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Matthew J Everly, Kimberly P Briley, Carl E Haisch, Georg Dieplinger, Paul Bolin, Scott A Kendrick, Claire Morgan, Angela Q Maldonado, Lorita M Rebellato
Controversy exists as to whether African American (AA) transplant recipients are at risk for developing de novo donor-specific anti-human leukocyte antigen (HLA) antibody (dnDSA). We studied 341 HLA-mismatched, primary renal allograft recipients who were consecutively transplanted between 3/1999 and 12/2010. Sera were collected sequentially pre- and post-transplant and tested for anti-HLA immunoglobulin G (IgG) via single antigen bead assay. Of the 341 transplant patients (225 AA and 116 non-AA), 107 developed dnDSA at a median of 9...
February 17, 2017: Transplant International: Official Journal of the European Society for Organ Transplantation
R E Cavicchi, Cayla Collett, Srivalli Telikepalli, Zhishang Hu, Michael Carrier, Dean C Ripple
An accurate assessment of particle characteristics and concentrations in pharmaceutical products by flow imaging requires accurate particle sizing and morphological analysis. Analysis of images begins with the definition of particle boundaries. Commonly a single threshold defines the level for a pixel in the image to be included in the detection of particles, but depending on the threshold level, this results in either missing translucent particles or oversizing of less transparent particles due to the halos and gradients in intensity near the particle boundaries...
February 13, 2017: Journal of Pharmaceutical Sciences
Thomas H Linz, W Hampton Henley, J Michael Ramsey
Multiplexing bead-based bioassays requires that each type of microsphere be uniquely encoded to distinguish one type from another. Microspheres are typically encoded using fluorescent dyes with different spectral properties and varying concentrations. However practical limits exist on the number of dyes that can be spectrally resolved or the number of distinguishable intensity levels with each dye. To expand the number of encoding levels, a novel method was developed that incorporates photobleaching kinetics into bead decoding, unlocking additional multiplexing levels unattainable by conventional decoding methods...
February 16, 2017: Lab on a Chip
H Clifford Sullivan, Robert S Liwski, Robert A Bray, Howard M Gebel
Technological advances in HLA laboratory testing undoubtedly improved the sensitivity and specificity of HLA antibody assessment, but not without introducing a set of challenges regarding data interpretation. In particular, the introduction of solid-phase single antigen bead (SAB) antibody assessment brought the belief that mean fluorescence intensity (MFI) was a quantifiable value. As such, MFI levels heavily influenced HLA antibody reporting, monitoring and clinical practice. However, given that SAB testing was neither intended for nor approved to be quantifiable, is the use of MFI in current clinical and laboratory practice valid? What, if anything, does this numerical value actually reveal about the pathogenic potential of the antibody? What are the pitfalls and caveats associated with reporting MFI? Herein, we travel the road to HLA antibody assessment and explore the reliability of MFI values to make clinical decisions...
February 15, 2017: American Journal of Transplantation
Todd M Gierahn, Marc H Wadsworth, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love, Alex K Shalek
Single-cell RNA-seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA-seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We use Seq-Well to profile thousands of primary human macrophages exposed to Mycobacterium tuberculosis.
February 13, 2017: Nature Methods
Dipankar Mondal, Debabrata Goswami
Multiphoton absorbing dye-coated trapped spherical bead at the focal plane of femtosecond optical tweezers shows nonlinear optical (NLO) phenomena. One such NLO process of two-photon fluorescence (TPF) has been used for the background-free imaging of a femtosecond laser-trapping event. Due to the high peak powers of femtosecond laser pulses with low average powers, it is possible to not only trap single nanospheres, but encourage optically directed self-assembly. The TPF signatures of trapped particles show evidence of such a directed self-assembly process which, in turn, can provide information about the structural dynamics during the process of cluster formation...
October 7, 2016: Methods and Applications in Fluorescence
Piotr Polanowski, Jeremiasz K Jeszka, Andrzej Sikorski
The static properties of two-dimensional athermal polymer solutions were studied by performing Monte Carlo lattice simulations using the cooperative motion algorithm (CMA) and taking into account the presence of explicit solvent molecules. The simulations were performed for a wide range of polymer chain lengths N (16-1024) and concentrations φ (0.0156-1). The results obtained for short chains (N < 256) were in good agreement with those given by previous simulations. For the longest chains (512 or 1024 beads), some unexpected behavior was observed in the dilute and semidilute regimes...
February 2017: Journal of Molecular Modeling
Anne C Jäger, Michelle L Alvarez, Carey P Davis, Ernesto Guzmán, Yonmee Han, Lisa Way, Paulina Walichiewicz, David Silva, Nguyen Pham, Glorianna Caves, Jocelyne Bruand, Felix Schlesinger, Stephanie J K Pond, Joe Varlaro, Kathryn M Stephens, Cydne L Holt
Human DNA profiling using PCR at polymorphic short tandem repeat (STR) loci followed by capillary electrophoresis (CE) size separation and length-based allele typing has been the standard in the forensic community for over 20 years. Over the last decade, Next-Generation Sequencing (NGS) matured rapidly, bringing modern advantages to forensic DNA analysis. The MiSeq FGx™ Forensic Genomics System, comprised of the ForenSeq™ DNA Signature Prep Kit, MiSeq FGx™ Reagent Kit, MiSeq FGx™ instrument and ForenSeq™ Universal Analysis Software, uses PCR to simultaneously amplify up to 231 forensic loci in a single multiplex reaction...
January 27, 2017: Forensic Science International. Genetics
Julian Strobel, Barbara Hauck-Dlimi, Volker Weisbach, Reinhold Eckstein, Juergen Zingsem, Erwin Strasser
BACKGROUND: Quantification of CD34+ cells in peripheral blood stem cell apheresis is normally performed by single platform flow cytometric measurements according to the ISHAGE protocol. Peripheral blood stem cell concentrates (PBSC) produced by apheresis normally contain many T cells. Those T cells can be used for production of donor lymphocyte infusion doses, if abundant amounts of CD34+ cells have been collected. Therefore, it is of interest to know both the CD3+ and the CD34+ cell count of allogeneic PBSC...
November 1, 2016: Clinical Laboratory
P H Geoghegan, A M Laffra, N K Hoogendorp, M C Taylor, M C Jermy
In an attempt to obtain a deeper understanding of the factors which determine the characteristics of expirated bloodstain patterns, the mechanism of formation of airborne droplets was studied. Hot wire anemometry measured air velocity, 25 mm from the lips, for 31 individuals spitting, coughing and blowing. Expirated stains were produced by the same mechanisms performed by one individual with different volumes of a synthetic blood substitute in their mouth. The atomization of the liquid at the lips was captured with high-speed video, and the resulting stain patterns were captured on paper targets...
February 2, 2017: International Journal of Legal Medicine
Liisa M Hirvonen, Merlin Fisher-Levine, Klaus Suhling, Andrei Nomerotski
TimepixCam is a novel fast optical imager based on an optimized silicon pixel sensor with a thin entrance window and read out by a Timepix Application Specific Integrated Circuit. The 256 × 256 pixel sensor has a time resolution of 15 ns at a sustained frame rate of 10 Hz. We used this sensor in combination with an image intensifier for wide-field time-correlated single photon counting imaging. We have characterised the photon detection capabilities of this detector system and employed it on a wide-field epifluorescence microscope to map phosphorescence decays of various iridium complexes with lifetimes of about 1 μs in 200 μm diameter polystyrene beads...
January 2017: Review of Scientific Instruments
Mario Villada-Balbuena, Mauricio D Carbajal-Tinoco
We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules...
January 28, 2017: Journal of Chemical Physics
Soraya Wilke Saliba, Erica Leandro Marciano Vieira, Rebeca Priscila de Melo Santos, Eduardo Candelario-Jalil, Bernd L Fiebich, Luciene Bruno Vieira, Antonio Lucio Teixeira, Antonio Carlos Pinheiro de Oliveira
BACKGROUND: The mammalian target of rapamycin (mTOR) is a kinase involved in a variety of physiological and pathological functions. However, the exact role of mTOR in excitotoxicity is poorly understood. Here, we investigated the effects of mTOR inhibition with rapamycin against neurodegeneration, and motor impairment, as well as inflammatory profile caused by an excitotoxic stimulus. METHODS: A single and unilateral striatal injection of quinolinic acid (QA) was used to induce excitotoxicity in mice...
January 31, 2017: Journal of Neuroinflammation
Wenjun Huang, Taraknath Mandal, Ronald G Larson
We present coarse-grained (CG) force fields for Hydroxypropyl-Methylcellulose Acetate Succinate (HPMCAS) polymers and the drug molecule phenytoin using a bead/stiff spring model, with each bead representing a HPMCAS monomer or monomer side group (hydroxypropyl acetate, acetate, or succinate), or a single phenytoin ring. We obtain the bonded and non-bonded interaction parameters in our CG model using the RDFs from atomistic simulations of short HPMCAS model oligomers (20-mer) and atomistic simulations of phenytoin molecules...
January 31, 2017: Molecular Pharmaceutics
Elisabeth Palzenberger, Ronja Reinhardt, Leila Muresan, Barbara Palaoro, Irene Tiemann-Boege
Characterizing polymorphisms on single molecules renders the phase of different alleles, and thus, haplotype information. Here, we describe a high-throughput method to genotype hundreds-of thousands single molecules in parallel using bead-emulsion haplotyping (BEH). Haplotyping via BEH is an emulsion-PCR-based method that was adapted to amplify multiple DNA fragments on paramagnetic, microscopic beads within a compartment formed by an aqueous-oil emulsion. This generates beads covered by thousands of clonal copies from several polymorphic regions of an initial DNA molecule that are then genotyped with fluorescently labeled probes...
2017: Methods in Molecular Biology
Cornelius S Bausch, Christian Heyn, Wolfgang Hansen, Insa M A Wolf, Björn-Philipp Diercks, Andreas H Guse, Robert H Blick
We present a radio-frequency impedance-based biosensor embedded inside a semiconductor microtube for the in-flow detection of single cells. An impedance-matched tank circuit and a tight wrapping of the electrodes around the sensing region, which creates a close, leakage current-free contact between cells and electrodes, yields a high signal-to-noise ratio. We experimentally show a twofold improved sensitivity of our three-dimensional electrode structure to conventional planar electrodes and support these findings by finite element simulations...
January 30, 2017: Scientific Reports
Catherine Findlay, Jason Morrison, C J Mundy, Julia Sedlmair, Carol J Hirschmugl, Kathleen M Gough
We have used thermal source Fourier Transform Infrared (FTIR) microtomographic imaging to compare sea ice diatoms growing under different light conditions. A prototype tomography accessory was designed to have sufficient degrees of freedom to align any tilted cylindrical sample relative to the axis of rotation, minimizing the off-axis path traced during rotation. The lightweight device rests on the motorized stage to position the sample in the field-of-view and enable mosaic imaging. Reconstruction routines were tested with simulated and real phantoms, to assess limitations in the Radon back-projection method employed...
January 30, 2017: Analyst
Nuonuo Zhang, Jianbing Jiang, Mengran Liu, Masahiko Taniguchi, Amit Kumar Mandal, Rosemary B Evans-Storms, J Bruce Pitner, David F Bocian, Dewey Holten, Jonathan S Lindsey
Synthetic bacteriochlorins absorb in the near-infrared (NIR) region and are versatile analogues of natural bacteriochlorophylls. The utilization of these chromophores in energy sciences and photomedicine requires the ability to tailor their physicochemical properties, including the incorporation of units to impart water solubility. Herein, we report the synthesis, from two common bacteriochlorin building blocks, of five wavelength-tunable, bioconjugatable and water-soluble bacteriochlorins along with two non-bioconjugatable benchmarks...
September 1, 2016: New Journal of Chemistry, Nouveau Journal de Chimie
Mine Dogan, Stephen M J Moysey, Ruud M Ramakers, Timothy A DeVol, Frederik J Beekman, Harald C Groen, Brian A Powell
A dynamic (99m)Tc tracer experiment was performed to investigate the capabilities of combined pre-clinical single photon emission computed tomography (SPECT) and x-ray computed tomography (CT) for investigating transport in a heterogeneous porous medium. The experiment was conducted by continuously injecting a (99m)Tc solution into a column packed with 8 layers (i.e., soil, silica gel, and 0.2-4 mm glass beads). Within the imaging results it was possible to correlate observed features with objects as small as 2 mm for the SPECT and 0...
January 27, 2017: Environmental Science & Technology
Minjeong Jang, Ilkyoo Koh, Seok Jae Lee, Jae-Ho Cheong, Pilnam Kim
Gastric cancer (GC) is a common aggressive malignant tumor with high incidence and mortality worldwide. GC is classified into intestinal and diffuse types according to the histo-morphological features. Because of distinctly different clinico-pathological features, new cancer therapy strategies and in vitro preclinical models for the two pathological variants of GC is necessary. Since extracellular matrix (ECM) influence the biological behavior of tumor cells, we hypothesized that GC might be more similarly modeled in 3D with matrix rather than in 2D...
January 27, 2017: Scientific Reports
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