Validating Phasing and Geometry of Large Focal Plane Arrays

The Kepler Mission is designed to survey our region of the Milky Way galaxy to discover hundreds of Earth-sized and smaller planets in or near the habitable zone. The Kepler photometer is an array of 42 CCDs (charge-coupled devices) in the focal plane of a 95-cm Schmidt camera onboard the Kepler spacecraft. Each 50x25-mm CCD has 2,200 x 1,024 pixels. The CCDs accumulate photons and are read out every six seconds to prevent saturation. The data is integrated for 30 minutes, and then the pixel data is transferred to onboard storage. The data is subsequently encoded and transmitted to the ground. During End-to-End Information System (EEIS) testing of the Kepler Mission System (KMS), there was a need to verify that the pixels requested by the science team operationally were correctly collected, encoded, compressed, stored, and transmitted by the FS, and subsequently received, decoded, uncompressed, and displayed by the Ground Segment (GS) without the outputs of any CCD modules being flipped, mirrored, or otherwise corrupted during the extensive FS and GS processing. This would normally be done by projecting an image on the focal plane array (FPA), collecting the data in a flight-like way, and making a comparison between the original data and the data reconstructed by the science data system. Projecting a focused image onto the FPA through the telescope would normally involve using a collimator suspended over the telescope opening. There were several problems with this approach: the collimation equipment is elaborate and expensive; as conceived, it could only illuminate a limited section of the FPA (.25 percent) during a given test; the telescope cover would have to be deployed during testing to allow the image to be projected into the telescope; the equipment was bulky and difficult to situate in temperature-controlled environments; and given all the above, test setup, execution, and repeatability were significant concerns. Instead of using this complicated approach of projecting an optical image on the FPA, the Kepler project developed a method using known defect features in the CCDs to verify proper collection and reassembly of the pixels, thereby avoiding the costs and risks of the optical projection approach. The CCDs composing the Kepler FPA, as all CCDs, had minor defects. At ambient temperature, some pixels look far brighter than they should. These ghot h pixels have a higher rate of charge leakage than the others due to manufacturing variations. They are usually stable over time, and appear at temperatures above 5 oC. The hot pixels on the Kepler FPA were mapped before photometer assembly during module testing. Selected hot pixels were used as target gstars h for the purposes of EEIS testing. gDead h pixels are permanently off, producing a permanently black pixel. These can also be used if there is some illumination of the FPA. During EEIS testing, Dark Current Full Frame Images (FFIs) taken at room temperature were used to create the hot pixel maps for all 84 Kepler photometer CCD channels. Data from two separate nights were used to create two hot pixel maps per channel, which were cross-correlated to remove cosmic ray events which appear to be hot pixels. These hot pixel maps obtained during EEIS testing were compared to the maps made during module testing to verify that the end-to-end data flow was correct

Domestic Cat Hepadnavirus: Molecular Epidemiology and Phylogeny in Cats in Hong Kong

Domestic cat hepadnavirus (DCH) is an emerging virus related to the hepatitis B virus (HBV). The pathogenic potential of DCH in cats remains to be established. The molecular prevalence of DCH varies widely in the regions investigated so far. The aim of this study was to determine the prevalence, load, and risk factors for DCH detection among cats in Hong Kong, and to generate molecular and epidemiological data on the DCH strains circulating in cats in Hong Kong. DCH DNA was detected using DCH-specific qPCR in 57/513 (11.1%) residual diagnostic blood samples from owned cats. The median viral load was 8.85 × 103 copies/mL of whole blood (range for the 5th to the 95th percentile, 3.33 × 103 to 2.2 × 105 copies per mL). Two outliers had higher viral loads of 1.88 × 107 copies/mL and 4.90 × 109 copies/mL. DCH was detected in cats from 3 months to 19 years of age. Sex, age, neuter status, breed, or elevated serum alanine aminotransferase were not statistically associated with DCH DNA detection. On phylogenetic analysis based on 12 complete genome sequences, the Hong Kong DCH viruses clustered in Genotype A with viruses from Australia and Asia (clade A1), distinct from viruses from Europe (clade A2). Sequence analysis found that DCH has similar epsilon and direct repeat regions to human HBV, suggesting a conserved method of replication. Based on our findings, the DCH strains circulating in Hong Kong are a continuum of the Asiatic strains

Sudden cardiac death while waiting: do we need the wearable cardioverter-defibrillator?

Sudden cardiac death (SCD) is the most frequent cause of cardiovascular death in industrialized nations. Patients with cardiomyopathy are at increased risk for SCD and may benefit from an implantable cardioverter-defibrillator (ICD). The risk of SCD is highest in the first months after myocardial infarction or first diagnosis of severe non-ischemic cardiomyopathy. On the other hand, left ventricular function may improve in a subset of patients to such an extent that an ICD might no longer be needed. To offer protection from a transient risk of SCD, the wearable cardioverter-defibrillator (WCD) is available. Results of the first randomized clinical trial investigating the role of the WCD after myocardial infarction were recently published. This review is intended to provide insight into data from the VEST trial, and to put these into perspective with studies and clinical experience. As a non-invasive, temporary therapy, the WCD may offer advantages over early ICD implantation. However, recent data demonstrate that patient compliance and education play a crucial role in this new concept of preventing SCD

Suppression of the 2010 Alexandrium fundyense bloom by changes in physical, biological, and chemical properties of the Gulf of Maine

Author Posting. © American Society of Limnology and Oceanography, 2011. This article is posted here by permission of American Society of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 56 (2011): 2411-2426, doi:10.4319/lo.2011.56.6.2411.For the period 2005–2009, the abundance of resting cysts in bottom sediments from the preceding autumn was a first-order predictor of the overall severity of spring–summer blooms of Alexandrium fundyense in the western Gulf of Maine and southern New England. Cyst abundance off mid-coast Maine was significantly higher in autumn 2009 than it was preceding a major regional bloom in 2005. A seasonal ensemble forecast was computed using a range of forcing conditions for the period 2004–2009, suggesting that a large bloom was likely in the western Gulf of Maine in 2010. This did not materialize, perhaps because environmental conditions in spring–summer 2010 were not favorable for growth of A. fundyense. Water mass anomalies indicate a regional-scale change in circulation with direct influence on A. fundyense's niche. Specifically, near-surface waters were warmer, fresher, more stratified, and had lower nutrients than during the period of observations used to construct the ensemble forecast. Moreover, a weaker-than-normal coastal current lessened A. fundyense transport into the western Gulf of Maine and Massachusetts Bay. Satellite ocean color observations indicate the 2010 spring phytoplankton bloom was more intense than usual. Early season nutrient depletion may have caused a temporal mismatch with A. fundyense's endogenous clock that regulates the timing of cyst germination. These findings highlight the difficulties of ecological forecasting in a changing oceanographic environment, and underscore the need for a sustained observational network to drive such forecasts.We gratefully acknowledge support of the National Oceanic Atmospheric Administration (grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program) and the Woods Hole Center for Oceans and Human Health through National Science Foundation grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences grant 1P50- ES01274201

Differential levels of plasma biomarkers of neurodegeneration in Lewy body dementia, Alzheimer’s disease, frontotemporal dementia and progressive supranuclear palsy

OBJECTIVES: This longitudinal study compared emerging plasma biomarkers for neurodegenerative disease between controls, patients with Alzheimer's disease (AD), Lewy body dementia (LBD), frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). METHODS: Plasma phosphorylated tau at threonine-181 (p-tau181), amyloid beta (Αβ)42, Aβ40, neurofilament light (NfL) and glial fibrillar acidic protein (GFAP) were measured using highly sensitive single molecule immunoassays (Simoa) in a multicentre cohort of 300 participants (controls=73, amyloid positive mild cognitive impairment (MCI+) and AD dementia=63, LBD=117, FTD=28, PSP=19). LBD participants had known positron emission tomography (PET)-Aβ status. RESULTS: P-tau181 was elevated in MCI+AD compared with all other groups. Aβ42/40 was lower in MCI+AD compared with controls and FTD. NfL was elevated in all dementias compared with controls while GFAP was elevated in MCI+AD and LBD. Plasma biomarkers could classify between MCI+AD and controls, FTD and PSP with high accuracy but showed limited ability in differentiating MCI+AD from LBD. No differences were detected in the levels of plasma biomarkers when comparing PET-Aβ positive and negative LBD. P-tau181, NfL and GFAP were associated with baseline and longitudinal cognitive decline in a disease specific pattern. CONCLUSION: This large study shows the role of plasma biomarkers in differentiating patients with different dementias, and at monitoring longitudinal change. We confirm that p-tau181 is elevated in MCI+AD, versus controls, FTD and PSP, but is less accurate in the classification between MCI+AD and LBD or detecting amyloid brain pathology in LBD. NfL was elevated in all dementia groups, while GFAP was elevated in MCI+AD and LBD

Fully digital data processing during cardiovascular implantable electronic device follow-up in a high-volume tertiary center

Background Increasing numbers of patients with cardiovascular implantable electronic devices (CIEDs) and limited follow-up capacities highlight unmet challenges in clinical electrophysiology. Integrated software (MediConnect®) enabling fully digital processing of device interrogation data has been commercially developed to facilitate follow-up visits. We sought to assess feasibility of fully digital data processing (FDDP) during ambulatory device follow-up in a high-volume tertiary hospital to provide guidance for future users of FDDP software. Methods A total of 391 patients (mean age, 70 years) presenting to the outpatient department for routine device follow-up were analyzed (pacemaker, 44%; implantable cardioverter defibrillator, 39%; cardiac resynchronization therapy device, 16%). Results Quality of data transfer and follow-up duration were compared between digital (n = 265) and manual processing of device data (n = 126). Digital data import was successful, complete and correct in 82% of cases when early software versions were used. When using the most recent software version the rate of successful digital data import increased to 100%. Software-based import of interrogation data was complete and without failure in 97% of cases. The mean duration of a follow-up visit did not differ between the two groups (digital 18.7 min vs. manual data transfer 18.2 min). Conclusions FDDP software was successfully implemented into the ambulatory follow-up of patients with implanted pacemakers and defibrillators. Digital data import into electronic patient management software was feasible and supported the physician’s workflow. The total duration of follow-up visits comprising technical device interrogation and clinical actions was not affected in the present tertiary center outpatient cohort

Your: Your Unified Reader

The advancement in signal processing and GPU based systems has enabled new transient detectors at various telescopes to perform much more sensitive searches than their predecessors. Typically the data output from the telescopes is in one of the two commonly used formats: psrfits and Sigproc filterbank. Software developed for transient searches often only works with one of these two formats, limiting their general applicability. Therefore, researchers have to write custom scripts to read/write the data in their format of choice before they can begin any data analysis relevant for their research. \textsc{Your} (Your Unified Reader) is a python-based library that unifies the data processing across multiple commonly used formats. \textsc{Your} implements a user-friendly interface to read and write in the data format of choice. It also generates unified metadata corresponding to the input data file for a quick understanding of observation parameters and provides utilities to perform common data analysis operations. \textsc{Your} also provides several state-of-the-art radio frequency interference mitigation (RFI) algorithms, which can now be used during any stage of data processing (reading, writing, etc.) to filter out artificial signals.Comment: 3 pages, Published in JOSS, Github: https://github.com/thepetabyteproject/you

Water masses and nutrient sources to the Gulf of Maine

Author Posting. © The Author(s), 2015. This article is posted here by permission of Sears Foundation for Marine Research for personal use, not for redistribution. The definitive version was published in Journal of Marine Research 73 (2015): 93-122, doi:10.1357/002224015815848811.The Gulf of Maine, a semienclosed basin on the continental shelf of the northwest Atlantic Ocean, is fed by surface and deep water flows from outside the gulf: Scotian Shelf Water (SSW) from the Nova Scotian shelf that enters the gulf at the surface and slope water that enters at depth and along the bottom through the Northeast Channel. There are two distinct types of slope water, Labrador Slope Water (LSW) and Warm Slope Water (WSW); it is these deep water masses that are the major source of dissolved inorganic nutrients to the gulf. It has been known for some time that the volume inflow of slope waters of either type to the Gulf of Maine is variable, that it covaries with the magnitude of inflowing SSW, and that periods of greater inflows of SSW have become more frequent in recent years, accompanied by reduced slope water inflows. We present here analyses of a 10-year record of data collected by moored sensors in Jordan Basin in the interior Gulf of Maine, and in the Northeast Channel, along with recent and historical hydrographic and nutrient data that help reveal the nature of SSW and slope water inflows. We show that proportional inflows of nutrient-rich slope waters and nutrient-poor SSWs alternate episodically with one another on timescales of months to several years, creating a variable nutrient field on which the biological productivities of the Gulf of Maine and Georges Bank depend. Unlike decades past, more recent inflows of slope waters of either type do not appear to be correlated with the North Atlantic Oscillation (NAO), which had been shown earlier to influence the relative proportions of the two types of slope waters that enter the gulf, WSW and LSW. We suggest that of greater importance than the NAO in recent years are recent increases in freshwater fluxes to the Labrador Sea, which may intensify the volume transport of the inshore, continental shelf limb of the Labrador Current and its continuation as the Nova Scotia Current. The result is more frequent, episodic influxes of colder, fresher, less dense, and low-nutrient SSW into the Gulf of Maine and concomitant reductions in the inflow of deep, nutrient-rich slope waters. We also discuss evidence that modified Gulf Stream ring water may have penetrated to Jordan Basin in the summer of 2013.Fundingwas provided by grants fromNOAAand the University of Maine.DJMwas also supported by theWoods Hole Center for Oceans and Human Health through National Science Foundation grant OCE-1314642 and National Institute of Environmental Health Sciences grant 1P01ES021923-01

An Extremes of outcome strategy provides evidence that multiple sclerosis severity is determined by alleles at the <i>HLA-DRB1</i> locus

Multiple sclerosis (MS) is a common inflammatory disease of the central nervous system unsurpassed for variability in disease outcome. A cohort of sporadic MS cases (n=63), taken from opposite extremes of the distribution of long-term outcome, was used to determine the role of the HLA-DRB1 locus on MS disease severity. Genotyping sets of benign and malignant MS patients showed that HLA-DRB1*01 was significantly underrepresented in malignant compared with benign cases. This allele appears to attenuate the progressive disability that characterizes MS in the long term. The observation was doubly replicated in (i) Sardinian benign and malignant patients and (ii) a cohort of affected sibling pairs discordant for HLA-DRB1*01. Among the latter, mean disability progression indices were significantly lower in those carrying the HLA-DRB1*01 allele compared with their disease-concordant siblings who did not. The findings were additionally supported by similar transmission distortion of HLA-DRB1*04 subtypes closely related to HLA-DRB1*01. The protective effect of HLA-DRB1*01 in sibling pairs may result from a specific epistatic interaction with the susceptibility allele HLA-DRB1*1501. A high-density (&gt;700) SNP examination of the MHC region in the benign and malignant patients could not identify variants differing significantly between the two groups, suggesting that HLA-DRB1 may itself be the disease-modifying locus. We conclude that HLA-DRB1*01, previously implicated in disease resistance, acts as an independent modifier of disease progression. These results closely link susceptibility to long-term outcome in MS, suggesting that shared quantitative MHC-based mechanisms are common to both, emphasizing the central role of this region in pathogenesis