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https://www.readbyqxmd.com/read/29149264/sim3c-simulation-of-hi-c-and-meta3c-proximity-ligation-sequencing-technologies
#1
Matthew Z DeMaere, Aaron E Darling
Background: Chromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization of genomes and metagenomes. Many variants of these protocols have been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family of sequencing protocols, potentially hindering the advancement of algorithms to exploit this new datatype. Findings: We describe a computational simulator that, given simple parameters and reference genome sequences, will simulate Hi-C sequencing on those sequences...
November 15, 2017: GigaScience
https://www.readbyqxmd.com/read/29148121/position-accuracy-of-implant-analogs-on-3d-printed-polymer-versus-conventional-dental-stone-casts-measured-using-a-coordinate-measuring-machine
#2
Marta Revilla-León, Óscar Gonzalez-Martín, Javier Pérez López, José Luis Sánchez-Rubio, Mutlu Özcan
PURPOSE: To compare the accuracy of implant analog positions on complete edentulous maxillary casts made of either dental stone or additive manufactured polymers using a coordinate measuring machine (CMM). MATERIAL AND METHODS: A completely edentulous maxillary model of a patient with 7 implant analogs was obtained. From this model, two types of casts were duplicated, namely conventional dental stone (CDS) using a custom tray impression technique after splinting (N = 5) and polymer cast using additive manufacturing based on the STL file generated...
November 17, 2017: Journal of Prosthodontics: Official Journal of the American College of Prosthodontists
https://www.readbyqxmd.com/read/29147536/a-complementary-pair-of-enantioselective-switchable-organocatalysts
#3
Guillaume De Bo, David A Leigh, Charlie T McTernan, Shoufeng Wang
A pair of enantioselective switchable bifunctional catalysts are shown to promote a range of conjugate addition reactions in up to 95 : 5 e.r. and 95% conversion. Each catalyst can be switched OFF using conditions that switch the other catalyst ON. Catalyst ON : OFF ratios of up to 98 : 2 and 1 : 99 were achieved, with a ratio of reaction rates of up to 16 : 1 between the ON and OFF states, maintained over complete ON-OFF-ON and OFF-ON-OFF cycles. However, simultaneous operation of the catalyst pair in the same reaction vessel, which in principle could allow product handedness to be switched by simple E-Z isomerisation of the catalyst pair, was unsuccessful...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29145618/the-histone-variant-h2a-z-promotes-initiation-of-meiotic-recombination-in-fission-yeast
#4
Shintaro Yamada, Kazuto Kugou, Da-Qiao Ding, Yurika Fujita, Yasushi Hiraoka, Hiroshi Murakami, Kunihiro Ohta, Takatomi Yamada
Meiotic recombination is initiated by programmed formation of DNA double strand breaks (DSBs), which are mainly formed at recombination hotspots. Meiotic DSBs require multiple proteins including the conserved protein Spo11 and its cofactors, and are influenced by chromatin structure. For example, local chromatin around hotspots directly impacts DSB formation. Moreover, DSB is proposed to occur in a higher-order chromatin architecture termed 'axis-loop', in which many loops protrude from cohesin-enriched axis...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145044/image-processing-for-precise-three-dimensional-registration-and-stitching-of-thick-high-resolution-laser-scanning-microscopy-image-stacks
#5
Chloé Murtin, Carole Frindel, David Rousseau, Kei Ito
The possible depth of imaging of laser-scanning microscopy is limited not only by the working distances of objective lenses but also by image degradation caused by attenuation and diffraction of light passing through the specimen. To tackle this problem, one can either flip the sample to record images from both sides of the specimen or consecutively cut off shallow parts of the sample after taking serial images of certain thickness. Multiple image substacks acquired in these ways should be combined afterwards to generate a single stack...
November 8, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29143488/isolation-and-characterization-of-novel-goose-parvovirus-related-virus-reveal-the-evolution-of-waterfowl-parvovirus
#6
P Li, S Lin, R Zhang, J Chen, D Sun, J Lan, S Song, Z Xie, S Jiang
Short beak and dwarfism syndrome (SBDS) has been constantly breaking out in China since 2015. It is caused by a novel goose parvovirus-related virus (NGPV) and can severely restrict the growth of ducks. In this study, seven NGPV stains were isolated from different regions in China between 2015 and 2016. To better understand the correlation between NGPV and goose parvovirus (GPV), we conducted complete genome sequencing and a comprehensive analysis of the NGPV genome. The phylogenetic and alignment analysis showed that NGPV is a branch of GPV, sharing 92...
November 16, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29143024/an-analysis-of-the-explosion-limits-of-hydrogen-oxygen-mixtures-with-nonlinear-chain-reactions
#7
Wenkai Liang, Chung K Law
The ignition boundary of hydrogen/oxygen mixtures is a Z-shaped curve in the pressure-temperature space, demonstrating the existence of three explosion limits. In this study, a general analysis governing all the three explosion limits in an isothermal environment is performed by considering both linear chain reactions (reactant-radical reactions) and nonlinear chain reactions (radical-radical reactions), in addition to the zeroth-order reactant-reactant reactions. For the nonlinear reactions, it is further shown that the linear-nonlinear coupling has the major influence, while the effect of nonlinear-nonlinear coupling is negligible...
November 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29142952/serum-ngal-and-cystatin-c-comparison-with-urinary-albumin-to-creatinine-ratio-and-inflammatory-biomarkers-as-early-predictors-of-renal-dysfunction-in-patients-with-type-2-diabetes
#8
Marcelo R Bacci, Ethel Z Chehter, Ligia A Azzalis, Beatriz Costa de Aguiar Alves, Fernando L A Fonseca
Introduction: Diabetic nephropathy is associated with specific histological changes. Early detection of poor glomerular and tubular function can be achieved with biomarkers of diabetes. The aim of this study was to evaluate the accuracy of kidney dysfunction biomarkers in type 2 diabetes (T2D). Methods: Patients with T2D were grouped according to their glycated hemoglobin level. Patients' urine and blood samples were taken to measure cystatin C (CysC), neutrophil gelatinase-associated lipocalin, beta-trace protein levels, and the first morning void albumin-to-creatinine ratio...
March 2017: KI Reports
https://www.readbyqxmd.com/read/29141996/the-distinct-transcriptomes-of-slow-and-fast-adult-muscles-are-delineated-by-noncoding-rnas
#9
Vered Raz, Muhammad Riaz, Zuotian Tatum, Szymon M Kielbasa, Peter A C 't Hoen
Adult muscles have a vast adaptation capacity, enabling function switches in response to altered conditions. During intensive physical activity, disease, or aging, adult skeletal muscles change and adjust their functions. The competence to adjust varies among muscles. Muscle-specific molecular mechanisms in healthy and normal conditions could designate changes in physiologic and pathologic conditions. We generated deep mRNA-sequencing data in adult fast and slow mouse muscles, and applying paired analysis, we identified that the muscle-specific signatures are composed of half of the muscle transcriptome...
November 15, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29141852/collagen-alignment-as-a-predictor-of-recurrence-after-ductal-carcinoma-in-situ
#10
Matthew W Conklin, Ronald E Gangnon, Brian L Sprague, Lisa van Germert, John M Hampton, Kevin W Eliceiri, Jeremy S Bredfeldt, Yuming Liu, Nuntida Surachaicharn, Polly A Newcomb, Andreas Friedl, Patricia Keely, Amy Trentham-Dietz
BACKGROUND: Collagen fibers surrounding breast ducts may influence breast cancer progression. Syndecan-1 interacts with constituents in the extracellular matrix, including collagen fibers, and may contribute to cancer cell migration. Thus, the orientation of collagen fibers surrounding ductal carcinoma in situ (DCIS) lesions and stromal syndecan-1 expression may predict recurrence. METHODS: We evaluated collagen fiber alignment and syndecan-1 expression in 227 women diagnosed with DCIS in 1995-2006 followed through 2014 (median 14...
November 15, 2017: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/29141638/diffusion-weighted-imaging-of-the-brains-of-dogs-with-idiopathic-epilepsy
#11
Antje Hartmann, Steffen Sager, Klaus Failing, Marion Sparenberg, Martin J Schmidt
BACKGROUND: Idiopathic epilepsy is one of the most common neurological disorders in dogs. Unfortunately, up to 30% of dogs with idiopathic epilepsy show no improvement under antiepileptic drug treatment. Diffusion-weighted imaging is used in human medicine to identify epileptogenic foci in the brain to allow for more invasive treatments such as deep brain stimulation or surgical removal. The aim of this study was to ass the feasibility of interictal diffusion-weighted MRI in dogs and to evaluate the distribution of diffusion in the brains of dogs with idiopathic epilepsy (IE) and to compare these values to previously published values from healthy beagle dogs...
November 15, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/29141363/-characteristics-of-high-resolution-diffusion-weighted-imaging-apparent-diffusion-coefficient-histogram-and-its-correlations-with-cancer-stages-in-patients-with-nasopharyngeal-carcinoma
#12
G J Wang, Y Wang, Y Ye, F Chen, Y T Lu, S L Li
Objective: To investigate the features of apparent diffusion coefficient (ADC) histogram parameters based on entire tumor volume data in high resolution diffusion weighted imaging of nasopharyngeal carcinoma (NPC) and to evaluate its correlations with cancer stages. Methods: This retrospective study included 154 cases of NPC patients[102 males and 52 females, mean age (48±11) years]who had received readout segmentation of long variable echo trains of MRI scan before radiation therapy. The area of tumor was delineated on each section of axial ADC maps to generate ADC histogram by using Image J...
November 7, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/29141320/-diagnosis-of-one-child-herpes-simplex-virus-type-1-encephalitis-with-next-generation-sequencing
#13
J Z Zhang, Q Chen, P Zheng
No abstract text is available yet for this article.
November 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29141312/-clinical-manifestation-and-gene-analyses-of-15-patients-with-intellectual-disability-or-developmental-delay-complicated-with-congenital-nystagmus
#14
Z J Gao, Q Jiang, Q Chen, K M Xu, Z Q Liu, X B Chen, X L Chen
Objective: To analyze the clinical and genetic features of 15 cases with intellectual disability or developmental delay (ID/DD) complicated with congenital nystagmus. Method: The clinical characteristics and the results of laboratory tests, images and genetics of 15 patients with ID/DD complicated with congenital nystagmus, confirmed by gene diagnosis in the Department of Neurology, Children's Hospital Affiliated to Capital Institute of Pediatrics from March 2015 to October 2016, were retrospectively analyzed...
November 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/29140363/snapshot-second-harmonic-generation-polarimeter-based-on-spectral-analysis
#15
Matthieu Dubreuil, Sylvain Rivet, Yann Le Grand
A new high-speed second-harmonic generation (SHG) polarimetric method is reported. It is based on the spectral analysis of the SHG radiation emitted by a nonlinear medium excited with circularly polarized femtosecond laser pulses. The setup uses only passive components for polarization encoding and a fast spectrometer for spectral analysis. The method is validated on a z-cut quartz plate, then on a collagen-rich biological tissue with a view to single image polarization-resolved SHG microscopy.
November 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/29138295/generation-of-specific-inhibitors-of-sumo-1-and-sumo-2-3-mediated-protein-protein-interactions-using-affimer-adhiron-technology
#16
David J Hughes, Christian Tiede, Natalie Penswick, Anna Ah-San Tang, Chi H Trinh, Upasana Mandal, Katarzyna Z Zajac, Thembaninskosi Gaule, Gareth Howell, Thomas A Edwards, Jianxin Duan, Eric Feyfant, Michael J McPherson, Darren C Tomlinson, Adrian Whitehouse
Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells...
November 14, 2017: Science Signaling
https://www.readbyqxmd.com/read/29137966/clinical-outcomes-of-complex-real-world-diabetic-patients-treated-with-amphilimus-sirolimus-eluting-stents-or-zotarolimus-eluting-stents-a-single-center-registry
#17
Rik Rozemeijer, Daniela Benedetto, Adriaan O Kraaijeveld, Michiel Voskuil, Mèra Stein, Leo Timmers, Saskia Z Rittersma, Pierfrancesco Agostoni, Pieter A Doevendans, Pieter R Stella
OBJECTIVE: To assess clinical outcomes of Amphilimus Sirolimus-Eluting Stents (A-SES) as compared to Zotarolimus-Eluting Stents (ZES) in complex real-world diabetic patients. BACKGROUND: Patients with diabetes mellitus represent one of the most challenging scenarios with high rates of restenosis and stent thrombosis in the current era of drug-eluting stents. Hence, we assessed the safety of A-SES versus ZES in complex diabetic patients. METHODS: In this observational study, we analyzed all consecutive patients with diabetes mellitus referred to our center from November 2012 to November 2014...
October 26, 2017: Cardiovascular Revascularization Medicine: Including Molecular Interventions
https://www.readbyqxmd.com/read/29136345/regional-lung-function-testing-in-children-using-electrical-impedance-tomography
#18
Barbara Vogt, Sarah Löhr, Zhanqi Zhao, Christian Falkenberg, Tobias Ankermann, Norbert Weiler, Inéz Frerichs
OBJECTIVE: To evaluate regional lung function in lung-healthy children before and after exercise challenge using electrical impedance tomography (EIT). METHODS: Regional lung function was examined using EIT in 100 lung-healthy children (three age subgroups: 74-121, 122-155, 156-195 months) at baseline and 10 min after exercise. Global lung function was assessed by spirometry using Z-Scores of FEV1 , FVC, FEV1 /FVC, and FEF75 . The same lung function measures were determined in 912 EIT image pixels to enable the spatial and temporal ventilation distribution analysis...
November 14, 2017: Pediatric Pulmonology
https://www.readbyqxmd.com/read/29134766/comparative-analyses-of-data-independent-acquisition-mass-spectrometric-approaches-dia-wisim-dia-and-untargeted-dia
#19
Frank Koopmans, Jenny T C Ho, August B Smit, Ka Wan Li
Data independent acquisition (DIA) is an emerging technology for quantitative proteomics. Current DIA focusses on the identification and quantitation of fragment ions that are generated from multiple peptides contained in the same selection-window of several to tens of m/z. An alternative approach is WiSIM-DIA, which combines conventional DIA with wide-SIM (wide-selected ion monitoring) windows to partition the precursor m/z space to produce high quality precursor ion chromatograms. However WiSIM-DIA has been under-explored; it remains unclear if it is a viable alternative to DIA...
November 14, 2017: Proteomics
https://www.readbyqxmd.com/read/29133957/hidden-magnetic-states-emergent-under-electric-field-in-a-room-temperature-composite-magnetoelectric-multiferroic
#20
J D Clarkson, I Fina, Z Q Liu, Y Lee, J Kim, C Frontera, K Cordero, S Wisotzki, F Sanchez, J Sort, S L Hsu, C Ko, L Aballe, M Foerster, J Wu, H M Christen, J T Heron, D G Schlom, S Salahuddin, N Kioussis, J Fontcuberta, X Marti, R Ramesh
The ability to control a magnetic phase with an electric field is of great current interest for a variety of low power electronics in which the magnetic state is used either for information storage or logic operations. Over the past several years, there has been a considerable amount of research on pathways to control the direction of magnetization with an electric field. More recently, an alternative pathway involving the change of the magnetic state (ferromagnet to antiferromagnet) has been proposed. In this paper, we demonstrate electric field control of the Anomalous Hall Transport in a metamagnetic FeRh thin film, accompanying an antiferromagnet (AFM) to ferromagnet (FM) phase transition...
November 13, 2017: Scientific Reports
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