Recent developments in the instrumentation and data analysis of synchrotron small‐angle X‐ray scattering (SAXS) on biomolecules in solution have made biological SAXS (BioSAXS) a mature and popular ...tool in structural biology. This article reports on an advanced endstation developed at beamline 13A of the 3.0 GeV Taiwan Photon Source for biological small‐ and wide‐angle X‐ray scattering (SAXS–WAXS or SWAXS). The endstation features an in‐vacuum SWAXS detection system comprising two mobile area detectors (Eiger X 9M/1M) and an online size‐exclusion chromatography system incorporating several optical probes including a UV–Vis absorption spectrometer and refractometer. The instrumentation and automation allow simultaneous SAXS–WAXS data collection and data reduction for high‐throughput biomolecular conformation and composition determinations. The performance of the endstation is illustrated with the SWAXS data collected for several model proteins in solution, covering a scattering vector magnitude q across three orders of magnitude. The crystal‐model fittings to the data in the q range ∼0.005–2.0 Å−1 indicate high similarity of the solution structures of the proteins to their crystalline forms, except for some subtle hydration‐dependent local details. These results open up new horizons of SWAXS in studying correlated local and global structures of biomolecules in solution.
A new endstation for biological small‐ and wide‐angle X‐ray scattering is detailed, which provides development opportunities for studying correlated local and global structures of biomolecules in solution.
From an analysis of the long cadence light curves of M and K dwarfs obtained by the K2 observations, 3589 flares on 548 M dwarfs and 1647 flares on 343 K dwarfs have been identified. We compared the ...M and K dwarfs' flares with the G dwarfs' flares reported by Shibayama et al. The later type stars' flare occurrence frequencies are higher than those of the earlier type stars, but the earlier type stars produce more powerful flares than those of the later type stars. For the stars of all spectral types, the flare activities, including the flare energy, peak amplitude, and percentage of magnetic activity, increase with faster rotation of stars. The longer the flare duration is, the more energy the flare releases, but an upper limit exists. The saturation energy of M, K, and G dwarfs are derived to be about 1 × 1035 erg, 4 × 1035 erg and 1 × 1036 erg, respectively, in the present study. We estimated the power-law indices of the flare frequency distributions of three spectral type stars. They are 1.82 0.02 (M dwarfs) and 1.86 0.02 (K dwarfs) in comparison to the 2.01 0.03 for the G dwarfs found by Shibayama et al. For stars with Prot ≤ 10 days, they are 1.78 0.02 (M dwarfs), 1.82 0.03 (K dwarfs), and 2.09 0.04 (G dwarfs). The power-law indices of flare frequency distributions of the fast-rotating M- and K-type stars are nearly the same. This indicates that the flare or magnetic mechanisms of different types of low-mass stars may be similar in some sense.
This Colloquium describes a new paradigm for creating strong quantum interactions of light and matter by way of single atoms and photons in nanoscopic lattices. Beyond the possibilities for ...quantitative improvements for familiar phenomena in atomic physics and quantum optics, there is a growing research community that is exploring novel quantum phases and phenomena that arise from atom-photon interactions in one- and two-dimensional nanophotonic lattices. Nanophotonic structures offer the intriguing possibility to control atom-photon interactions by engineering the medium properties through which they interact. An important aspect of these new research lines is that they have become possible only by pushing the state-of-the-art capabilities in nanophotonic device fabrication and by the integration of these capabilities into the realm of ultracold atoms. This Colloquium attempts to inform a broad physics community of the emerging opportunities in this new field on both theoretical and experimental fronts. The research is inherently multidisciplinary, spanning the fields of nanophotonics, atomic physics, quantum optics, and condensed matter physics.
Summary Background Outbreaks of urinary tract infections (UTIs) due to contaminated ureteroscopes have been rarely reported. Aim To report such an outbreak at a regional teaching hospital in southern ...Taiwan. Methods From October to December 2010, ertapenem-resistant Enterobacter cloacae were identified from urine cultures of 15 patients who had undergone ureteroscopy prior to the infection. Three batches of surveillance cultures were obtained from the environmental objects and healthcare workers related to the procedures. Pulsed-field gel electrophoresis (PFGE) was used for bacterial typing. Antimicrobial susceptibility was assessed by disc diffusion and E-test methods. Polymerase chain reaction and sequencing were used to analyse β-lactamase genes. Findings A total of 70 specimens were obtained during the first surveillance operation. One ertapenem-resistant E. cloacae was isolated from a ureteroscope. Although the disinfection protocols for ureteroscopes were revised and implemented, seven additional UTI cases were identified thereafter. The pathogen was identified from two subsequent surveillance cultures and was not eliminated until ethylene oxide sterilization was added to the disinfection protocol. PFGE revealed that all 15 isolates from the patients and the three isolates from the ureteroscope shared a common pattern with minor variance. Most isolates were resistant to gentamicin, levofloxacin, ceftriaxone, ceftazidime, and ertapenem. All isolates were susceptible to amikacin, imipenem, and meropenem. SHV-12 and IMP-8 genes were simultaneously identified in 16 of the 18 isolates. Conclusion The outbreak of ertapenem-resistant E. cloacae was caused by a contaminated ureteroscope and was terminated by the implementation of a revised disinfection protocol for ureteroscopes.
From a study of the light curves of the M dwarfs observed by the Kepler space telescope in its primary mission, a number of flare events with the peak flux increases reaching more than the nominal ...stellar luminosity have been found. One of them, KIC 9201463, produced an extreme flare with the peak flux increase jumping to five times the quiet-time value. In relative terms, this class of hyperflares is much stronger than the superflares of the solar-type stars and could have a very important influence on the atmospheric evolution and the potential development of biospheres of habitable super-Earths orbiting around M dwarf stars. A cross-correlation of the flare activities of some of these M dwarf stars and their H equivalent width (EW) values derived from the LAMOST project indicates that the H EW values can be used to monitor the occurrence of hyperflares as well as the level of flare activity of different classes of M dwarfs with fast to slow rotations, and hence the long-term environmental effects of star-planet interaction of exoplanets.
To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)—BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic ...Gen-Probe Prodesse assays—on the detection of viral respiratory infections.
A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay.
Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848–0.949), 0.949 (95% confidence interval, 0.882–0.979) and 0.954 (95% confidence interval, 0.871–0.985), respectively. The three mPCRs were comparable in terms of detection of FluA.
Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.
The optical design and performance of the recently opened 13A biological small‐angle X‐ray scattering (SAXS) beamline at the 3.0 GeV Taiwan Photon Source of the National Synchrotron Radiation ...Research Center are reported. The beamline is designed for studies of biological structures and kinetics in a wide range of length and time scales, from angstrom to micrometre and from microsecond to minutes. A 4 m IU24 undulator of the beamline provides high‐flux X‐rays in the energy range 4.0–23.0 keV. MoB4C double‐multilayer and Si(111) double‐crystal monochromators (DMM/DCM) are combined on the same rotating platform for a smooth rotation transition from a high‐flux beam of ∼4 × 1014 photons s−1 to a high‐energy‐resolution beam of ΔE/E ≃ 1.5 × 10−4; both modes share a constant beam exit. With a set of Kirkpatrick–Baez (KB) mirrors, the X‐ray beam is focused to the farthest SAXS detector position, 52 m from the source. A downstream four‐bounce crystal collimator, comprising two sets of Si(311) double crystals arranged in a dispersive configuration, optionally collimate the DCM (vertically diffracted) beam in the horizontal direction for ultra‐SAXS with a minimum scattering vector q down to 0.0004 Å−1, which allows resolving ordered d‐spacing up to 1 µm. A microbeam, of 10–50 µm beam size, is tailored by a combined set of high‐heat‐load slits followed by micrometre‐precision slits situated at the front‐end 15.5 m position. The second set of KB mirrors then focus the beam to the 40 m sample position, with a demagnification ratio of ∼1.5. A detecting system comprising two in‐vacuum X‐ray pixel detectors is installed to perform synchronized small‐ and wide‐angle X‐ray scattering data collections. The observed beamline performance proves the feasibility of having compound features of high flux, microbeam and ultra‐SAXS in one beamline.
The optical design and performance of the BioSAXS beamline at the Taiwan Photon Source are reported
Quantum simulation with cold atoms in optical lattices is an attractive avenue for explorations of quantum many-body physics. A principal challenge in the field is to increase the energy and length ...scales in current set-ups, thereby reducing temperature and coherence-time requirements. Here, we present a new paradigm for high-density, two-dimensional optical lattices in photonic crystal waveguides. Specially engineered two-dimensional photonic crystals provide a practical platform to trap atoms and engineer their interactions in ways that surpass the limitations of current technologies and enable investigations of novel quantum many-body matter. Our schemes remove the constraint on the lattice constant set by the free-space optical wavelength in favour of deeply sub-wavelength atomic arrays. We further describe possibilities for atom-atom interactions mediated by photons in two-dimensional photonic crystal waveguides with energy scales several orders of magnitude larger than for exchange interactions in free-space lattices and with the capability to engineer strongly long-range interactions.
Carboxylated/oxidized diamond nanoparticles (nominal size 100 nm) exhibit exceptionally high affinity for proteins through both hydrophilic and hydrophobic forces. The affinity is so high that ...proteins in dilute solution can be easily captured by diamonds, simply separated by centrifugation, and directly analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). No preseparation of the adsorbed molecules from diamonds is required for the mass spectrometric analysis. Compared to conventional MALDI-TOF-MS, an enhancement in detection sensitivity by more than 2 orders of magnitude is achieved for dilute solution containing cytochrome c, myoglobin, and albumin because of preconcentration of the probed molecules. The lowest concentration detectable is 100 pM for a 1-mL solution. Aside from the enhanced sensitivity, the overall performance of this technique does not show any sign of deterioration for highly contaminated protein solutions, and furthermore, no significant peak broadening and band shift were observed in the mass spectra. The promise of this new method for clinical proteomics research is demonstrated with an application to human blood serum.
In this work, we present measurements of the E-mode (EE) polarization power spectrum and temperature-E-mode (TE) cross-power spectrum of the cosmic microwave background using data collected by ...SPT-3G, the latest instrument installed on the South Pole Telescope. This analysis uses observations of a 1500 deg2 region at 95, 150, and 220 GHz taken over a four-month period in 2018. We report binned values of the EE and TE power spectra over the angular multipole range 300≤ℓ<3000, using the multifrequency data to construct six semi-independent estimates of each power spectrum and their minimum-variance combination. These measurements improve upon the previous results of SPTpol across the multipole ranges 300 ≤ ℓ ≤ 1400 for EE and 300 ≤ ℓ ≤ 1700 for TE, resulting in constraints on cosmological parameters comparable to those from other current leading ground-based experiments. We find that the SPT-3G data set is well fit by a ΛCDM cosmological model with parameter constraints consistent with those from Planck and SPTpol data. From SPT-3G data alone, we find H0=68.8±1.5 km s-1 Mpc-1 and σ8=0.789±0.016, with a gravitational lensing amplitude consistent with the ΛCDM prediction (AL=0.98±0.12). We combine the SPT-3G and the Planck data sets and obtain joint constraints on the ΛCDM model. The volume of the 68% confidence region in six-dimensional ΛCDM parameter space is reduced by a factor of 1.5 compared to Planck-only constraints, with no significant shifts in central values. We note that the results presented here are obtained from data collected during just half of a typical observing season with only part of the focal plane operable, and that the active detector count has since nearly doubled for observations made with SPT-3G after 2018.
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