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Xiqi Li, Cesar A Arias, Samuel L Aitken, Jessica Galloway Peña, Diana Panesso, Michael Chang, Lorena Diaz, Rafael Rios, Yazan Numan, Sammi Ghaoui, Sruti DebRoy, Micah M Bhatti, Dawn E Simmons, Isaam Raad, Ray Hachem, Stephanie A Folan, Pranoti Sahasarabhojane, Awdhesh Kalia, Samuel A Shelburne
Background: Pathobionts, bacteria that are typically human commensals but can cause disease, contribute significantly to antimicrobial resistance. Staphylococcus epidermidis is a prototypical pathobiont as it is a ubiquitous human commensal but also a leading cause of healthcare-associated bacteremia. We sought to determine the etiology of a recent increase in invasive S. epidermidis isolates resistant to linezolid. Methods: Whole-genome sequencing (WGS) was performed on 176 S...
March 12, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
Holger Winkels, Erik Ehinger, Melanie Vassallo, Konrad Buscher, Huy Dinh, Kouji Kobiyama, Anouk Hamers, Clément Cochain, Ehsan Vafadarnejad, Antoine-Emmanuel Saliba, Alma Zernecke, Akula Pramod, Amlan Ghosh, Nathaly Anto Michel, Natalie Hoppe, Ingo Hilgendorf, Andreas Zirlik, Catherine Hedrick, Klaus Ley, Dennis Wolf
<u>Rationale:</u> Atherosclerosis is a chronic inflammatory disease that is driven by the interplay of pro- and anti-inflammatory leukocytes in the aorta. Yet, the phenotypic and transcriptional diversity of aortic leukocytes is only poorly understood. <u>Objective:</u> We characterized leukocytes from healthy and atherosclerotic mouse aortas in-depth by single cell RNA-sequencing (scRNAseq) and mass cytometry (CyTOF) to define an atlas of the immune cell landscape in atherosclerosis...
March 15, 2018: Circulation Research
Bo Zhang, Mouzhe Xie, Lei Bruschweiler-Li, Rafael Brüschweiler
Understanding and harnessing the interactions between nanoparticles and biological molecules is at the forefront of applications of nanotechnology to modern biology. Metabolomics has emerged as a prominent player in systems biology as a complement to genomics, transcriptomics and proteomics. Its focus is the systematic study of metabolite identities and concentration changes in living systems. Despite significant progress over the recent past, important challenges in metabolomics remain, such as the deconvolution of the spectra of complex mixtures with strong overlaps, the sensitive detection of metabolites at low abundance, unambiguous identification of known metabolites, structure determination of unknown metabolites and standardized sample preparation for quantitative comparisons...
March 13, 2018: Metabolites
Anastasia A Andrianova, Thomas DiProspero, Clayton Geib, Irina P Smoliakova, Evguenii I Kozliak, Alena Kubátová
The capability to characterize lignin, lignocellulose, and their degradation products is essential for the development of new renewable feedstocks. Electrospray ionization high-resolution time-of-flight mass spectrometry (ESI-HR TOF-MS) method was developed expanding the lignomics toolkit while targeting the simultaneous detection of low and high molecular weight (MW) lignin species. The effect of a broad range of electrolytes and various ionization conditions on ion formation and ionization effectiveness was studied using a suite of mono-, di-, and triarene lignin model compounds as well as kraft alkali lignin...
March 12, 2018: Journal of the American Society for Mass Spectrometry
Melisa Okanovic, Burghard Hillig, Felix Breuer, Peter Jakob, Martin Blaimer
PURPOSE: To improve 2D noncontrast-enhanced MRA by using a helical time-of-flight (TOF) acquisition technique and a slice-super-resolution reconstruction. METHODS: The TOF technique is combined with a helical trajectory with golden-angle-based radial projection reordering. A continuous spatial shift in slice direction is realized by adjusting the frequency of the excitation pulse between the individual projections. The limited resolution along the shift direction is improved by a deconvolution with simulated slice profile...
March 11, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Patrick W Hales, Victoria Smith, Deepi Dhanoa-Hayre, Patricia O'Hare, Kshitij Mankad, Felice d'Arco, Jessica Cooper, Ramneek Kaur, Kim Phipps, Richard Bowman, Darren Hargrave, Christopher Clark
Background: Radiological biomarkers which correlate with visual function are needed to improve the clinical management of optic pathway glioma (OPG) patients. Currently, these are not available using conventional magnetic resonance imaging (MRI) sequences. The aim of this study was to determine whether diffusion MRI could be used to delineate the entire optic pathway in OPG patients, and provide imaging biomarkers within this pathway which correlate with a patient's visual acuity (VA)...
2018: NeuroImage: Clinical
Louise J C J den Biggelaar, Simone J P M Eussen, Simone J S Sep, Andrea Mari, Ele Ferrannini, Marleen M van Greevenbroek, Carla J van der Kallen, Casper G Schalkwijk, Ilja C W Arts, Coen D A Stehouwer, Pieter C Dagnelie
PURPOSE: Type 2 diabetes mellitus (T2DM) is characterized by both impaired pancreatic β-cell function (BCF) and insulin resistance. In the etiology of T2DM, BCF basically determines whether a person with a certain degree of insulin resistance develops T2DM, as β-cells are able to compensatorily increase insulin secretion. The effects of dietary intake on BCF are largely unknown. Our study aim was to investigate whether dietary macronutrient intake predicts BCF. METHODS: Prospective data (median follow-up 7 years) of 303 individuals recruited from the CODAM study population (aged 40-70 years, 39% women) were analyzed...
March 10, 2018: European Journal of Nutrition
Rebecca S Just, Jodi A Irwin
Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input...
February 21, 2018: Forensic Science International. Genetics
Guillaume Falgayrac, Damian Siepka, Elżbieta A Stefaniak, Guillaume Penel, Sophie Sobanska
The influence of six common substrates on the Raman imaging of micron-sized inorganic aerosol particles was examined. Laboratory-generated single-component particles of calcite (CaCO3 ) and mixed particles of calcite (CaCO3 ), nitratine (NaNO3 ), hematite (Fe2 O3 ) and anglesite (PbSO4 ) were deposited by cascade impaction on Ag, In, Si, SiO2 , microscope slide and TEM-grid substrates. The spectral contribution of substrates to Raman images of the deposited particles was evaluated by Multivariate Curve Resolution...
July 19, 2018: Analytica Chimica Acta
Christopher P Caridi, Laetitia Delabaere, Harianto Tjong, Hannah Hopp, Devika Das, Frank Alber, Irene Chiolo
Heterochromatin is mostly composed of long stretches of repeated DNA sequences prone to ectopic recombination during double-strand break (DSB) repair. In Drosophila, "safe" homologous recombination (HR) repair of heterochromatic DSBs relies on a striking relocalization of repair sites to the nuclear periphery. Central to understanding heterochromatin repair is the ability to investigate the 4D dynamics (movement in space and time) of repair sites. A specific challenge of these studies is preventing phototoxicity and photobleaching effects while imaging the sample over long periods of time, and with sufficient time points and Z-stacks to track repair foci over time...
2018: Methods in Enzymology
Matthew Sonnett, Eyan Yeung, Martin Wühr
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitations...
March 9, 2018: Analytical Chemistry
Anna K Trull, Jelle van der Horst, Lucas J van Vliet, Jeroen Kalkman
We present a comparison of image reconstruction techniques for optical projection tomography. We compare conventional filtered back projection, sinogram filtering using the frequency-distance relationship (FDR), image deconvolution, and 2D point-spread-function-based iterative reconstruction. The latter three methods aim to remove the spatial blurring in the reconstructed image originating from the limited depth of field caused by the point spread function of the imaging system. The methods are compared based on simulated data, experimental optical projection tomography data of single fluorescent beads, and high-resolution optical projection tomography imaging of an entire zebrafish larva...
March 10, 2018: Applied Optics
Kum Ju Chae, Jin Mo Goo, Su Yeon Ahn, Jin Young Yoo, Soon Ho Yoon
[This corrects the article on p. 147 in vol. 19, PMID: 29354011.].
March 2018: Korean Journal of Radiology: Official Journal of the Korean Radiological Society
Guang Xu, Jacek Stupak, Li Yang, Luokai Hu, Bo Guo, Jianjun Li
Mass spectrometry (MS) has played a vital role across a broad range of fields and applications in proteomics. The development of high-resolution MS for the past decades has significantly advanced biology, such as protein structure, function, post translational modification and global protein dynamics. In MS, two ionization techniques are often used-electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). ESI mass spectra are generally crowded by signals of multiple charge values for each molecular mass and an isotopic cluster for each nominal mass-to-charge (m/z) value...
March 8, 2018: Rapid Communications in Mass Spectrometry: RCM
M Modzel, K A Solanko, M Szomek, S K Hansen, A Dupont, L J Nåbo, J Kongsted, D Wüstner
Analysis of intracellular cholesterol transport by fluorescence microscopy requires suitable fluorescent analogues of cholesterol. Most existing cholesterol analogues contain lipophilic dyes which can compromise the sterol properties in membranes. An alternative strategy is to introduce additional double bonds into the sterol ring system resulting in intrinsic fluorescence, while at the same time keeping the cholesterol-like properties of the analogues. Existing polyene sterols, such as dehydroergosterol (DHE) or cholestatrienol (CTL), however, contain only three double bonds and suffer from low brightness, significant photobleaching and excitation/emission in the ultraviolet region...
March 8, 2018: Journal of Microscopy
Elsa Omer, Ronan Cariou, Gérald Remaud, Yann Guitton, Hélène Germon, Paul Hill, Gaud Dervilly-Pinel, Bruno Le Bizec
An untargeted strategy aiming at identifying non-intentionally added substances (NIAS) migrating from coatings was developed. This innovative approach was applied to two polyester-polyurethane lacquers, for which suppliers previously provided the identity of the monomers involved. Lacquers were extracted with acetonitrile and analyzed by liquid chromatography-high resolution mass spectrometry (LC-HRMS). Data, acquired in the full scan mode, were processed using an open-source R-environment (xcms and CAMERA packages) to list the detected features and deconvolute them in groups related to individual compounds...
March 8, 2018: Analytical and Bioanalytical Chemistry
Niya Wang, Lulu Chen, Yue Wang
Tissue heterogeneity is both a major confounding factor and an underexploited information source. While a handful of reports have demonstrated the potential of supervised methods to deconvolve tissue heterogeneity, these approaches require a priori information on the marker genes or composition of known subpopulations. To address the critical problem of the absence of validated marker genes for many (including novel) subpopulations, we develop a novel unsupervised deconvolution method, Convex Analysis of Mixtures (CAM), within a well-grounded mathematical framework, to dissect mixed gene expressions in heterogeneous tissue samples...
2018: Methods in Molecular Biology
M Rahimi, M Zahedifar, E Sadeghi
Lithium tetraborate (Li2B4O7) nanoparticles (NPs) doped with manganese (Mn) were prepared for the first time by the solid-state sintering method. NPs were characterized using X-ray diffraction, scanning electron microscopy, photoluminescence and thermoluminescence (TL) techniques. The synthesized NPs exhibited highest TL response at 0.3 wt% of Mn dopant under gamma irradiation. TL dose response is linear for the absorbed dose from 1 Gy to 20 kGy and beyond this range behaves sub-linear. Such feature makes the synthesized nanophosphor as a promising material for high-dose dosimetry applications...
March 1, 2018: Radiation Protection Dosimetry
Hao Yan, Owen Carmichael, Debashis Paul, Jie Peng
We present a novel method for estimation of the fiber orientation distribution (FOD) function based on diffusion-weighted magnetic resonance imaging (D-MRI) data. We formulate the problem of FOD estimation as a regression problem through spherical deconvolution and a sparse representation of the FOD by a spherical needlets basis that forms a multi-resolution tight frame for spherical functions. This sparse representation allows us to estimate the FOD by ℓ1 -penalized regression under a non-negativity constraint on the estimated FOD...
February 8, 2018: Medical Image Analysis
Jing Zhang, Jingling Huang, Carmen Say, Robert L Dorit, K T Queeney
HYPOTHESIS: The nucleation of biofilms is known to be affected by both the chemistry and topography of the underlying substrate, particularly when topography includes nanoscale (<100 nm) features. However, determining the role of topography vs. chemistry is complicated by concomitant variation in both as a result of typical surface modification techniques. Analyzing the behavior of biofilm-forming bacteria exposed to surfaces with systematic, independent variation of both topography and surface chemistry should allow differentiation of the two effects...
February 24, 2018: Journal of Colloid and Interface Science
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