Regional and seasonal patterns of epipelagic fish assemblages from the central California Current

The coastal Pacific Ocean off northern and central California encompasses the strongest seasonal upwelling zone in the California Current ecosystem. Headlands and bays here generate complex circulation features and confer unusual oceanographic complexity. We sampled the coastal epipelagic fish community of this region with a surface trawl in the summer and fall of 2000–05 to assess patterns of spatial and temporal community structure. Fifty-three species of fish were captured in 218 hauls at 34 fixed stations, with clupeiform species dominating. To examine spatial patterns, samples were grouped by location relative to a prominent headland at Point Reyes and the resulting two regions, north coast and Gulf of the Farallones, were plotted by using nonmetric multidimensional scaling. Seasonal and interannual patterns were also examined, and representative species were identified for each distinct community. Seven oceanographic variables measured concurrently with trawling were plotted by principal components analysis and tested for correlation with biotic patterns. We found significant differences in community structure by region, year, and season, but no interaction among main effects. Significant differences in oceanographic conditions mirrored the biotic patterns, and a match between biotic and hydrographic structure was detected. Dissimilarity between assemblages was mostly the result of differences in abundance and frequency of occurrence of about twelve common species. Community patterns were best described by a subset of hydrographic variables, including water depth, distance from shore, and any one of several correlated variables associated with upwelling intensity. Rather than discrete communities with clear borders and distinct member species, we found gradients in community structure and identified stations with similar fish communities by region and by proximity to features such as the San Francisco Bay

Structure-Guided Recombination Creates an Artificial Family of Cytochromes P450

Creating artificial protein families affords new opportunities to explore the determinants of structure and biological function free from many of the constraints of natural selection. We have created an artificial family comprising ~3,000 P450 heme proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven crossover locations chosen to minimize structural disruption. Members of this protein family differ from any known sequence at an average of 72 and by as many as 109 amino acids. Most (>73%) of the properly folded chimeric P450 heme proteins are catalytically active peroxygenases; some are more thermostable than the parent proteins. A multiple sequence alignment of 955 chimeras, including both folded and not, is a valuable resource for sequence-structure-function studies. Logistic regression analysis of the multiple sequence alignment identifies key structural contributions to cytochrome P450 heme incorporation and peroxygenase activity and suggests possible structural differences between parents CYP102A1 and CYP102A2

Design and Use of a Systematic Site Visit Protocol: Implications for Novice Evaluators and Mentors

Site visits are frequently used by evaluators to gain first-hand experience and knowledge about program implementation. However, few peer-reviewed articles describe the procedures used for designing and conducting site visits. This article describes the process of constructing and using a systematic site visit protocol. Theories and concepts of evaluation, including the measurement of fidelity and quality and the importance of context to site-level implementation, guided the construction of this protocol. Using a systematic method for program inquiry can improve the consistency of qualitative observations of program activities by enhancing intentionality, transparency, and emergence within the site visit process. The method presented may be especially helpful to novice evaluators and their mentors in learning about and teaching the process of conducting site visits

Climate Change Sensitivity Assessment on Upper Mississippi River Basin Streamflows Using SWAT

The Soil and Water Assessment Tool (SWAT) model was used to assess the impacts of potential future climate change on the hydrology of the Upper Mississippi River Basin (UMRB). Calibration and validation of SWAT were performed on a monthly basis for 1968-87 and 1988-97, respectively; R2 and Nash-Sutcliffe simulation efficiency (E) values computed for the monthly comparisons were 0.74 and 0.65 for the calibration period and 0.81 and 0.75 for the validation period. The impacts of eight 20-year (1971- 90) scenarios were then analyzed, relative to a scenario baseline. A doubling of atmospheric CO2 concentrations was predicted to result in an average annual flow increase of 35 percent. An average annual flow decrease of 15 percent was estimated for a constant temperature increase of 4°C. Essentially linear impacts were predicted among precipitation change scenarios of -20, -10, 10, and 20 percent, which resulted in average annual flow changes at Grafton, Illinois, of -51, -27, 28, and 58 percent, respectively. The final two scenarios accounted for variable monthly temperature and precipitation changes obtained from a previous climate projection with and without the effects of CO2 doubling. The resultant average annual flows were predicted to increase by 15 and 52 percent in response to these climatic changes. Overall, the results indicate that the UMRB hydrology is very sensitive to potential future climate changes and that these changes could stimulate increased periods of flooding or drought

SnapShot: Cortical Development

Stem Cell and Regenerative Biolog

Advancement of a Soil Parameters Geodatabase for the Modeling Assessment of Conservation Practice Outcomes in the United States

US-ModSoilParms-TEMPLE is a database composed of a set of geographic databases functionally storing soil-spatial units and soil hydraulic, physical, and chemical parameters for three agriculture management simulation models, SWAT, APEX, and ALMANAC. This paper introduces the updated US-ModSoilParms-TEMPLE, which covers the entire United States and is organized as a framework of 22 nested and hydrologically-ordered regional geographic databases with internal spatial segmentation drainage-defined at a conveniently manageable tile (Watershed Boundary Dataset’s, WBD, 8-digit Subbasin) level. Spatial features are stored in multiple formats (raster and vector) and resolutions (10-meter and 30-meter), while being in direct relationship with the table of attributes storing the models’ parameters. A significant number of former parameter voids, determined by the local incompleteness of the source datasets, were filled using a methodology leveraging upon the hierarchy of the Soil Taxonomy information and the geographic location of the gaps. The functionality of each geographic database was extended by adding customized tools, which streamline the incorporation into geoprocessing workflows, the aggregation and extraction of data sets, and finally the export to other model support software user environments. These tools are attached and conveniently distributed along with detailed metadata documentation within each of the developed regional geographic databases. The system hosting this framework is developed using a proprietary software format (ESRI® File Geodatabase), however, a companion version of the framework of 8-digit tiles is also developed and provided using openly accessible formats. The experience shared in this paper might help other efforts in developing hydrology-oriented geographical databases

A Soil Parameters Geodatabase for the Modeling Assessment of Agricultural Conservation Practices Effects in the United States

Soil parameters for hydrology modeling in cropland dominated areas, from the regional to local scale, are part of critical biophysical information whose deficiency may increase the uncertainty of simulated conservation effects and predicting potential. Despite this importance, soil physical and hydraulic parameters lack common, wide-coverage repositories combined to digital maps as required by various hydrology-based agricultural water quality models. This paper describes the construction of a geoprocessing workflow and the resultant hydrology-structured soil hydraulic, physical, and chemical parameters geographic database for the entire United States, named US-SOILM-CEAP. This database is designed to store a-priori values for a suit of models, such as SWAT (Soil and Water Assessment Tool), APEX (Agricultural Policy Environmental EXtender) and ALMANAC (Agricultural Land Management Alternatives with Numerical Assessment Criteria), which are commonly used for the across scale assessment of agricultural hydrology and conservation practice scenarios. The Soil Survey Geographic (SSURGO) database developed by the U.S. Department of Agriculture provided the main source data for this development. Additional spatial information, a geographic information system platform and Python computer programming language code were used to create hydrology-based tile coverage of the areal soil units linked to the specific and detailed attributes required by each model. The created repository adds value to the source soil survey data, while maintaining and extending the detailed information necessary for the across scale and combined application of the models. Ultimately, our multi-model database provides a comprehensive product achieving joined informational-mapping-geoprocessing functionality with the explicit maintenance of the original conceptual links between soil series and composing soil layers, allowing for efficient data retrieval, analysis and service as input for modeling conservation effects

Antibody-Based Ticagrelor Reversal Agent in Healthy Volunteers.

BACKGROUND: Ticagrelor is an oral P2Y12 inhibitor that is used with aspirin to reduce the risk of ischemic events among patients with acute coronary syndromes or previous myocardial infarction. Spontaneous major bleeding and bleeding associated with urgent invasive procedures are concerns with ticagrelor, as with other antiplatelet drugs. The antiplatelet effects of ticagrelor cannot be reversed with platelet transfusion. A rapid-acting reversal agent would be useful. METHODS: In this randomized, double-blind, placebo-controlled, phase 1 trial, we evaluated intravenous PB2452, a monoclonal antibody fragment that binds ticagrelor with high affinity, as a ticagrelor reversal agent. We assessed platelet function in healthy volunteers before and after 48 hours of ticagrelor pretreatment and again after the administration of PB2452 or placebo. Platelet function was assessed with the use of light transmission aggregometry, a point-of-care P2Y12 platelet-reactivity test, and a vasodilator-stimulated phosphoprotein assay. RESULTS: Of the 64 volunteers who underwent randomization, 48 were assigned to receive PB2452 and 16 to receive placebo. After 48 hours of ticagrelor pretreatment, platelet aggregation was suppressed by approximately 80%. PB2452 administered as an initial intravenous bolus followed by a prolonged infusion (8, 12, or 16 hours) was associated with a significantly greater increase in platelet function than placebo, as measured by multiple assays. Ticagrelor reversal occurred within 5 minutes after the initiation of PB2452 and was sustained for more than 20 hours (P\u3c0.001 after Bonferroni adjustment across all time points for all assays). There was no evidence of a rebound in platelet activity after drug cessation. Adverse events related to the trial drug were limited mainly to issues involving the infusion site. CONCLUSIONS: In healthy volunteers, the administration of PB2452, a specific reversal agent for ticagrelor, provided immediate and sustained reversal of the antiplatelet effects of ticagrelor, as measured by multiple assays. (Funded by PhaseBio Pharmaceuticals; ClinicalTrials.gov number, NCT03492385.)

Climate Change Sensitivity Assessment on Upper Mississippi River Basin Streamflows using SWAT

The Soil and Water Assessment Tool (SWAT) model was used to assess the effects of potential future climate change on the hydrology of the Upper Mississippi River Basin (UMRB). Calibration and validation of SWAT were performed using monthly stream flows for 1968–1987 and 1988–1997, respectively. The R2 and Nash-Sutcliffe simulation efficiency values computed for the monthly comparisons were 0.74 and 0.69 for the calibration period and 0.82 and 0.81 for the validation period. The effects of nine 30-year (1968 to 1997) sensitivity runs and six climate change scenarios were then analyzed, relative to a scenario baseline. A doubling of atmospheric CO2 to 660 ppmv (while holding other climate variables constant) resulted in a 36 percent increase in average annual streamflow while average annual flow changes of −49, −26, 28, and 58 percent were predicted for precipitation change scenarios of −20, −10, 10, and 20 percent, respectively. Mean annual streamflow changes of 51,10, 2, −6, 38, and 27 percent were predicted by SWAT in response to climate change projections generated from the CISRO-RegCM2, CCC, CCSR, CISRO-Mk2, GFDL, and HadCMS general circulation model scenarios. High seasonal variability was also predicted within individual climate change scenarios and large variability was indicated between scenarios within specific months. Overall, the climate change scenarios reveal a large degree of uncertainty in current climate change forecasts for the region. The results also indicate that the simulated UMRB hydrology is very sensitive to current forecasted future climate changes