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https://www.readbyqxmd.com/read/28488874/an-optically-modulated-self-assembled-resonance-energy-transfer-pass-gate
#1
Craig D LaBoda, Alvin R Lebeck, Chris L Dwyer
We demonstrate an optically controlled molecular-scale pass gate that uses the photoinduced dark states of fluorescent molecules to modulate the flow of excitons. The device consists of four fluorophores spatially arranged on a self-assembled DNA nanostructure. Together, they form a resonance energy transfer (RET) network resembling a standard transistor with a source, channel, drain, and gate. When the gate fluorophore is directly excited, the device is toggled on. Excitons flow freely from the source to the drain, producing strong output fluorescence...
May 10, 2017: Nano Letters
https://www.readbyqxmd.com/read/28470816/patient-specific-methods-for-room-mounted-x-ray-imagers-for-monoscopic-stereoscopic-prostate-motion-monitoring
#2
M Tynan R Stevens, Dave D Parsons, James L Robar
PURPOSE: To investigate the improvement of combined monoscopic/stereoscopic prostate motion monitoring with room-mounted dual x-ray systems by adopting patient specific methods. METHODS: The linac couch was used as a motion stage to simulate 40 highly dynamic real patient prostate trajectories. For each trajectory, 40 s pretreatment and 120 s treatment periods were extracted to represent a typical treatment fraction. Motion was monitored via continuous stereoscopic x-ray imaging of a single gold fiducial and images were retrospectively divided into periods of stereoscopic and monoscopic imaging to simulate periodic blocking of the room-mounted system by the gantry during arc-based therapy...
May 4, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28465380/the-angiopoietin-tie2-signaling-axis-in-systemic-inflammation
#3
Samir M Parikh
Systemic inflammation is a hallmark of commonly encountered diseases ranging from bacterial sepsis to sterile syndromes such as major trauma. Derangements in the host vasculature contribute to the cardinal manifestations of sepsis in profound ways. Recent studies of control pathways regulating the vascular endothelium have illuminated how this single cell layer toggles between quiescence and activation to affect the development of shock and multiorgan dysfunction. This article focuses on one such control pathway, the Tie2 receptor and its ligands the angiopoietins, to describe a growing body of genetic, biochemical, mechanistic, and human studies that implicate Tie2 as a critical switch...
May 2, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28418225/an-iterative-module-in-the-azalomycin%C3%A2-f-polyketide-synthase-contains-a-switchable-enoylreductase-domain
#4
Wei Xu, Guifa Zhai, Yuanzhen Liu, Yuan Li, Yanrong Shi, Kui Hong, Hui Hong, Peter F Leadlay, Zixin Deng, Yuhui Sun
Detailed analysis of the modular Type I polyketide synthase (PKS) involved in the biosynthesis of the marginolactone azalomycin F in mangrove Streptomyces sp. 211726 has shown that only nineteen extension modules are required to accomplish twenty cycles of polyketide chain elongation. Analysis of the products of a PKS mutant specifically inactivated in the dehydratase domain of extension-module 1 showed that this module catalyzes two successive elongations with different outcomes. Strikingly, the enoylreductase domain of this module can apparently be "toggled" off and on : it functions in only the second of these two cycles...
May 8, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28415246/synchronization-dynamics-on-the-picosecond-time-scale-in-coupled-josephson-junction-neurons
#5
K Segall, M LeGro, S Kaplan, O Svitelskiy, S Khadka, P Crotty, D Schult
Conventional digital computation is rapidly approaching physical limits for speed and energy dissipation. Here we fabricate and test a simple neuromorphic circuit that models neuronal somas, axons, and synapses with superconducting Josephson junctions. The circuit models two mutually coupled excitatory neurons. In some regions of parameter space the neurons are desynchronized. In others, the Josephson neurons synchronize in one of two states, in-phase or antiphase. An experimental alteration of the delay and strength of the connecting synapses can toggle the system back and forth in a phase-flip bifurcation...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28374330/timing-of-pmma-cement-application-for-pedicle-screw-augmentation-affects-screw-anchorage
#6
Werner Schmoelz, Christian Heinz Heinrichs, Sven Schmidt, Angel R Piñera, Felix Tome-Bermejo, Javier M Duart, Marlies Bauer, Luis Álvarez Galovich
INTRODUCTION: Cement augmentation is an established method to increase the pedicle screw (PS) anchorage in osteoporotic vertebral bodies. The ideal timing for augmentation when a reposition maneuver is necessary is controversial. While augmentation of the PS before reposition maneuver may increase the force applied it on the vertebrae, it bears the risk to impair PS anchorage, whereas augmenting the PS after the maneuver may restore this anchorage and prevent early screw loosening. The purpose of the present study was to evaluate the effect of cement application timing on PS anchorage in the osteoporotic vertebral body...
April 3, 2017: European Spine Journal
https://www.readbyqxmd.com/read/28362798/interrogating-the-topological-robustness-of-gene-regulatory-circuits-by-randomization
#7
Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, Jose N Onuchic
One of the most important roles of cells is performing their cellular tasks properly for survival. Cells usually achieve robust functionality, for example, cell-fate decision-making and signal transduction, through multiple layers of regulation involving many genes. Despite the combinatorial complexity of gene regulation, its quantitative behavior has been typically studied on the basis of experimentally verified core gene regulatory circuitry, composed of a small set of important elements. It is still unclear how such a core circuit operates in the presence of many other regulatory molecules and in a crowded and noisy cellular environment...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28274123/a-glucose-sensing-toggle-switch-for-autonomous-high-productivity-genetic-control
#8
William Bothfeld, Grace Kapov, Keith E J Tyo
Many biosynthetic strategies are coupled to growth, which is inherently limiting, as (1) excess feedstock (e.g., sugar) may be converted to biomass, instead of product, (2) essential genes must be maintained, and (3) growth toxicity must be managed. A decoupled growth and production phase strategy could avoid these issues. We have developed a toggle switch that uses glucose sensing to enable this two-phase strategy. Temporary glucose starvation precisely and autonomously activates product pathway expression in rich or minimal media, obviating the requirement for expensive inducers...
March 30, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28219948/genomic-integration-of-wnt-%C3%AE-catenin-and-bmp-smad1-signaling-coordinates-foregut-and-hindgut-transcriptional-programs
#9
Mariana L Stevens, Praneet Chaturvedi, Scott A Rankin, Melissa Macdonald, Sajjeev Jagannathan, Masashi Yukawa, Artem Barski, Aaron M Zorn
Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how these signals are interpreted in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts as a genome-wide toggle between foregut and hindgut programs...
April 1, 2017: Development
https://www.readbyqxmd.com/read/28048656/su-f-t-301-planar-dose-pass-rate-inflation-due-to-the-mapcheck-measurement-uncertainty-function
#10
D Bailey, J Spaans, L Kumaraswamy, M Podgorsak
PURPOSE: To quantify the effect of the Measurement Uncertainty function on planar dosimetry pass rates, as analyzed with Sun Nuclear Corporation analytic software ("MapCHECK" or "SNC Patient"). This optional function is toggled on by default upon software installation, and automatically increases the user-defined dose percent difference (%Diff) tolerance for each planar dose comparison. METHODS: Dose planes from 109 IMRT fields and 40 VMAT arcs were measured with the MapCHECK 2 diode array, and compared to calculated planes from a commercial treatment planning system...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28046456/we-de-bra-08-a-linear-accelerator-target-allowing-rapid-switching-between-treatment-and-high-contrast-imaging-modes
#11
M Yewondwossen, J Robar, D Parsons
PURPOSE: During radiotherapy treatment, lung tumors can display substantial respiratory motion. This motion usually necessitates enlarged treatment margins to provide full tumour coverage. Unfortunately, these margins limit the dose that can be prescribed for tumour control and cause complications to normal tissue. Options for real-time methods of direct detection of tumour position, and particularly those that obviate the need for inserted fiducial markers, are limited. We propose a method of tumor tracking without implanted fiducial markers using a novel fast switching-target that toggles between a FFF copper/tungsten therapy mode and a FFF low-Z target mode for imaging...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28027639/helical-self-assembly-induced-singlet-triplet-emissive-switching-in-a-mechanically-sensitive-system
#12
Hongwei Wu, Yunyun Zhou, Liyuan Yin, Cheng Hang, Xin Li, Hans Ågren, Tao Yi, Qing Zhang, Liangliang Zhu
In nanoscience, chirality has shown a significant ability to tune materials' electronic properties, whereas imposing macrochirality into the regulation of singlet-triplet features of organic optoelectronics remains a challenging research topic. Since the tuning for singlet and triplet excited-state properties in a single π-functional molecule connects to its multicolor luminescent application and potential improvement of internal quantum efficiency, we here report that supramolecular chirality can be employed to toggle the singlet and triplet emissions in a well-designed asterisk-shaped molecule...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28024385/controlling-stiction-in-nano-electro-mechanical-systems-using-liquid-crystals
#13
Oleksandr Buchnev, Nina Podoliak, Thomas Frank, Malgosia Kaczmarek, Liudi Jiang, Vassili A Fedotov
Stiction is one of the major reliability issues limiting practical application of nano-electro-mechanical systems (NEMS), an emerging device technology that exploits mechanical movements on the scale of an integrated electronic circuit. We report on a discovery that stiction can be eliminated by infiltrating NEMS with nematic liquid crystals. We demonstrate this experimentally using a NEMS-based tunable photonic metamaterial, where reliable switching of optical response was achieved for the entire range of nanoscopic structural displacements admitted by the metamaterial design...
December 27, 2016: ACS Nano
https://www.readbyqxmd.com/read/27941807/self-organized-amniogenesis-by-human-pluripotent-stem-cells-in-a-biomimetic-implantation-like-niche
#14
Yue Shao, Kenichiro Taniguchi, Katherine Gurdziel, Ryan F Townshend, Xufeng Xue, Koh Meng Aw Yong, Jianming Sang, Jason R Spence, Deborah L Gumucio, Jianping Fu
Amniogenesis-the development of amnion-is a critical developmental milestone for early human embryogenesis and successful pregnancy. However, human amniogenesis is poorly understood due to limited accessibility to peri-implantation embryos and a lack of in vitro models. Here we report an efficient biomaterial system to generate human amnion-like tissue in vitro through self-organized development of human pluripotent stem cells (hPSCs) in a bioengineered niche mimicking the in vivo implantation environment...
April 2017: Nature Materials
https://www.readbyqxmd.com/read/27927198/a-computational-method-for-the-investigation-of-multistable-systems-and-its-application-to-genetic-switches
#15
Miriam Leon, Mae L Woods, Alex J H Fedorec, Chris P Barnes
BACKGROUND: Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic switches can be used for recording the presence of different environmental signals, for changing phenotype using synthetic inputs and as building blocks for higher-level sequential logic circuits. Understanding how multistable switches can be constructed and how they function within larger biological systems is therefore key to synthetic biology...
December 7, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27811141/a-glucocorticoid-and-diet-responsive-pathway-toggles-adipocyte-precursor-cell-activity-in-vivo
#16
Janica C Wong, Katherine C Krueger, Maria José Costa, Abhishek Aggarwal, Hongqing Du, Tracey L McLaughlin, Brian J Feldman
Obesity is driven by excess caloric intake, which leads to the expansion of adipose tissue by hypertrophy and hyperplasia. Adipose tissue hyperplasia results from the differentiation of adipocyte precursor cells (APCs) that reside in adipose depots. Investigation into this process has elucidated a network of mostly transcription factors that drive APCs through the differentiation process. Using in vitro and in vivo approaches, our study revealed a signaling pathway that inhibited the initiation of the adipocyte differentiation program...
October 25, 2016: Science Signaling
https://www.readbyqxmd.com/read/27781448/super-transient-scaling-in-time-delay-autonomous-boolean-network-motifs
#17
Otti D'Huys, Johannes Lohmann, Nicholas D Haynes, Daniel J Gauthier
Autonomous Boolean networks are commonly used to model the dynamics of gene regulatory networks and allow for the prediction of stable dynamical attractors. However, most models do not account for time delays along the network links and noise, which are crucial features of real biological systems. Concentrating on two paradigmatic motifs, the toggle switch and the repressilator, we develop an experimental testbed that explicitly includes both inter-node time delays and noise using digital logic elements on field-programmable gate arrays...
September 2016: Chaos
https://www.readbyqxmd.com/read/27768683/intrinsic-noise-profoundly-alters-the-dynamics-and-steady-state-of-morphogen-controlled-bistable-genetic-switches
#18
Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27618190/a-chemical-inducible-crispr-cas9-system-for-rapid-control-of-genome-editing
#19
Kaiwen Ivy Liu, Muhammad Nadzim Bin Ramli, Cheok Wei Ariel Woo, Yuanming Wang, Tianyun Zhao, Xiujun Zhang, Guo Rong Daniel Yim, Bao Yi Chong, Ali Gowher, Mervyn Zi Hao Chua, Jonathan Jung, Jia Hui Jane Lee, Meng How Tan
CRISPR-Cas9 has emerged as a powerful technology that enables ready modification of the mammalian genome. The ability to modulate Cas9 activity can reduce off-target cleavage and facilitate precise genome engineering. Here we report the development of a Cas9 variant whose activity can be switched on and off in human cells with 4-hydroxytamoxifen (4-HT) by fusing the Cas9 enzyme with the hormone-binding domain of the estrogen receptor (ERT2). The final optimized variant, termed iCas, showed low endonuclease activity without 4-HT but high editing efficiency at multiple loci with the chemical...
November 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27539010/the-switch-in-a-genetic-toggle-system-with-l%C3%A3-vy-noise
#20
Yong Xu, Yongge Li, Hao Zhang, Xiaofan Li, Jürgen Kurths
A bistable toggle switch is a paradigmatic model in the field of biology. The dynamics of the system induced by Gaussian noise has been intensively investigated, but Gaussian noise cannot incorporate large bursts typically occurring in real experiments. This paper aims to examine effects of variations from one protein imposed by a non-Gaussian Lévy noise, which is able to describe even large jumps, on the coherent switch and the on/off switch via the steady-state probability density, the joint steady-state probability density, and the mean first passage time...
2016: Scientific Reports
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