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https://www.readbyqxmd.com/read/28641402/ec-tagging-allows-cell-type-specific-rna-analysis
#1
Naoki Hida, Mohamed Y Aboukilila, Dana A Burow, Rakesh Paul, Marc M Greenberg, Michael Fazio, Samantha Beasley, Robert C Spitale, Michael D Cleary
Purification of cell type-specific RNAs remains a significant challenge. One solution involves biosynthetic tagging of target RNAs. RNA tagging via incorporation of 4-thiouracil (TU) in cells expressing transgenic uracil phosphoribosyltransferase (UPRT), a method known as TU-tagging, has been used in multiple systems but can have limited specificity due to endogenous pathways of TU incorporation. Here, we describe an alternative method that requires the activity of two enzymes: cytosine deaminase (CD) and UPRT...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641399/compannotate-a-comparative-approach-to-annotate-base-pairing-interactions-in-rna-3d-structures
#2
Shahidul Islam, Ping Ge, Shaojie Zhang
The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28641383/neuroprotection-in-stroke-the-importance-of-collaboration-and-reproducibility
#3
Ain A Neuhaus, Yvonne Couch, Gina Hadley, Alastair M Buchan
Acute ischaemic stroke accounts for 6.5 million deaths per year, and by 2030 will result in the annual loss of over 200 million disability-adjusted life years globally. There have been considerable recent advances in the gold standard of acute ischaemic stroke treatment, some aspects of which-aspirin to prevent recurrence, and treating patients in specialized stroke wards-are widely applicable. Recanalization of the occluded artery through thrombolysis and/or endovascular thrombectomy is restricted to only a small proportion of patients, due to contra-indications and the costs associated with establishing the infrastructure to deliver these treatments...
June 20, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28641350/-laparoscopic-assisted-mobilisation-and-resection-of-a-sacrococcygeal-teratoma-altman-type-iii
#4
Jan Gödeke, Veronika Engel, Oliver Münsterer
Objective This video is a step-by-step illustration of the laparoscopic-assisted mobilisation and resection of a sacrococcygeal teratoma Altman type III. Indication Laparoscopic supralevatory tumour mobilisation is an established method in selected centres and can be the initial step in approaching sacrococcygeal teratomas with an intrapelvic portion, facilitating a complete (R0) resection. Method Laparoscopic surgery is performed in supine position with a 5 mm umbilical trocar, a 5 mm trocar in the right upper abdomen, and two 3 mm trocars in the left middle and lower abdomen...
June 2017: Zentralblatt Für Chirurgie
https://www.readbyqxmd.com/read/28641331/-surgical-treatment-of-pseudotumours-of-the-lung
#5
Zsolt Sziklavari, Annete Droste, Reiner Neu, Hans-Stefan Hofmann, Michael Ried
Introduction Pseudotumour of the lung is a collective term for various subentities. Some subgroups are considered to be intermediary malignant tumours. A pseudotumour is a rare condition, which makes it difficult to estimate its incidence and prevalence. Methods Retrospective analysis of all surgically treated patients between 2008 and 2015 diagnosed with a pseudotumour of the lung. The primary endpoint of this study was to estimate the rates of local recurrence and metastasis. Secondary endpoints were to determine the nomenclature, medical history, treatment, and the perioperative course...
June 22, 2017: Zentralblatt Für Chirurgie
https://www.readbyqxmd.com/read/28641322/scuba-diving-and-otology-a-systematic-review-with-recommendations-on-diagnosis-treatment-and-post-operative-care
#6
REVIEW
Devon M Livingstone, Kristine A Smith, Beth Lange
Scuba diving is a popular recreational and professional activity with inherent risks. Complications related to barotrauma and decompression illness can pose significant morbidity to a diver's hearing and balance systems. The majority of dive-related injuries affect the head and neck, particularly the outer, middle and inner ear. Given the high incidence of otologic complications from diving, an evidence-based approach to the diagnosis and treatment of otic pathology is a necessity. We performed a systematic and comprehensive literature review including the pathophysiology, diagnosis, and treatment of otologic pathology related to diving...
June 2017: Diving and Hyperbaric Medicine: the Journal of the South Pacific Underwater Medicine Society
https://www.readbyqxmd.com/read/28641288/the-crista-fenestra-and-its-impact-on-the-surgical-approach-to-the-scala-tympani-during-cochlear-implantation
#7
Roberto D Angeli, Joel Lavinsky, Enio T Setogutti, Luiz Lavinsky
OBJECTIVE: The aim of this work was to describe the dimensions of the crista fenestra and determine its presence by means of high-resolution computed tomography (CT) for the purpose of cochlear implantation via the round window approach. METHODS: A series of 10 adult human temporal bones underwent high-resolution CT scanning and were further dissected for microscopic study of the round window niche. RESULTS: In all of the specimens, the round window membrane was fully visualized after the complete removal of bony overhangs...
June 23, 2017: Audiology & Neuro-otology
https://www.readbyqxmd.com/read/28641266/an-approach-to-identifying-phenomena-accompanying-micro-and-nanoparticles-in-contact-with-irregular-vessel-walls
#8
K Talaska, A Ferreira
OBJECTIVE: The objective of this manuscript is to present the method for determining the nature and values of the forces needed to set micro and nanoparticles sitting immobile at the blood vessel wall in motion. METHODS: The problem was tackled in two ways. Microparticles were examined as objects coming into contact with the wall with the actual large arteriole-type vessel structure. The forces acting on microparticles 10 μm, 30 μm and 50 μm in diameter were determined: drag force FD, lift force FL, electrostatic force FE and gravity force FG...
June 19, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28641261/robust-web-image-annotation-via-exploring-multi-facet-and-structural-knowledge
#9
Mengqiu Hu, Yang Yang, Fumin Shen, Luming Zhang, Heng Tao Shen, Xuelong Li
Driven by the rapid development of Internet and digital technologies, we have witnessed the explosive growth of Web images in recent years. Seeing that labels can reflect the semantic contents of the images, automatic image annotation, which can further facilitate the procedure of image semantic indexing, retrieval and other image management tasks, has become one of the most crucial research directions in multimedia. Most of the existing annotation methods heavily rely on well-labeled training data (expensive to collect) and/or single view of visual features (insufficient representative power)...
June 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641252/an-embedded-marked-point-process-framework-for-three-level-object-population-analysis
#10
Csaba Benedek
In this paper we introduce a probabilistic approach for extracting complex hierarchical object structures from digital images used by various vision applications. The proposed framework extends conventional Marked Point Process (MPP) models by (i) admitting object-subobject ensembles in parent-child relationships and (ii) allowing corresponding objects to form coherent object groups, by a Bayesian segmentation of the population. Different from earlier, highly domain specific attempts on MPP generalization, the proposed model is defined at an abstract level, providing clear interfaces for applications in various domains...
June 15, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28641249/eit-imaging-regularization-based-on-spectral-graph-wavelets
#11
Bo Gong, Benjamin Schullcke, Sabine Krueger-Ziolek, Marko Vauhkonen, Gerhard Wolf, Ullrich Mueller-Lisse, Knut Moeller
The objective of Electrical Impedance Tomographic reconstruction is to identify the distribution of tissue conductivity from electrical boundary conditions. This is an ill-posed inverse problem usually solved under the finite element method framework. In previous studies, standard sparse regularization was used for difference EIT to achieve a sparse solution. However, regarding element-wise sparsity, standard sparse regularization interferes with the smoothness of conductivity distribution between neighboring elements and is sensitive to noise...
June 16, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28641247/modeling-task-fmri-data-via-deep-convolutional-autoencoder
#12
Heng Huang, Xintao Hu, Yu Zhao, Milad Makkie, Qinglin Dong, Shijie Zhao, Lei Guo, Tianming Liu
Task-based fMRI (tfMRI) has been widely used to study functional brain networks under task performance. Modeling tfMRI data is challenging due to at least two problems: the lack of the ground truth of underlying neural activity and the highly complex intrinsic structure of tfMRI data. To better understand brain networks based on fMRI data, data-driven approaches have been proposed, for instance, Independent Component Analysis (ICA) and Sparse Dictionary Learning (SDL). However, both ICA and SDL only build shallow models, and they are under the strong assumption that original fMRI signal could be linearly decomposed into time series components with their corresponding spatial maps...
June 15, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28641244/computerized-lung-sound-screening-for-pediatric-auscultation-in-noisy-field-environments
#13
Dimitra Emmanouilidou, Eric D McCollum, Daniel E Park, Mounya Elhilali
GOAL: Chest auscultations offer a non-invasive and low-cost tool for monitoring lung disease. However, they present many shortcomings including inter-listener variability, subjectivity, and vulnerability to noise and distortions. The current work proposes a computer-aided approach to process lung signals acquired in the field under adverse noisy conditions, by improving the signal quality and offering automated iden- tification of abnormal auscultations indicative of respiratory pathologies...
June 19, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28641242/arrhythmia-mechanism-and-scaling-effect-on-the-spectral-properties-of-electroanatomical-maps-with-manifold-harmonics
#14
Margarita Sanroman-Junquera, Inmaculada Mora-Jimenez, Arcadi Garcia-Alberola, Antonio J Caamano, Beatriz Trenor, Jose Luis Rojo-Alvarez
Spatial and temporal processing of intracardiac electrograms provides relevant information to support the arrhythmia ablation during electrophysiological studies. Current Cardiac Navigation Systems (CNS) and Electrocardiographic Imaging (ECGI) build detailed three-dimensional electroanatomical maps (EAM), which represent the spatial anatomical distribution of bioelectrical features, such as activation time or voltage. We present a principled methodology for spectral analysis of both EAM geometry and bioelectrical feature in CNS or ECGI, including their spectral representation, cut-off frequency, or spatial sampling rate (SSR)...
June 15, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28641237/tunable-excited-state-intramolecular-proton-transfer-reactions-with-nh-or-oh-as-a-proton-donor-a-theoretical-investigation
#15
Yuanyuan Li, Keke Wen, Songyan Feng, Huijuan Yuan, Beibei An, Qiuling Zhu, Xugeng Guo, Jinglai Zhang
Excited-state intramolecular proton transfer (ESIPT) reactions occurring in the S1 state for five molecules, which possess five/six-membered ring intramolecular NH···N or OH···N hydrogen bonds bearing quinoline or 2-phenylpyridine moiety, have been described in detail by the time-dependent density functional theory (TD-DFT) approach using the B3LYP hybrid functional. For the five molecules, the constrained potential energy profiles along the ESIPT reactions show that proton transfer is barrierless in molecules possessing six-membered ring intramolecular H-bonds, which is smoother than that with certain barriers in five-membered ring H-bonding systems...
June 15, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28641210/comparative-analysis-of-polyspecificity-of-the-endogenous-trna-synthetase-of-different-expression-host-towards-photocrosslinking-amino-acids-using-an-in-silico-approach
#16
Nadarajan Saravanan Prabhu, Hyungdon Yun
Photo-induced covalent crosslinking has emerged as the powerful strategy for analyzing and characterizing the protein-protein interaction and mapping protein 3D conformations. In the last decades, a number of photocrosslinking amino acids have been reported but only a few have been efficiently utilized for photocrosslinking purposes. Recently, incorporation of diazirine containing photoactivatable analogs such as photo-methionine, photo-leucine, photo-isoleucine and photo-lysine into target proteins were accomplished in live cells (Human A549cells, HEK 293) by depleting corresponding natural amino acid and supplementing these analogs in the medium...
June 8, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28641208/an-associative-account-of-the-development-of-word-learning
#17
Vladimir M Sloutsky, Hyungwook Yim, Xin Yao, Simon Dennis
Word learning is a notoriously difficult induction problem because meaning is underdetermined by positive examples. How do children solve this problem? Some have argued that word learning is achieved by means of inference: young word learners rely on a number of assumptions that reduce the overall hypothesis space by favoring some meanings over others. However, these approaches have difficulty explaining how words are learned from conversations or text, without pointing or explicit instruction. In this research, we propose an associative mechanism that can account for such learning...
June 19, 2017: Cognitive Psychology
https://www.readbyqxmd.com/read/28641203/current-trends-in-electrochemical-sensing-and-biosensing-of-dna-methylation
#18
REVIEW
Ludmila Krejcova, Lukas Richtera, David Hynek, Jan Labuda, Vojtech Adam
DNA methylation plays an important role in physiological and pathological processes. Several genetic diseases and most malignancies tend to be associated with aberrant DNA methylation. Among other analytical methods, electrochemical approaches have been successfully employed for characterisation of DNA methylation patterns that are essential for the diagnosis and treatment of particular diseases. This article discusses current trends in the electrochemical sensing and biosensing of DNA methylation. Particularly, it provides an overview of applied electrode materials, electrode modifications and biorecognition elements applications with an emphasis on strategies that form the core DNA methylation detection approaches...
June 8, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28641186/composition-of-dissolved-organic-matter-dom-from-periodically-submerged-soils-in-the-three-gorges-reservoir-areas-as-determined-by-elemental-and-optical-analysis-infrared-spectroscopy-pyrolysis-gc-ms-and-thermally-assisted-hydrolysis-and-methylation
#19
Tao Jiang, Joeri Kaal, Jian Liang, Yaoling Zhang, Shiqiang Wei, Dingyong Wang, Nelson W Green
Soil-derived dissolved organic matter (DOM) has a major influence in biogeochemical processes related to contaminant dynamics and greenhouse gas emissions, due to its reactivity and its bridging role between the soil and aquatic systems. Within the Three Gorges Reservoir (TGR, China) area, an extensive water-fluctuation zone periodically submerges the surrounding soils. Here we report a characterization study of soil-derived DOM across the TGR areas, using elemental and optical analysis, infrared spectroscopy (FTIR), pyrolysis-GC-MS (Py-GC-MS) and thermally assisted hydrolysis and methylation (THM-GC-MS)...
June 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28641184/estimation-of-u-s-sewer-residence-time-distributions-for-national-scale-risk-assessment-of-down-the-drain-chemicals
#20
Katherine E Kapo, Michael Paschka, Raghu Vamshi, Megan Sebasky, Kathleen McDonough
Sewer residence time (the amount of time a given volume of wastewater resides in a sewer system prior to treatment) can have a significant influence on predictions of environmental fate and transport of wastewater constituents and corresponding risk assessment. In this study, a geographic information systems-based approach for estimating the distribution of sewer residence times for the U.S. was developed using road networks as a spatial proxy for sewer networks. The suitability of the approach was evaluated using case study municipalities, and the approach was subsequently extrapolated to 3422 wastewater treatment facilities of varying size across the U...
June 19, 2017: Science of the Total Environment
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