135 research outputs found

    Advancing brain barriers RNA sequencing: guidelines from experimental design to publication

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    Background: RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing differential gene expression and thus characterization of specific tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers research. This has led to availability of both, bulk and single-cell RNA-Seq datasets over the last few years. If appropriately performed, the RNA-Seq studies provide powerful datasets that allow for significant deepening of knowledge on the molecular mechanisms that establish the brain barriers. However, RNA-Seq studies comprise complex workflows that require to consider many options and variables before, during and after the proper sequencing process.Main body: In the current manuscript, we build on the interdisciplinary experience of the European PhD Training Network BtRAIN (https://www.btrain-2020.eu/) where bioinformaticians and brain barriers researchers collaborated to analyze and establish RNA-Seq datasets on vertebrate brain barriers. The obstacles BtRAIN has identified in this process have been integrated into the present manuscript. It provides guidelines along the entire workflow of brain barriers RNA-Seq studies starting from the overall experimental design to interpretation of results. Focusing on the vertebrate endothelial blood–brain barrier (BBB) and epithelial blood-cerebrospinal-fluid barrier (BCSFB) of the choroid plexus, we provide a step-by-step description of the workflow, highlighting the decisions to be made at each step of the workflow and explaining the strengths and weaknesses of individual choices made. Finally, we propose recommendations for accurate data interpretation and on the information to be included into a publication to ensure appropriate accessibility of the data and reproducibility of the observations by the scientific community.Conclusion: Next generation transcriptomic profiling of the brain barriers provides a novel resource for understanding the development, function and pathology of these barrier cells, which is essential for understanding CNS homeostasis and disease. Continuous advancement and sophistication of RNA-Seq will require interdisciplinary approaches between brain barrier researchers and bioinformaticians as successfully performed in BtRAIN. The present guidelines are built on the BtRAIN interdisciplinary experience and aim to facilitate collaboration of brain barriers researchers with bioinformaticians to advance RNA-Seq study design in the brain barriers community

    Search for a narrow baryonic state decaying to pKS0{pK^0_S} and pKS0{\overline{p}K^0_S} in deep inelastic scattering at HERA

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    A search for a narrow baryonic state in the pKS0pK^0_S and pKS0\overline{p}K^0_S system has been performed in epep collisions at HERA with the ZEUS detector using an integrated luminosity of 358 pb1^{-1} taken in 2003-2007. The search was performed with deep inelastic scattering events at an epep centre-of-mass energy of 318 GeV for exchanged photon virtuality, Q2Q^2, between 20 and 100 GeV2\rm{} GeV^{2}. Contrary to evidence presented for such a state around 1.52 GeV in a previous ZEUS analysis using a sample of 121 pb1^{-1} taken in 1996-2000, no resonance peak was found in the p(p)KS0p(\overline{p})K^0_S invariant-mass distribution in the range 1.45-1.7 GeV. Upper limits on the production cross section are set

    Measurement of the cross-section ratio sigma(psi(2S))/sigma(J/psi(1S)) in deep inelastic exclusive ep scattering at HERA

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    The exclusive deep inelastic electroproduction of ψ(2S) and J/ψ(1S) at an ep centre-of-mass energy of 317 GeV has been studied with the ZEUS detector at HERA in the kinematic range 2<Q2<80 GeV2, 30<W<210 GeV and |t|<1 GeV2, where Q2 is the photon virtuality, W is the photon–proton centre-of-mass energy and t is the squared four-momentum transfer at the proton vertex. The data for 2<Q2<5 GeV2 were taken in the HERA I running period and correspond to an integrated luminosity of 114 pb−1. The data for 5<Q2<80 GeV2 are from both HERA I and HERA II periods and correspond to an integrated luminosity of 468 pb−1. The decay modes analysed were μ+μ− and View the MathML source for the ψ(2S) and μ+μ− for the J/ψ(1S). The cross-section ratio σψ(2S)/σJ/ψ(1S) has been measured as a function of View the MathML source  and t. The results are compared to predictions of QCD-inspired models of exclusive vector-meson production

    Combined QCD and electroweak analysis of HERA data

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    A simultaneous fit of parton distribution functions (PDFs) and electroweak parameters to HERA data on deep inelastic scattering is presented. The input data are the neutral current and charged current inclusive cross sections which were previously used in the QCD analysis leading to the HERAPDF2.0 PDFs. In addition, the polarisation of the electron beam was taken into account for the ZEUS data recorded between 2004 and 2007. Results on the vector and axial-vector couplings of the Z boson to u- and d-type quarks, on the value of the electroweak mixing angle and the mass of the W boson are presented. The values obtained for the electroweak parameters are in agreement with Standard Model predictions

    Alzheimer's Disease: a Review of its Visual System Neuropathology. Optical Coherence Tomography-a Potential Role As a Study Tool in Vivo

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    Alzheimer's disease (AD) is a prevalent, long-term progressive degenerative disorder with great social impact. It is currently thought that, in addition to neurodegeneration, vascular changes also play a role in the pathophysiology of the disease. Visual symptoms are frequent and are an early clinical manifestation; a number of psychophysiologic changes occur in visual function, including visual field defects, abnormal contrast sensitivity, abnormalities in color vision, depth perception deficits, and motion detection abnormalities. These visual changes were initially believed to be solely due to neurodegeneration in the posterior visual pathway. However, evidence from pathology studies in both animal models of AD and humans has demonstrated that neurodegeneration also takes place in the anterior visual pathway, with involvement of the retinal ganglion cells' (RGCs) dendrites, somata, and axons in the optic nerve. These studies additionally showed that patients with AD have changes in retinal and choroidal microvasculature. Pathology findings have been corroborated in in-vivo assessment of the retina and optic nerve head (ONH), as well as the retinal and choroidal vasculature. Optical coherence tomography (OCT) in particular has shown great utility in the assessment of these changes, and it may become a useful tool for early detection and monitoring disease progression in AD. The authors make a review of the current understanding of retinal and choroidal pathological changes in patients with AD, with particular focus on in-vivo evidence of retinal and choroidal neurodegenerative and microvascular changes using OCT technology.info:eu-repo/semantics/publishedVersio

    Production of exclusive dijets in diffractive deep inelastic scattering at HERA

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    Production of exclusive dijets in diffractive deep inelastic e±p scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 372 pb-1. The measurement was performed for γ∗–p centre-of-mass energies in the range 9025GeV2. Energy flows around the jet axis are presented. The cross section is presented as a function of β and ϕ, where β=x/xIP, x is the Bjorken variable and xIP is the proton fractional longitudinal momentum loss. The angle ϕ is defined by the γ∗–dijet plane and the γ∗–e± plane in the rest frame of the diffractive final state. The ϕ cross section is measured in bins of β. The results are compared to predictions from models based on different assumptions about the nature of the diffractive exchange.</w<250gev

    Combination of measurements of inclusive deep inelastic e(+/-)p scattering cross sections and QCD analysis of HERA data

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    Combination of Differential D^{*\pm} Cross-Section Measurements in Deep-Inelastic ep Scattering at HERA

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    H1 and ZEUS have published single-differential cross sections for inclusive D^{*\pm}-meson production in deep-inelastic ep scattering at HERA from their respective final data sets. These cross sections are combined in the common visible phase-space region of photon virtuality Q2 > 5 GeV2, electron inelasticity 0.02 1.5 GeV and pseudorapidity |eta(D^*)| 1.5 GeV2. Perturbative next-to-leadingorder QCD predictions are compared to the results.H1 and ZEUS have published single-differential cross sections for inclusive D±^{∗±}-meson production in deep-inelastic ep scattering at HERA from their respective final data sets. These cross sections are combined in the common visible phase-space region of photon virtuality Q2^{2} > 5 GeV2^{2}, electron inelasticity 0.02 1.5 GeV and pseudorapidity |η(D^{∗})| 1.5 GeV2^{2}. Perturbative next-to-leading-order QCD predictions are compared to the results.H1 and ZEUS have published single-differential cross sections for inclusive D^{*\pm}-meson production in deep-inelastic ep scattering at HERA from their respective final data sets. These cross sections are combined in the common visible phase-space region of photon virtuality Q2 > 5 GeV2, electron inelasticity 0.02 1.5 GeV and pseudorapidity |eta(D^*)| 1.5 GeV2. Perturbative next-to-leadingorder QCD predictions are compared to the results

    Combination of differential D*(+/-) cross-section measurements in deep-inelastic ep scattering at HERA

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    Combination of differential D*(+/-) cross-section measurements in deep-inelastic ep scattering at HERA

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    H1 and ZEUS have published single-differential cross sections for inclusive D∗±-meson production in deep-inelastic ep scattering at HERA from their respective final data sets. These cross sections are combined in the common visible phase-space region of photon virtuality Q2&gt; 5 GeV2, electron inelasticity 0.02 &lt; y &lt; 0.7 and the D∗± meson’s transverse momentum pT(D∗) &gt; 1.5 GeV and pseudorapidity |η(D∗)| &lt; 1.5. The combination procedure takes into account all correlations, yielding significantly reduced experimental uncertainties. Double-differential cross sections d2σ/dQ2dy are combined with earlier D∗± data, extending the kinematic range down to Q2&gt; 1.5 GeV2. Perturbative next-to-leading-order QCD predictions are compared to the results
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