Detection of Tropheryma whippelii DNA in a patient with AIDS

A case of an AIDS patient infected with the Whipple's disease bacterium, Tropheryma whippelii, is reported. A DNA fragment with sequence specificity for the 16S rRNA gene of the bacterium was detected by PCR in a duodenal biopsy specimen from a 55-year-old male patient with AIDS and diarrhea. The biopsy specimen contained periodic acid-Schiff stain-positive macrophages which did not, however, resemble the sickleform-particle-containing cells characteristic of Whipple's disease. This observation raises two possibilities: either the patient had a coincidence of AIDS and Whipple's disease or Tropheryma whippelii acted as an opportunistic pathogen in this immunodeficient patient. The latter explanation is of interest in light of the ongoing discussion of immunologic abnormalities as predisposing factors for Whipple's disease

Effects of closed-loop automatic control of the inspiratory fraction of oxygen (FiO(2)-C) on outcome of extremely preterm infants - study protocol of a randomized controlled parallel group multicenter trial for safety and efficacy

Background: Most extremely low gestational age neonates (ELGANS, postmenstrual age at birth (PMA) < 28 completed weeks) require supplemental oxygen and experience frequent intermittent hypoxemic and hyperoxemic episodes. Hypoxemic episodes and exposure to inadequately high concentrations of oxygen are associated with an increased risk of retinopathy of prematurity (ROP), chronic lung disease of prematurity (BPD), necrotizing enterocolitis (NEC), neurodevelopmental impairment (NDI), and death beyond 36 weeks PMA. Closed-loop automated control of the inspiratory fraction of oxygen (FiO2-C) reduces time outside the hemoglobin oxygen saturation (SpO2) target range, number and duration of hypo- and hyperoxemic episodes and caregivers’ workload. Effects on clinically important outcomes in ELGANs such as ROP, BPD, NEC, NDI and mortality have not yet been studied. Methods: An outcome-assessor-blinded, randomized controlled, parallel-group trial was designed and powered to study the effect of FiO2-C (in addition to routine manual control (RMC) of FiO2), compared to RMC only, on death and severe complications related to hypoxemia and/or hyperoxemia. 2340 ELGANS with a GA of 23 + 0/7 to 27 + 6/ 7 weeks will be recruited in approximately 75 European tertiary care neonatal centers. Study participants are randomly assigned to RMC (control-group) or FiO2-C in addition to RMC (intervention-group). Central randomization is stratified for center, gender and PMA at birth (< 26 weeks and ≥ 26 weeks). FiO2-C is provided by commercially available and CE-marked ventilators with an FiO2-C algorithm intended for use in newborn infants. The primary outcome variable (composite of death, severe ROP, BPD or NEC) is assessed at 36 weeks PMA (or, in case of ROP, until complete vascularization of the retina, respectively). The co-primary outcome variable (composite outcome of death, language/cognitive delay, motor impairment, severe visual impairment or hearing impairment) is assessed at 24 months corrected age. Discussion: Short-term studies on FiO2-C showed improved time ELGANs spent within their assigned SpO2 target range, but effects of FiO2-C on clinical outcomes are yet unknown and will be addressed in the FiO2-C trial. This will ensure an appropriate assessment of safety and efficacy before FiO2-C may be implemented as standard therap

Ultrasensitive force and displacement detection using trapped ions

The ability to detect extremely small forces is vital for a variety of disciplines including precision spin-resonance imaging, microscopy, and tests of fundamental physical phenomena. Current force-detection sensitivity limits have surpassed 1 $aN/\sqrt{Hz}$ (atto $=10^{-18}$) through coupling of micro or nanofabricated mechanical resonators to a variety of physical systems including single-electron transistors, superconducting microwave cavities, and individual spins. These experiments have allowed for probing studies of a variety of phenomena, but sensitivity requirements are ever-increasing as new regimes of physical interactions are considered. Here we show that trapped atomic ions are exquisitely sensitive force detectors, with a measured sensitivity more than three orders of magnitude better than existing reports. We demonstrate detection of forces as small as 174 $yN$ (yocto $=10^{-24}$), with a sensitivity 390$\pm150$ $yN/\sqrt{Hz}$ using crystals of $n=60$ $^{9}$Be$^{+}$ ions in a Penning trap. Our technique is based on the excitation of normal motional modes in an ion trap by externally applied electric fields, detection via and phase-coherent Doppler velocimetry, which allows for the discrimination of ion motion with amplitudes on the scale of nanometers. These experimental results and extracted force-detection sensitivities in the single-ion limit validate proposals suggesting that trapped atomic ions are capable of detecting of forces with sensitivity approaching 1 $yN/\sqrt{Hz}$. We anticipate that this demonstration will be strongly motivational for the development of a new class of deployable trapped-ion-based sensors, and will permit scientists to access new regimes in materials science.Comment: Expanded introduction and analysis. Methods section added. Subject to press embarg

Heralded single photon absorption by a single atom

The emission and absorption of single photons by single atomic particles is a fundamental limit of matter-light interaction, manifesting its quantum mechanical nature. At the same time, as a controlled process it is a key enabling tool for quantum technologies, such as quantum optical information technology [1, 2] and quantum metrology [3, 4, 5, 6]. Controlling both emission and absorption will allow implementing quantum networking scenarios [1, 7, 8, 9], where photonic communication of quantum information is interfaced with its local processing in atoms. In studies of single-photon emission, recent progress includes control of the shape, bandwidth, frequency, and polarization of single-photon sources [10, 11, 12, 13, 14, 15, 16, 17], and the demonstration of atom-photon entanglement [18, 19, 20]. Controlled absorption of a single photon by a single atom is much less investigated; proposals exist but only very preliminary steps have been taken experimentally such as detecting the attenuation and phase shift of a weak laser beam by a single atom [21, 22], and designing an optical system that covers a large fraction of the full solid angle [23, 24, 25]. Here we report the interaction of single heralded photons with a single trapped atom. We find strong correlations of the detection of a heralding photon with a change in the quantum state of the atom marking absorption of the quantum-correlated heralded photon. In coupling a single absorber with a quantum light source, our experiment demonstrates previously unexplored matter-light interaction, while opening up new avenues towards photon-atom entanglement conversion in quantum technology.Comment: 10 pages, 4 figure

Ion traps with enhanced optical and physical access

Small, controllable, highly accessible quantum systems can serve as probes at the single quantum level to study multiple physical effects, for example in quantum optics or for electric and magnetic field sensing. The applicability of trapped atomic ions as probes is highly dependent on the measurement situation at hand and thus calls for specialized traps. Previous approaches for ion traps with enhanced optical access included traps consisting of a single ring electrode or two opposing endcap electrodes. Other possibilities are planar trap geometries, which have been investigated for Penning traps and rf-trap arrays. By not having the electrodes lie in a common plane the optical access in the latter cases can be substantially increased. Here, we discuss the fabrication and experimental characterization of a novel radio-frequency (rf) ion trap geometry. It has a relatively simple structure and provides largely unrestricted optical and physical access to the ion, of up to 96% of the total 4pi solid angle in one of the three traps tested. We also discuss potential applications in quantum optics and field sensing. As a force sensor, we estimate sensitivity to forces smaller than 1 yN Hz^(-1/2).Comment: 6 pages, 3 figures. Corrections of some typos, application section expanded to account for reviewer comment

Photon-Atom Coupling with Parabolic Mirrors

Efficient coupling of light to single atomic systems has gained considerable attention over the past decades. This development is driven by the continuous growth of quantum technologies. The efficient coupling of light and matter is an enabling technology for quantum information processing and quantum communication. And indeed, in recent years much progress has been made in this direction. But applications aside, the interaction of photons and atoms is a fundamental physics problem. There are various possibilities for making this interaction more efficient, among them the apparently 'natural' attempt of mode-matching the light field to the free-space emission pattern of the atomic system of interest. Here we will describe the necessary steps of implementing this mode-matching with the ultimate aim of reaching unit coupling efficiency. We describe the use of deep parabolic mirrors as the central optical element of a free-space coupling scheme, covering the preparation of suitable modes of the field incident onto these mirrors as well as the location of an atom at the mirror's focus. Furthermore, we establish a robust method for determining the efficiency of the photon-atom coupling.Comment: Book chapter in compilation "Engineering the Atom-Photon Interaction" published by Springer in 2015, edited by A. Predojevic and M. W. Mitchell, ISBN 9783319192307, http://www.springer.com/gp/book/9783319192307. Only change to version1: now with hyperlinks to arXiv eprints of other book chapters mentioned in this on

RKappa: Statistical sampling suite for Kappa models

We present RKappa, a framework for the development and analysis of rule-based models within a mature, statistically empowered R environment. The infrastructure allows model editing, modification, parameter sampling, simulation, statistical analysis and visualisation without leaving the R environment. We demonstrate its effectiveness through its application to Global Sensitivity Analysis, exploring it in "parallel" and "concurrent" implementations. The pipeline was designed for high performance computing platforms and aims to facilitate analysis of the behaviour of large-scale systems with limited knowledge of exact mechanisms and respectively sparse availability of parameter values, and is illustrated here with two biological examples. The package is available on github: https://github.com/lptolik/R4KappaComment: Hybrid Systems and Biology 2014, Vienn