HI in the Outskirts of Nearby Galaxies

The HI in disk galaxies frequently extends beyond the optical image, and can trace the dark matter there. I briefly highlight the history of high spatial resolution HI imaging, the contribution it made to the dark matter problem, and the current tension between several dynamical methods to break the disk-halo degeneracy. I then turn to the flaring problem, which could in principle probe the shape of the dark halo. Instead, however, a lot of attention is now devoted to understanding the role of gas accretion via galactic fountains. The current $\rm \Lambda$ cold dark matter theory has problems on galactic scales, such as the core-cusp problem, which can be addressed with HI observations of dwarf galaxies. For a similar range in rotation velocities, galaxies of type Sd have thin disks, while those of type Im are much thicker. After a few comments on modified Newtonian dynamics and on irregular galaxies, I close with statistics on the HI extent of galaxies.Comment: 38 pages, 17 figures, invited review, book chapter in "Outskirts of Galaxies", Eds. J. H. Knapen, J. C. Lee and A. Gil de Paz, Astrophysics and Space Science Library, Springer, in pres

A Kinematically Complete Measurement of the Proton Structure Function F2 in the Resonance Region and Evaluation of Its Moments

We measured the inclusive electron-proton cross section in the nucleon resonance region (W < 2.5 GeV) at momentum transfers Q**2 below 4.5 (GeV/c)**2 with the CLAS detector. The large acceptance of CLAS allowed for the first time the measurement of the cross section in a large, contiguous two-dimensional range of Q**2 and x, making it possible to perform an integration of the data at fixed Q**2 over the whole significant x-interval. From these data we extracted the structure function F2 and, by including other world data, we studied the Q**2 evolution of its moments, Mn(Q**2), in order to estimate higher twist contributions. The small statistical and systematic uncertainties of the CLAS data allow a precise extraction of the higher twists and demand significant improvements in theoretical predictions for a meaningful comparison with new experimental results.Comment: revtex4 18 pp., 12 figure

eta-prime photoproduction on the proton for photon energies from 1.527 to 2.227 GeV

Differential cross sections for the reaction gamma p -> eta-prime p have been measured with the CLAS spectrometer and a tagged photon beam with energies from 1.527 to 2.227 GeV. The results reported here possess much greater accuracy than previous measurements. Analyses of these data indicate for the first time the coupling of the etaprime N channel to both the S_11(1535) and P_11(1710) resonances, known to couple strongly to the eta N channel in photoproduction on the proton, and the importance of j=3/2 resonances in the process.Comment: 6 pages, 3 figure

Measurement of the Deuteron Structure Function F2 in the Resonance Region and Evaluation of Its Moments

Inclusive electron scattering off the deuteron has been measured to extract the deuteron structure function F2 with the CEBAF Large Acceptance Spectrometer (CLAS) at the Thomas Jefferson National Accelerator Facility. The measurement covers the entire resonance region from the quasi-elastic peak up to the invariant mass of the final-state hadronic system W~2.7 GeV with four-momentum transfers Q2 from 0.4 to 6 (GeV/c)^2. These data are complementary to previous measurements of the proton structure function F2 and cover a similar two-dimensional region of Q2 and Bjorken variable x. Determination of the deuteron F2 over a large x interval including the quasi-elastic peak as a function of Q2, together with the other world data, permit a direct evaluation of the structure function moments for the first time. By fitting the Q2 evolution of these moments with an OPE-based twist expansion we have obtained a separation of the leading twist and higher twist terms. The observed Q2 behaviour of the higher twist contribution suggests a partial cancellation of different higher twists entering into the expansion with opposite signs. This cancellation, found also in the proton moments, is a manifestation of the "duality" phenomenon in the F2 structure function

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

A connectome of the adult drosophila central brain

The neural circuits responsible for behavior remain largely unknown. Previous efforts have reconstructed the complete circuits of small animals, with hundreds of neurons, and selected circuits for larger animals. Here we (the FlyEM project at Janelia and collaborators at Google) summarize new methods and present the complete circuitry of a large fraction of the brain of a much more complex animal, the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses, and proofread such large data sets; new methods that define cell types based on connectivity in addition to morphology; and new methods to simplify access to a large and evolving data set. From the resulting data we derive a better definition of computational compartments and their connections; an exhaustive atlas of cell examples and types, many of them novel; detailed circuits for most of the central brain; and exploration of the statistics and structure of different brain compartments, and the brain as a whole. We make the data public, with a web site and resources specifically designed to make it easy to explore, for all levels of expertise from the expert to the merely curious. The public availability of these data, and the simplified means to access it, dramatically reduces the effort needed to answer typical circuit questions, such as the identity of upstream and downstream neural partners, the circuitry of brain regions, and to link the neurons defined by our analysis with genetic reagents that can be used to study their functions. Note: In the next few weeks, we will release a series of papers with more involved discussions. One paper will detail the hemibrain reconstruction with more extensive analysis and interpretation made possible by this dense connectome. Another paper will explore the central complex, a brain region involved in navigation, motor control, and sleep. A final paper will present insights from the mushroom body, a center of multimodal associative learning in the fly brain

A connectome and analysis of the adult Drosophila central brain

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain

Tensor Polarization of the phi meson Photoproduced at High t

As part of a measurement of the cross section of $\phi$ meson photoproduction to high momentum transfer, we measured the polar angular decay distribution of the outgoing $K^+$ in the channel $\phi \to K^+K^-$ in the $\phi$ center-of-mass frame (the helicity frame). We find that s-channel helicity conservation (SCHC) holds in the kinematical range where $t$-channel exchange dominates (up to $-t \sim 2.5$ GeV$^2$ for $E_{\gamma}$=3.6 GeV). Above this momentum, $u$-channel production of a $\phi$ meson dominates and induces a violation of SCHC. The deduced value of the $\phi NN$ coupling constant lies in the upper range of previously reported values.Comment: 6 pages; 5 figure

Measurement of the xx- and Q2Q^2-Dependence of the Asymmetry A1A_1 on the Nucleon

We report results for the virtual photon asymmetry $A_1$ on the nucleon from new Jefferson Lab measurements. The experiment, which used the CEBAF Large Acceptance Spectrometer and longitudinally polarized proton ($^{15}$NH$_3$) and deuteron ($^{15}$ND$_3$) targets, collected data with a longitudinally polarized electron beam at energies between 1.6 GeV and 5.7 GeV. In the present paper, we concentrate on our results for $A_1(x,Q^2)$ and the related ratio $g_1/F_1(x,Q^2)$ in the resonance and the deep inelastic regions for our lowest and highest beam energies, covering a range in momentum transfer $Q^2$ from 0.05 to 5.0 GeV$^2$ and in final-state invariant mass $W$ up to about 3 GeV. Our data show detailed structure in the resonance region, which leads to a strong $Q^2$--dependence of $A_1(x,Q^2)$ for $W$ below 2 GeV. At higher $W$, a smooth approach to the scaling limit, established by earlier experiments, can be seen, but $A_1(x,Q^2)$ is not strictly $Q^2$--independent. We add significantly to the world data set at high $x$, up to $x = 0.6$. Our data exceed the SU(6)-symmetric quark model expectation for both the proton and the deuteron while being consistent with a negative $d$-quark polarization up to our highest $x$. This data setshould improve next-to-leading order (NLO) pQCD fits of the parton polarization distributions.Comment: 7 pages LaTeX, 5 figure

Beam Spin Asymmetries in DVCS with CLAS at 4 .8 GeV

We report measurements of the beam spin asymmetry in Deeply Virtual Compton Scattering (DVCS) at an electron beam energy of 4.8 GeV using the CLAS detector at the Thomas Jefferson National Accelerator Facility. The DVCS beam spin asymmetry has been measured in a wide range of kinematics, 1(GeV/c)$^2$ $<Q^2<2.8$(GeV/c)$^2$, $0.12<x_B<0.48$, and 0.1 (GeV/c)$^2$ $<-t<0.8$(GeV/c)$^2$, using the reaction \pEpX. The number of H$(e,e^{\prime}\gamma p)$ and H$(e,e^{\prime}\pi^0 p)$ events are separated in each $(Q^2,x_B,t)$ bin by a fit to the line shape of the H$(e,e^{\prime}p)X$ $M_x^2$ distribution. The validity of the method was studied in detail using experimental and simulated data. It was shown, that with the achieved missing mass squared resolution and the available statistics, the separation of DVCS-BH and $\pi^0$ events can reliably be done with less than 5% uncertainty. The $Q^2$- and $t$-dependences of the $\sin\phi$ moments of the asymmetry are extracted and compared with theoretical calculations