Complete Genome Sequences of Chop, DelRio, and GrandSlam, Three Gordonia Phages Isolated from Soil in Central Arkansas.

Chop, DelRio, and GrandSlam are phage with a Siphoviridae morphotype isolated from soil in Arkansas using the host Gordonia terrae 3612. All three are temperate, and their genomes share at least 96% nucleotide identity. These phage are assigned to cluster DI based on gene content similarity to other sequenced actinobacteriophage.

Recurrent Colon Cancer: Presentation With Disseminated Intravascular Coagulation From Disseminated Carcinomatosis of the Bone Marrow.

Diffuse carcinomatosis of the bone marrow (DCBM) is a rare clinical condition characterized by diffuse bone marrow involvement with hematological changes. This case study concerns a patient who presented with DCBM secondary to colon cancer with diffuse intravascular coagulation. This is a rare presentation of DCBM in colon cancer. The case study also elaborates on clinical features, pathogenesis, and therapy of this unique presentation.

Electrolyte Replacement in Bartter Syndrome With Abnormal Small Bowel: A Case Report.

Bartter syndrome is a rare disorder that is characterized by weakness and fatigue with laboratory findings of hypokalemia and metabolic alkalosis with increased aldosterone and angiotensin. It specifically acts on the ascending loop of Henle, characterized by miscoded proteins affecting NaCl transports and channels. Patients will require replacement of potassium and sometimes magnesium due to the kidneys' inability to reabsorb these ions. So what happens when the body's other primary mechanism of absorption of these elements are taken out? In this article, we present the case of a 47-year-old woman with Bartter syndrome on oral potassium 40 mg BID (twice a day) and magnesium oxide 800 TID (thrice a day), who recently had a small bowel resection that required intravenous potassium and magnesium throughout her hospital admission. Significant questions arose as to how her electrolytes should be managed, given her unusual presentation with rare underlying disorder. We discuss the implications of her bowel resection in the context of Bartter syndrome and our views on her future course based on available literature.

Chronic Myelomonocytic Leukemia Presenting With Polyserositis and Seropositivity for Rheumatoid Arthritis.

Chronic myelomonocytic leukemia (CMML) is a rare clonal stem cell disorder associated with clinical and pathologic of myelodysplasia and myeloproliferation. Systemic autoimmune/inflammatory disorders (SAID) and polyserositis have been associated with CMML. These manifestations can be observed concomitantly, shortly before diagnosis or anytime along the course of illness. We report a case of myeloproliferative CMML who presented with polyserositis and positive serology for rheumatoid arthritis. Retrospective studies of myelodysplasia/CMML have reported 15% to 25% incidence of SAID. The most commonly observed disorders include systemic vasculitis, connective tissue diseases, polychondritis, seronegative arthritis, and immune thrombocytopenia. SAID does not confer adverse prognosis in retrospective studies. Polyserositis is less common; this may result from leukemic infiltrate or result from autoimmunity. Treatment of serositis includes steroids and cytoreductive agents. Serositis may confer poor prognosis and hypomethylating therapy may improve the outcome.

Capillary Leak Syndrome From Rituximab Therapy of Lymphoma.

Capillary leak syndrome (CLS) is characterized by plasma extravasation into the interstitium with resultant hypotension, anasarca, hemoconcentration, and hypoalbuminemia in the absence of albuminuria. Initially reported in Clarkson's disease (systemic capillary leak syndrome), CLS has been observed in multiple disease settings, the most common being sepsis. In oncology, CLS has been reported more often as a complication from therapy, and less often from malignancy. In this case study, we documented clinical manifestation, laboratory features, and radiological findings of CLS from rituximab therapy when employed in combination with a multi-agent chemotherapy regimen (EPOCH-R). Differentiating drug-induced CLS from sepsis, which presents with the same clinical features, is important in avoiding further exposure to rituximab, which could be fatal to the patient.

Delayed acute pancreatitis induced by nilotinib in a patient with chronic myeloid leukemia attaining sustained complete molecular response.

Advent of tyrosine kinase inhibitors (TKI) have revolutionized therapy of chronic myeloid leukemia. Imatinib was the first agent utilized in the therapy of CML. Nilotinib, a second generation TKI, results in an increase in number of patients achieving major molecular response at an earlier time point. Asymptomatic elevations in pancreatic enzyme is common and acute pancreatitis within weeks to months from start of therapy has been observed. Delayed onset pancreatitis has not been reported. We report a case of delayed onset pancreatitis in a patient with sustained complete molecular response. On account of the deep response, we were able to avoid starting alternate tyrosine kinase inhibitors that could also result in pancreatitis as a class effect.

On-orbit calibration of SeaWiFS.

Ocean color climate data records (CDRs) require water-leaving radiances with 5% absolute and 1% relative accuracies as input. Because of the amplification of any sensor calibration errors by the atmospheric correction, the 1% relative accuracy requirement translates into a 0.1% long-term radiometric stability requirement for top-of-the-atmosphere (TOA) radiances. The rigorous prelaunch and on-orbit calibration program developed and implemented for Sea-viewing Wide Field-of-view Sensor (SeaWiFS) by the NASA Ocean Biology Processing Group (OBPG) has led to the incorporation of significant changes into the on-orbit calibration methodology over the 13-year lifetime of the instrument. Evolving instrument performance and ongoing algorithm refinement have resulted in updates to approaches for the lunar, solar, and vicarious calibration of SeaWiFS. The uncertainties in the calibrated TOA radiances are addressed in terms of accuracy (biases in the measurements), precision (scatter in the measurements), and stability (repeatability of the measurements). The biases are 2%-3% from lunar calibration and 1%-2% from vicarious calibration. The precision is 0.16% from solar signal-to-noise ratios, 0.13% from lunar residuals, and 0.10% from vicarious gains. The long-term stability of the TOA radiances, derived from the lunar time series, is 0.13%. The stability of the vicariously calibrated TOA radiances, incorporating the uncertainties of the in situ measurements and the atmospheric correction, is 0.30%. This stability of the radiometric calibration of SeaWiFS over its 13-year on-orbit lifetime has allowed the OBPG to produce CDRs from the ocean color data set.

Dynamic range and sensitivity requirements of satellite ocean color sensors: learning from the past.

Sensor design and mission planning for satellite ocean color measurements requires careful consideration of the signal dynamic range and sensitivity (specifically here signal-to-noise ratio or SNR) so that small changes of ocean properties (e.g., surface chlorophyll-a concentrations or Chl) can be quantified while most measurements are not saturated. Past and current sensors used different signal levels, formats, and conventions to specify these critical parameters, making it difficult to make cross-sensor comparisons or to establish standards for future sensor design. The goal of this study is to quantify these parameters under uniform conditions for widely used past and current sensors in order to provide a reference for the design of future ocean color radiometers. Using measurements from the Moderate Resolution Imaging Spectroradiometer onboard the Aqua satellite (MODISA) under various solar zenith angles (SZAs), typical (L(typical)) and maximum (L(max)) at-sensor radiances from the visible to the shortwave IR were determined. The L(typical) values at an SZA of 45° were used as constraints to calculate SNRs of 10 multiband sensors at the same L(typical) radiance input and 2 hyperspectral sensors at a similar radiance input. The calculations were based on clear-water scenes with an objective method of selecting pixels with minimal cross-pixel variations to assure target homogeneity. Among the widely used ocean color sensors that have routine global coverage, MODISA ocean bands (1 km) showed 2-4 times higher SNRs than the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) (1 km) and comparable SNRs to the Medium Resolution Imaging Spectrometer (MERIS)-RR (reduced resolution, 1.2 km), leading to different levels of precision in the retrieved Chl data product. MERIS-FR (full resolution, 300 m) showed SNRs lower than MODISA and MERIS-RR with the gain in spatial resolution. SNRs of all MODISA ocean bands and SeaWiFS bands (except the SeaWiFS near-IR bands) exceeded those from prelaunch sensor specifications after adjusting the input radiance to L(typical). The tabulated L(typical), L(max), and SNRs of the various multiband and hyperspectral sensors under the same or similar radiance input provide references to compare sensor performance in product precision and to help design future missions such as the Geostationary Coastal and Air Pollution Events (GEO-CAPE) mission and the Pre-Aerosol-Clouds-Ecosystems (PACE) mission currently being planned by the U.S. National Aeronautics and Space Administration (NASA).

Cross calibration of SeaWiFS and MODIS using on-orbit observations of the Moon.

Observations of the Moon provide a primary technique for the on-orbit cross calibration of Earth remote sensing instruments. Monthly lunar observations are major components of the on-orbit calibration strategies of SeaWiFS and MODIS. SeaWiFS has collected more than 132 low phase angle and 59 high phase angle lunar observations over 12 years, Terra MODIS has collected more than 82 scheduled and 297 unscheduled lunar observations over nine years, and Aqua MODIS has collected more than 61 scheduled and 171 unscheduled lunar observations over seven years. The NASA Ocean Biology Processing Group Calibration and Validation Team and the NASA MODIS Characterization Support Team use the USGS RObotic Lunar Observatory (ROLO) photometric model of the Moon to compare these time series of lunar observations over time and varying observing geometries. The cross-calibration results show that Terra MODIS and Aqua MODIS agree, band to band, at the 1%-3% level, while SeaWiFS and either MODIS instrument agree at the 3%-8% level. The combined uncertainties of these comparisons are 1.3% for Terra and Aqua MODIS, 1.4% for SeaWiFS and Terra MODIS, and 1.3% for SeaWiFS and Aqua MODIS. Any residual phase dependence in the ROLO model, based on these observations, is less than 1.7% over the phase angle range of -80° to -6° and +5° to +82°. The lunar cross calibration of SeaWiFS, Terra MODIS, and Aqua MODIS is consistent with the vicarious calibration of ocean color products for these instruments, with the vicarious gains mitigating the calibration biases for the ocean color bands.

Point-spread function of the ocean color bands of the Moderate Resolution Imaging Spectroradiometer on Aqua.

The Moderate Resolution Imaging Spectroradiometer (MODIS) on the Aqua platform has nine spectral bands with center wavelengths from 412 to 870 nm that are used to produce the standard ocean color data products. Ocean scenes usually contain high contrast due to the presence of bright clouds over dark water. About half of the MODIS Aqua ocean pixels are flagged as spatial stray light contaminated. The MODIS has been characterized for stray light effects prelaunch. In this paper, we derive point-spread functions for the MODIS Aqua ocean bands based on prelaunch line-spread function measurements. The stray light contamination of ocean scenes is evaluated based on artificial test scenes and on-orbit data.

New aerosol models for the retrieval of aerosol optical thickness and normalized water-leaving radiances from the SeaWiFS and MODIS sensors over coastal regions and open oceans.

We describe the development of a new suite of aerosol models for the retrieval of atmospheric and oceanic optical properties from the SeaWiFS and MODIS sensors, including aerosol optical thickness (τ), angstrom coefficient (α), and water-leaving radiance (L(w)). The new aerosol models are derived from Aerosol Robotic Network (AERONET) observations and have bimodal lognormal distributions that are narrower than previous models used by the Ocean Biology Processing Group. We analyzed AERONET data over open ocean and coastal regions and found that the seasonal variability in the modal radii, particularly in the coastal region, was related to the relative humidity. These findings were incorporated into the models by making the modal radii, as well as the refractive indices, explicitly dependent on relative humidity. From these findings, we constructed a new suite of aerosol models. We considered eight relative humidity values (30%, 50%, 70%, 75%, 80%, 85%, 90%, and 95%) and, for each relative humidity value, we constructed ten distributions by varying the fine-mode fraction from zero to 1. In all, 80 distributions (8 Rh×10 fine-mode fractions) were created to process the satellite data. We also assumed that the coarse-mode particles were nonabsorbing (sea salt) and that all observed absorptions were entirely due to fine-mode particles. The composition of the fine mode was varied to ensure that the new models exhibited the same spectral dependence of single scattering albedo as observed in the AERONET data. The reprocessing of the SeaWiFS data show that, over deep ocean, the average τ(865) values retrieved from the new aerosol models was 0.100±0.004, which was closer to the average AERONET value of 0.086±0.066 for τ(870) for the eight open-ocean sites used in this study. The average τ(865) value from the old models was 0.131±0.005. The comparison of monthly mean aerosol optical thickness retrieved from the SeaWiFS sensor with AERONET data over Bermuda and Wallops Island show very good agreement with one another. In fact, 81% of the data points over Bermuda and 78% of the data points over Wallops Island fall within an uncertainty of ±0.02 in optical thickness. As a part of the reprocessing effort of the SeaWiFS data, we also revised the vicarious calibration gain factors, which resulted in significant improvement in angstrom coefficient (α) retrievals. The average value of α from the new models over Bermuda is 0.841±0.171, which is in good agreement with the AERONET value of 0.891±0.211. The average value of α retrieved using old models is 0.394±0.087, which is significantly lower than the AERONET value.

A decade of satellite ocean color observations.

After the successful Coastal Zone Color Scanner (CZCS, 1978-1986) demonstration that quantitative estimations of geophysical variables such as chlorophyll a and diffuse attenuation coefficient could be derived from top of the atmosphere radiances, a number of international missions with ocean color capabilities were launched beginning in the late 1990s. Most notable were those with global data acquisition capabilities, i.e., the Ocean Color and Temperature Sensor (OCTS,Japan, 1996-1997), the Sea-viewing Wide Field-of-view Sensor (SeaWiFS, United States, 1997-present), two Moderate Resolution Imaging Spectroradiometers (MODIS, United States, Terra/2000-present and Aqua/2002-present), the Global Imager (GLI, Japan, 2002-2003), and the Medium Resolution Imaging Spectrometer (MERIS, European Space Agency, 2002-present). These missions have provided data of exceptional quality and continuity, allowing for scientific inquiries into a wide variety of marine research topics not possible with the CZCS. This review focuses on the scientific advances made over the past decade using these data sets.

Cross calibration of ocean-color bands from moderate resolution imaging spectroradiometer on Terra platform.

Ocean-color applications require maximum uncertainties in blue-wavelength water-leaving radiances in oligotrophic ocean of approximately 5%. Water-leaving radiances from Moderate Resolution Imaging Spectroradiometer (MODIS) on the Terra satellite, however, exhibit temporal drift of the order of 15% as well as sensor changes in response versus scan and polarization sensitivity, which cannot be tracked by onboard calibrators. This paper introduces an instrument characterization approach that uses Earth-view data as a calibration source. The approach models the top of the atmosphere signal over ocean that the instrument is expected to measure, including its polarization, with water-leaving radiances coming from another well-calibrated global sensor. The cross calibration allows for significant improvement in derived MODIS-Terra ocean-color products, with largest changes in the blue wavelengths.

SeaWiFS on-orbit gain and detector calibrations: effect on ocean products.

The NASA Ocean Biology Processing Group's Calibration and Validation Team has analyzed the mission-long Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) on-orbit gain and detector calibration time series to verify that lunar calibrations, obtained at nonstandard gains and radiance ranges, are valid for Earth data collected at standard gains and typical ocean, cloud, and land radiances. For gain calibrations, a constant voltage injected into the postdetector electronics allows gain ratios to be computed for all four detectors in each band. The on-orbit lunar gain ratio time series show small drifts for the near infrared bands. These drifts are propagated into the ocean color data through the atmospheric correction parameter epsilon, which uses the 765/865 nm band ratio. An anomaly analysis of global mean normalized water-leaving radiances at 510 nm shows a small decrease over the mission, while an analysis of epsilon shows a corresponding increase. The drifts in the lunar time series for the 765 and 865 nm bands were corrected. An analysis of the revised water-leaving radiances at 510 nm shows the drift has been eliminated, while an analysis of epsilon shows a reduced drift. For detector calibrations, solar diffuser observations made by the individual detectors in each band allows the response of the detectors to be monitored separately. The mission-long time series of detector calibration data show that the variations in the response of the individual detectors are less than 0.5% over the mission for all bands except the 865 nm band, where the variations are less than 1%.

Atmospheric correction for NO2 absorption in retrieving water-leaving reflectances from the SeaWiFS and MODIS measurements.

The absorption by atmospheric nitrogen dioxide (NO2) gas in the visible has been traditionally neglected in the retrieval of oceanic parameters from satellite measurements. Recent measurements of NO2 from spaceborne sensors show that over the Eastern United States the NO2 column amount often exceeds 1 Dobson Unit (approximately 2.69x10(16) molecules/cm2). Our radiative transfer sensitivity calculations show that under high NO2 conditions (approximately 1x10(16) molecules/cm2) the error in top-of-atmosphere (TOA) reflectance in the blue channels of the sea-viewing wide field-of-view sensor (SeaWiFS) and moderate-resolution imaging spectroradiometer (MODIS) sensors is approximately 1%. This translates into approximately 10% error in water-leaving radiance for clear waters and to higher values (>20%) in the coastal areas. We have developed an atmospheric-correction algorithm that allows an accurate retrieval of normalized water-leaving radiances (nLws) in the presence of NO2 in the atmosphere. The application of the algorithm to 52 MODIS scenes over the Chesapeake Bay area show a decrease in the frequency of negative nLw estimates in the 412 nm band and an increase in the value of nLws in the same band. For the particular scene reported in this paper, the mean value of nLws in the 412 nm band increased by 17%, which is significant, because for the MODIS sensor the error in nLws attributable to the digitization error in the observed TOA reflectance over case 2 waters is approximately 2.5%.

On-orbit vicarious calibration of ocean color sensors using an ocean surface reflectance model.

Recent advances in global biogeochemical research demonstrate a critical need for long-term ocean color satellite data records of consistent high quality. To achieve that quality, spaceborne instruments require on-orbit vicarious calibration, where the integrated instrument and atmospheric correction system is adjusted using in situ normalized water-leaving radiances, such as those collected by the marine optical buoy (MOBY). Unfortunately, well-characterized time-series of in situ data are scarce for many historical satellite missions, in particular, the NASA coastal zone color scanner (CZCS) and the ocean color and temperature scanner (OCTS). Ocean surface reflectance models (ORMs) accurately reproduce spectra observed in clear marine waters, using only chlorophyll a (C(a)) as input, a measurement for which long-term in situ time series exist. Before recalibrating CZCS and OCTS using modeled radiances, however, we evaluate the approach with the Sea-viewing Wide-Field-of-view Sensor (SeaWiFS). Using annual C(a) climatologies as input into an ORM, we derive SeaWiFS vicarious gains that differ from the operational MOBY gains by less than +/-0.9% spectrally. In the context of generating decadal C(a) climate data records, we quantify the downstream effects of using these modeled gains by generating satellite-to-in situ data product validation statistics for comparison with the operational SeaWiFS results. Finally, we apply these methods to the CZCS and OCTS ocean color time series.

Sensor-independent approach to the vicarious calibration of satellite ocean color radiometry.

The retrieval of ocean color radiometry from space-based sensors requires on-orbit vicarious calibration to achieve the level of accuracy desired for quantitative oceanographic applications. The approach developed by the NASA Ocean Biology Processing Group (OBPG) adjusts the integrated instrument and atmospheric correction system to retrieve normalized water-leaving radiances that are in agreement with ground truth measurements. The method is independent of the satellite sensor or the source of the ground truth data, but it is specific to the atmospheric correction algorithm. The OBPG vicarious calibration approach is described in detail, and results are presented for the operational calibration of SeaWiFS using data from the Marine Optical Buoy (MOBY) and observations of clear-water sites in the South Pacific and southern Indian Ocean. It is shown that the vicarious calibration allows SeaWiFS to reproduce the MOBY radiances and achieve good agreement with radiometric and chlorophyll a measurements from independent in situ sources. We also find that the derived vicarious gains show no significant temporal or geometric dependencies, and that the mission-average calibration reaches stability after approximately 20-40 high-quality calibration samples. Finally, we demonstrate that the performance of the vicariously calibrated retrieval system is relatively insensitive to the assumptions inherent in our approach.

SeaWiFS long-term solar diffuser reflectance and sensor noise analyses.

The NASA Ocean Biology Processing Group's Calibration and Validation (Cal/Val) team has undertaken an analysis of the mission-long Sea-Viewing Wide Field-of-View Sensor (SeaWiFS) solar calibration time series to assess the long-term degradation of the solar diffuser reflectance over 9 years on orbit. The SeaWiFS diffuser is an aluminum plate coated with YB71 paint. The bidirectional reflectance distribution function of the diffuser was not fully characterized before launch, so the Cal/Val team has implemented a regression of the solar incidence angles and the drift in the node of the satellite's orbit against the diffuser time series to correct for solar incidence angle effects. An exponential function with a time constant of 200 days yields the best fit to the diffuser time series. The decrease in diffuser reflectance over the mission is wavelength dependent, ranging from 9% in the blue (412 nm) to 5% in the red and near infrared (670-865 nm). The Cal/Val team has developed a methodology for computing the signal-to-noise ratio (SNR) for SeaWiFS on orbit from the diffuser time series corrected for both the varying solar incidence angles and the diffuser reflectance degradation. A sensor noise model is used to compare on-orbit SNRs computed for radiances reflected from the diffuser with prelaunch SNRs measured at typical radiances specified for the instrument. To within the uncertainties in the measurements, the SNRs for SeaWiFS have not changed over the mission. The on-orbit performance of the SeaWiFS solar diffuser should offer insight into the long-term on-orbit performance of solar diffusers on other instruments, such as the Moderate-Resolution Imaging Spectrometer [currently flying on the Earth Observing System (EOS) Terra and Aqua satellites], the Visible and Infrared Radiometer Suite [scheduled to fly on the NASA National Polar-orbiting Operational Environmental Satellite System (NPOESS) and NPOESS Preparatory Project (NPP) satellites] and the Advanced Baseline Imager [scheduled to fly on the National Oceanic and Atmospheric Administration Geostationary Environmental Operational Satellite Series R (GOES-R) satellites].

Climate-driven trends in contemporary ocean productivity.

Contributing roughly half of the biosphere's net primary production (NPP), photosynthesis by oceanic phytoplankton is a vital link in the cycling of carbon between living and inorganic stocks. Each day, more than a hundred million tons of carbon in the form of CO2 are fixed into organic material by these ubiquitous, microscopic plants of the upper ocean, and each day a similar amount of organic carbon is transferred into marine ecosystems by sinking and grazing. The distribution of phytoplankton biomass and NPP is defined by the availability of light and nutrients (nitrogen, phosphate, iron). These growth-limiting factors are in turn regulated by physical processes of ocean circulation, mixed-layer dynamics, upwelling, atmospheric dust deposition, and the solar cycle. Satellite measurements of ocean colour provide a means of quantifying ocean productivity on a global scale and linking its variability to environmental factors. Here we describe global ocean NPP changes detected from space over the past decade. The period is dominated by an initial increase in NPP of 1,930 teragrams of carbon a year (Tg C yr(-1)), followed by a prolonged decrease averaging 190 Tg C yr(-1). These trends are driven by changes occurring in the expansive stratified low-latitude oceans and are tightly coupled to coincident climate variability. This link between the physical environment and ocean biology functions through changes in upper-ocean temperature and stratification, which influence the availability of nutrients for phytoplankton growth. The observed reductions in ocean productivity during the recent post-1999 warming period provide insight on how future climate change can alter marine food webs.

Moderate-resolution imaging spectroradiometer ocean color polarization correction.

The polarization correction for the Moderate-Resolution Imaging Spectroradiometer (MODIS) instruments on the Terra and Aqua satellites is described. The focus is on the prelaunch polarization characterization and on the derivation of polarization correction coefficients for the processing of ocean color data. The effect of the polarization correction is demonstrated. The radiances at the top of the atmosphere need to be corrected by as much as 3.2% in the 412 nm band. The effect on the water-leaving radiances can exceed 50%. The polarization correction produces good agreement of the MODIS Aqua water-leaving radiance time series with data from another, independent satellite-based ocean color sensor, the Sea-Viewing Wide Field-of-View Sensor (SeaWiFS).