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https://www.readbyqxmd.com/read/28214361/identification-of-arabidopsis-genic-and-non-genic-promoters-by-paired-end-sequencing-of-tss-tags
#1
Mutsutomo Tokizawa, Kazutaka Kusunoki, Hiroyuki Koyama, Atsushi Kurotani, Tetsuya Sakurai, Yutaka Suzuki, Tomoaki Sakamoto, Tetsuya Kurata, Yoshiharu Y Yamamoto
Information about transcription start sites (TSSs) provides foundational data for analyses of promoter architecture. In this report, we used paired- and single-end deep sequencing to analyze Arabidopsis TSS tags from several libraries prepared from roots, shoots, flowers, and etiolated seedlings. The clustering of approximately 33 million mapped TSS tags led to the identification of 324,461 promoters that covered 79.7% (21,672/27,206) of protein-coding genes in the Arabidopsis genome. In addition, we identified intragenic, antisense, and Orphan promoters that were not associated with any gene models...
February 18, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28214332/comparison-of-several-white-matter-tracts-in-feline-and-canine-brain-by-using-magnetic-resonance-diffusion-tensor-imaging
#2
Olivier Jacqmot, Bert Van Thielen, Alex Michotte, Inneke Willekens, Filip Verhelle, Peter Goossens, Filip De Ridder, Jan Pieter Clarys, Anne Vanbinst, Cindy Peleman, Johan de Mey
Recently, we published a first anatomical Diffusion Tensor Imaging (DTI) atlas regarding white matter tracts in the canine brain. The purpose of this study was to show the significance of DTI in the revelation of the white matter fibres in the feline brain (i.e. to obtain an anatomical DTI atlas of images) and to descriptively compare these to previously obtained white matter fibre images of the canine brain. DTI MR Images of 4 cats euthanised for reasons other than neurological disorders were obtained with a 3 T system...
February 18, 2017: Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology
https://www.readbyqxmd.com/read/28214015/anomalous-network-architecture-of-the-resting-brain-in-children-who-stutter
#3
Soo-Eun Chang, Michael Angstadt, Ho Ming Chow, Andrew C Etchell, Emily O Garnett, Ai Leen Choo, Daniel Kessler, Robert C Welsh, Chandra Sripada
PURPOSE: We combined a large longitudinal neuroimaging dataset that includes children who do and do not stutter and a whole-brain network analysis in order to examine the intra- and inter-network connectivity changes associated with stuttering. Additionally, we asked whether whole brain connectivity patterns observed at the initial year of scanning could predict persistent stuttering in later years. METHODS: A total of 224 high-quality resting state fMRI scans collected from 84 children (42 stuttering, 42 controls) were entered into an independent component analysis (ICA), yielding a number of distinct network connectivity maps ("components") as well as expression scores for each component that quantified the degree to which it is expressed for each child...
January 25, 2017: Journal of Fluency Disorders
https://www.readbyqxmd.com/read/28213810/how-to-tackle-natural-focal-infections-from-risk-assessment-to-vaccination-strategies
#4
Luca Busani, Alexander E Platonov, Onder Ergonul, Giovanni Rezza
Natural focal diseases are caused by biological agents associated with specific landscapes. The natural focus of such diseases is defined as any natural ecosystem containing the pathogen's population as an essential component. In such context, the agent circulates independently on human presence, and humans may become accidentally infected through contact with vectors or reservoirs. Some viruses (i.e., tick-borne encephalitis and Congo-Crimean hemorrhagic fever virus) are paradigmatic examples of natural focal diseases...
February 18, 2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28213793/automation-of-peak-tracking-analysis-of-stepwise-perturbed-nmr-spectra
#5
Tommaso Banelli, Marco Vuano, Federico Fogolari, Andrea Fusiello, Gennaro Esposito, Alessandra Corazza
We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered...
February 17, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28213666/patterns-of-abnormal-gastric-pacemaking-after-sleeve-gastrectomy-defined-by-laparoscopic-high-resolution-electrical-mapping
#6
Rachel Berry, Leo K Cheng, Peng Du, Niranchan Paskaranandavadivel, Timothy R Angeli, Terence Mayne, Grant Beban, Gregory O'Grady
BACKGROUND: Laparoscopic sleeve gastrectomy (LSG) is increasingly being applied to treat obesity. LSG includes excision of the normal gastric pacemaker, which could induce electrical dysrhythmias impacting on post-operative symptoms and recovery, but these implications have not been adequately investigated. This study aimed to define the effects of LSG on gastric slow-wave pacemaking using laparoscopic high-resolution (HR) electrical mapping. METHODS: Laparoscopic HR mapping was performed before and after LSG using flexible printed circuit arrays (64-96 electrodes; 8-12 cm(2); n = 8 patients) deployed through a 12 mm trocar and positioned on the gastric serosa...
February 17, 2017: Obesity Surgery
https://www.readbyqxmd.com/read/28213646/auditory-feedback-to-support-image-guided-medical-needle-placement
#7
David Black, Julian Hettig, Maria Luz, Christian Hansen, Ron Kikinis, Horst Hahn
PURPOSE: During medical needle placement using image-guided navigation systems, the clinician must concentrate on a screen. To reduce the clinician's visual reliance on the screen, this work proposes an auditory feedback method as a stand-alone method or to support visual feedback for placing the navigated medical instrument, in this case a needle. METHODS: An auditory synthesis model using pitch comparison and stereo panning parameter mapping was developed to augment or replace visual feedback for navigated needle placement...
February 17, 2017: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#8
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28213506/role-of-apamin-sensitive-calcium-activated-small-conductance-potassium-currents-on-the-mechanisms-of-ventricular-fibrillation-in-pacing-induced-failing-rabbit-hearts
#9
Dechun Yin, Yu-Cheng Hsieh, Wei-Chung Tsai, Adonis Zhi-Yang Wu, Zhaolei Jiang, Yi-Hsin Chan, Dongzhu Xu, Na Yang, Changyu Shen, Zhenhui Chen, Shien-Fong Lin, Peng-Sheng Chen, Thomas H Everett
BACKGROUND: Ventricular fibrillation (VF) during heart failure is characterized by stable reentrant spiral waves (rotors). Apamin-sensitive small-conductance calcium-activated potassium currents (IKAS) are heterogeneously upregulated in failing hearts. We hypothesized that IKAS influences the location and stability of rotors during VF. METHODS AND RESULTS: Optical mapping was performed on 9 rabbit hearts with pacing-induced heart failure. The epicardial right ventricular and left ventricular surfaces were simultaneously mapped in a Langendorff preparation...
February 2017: Circulation. Arrhythmia and Electrophysiology
https://www.readbyqxmd.com/read/28213475/wheat-landrace-genome-diversity
#10
Luzie U Wingen, Claire West, Michelle Leverington-Waite, Sarah Collier, Simon Orford, Richard Goram, Cai-Yun Yang, Julie King, Alexandra M Allen, Amanda Burridge, Keith J Edwards, Simon Griffiths
Understanding the genomic complexity of bread wheat (Triticum aestivum L.) is a cornerstone in the quest to unravel the processes of domestication and the following adaptation of domesticated wheat to a wide variety of environments across the globe. Additionally, it is of importance for future improvement of the crop, particularly in the light of climate change. Focussing on the adaptation after domestication, a nested association mapping (NAM) panel of 60 segregating bi-parental populations were developed mainly involving landrace accessions from the core set of the Watkins hexaploid wheat collection optimized for genetic diversity (WINGEN et al...
February 17, 2017: Genetics
https://www.readbyqxmd.com/read/28213448/detection-and-monitoring-of-acute-myocarditis-applying-quantitative-cardiovascular-magnetic-resonance
#11
Florian von Knobelsdorff-Brenkenhoff, Johannes Schüler, Serkan Dogangüzel, Matthias A Dieringer, Andre Rudolph, Andreas Greiser, Peter Kellman, Jeanette Schulz-Menger
BACKGROUND: Cardiovascular magnetic resonance based on the Lake Louise Criteria is used to make the diagnosis of acute myocarditis. Novel quantitative parametric mapping techniques promise to overcome some of its limitations. We aimed to evaluate quantitative cardiovascular magnetic resonance to detect and monitor acute myocarditis. METHODS AND RESULTS: Eighteen patients with clinical diagnosis of acute myocarditis (25 years [23-38 years]; 78% males) were prospectively enrolled and repeatedly underwent cardiovascular magnetic resonance at 1...
February 2017: Circulation. Cardiovascular Imaging
https://www.readbyqxmd.com/read/28213446/acetylcholine-release-in-prefrontal-cortex-promotes-gamma-oscillations-and-theta-gamma-coupling-during-cue-detection
#12
W M Howe, H J Gritton, N Lusk, Erik A Roberts, Vaughn L Hetrick, Joshua D Berke, Martin Sarter
The capacity for using external cues to guide behavior ("cue detection") constitutes an essential aspect of attention and goal-directed behavior. The cortical cholinergic input system, via phasic increases in prefrontal acetylcholine release, plays an essential role in attention by mediating such cue detection. However, the relationship between cholinergic signaling during cue detection and neural activity dynamics in prefrontal networks remains unclear. Here we combined sub-second measures of cholinergic signaling, neurophysiological recordings, and cholinergic receptor blockade to delineate the cholinergic contributions to prefrontal oscillations during cue detection in rats...
February 17, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28213285/mechanical-and-chemical-studies-on-eps-from-sulfobacillus-thermosulfidooxidans-from-planktonic-to-biofilm-cells
#13
Qian Li, Wolfgang Sand
Bacteria attach to minerals and form biofilms, which can initiate and enhance bioleaching. Extracellular polymeric substances (EPS) play a crucial role during the whole process. Little is known how the cell surface/EPS mechanically and chemically respond to transformation from planktonic to biofilm cells. In this study the attachment and biofilm formation by Sulfobacillus thermosulfidooxidans were followed during pyrite leaching. Adhesiveness and stiffness of the cell/biofilm and the pyrite surface were checked by atomic force microscopy (AFM) in force mapping mode under real living conditions...
February 10, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28213271/woodchuck-sodium-taurocholate-cotransporting-polypeptide-supports-low-level-hepatitis-b-and-d-virus-entry
#14
Liran Fu, Hongjie Hu, Yang Liu, Zhiyi Jing, Wenhui Li
Sodium taurocholate cotransporting polypeptide (NTCP) is the functional receptor for human hepatitis B virus (HBV) and its satellite hepatitis D virus (HDV). Species barriers to HBV/HDV infection are mainly determined at entry level by variations in the sequences of particular NTCP orthologs. In this study, we sought to determine whether the NTCP ortholog in woodchuck (Marmota monax), woodchuck NTCP (wNTCP) supports viral infection. We found that wNTCP is capable of supporting HBV/HDV infection in HepG2 cells, but to much lower extent than human NTCP (hNTCP), which is about 90% reduction of hNTCP...
February 14, 2017: Virology
https://www.readbyqxmd.com/read/28213235/preparation-and-characterization-of-a-packed-bead-immobilized-trypsin-reactor-integrated-into-a-pdms-microfluidic-chip-for-rapid-protein-digestion
#15
Adam Kecskemeti, Attila Gaspar
This paper demonstrates the design, efficiency and applicability of a simple, inexpensive and high sample throughput microchip immobilized enzymatic reactor (IMER) for rapid protein digestion. The IMER contains conventional silica particles with covalently immobilized trypsin packed inside of a poly(dimethylsiloxane) (PDMS) microchip channel (10mm×1mm×35µm). The microchip consists of 9 different channels, enabling 9 simultaneous protein digestions. Trypsin was covalently immobilized using carbodiimide activation, the ideal trypsin/silica particle ratio (i...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28213194/subcortical-mapping-using-an-electrified-cusa-in-pediatric-supratentorial-surgery
#16
Jonathan Roth, Akiva Korn, Yifat Bitan-Talmor, Rivka Kaufman, Margaret Ekstein, Shlomi Constantini
BACKGROUND: Intraoperative electrophysiology is increasingly used for various lesion resections, both in adult and pediatric brain surgery. Subcortical mapping is often used in adult surgery when lesions lie in proximity to the corticospinal tract (CST). We describe a novel technique of continuous subcortical mapping using an electrified Cavitron UltraSonic Aspirator (CUSA) in children with supratentorial lesions. METHODS: We evaluated the method of subcortical mapping using a CUSA as a stimulation probe...
February 14, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28213116/pushing-the-limits-of-ultra-high-resolution-human-brain-imaging-with-sms-epi-demonstrated-for-columnar-level-fmri
#17
David A Feinberg, An T Vu, Alexander Beckett
Encoding higher spatial resolution in simultaneous multi-slice (SMS) EPI is highly dependent on gradient performance, high density receiver coil arrays and pulse sequence optimization. We simulate gradient amplitude and slew rate determination of EPI imaging performance in terms of minimum TE, echo spacing (ES) and spatial resolution. We discuss the effects of image zooming in pulse sequences that have been used for sub-millimeter resolutions and the trade-offs in using partial Fourier and parallel imaging to reduce TE, PSF and ES...
February 14, 2017: NeuroImage
https://www.readbyqxmd.com/read/28213113/a-variational-bayesian-inference-method-for-parametric-imaging-of-pet-data
#18
M Castellaro, G Rizzo, M Tonietto, M Veronese, F E Turkheimer, M A Chappell, A Bertoldo
In dynamic Positron Emission Tomography (PET) studies, compartmental models provide the richest information on the tracer kinetics of the tissue. Inverting such models at the voxel level is however quite challenging due to the low signal-to-noise ratio of the time activity curves. In this study, we propose the use of a Variational Bayesian (VB) approach to efficiently solve this issue and thus obtain robust quantitative parametric maps. VB was adapted to the non-uniform noise distribution of PET data. Moreover, we propose a novel hierarchical scheme to define the model parameter priors directly from the images in case such information are not available from the literature, as often happens with new PET tracers...
February 14, 2017: NeuroImage
https://www.readbyqxmd.com/read/28213059/multidisciplinary-team-learning-in-the-management-of-the-morbidly-adherent-placenta-outcome-improvements-over-time
#19
Alireza A Shamshirsaz, Karin A Fox, Hadi Erfani, Steven L Clark, Bahram Salmanian, B Wycke Baker, Michael Coburn, Amir A Shamshirsaz, Zhoobin H Bateni, Jimmy Espinoza, Ahmed A Nassr, Edwina J Popek, Shiu-Ki Hui, Jun Teruya, Celestine Shauching Tung, Jeffery A Jones, Martha Rac, Gary A Dildy, Michael A Belfort
BACKGROUND: Morbidly adherent placenta (MAP) is a serious obstetric complication causing mortality and morbidity. OBJECTIVE: To evaluate whether outcomes of patients with morbidly adherent placenta improve with increasing experience within a well-established multidisciplinary team at a single referral center. STUDY DESIGN: All singleton pregnancies with pathology-confirmed MAP (including placenta accreta, increta or percreta) managed by a multidisciplinary team between January 2011 and August 2016 were included in this retrospective study...
February 14, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28213055/electrophysiological-measurements-that-can-explain-and-guide-temporary-accelerated-pacing-to-avert-re-occurrence-of-torsade-de-pointes-arrhythmias-in-the-canine-chronic-atrioventricular-block-model
#20
Sofieke C Wijers, Alexandre Bossu, Albert Dunnink, Jet D M Beekman, Rosanne Varkevisser, Alfonso Aranda Hernández, Mathias Meine, Marc A Vos
BACKGROUND: Pacing at higher rates is known to suppress Torsade de Pointes (TdP) arrhythmias. Nevertheless, exact application and mechanism need further clarification. In the anesthetized, canine, chronic atrioventricular block model, ventricular remodeling is responsible for a high and reproducible incidence of TdP upon a challenge with dofetilide. OBJECTIVE: We used this model to investigate by what mechanism accelerated pacing averts TdP and what repolarization parameter could be used to guide temporary applied accelerated pacing (TAP)...
February 14, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
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