Abstract
The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases ...(https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.
The MODIS is a key instrument for NASA’s EOS program, currently operated onboard the Terra and Aqua spacecraft launched in 1999 and 2002, respectively. The VIIRS is a MODIS follow-on instrument for ...the JPSS program. Adding to the ones operated onboard the S-NPP and NOAA-20 satellites launched in 2011 and 2017, respectively, three nearly identical VIIRS instruments will also be launched. This will enable the data records from MODIS and VIIRS to be extended beyond 2040. In addition to various applications and scientific studies of the Earth’s system, long-term data records from MODIS and VIIRS observations will greatly benefit the space-based climate observing system. This is attributed to the high-quality measurements and extensive calibration efforts, from pre-launch to post-launch. This paper provides an overview of MODIS and VIIRS calibration history and approaches applied to establish and maintain sensor calibration traceability and accuracy. It illustrates calibration and performance issues through different phases of the mission using examples derived from ground testing equipment, on-board calibrators, and other calibration targets. Moreover, discussed in this paper are outstanding challenges and future efforts to maintain and improve sensor calibration stability and long-term data quality, and to better support the space-based climate observing system.
The biogeochemical and stoichiometric signature of vegetation fire may influence post‐fire ecosystem characteristics and the evolution of plant ‘fire traits’. Phosphorus (P), a potentially limiting ...nutrient in many fire‐prone environments, might be particularly important in this context; however, the effects of fire on P cycling often vary widely. We conducted a global‐scale meta‐analysis using data from 174 soil studies and 39 litter studies, and found that fire led to significantly higher concentrations of soil mineral P as well as significantly lower soil and litter carbon:P and nitrogen:P ratios. These results demonstrate that fire has a P‐rich signature in the soil–plant system that varies with vegetation type. Further, they suggest that burning can ease P limitation and decouple the biogeochemical cycling of P, carbon and nitrogen. These effects resemble a transient reversion to an earlier stage of ecosystem development, and likely underpin at least some of fire's impacts on ecosystems and organisms.
Emotional suppression has been associated with generally negative social consequences (
Butler et al., 2003
;
Gross & John, 2003
). A cultural perspective suggests, however, that these consequences ...may be moderated by cultural values. We tested this hypothesis in a two-part study, and found that, for Americans holding Western-European values, habitual suppression was associated with self-protective goals and negative emotion. In addition, experimentally elicited suppression resulted in reduced interpersonal responsiveness during face-to-face interaction, along with negative partner-perceptions and hostile behavior. These deleterious effects were reduced when individuals with more Asian values suppressed, and these reductions were mediated by cultural differences in the responsiveness of the suppressors. These findings suggest that many of suppression's negative social impacts may be moderated by cultural values.
Nuclear magnetic resonance (NMR) logging provides a new means of estimating the hydraulic conductivity (K) of unconsolidated aquifers. The estimation of K from the measured NMR parameters can be ...performed using the Schlumberger‐Doll Research (SDR) equation, which is based on the Kozeny–Carman equation and initially developed for obtaining permeability from NMR logging in petroleum reservoirs. The SDR equation includes empirically determined constants. Decades of research for petroleum applications have resulted in standard values for these constants that can provide accurate estimates of permeability in consolidated formations. The question we asked: Can standard values for the constants be defined for hydrogeologic applications that would yield accurate estimates of K in unconsolidated aquifers? Working at 10 locations at three field sites in Kansas and Washington, USA, we acquired NMR and K data using direct‐push methods over a 10‐ to 20‐m depth interval in the shallow subsurface. Analysis of pairs of NMR and K data revealed that we could dramatically improve K estimates by replacing the standard petroleum constants with new constants, optimal for estimating K in the unconsolidated materials at the field sites. Most significant was the finding that there was little change in the SDR constants between sites. This suggests that we can define a new set of constants that can be used to obtain high resolution, cost‐effective estimates of K from NMR logging in unconsolidated aquifers. This significant result has the potential to change dramatically the approach to determining K for hydrogeologic applications.
The Suomi National Polar-orbiting Partnership (S-NPP) Visible Infrared Imaging Radiometer Suite (VIIRS) has successfully operated for more than three years since its launch in October 2011. Fifteen ...of the 22 VIIRS spectral bands are in the reflective solar spectral region, covering wavelengths from 0.41 to 2.3 μm. Similar to its heritage sensor, i.e., Moderate Resolution Imaging Spectroradiometer (MODIS) on NASA Terra and Aqua spacecraft, the measurements of these spectral bands are routinely calibrated on orbit by a solar diffuser (SD) and an SD stability monitor (SDSM) system. In addition, lunar observations are regularly scheduled and implemented, allowing the reflective solar band (RSB) calibration stability to be independently monitored. This paper provides an overview of VIIRS RSB on-orbit calibration activities and methodologies, with a focus on the approaches and strategies developed for the lunar calibration. Results derived from VIIRS lunar observations are used to assess its RSB on-orbit performance and to compare with that derived from the SD measurements. Also discussed in this paper are issues identified since launch through comparisons of VIIRS SD and lunar calibration, remaining challenges, and future improvements. Specifically, potential impacts due to degradation caused by the telescope mirror coating contamination on both SD and lunar calibration are assessed. As demonstrated in this paper, VIIRS lunar calibration activities have been successfully planned and executed, in support of its RSB on-orbit calibration. Overall, the long-term response trending derived from lunar calibrations has been consistent with that derived from SD observations. In addition to small features in SD measurements, noticeable seasonal variations, on the order of 1%, between the lunar measurements and the model have been identified. These variations are likely due to the effect of different lunar viewing angles on the lunar irradiance reference model. Future improvements to the sensor's lunar response trending could be achieved with an improved lunar irradiance model.
Respiratory sinus arrhythmia (RSA) figures prominently in emotional responding, but its exact role remains unclear. The present study tests two hypotheses: (1) Between‐person differences in resting ...RSA are related to emotional reactivity, and (2) within‐person changes in RSA are related to regulatory efforts. Pairs of women watched an upsetting film and discussed it. One woman in each of the experimental dyads was asked to either suppress or to reappraise during the conversation. Their partners and both members of the control dyads conversed naturally. Between‐person differences in resting RSA were assessed with paced breathing, and within‐person changes in RSA were calculated from baseline to the conversation accounting for respiration. Women with higher resting RSA experienced and expressed more negative emotion, and women who attempted to regulate their emotions either by suppressing or reappraising showed larger increases in RSA than controls.
Nuclear magnetic resonance (NMR) logging is a promising method for estimating hydraulic conductivity (K). During the past ∼60 years, NMR logging has been used for petroleum applications, and ...different models have been developed for deriving estimates of permeability. These models involve calibration parameters whose values were determined through decades of research on sandstones and carbonates. We assessed the use of five models to derive estimates of K in glacial aquifers from NMR logging data acquired in two wells at each of two field sites in central Wisconsin, USA. Measurements of K, obtained with a direct push permeameter (DPP), K
, were used to obtain the calibration parameters in the Schlumberger-Doll Research, Seevers, Timur-Coates, Kozeny-Godefroy, and sum-of-echoes (SOE) models so as to predict K from the NMR data; and were also used to assess the ability of the models to predict K
. We obtained four well-scale calibration parameter values for each model using the NMR and DPP measurements in each well; and one study-scale parameter value for each model by using all data. The SOE model achieved an agreement with K
that matched or exceeded that of the other models. The Timur-Coates estimates of K were found to be substantially different from K
. Although the well-scale parameter values for the Schlumberger-Doll, Seevers, and SOE models were found to vary by less than a factor of 2, more research is needed to confirm their general applicability so that site-specific calibration is not required to obtain accurate estimates of K from NMR logging data.
Groundwater consumption by phreatophytes is a difficult-to-measure but important component of the water budget in many arid and semiarid environments. Over the past 70 years the consumptive use of ...groundwater by phreatophytes has been estimated using a method that analyzes diurnal trends in hydrographs from wells that are screened across the water table (White, 1932). The reliability of estimates obtained with this approach has never been rigorously evaluated using saturated-unsaturated flow simulation. We present such an evaluation for common flow geometries and a range of hydraulic properties. Results indicate that the major source of error in the White method is the uncertainty in the estimate of specific yield. Evapotranspirative consumption of groundwater will often be significantly overpredicted with the White method if the effects of drainage time and the depth to the water table on specific yield are ignored. We utilize the concept of readily available specific yield as the basis for estimation of the specific yield value appropriate for use with the White method. Guidelines are defined for estimating readily available specific yield based on sediment texture. Use of these guidelines with the White method should enable the evapotranspirative consumption of groundwater to be more accurately quantified.
A small‐diameter nuclear magnetic resonance (NMR) logging tool has been developed and field tested at various sites in the United States and Australia. A novel design approach has produced relatively ...inexpensive, small‐diameter probes that can be run in open or PVC‐cased boreholes as small as 2 inches in diameter. The complete system, including surface electronics and various downhole probes, has been successfully tested in small‐diameter monitoring wells in a range of hydrogeological settings. A variant of the probe that can be deployed by a direct‐push machine has also been developed and tested in the field. The new NMR logging tool provides reliable, direct, and high‐resolution information that is of importance for groundwater studies. Specifically, the technology provides direct measurement of total water content (total porosity in the saturated zone or moisture content in the unsaturated zone), and estimates of relative pore‐size distribution (bound vs. mobile water content) and hydraulic conductivity. The NMR measurements show good agreement with ancillary data from lithologic logs, geophysical logs, and hydrogeologic measurements, and provide valuable information for groundwater investigations.
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