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https://www.readbyqxmd.com/read/28212749/comparative-analysis-of-single-cell-rna-sequencing-methods
#1
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard
Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2. While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs)...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28210188/non-contact-photoacoustic-imaging-using-a-commercial-heterodyne-interferometer
#2
Chao Tian, Ting Feng, Cheng Wang, Shengchun Liu, Qian Cheng, David E Oliver, Xueding Wang, Guan Xu
Most current photoacoustic imaging (PAI) systems employ piezoelectric transducers to receive photoacoustic signals, which requires coupling medium to facilitate photoacoustic wave propagation and are not favored in many applications. Here, we report an all-optical non-contact PAI system based on a commercial heterodyne interferometer working at 1550 nm. The interferometer remotely detects ultrasound-induced surface vibration and does not involve any physical contact with the sample. The theoretically predicated and experimentally measured noise equivalent detection limits of the optical sensor are about 4...
December 1, 2016: IEEE Sensors Journal
https://www.readbyqxmd.com/read/28208500/sign-changes-as-a-universal-concept-in-first-passage-time-calculations
#3
Wilhelm Braun, Rüdiger Thul
First-passage-time problems are ubiquitous across many fields of study, including transport processes in semiconductors and biological synapses, evolutionary game theory and percolation. Despite their prominence, first-passage-time calculations have proven to be particularly challenging. Analytical results to date have often been obtained under strong conditions, leaving most of the exploration of first-passage-time problems to direct numerical computations. Here we present an analytical approach that allows the derivation of first-passage-time distributions for the wide class of nondifferentiable Gaussian processes...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28207908/isolation-and-determination-of-ivermectin-in-post-mortem-and-in-vivo-tissues-of-dung-beetles-using-a-continuous-solid-phase-extraction-method-followed-by-lc-esi-ms-ms
#4
Antonio J Ortiz, Vieyle Cortez, Abdelmonaim Azzouz, José R Verdú
A new analytical method based on solvent extraction, followed by continuous solid-phase extraction (SPE) clean-up using a polymeric sorbent, was demonstrated to be applicable for the detection of ivermectin in complex biological matrices of dung beetles (hemolymph, excreta or dry tissues) using liquid chromatography combined with positive electrospray ionization tandem mass spectrometry (LC/ESI+-MS/MS). Using a signal-to-noise ratio of 3:1, the limit of detection (LOD) in the insect matrices at trace levels was 0...
2017: PloS One
https://www.readbyqxmd.com/read/28207405/compressive-sensing-based-structure-identification-for-multilayer-networks
#5
Guofeng Mei, Xiaoqun Wu, Yingfei Wang, Mi Hu, Jun-An Lu, Guanrong Chen
The coexistence of multiple types of interactions within social, technological, and biological networks has motivated the study of the multilayer nature of real-world networks. Meanwhile, identifying network structures from dynamical observations is an essential issue pervading over the current research on complex networks. This paper addresses the problem of structure identification for multilayer networks, which is an important topic but involves a challenging inverse problem. To clearly reveal the formalism, the simplest two-layer network model is considered and a new approach to identifying the structure of one layer is proposed...
February 13, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28207404/a-noise-reduction-technique-based-on-nonlinear-kernel-function-for-heart-sound-analysis
#6
Ashok Mondal, Ishan Saxena, Hong Tang, Poulami Banerjee
The main difficulty encountered in interpretation of cardiac sound is interference of noise. The contaminated noise obscures the relevant information which are useful for recognition of heart diseases. The unwanted signals are produced mainly by lungs and surrounding environment. In this paper, a novel heart sound de-noising technique has been introduced based on a combined framework of wavelet packet transform (WPT) and singular value decomposition (SVD). The most informative node of wavelet tree is selected on the criteria of mutual information measurement...
February 13, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28196398/factors-of-influence-and-social-correlates-of-parturition-in-captive-campbell-s-monkeys-case-study-and-breeding-data
#7
Alban Lemasson, Ronan Jubin, Philippe Bec, Martine Hausberger
How nonhuman primates deal with birth, at the moment of delivery, and during the following days, remains poorly explored because of the unpredictability of this event, particularly for forest-dwelling arboreal species. Available studies highlight intra- and interspecific variation which suggest flexibility of the timing of delivery, of behavior associated with labor contractions and parturition, and the social context and ambient noise surrounding delivery. Here, we present the findings of a two-decade survey of reproduction in a population of captive Campbell's monkeys...
February 14, 2017: American Journal of Primatology
https://www.readbyqxmd.com/read/28194103/reassessment-of-non-monosynaptic-excitation-from-the-motor-cortex-to-motoneurons-in-single-motor-units-of-the-human-biceps-brachii
#8
Tsuyoshi Nakajima, Toshiki Tazoe, Masanori Sakamoto, Takashi Endoh, Satoshi Shibuya, Leonardo A Elias, Rinaldo A Mezzarane, Tomoyoshi Komiyama, Yukari Ohki
Corticospinal excitation is mediated by polysynaptic pathways in several vertebrates, including dexterous monkeys. However, indirect non-monosynaptic excitation has not been clearly observed following transcranial electrical stimulation (TES) or cervicomedullary stimulation (CMS) in humans. The present study evaluated indirect motor pathways in normal human subjects by recording the activities of single motor units (MUs) in the biceps brachii (BB) muscle. The pyramidal tract was stimulated with weak TES, CMS, and transcranial magnetic stimulation (TMS) contralateral to the recording side...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28193022/development-of-an-ion-mobility-spectrometry-orbitrap-mass-spectrometer-platform
#9
Yehia M Ibrahim, Sandilya V B Garimella, Spencer A Prost, Roza Wojcik, Randolph V Norheim, Erin S Baker, Ivan Rusyn, Richard D Smith
Complex samples benefit from multidimensional measurements where higher resolution enables more complete characterization of biological and environmental systems. To address this challenge, we developed a drift tube-based ion mobility spectrometry-Orbitrap mass spectrometer (IMS-Orbitrap MS) platform. To circumvent the time scale disparity between the fast IMS separation and the much slower Orbitrap MS acquisition, we utilized a dual gate and pseudorandom sequences to multiplex the injection of ions and allow operation in signal averaging (SA), single multiplexing (SM), and double multiplexing (DM) IMS modes to optimize the signal-to-noise ratio of the measurements...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28192423/elucidation-of-molecular-kinetic-schemes-from-macroscopic-traces-using-system-identification
#10
Miguel Fribourg, Diomedes E Logothetis, Javier González-Maeso, Stuart C Sealfon, Belén Galocha-Iragüen, Fernando Las-Heras Andrés, Vladimir Brezina
Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology...
February 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28192413/evolution-of-a-split-rna-polymerase-as-a-versatile-biosensor-platform
#11
Jinyue Pu, Julia Zinkus-Boltz, Bryan C Dickinson
Biosensors that transduce target chemical and biochemical inputs into genetic outputs are essential for bioengineering and synthetic biology. Current biosensor design strategies are often limited by a low signal-to-noise ratio, the extensive optimization required for each new input, and poor performance in mammalian cells. Here we report the development of a proximity-dependent split RNA polymerase (RNAP) as a general platform for biosensor engineering. After discovering that interactions between fused proteins modulate the assembly of a split T7 RNAP, we optimized the split RNAP components for protein-protein interaction detection by phage-assisted continuous evolution (PACE)...
February 13, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28191877/a-virtual-clinical-trial-comparing-static-versus-dynamic-pet-imaging-in-measuring-response-to-breast-cancer-therapy
#12
Kristen A Wangerin, Mark Muzi, Lanell Peterson, Hannah Linden, Alena Novakova, David Mankoff, Paul Kinahan
OBJECTIVE: We developed a method to evaluate variations in the PET imaging process in order to characterize the relative ability of static and dynamic metrics to measure breast cancer response to therapy in a clinical trial setting. METHODS: We performed a virtual clinical trial by generating 540 i.i.d. PET imaging study realizations for each of 22 original dynamic fluorodeoxyglucose (18F-FDG) breast cancer patient studies pre- and post-therapy. Each noise realization accounted for known sources of uncertainty in the imaging process, such as biological variability and SUV uptake time...
February 13, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28191646/non-invasive-evaluation-of-blood-oxygen-saturation-and-hematocrit-from-t1-and-t2-relaxation-times-in-vitro-validation-in-fetal-blood
#13
Sharon Portnoy, Mike Seed, John G Sled, Christopher K Macgowan
PURPOSE: We propose an analytical method for calculating blood hematocrit (Hct) and oxygen saturation (sO2 ) from measurements of its T1 and T2 relaxation times. THEORY: Through algebraic substitution, established two-compartment relationships describing R1=T1-1 and R2=T2-1 as a function of hematocrit and oxygen saturation were rearranged to solve for Hct and sO2 in terms of R1 and R2 . Resulting solutions for Hct and sO2 are the roots of cubic polynomials. METHODS: Feasibility of the method was established by comparison of Hct and sO2 estimates obtained from relaxometry measurements (at 1...
February 12, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28190869/single-molecule-detection-thermal-fluctuation-and-life
#14
Toshio Yanagida, Yoshiharu Ishii
Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28188592/redirecting-reproductive-immunology-research-toward-pregnancy-as-a-period-of-temporary-immune-tolerance
#15
Norbert Gleicher, Vitaly A Kushnir, David H Barad
Referring to two recent publications, we here propose that clinical reproductive immunology has for decades stagnated because reproductive medicine, including assisted reproduction (AR), has failed to accept embryo implantation as an immune system-driven process, dependent on establishment of maternal tolerance toward the implanting fetal semi-allograft (and complete allograft in cases of oocyte donation). Pregnancy represents a biologically unique period of temporary (to the period of gestation restricted) tolerance, otherwise only known in association with parasitic infections...
February 10, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28183729/organelles-understanding-noise-and-heterogeneity-in-cell-biology-at-an-intermediate-scale
#16
REVIEW
Amy Y Chang, Wallace F Marshall
Many studies over the years have shown that non-genetic mechanisms for producing cell-to-cell variation can lead to highly variable behaviors across genetically identical populations of cells. Most work to date has focused on gene expression noise as the primary source of phenotypic heterogeneity, yet other sources may also contribute. In this Commentary, we explore organelle-level heterogeneity as a potential secondary source of cellular 'noise' that contributes to phenotypic heterogeneity. We explore mechanisms for generating organelle heterogeneity and present evidence of functional links between organelle morphology and cellular behavior...
February 9, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28182661/representing-high-throughput-expression-profiles-via-perturbation-barcodes-reveals-compound-targets
#17
Tracey M Filzen, Peter S Kutchukian, Jeffrey D Hermes, Jing Li, Matthew Tudor
High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations. As profiling campaigns expand in scope, it is important to homogenize, summarize, and analyze the resulting data in a manner that captures significant biological signals in spite of various noise sources such as batch effects and stochastic variation. We used the L1000 platform for large-scale profiling of 978 representative genes across thousands of compound treatments...
February 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28181720/organic-bioelectronics-in-medicine
#18
S Löffler, K Melican, K P R Nilsson, A Richter-Dahlfors
A major challenge in the growing field of bioelectronic medicine is the development of tissue interface technologies promoting device integration with biological tissues. Materials based on organic bioelectronics show great promise due to a unique combination of electronic and ionic conductivity properties. In this review, we outline exciting developments in the field of organic bioelectronics and demonstrate the medical importance of these active, electronically controllable materials. Importantly, organic bioelectronics offer a means to control cell-surface attachment as required for many device-tissue applications...
February 9, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28176808/comparative-study-of-the-collective-dynamics-of-proteins-and-inorganic-nanoparticles
#19
Esmael J Haddadian, Hao Zhang, Karl F Freed, Jack F Douglas
Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28167969/bioaerosols-noise-and-ultraviolet-radiation-exposures-for-municipal-solid-waste-handlers
#20
France Ncube, Esper Jacobeth Ncube, Kuku Voyi
Few studies have investigated the occupational hazards of municipal solid waste workers, particularly in developing countries. Resultantly these workers are currently exposed to unknown and unabated occupational hazards that may endanger their health. We determined municipal solid waste workers' work related hazards and associated adverse health endpoints. A multifaceted approach was utilised comprising bioaerosols sampling, occupational noise, thermal conditions measurement, and field based waste compositional analysis...
2017: Journal of Environmental and Public Health
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