Testing and Modeling of the Mars Atmospheric Processing Module

Here we report further progress in the development of the MARCO POLO-Mars Pathfinder Atmospheric Processing Module (APM). The APM is designed to demonstrate in situ resource utilization (ISRU) of the Martian atmosphere, which primarily consists of carbon dioxide (CO2). The APM is part of a larger project with the overall goal of collecting and utilizing CO2 found in the atmosphere and water in the regolith of Mars to produce methane and oxygen to be used as rocket propellant, eliminating the need to import those to Mars for human missions, thus significantly reducing costs. The initial focus of NASA's new ISRU Project is modeling of key ISRU components, such as the CO2 Freezers and the Sabatier reactor of the APM. We have designed models of those components and verified the models with the APM by gathering additional data for the Sabatier reactor. Future efforts will be focused on simultaneous operations of the APM and other MARCO POLO-Mars Pathfinder modules

Ensembl Genomes 2013: scaling up access to genome-wide data

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future

The Primordial Inflation Polarization Explorer (PIPER): Current Status and Performance of the First Flight

The Primordial Inflation Polarization ExploreR (PIPER) is a balloon-borne instrument optimized to measure the polarization of the CMB at large angular scales. It will map 85% of the sky over a series of conventional balloon flights from the Northern and Southern hemispheres, measuring the B-mode polarization power spectrumover a range of multipoles from 2-300 covering both the reionization bump and the recombination peak, with sensitivity to measure the tensor-to-scalar ratio down to r = 0.007. PIPER will observe in four frequency bands centered at 200, 270, 350, and 600 GHz to characterize dust foregrounds. The instrument has background-limited sensitivity provided by fully cryogenic (1.7 K) optics focusing the sky signal onto kilo-pixel arrays of time-domain multiplexed Transition-Edge Sensor (TES) bolometers held at 100 mK. Polarization sensitivity and systematiccontrol are provided by front-end Variable-delay Polarization Modulators (VPMs). PIPER had its engineering flight in October 2017 from Fort Sumner, New Mexico. This papers outlines the major components in the PIPER system discussing the conceptual design as well as specific choices made for PIPER. We also report on the results of the engineering flight, looking at the functionality of the payload systems, particularly VPM, as well as pointing out areas of improvement

Sub-Kelvin cooling for two kilopixel bolometer arrays in the PIPER receiver

The Primordial Inflation Polarization Explorer (PIPER) is a balloon-borne telescope mission to search for inflationary gravitational waves from the early universe. PIPER employs two 32 × 40 arrays of superconducting transition-edge sensors, which operate at 100 mK. An open bucket Dewar of liquid helium maintains the receiver and telescope optics at 1.7 K. We describe the thermal design of the receiver and sub-Kelvin cooling with a continuous adiabatic demagnetization refrigerator (CADR). The CADR operates between 70 and 130 mK and provides ≈10 μW cooling power at 100 mK, nearly five times the loading of the two detector assemblies. We describe electronics and software to robustly control the CADR, overall CADR performance in flightlike integrated receiver testing, and practical considerations for implementation in the balloon float environment

Ensembl Genomes 2016: more genomes, more complexity

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces

Pathologists should probably forget about kappa. Percent agreement, diagnostic specificity and related metrics provide more clinically applicable measures of interobserver variability

Kappa statistics have been widely used in the pathology literature to compare interobserver diagnostic variability (IOV) among different pathologists but there has been limited discussion about the clinical significance of kappa scores. Five representative and recent pathology papers were queried using clinically relevant specific questions to learn how IOV was evaluated and how the clinical applicability of results was interpreted. The papers supported our anecdotal impression that pathologists usually assess IOV using Cohen's or Fleiss' kappa statistics and interpret the results using some variation of the scale proposed by Landis and Koch. The papers did not cite or propose specific guidelines to comment on the clinical applicability of results. The solutions proposed to decrease IOV included the development of better diagnostic criteria and additional educational efforts, but the possibility that the entities themselves represented a continuum of morphologic findings rather than distinct diagnostic categories was not considered in any of the studies. A dataset from a previous study of IOV reported by Thunnissen et al. was recalculated to estimate percent agreement among 19 international lung pathologists for the diagnosis of 74 challenging lung neuroendocrine neoplasms. Kappa scores and diagnostic sensitivity, specificity, positive and negative predictive values were calculated using the majority consensus diagnosis for each case as the gold reference diagnosis for that case. Diagnostic specificity estimates among multiple pathologists were > 90%, although kappa scores were considerably more variable. We explain why kappa scores are of limited clinical applicability in pathology and propose the use of positive and negative percent agreement and diagnostic specificity against a gold reference diagnosis to evaluate IOV among two and multiple raters, respectively