Photodisintegration of 4^4He into p+t

The two-body photodisintegration of $^4$He into a proton and a triton has been studied using the CEBAF Large-Acceptance Spectrometer (CLAS) at Jefferson Laboratory. Real photons produced with the Hall-B bremsstrahlung-tagging system in the energy range from 0.35 to 1.55 GeV were incident on a liquid $^4$He target. This is the first measurement of the photodisintegration of $^4$He above 0.4 GeV. The differential cross sections for the $\gamma$$^4$He$\to pt$ reaction have been measured as a function of photon-beam energy and proton-scattering angle, and are compared with the latest model calculations by J.-M. Laget. At 0.6-1.2 GeV, our data are in good agreement only with the calculations that include three-body mechanisms, thus confirming their importance. These results reinforce the conclusion of our previous study of the three-body breakup of $^3$He that demonstrated the great importance of three-body mechanisms in the energy region 0.5-0.8 GeV .Comment: 13 pages submitted in one tgz file containing 2 tex file and 22 postscrip figure

Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data

Apparent occupancy levels of proteins bound to DNA in vivo can now be routinely measured on a genomic scale. A challenge in relating these occupancy levels to assembly mechanisms that are defined with biochemically isolated components lies in the veracity of assumptions made regarding the in vivo system. Assumptions regarding behavior of molecules in vivo can neither be proven true nor false, and thus is necessarily subjective. Nevertheless, within those confines, connecting in vivo protein-DNA interaction observations with defined biochemical mechanisms is an important step towards fully defining and understanding assembly/disassembly mechanisms in vivo. To this end, we have developed a computational program PathCom that models in vivo protein-DNA occupancy data as biochemical mechanisms under the assumption that occupancy levels can be related to binding duration and explicitly defined assembly/disassembly reactions. We exemplify the process with the assembly of the general transcription factors (TBP, TFIIB, TFIIE, TFIIF, TFIIH, and RNA polymerase II) at the genes of the budding yeast Saccharomyces. Within the assumption inherent in the system our modeling suggests that TBP occupancy at promoters is rather transient compared to other general factors, despite the importance of TBP in nucleating assembly of the preinitiation complex. PathCom is suitable for modeling any assembly/disassembly pathway, given that all the proteins (or species) come together to form a complex

Monitoring the orientation of rare-earth-doped nanorods for flow shear tomography

Rare-earth phosphors exhibit unique luminescence polarization features originating from the anisotropic symmetry of the emitter ion's chemical environment. However, to take advantage of this peculiar property, it is necessary to control and measure the ensemble orientation of the host particles with a high degree of precision. Here, we show a methodology to obtain the photoluminescence polarization of Eu-doped LaPO4 nano rods assembled in an electrically modulated liquid-crystalline phase. We measure Eu3+ emission spectra for the three main optimal configurations ({\sigma}, {\pi} and {\alpha}, depending on the direction of observation and the polarization axes) and use them as a reference for the nano rod orientation analysis. Based on the fact that flowing nano rods tend to orient along the shear strain profile, we use this orientation analysis to measure the local shear rate in a flowing liquid. The potential of this approach is then demonstrated through tomographic imaging of the shear rate distribution in a microfluidic system.Comment: 8 pages, 3 figures + supplementary files for experimental and numerical method

Beam-Recoil Polarization Transfer in the Nucleon Resonance Region in the Exclusive e⃗p→e′K+Λ⃗\vec{e}p \to e'K^+\vec{\Lambda} and e⃗p→e′K+Σ⃗0\vec{e}p \to e'K^+\vec{\Sigma}^0 Reactions at CLAS

Beam-recoil transferred polarizations for the exclusive $\vec{e}p \to e'K^+ \vec{\Lambda},\vec{\Sigma}^0$ reactions have been measured using the CLAS spectrometer at Jefferson Laboratory. New measurements have been completed at beam energies of 4.261 and 5.754 GeV that span a range of momentum transfer $Q^2$ from 0.7 to 5.4 GeV$^2$, invariant energy $W$ from 1.6 to 2.6 GeV, and the full center-of-mass angular range of the $K^+$ meson. These new data add to the existing CLAS $K^+\Lambda$ measurements at 2.567 GeV, and provide the first-ever data for the $K^+\Sigma^0$ channel in electroproduction. Comparisons of the data with several theoretical models are used to study the sensitivity to s-channel resonance contributions and the underlying reaction mechanism. Interpretations within two semi-classical partonic models are made to probe the underlying reaction mechanism and the $s\bar{s}$ quark-pair creation dynamics.Comment: 48 pages, 22 figure

Separated Structure Functions for the Exclusive Electroproduction of K+ΛK^+\Lambda and K+Σ0K^+\Sigma^0 Final States

We report measurements of the exclusive electroproduction of $K^+\Lambda$ and $K^+\Sigma^0$ final states from a proton target using the CLAS detector at the Thomas Jefferson National Accelerator Facility. The separated structure functions $\sigma_T$, $\sigma_L$, $\sigma_{TT}$, and $\sigma_{LT}$ were extracted from the $\Phi$- and $\epsilon$-dependent differential cross sections taken with electron beam energies of 2.567, 4.056, and 4.247 GeV. This analysis represents the first $\sigma_L/\sigma_T$ separation with the CLAS detector, and the first measurement of the kaon electroproduction structure functions away from parallel kinematics. The data span a broad range of momentum transfers from $0.5\leq Q^2\leq 2.8$ GeV$^2$ and invariant energy from $1.6\leq W\leq 2.4$ GeV, while spanning nearly the full center-of-mass angular range of the kaon. The separated structure functions reveal clear differences between the production dynamics for the $\Lambda$ and $\Sigma^0$ hyperons. These results provide an unprecedented data sample with which to constrain current and future models for the associated production of strangeness, which will allow for a better understanding of the underlying resonant and non-resonant contributions to hyperon production.Comment: 61 pages, 26 figures, 5 table

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Lawson criterion for ignition exceeded in an inertial fusion experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion

Evaluation of three field-based methods for quantifying soil carbon

Citation: Izaurralde, Roberto C., Charles W. Rice, Lucian Wielopolski, Michael H. Ebinger, James B. Reeves Iii, Allison M. Thomson, Ronny Harris, et al. “Evaluation of Three Field-Based Methods for Quantifying Soil Carbon.” PLOS ONE 8, no. 1 (January 31, 2013): e55560. https://doi.org/10.1371/journal.pone.0055560.Three advanced technologies to measure soil carbon (C) density (g C mˉ²) are deployed in the field and the results compared against those obtained by the dry combustion (DC) method. The advanced methods are: a) Laser Induced Breakdown Spectroscopy (LIBS), b) Diffuse Reflectance Fourier Transform Infrared Spectroscopy (DRIFTS), and c) Inelastic Neutron Scattering (INS). The measurements and soil samples were acquired at Beltsville, MD, USA and at Centro International para el Mejoramiento del Maı´z y el Trigo (CIMMYT) at El Bata´n, Mexico. At Beltsville, soil samples were extracted at three depth intervals (0–5, 5–15, and 15–30 cm) and processed for analysis in the field with the LIBS and DRIFTS instruments. The INS instrument determined soil C density to a depth of 30 cm via scanning and stationary measurements. Subsequently, soil core samples were analyzed in the laboratory for soil bulk density (kg mˉ³), C concentration (g kgˉ¹) by DC, and results reported as soil C density (kg mˉ²). Results from each technique were derived independently and contributed to a blind test against results from the reference (DC) method. A similar procedure was employed at CIMMYT in Mexico employing but only with the LIBS and DRIFTS instruments. Following conversion to common units, we found that the LIBS, DRIFTS, and INS results can be compared directly with those obtained by the DC method. The first two methods and the standard DC require soil sampling and need soil bulk density information to convert soil C concentrations to soil C densities while the INS method does not require soil sampling. We conclude that, in comparison with the DC method, the three instruments (a) showed acceptable performances although further work is needed to improve calibration techniques and (b) demonstrated their portability and their capacity to perform under field conditions

Yeast TFIIE. Cloning, expression, and homology to vertebrate proteins.

Genes encoding both the 66- and the 43-kDa subunits of yeast RNA polymerase II initiation factor a, designated TFA1 and TFA2, have been isolated. Both genes are essential for cell viability. The bacterially expressed gene products could replace factor a in transcription in vitro, and both recombinant subunits were required for activity. The deduced amino acid sequences of the TFA1 and TFA2 gene products were homologous to those of the large and small subunits of human TFIIE, respectively, identifying factor a as the yeast homolog of TFIIE