Kantola, Osmo Tervonen, Vesa Kiviniemi
This study investigated lag structure in the resting-state fMRI by applying a novel independent component (ICA) method to magnetic resonance encephalography (MREG) data. Briefly, the spatial ICA (sICA) was used for defining the frontal and back nodes of the default mode network (DMN), and the temporal ICA (tICA), which is enabled by the high temporal resolution of MREG (TR=100ms), was used to separate both neuronal and physiological components of these two spatial map regions. Subsequently, lag structure was investigated between the frontal (DMNvmpf) and posterior (DMNpcc) DMN nodes using both conventional method with all-time points and a sliding-window approach...
January 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28069594/sigmod-an-exact-and-efficient-method-to-identify-a-strongly-interconnected-disease-associated-module-in-a-gene-network
#12
Yuanlong Liu, Myriam Brossard, Damian Roqueiro, Patricia Margaritte-Jeannin, Chloé Sarnowski, Emmanuelle Bouzigon, Florence Demenais
MOTIVATION: Apart from single marker-based tests classically used in genome-wide association studies (GWAS), network-assisted analysis has become a promising approach to identify a set of genes associated with disease. To date, most network-assisted methods aim at finding genes connected in a background network, whatever the density or strength of their connections. This can hamper the findings as sparse connections are non-robust against noise from either the GWAS results or the network resource...
January 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28069376/translational-issues-in-cochlear-synaptopathy
#13
REVIEW
Ann E Hickox, Erik Larsen, Michael G Heinz, Leslie Shinobu, Jonathon P Whitton
Understanding the biology of the previously underappreciated sensitivity of cochlear synapses to noise insult, and its clinical consequences, is becoming a mission for a growing number of auditory researchers. In addition, several research groups have become interested in developing therapeutic approaches that can reverse synaptopathy and restore hearing function. One of the major challenges to realizing the potential of synaptopathy rodent models is that current clinical audiometric approaches cannot yet reveal the presence of this subtle cochlear pathology in humans...
January 6, 2017: Hearing Research
https://www.readbyqxmd.com/read/28068790/temporomandibular-disorders-old-ideas-and-new-concepts
#14
Thomas List, Rigmor Højland Jensen
Background Temporomandibular disorders (TMD) is an umbrella term for pain and dysfunction involving the masticatory muscles and the temporomandibular joints (TMJs). TMD is the most common orofacial pain condition. Its prominent features include regional pain in the face and preauricular area, limitations in jaw movement, and noise from the TMJs during jaw movements. TMD affects up to 15% of adults and 7% of adolescents. Chronic pain is the overwhelming reason that patients with TMD seek treatment. TMD can associate with impaired general health, depression, and other psychological disabilities, and may affect the quality of life of the patient...
January 1, 2017: Cephalalgia: An International Journal of Headache
https://www.readbyqxmd.com/read/28068481/micrornas-and-periodontal-homeostasis
#15
X Luan, X Zhou, J Trombetta-eSilva, M Francis, A K Gaharwar, P Atsawasuwan, T G H Diekwisch
MicroRNAs (miRNAs) are a group of small RNAs that control gene expression in all aspects of eukaryotic life, primarily through RNA silencing mechanisms. The purpose of the present review is to introduce key miRNAs involved in periodontal homeostasis, summarize the mechanisms by which they affect downstream genes and tissues, and provide an introduction into the therapeutic potential of periodontal miRNAs. In general, miRNAs function synergistically to fine-tune the regulation of biological processes and to remove expression noise rather than by causing drastic changes in expression levels...
January 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28068315/hyperspectral-phasor-analysis-enables-multiplexed-5d-in-vivo-imaging
#16
Francesco Cutrale, Vikas Trivedi, Le A Trinh, Chi-Li Chiu, John M Choi, Marcela S Artiga, Scott E Fraser
Time-lapse imaging of multiple labels is challenging for biological imaging as noise, photobleaching and phototoxicity compromise signal quality, while throughput can be limited by processing time. Here, we report software called Hyper-Spectral Phasors (HySP) for denoising and unmixing multiple spectrally overlapping fluorophores in a low signal-to-noise regime with fast analysis. We show that HySP enables unmixing of seven signals in time-lapse imaging of living zebrafish embryos.
January 9, 2017: Nature Methods
https://www.readbyqxmd.com/read/28068090/femtosecond-to-millisecond-dynamics-of-light-induced-allostery-in-the-avena-sativa-lov-domain
#17
Agnieszka A Gil, Sergey P Laptenok, Jarrod B French, James N Iuliano, Andras Lukacs, Christopher R Hall, Igor V Sazanovich, Gregory M Greetham, Adelbert Bacher, Boris Illarionov, Markus Fischer, Peter J Tonge, Stephen R Meech
The rational engineering of photosenor proteins underpins the field of optogenetics, in which light is used for spatio-temporal control of cell signalling. Optogenetic elements function by converting electronic excitation of an embedded chromophore into structural changes on the μs-sec timescale, which then modulate the activity of output domains responsible for biological signalling. Using time resolved vibrational spectroscopy coupled with isotope labelling we have mapped the structural evolution of the LOV2 domain of the flavin binding phototropin Avena sativa (AsLOV2) over 10 decades of time, reporting structural dynamics between 100 femtoseconds and one millisecond after optical ex-citation...
January 9, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28067287/smartphone-based-low-light-detection-for-bioluminescence-application
#18
Huisung Kim, Youngkee Jung, Iyll-Joon Doh, Roxana Andrea Lozano-Mahecha, Bruce Applegate, Euiwon Bae
We report a smartphone-based device and associated imaging-processing algorithm to maximize the sensitivity of standard smartphone cameras, that can detect the presence of single-digit pW of radiant flux intensity. The proposed hardware and software, called bioluminescent-based analyte quantitation by smartphone (BAQS), provides an opportunity for onsite analysis and quantitation of luminescent signals from biological and non-biological sensing elements which emit photons in response to an analyte. A simple cradle that houses the smartphone, sample tube, and collection lens supports the measuring platform, while noise reduction by ensemble averaging simultaneously lowers the background and enhances the signal from emitted photons...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28065937/dynomics-to-identify-delays-and-co-expression-patterns-across-time-course-experiments
#19
Jasmin Straube, Bevan Emma Huang, Kim-Anh Lê Cao
Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time. Integration of such data aims to identify molecules that show similar expression changes over time; such molecules may be co-regulated and thus involved in similar biological processes. Combining data sources presents a systematic approach to study molecular behaviour. It can compensate for missing data in one source, and can reduce false positives when multiple sources highlight the same pathways...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28064496/alkaline-phosphatase-triggered-simultaneous-hydrogelation-and-chemiluminescence
#20
Zijuan Hai, Jindan Li, Jingjing Wu, Jiacheng Xu, Gaolin Liang
Chemiluminescence (CL) has a higher signal-to-noise ratio than fluorescence, but the use of CL to track an enzyme-instructed self-assembly (EISA) process has not been reported. In this work, by coincubation of the hydrogelator precursor Fmoc-Phe-Phe-Tyr(H2PO3)-OH (1P) and the CL agent AMPPD (2) with alkaline phosphatase (ALP), we employed CL to directly characterize and image the simultaneous EISA process of 1P. Hydrogelation processes of 1P with and without 2 and the CL properties of 2 with and without 1P under ALP catalysis were systematically studied...
January 11, 2017: Journal of the American Chemical Society
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