Long-Baseline Neutrino Facility (LBNF) and Deep Underground Neutrino Experiment (DUNE) Conceptual Design Report Volume 2: The Physics Program for DUNE at LBNF

The Physics Program for the Deep Underground Neutrino Experiment (DUNE) at the Fermilab Long-Baseline Neutrino Facility (LBNF) is described

COMPASS identifies T-cell subsets correlated with clinical outcomes.

Advances in flow cytometry and other single-cell technologies have enabled high-dimensional, high-throughput measurements of individual cells as well as the interrogation of cell population heterogeneity. However, in many instances, computational tools to analyze the wealth of data generated by these technologies are lacking. Here, we present a computational framework for unbiased combinatorial polyfunctionality analysis of antigen-specific T-cell subsets (COMPASS). COMPASS uses a Bayesian hierarchical framework to model all observed cell subsets and select those most likely to have antigen-specific responses. Cell-subset responses are quantified by posterior probabilities, and human subject-level responses are quantified by two summary statistics that describe the quality of an individual's polyfunctional response and can be correlated directly with clinical outcome. Using three clinical data sets of cytokine production, we demonstrate how COMPASS improves characterization of antigen-specific T cells and reveals cellular 'correlates of protection/immunity' in the RV144 HIV vaccine efficacy trial that are missed by other methods. COMPASS is available as open-source software

Expression profile of human Fc receptors in mucosal tissue: implications for antibody-dependent cellular effector functions targeting HIV-1 transmission

The majority of new Human Immunodeficiency Virus (HIV)-1 infections are acquired via sexual transmission at mucosal surfaces. Partial efficacy (31.2%) of the Thai RV144 HIV-1 vaccine trial has been correlated with Antibody-dependent Cellular Cytotoxicity (ADCC) mediated by non-neutralizing antibodies targeting the V1V2 region of the HIV-1 envelope. This has led to speculation that ADCC and other antibody-dependent cellular effector functions might provide an important defense against mucosal acquisition of HIV-1 infection. However, the ability of antibody-dependent cellular effector mechanisms to impact on early mucosal transmission events will depend on a variety of parameters including effector cell type, frequency, the class of Fc-Receptor (FcR) expressed, the number of FcR per cell and the glycoslyation pattern of the induced antibodies. In this study, we characterize and compare the frequency and phenotype of IgG (CD16 [FcγRIII], CD32 [FcγRII] and CD64 [FcγRI]) and IgA (CD89 [FcαR]) receptor expression on effector cells within male and female genital mucosal tissue, colorectal tissue and red blood cell-lysed whole blood. The frequency of FcR expression on CD14+ monocytic cells, myeloid dendritic cells and natural killer cells were similar across the three mucosal tissue compartments, but significantly lower when compared to the FcR expression profile of effector cells isolated from whole blood, with many cells negative for all FcRs. Of the three tissues tested, penile tissue had the highest percentage of FcR positive effector cells. Immunofluorescent staining was used to determine the location of CD14+, CD11c+ and CD56+ cells within the three mucosal tissues. We show that the majority of effector cells across the different mucosal locations reside within the subepithelial lamina propria. The potential implication of the observed FcR expression patterns on the effectiveness of FcR-dependent cellular effector functions to impact on the initial events in mucosal transmission and dissemination warrants further mechanistic studies

Remote Data Retrieval for Bioinformatics Applications: An Agent Migration Approach

Some of the approaches have been developed to retrieve data automatically from one or multiple remote biological data sources. However, most of them require researchers to remain online and wait for returned results. The latter not only requires highly available network connection, but also may cause the network overload. Moreover, so far none of the existing approaches has been designed to address the following problems when retrieving the remote data in a mobile network environment: (1) the resources of mobile devices are limited; (2) network connection is relatively of low quality; and (3) mobile users are not always online. To address the aforementioned problems, we integrate an agent migration approach with a multi-agent system to overcome the high latency or limited bandwidth problem by moving their computations to the required resources or services. More importantly, the approach is fit for the mobile computing environments. Presented in this paper are also the system architecture, the migration strategy, as well as the security authentication of agent migration. As a demonstration, the remote data retrieval from GenBank was used to illustrate the feasibility of the proposed approach

The very forward CASTOR calorimeter of the CMS experiment

The physics motivation, detector design, triggers, calibration, alignment, simulation, and overall performance of the very forward CASTOR calorimeter of the CMS experiment are reviewed. The CASTOR Cherenkov sampling calorimeter is located very close to the LHC beam line, at a radial distance of about 1cm from the beam pipe, and at 14.4m from the CMS interaction point, covering the pseudorapidity range of -6.6 < η < -5.2. It was designed to withstand high ambient radiation and strong magnetic fields. The performance of the detector in measurements of forward energy density, jets, and processes characterized by rapidity gaps, is reviewed using data collected in proton and nuclear collisions at the LHC

Measurements of production cross sections of WZ and same-sign WW boson pairs in association with two jets in proton-proton collisions at √s = 13 TeV

The first measurements of production cross sections of polarized same-sign W$^{±}$ W$^{±}$ boson pairs in proton-proton collisions are reported. The measurements are based on a data sample collected with the CMS detector at the LHC at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 137fb$^{-1}$. Events are selected by requiring exactly two same-sign leptons, electrons or muons, moderate missing transverse momentum, and two jets with a large rapidity separation and a large dijet mass to enhance the contribution of same-sign W$^{±}$ W$^{±}$ scattering events. An observed (expected) 95% confidence level upper limit of 1.17 (0.88) fbis set on the production cross section for longitudinally polarized same-sign W$^{±}$ W$^{±}$ boson pairs. The electroweak production of same-sign W$^{±}$ W$^{±}$ boson pairs with at least one of the W bosons longitudinally polarized is measured with an observed (expected) significance of 2.3 (3.1) standard deviations

Combined searches for the production of supersymmetric top quark partners in proton–proton collisions at √s=13Te

A combination of searches for top squark pair production using proton–proton collision data at a center-of-mass energy of 13TeV at the CERN LHC, corresponding to an integrated luminosity of 137fb$^{-1}$ collected by the CMS experiment, is presented. Signatures with at least 2 jets and large missing transverse momentum are categorized into events with 0, 1, or 2 leptons. New results for regions of parameter space where the kinematical properties of top squark pair production and top quark pair production are very similar are presented. Depending on the model, the combined result excludes a top squark mass up to 1325GeV for a massless neutralino, and a neutralino mass up to 700GeV for a top squark mass of 1150GeV. Top squarks with masses from 145 to 295GeV, for neutralino masses from 0 to 100GeV, with a mass difference between the top squark and the neutralino in a window of 30GeV around the mass of the top quark, are excluded for the first time with CMS data. The results of theses searches are also interpreted in an alternative signal model of dark matter production via a spin-0 mediator in association with a top quark pair. Upper limits are set on the cross section for mediator particle masses of up to 420GeV

Search for high-mass resonances decaying to a jet and a Lorentz-boosted resonance in proton-proton collisions at √s = 13 TeV

A search is reported for high-mass hadronic resonances that decay to a parton and a Lorentz-boosted resonance, which in turn decays into a pair of partons. The search is based on data collected with the CMS detector at the LHC in proton-proton collisions at , corresponding to an integrated luminosity of 138. The boosted resonance is reconstructed as a single wide jet with substructure consistent with a two-body decay. The high-mass resonance is thus considered as a dijet system. The jet substructure information and the kinematic properties of cascade resonance decays are exploited to disentangle the signal from the large quantum chromodynamics multijet background. The dijet mass spectrum is analyzed for the presence of new high-mass resonances, and is found to be consistent with the standard model background predictions. Results are interpreted in a warped extra dimension model where the high-mass resonance is a Kaluza–Klein gluon, the boosted resonance is a radion, and the final state partons are all gluons. Limits on the production cross section are set as a function of the Kaluza–Klein gluon and radion masses. These limits exclude at 95% confidence level models with Kaluza–Klein gluon masses in the range 2.0 to 4.3 TeV and radion masses in the range 0.20 to 0.74 TeV. By exploring a novel experimental signature, the observed limits on the Kaluza–Klein gluon mass are extended by up to about 1 TeV compared to previous searches