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https://www.readbyqxmd.com/read/29780628/comprehensive-targeted-super-deep-next-generation-sequencing-enhances-differential-diagnosis-of-solitary-pulmonary-nodules
#1
Mingzhi Ye, Shiyong Li, Weizhe Huang, Chunli Wang, Liping Liu, Jun Liu, Jilong Liu, Hui Pan, Qiuhua Deng, Hailing Tang, Long Jiang, Weizhe Huang, Xi Chen, Di Shao, Zhiyu Peng, Renhua Wu, Jing Zhong, Zhe Wang, Xiaoping Zhang, Karsten Kristiansen, Jian Wang, Ye Yin, Mao Mao, Jianxing He, Wenhua Liang
Background: A non-invasive method to predict the malignancy of surgery-candidate solitary pulmonary nodules (SPN) is urgently needed. Methods: Super-depth next generation sequencing (NGS) of 35 paired tissues and plasma DNA was performed as an attempt to develop an early diagnosis approach. Results: Only ~6% of malignant nodule patients had driver mutations in the circulating tumour DNA (ctDNA) with >10,000-fold sequencing depth, and the concordance of mutation between tDNA and ctDNA was 3...
April 2018: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29777912/a-super-enhancer-maintains-homeostatic-expression-of-regnase-1
#2
Riyun Yang, Yuanyuan Wu, Yue Ming, Yuanpei Xu, Shouyan Wang, Jianbo Shen, Chenlu Wang, Xia Chen, Yongming Wang, Renfang Mao, Yihui Fan
Regnase-1 is not only a key component in maintaining intracellular homeostasis but also a critical negative regulator in preventing autoimmune diseases and cancer development. To keep homeostatic state, Regnase-1 has to be maintained at a desired level in multiple cell types. However, the molecular mechanism of keeping a certain transcriptional level of Reganase-1 is largely unknown. In this study, we found a super-enhancer (Reg-1-SE) around Regnase-1 gene is able to control the homeostatic expression of Regnase-1...
May 16, 2018: Gene
https://www.readbyqxmd.com/read/29777141/quantum-optically-enhanced-storm-quest-for-multi-emitter-localization
#3
Marc Aßmann
Super-resolution imaging has introduced new capabilities to investigate processes at the nanometer scale by optical means. However, most super-resolution techniques require either sparse excitation of few emitters or analysis of high-order cumulants in order to identify several emitters in close vicinity. Here, we present an approach that draws upon methods from quantum optics to perform localization super-resolution imaging of densely packed emitters and determine their number automatically: Quantum-optically enhanced STORM (QUEST)...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29774907/plasmon-response-evaluation-based-on-image-derived-arbitrary-nanostructures
#4
S Trautmann, M Richard-Lacroix, A Dathe, H Schneidewind, J Dellith, W Fritzsche, V Deckert
The optical response of realistic 3D plasmonic substrates composed of randomly shaped particles of different size and interparticle distance distributions in addition to nanometer scale surface roughness is intrinsically challenging to simulate due to computational limitations. Here, we present a Finite Element Method (FEM)-based methodology that bridges in-depth theoretical investigations and experimental optical response of plasmonic substrates composed of such silver nanoparticles. Parametrized scanning electron microscopy (SEM) images of surface enhanced Raman spectroscopy (SERS) active substrate and tip-enhanced Raman spectroscopy (TERS) probes are used to simulate the far-and near-field optical response...
May 18, 2018: Nanoscale
https://www.readbyqxmd.com/read/29773832/distinct-epigenetic-landscapes-underlie-the-pathobiology-of-pancreatic-cancer-subtypes
#5
Gwen Lomberk, Yuna Blum, Rémy Nicolle, Asha Nair, Krutika Satish Gaonkar, Laetitia Marisa, Angela Mathison, Zhifu Sun, Huihuang Yan, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Tamas Ordog, Jeong-Heon Lee, Gavin Oliver, Eric Klee, Vincent Moutardier, Odile Gayet, Benjamin Bian, Pauline Duconseil, Marine Gilabert, Martin Bigonnet, Stephane Garcia, Olivier Turrini, Jean-Robert Delpero, Marc Giovannini, Philippe Grandval, Mohamed Gasmi, Veronique Secq, Aurélien De Reyniès, Nelson Dusetti, Juan Iovanna, Raul Urrutia
Recent studies have offered ample insight into genome-wide expression patterns to define pancreatic ductal adenocarcinoma (PDAC) subtypes, although there remains a lack of knowledge regarding the underlying epigenomics of PDAC. Here we perform multi-parametric integrative analyses of chromatin immunoprecipitation-sequencing (ChIP-seq) on multiple histone modifications, RNA-sequencing (RNA-seq), and DNA methylation to define epigenomic landscapes for PDAC subtypes, which can predict their relative aggressiveness and survival...
May 17, 2018: Nature Communications
https://www.readbyqxmd.com/read/29771329/regulation-of-the-neuropathy-associated-pmp22-gene-by-a-distal-super-enhancer
#6
Harrison Pantera, John J Moran, Holly A Hung, Evgenia Pak, Amalia Dutra, John Svaren
Peripheral nerve myelination is adversely affected in the most common form of the hereditary peripheral neuropathy called Charcot-Marie-Tooth Disease. This form, classified as CMT1A, is caused by a 1.4 Mb duplication on chromosome 17, which includes the abundantly expressed Schwann cell myelin gene, Peripheral Myelin Protein 22 (PMP22). This is one of the most common copy number variants causing neurological disease. Overexpression of Pmp22 in rodent models recapitulates several aspects of neuropathy, and reduction of Pmp22 in such models results in amelioration of the neuropathy phenotype...
May 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29769037/a-method-for-estimating-relative-changes-in-the-synaptic-density-in-drosophila-central-nervous-system
#7
Dipti Rai, Swagata Dey, Krishanu Ray
BACKGROUND: Synapse density is an essential indicator of development and functioning of the central nervous system. It is estimated indirectly through the accumulation of pre and postsynaptic proteins in tissue sections. 3D reconstruction of the electron microscopic images in serial sections is one of the most definitive means of estimating the formation of active synapses in the brain. It is tedious and highly skill-dependent. Confocal imaging of whole mounts or thick sections of the brain provides a natural alternative for rapid gross estimation of the synapse density in large areas...
May 16, 2018: BMC Neuroscience
https://www.readbyqxmd.com/read/29768130/super-pill-is-less-effective-than-an-ordinary-mint-in-altering-subjective-psychological-feeling-states-within-a-few-minutes
#8
Attila Szabo, Lilla Jobbágy, Ferenc Köteles
Expectations shape human behavior. Initial drug use might be associated with information-based expectations. In this study, we presumed that changes in affect and perceived physical wellbeing will be stronger after receiving an active placebo (Tic Tac mint; n = 40), than a pure placebo (inert pill; n = 40) given as a mood-enhancing "super pill." After baseline measures, participants completed a treatment-expectancy scale, ingested the mint/super pill, and attended to the effects over 3-minutes. Subsequently, they completed again the psychological tests...
April 2018: Journal of General Psychology
https://www.readbyqxmd.com/read/29767502/low-voltage-solution-processed-hybrid-light-emitting-transistors
#9
Mujeeb Ullah Chaudhry, Kornelius Tetzner, Yen-Hung Lin, Sungho Nam, Christopher Pearson, Chris Groves, Michael C Petty, Thomas D Anthopoulos, Donal D C Bradley
We report the development of low operating voltages in inorganic-organic hybrid light-emitting transistors (HLETs) based on solution-processed ZrOx gate dielectric and a hybrid multilayer channel consisting of the heterojunction In3 O2 /ZnO and the organic polymer 'Super Yellow' acting as n- and p-channel/emissive layers, respectively. Resulting HLETs operate at the lowest voltages reported to-date (<10 V) and combine high electron mobility (22 cm2 /Vs) with appreciable current on/off ratios (≈103 ) and an external quantum efficiency of 2×10-2 % at 700 cd/m2 ...
May 16, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29765516/selective-dissociation-between-lsd1-and-gfi1b-by-a-lsd1-inhibitor-ncd38-induces-the-activation-of-erg-super-enhancer-in-erythroleukemia-cells
#10
Ryusuke Yamamoto, Masahiro Kawahara, Shinji Ito, Junko Satoh, Goichi Tatsumi, Masakatsu Hishizawa, Takayoshi Suzuki, Akira Andoh
Lysine-specific demethylase 1 (LSD1) is a histone modifier for transcriptional repression involved in the regulation of hematopoiesis. We previously reported that a LSD1 inhibitor NCD38 induces transdifferentiation from erythroid lineage to granulomonocytic lineage and exerts anti-leukemia effect through de-repression of the specific super-enhancers of hematopoietic regulators including ERG in a human erythroleukemia cell line, HEL. However, the mechanistic basis for this specificity of NCD38 has remained unclear...
April 20, 2018: Oncotarget
https://www.readbyqxmd.com/read/29762557/sparsity-based-reconstruction-for-super-resolved-limited-view-photoacoustic-computed-tomography-deep-in-a-scattering-medium
#11
David M Egolf, Ryan K W Chee, Roger J Zemp
Delay-and-sum beamforming (DSB) of photoacoustic data does not incorporate a priori spatial sparsity of the imaging target. By incorporating this information into beamforming for limited-view photoacoustic computed tomography, we experimentally obtained enhanced resolution images of wires at a depth of 8.5 mm in a tissue mimicking scattering medium. Using a 21 MHz transducer, we improved the resolution from the 200 to 250 μm achieved by DSB to 75 μm. The sparsity-based technique also generated a cleaner image with a background signal level of roughly -50  dB, much lower than the roughly -18  dB background signal level of DSB...
May 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29760797/-lmo1-super-enhancer-polymorphism-rs2168101-g-t-correlates-with-decreased-neuroblastoma-risk-in-chinese-children
#12
Jing He, Xiaohong Zhang, Jiao Zhang, Ruizhong Zhang, Tianyou Yang, Jinhong Zhu, Huimin Xia, Yan Zou
Neuroblastoma is one of the most frequently occurring childhood cancers. The rs2168101 G>T polymorphism observed in the LMO1 gene is located at a conserved GATA transcription factor binding motif. This polymorphism was reported to be significantly associated with neuroblastoma susceptibility. However, whether this and other functional polymorphisms can affect neuroblastoma risk of Chinese children remains unknown. We conducted a two-center hospital-based case-control study with a total of 374 cases and 812 controls to assess the role of five LMO1 gene polymorphisms in the neuroblastoma risk...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29757144/computational-prediction-of-ctcf-cohesin-based-intra-tad-loops-that-insulate-chromatin-contacts-and-gene-expression-in-mouse-liver
#13
Bryan J Matthews, David J Waxman
CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues...
May 14, 2018: ELife
https://www.readbyqxmd.com/read/29755129/molecular-mechanism-of-the-tp53-mdm2-ar-akt-signalling-network-regulation-by-usp12
#14
Urszula L McClurg, Nay C T H Chit, Mahsa Azizyan, Joanne Edwards, Arash Nabbi, Karl T Riabowol, Sirintra Nakjang, Stuart R McCracken, Craig N Robson
The TP53-MDM2-AR-AKT signalling network plays a critical role in the development and progression of prostate cancer. However, the molecular mechanisms regulating this signalling network are not completely defined. By conducting transcriptome analysis, denaturing immunoprecipitations and immunopathology, we demonstrate that the TP53-MDM2-AR-AKT cross-talk is regulated by the deubiquitinating enzyme USP12 in prostate cancer. Our findings explain why USP12 is one of the 12 most commonly overexpressed cancer-associated genes located near an amplified super-enhancer...
May 14, 2018: Oncogene
https://www.readbyqxmd.com/read/29754476/targeting-super-enhancers-for-disease-treatment-and-diagnosis
#15
Ha Youn Shin
The transcriptional regulation of genes determines the fate of animal cell differentiation and subsequent organ development. With the recent progress in genome-wide technologies, the genomic landscapes of enhancers have been broadly explored in mammalian genomes, which led to the discovery of novel specific subsets of enhancers, termed superenhancers. Super-enhancers are large clusters of enhancers covering the long region of regulatory DNA and are densely occupied by transcription factors, active histone marks, and co-activators...
May 10, 2018: Molecules and Cells
https://www.readbyqxmd.com/read/29743689/electron-magnetic-reconnection-without-ion-coupling-in-earth-s-turbulent-magnetosheath
#16
T D Phan, J P Eastwood, M A Shay, J F Drake, B U Ö Sonnerup, M Fujimoto, P A Cassak, M Øieroset, J L Burch, R B Torbert, A C Rager, J C Dorelli, D J Gershman, C Pollock, P S Pyakurel, C C Haggerty, Y Khotyaintsev, B Lavraud, Y Saito, M Oka, R E Ergun, A Retino, O Le Contel, M R Argall, B L Giles, T E Moore, F D Wilder, R J Strangeway, C T Russell, P A Lindqvist, W Magnes
Magnetic reconnection in current sheets is a magnetic-to-particle energy conversion process that is fundamental to many space and laboratory plasma systems. In the standard model of reconnection, this process occurs in a minuscule electron-scale diffusion region1,2 . On larger scales, ions couple to the newly reconnected magnetic-field lines and are ejected away from the diffusion region in the form of bi-directional ion jets at the ion Alfvén speed3-5 . Much of the energy conversion occurs in spatially extended ion exhausts downstream of the diffusion region 6 ...
May 2018: Nature
https://www.readbyqxmd.com/read/29741610/aff4-promotes-tumorigenesis-and-tumor-initiation-capacity-of-head-and-neck-squamous-cell-carcinoma-cells-by-regulating-sox2
#17
Peng Deng, Jiongke Wang, Xuefeng Zhang, Xingyu Wu, Ning Ji, Jing Li, Min Zhou, Lu Jiang, Xin Zeng, Qianming Chen
Super elongation complex (SEC) controls gene transcription by releasing Pol II from pausing. Previous studies have shown that dysfunction of SEC was associated with multiple human cancers, such as leukemia and breast cancer. However, the role of SEC in head and neck squamous cell carcinoma (HNSCC) development remains largely unknown. In this study, we found expression of AF4/FMR2 family member 4 (AFF4), the core component of SEC, was upregulated dramatically in HNSCC cell lines and tumor tissues. By using siRNA-mediated depletion and overexpression of AFF4, we demonstrated AFF4 promoted proliferation, migration and invasion of HNSCC cells...
May 8, 2018: Carcinogenesis
https://www.readbyqxmd.com/read/29740163/directional-subradiance-from-helical-phase-imprinted-multiphoton-states
#18
H H Jen
We theoretically investigate the far-field scattering properties of multiphoton super- and subradiant states which can be prepared by multiphoton excitations with orbital angular momentum (OAM). Due to multiphoton interference, the far-field patterns of the subradiant modes show directional scattering along the excitation direction or transverse scattering with number of peaks equal to the number of atoms. When more atoms are involved, we consider structures of stacked and concentric rings, which respectively show enhanced directional scattering and smoothed emission patterns...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29737993/investigating-the-dynamics-of-excitons-in-monolayer-wse-2-before-and-after-organic-super-acid-treatment
#19
Xin Chen, Zhuo Wang, Lei Wang, Hai-Yu Wang, Yuan-Yuan Yue, Hai Wang, Xue-Peng Wang, Andrew T S Wee, Cheng-Wei Qiu, Hong-Bo Sun
Due to the large photoluminescence quantum yield, high mobility and good stability, organic super acid treated two-dimensional WSe2 has drawn much attention. However, reports about the influence of organic super acid treatment on the dynamic processes of excitons of monolayer WSe2 are still rare. In this work, through the broadband transient absorption spectra obtained using a femtosecond pump-probe system, we determine the dynamics of A' and C excitons in monolayer and bulk WSe2 at room temperature. Besides this, we also observe the relaxation process of the holes between the two spin split states in the valence band maximum in organic super acid treated monolayer WSe2...
May 8, 2018: Nanoscale
https://www.readbyqxmd.com/read/29733581/dual-analyte-fluorescent-sensor-based-on-5-helicene-derivative-with-super-large-stokes-shift-for-the-selective-determinations-of-cu2-or-zn2-in-buffer-solutions-and-its-application-in-living-cell
#20
Siwakorn Sakunkaewkasem, Anuwut Petdum, Waraporn Panchan, Jitnapa Sirirak, Adisri Charoenpanich, Thanasat Sooksimuang, Nantanit Wanichacheva
A new fluorescent sensor, M201-DPA, based on [5]helicene derivative was utilized as dual-analyte sensor for determination of Cu2+ or Zn2+ in different media and different emission wavelengths. The sensor could provide selective and bifunctional determination of Cu2+ in HEPES buffer containing Triton-X100 and Zn2+ in Tris buffer/methanol without the interfering from each other and other ions. In HEPES buffer, M201-DPA demonstrated the selective ON-OFF fluorescence quenching at 524 nm toward Cu2+. On the other hand, in Tris buffer/methanol, M201-DPA showed the selective OFF-ON fluorescence enhancement upon the addition of Zn2+, which was specified by the hypsochromic shift at 448 nm...
May 7, 2018: ACS Sensors
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