178 research outputs found
The Human Airway Epithelial Basal Cell Transcriptome
The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population.. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels.The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium
Unsupervised discovery of tissue architecture in multiplexed imaging
Multiplexed imaging and spatial transcriptomics enable highly resolved spatial characterization of cellular phenotypes, but still largely depend on laborious manual annotation to understand higher-order patterns of tissue organization. As a result, higher-order patterns of tissue organization are poorly understood and not systematically connected to disease pathology or clinical outcomes. To address this gap, we developed an approach called UTAG to identify and quantify microanatomical tissue structures in multiplexed images without human intervention. Our method combines information on cellular phenotypes with the physical proximity of cells to accurately identify organ-specific microanatomical domains in healthy and diseased tissue. We apply our method to various types of images across healthy and disease states to show that it can consistently detect higher-level architectures in human tissues, quantify structural differences between healthy and diseased tissue, and reveal tissue organization patterns at the organ scale
RNA-Seq quantification of the human small airway epithelium transcriptome
<p>Abstract</p> <p>Background</p> <p>The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6<sup>th </sup>generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting state and in response to chronic cigarette smoking using massive parallel mRNA sequencing (RNA-Seq).</p> <p>Results</p> <p>The data demonstrate that 48% of SAE expressed genes are ubiquitous, shared with many tissues, with 52% enriched in this cell population. The most highly expressed gene, SCGB1A1, is characteristic of Clara cells, the cell type unique to the human SAE. Among other genes expressed by the SAE are those related to Clara cell differentiation, secretory mucosal defense, and mucociliary differentiation. The high sensitivity of RNA-Seq permitted quantification of gene expression related to infrequent cell populations such as neuroendocrine cells and epithelial stem/progenitor cells. Quantification of the absolute smoking-induced changes in SAE gene expression revealed that, compared to ubiquitous genes, more SAE-enriched genes responded to smoking with up-regulation, and those with the highest basal expression levels showed most dramatic changes. Smoking had no effect on SAE gene splicing, but was associated with a shift in molecular pattern from Clara cell-associated towards the mucus-secreting cell differentiation pathway with multiple features of cancer-associated molecular phenotype.</p> <p>Conclusions</p> <p>These observations provide insights into the unique biology of human SAE by providing quantit-ative assessment of the global transcriptome under physiological conditions and in response to the stress of chronic cigarette smoking.</p
Baby MIND: A magnetised spectrometer for the WAGASCI experiment
The WAGASCI experiment being built at the J-PARC neutrino beam line will
measure the difference in cross sections from neutrinos interacting with a
water and scintillator targets, in order to constrain neutrino cross sections,
essential for the T2K neutrino oscillation measurements. A prototype Magnetised
Iron Neutrino Detector (MIND), called Baby MIND, is being constructed at CERN
to act as a magnetic spectrometer behind the main WAGASCI target to be able to
measure the charge and momentum of the outgoing muon from neutrino charged
current interactions.Comment: Poster presented at NuPhys2016 (London, 12-14 December 2016). Title +
4 pages, LaTeX, 6 figure
Synchronization of the Distributed Readout Frontend Electronics of the Baby MIND Detector
Baby MIND is a new downstream muon range detector for the WGASCI experiment. This article discusses the distributed readout system and its timing requirements. The paper presents the design of the synchronization subsystem and the results of its test
Baby MIND Experiment Construction Status
Baby MIND is a magnetized iron neutrino detector, with novel design features,
and is planned to serve as a downstream magnetized muon spectrometer for the
WAGASCI experiment on the T2K neutrino beam line in Japan. One of the main
goals of this experiment is to reduce systematic uncertainties relevant to
CP-violation searches, by measuring the neutrino contamination in the
anti-neutrino beam mode of T2K. Baby MIND is currently being constructed at
CERN, and is planned to be operational in Japan in October 2017.Comment: Poster presented at NuPhys2016 (London, 12-14 December 2016). 4
pages, LaTeX, 7 figure
Baby MIND: A magnetized segmented neutrino detector for the WAGASCI experiment
T2K (Tokai-to-Kamioka) is a long-baseline neutrino experiment in Japan
designed to study various parameters of neutrino oscillations. A near detector
complex (ND280) is located 280~m downstream of the production target and
measures neutrino beam parameters before any oscillations occur. ND280's
measurements are used to predict the number and spectra of neutrinos in the
Super-Kamiokande detector at the distance of 295~km. The difference in the
target material between the far (water) and near (scintillator, hydrocarbon)
detectors leads to the main non-cancelling systematic uncertainty for the
oscillation analysis. In order to reduce this uncertainty a new
WAter-Grid-And-SCintillator detector (WAGASCI) has been developed. A magnetized
iron neutrino detector (Baby MIND) will be used to measure momentum and charge
identification of the outgoing muons from charged current interactions. The
Baby MIND modules are composed of magnetized iron plates and long plastic
scintillator bars read out at the both ends with wavelength shifting fibers and
silicon photomultipliers. The front-end electronics board has been developed to
perform the readout and digitization of the signals from the scintillator bars.
Detector elements were tested with cosmic rays and in the PS beam at CERN. The
obtained results are presented in this paper.Comment: In new version: modified both plots of Fig.1 and added one sentence
in the introduction part explaining Baby MIND role in WAGASCI experiment,
added information for the affiliation
Scintillator counters with WLS fiber/MPPC readout for the side muon range detector (SMRD)of the T2K experiment
The T2K neutrino experiment at J-PARC uses a set of near detectors to measure
the properties of an unoscillated neutrino beam and neutrino interaction
cross-sections. One of the sub-detectors of the near-detector complex, the side
muon range detector (SMRD), is described in the paper. The detector is designed
to help measure the neutrino energy spectrum, to identify background and to
calibrate the other detectors. The active elements of the SMRD consist of 0.7
cm thick extruded scintillator slabs inserted into air gaps of the UA1 magnet
yokes. The readout of each scintillator slab is provided through a single WLS
fiber embedded into a serpentine shaped groove. Two Hamamatsu multi-pixel
avalanche photodiodes (MPPC's) are coupled to both ends of the WLS fiber. This
design allows us to achieve a high MIP detection efficiency of greater than
99%. A light yield of 25-50 p.e./MIP, a time resolution of about 1 ns and a
spatial resolution along the slab better than 10 cm were obtained for the SMRD
counters.Comment: 7 pages, 4 figures; talk at TIPP09, March 12-17, Tsukuba, Japan; to
be published in the conference proceeding
- …