| 1. |
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| 2. |
- Beal, Jacob, et al.
(author)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
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| 5. |
- Campbell, PJ, et al.
(author)
-
Pan-cancer analysis of whole genomes
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
-
Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 6. |
- Abelev, B., et al.
(author)
-
Centrality, rapidity and transverse momentum dependence of J/Psi suppression in Pb-Pb collisions at root(NN)-N-S=2.76TeV
- 2014
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 734, s. 314-327
-
Journal article (peer-reviewed)abstract
- The inclusive J/.nuclear modification factor (R-AA) in Pb-Pb collisions at root(NN)-N-S = 2.76TeVhas been measured by ALICE as a function of centrality in the e+ e-decay channel at mid-rapidity (| y| < 0.8) and as a function of centrality, transverse momentum and rapidity in the + -decay channel at forward-rapidity (2.5 < y < 4). The J/.yields measured in Pb-Pb are suppressed compared to those in ppcollisions scaled by the number of binary collisions. The RAAintegrated over a centrality range corresponding to 90% of the inelastic Pb-Pb cross section is 0.72 - 0.06(stat.) - 0.10(syst.) at mid-rapidity and 0.58 - 0.01(stat.) - 0.09(syst.) at forward-rapidity. At low transverse momentum, significantly larger values of RAAare measured at forward-rapidity compared to measurements at lower energy. These features suggest that a contribution to the J/.yield originates from charm quark (re) combination in the deconfined partonic medium. (C) 2014 The Authors. Published by Elsevier B. V.
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| 7. |
- Abelev, B, et al.
(author)
-
Directed Flow of Charged Particles at Midrapidity Relative to the Spectator Plane in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV.
- 2013
-
In: Physical Review Letters. - 1079-7114. ; 111:23
-
Journal article (peer-reviewed)abstract
- The directed flow of charged particles at midrapidity is measured in Pb-Pb collisions at sqrt[s_{NN}]=2.76 TeV relative to the collision symmetry plane defined by the spectator nucleons. A negative slope of the rapidity-odd directed flow component with approximately 3 times smaller magnitude than found at the highest RHIC energy is observed. This suggests a smaller longitudinal tilt of the initial system and disfavors the strong fireball rotation predicted for the LHC energies. The rapidity-even directed flow component is measured for the first time with spectators and found to be independent of pseudorapidity with a sign change at transverse momenta p_{T} between 1.2 and 1.7 GeV/c. Combined with the observation of a vanishing rapidity-even p_{T} shift along the spectator deflection this is strong evidence for dipolelike initial density fluctuations in the overlap zone of the nuclei. Similar trends in the rapidity-even directed flow and the estimate from two-particle correlations at midrapidity, which is larger by about a factor of 40, indicate a weak correlation between fluctuating participant and spectator symmetry planes. These observations open new possibilities for investigation of the initial conditions in heavy-ion collisions with spectator nucleons.
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| 8. |
- Abelev, B., et al.
(author)
-
Energy dependence of the transverse momentum distributions of charged particles in pp collisions measured by ALICE
- 2013
-
In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 73:12
-
Journal article (peer-reviewed)abstract
- Differential cross sections of charged particles in inelastic pp collisions as a function of pT have been measured at root s = 0.9, 2.76 and 7 TeV at the LHC. The pT spectra are compared to NLO-pQCD calculations. Though the differential cross section for an individual root s cannot be described by NLO-pQCD, the relative increase of cross section with root s is in agreement with NLO-pQCD. Based on these measurements and observations, procedures are discussed to construct pp reference spectra at root s = 2.76 and 5.02 TeV up to pT = 50 GeV/c as required for the calculation of the nuclear modification factor in nucleus-nucleus and proton-nucleus collisions.
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| 9. |
- Abelev, B., et al.
(author)
-
Freeze-out radii extracted from three-pion cumulants in pp, p-Pb and Pb-Pb collisions at the LHC
- 2014
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 739, s. 139-151
-
Journal article (peer-reviewed)abstract
- In high-energy collisions, the spatio-temporal size of the particle production region can be measured using the Bose-Einstein correlations of identical bosons at low relative momentum. The source radii are typically extracted using two-pion correlations, and characterize the system at the last stage of interaction, called kinetic freeze-out. In low-multiplicity collisions, unlike in high-multiplicity collisions, two-pion correlations are substantially altered by background correlations, e. g. mini-jets. Such correlations can be suppressed using three-pion cumulant correlations. We present the first measurements of the size of the system at freeze-out extracted from three-pion cumulant correlations in pp, p-Pb and Pb-Pb collisions at the LHC with ALICE. At similar multiplicity, the invariant radii extracted in p-Pb collisions are found to be 5-15% larger than those in pp, while those in Pb-Pb are 35-55% larger than those in p-Pb. Our measurements disfavor models which incorporate substantially stronger collective expansion in p-Pb as compared to pp collisions at similar multiplicity. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license
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| 10. |
- Abelev, B., et al.
(author)
-
J/psi production and nuclear effects in p-Pb collisions at=5.02 TeV
- 2014
-
In: Journal of High Energy Physics. - 1029-8479. ; :2
-
Journal article (peer-reviewed)abstract
- Inclusive J/psi production has been studied with the ALICE detector in p-Pb collisions at the nucleon-nucleon center of mass energy = 5.02 TeV at the CERN LHC. The measurement is performed in the center of mass rapidity domains 2.03 < y (cms) < 3.53 and -4.46 < y (cms) < -2.96, down to zero transverse momentum, studying the mu (+) mu (-) decay mode. In this paper, the J/psi production cross section and the nuclear modification factor R (pPb) for the rapidities under study are presented. While at forward rapidity, corresponding to the proton direction, a suppression of the J/psi yield with respect to binary-scaled pp collisions is observed, in the backward region no suppression is present. The ratio of the forward and backward yields is also measured differentially in rapidity and transverse momentum. Theoretical predictions based on nuclear shadowing, as well as on models including, in addition, a contribution from partonic energy loss, are in fair agreement with the experimental results.
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| 11. |
- Abelev, B., et al.
(author)
-
K*(892)(0) and phi(1020) production in Pb-Pb collisions at root s(NN)=2.76 TeV
- 2015
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 91:2
-
Journal article (peer-reviewed)abstract
- The yields of the K*(892)(0) and phi(1020) resonances are measured in Pb-Pb collisions at root s(NN) = 2.76 TeV through their hadronic decays using the ALICE detector. The measurements are performed in multiple centrality intervals at mid-rapidity (vertical bar y vertical bar < 0.5) in the transverse-momentum ranges 0.3 < p(T) < 5 GeV/c for the K*(892)(0) and 0.5 < p(T) < 5 GeV/c for the phi(1020). The yields of K*(892)(0) are suppressed in central Pb-Pb collisions with respect to pp and peripheral Pb-Pb collisions (perhaps due to rescattering of its decay products in the hadronic medium), while the longer-lived phi(1020) meson is not suppressed. These particles are also used as probes to study the mechanisms of particle production. The shape of the pT distribution of the phi(1020) meson, but not its yield, is reproduced fairly well by hydrodynamic models for central Pb-Pb collisions. In central Pb-Pb collisions at low and intermediate p(T), the p/phi(1020) ratio is flat in p(T), while the p/pi and phi(1020)/pi ratios show a pronounced increase and have similar shapes to each other. These results indicate that the shapes of the p(T) distributions of these particles in central Pb-Pb collisions are determined predominantly by the particle masses and radial flow. Finally, phi(1020) production in Pb-Pb collisions is enhanced, with respect to the yield in pp collisions and the yield of charged pions, by an amount similar to the Lambda and Xi.
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| 12. |
- Abelev, B, et al.
(author)
-
K_{S}^{0} and Λ Production in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV.
- 2013
-
In: Physical Review Letters. - 1079-7114. ; 111:22
-
Journal article (peer-reviewed)abstract
- The ALICE measurement of K_{S}^{0} and Λ production at midrapidity in Pb-Pb collisions at sqrt[s_{NN}]=2.76 TeV is presented. The transverse momentum (p_{T}) spectra are shown for several collision centrality intervals and in the p_{T} range from 0.4 GeV/c (0.6 GeV/c for Λ) to 12 GeV/c. The p_{T} dependence of the Λ/K_{S}^{0} ratios exhibits maxima in the vicinity of 3 GeV/c, and the positions of the maxima shift towards higher p_{T} with increasing collision centrality. The magnitude of these maxima increases by almost a factor of three between most peripheral and most central Pb-Pb collisions. This baryon excess at intermediate p_{T} is not observed in pp interactions at sqrt[s]=0.9 TeV and at sqrt[s]=7 TeV. Qualitatively, the baryon enhancement in heavy-ion collisions is expected from radial flow. However, the measured p_{T} spectra above 2 GeV/c progressively decouple from hydrodynamical-model calculations. For higher values of p_{T}, models that incorporate the influence of the medium on the fragmentation and hadronization processes describe qualitatively the p_{T} dependence of the Λ/K_{S}^{0} ratio.
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| 13. |
- Abelev, B., et al.
(author)
-
Long-range angular correlations of pi, K and p in p-Pb collisions at root s(NN)=5.02 TeV
- 2013
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 726:1-3, s. 164-177
-
Journal article (peer-reviewed)abstract
- Angular correlations between unidentified charged trigger particles and various species of charged associated particles (unidentified particles, pions, kaons, protons and antiprotons) are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV in the transverse-momentum range 0.3 < p(T) < 4 GeV/c. The correlations expressed as associated yield per trigger particle are obtained in the pseudorapidity range vertical bar n(lab)vertical bar < 0.8. Fourier coefficients are extracted from the long-range correlations projected onto the azimuthal angle difference and studied as a function of p(T) and in intervals of event multiplicity. In high-multiplicity events, the second-order coefficient for protons, 4, is observed to be smaller than that for pions, v(2)(pi), up to about p(T) = 2 GeV/c. To reduce correlations due to jets, the per-trigger yield measured in low-multiplicity events is subtracted from that in high-multiplicity events. A two-ridge structure is obtained for all particle species. The Fourier decomposition of this structure shows that the second-order coefficients for pions and kaons are similar. The v(2)(p) is found to be smaller at low P-T and larger at higher p(T) than v(2)(pi), with a crossing occurring at about 2 GeV/c. This is qualitatively similar to the elliptic-flow pattern observed in heavy-ion collisions. A mass ordering effect at low transverse momenta is consistent with expectations from hydrodynamic model calculations assuming a collectively expanding system. (C) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 14. |
- Abelev, B., et al.
(author)
-
Measurement of electrons from semileptonic heavy-flavor hadron decays in pp collisions at root s=2.76 TeV
- 2015
-
In: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 91:1
-
Journal article (peer-reviewed)abstract
- The p(T)-differential production cross section of electrons from semileptonic decays of heavy-flavor hadrons has been measured at midrapidity in proton-proton collisions at root s = 2.76 TeV in the transverse momentum range 0.5 < p(T) < 12 GeV/c with the ALICE detector at the LHC. The analysis was performed using minimum bias events and events triggered by the electromagnetic calorimeter. Predictions from perturbative QCD calculations agree with the data within the theoretical and experimental uncertainties.
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| 15. |
- Abelev, B., et al.
(author)
-
Measurement of quarkonium production at forward rapidity in collisions at TeV
- 2014
-
In: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 74:8
-
Journal article (peer-reviewed)abstract
- The inclusive production cross sections at forward rapidity of , , (1S) and (2S) are measured in collisions at with the ALICE detector at the LHC. The analysis is based on a data sample corresponding to an integrated luminosity of 1.35 pb. Quarkonia are reconstructed in the dimuon-decay channel and the signal yields are evaluated by fitting the invariant mass distributions. The differential production cross sections are measured as a function of the transverse momentum and rapidity , over the ranges GeV/c for , GeV/c for all other resonances and for . The measured cross sections integrated over and , and assuming unpolarized quarkonia, are: b, b, nb and nb, where the first uncertainty is statistical and the second one is systematic. The results are compared to measurements performed by other LHC experiments and to theoretical models.
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| 16. |
- Abelev, B., et al.
(author)
-
Measurement of visible cross sections in proton-lead collisions at root s(NN)=5.02 TeV in van der Meer scans with the ALICE detector
- 2014
-
In: Journal of Instrumentation. - 1748-0221. ; 9
-
Journal article (peer-reviewed)abstract
- In 2013, the Large Hadron Collider provided proton-lead and lead-proton collisions at the center-of-mass energy per nucleon pair root s(NN) = 5.02 TeV. Van der Meer scans were performed for both configurations of colliding beams, and the cross section was measured for two reference processes, based on particle detection by the T0 and V0 detectors, with pseudo-rapidity coverage 4.6 < eta < 4.9, -3.3 < eta < -3.0 and 2.8 < eta < 5.1, -3.7 < eta < -1.7, respectively. Given the asymmetric detector acceptance, the cross section was measured separately for the two configurations. The measured visible cross sections are used to calculate the integrated luminosity of the proton-lead and lead-proton data samples, and to indirectly measure the cross section for a third, configuration-independent, reference process, based on neutron detection by the Zero Degree Calorimeters.
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| 17. |
- Abelev, B., et al.
(author)
-
Multi-strange baryon production at mid-rapidity in Pb-Pb collisions at root s(NN)=2.76 TeV
- 2014
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 728, s. 216-227
-
Journal article (peer-reviewed)abstract
- The production of Xi(-) and Omega(-) baryons and their anti-particles in Pb-Pb collisions root s(NN) = 2.76 TeV has been measured using the ALICE detector. The transverse momentum spectra at mid-rapidity (vertical bar y vertical bar < 0.5) for charged Xi and Omega hyperons have been studied in the range 0.6 < P-T < 8.0 GeV/c and 1.2 < p(T) < 7.0 GeV/c, respectively, and in several centrality intervals (from the most central 0-.10% to the most peripheral 60-80% collisions). These spectra have been compared with the predictions of recent hydrodynamic models. In particular, the Krakow and EPOS models give a satisfactory description of the data, with the latter covering a wider P-T range. Mid-rapidity yields, integrated over p(T), have been determined. The hyperon-to-pion ratios are similar to those at RHIC: they rise smoothly with centrality up to < N-part > similar to 150 and saturate thereafter. The enhancements (yields per participant nucleon relative to those in pp collisions) increase both with the strangeness content of the baryon and with centrality, but are less pronounced than at lower energies. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.
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| 18. |
- Abelev, B., et al.
(author)
-
Multiplicity dependence of pion, kaon, proton and lambda production in p-Pb collisions at root s(NN)=5.02 TeV
- 2014
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 728, s. 25-38
-
Journal article (peer-reviewed)abstract
- In this Letter, comprehensive results on pi(+/-), K-+/-, K-S(0), p((p) over bar) and A((A) over bar) production at mid-rapidity (0 < y(CMS) < 0.5) in p-Pb collisions at root s(NN) = 5.02 TeV, measured by the ALICE detector at the LHC, are reported. The transverse momentum distributions exhibit a hardening as a function of event multiplicity, which is stronger for heavier particles. This behavior is similar to what has been observed in pp and Pb-Pb collisions at the LHC. The measured pr distributions are compared to d-Au, Au-Au and Pb-Pb results at lower energy and with predictions based on QCD-inspired and hydrodynamic models. (C) 2013 The Authors. Published by Elsevier B.V. All rights reserved.
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| 19. |
- Abelev, B., et al.
(author)
-
Multiplicity dependence of two-particle azimuthal correlations in pp collisions at the LHC
- 2013
-
In: Journal of High Energy Physics. - 1029-8479. ; :9
-
Journal article (peer-reviewed)abstract
- We present the measurements of particle pair yields per trigger particle obtained from di-hadron azimuthal correlations in pp collisions at root s = 0.9, 2.76, and 7TeV recorded with the ALICE detector. The yields are studied as a function of the charged particle multiplicity. Taken together with the single particle yields the pair yields provide information about parton fragmentation at low transverse momenta, as well as on the contribution of multiple parton interactions to particle production. Data are compared to calculations using the PYTHIA6, PYTHIA8, and PHOJET event generators.
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| 20. |
- Abelev, B., et al.
(author)
-
Performance of the ALICE experiment at the CERN LHC
- 2014
-
In: International Journal of Modern Physics A. - 0217-751X. ; 29:24
-
Research review (peer-reviewed)abstract
- ALICE is the heavy-ion experiment at the CERN Large Hadron Collider. The experiment continuously took data during the first physics campaign of the machine from fall 2009 until early 2013, using proton and lead-ion beams. In this paper we describe the running environment and the data handling procedures, and discuss the performance of the ALICE detectors and analysis methods for various physics observables.
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| 21. |
- Abelev, B., et al.
(author)
-
Production of charged pions, kaons and protons at large transverse momenta in pp and Pb-Pb collisions at root s(NN)=2.76 TeV
- 2014
-
In: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 736, s. 196-207
-
Journal article (peer-reviewed)abstract
- Transverse momentum spectra of pi(+/-), K-+/- and p((p) over bar) up to p(T) = 20 GeV/c at mid-rapidity in pp, peripheral (60-80%) and central (0-5%) Pb-Pb collisions at v root s(NN) = 2.76 TeV have been measured using the ALICE detector at the Large Hadron Collider. The proton-to-pion and the kaon-to-pionratios both show a distinct peak at p(T) approximate to 3 GeV/c in central Pb-Pb collisions. Below the peak, p(T) < 3 GeV/c, both ratios are in good agreement with hydrodynamical calculations, suggesting that the peak itself is dominantly the result of radial flow rather than anomalous hadronization processes. For p(T) > 10 GeV/c particle ratios in pp and Pb-Pb collisions are in agreement and the nuclear modification factors for pi(+/-), K-+/- and p((p) over bar) indicate that, within the systematic and statistical uncertainties, the suppression is the same. This suggests that the chemical composition of leading particles from jets in the medium is similar to that of vacuum jets. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license
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| 22. |
- Abelev, B., et al.
(author)
-
Technical Design Report for the Upgrade of the ALICE Inner Tracking System
- 2014
-
In: Journal of Physics G: Nuclear and Particle Physics. - : IOP Publishing. - 0954-3899 .- 1361-6471. ; 41:8
-
Journal article (peer-reviewed)abstract
- LICE (A Large Ion Collider Experiment) is studying the physics of strongly interacting matter, and in particular the properties of the Quark–Gluon Plasma (QGP), using proton–proton, proton–nucleus and nucleus–nucleus collisions at the CERN LHC (Large Hadron Collider). The ALICE Collaboration is preparing a major upgrade of the experimental apparatus, planned for installation in the second long LHC shutdown in the years 2018–2019. A key element of the ALICE upgrade is the construction of a new, ultra-light, high-resolution Inner Tracking System (ITS) based on monolithic CMOS pixel detectors. The primary focus of the ITS upgrade is on improving the performance for detection of heavy-flavour hadrons, and of thermal photons and low-mass di-electrons emitted by the QGP. With respect to the current detector, the new Inner Tracking System will significantly enhance the determination of the distance of closest approach to the primary vertex, the tracking efficiency at low transverse momenta, and the read-out rate capabilities. This will be obtained by seven concentric detector layers based on a 50 μm thick CMOS pixel sensor with a pixel pitch of about 30×30 μm2. This document, submitted to the LHCC (LHC experiments Committee) in September 2013, presents the design goals, a summary of the R&D activities, with focus on the technical implementation of the main detector components, and the projected detector and physics performance.
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| 23. |
- Abelev, B., et al.
(author)
-
Two- and three-pion quantum statistics correlations in Pb-Pb collisions at root S-NN=2.76 TeV at the CERN Large Hadron Collider
- 2014
-
In: Physical Review C (Nuclear Physics). - 0556-2813. ; 89:2
-
Journal article (peer-reviewed)abstract
- Correlations induced by quantum statistics are sensitive to the spatiotemporal extent as well as dynamics of particle-emitting sources in heavy-ion collisions. In addition, such correlations can be used to search for the presence of a coherent component of pion production. Two- and three-pion correlations of same and mixed charge are measured at low relative momentum to estimate the coherent fraction of charged pions in Pb-Pb collisions at root S-NN = 2.76 TeV at the CERN Large Hadron Collider with ALICE. The genuine three-pion quantum statistics correlation is found to be suppressed relative to the two-pion correlation based on the assumption of fully chaotic pion emission. The suppression is observed to decrease with triplet momentum. The observed suppression at low triplet momentum may correspond to a coherent fraction in charged-pion emission of 23% +/- 8%.
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| 24. |
- Chen, DS, et al.
(author)
-
Single cell atlas for 11 non-model mammals, reptiles and birds
- 2021
-
In: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 12:1, s. 7083-
-
Journal article (peer-reviewed)abstract
- The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.
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| 25. |
- Wang, Fang, et al.
(author)
-
Emerging contaminants: A One Health perspective
- 2024
-
In: Innovation. - 2666-6758. ; 5
-
Research review (peer-reviewed)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
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| 26. |
- You, Xiaohu, et al.
(author)
-
Towards 6G wireless communication networks: vision, enabling technologies, and new paradigm shifts
- 2021
-
In: Science China Information Sciences. - : Science Press. - 1674-733X .- 1869-1919. ; 64:1
-
Research review (peer-reviewed)abstract
- The fifth generation (5G) wireless communication networks are being deployed worldwide from 2020 and more capabilities are in the process of being standardized, such as mass connectivity, ultra-reliability, and guaranteed low latency. However, 5G will not meet all requirements of the future in 2030 and beyond, and sixth generation (6G) wireless communication networks are expected to provide global coverage, enhanced spectral/energy/cost efficiency, better intelligence level and security, etc. To meet these requirements, 6G networks will rely on new enabling technologies, i.e., air interface and transmission technologies and novel network architecture, such as waveform design, multiple access, channel coding schemes, multi-antenna technologies, network slicing, cell-free architecture, and cloud/fog/edge computing. Our vision on 6G is that it will have four new paradigm shifts. First, to satisfy the requirement of global coverage, 6G will not be limited to terrestrial communication networks, which will need to be complemented with non-terrestrial networks such as satellite and unmanned aerial vehicle (UAV) communication networks, thus achieving a space-air-ground-sea integrated communication network. Second, all spectra will be fully explored to further increase data rates and connection density, including the sub-6 GHz, millimeter wave (mmWave), terahertz (THz), and optical frequency bands. Third, facing the big datasets generated by the use of extremely heterogeneous networks, diverse communication scenarios, large numbers of antennas, wide bandwidths, and new service requirements, 6G networks will enable a new range of smart applications with the aid of artificial intelligence (AI) and big data technologies. Fourth, network security will have to be strengthened when developing 6G networks. This article provides a comprehensive survey of recent advances and future trends in these four aspects. Clearly, 6G with additional technical requirements beyond those of 5G will enable faster and further communications to the extent that the boundary between physical and cyber worlds disappears.
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| 27. |
-
- 2019
-
Journal article (peer-reviewed)
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| 28. |
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| 29. |
- Jin, Ying-Hui, et al.
(author)
-
Chemoprophylaxis, diagnosis, treatments, and discharge management of COVID-19 : An evidence-based clinical practice guideline (updated version)
- 2020
-
In: Military Medical Research. - : Springer Science and Business Media LLC. - 2054-9369. ; 7:1
-
Journal article (peer-reviewed)abstract
- The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of a rapidly spreading illness, coronavirus disease 2019 (COVID-19), affecting more than seventeen million people around the world. Diagnosis and treatment guidelines for clinicians caring for patients are needed. In the early stage, we have issued "A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)"; now there are many direct evidences emerged and may change some of previous recommendations and it is ripe for develop an evidence-based guideline. We formed a working group of clinical experts and methodologists. The steering group members proposed 29 questions that are relevant to the management of COVID-19 covering the following areas: chemoprophylaxis, diagnosis, treatments, and discharge management. We searched the literature for direct evidence on the management of COVID-19, and assessed its certainty generated recommendations using the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. Recommendations were either strong or weak, or in the form of ungraded consensus-based statement. Finally, we issued 34 statements. Among them, 6 were strong recommendations for, 14 were weak recommendations for, 3 were weak recommendations against and 11 were ungraded consensus-based statement. They covered topics of chemoprophylaxis (including agents and Traditional Chinese Medicine (TCM) agents), diagnosis (including clinical manifestations, reverse transcription-polymerase chain reaction (RT-PCR), respiratory tract specimens, IgM and IgG antibody tests, chest computed tomography, chest x-ray, and CT features of asymptomatic infections), treatments (including lopinavir-ritonavir, umifenovir, favipiravir, interferon, remdesivir, combination of antiviral drugs, hydroxychloroquine/chloroquine, interleukin-6 inhibitors, interleukin-1 inhibitors, glucocorticoid, qingfei paidu decoction, lianhua qingwen granules/capsules, convalescent plasma, lung transplantation, invasive or noninvasive ventilation, and extracorporeal membrane oxygenation (ECMO)), and discharge management (including discharge criteria and management plan in patients whose RT-PCR retesting shows SARS-CoV-2 positive after discharge). We also created two figures of these recommendations for the implementation purpose. We hope these recommendations can help support healthcare workers caring for COVID-19 patients.
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| 30. |
- Kanoni, Stavroula, et al.
(author)
-
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
- 2022
-
In: Genome biology. - : Springer Science and Business Media LLC. - 1474-760X .- 1465-6906 .- 1474-7596. ; 23:1
-
Journal article (peer-reviewed)abstract
- Genetic variants within nearly 1000 loci are known to contribute to modulation of blood lipid levels. However, the biological pathways underlying these associations are frequently unknown, limiting understanding of these findings and hindering downstream translational efforts such as drug target discovery.To expand our understanding of the underlying biological pathways and mechanisms controlling blood lipid levels, we leverage a large multi-ancestry meta-analysis (N=1,654,960) of blood lipids to prioritize putative causal genes for 2286 lipid associations using six gene prediction approaches. Using phenome-wide association (PheWAS) scans, we identify relationships of genetically predicted lipid levels to other diseases and conditions. We confirm known pleiotropic associations with cardiovascular phenotypes and determine novel associations, notably with cholelithiasis risk. We perform sex-stratified GWAS meta-analysis of lipid levels and show that 3-5% of autosomal lipid-associated loci demonstrate sex-biased effects. Finally, we report 21 novel lipid loci identified on the X chromosome. Many of the sex-biased autosomal and X chromosome lipid loci show pleiotropic associations with sex hormones, emphasizing the role of hormone regulation in lipid metabolism.Taken together, our findings provide insights into the biological mechanisms through which associated variants lead to altered lipid levels and potentially cardiovascular disease risk.
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| 31. |
- Kristan, Matej, et al.
(author)
-
The Ninth Visual Object Tracking VOT2021 Challenge Results
- 2021
-
In: 2021 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2021). - : IEEE COMPUTER SOC. - 9781665401913 ; , s. 2711-2738
-
Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2021 is the ninth annual tracker benchmarking activity organized by the VOT initiative. Results of 71 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in recent years. The VOT2021 challenge was composed of four sub-challenges focusing on different tracking domains: (i) VOT-ST2021 challenge focused on short-term tracking in RGB, (ii) VOT-RT2021 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2021 focused on long-term tracking, namely coping with target disappearance and reappearance and (iv) VOT-RGBD2021 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2021 dataset was refreshed, while VOT-RGBD2021 introduces a training dataset and sequestered dataset for winner identification. The source code for most of the trackers, the datasets, the evaluation kit and the results along with the source code for most trackers are publicly available at the challenge website(1).
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| 32. |
- Kristanl, Matej, et al.
(author)
-
The Seventh Visual Object Tracking VOT2019 Challenge Results
- 2019
-
In: 2019 IEEE/CVF INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW). - : IEEE COMPUTER SOC. - 9781728150239 ; , s. 2206-2241
-
Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge VOT2019 is the seventh annual tracker benchmarking activity organized by the VOT initiative. Results of 81 trackers are presented; many are state-of-the-art trackers published at major computer vision conferences or in journals in the recent years. The evaluation included the standard VOT and other popular methodologies for short-term tracking analysis as well as the standard VOT methodology for long-term tracking analysis. The VOT2019 challenge was composed of five challenges focusing on different tracking domains: (i) VOT-ST2019 challenge focused on short-term tracking in RGB, (ii) VOT-RT2019 challenge focused on "real-time" short-term tracking in RGB, (iii) VOT-LT2019 focused on long-term tracking namely coping with target disappearance and reappearance. Two new challenges have been introduced: (iv) VOT-RGBT2019 challenge focused on short-term tracking in RGB and thermal imagery and (v) VOT-RGBD2019 challenge focused on long-term tracking in RGB and depth imagery. The VOT-ST2019, VOT-RT2019 and VOT-LT2019 datasets were refreshed while new datasets were introduced for VOT-RGBT2019 and VOT-RGBD2019. The VOT toolkit has been updated to support both standard short-term, long-term tracking and tracking with multi-channel imagery. Performance of the tested trackers typically by far exceeds standard baselines. The source code for most of the trackers is publicly available from the VOT page. The dataset, the evaluation kit and the results are publicly available at the challenge website(1).
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| 33. |
- Liu, Yuzhong, et al.
(author)
-
Weaving of organic threads into a crystalline covalent organic framework
- 2016
-
In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 351:6271, s. 365-369
-
Journal article (peer-reviewed)abstract
- A three-dimensional covalent organic framework (COF-505) constructed from helical organic threads, designed to be mutually weaving at regular intervals, has been synthesized by imine condensation reactions of aldehyde functionalized copper(I)-bisphenanthroline tetrafluoroborate, Cu(PDB)2(BF4), and benzidine (BZ). The copper centers are topologically independent of the weaving within the COF structure and serve as templates for bringing the threads into a woven pattern rather than the more commonly observed parallel arrangement. The copper(I) ions can be reversibly removed and added without loss of the COF structure, for which a tenfold increase in elasticity accompanies its demetalation. The threads in COF-505 have many degrees of freedom for enormous deviations to take place between them, throughout the material, without undoing the weaving of the overall structure.
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| 34. |
- Sheng, Xiang, et al.
(author)
-
A Combined Experimental-Theoretical Study of the LigW-Catalyzed Decarboxylation of 5-Carboxyvanillate in the Metabolic Pathway for Lignin Degradation
- 2017
-
In: ACS Catalysis. - : American Chemical Society (ACS). - 2155-5435. ; 7:8, s. 4968-4974
-
Journal article (peer-reviewed)abstract
- Although it is a member of the amidohydrolase superfamily, LigW catalyzes the nonoxidative decarboxylation of 5-carboxyvanillate to form vanillate in the metabolic pathway for bacterial lignin degradation. We now show that membrane inlet mass spectrometry (MIMS) can be used to measure transient CO2 concentrations in real time, thereby permitting us to establish that C-C bond cleavage proceeds to give CO2 rather than HCO3- as the initial product in the LigW-catalyzed reaction. Thus, incubation of LigW at pH 7.0 with the substrate 5-carboxyvanillate results in an initial burst of CO2 formation that gradually decreases to an equilibrium value as CO2 is nonenzymatically hydrated to HCO3-. The burst of CO2 is completely eliminated with the simultaneous addition of substrate and excess carbonic anhydrase to the enzyme, demonstrating that CO2 is the initial reaction product. This finding is fully consistent with the results of density functional theory calculations, which also provide support for a mechanism in which protonation of the C5 carbon takes place prior to C-C bond cleavage. The calculated barrier of 16.8 kcal/mol for the rate-limiting step, the formation of the C5-protonated intermediate, compares well with the observed kcat value of 27 for Sphingomonas paucimobilis LigW, which corresponds to an energy barrier of 16 kcal/mol. The MIMS-based strategy is superior to alternate methods of establishing whether CO2 or HCO3- is the initial reaction product, such as the use of pH-dependent dyes to monitor very small changes in solution pH. Moreover, the MIMS-based assay is generally applicable to studies of all enzymes that produce and/or consume small-molecule, neutral gases.
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| 35. |
- Tang, Ting-Ting, et al.
(author)
-
Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
-
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
-
Journal article (peer-reviewed)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 36. |
- Wang, Cheng-Xiang, et al.
(author)
-
On the Road to 6G: Visions, Requirements, Key Technologies, and Testbeds
- 2023
-
In: IEEE Communications Surveys and Tutorials. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1553-877X. ; 25:2, s. 905-974
-
Journal article (peer-reviewed)abstract
- Fifth generation (5G) mobile communication systems have entered the stage of commercial deployment, providing users with new services, improved user experiences as well as a host of novel opportunities to various industries. However, 5G still faces many challenges. To address these challenges, international industrial, academic, and standards organizations have commenced research on sixth generation (6G) wireless communication systems. A series of white papers and survey papers have been published, which aim to define 6G in terms of requirements, application scenarios, key technologies, etc. Although ITU-R has been working on the 6G vision and it is expected to reach a consensus on what 6G will be by mid-2023, the related global discussions are still wide open and the existing literature has identified numerous open issues. This paper first provides a comprehensive portrayal of the 6G vision, technical requirements, and application scenarios, covering the current common understanding of 6G. Then, a critical appraisal of the 6G network architecture and key technologies is presented. Furthermore, existing testbeds and advanced 6G verification platforms are detailed for the first time. In addition, future research directions and open challenges are identified to stimulate the on-going global debate. Finally, lessons learned to date concerning 6G networks are discussed.
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| 37. |
- Wang, Zhaoming, et al.
(author)
-
Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
-
In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
-
Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 38. |
- Yu, Sheng-Xiang, et al.
(author)
-
Phylogeny of Impatiens (Balsaminaceae) : integrating molecular and morphological evidence into a new classification
- 2016
-
In: Cladistics. - : Wiley-Blackwell. - 0748-3007 .- 1096-0031. ; 32:2, s. 179-197
-
Journal article (peer-reviewed)abstract
- Impatiens L. is one of the largest angiosperm genera, containing over 1000 species, and is notorious for its taxonomic difficulty. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the genus to date based on a total evidence approach. Forty-six morphological characters, mainly obtained from our own investigations, are combined with sequence data from three genetic regions, including nuclear ribosomal ITS and plastid atpB-rbcL and trnL-F. We include 150 Impatiens species representing all clades recovered by previous phylogenetic analyses as well as three outgroups. Maximum-parsimony and Bayesian inference methods were used to infer phylogenetic relationships. Our analyses concur with previous studies, but in most cases provide stronger support. Impatiens splits into two major clades. For the first time, we report that species with three-colpate pollen and four carpels form a monophyletic group (clade I). Within clade II, seven well-supported subclades are recognized. Within this phylogenetic framework, character evolution is reconstructed, and diagnostic morphological characters for different clades and subclades are identified and discussed. Based on both morphological and molecular evidence, a new classification outline is presented, in which Impatiens is divided into two subgenera, subgen. Clavicarpa and subgen. Impatiens; the latter is further subdivided into seven sections.
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| 39. |
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| 40. |
- Aaltonen, T., et al.
(author)
-
Tevatron Run II combination of the effective leptonic electroweak mixing angle
- 2018
-
In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 97:11
-
Journal article (peer-reviewed)abstract
- Drell-Yan lepton pairs produced in the process p (p) over bar -> l(+)l(-) + X through an intermediate gamma*/Z boson have an asymmetry in their angular distribution related to the spontaneous symmetry breaking of the electroweak force and the associated mixing of its neutral gauge bosons. The CDF and D0 experiments have measured the effective-leptonic electroweak mixing parameter sin(2) theta(lept)(eff) using electron and muon pairs selected from the full Tevatron proton-antiproton data sets collected in 2001-2011, corresponding to 9-10 fb(-1) of integrated luminosity. The combination of these measurements yields the most precise result from hadron colliders, sin(2)theta(lept)(eff) = 0.23148 +/- 0.00033. This result is consistent with, and approaches in precision, the best measurements from electron-positron colliders. The standard model inference of the on-shell electroweak mixing parameter sin(2) theta(W), or equivalently the W-boson mass M-W, using the ZFITTER software package yields sin(2) theta(W) = 0.22324 +/- 0.00033 or equivalently, M-W = 80.367 +/- 0.017 GeV/c(2).
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| 41. |
- Abazov, V. M., et al.
(author)
-
Measurement of the Effective Weak Mixing Angle in p¯p→Z/γ∗→ℓ+ℓ− Events
- 2018
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 120:24
-
Journal article (peer-reviewed)abstract
- We present a measurement of the effective weak mixing angle parameter sin(2)theta(l)(eff) in p (p) over bar -> Z/gamma* -> mu(+)mu(-) events at a center-of-mass energy of 1.96 TeV, collected by the D0 detector at the Fermilab Tevatron Collider and corresponding to 8.6 fb(-1) of integrated luminosity. The measured value of sin(2)theta(l)(eff)[mu mu] = 0.23016 +/- 0.00064 is further combined with the result from the D0 measurement in p (p) over bar -> Z/gamma* -> e(+)e(-) events, resulting in sin(2)theta(l)(eff)[comb] = 0.23095 +/- 0.00040. This combined result is the most precise measurement from a single experiment at a hadron collider and is the most precise determination using the coupling of the Z/gamma* to light quarks.
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| 42. |
- Alcorn, J, et al.
(author)
-
Basic instrumentation for Hall A at Jefferson Lab
- 2004
-
In: Nuclear Instruments & Methods in Physics Research. Section A: Accelerators, Spectrometers, Detectors, and Associated Equipment. - : Elsevier BV. - 0167-5087 .- 0168-9002. ; 522:3, s. 294-346
-
Journal article (peer-reviewed)abstract
- The instrumentation in Hall A at the Thomas Jefferson National Accelerator Facility was designed to study electro-and photo-induced reactions at very high luminosity and good momentum and angular resolution for at least one of the reaction products. The central components of Hall A are two identical high resolution spectrometers, which allow the vertical drift chambers in the focal plane to provide a momentum resolution of better than 2 x 10(-4). A variety of Cherenkov counters, scintillators and lead-glass calorimeters provide excellent particle identification. The facility has been operated successfully at a luminosity well in excess of 10(38) CM-2 s(-1). The research program is aimed at a variety of subjects, including nucleon structure functions, nucleon form factors and properties of the nuclear medium. (C) 2003 Elsevier B.V. All rights reserved.
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| 43. |
- Algaba, Juan-Carlos, et al.
(author)
-
Broadband Multi-wavelength Properties of M87 during the 2017 Event Horizon Telescope Campaign
- 2021
-
In: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 911:1
-
Research review (peer-reviewed)abstract
- In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in capturing the first direct image of the center of the M87 galaxy. The asymmetric ring morphology and size are consistent with theoretical expectations for a weakly accreting supermassive black hole of mass ∼6.5 × 109 M o˙. The EHTC also partnered with several international facilities in space and on the ground, to arrange an extensive, quasi-simultaneous multi-wavelength campaign. This Letter presents the results and analysis of this campaign, as well as the multi-wavelength data as a legacy data repository. We captured M87 in a historically low state, and the core flux dominates over HST-1 at high energies, making it possible to combine core flux constraints with the more spatially precise very long baseline interferometry data. We present the most complete simultaneous multi-wavelength spectrum of the active nucleus to date, and discuss the complexity and caveats of combining data from different spatial scales into one broadband spectrum. We apply two heuristic, isotropic leptonic single-zone models to provide insight into the basic source properties, but conclude that a structured jet is necessary to explain M87's spectrum. We can exclude that the simultaneous γ-ray emission is produced via inverse Compton emission in the same region producing the EHT mm-band emission, and further conclude that the γ-rays can only be produced in the inner jets (inward of HST-1) if there are strongly particle-dominated regions. Direct synchrotron emission from accelerated protons and secondaries cannot yet be excluded.
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| 44. |
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| 45. |
- Calabrese, Claudia, et al.
(author)
-
Genomic basis for RNA alterations in cancer
- 2020
-
In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 578:7793, s. 129-136
-
Journal article (peer-reviewed)abstract
- Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed 'bridged' fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
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| 46. |
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| 47. |
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| 48. |
- Cho-Ngwa, Fidelis, et al.
(author)
-
Identification of in vivo released products of Onchocerca with diagnostic potential, and characterization of a dominant member, the OV1CF intermediate filament
- 2011
-
In: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 11:4, s. 778-783
-
Journal article (peer-reviewed)abstract
- A sensitive and specific test for the routine diagnosis of active Onchocerca infection is currently lacking. A major drawback in the development of such a test has been the paucity of knowledge of suitable parasite antigens that can serve as targets in antigen-detection assays. In the present investigation, we employed mass spectrometry, bioinformatics and molecular techniques to identify and characterize several potentially diagnostic Onchocerca antigens in the in vivo nodular fluid, which is being investigated for the first time. The majority of the 27 identified antigens lacked a secretory signal. One of them, also identified and characterized in greater detail with the aid of previously developed monoclonal antibodies (Mabs), was a dominant circulating cytoplasmic intermediate filament protein, previously identified and named, OV1CF. Although OV1CF lacks a secretory signal in its amino acid sequence and is not detected in the pure 42h in vitro released products, it is easily detected in the in vivo nodular fluid. We conclude that these in vivo released products offer promise as diagnostics markers in onchocerciasis.
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| 49. |
- Dinh, Thanh Theresa, et al.
(author)
-
An NKX-COUP-TFII morphogenetic code directs mucosal endothelial addressin expression
- 2022
-
In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Journal article (peer-reviewed)abstract
- Immunoglobulin family and carbohydrate vascular addressins encoded by Madcam1 and St6gal1 control lymphocyte homing into intestinal tissues, regulating immunity and inflammation. The addressins are developmentally programmed to decorate endothelial cells lining gut post-capillary and high endothelial venules (HEV), providing a prototypical example of organ- and segment-specific endothelial specialization. We identify conserved NKX-COUP-TFII composite elements (NCCE) in regulatory regions of Madcam1 and St6gal1 that bind intestinal homeodomain protein NKX2-3 cooperatively with venous nuclear receptor COUP-TFII to activate transcription. The Madcam1 element also integrates repressive signals from arterial/capillary Notch effectors. Pan-endothelial COUP-TFII overexpression induces ectopic addressin expression in NKX2-3+ capillaries, while NKX2-3 deficiency abrogates expression by HEV. Phylogenetically conserved NCCE are enriched in genes involved in neuron migration and morphogenesis of the heart, kidney, pancreas and other organs. Our results define an NKX-COUP-TFII morphogenetic code that targets expression of mucosal vascular addressins.
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| 50. |
- Du, Jie, et al.
(author)
-
Effects of rainfall intensity and slope on interception and precipitation partitioning by forest litter layer
- 2019
-
In: Catena. - : Elsevier BV. - 0341-8162. ; 172, s. 711-718
-
Journal article (peer-reviewed)abstract
- Rainfall interception and other hydrologic processes affected by the forest litter layer are usually related to litter characteristics and rainfall conditions, with limited studies that consider the influence of slope. To simulate the hydrological functions of the litter layer at different slope gradients, artificial rainfall experiments were conducted at four rainfall intensities (from 30 to 120 mm hr−1) in horizontal and inclined trays (with the slope of 0° 10° 20° and 30°) with litter of Pinus tabuliformis or Quercus variabilis. The results indicated that (1) the dynamic process of litter interception had 3 phases: a rapid intercepted phase within the first 5 min, a moderate intercepted phase and a post-rainfall drainage phase; (2) the maximum interception storage (Cmax) and the minimum interception storage (Cmin) of Q. variabilis were larger than those of P. tabuliformis; (3) Cmax and Cmin were correlated with slope for both types of litter, whereas only Cmax was correlated with rainfall intensity; and (4) lateral flow amount significantly increased with both slope gradient and rainfall intensity only for Quercus variabilis, whereas drainage volume showed significant correlation with rainfall intensity. Moreover, the ratio of lateral runoff and drainage was affected by slope gradient whereas percentage of litter interception had a good relationship with rainfall intensity, rather than slope, with litter interception and drainage contributing the smallest and the largest proportions, respectively. Overall, the results demonstrate the effect of rainfall and slope factors on hydrological processes in the forest litter layer.
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