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Transverse momentum spectra of π±, K± and p(p¯) up to pT = 20 GeV/c at mid-rapidity in pp and Pb-Pb collisions at sNN−−−√= 2.76 TeV have been measured using the ALICE detector at the Large Hadron Collider. The proton-to-pion and the kaon-to-pion ratios both show a distinct peak at pT≈3GeV/c in central Pb-Pb collisions. Below the peak, pT < 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 pT > 10 GeV/c particle ratios in pp and Pb-Pb collisions are in agreement and the nuclear modification factors for π±, K± and p(p¯) 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.
The pT-differential production cross section of electrons from semileptonic decays of heavy-flavor hadrons has been measured at mid-rapidity in proton-proton collisions at s√=2.76 TeV in the transverse momentum range 0.5 < pT < 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.
The pT-differential production cross section of electrons from semileptonic decays of heavy-flavor hadrons has been measured at mid-rapidity in proton-proton collisions at s√=2.76 TeV in the transverse momentum range 0.5 < pT < 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.
The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time. The ultrafine φ-slicing data-collection method is introduced and validated and its application in finding the optimal rotation angle, a suitable rotation speed and a sufficient X-ray dose are presented. An improvement of the data quality up to slicing at one tenth of the mosaicity has been observed, which is much finer than expected based on previous findings. The influence of key data-collection parameters on data quality is discussed.
The exact pathophysiology of contrast-induced nephropathy (CIN) is not fully clarified, yet the osmotic characteristics of contrast media (CM) have been a significant focus in many investigations of CIN. Osmotic effects of CM specific to the kidney include transient decreases in blood flow, filtration fraction, and glomerular filtration rate. Potentially significant secondary effects include an osmotically induced diuresis with a concomitant dehydrating effect. Clinical experiences that have compared the occurrence of CIN between the various classes of CM based on osmolality have suggested a much less than anticipated advantage, if any, with a lower osmolality. Recent animal experiments actually suggest that induction of a mild osmotic diuresis in association with iso-osmolar agents tends to offset potentially deleterious renal effects of high viscosity-mediated intratubular CM stagnation.
Background: Denosumab treatment for up to 8 years in the FREEDOM study and Extension was associated with low fracture incidence. It was not clear whether subjects who discontinued during the study conduct had a higher risk of fracture than those who remained enrolled, thereby underestimating the true fracture risk for the entire trial cohort. Thus, we explored the influence of early withdrawals on nonvertebral fracture incidence during the Extension study.
Methods: To understand the potential effect of depletion of susceptible subjects on fracture incidence, we first evaluated subject characteristics in patients who were enrolled in the Extension vs those who were not. We subsequently employed a Kaplan-Meier multiple imputation (KMMI) approach to consider subjects who discontinued as if they remained enrolled with a 0%, 20%, 50%, and 100% increase in fracture risk compared with participants remaining on study.
Results: Extension enrollees were generally similar to nonparticipants in median age (71.9 and 73.1 years, respectively), mean total hip bone mineral density T-score (–1.9 and –2.0, respectively), and probability of fracture risk by Fracture Risk Assessment Tool (FRAX®) at FREEDOM baseline (16.9% and 17.7% for major osteoporotic fracture and 6.7% and 7.4% for hip fracture, respectively). When we assumed a doubled fracture risk (100% increase) after discontinuation in KMMI analyses, nonvertebral fracture rate estimates were only marginally higher than the observed rates for both the crossover group (10.32% vs 9.16%, respectively) and the long-term group (7.63% vs 6.63%, respectively).
Conclusion: The observation of continued denosumab efficacy over 8 years of treatment was robust and does not seem to be explained by depletion of susceptible subjects.
Trial registration: ClincalTrials.gov registration number NCT00523341; registered August 30, 2007
GABARAP belongs to an evolutionary highly conserved gene family that has a fundamental role in autophagy. There is ample evidence for a crosstalk between autophagy and apoptosis as well as the immune response. However, the molecular details for these interactions are not fully characterized. Here, we report that the ablation of murine GABARAP, a member of the Atg8/LC3 family that is central to autophagosome formation, suppresses the incidence of tumor formation mediated by the carcinogen DMBA and results in an enhancement of the immune response through increased secretion of IL-1β, IL-6, IL-2 and IFN-γ from stimulated macrophages and lymphocytes. In contrast, TGF-β1 was significantly reduced in the serum of these knockout mice. Further, DMBA treatment of these GABARAP knockout mice reduced the cellularity of the spleen and the growth of mammary glands through the induction of apoptosis. Gene expression profiling of mammary glands revealed significantly elevated levels of Xaf1, an apoptotic inducer and tumor-suppressor gene, in knockout mice. Furthermore, DMBA treatment triggered the upregulation of pro-apoptotic (Bid, Apaf1, Bax), cell death (Tnfrsf10b, Ripk1) and cell cycle inhibitor (Cdkn1a, Cdkn2c) genes in the mammary glands. Finally, tumor growth of B16 melanoma cells after subcutaneous inoculation was inhibited in GABARAP-deficient mice. Together, these data provide strong evidence for the involvement of GABARAP in tumorigenesis in vivo by delaying cell death and its associated immune-related response.
Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest for Orthologs Consortium. We review the recent advances and outstanding challenges in this field, as revealed at a symposium and meeting held at the University of Southern California in 2017. Key advances have been made both at the level of orthology algorithm development and with respect to coordination across the community of algorithm developers and orthology end-users. Applications spanned a broad range, including gene function prediction, phylostratigraphy, genome evolution, and phylogenomics. The meetings highlighted the increasing use of meta-analyses integrating results from multiple different algorithms, and discussed ongoing challenges in orthology inference as well as the next steps toward improvement and integration of orthology resources.
A measurement of the production of prompt +c baryons in Pb–Pb collisions at √sNN = 5.02 TeV with the ALICE detector at the LHC is reported. The +c and − c were reconstructed at midrapidity (|y| < 0.5) via the hadronic decay channel +c → pK0 S (and charge conjugate) in the transverse momentum and centrality intervals 6 < pT < 12 GeV/c and 0–80%. The +c /D0 ratio, which is sensitive to the charm quark hadronisation mechanisms in the medium, is measured and found to be larger than the ratio measured in minimum-bias pp collisions at √s = 7 TeV and in p–Pb collisions at √sNN = 5.02 TeV. In particular, the values in p–Pb and Pb–Pb collisions differ by about two standard deviations of the combined statistical and systematic uncertainties in the common pT interval covered by the measurements in the two collision systems. The + c /D0 ratio is also compared with model calculations including different implementations of charm quark hadronisation. The measured ratio is reproduced by models implementing a pure coalescence scenario, while adding a fragmentation contribution leads to an underestimation. The + c nuclear modification factor, RAA, is also presented. The measured values of the RAA of + c , D+ s and non-strange D mesons are compatible within the combined statistical and systematic uncertainties. They show, however, a hint of a hierarchy (RD0 AA < RD+ s AA < R+ c AA ), conceivable with a contribution from coalescence mechanisms to charm hadron formation in the medium.
The production yield of prompt D mesons and their elliptic flow coefficient v2 were measured with the Event-Shape Engineering (ESE) technique applied to mid-central (10–30% and 30–50% centrality classes) Pb-Pb collisions at the centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV, with the ALICE detector at the LHC. The ESE technique allows the classification of events, belonging to the same centrality, according to the azimuthal anisotropy of soft particle production in the collision. The reported measurements give the opportunity to investigate the dynamics of charm quarks in the Quark-Gluon Plasma and provide information on their participation in the collective expansion of the medium. D mesons were reconstructed via their hadronic decays at mid-rapidity, |η| < 0.8, in the transverse momentum interval 1 < pT < 24 GeV/c. The v2 coefficient is found to be sensitive to the event-shape selection confirming a correlation between the D-meson azimuthal anisotropy and the collective expansion of the bulk matter, while the per-event D-meson yields do not show any significant modification within the current uncertainties.
The ALICE Collaboration has measured the energy dependence of exclusive photoproduction of J/ψ vector mesons off proton targets in ultra–peripheral p–Pb collisions at a centre-of-mass energy per nucleon pair sNN−−−√=5.02 TeV. The e+e− and μ+μ− decay channels are used to measure the cross section as a function of the rapidity of the J/ψ in the range −2.5<y<2.7, corresponding to an energy in the γp centre-of-mass in the interval 40<Wγp<550 GeV. The measurements, which are consistent with a power law dependence of the exclusive J/ψ photoproduction cross section, are compared to previous results from HERA and the LHC and to several theoretical models. They are found to be compatible with previous measurements.
Two-particle correlations in high-energy collision experiments enable the extraction of particle source radii by using the Bose-Einstein enhancement of pion production at low relative momentum q ∝ 1/R. It was previously observed that in pp collisions at s√ = 7TeV the average pair transverse momentum kT range of such analyses is limited due to large background correlations which were attributed to mini-jet phenomena. To investigate this further, an event-shape dependent analysis of Bose-Einstein correlations for pion pairs is performed in this work. By categorizing the events by their transverse sphericity ST into spherical (ST > 0:7) and jet-like (ST < 0:3) events a method was developed that allows for the determination of source radii for much larger values of kT for the first time. Spherical events demonstrate little or no background correlations while jet-like events are dominated by them. This observation agrees with the hypothesis of a mini-jet origin of the non-femtoscopic background correlations and gives new insight into the physics interpretation of the kT dependence of the radii. The emission source size in spherical events shows a substantially diminished kT dependence, while jet-like events show indications of a negative trend with respect to kT in the highest multiplicity events. Regarding the emission source shape, the correlation functions for both event sphericity classes show good agreement with an exponential shape, rather than a Gaussian one.
The second (v2) and third (v3) flow harmonic coefficients of J/ψ mesons are measured at forward rapidity (2.5 < y < 4.0) in Pb-Pb collisions at sNN−−−√=5.02 TeV with the ALICE detector at the LHC. Results are obtained with the scalar product method and reported as a function of transverse momentum, pT, for various collision centralities. A positive value of J/ψ v3 is observed with 3.7σ significance. The measurements, compared to those of prompt D0 mesons and charged particles at mid-rapidity, indicate an ordering with vn(J/ψ) < vn(D0) < vn(h±) (n = 2, 3) at low and intermediate pT up to 6 GeV/c and a convergence with v2(J/ψ) ≈ v2(D0) ≈ v2(h±) at high pT above 6–8 GeV/c. In semi-central collisions (5–40% and 10–50% centrality intervals) at intermediate pT between 2 and 6 GeV/c, the ratio v3/v2 of J/ψ mesons is found to be significantly lower (4.6σ) with respect to that of charged particles. In addition, the comparison to the prompt D0-meson ratio in the same pT interval suggests an ordering similar to that of the v2 and v3 coefficients. The J/ψ v2 coefficient is further studied using the Event Shape Engineering technique. The obtained results are found to be compatible with the expected variations of the eccentricity of the initial-state geometry.
This paper compares measurements of gaseous and particulate emissions from a wide range of biomass-burning plumes intercepted by the NASA DC-8 research aircraft during the three phases of the ARCTAS-2008 experiment: ARCTAS-A, based out of Fairbanks, Alaska USA (3 April to 19 April 2008); ARCTAS-B based out of Cold Lake, Alberta, Canada (29 June to 13 July 2008); and ARCTAS-CARB, based out of Palmdale, California, USA (18 June to 24 June 2008). Extensive investigations of boreal fire plume evolution were undertaken during ARCTAS-B, where four distinct fire plumes that were intercepted by the aircraft over a range of down-wind distances (0.1 to 16 hr transport times) were studied in detail. Based on these analyses, there was no evidence for ozone production and a box model simulation of the data confirmed that net ozone production was slow (on average 1 ppbv h−1 in the first 3 h and much lower afterwards) due to limited NOx. Peroxyacetyl nitrate concentrations (PAN) increased with plume age and the box model estimated an average production rate of ~80 pptv h−1 in the first 3 h. Like ozone, there was also no evidence for net secondary inorganic or organic aerosol formation. There was no apparent increase in aerosol mass concentrations in the boreal fire plumes due to secondary organic aerosol (SOA) formation; however, there were indications of chemical processing of the organic aerosols. In addition to the detailed studies of boreal fire plume evolution, about 500 smoke plumes intercepted by the NASA DC-8 aircraft were segregated by fire source region. The normalized excess mixing ratios (i.e. ΔX/ΔCO) of gaseous (carbon dioxide, acetonitrile, hydrogen cyanide, toluene, benzene, methane, oxides of nitrogen (NOx), ozone, PAN) and fine aerosol particulate components (nitrate, sulfate, ammonium, chloride, organic aerosols and water soluble organic carbon) of these plumes were compared.
This paper compares measurements of gaseous and particulate emissions from a wide range of biomass-burning plumes intercepted by the NASA DC-8 research aircraft during the three phases of the ARCTAS-2008 experiment: ARCTAS-A, based out of Fairbanks, Alaska, USA (3 April to 19 April 2008); ARCTAS-B based out of Cold Lake, Alberta, Canada (29 June to 13 July 2008); and ARCTAS-CARB, based out of Palmdale, California, USA (18 June to 24 June 2008). Approximately 500 smoke plumes from biomass burning emissions that varied in age from minutes to days were segregated by fire source region and urban emission influences. The normalized excess mixing ratios (NEMR) of gaseous (carbon dioxide, acetonitrile, hydrogen cyanide, toluene, benzene, methane, oxides of nitrogen and ozone) and fine aerosol particulate components (nitrate, sulfate, ammonium, chloride, organic aerosols and water soluble organic carbon) of these plumes were compared. A detailed statistical analysis of the different plume categories for different gaseous and aerosol species is presented in this paper.
The comparison of NEMR values showed that CH4 concentrations were higher in air-masses that were influenced by urban emissions. Fresh biomass burning plumes mixed with urban emissions showed a higher degree of oxidative processing in comparison with fresh biomass burning only plumes. This was evident in higher concentrations of inorganic aerosol components such as sulfate, nitrate and ammonium, but not reflected in the organic components. Lower NOx NEMRs combined with high sulfate, nitrate and ammonium NEMRs in aerosols of plumes subject to long-range transport, when comparing all plume categories, provided evidence of advanced processing of these plumes.
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium’s collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
Formalin‐fixed, paraffin‐embedded (FFPE ), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT )‐SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PC a) and diffuse large B‐cell lymphoma (DLBCL ) samples. We show that the proteome patterns of FFPE PC a tissue samples and their analogous fresh‐frozen (FF ) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PC a tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PC a and DLBCL have been discovered.
The Kinase Chemogenomic Set (KCGS): an open science resource for kinase vulnerability identification
(2021)
We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS), current Version 1.0, is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.
The Kinase Chemogenomic Set (KCGS): An open science resource for kinase vulnerability identification
(2019)
We describe the assembly and annotation of a chemogenomic set of protein kinase inhibitors as an open science resource for studying kinase biology. The set only includes inhibitors that show potent kinase inhibition and a narrow spectrum of activity when screened across a large panel of kinase biochemical assays. Currently, the set contains 187 inhibitors that cover 215 human kinases. The kinase chemogenomic set (KCGS) is the most highly annotated set of selective kinase inhibitors available to researchers for use in cell-based screens.
Cytotoxic T-lymphocytes play an important role in the protection against viral infections, which they detect through the recognition of virus-derived peptides, presented in the context of MHC class I molecules at the surface of the infected cell. The transporter associated with antigen processing (TAP) plays an essential role in MHC class I–restricted antigen presentation, as TAP imports peptides into the ER, where peptide loading of MHC class I molecules takes place. In this study, the UL49.5 proteins of the varicelloviruses bovine herpesvirus 1 (BHV-1), pseudorabies virus (PRV), and equine herpesvirus 1 and 4 (EHV-1 and EHV-4) are characterized as members of a novel class of viral immune evasion proteins. These UL49.5 proteins interfere with MHC class I antigen presentation by blocking the supply of antigenic peptides through inhibition of TAP. BHV-1, PRV, and EHV-1 recombinant viruses lacking UL49.5 no longer interfere with peptide transport. Combined with the observation that the individually expressed UL49.5 proteins block TAP as well, these data indicate that UL49.5 is the viral factor that is both necessary and sufficient to abolish TAP function during productive infection by these viruses. The mechanisms through which the UL49.5 proteins of BHV-1, PRV, EHV-1, and EHV-4 block TAP exhibit surprising diversity. BHV-1 UL49.5 targets TAP for proteasomal degradation, whereas EHV-1 and EHV-4 UL49.5 interfere with the binding of ATP to TAP. In contrast, TAP stability and ATP recruitment are not affected by PRV UL49.5, although it has the capacity to arrest the peptide transporter in a translocation-incompetent state, a property shared with the BHV-1 and EHV-1 UL49.5. Taken together, these results classify the UL49.5 gene products of BHV-1, PRV, EHV-1, and EHV-4 as members of a novel family of viral immune evasion proteins, inhibiting TAP through a variety of mechanisms.