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https://www.readbyqxmd.com/read/28102959/x-ray-scatter-correction-for-multi-source-interior-computed-tomography
#1
Hao Gong, Hao Yan, Xun Jia, Bin Li, Ge Wang, Guohua Cao
PURPOSE: The schemes of multi-source interior computed tomography (CT) have shown promise for ultra-fast, organ-oriented, and low-dose dynamic imaging. Besides forward scattering, x-ray cross scattering from multiple x-ray sources activated simultaneously can further degrade image quality. Here, we investigate the overall x-ray scattering artifact in a recently proposed multi-source interior CT architecture, and present two methods for scatter correction. METHODS: Compared to single-source global CT, scattering in multi-source interior CT architecture is affected by two new factors: cross scattering from simultaneously activated multiple x-ray sources and region-of-interest (ROI) oriented interior CT mode...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102958/sliding-window-prior-data-assisted-compressed-sensing-for-mri-tracking-of-lung-tumors
#2
Eugene Yip, Jihyun Yun, Keith Wachowicz, Zsolt Gabos, Satyapal Rathee, B G Fallone
PURPOSE: Hybrid magnetic resonance imaging and radiation therapy devices are capable of imaging in real-time to track intrafractional lung tumor motion during radiotherapy. Highly accelerated magnetic resonance (MR) imaging methods can potentially reduce system delay time and/or improves imaging spatial resolution, and provide flexibility in imaging parameters. Prior Data Assisted Compressed Sensing (PDACS) has previously been proposed as an acceleration method that combines the advantages of 2D compressed sensing and the KEYHOLE view-sharing technique...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102949/simultaneous-pet-mr-imaging-with-a-radio-frequency-penetrable-pet-insert
#3
Alexander M Grant, Brian J Lee, Chen-Ming Chang, Craig S Levin
PURPOSE: A brain sized radio frequency (RF)-penetrable PET insert has been designed for simultaneous operation with MRI systems. This system takes advantage of electro-optical coupling and battery power to electrically float the PET insert relative to the MRI ground, permitting RF signals to be transmitted through small gaps between the modules that form the PET ring. This design facilitates the use of the built-in body coil for RF transmission and thus could be inserted into any existing MR site wishing to achieve simultaneous PET/MR imaging...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102912/different-spatio-temporal-eeg-features-drive-the-successful-decoding-of-binaural-and-monaural-cues-for-sound-localization
#4
Adam Bednar, Francis M Boland, Edmund C Lalor
The human ability to localize sound is essential for monitoring the environment and helps us to analyze complex auditory scenes. Although the acoustic cues mediating sound localization have been established, it remains unknown how these cues are represented in human cortex. In particular, it is still a point of contention whether binaural and monaural cues are processed by the same or distinct cortical networks. In this study, participants listened to a sequence of auditory stimuli from different spatial locations while we recorded their neural activity using electroencephalography (EEG)...
January 19, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28102863/a-taxonomy-of-medical-uncertainties-in-clinical-genome-sequencing
#5
Paul K J Han, Kendall L Umstead, Barbara A Bernhardt, Robert C Green, Steven Joffe, Barbara Koenig, Ian Krantz, Leo B Waterston, Leslie G Biesecker, Barbara B Biesecker
PURPOSE: Clinical next-generation sequencing (CNGS) is introducing new opportunities and challenges into the practice of medicine. Simultaneously, these technologies are generating uncertainties of an unprecedented scale that laboratories, clinicians, and patients are required to address and manage. We describe in this report the conceptual design of a new taxonomy of uncertainties around the use of CNGS in health care. METHODS: Interviews to delineate the dimensions of uncertainty in CNGS were conducted with genomics experts and themes were extracted in order to expand on a previously published three-dimensional taxonomy of medical uncertainty...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102861/clinical-utility-of-next-generation-sequencing-for-inherited-bone-marrow-failure-syndromes
#6
Hideki Muramatsu, Yusuke Okuno, Kenichi Yoshida, Yuichi Shiraishi, Sayoko Doisaki, Atsushi Narita, Hirotoshi Sakaguchi, Nozomu Kawashima, Xinan Wang, Yinyan Xu, Kenichi Chiba, Hiroko Tanaka, Asahito Hama, Masashi Sanada, Yoshiyuki Takahashi, Hitoshi Kanno, Hiroki Yamaguchi, Shouichi Ohga, Atsushi Manabe, Hideo Harigae, Shinji Kunishima, Eiichi Ishii, Masao Kobayashi, Kenichi Koike, Kenichiro Watanabe, Etsuro Ito, Minoru Takata, Miharu Yabe, Seishi Ogawa, Satoru Miyano, Seiji Kojima
PURPOSE: Precise genetic diagnosis of inherited bone marrow failure syndromes (IBMFS), a heterogeneous group of genetic disorders, is challenging but essential for precise clinical decision making. METHODS: We analyzed 121 IBMFS patients using a targeted sequencing covering 184 associated genes and 250 IBMFS patients using whole-exome sequencing (WES). RESULTS: We achieved successful genetic diagnoses for 53 of 121 patients (44%) using targeted sequencing and for 68 of 250 patients (27%) using WES...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28102837/precise-and-efficient-scarless-genome-editing-in-stem-cells-using-correct
#7
Dylan Kwart, Dominik Paquet, Shaun Teo, Marc Tessier-Lavigne
CRISPR/Cas9 is a promising tool for genome-editing DNA in cells with single-base-pair precision, which allows novel in vitro models of human disease to be generated-e.g., in pluripotent stem cells. However, the accuracy of intended sequence changes can be severely diminished by CRISPR/Cas9's propensity to re-edit previously modified loci, causing unwanted mutations (indels) alongside intended changes. Here we describe a genome-editing framework termed consecutive re-guide or re-Cas steps to erase CRISPR/Cas-blocked targets (CORRECT), which, by exploiting the use of highly efficacious CRISPR/Cas-blocking mutations in two rounds of genome editing, enables accurate, efficient and scarless introduction of specific base changes-for example, in human induced pluripotent (iPS) stem cells...
February 2017: Nature Protocols
https://www.readbyqxmd.com/read/28102781/a-neurodevelopmental-disorder-with-a-nonsense-mutation-in-the-ox-2-antigen-domain-of-the-amyloid-precursor-protein-app-gene
#8
Khue Vu Nguyen, Karen Leydiker, Raymond Wang, Jose Abdenur, William L Nyhan
We report a patient, an infant with a neurodevelopmental disorder manifesting intractable complex partial epilepsy, bull's eye maculopathy, microcephaly, bilateral cataracts, truncal hypotonia, and spasticity of all four extremities. Sequencing of genomic DNA revealed mutations in (a) exon 8 (Ox-2 antigen domain) of the amyloid precursor protein (APP) gene: c.1075C>T, p.Arg359(*) (b) exon 8 of the senataxin (SETX) gene: c.4738C>T, p.Arg1580Cys, and (c) exon 2 of the ceroid-lipofuscinosis, neuronal 8 (CLN8) gene: c...
January 19, 2017: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/28102740/update-on-functional-and-genetic-laboratory-assays-for-the-detection-of-platelet-microvesicles
#9
Maxime Laroche, Claire Dunois, Anne Marie Vissac, Jean Amiral
Functional and genetic assays for measuring platelet microvesicles (PMVs) are presented and discussed. Functional assays concern two groups of methods: a) homogeneous assays using the cofactor activity of phospholipids (PPLs) contained in PMVs and present in assayed plasmas, and a coagulation or a thrombin generation assay (TGA) as "end points"; b) capture-based assays, in which PMVs bind to an immobilized ligand, such as Annexin V in the presence of calcium, or monoclonal antibodies (MoAbs) specific for membrane proteins...
January 19, 2017: Platelets
https://www.readbyqxmd.com/read/28102702/immunomodulating-peptides-for-food-allergy-prevention-and-treatment
#10
Daniel Lozano-Ojalvo, Rosina López-Fandiño
Among the most promising strategies currently assayed against IgE-mediated allergic diseases stands the possibility of using immunomodulating peptides to induce oral tolerance towards offending food allergens or even to prevent allergic sensitization. This review focuses on the beneficial effects of food derived immunomodulating peptides on food allergy, which can be directly exerted in the intestinal tract or once being absorbed through the intestinal epithelial barrier to interact with immune cells. Food peptides influence intestinal homeostasis by maintaining and reinforcing barrier function or affecting intestinal cell-signalling to nearby immune cells and mucus secretion...
January 19, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28102682/identification-of-serratane-synthase-gene-from-the-fern-lycopodium-clavatum
#11
Yusuke Saga, Takeshi Araki, Hiroshi Araya, Kazuki Saito, Mami Yamazaki, Hideyuki Suzuki, Tetsuo Kushiro
Ferns are known to produce onoceroids including onoceranes and serratanes having unusual structures among triterpenes. From the fern Lycopodium clavatum, a novel onoceroid synthase gene was cloned that showed high sequence identity with a previously identified α-onocerin synthase. Functional analysis by coexpression with pre-α-onocerin synthase in yeast led to the production of tohogenol and serratenediol. The result suggested that serratanes are directly biosynthesized from pre-α-onocerin and not from α-onocerin as previously assumed...
January 19, 2017: Organic Letters
https://www.readbyqxmd.com/read/28102674/2d-ir-spectroscopy-shows-that-optimised-dna-minor-groove-binding-of-hoechst33258-follows-an-induced-fit-model
#12
Lennart A I Ramakers, Gordon Hithell, John J May, Gregory M Greetham, Paul M Donaldson, Michael Towrie, Anthony W Parker, Glenn A Burley, Neil T Hunt
The induced fit binding model describes a conformational change occurring when a small molecule binds to its biomacromolecular target. The result is enhanced non-covalent interactions between ligand and biomolecule. Induced fit is well-established for small molecule-protein interactions, but its relevance to small molecule-DNA binding is less clear. We investigate the molecular determinants of Hoechst33258 binding to its preferred A-tract sequence relative to a sub-optimal alternating A-T sequence. Results from 2-dimensional infrared spectroscopy, which is sensitive to H-bonding and molecular structure changes, show that Hoechst33258 binding results in loss of minor groove spine of hydration in both sequences, but an additional perturbation of the base propeller twists occurs in the A-tract binding region...
January 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28102546/ataluren-and-similar-compounds-specific-therapies-for-premature-termination-codon-class-i-mutations-for-cystic-fibrosis
#13
REVIEW
Aisha A Aslam, Colin Higgins, Ian P Sinha, Kevin W Southern
BACKGROUND: Cystic fibrosis is a common life-shortening genetic disorder in the Caucasian population (less common in other ethnic groups) caused by the mutation of a single gene that codes for the production of the cystic fibrosis transmembrane conductance regulator protein. This protein coordinates the transport of salt (and bicarbonate) across cell surfaces and the mutation most notably affects the airways. In the lungs of people with cystic fibrosis, defective protein results in a dehydrated surface liquid and compromised mucociliary clearance...
January 19, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28102479/peripherally-inserted-central-catheter-related-bloodstream-infection-caused-by-kocuria-marina-in-an-elderly-man
#14
Nobuaki Mori, Yuichi Nishihara, Hideki Tayama, Akiko Higuchi, Yasuko Aoki
BACKGROUND: Kocuria species are Gram-positive, aerobic cocci, and members of the Micrcoccaceae family that are known to be opportunistic pathogens. Although there have been sporadic reports of infections caused by Kocuria species, little is known regarding their human pathogenicity and clinical characteristics. CASE REPORT: We herein report a case of a peripherally inserted central catheter (PICC)-related bloodstream infection caused by Kocuria marina in a 90-year-old Japanese with multiple cancer...
January 19, 2017: Infection
https://www.readbyqxmd.com/read/28102461/rnahelix-computational-modeling-of-nucleic-acid-structures-with-watson-crick-and-non-canonical-base-pairs
#15
Dhananjay Bhattacharyya, Sukanya Halder, Sankar Basu, Debasish Mukherjee, Prasun Kumar, Manju Bansal
Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs...
January 19, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28102441/the-effect-of-land-use-on-bacterial-communities-in-saline-alkali-soil
#16
Mu Peng, Hongbai Jia, Qiuyu Wang
Saline-alkali soil can inhibit the growth of crops as a consequence of cellular damage through oxidation of lipids and proteins and degradation of nucleic acids, ultimately leading to cell death. The bacterial community composition and diversity in saline-alkali soil across different land uses, such as agricultural land, forest land, and grassland, were evaluated using high-throughput sequencing of the bacterial 16S rRNA gene. Significant differences in the soil physicochemical characteristics and bacterial community among different land uses were observed in this study...
January 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28102432/synthesis-of-human-parainfluenza-virus-4-nucleocapsid-like-particles-in-yeast-and-their-use-for-detection-of-virus-specific-antibodies-in-human-serum
#17
Aistė Bulavaitė, Rita Lasickienė, Paulius Lukas Tamošiūnas, Martynas Simanavičius, Kęstutis Sasnauskas, Aurelija Žvirblienė
The aim of this study was to produce human parainfluenza virus type 4 (HPIV4) nucleocapsid (N) protein in yeast Saccharomyces cerevisiae expression system, to explore its structural and antigenic properties and to evaluate its applicability in serology. The use of an optimized gene encoding HPIV4 N protein amino acid (aa) sequence GenBank AGU90031.1 allowed high yield of recombinant N protein forming nucleocapsid-like particles (NLPs) in yeast. A substitution L332D disrupted self-assembly of NLPs, confirming the role of this position in the N proteins of Paramyxovirinae...
January 19, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28102381/maldi-imaging-enables-direct-observation-of-kinetic-and-thermodynamic-products-of-mixed-peptide-fiber-assembly
#18
Karima Medini, Brandi West, David E Williams, Margaret A Brimble, Juliet A Gerrard
Controlling the self-assembly of multicomponent systems provides a key to designing new materials and understanding the molecular complexity of biology. Here, we demonstrate the first use of MALDI-imaging to characterize a multicomponent self-assembling peptide fiber. Observations of mixed peptide systems over time demonstrate how simple sequence variation can change the balance between kinetic and thermodynamic products.
January 19, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28102380/novel-high-temperature-ferroelectric-domain-morphology-in-pbtio3-ultrathin-films
#19
Jacob B J Chapman, Anna V Kimmel, Dorothy M Duffy
Exotic domain morphologies in ferroic materials are an exciting avenue for the development of novel nanoelectronics. In this work we have used large scale molecular dynamics to construct a strain-temperature phase diagram of the domain morphology of PbTiO3 ultrathin films. Sampling a wide interval of strain values over a temperature range up to the Curie temperature Tc, we found that epitaxial strain induces the formation of a variety of closure- and in-plane domain morphologies. The local strain and ferroelectric-antiferrodistortive coupling at the film surface vary for the strain mediated transition sequence and this could offer a route for experimental observation of the morphologies...
January 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28102365/viral-phylogenomics-using-an-alignment-free-method-a-three-step-approach-to-determine-optimal-length-of-k-mer
#20
Qian Zhang, Se-Ran Jun, Michael Leuze, David Ussery, Intawat Nookaew
The development of rapid, economical genome sequencing has shed new light on the classification of viruses. As of October 2016, the National Center for Biotechnology Information (NCBI) database contained >2 million viral genome sequences and a reference set of ~4000 viral genome sequences that cover a wide range of known viral families. Whole-genome sequences can be used to improve viral classification and provide insight into the viral "tree of life". However, due to the lack of evolutionary conservation amongst diverse viruses, it is not feasible to build a viral tree of life using traditional phylogenetic methods based on conserved proteins...
January 19, 2017: Scientific Reports
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