Simulating the WFIRST coronagraph Integral Field Spectrograph

A primary goal of direct imaging techniques is to spectrally characterize the atmospheres of planets around other stars at extremely high contrast levels. To achieve this goal, coronagraphic instruments have favored integral field spectrographs (IFS) as the science cameras to disperse the entire search area at once and obtain spectra at each location, since the planet position is not known a priori. These spectrographs are useful against confusion from speckles and background objects, and can also help in the speckle subtraction and wavefront control stages of the coronagraphic observation. We present a software package, the Coronagraph and Rapid Imaging Spectrograph in Python (crispy) to simulate the IFS of the WFIRST Coronagraph Instrument (CGI). The software propagates input science cubes using spatially and spectrally resolved coronagraphic focal plane cubes, transforms them into IFS detector maps and ultimately reconstructs the spatio-spectral input scene as a 3D datacube. Simulated IFS cubes can be used to test data extraction techniques, refine sensitivity analyses and carry out design trade studies of the flight CGI-IFS instrument. crispy is a publicly available Python package and can be adapted to other IFS designs.Comment: 15 page

Phase transition curves for mesoscopic superconducting samples

We compute the phase transition curves for mesoscopic superconductors. Special emphasis is given to the limiting shape of the curve when the magnetic flux is large. We derive an asymptotic formula for the ground state of the Schr\"odinger equation in the presence of large applied flux. The expansion is shown to be sensitive to the smoothness of the domain. The theoretical results are compared to recent experiments.Comment: 8 pages, 1 figur

WFIRST CGI Integral Field Spectrograph Performance and Post-Processing in the OS6 Observing Scenario

The WFIRST coronagraph instrument (CGI) will have an integral field spectrograph (IFS) backend to disperse the entire field of view at once and obtain spatially-resolved, low-resolution spectra of the speckles and science scene. The IFS will be key to understanding the spectral nature of the speckles, obtain science spectra of planets and disks, and will be used for broadband wavefront control. In order to characterize, predict, and optimize the performance of the instrument, we present a detailed model of the IFS in the context of the new OS6 observing scenario. The simulation includes spatial, spectral, and temporal variations of the speckle field on the IFS detector plane, which allows us to explore several post-processing methods and assess what gains can be expected. The simulator includes the latest models of the detector behavior when operating in photon-counting mode

Flux-Induced Vortex in Mesoscopic Superconducting Loops

We predict the existence of a quantum vortex for an unusual situation. We study the order parameter in doubly connected superconducting samples embedded in a uniform magnetic field. For samples with perfect cylindrical symmetry, the order parameter has been known for long and no vortices are present in the linear regime. However, if the sample is not symmetric, there exist ranges of the field for which the order parameter vanishes along a line, parallel to the field. In many respects, the behavior of this line is qualitatively different from that of the vortices encountered in type II superconductivity. For samples with mirror symmetry, this flux-induced vortex appears at the thin side for small fluxes and at the opposite side for large fluxes. We propose direct and indirect experimental methods which could test our predictions.Comment: 6 pages, Latex, 4 figs., uses RevTex, extended to situations far from cylindrical symmetr

Rapid-prototyping a tabletop integral field spectrograph

We successfully rapid-prototyped a mostly off-the-shelf, partially 3D-printed pathfinder version of an integral field spectrograph (IFS) in order to compress the design/build/test schedule of a final, mostly-custom IFS, by accelerating the start date of data pipeline development, thus allowing this development to progress in parallel with the design, procurement, fabrication, and alignment of the final IFS version. This parallel-path development schedule enabled us to successfully design, build, align, test, and extract a data cube from the new IFS within only 1 year, even in the face of several design setbacks. We have begun using the now-functional IFS for development of IFS sensing and control algorithms, and have also begun implementing motorized alignment upgrades that enable the systematic characterization of the tolerance (or required compensation) of its data cube extraction to misaligned images, in support of NASA's WFIRST and PISCES IFS. © 2019 SPIE

New NIR spectro-polarimetric modes for the SCExAO instrument

Polarization Differential Imaging (PDI) is one of the most productive modes of current high-contrast imagers. Dozens of new protoplanetary, transition and debris disks were imaged recently for the first time, helping us understand the processes of planet formation, and giving clues on the mass of potential planets inside these disks, even if they cannot be imaged directly. The Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) instrument is equipped with a fast visible dual-camera polarimetric module, VAMPIRES, already producing valuable scientific observations of protoplanetary disks and dust shells. In addition, we recently commissioned two new polarimetric modules in the infrared. The first one is a spectro-polarimetric mode using the CHARIS Integral Field Spectrograph (IFS). A Wollaston prism was added in front of the IFS, reducing the field-of-view to 2x1 arcsec to accommodate for the imaging of both polarizations on the same detector without sacrificing the spectral resolution of the instrument, in any of its spectral modes. The second module, similar to VAMPIRES, uses a low-noise high frame rate C-RED ONE camera combined with a Ferroelectric Liquid Crystal (FLC) device to modulate and record the polarization at high-speed, freezing effectively the atmospheric speckles for higher precision. We present on-sky results of the new polarimetric capabilities taken during the commissioning phase. In addition, we show future capabilities that are already scheduled to increase the performance of these modules, especially the addition of non-redundant masks, as well as a polarimetric vector Apodizing Phase Plate (vAPP) coronagraph

Elevated reticulocyte count – a clue to the diagnosis of haemolytic-uraemic syndrome (HUS) associated with gemcitabine therapy for metastatic duodenal papillary carcinoma: a case report

In adults, the haemolytic-uraemic syndrome (HUS) is associated with probable causative factors in the minority of all cases. Cytotoxic drugs are one of these potential causative agents. Although metastatic cancer by itself is a recognized risk-factor for the development of HUS, therapy with mitomycin-C, with cis-platinum, and with bleomycin carries a significant, albeit extremely small, risk for the development of HUS, compared with all other cytotoxic drugs. Gemcitabine is a novel cytotoxic drug with promising activity against pancreatic adenocarcinoma. We are reporting on one patient with metastatic duodenal papillary carcinoma developing HUS while on weekly gemcitabine therapy. The presenting features in this patient were non-cardiac pulmonary oedema, renal failure, thrombocytopenia and haemolytic anaemia. The diagnosis of HUS was made on the day of admission of the patient to this institution. Upon aggressive therapy, including one single haemodialysis and five plasmaphereses, the patient recovered uneventfully, with modestly elevated creatinine-values as a remnant of the acute illness. Re-exposure to gemcitabine 6 months after the episode of HUS instituted for progressive carcinoma, thus far has not caused another episode of HUS. © 1999 Cancer Research Campaig

The Tug1 locus is essential for male fertility

Background: Several long noncoding RNAs (lncRNAs) have been shown to function as central components of molecular machines that play fundamental roles in biology. While the number of annotated lncRNAs in mammalian genomes has greatly expanded, their functions remain largely uncharacterized. This is compounded by the fact that identifying lncRNA loci that have robust and reproducible phenotypes when mutated has been a challenge. Results: We previously generated a cohort of 20 lncRNA loci knockout mice. Here, we extend our initial study and provide a more detailed analysis of the highly conserved lncRNA locus, Taurine Upregulated Gene 1 (Tug1). We report that Tug1 knockout male mice are sterile with complete penetrance due to a low sperm count and abnormal sperm morphology. Having identified a lncRNA loci with a robust phenotype, we wanted to determine which, if any, potential elements contained in the Tug1 genomic region (DNA, RNA, protein, or the act of transcription) have activity. Using engineered mouse models and cell-based assays, we provide evidence that the Tug1 locus harbors three distinct regulatory activities - two noncoding and one coding: (i) a cis DNA repressor that regulates many neighboring genes, (ii) a lncRNA that can regulate genes by a trans-based function, and finally (iii) Tug1 encodes an evolutionary conserved peptide that when overexpressed impacts mitochondrial membrane potential. Conclusions: Our results reveal an essential role for the Tug1 locus in male fertility and uncover three distinct regulatory activities in the Tug1 locus, thus highlighting the complexity present at lncRNA loci

The what and where of adding channel noise to the Hodgkin-Huxley equations

One of the most celebrated successes in computational biology is the Hodgkin-Huxley framework for modeling electrically active cells. This framework, expressed through a set of differential equations, synthesizes the impact of ionic currents on a cell's voltage -- and the highly nonlinear impact of that voltage back on the currents themselves -- into the rapid push and pull of the action potential. Latter studies confirmed that these cellular dynamics are orchestrated by individual ion channels, whose conformational changes regulate the conductance of each ionic current. Thus, kinetic equations familiar from physical chemistry are the natural setting for describing conductances; for small-to-moderate numbers of channels, these will predict fluctuations in conductances and stochasticity in the resulting action potentials. At first glance, the kinetic equations provide a far more complex (and higher-dimensional) description than the original Hodgkin-Huxley equations. This has prompted more than a decade of efforts to capture channel fluctuations with noise terms added to the Hodgkin-Huxley equations. Many of these approaches, while intuitively appealing, produce quantitative errors when compared to kinetic equations; others, as only very recently demonstrated, are both accurate and relatively simple. We review what works, what doesn't, and why, seeking to build a bridge to well-established results for the deterministic Hodgkin-Huxley equations. As such, we hope that this review will speed emerging studies of how channel noise modulates electrophysiological dynamics and function. We supply user-friendly Matlab simulation code of these stochastic versions of the Hodgkin-Huxley equations on the ModelDB website (accession number 138950) and http://www.amath.washington.edu/~etsb/tutorials.html.Comment: 14 pages, 3 figures, review articl