Far-infrared polarimetry from the Stratospheric Observatory for Infrared Astronomy

Multi-wavelength imaging polarimetry at far-infrared wavelengths has proven to be an excellent tool for studying the physical properties of dust, molecular clouds, and magnetic fields in the interstellar medium. Although these wavelengths are only observable from airborne or space-based platforms, no first-generation instrument for the Stratospheric Observatory for Infrared Astronomy (SOFIA) is presently designed with polarimetric capabilities. We study several options for upgrading the High-resolution Airborne Wideband Camera (HAWC) to a sensitive FIR polarimeter. HAWC is a 12 x 32 pixel bolometer camera designed to cover the 53 - 215 micron spectral range in 4 colors, all at diffraction-limited resolution (5 - 21 arcsec). Upgrade options include: (1) an external set of optics which modulates the polarization state of the incoming radiation before entering the cryostat window; (2) internal polarizing optics; and (3) a replacement of the current detector array with two state-of-the-art superconducting bolometer arrays, an upgrade of the HAWC camera as well as polarimeter. We discuss a range of science studies which will be possible with these upgrades including magnetic fields in star-forming regions and galaxies and the wavelength-dependence of polarization.Comment: 12 pages, 5 figure

MAPU 2.0: high-accuracy proteomes mapped to genomes

The MAPU 2.0 database contains proteomes of organelles, tissues and cell types measured by mass spectrometry (MS)-based proteomics. In contrast to other databases it is meant to contain a limited number of experiments and only those with very high-resolution and -accuracy data. MAPU 2.0 displays the proteomes of organelles, tissues and body fluids or conversely displays the occurrence of proteins of interest in all these proteomes. The new release addresses MS-specific problems including ambiguous peptide-to-protein assignments and it provides insight into general functional features on the protein level ranging from gene ontology classification to comprehensive SwissProt annotation. Moreover, the derived proteomic data are used to annotate the genomes using Distributed Annotation Service (DAS) via EnsEMBL services. MAPU 2.0 is a model for a database specifically designed for high-accuracy proteomics and a member of the ProteomExchange Consortium. It is available on line at http://www.mapuproteome.com

CMB polarimetry with BICEP: instrument characterization, calibration, and performance

BICEP is a ground-based millimeter-wave bolometric array designed to target the primordial gravity wave signature on the polarization of the cosmic microwave background (CMB) at degree angular scales. Currently in its third year of operation at the South Pole, BICEP is measuring the CMB polarization with unprecedented sensitivity at 100 and 150 GHz in the cleanest available 2% of the sky, as well as deriving independent constraints on the diffuse polarized foregrounds with select observations on and off the Galactic plane. Instrument calibrations are discussed in the context of rigorous control of systematic errors, and the performance during the first two years of the experiment is reviewed.Comment: 12 pages, 15 figures, updated version of a paper accepted for Millimeter and Submillimeter Detectors and Instrumentation for Astronomy IV, Proceedings of SPIE, 7020, 200

Absolute polarization angle calibration using polarized diffuse Galactic emission observed by BICEP

We present a method of cross-calibrating the polarization angle of a polarimeter using BICEP Galactic observations. \bicep\ was a ground based experiment using an array of 49 pairs of polarization sensitive bolometers observing from the geographic South Pole at 100 and 150 GHz. The BICEP polarimeter is calibrated to +/-0.01 in cross-polarization and less than +/-0.7 degrees in absolute polarization orientation. BICEP observed the temperature and polarization of the Galactic plane (R.A= 100 degrees ~ 270 degrees and Dec. = -67 degrees ~ -48 degrees). We show that the statistical error in the 100 GHz BICEP Galaxy map can constrain the polarization angle offset of WMAP Wband to 0.6 degrees +\- 1.4 degrees. The expected 1 sigma errors on the polarization angle cross-calibration for Planck or EPIC are 1.3 degrees and 0.3 degrees at 100 and 150 GHz, respectively. We also discuss the expected improvement of the BICEP Galactic field observations with forthcoming BICEP2 and Keck observations.Comment: 13 pages, 10 figures and 2 tables. To appear in Proceedings of SPIE Astronomical Telescopes and Instrumentation 201

The Influence of Physiological Status on age Prediction of Anopheles Arabiensis Using Near Infra-red spectroscopy

Determining the age of malaria vectors is essential for evaluating the impact of interventions that reduce the survival of wild mosquito populations and for estimating changes in vectorial capacity. Near infra-red spectroscopy (NIRS) is a simple and non-destructive method that has been used to determine the age and species of Anopheles gambiae s.l. by analyzing differences in absorption spectra. The spectra are affected by biochemical changes that occur during the life of a mosquito and could be influenced by senescence and also the life history of the mosquito, i.e., mating, blood feeding and egg-laying events. To better understand these changes, we evaluated the influence of mosquito physiological status on NIR energy absorption spectra. Mosquitoes were kept in individual cups to permit record keeping of each individual insect’s life history. Mosquitoes of the same chronological age, but at different physiological stages, were scanned and compared using cross-validations. We observed a slight trend within some physiological stages that suggest older insects tend to be predicted as being physiologically more mature. It was advantageous to include mosquitoes of different chronological ages and physiological stages in calibrations, as it increases the robustness of the model resulting in better age predictions. Progression through different physiological statuses of An. arabiensis influences the chronological age prediction by the NIRS. Entomologists that wish to use NIR technology to predict the age of field-caught An. gambiae s.l from their study area should use a calibration developed from their field strain using mosquitoes of diverse chronological ages and physiological stages to increase the robustness and accuracy of the predictions.\u

Organisational barriers to the facilitation of overseas volunteering and training placements in the NHS

Background Undertaking a period of voluntary work or a professional placement overseas has long been a feature of medical training in the UK. There are now a number of high profile National Health Service (NHS) initiatives aimed at increasing access to such opportunities for staff at all levels. We present findings from a qualitative study involving a range of NHS staff and other stakeholders which explored barriers to participation in these activities. Methods A grounded theory methodology was drawn upon to conduct thematic based analysis. Our data included in-depth, semi-structured interviews with a range of returned volunteers, non-volunteers and other stakeholders (n=51) who were, or had been, employed by the NHS. Results There are significant barriers to placement and volunteering activity stemming from structural and organisational shortcomings within the NHS. Difficulties in filling clinical roles has a significant impact on the ability of staff to plan and undertake independent placements. There is currently no clearly defined pathway within the NHS by which the majority of grades can apply for, or organise, a period of overseas voluntary or professional placement activity. There were divergent views on the relevance and usefulness of overseas professional placements. Conclusions We argue that in the context of current UK policy initiatives aimed at facilitating overseas volunteer and professional placement activity, urgent attention needs to be given to the structural and organisational framework within which such initiatives will be required to work

Antenna-coupled TES bolometers used in BICEP2, Keck array, and SPIDER

We have developed antenna-coupled transition-edge sensor (TES) bolometers for a wide range of cosmic microwave background (CMB) polarimetry experiments, including BICEP2, Keck Array, and the balloon borne SPIDER. These detectors have reached maturity and this paper reports on their design principles, overall performance, and key challenges associated with design and production. Our detector arrays repeatedly produce spectral bands with 20%-30% bandwidth at 95, 150, or 220~GHz. The integrated antenna arrays synthesize symmetric co-aligned beams with controlled side-lobe levels. Cross-polarized response on boresight is typically ~0.5%, consistent with cross-talk in our multiplexed readout system. End-to-end optical efficiencies in our cameras are routinely 35% or higher, with per detector sensitivities of NET~300 uKrts. Thanks to the scalability of this design, we have deployed 2560 detectors as 1280 matched pairs in Keck Array with a combined instantaneous sensitivity of ~9 uKrts, as measured directly from CMB maps in the 2013 season. Similar arrays have recently flown in the SPIDER instrument, and development of this technology is ongoing.Comment: 16 pgs, 20 fig

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

BACKGROUND: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. RESULTS: We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. CONCLUSION: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm – this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN – have comparable overall performance with different strengths and weaknesses