Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution

Behavioral Changes in Aging but Not Young Mice after Neonatal Exposure to the Polybrominated Flame Retardant DecaBDE

BACKGROUND: After several decades of commercial use, the flame-retardant chemicals polybrominated diphenyl ethers (PBDEs) and their metabolites are pervasive environmental contaminants and are detected in the human body. Decabrominated diphenyl ether (decaBDE) is currently the only PBDE in production in the United States. OBJECTIVES: Little is known about the health effects of decaBDE. In the present study we examined the effects of neonatal decaBDE exposure on behavior in mice at two ages. METHODS: Neonatal male and female C57BL6/J mice were exposed to a daily oral dose of 0, 6, or 20 mg/kg decaBDE from postnatal days 2 through 15. Two age groups were examined: a cohort that began training during young adulthood and an aging cohort of littermates that began training at 16 months of age. Both cohorts were tested on a series of operant procedures that included a fixed-ratio I schedule of reinforcement, a fixed-interval (FI) 2-min schedule, and a light-dark visual discrimination. RESULTS: We observed minimal effects on the light-dark discrimination in the young cohort, with no effects on the other tasks. The performance of the aging cohort was significantly affected by decaBDE. On the FI schedule, decaBDE exposure increased the overall response rate. On the light-dark discrimination, older treated mice learned the task more slowly, made fewer errors on the first-response choice of a trial but more perseverative errors after an initial error, and had lower latencies to respond compared with controls. Effects were observed in both dose groups and sexes on various measures. CONCLUSIONS: These findings suggest that neonatal decaBDE exposure produces effects on behavioral tasks in older but not younger animals. The behavioral mechanisms responsible for the pattern of observed effects may include increased impulsivity, although further research is required

Observations of the December 13 and 14, 2006, Solar Particle Events in the 80 MeV/n - 3 GeV/n range from space with PAMELA detector

We present the space spectrometer PAMELA observations of proton and helium fluxes during the December 13 and 14, 2006 solar particle events. This is the first direct measurement of the solar energetic particles in space with a single instrument in the energy range from $\sim$ 80 MeV/n up to $\sim$ 3 GeV/n. In the event of December 13 measured energy spectra of solar protons and helium were compared with results obtained by neutron monitors and other detectors. Our measurements show a spectral behaviour different from those derived from the neutron monitor network. No satisfactory analytical fitting was found for the energy spectra. During the first hours of the December 13 event solar energetic particles spectra were close to the exponential form demonstrating rather significant temporal evolution. Solar He with energy up to ~1 GeV/n was recorded on December 13. In the event of December 14 energy of solar protons reached ~600 MeV whereas maximum energy of He was below 100 MeV/n. The spectra were slightly bended in the lower energy range and preserved their form during the second event. Difference in the particle flux appearance and temporal evolution in these two events may argue for a special conditions leading to acceleration of solar particles up to relativistic energies.Comment: Accepted for publication on Astrophysical journa

Wavefront Measurement for Laser-Guiding Diagnostic

The wavefront of a short laser pulse after interaction in a laser-plasma accelerator (LPA) was measured to diagnose laser-guiding quality. Experiments were performed on a 100 TW class laser at the LOASIS facility of LBNL using a hydrogenfilled capillary discharge waveguide. Laser-guiding with a pre-formed plasma channel allows the laser pulse to propagate over many Rayleigh lengths at high intensity and is crucial to accelerate electrons to the highest possible energy. Efficient coupling of laser energy into the plasma is realized when the laser and the channel satisfy a matched guiding condition, in which the wavefront remains flat within the channel. Using a wavefront sensor, the laser-guiding quality was diagnosed based on the wavefront of the laser pulse exiting the plasma channel. This wavefront diagnostic will contribute to achieving controlled, matched guiding in future experiments

Eradication of common pathogens at days 2, 3 and 4 of moxifloxacin therapy in patients with acute bacterial sinusitis

BACKGROUND: Acute bacterial sinusitis (ABS) is a common infection in clinical practice. Data on time to bacteriologic eradication after antimicrobial therapy are lacking for most agents, but are necessary in order to optimize therapy. This was a prospective, single-arm, open-label, multicenter study to determine the time to bacteriologic eradication in ABS patients (maxillary sinusitis) treated with moxifloxacin. METHODS: Adult patients with radiologically and clinically confirmed ABS received once-daily moxifloxacin 400 mg for 10 days. Middle meatus secretion sampling was performed using nasal endoscopy pre-therapy, and repeated on 3 consecutive days during treatment. Target enrollment was 30 bacteriologically evaluable patients (pre-therapy culture positive for Streptococcus pneumoniae, Haemophilus influenzae or Moraxella catarrhalis and evaluable cultures for at least Day 2 and Day 3 during therapy visits), including at least 10 each with S. pneumoniae or H. influenzae. RESULTS: Of 192 patients enrolled, 42 were bacteriologically evaluable, with 48 pathogens isolated. Moxifloxacin was started on Day 1. Baseline bacteria were eradicated in 35/42 (83.3%) patients by day 2, 42/42 (100%) patients by day 3, and 41/42 (97.6%) patients by day 4. In terms of individual pathogens, 12/18 S. pneumoniae, 22/23 H. influenzae and 7/7 M. catarrhalis were eradicated by day 2 (total 41/48; 85.4%), and 18/18 S. pneumoniae and 23/23 H. influenzae were eradicated by day 3. On Day 4, S. pneumoniae was isolated from a patient who had negative cultures on Days 2 and 3. Thus, the Day 4 eradication rate was 47/48 (97.9%). Clinical success was achieved in 36/38 (94.7%) patients at the test of cure visit. CONCLUSION: In patients with ABS (maxillary sinusitis), moxifloxacin 400 mg once daily for 10 days resulted in eradication of baseline bacteria in 83.3% of patients by Day 2, 100% by Day 3 and 97.6% by Day 4

Observation of the TeV gamma-ray source MGRO J1908+06 with ARGO-YBJ

The extended gamma ray source MGRO J1908+06, discovered by the Milagro air shower detector in 2007, has been observed for about 4 years by the ARGO-YBJ experiment at TeV energies, with a statistical significance of 6.2 standard deviations. The peak of the signal is found at a position consistent with the pulsar PSR J1907+0602. Parametrizing the source shape with a two-dimensional Gauss function we estimate an extension \sigma = 0.49 \pm 0.22 degrees, consistent with a previous measurement by the Cherenkov Array H.E.S.S.. The observed energy spectrum is dN/dE = 6.1 \pm 1.4 \times 10^-13 (E/4 TeV)^{-2.54 \pm 0.36} photons cm^-2 s^-1 TeV^-1, in the energy range 1-20 TeV. The measured gamma ray flux is consistent with the results of the Milagro detector, but is 2-3 times larger than the flux previously derived by H.E.S.S. at energies of a few TeV. The continuity of the Milagro and ARGO-YBJ observations and the stable excess rate observed by ARGO-YBJ along 4 years of data taking support the identification of MGRO J1908+06 as the steady powerful TeV pulsar wind nebula of PSR J1907+0602, with an integrated luminosity above 1 TeV about 1.8 times the Crab Nebula luminosity.Comment: 6 pages, accepted for pubblication by ApJ. Replaced to correct the author lis

Recoil Polarization for Delta Excitation in Pion Electroproduction

We measured angular distributions of recoil-polarization response functions for neutral pion electroproduction for W=1.23 GeV at Q^2=1.0 (GeV/c)^2, obtaining 14 separated response functions plus 2 Rosenbluth combinations; of these, 12 have been observed for the first time. Dynamical models do not describe quantities governed by imaginary parts of interference products well, indicating the need for adjusting magnitudes and phases for nonresonant amplitudes. We performed a nearly model-independent multipole analysis and obtained values for Re(S1+/M1+)=-(6.84+/-0.15)% and Re(E1+/M1+)=-(2.91+/-0.19)% that are distinctly different from those from the traditional Legendre analysis based upon M1+ dominance and sp truncation.Comment: 5 pages, 2 figures, for PR