Virginia\u27s Pfiesteria Monitoring Program: Water Quality

During the summer and early fall of 1998, 34 estuarine stations in Virginia were sampled for Pfiesteria like organisms (PLOs) and associated water quality conditions. Stations were sampled either bimonthly (20 stations) or monthly (14 stations) from June to October 1998. At each station, a set of live and Lugol\u27 s preserved samples were collected for presumptive counts of PLOs and water quality conditions were determined. Water quality parame­ters measured included standard field parameters, nutrients (total, dissolved, and particulate), chlorophyll a, and conventional water quality indicators. Although PLOs were relatively low in 1998 as compared to 1997, presump­tive PLO counts revealed higher PLO levels at stations located in the Northern Neck area (Potomac Embayments, Rappallannock River, and other smaller watersheds). The water quality parameters of pH, dissolved oxygen, and temperature were correlated with higher PLO counts, while several nutrients, salinity, and turbidity ,vere negatively correlated with PLOs. In the August 1997, relatively minor fish kills in the Pocomoke River and the Pocomoke Sound on the Virginia and Maryland border were attnbuted to the toxic dinoflagellate, Pfiesteria piscicida. Pfiesteria piscicida was first identified as a fish-killing dinoflagellate in fish tank at North Carolina State University (Noga et al., 1993 ). Pfiesteria piscicda has since been implicated in large widespread fish kills in North Carolina\u27s estuaries (Burkholder et al., 1992, 1995)

Penetration and effectiveness of micronized copper in refractory wood species

The North American wood decking market mostly relies on easily treatable Southern yellow pine (SYP), which is being impregnated with micronized copper (MC) wood preservatives since 2006. These formulations are composed of copper (Cu) carbonate particles (CuCO3 center dot Cu(OH)(2)), with sizes ranging from 1 nm to 250 mu m, according to manufacturers. MC-treated SYP wood is protected against decay by solubilized Cu2+ ions and unreacted CuCO3 center dot Cu(OH)(2) particles that successively release Cu2+ ions (reservoir effect). The wood species used for the European wood decking market differ from the North American SYP. One of the most common species is Norway spruce wood, which is poorly treatable i.e. refractory due to the anatomical properties, like pore size and structure, and chemical composition, like pit membrane components or presence of wood extractives. Therefore, MC formulations may not suitable for refractory wood species common in the European market, despite their good performance in SYP. We evaluated the penetration effectiveness of MC azole (MCA) in easily treatable Scots pine and in refractory Norway spruce wood. We assessed the effectiveness against the Cu-tolerant wood-destroying fungus Rhodonia placenta. Our findings show that MCA cannot easily penetrate refractory wood species and could not confirm the presence of a reservoir effect

Adaptive optics and phase diversity imaging for responsive space applications.

The combination of phase diversity and adaptive optics offers great flexibility. Phase diverse images can be used to diagnose aberrations and then provide feedback control to the optics to correct the aberrations. Alternatively, phase diversity can be used to partially compensate for aberrations during post-detection image processing. The adaptive optic can produce simple defocus or more complex types of phase diversity. This report presents an analysis, based on numerical simulations, of the efficiency of different modes of phase diversity with respect to compensating for specific aberrations during post-processing. It also comments on the efficiency of post-processing versus direct aberration correction. The construction of a bench top optical system that uses a membrane mirror as an active optic is described. The results of characterization tests performed on the bench top optical system are presented. The work described in this report was conducted to explore the use of adaptive optics and phase diversity imaging for responsive space applications

Ocean Winds and Turbulent Air-Sea Fluxes Inferred From Remote Sensing

Air-sea turbulent fluxes determine the exchange of momentum, heat, freshwater, and gas between the atmosphere and ocean. These exchange processes are critical to a broad range of research questions spanning length scales from meters to thousands of kilometers and time scales from hours to decades. Examples are discussed (section 2). The estimation of surface turbulent fluxes from satellite is challenging and fraught with considerable errors (section 3); however, recent developments in retrievals (section 3) will greatly reduce these errors. Goals for the future observing system are summarized in section 4. Surface fluxes are defined as the rate per unit area at which something (e.g., momentum, energy, moisture, or CO Z ) is transferred across the air/sea interface. Wind- and buoyancy-driven surface fluxes are called surface turbulent fluxes because the mixing and transport are due to turbulence. Examples of nonturbulent processes are radiative fluxes (e.g., solar radiation) and precipitation (Schmitt et al., 2010). Turbulent fluxes are strongly dependent on wind speed; therefore, observations of wind speed are critical for the calculation of all turbulent surface fluxes. Wind stress, the vertical transport of horizontal momentum, also depends on wind direction. Stress is very important for many ocean processes, including upper ocean currents (Dohan and Maximenko, 2010) and deep ocean currents (Lee et al., 2010). On short time scales, this horizontal transport is usually small compared to surface fluxes. For long-term processes, transport can be very important but again is usually small compared to surface fluxes

Bandage: interactive visualization of de novo genome assemblies.

UNLABELLED: Although de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Rapid detection of 2-hydroxyglutarate in frozen sections of IDH mutant tumors by MALDI-TOF mass spectrometry

All isocitrate dehydrogenase (IDH) mutant solid neoplasms exhibit highly elevated levels of D-2-hydroxyglutarate (D-2HG). Detection of 2HG in tumor tissues currently is performed by gas or liquid chromatography-mass spectrometry (GC- or LC-MS) or biochemical detection. While these methods are highly accurate, a considerable amount of time for tissue preparation and a relatively high amount of tissue is required for testing. We here present a rapid approach to detect 2HG in brain tumor tissue based on matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI-TOF). We analyzed 26 brain tumor samples with known IDH1 or IDH2 mutation and compared readouts to those from 28 brain tumor samples of wildtype IDH status. IDH mutant samples exhibited a clear positive signal for 2HG which was not observed in any of the IDH wildtype tumors. Our analytical pipeline allowed for 2HG detection in less than 5 min. Data were validated by determining 2HG levels in all tissues with a biochemical assay. In conclusion, we developed a protocol for rapid detection of 2HG levels and illustrate the possibility to use MALDI-TOF for the detection of metabolites on frozen tissue sections in a diagnostic setting

Well-differentiated Papillary Mesothelioma With Invasive Foci

Well-differentiated papillary mesotheliomas (WDPMs) are usually encountered as incidental findings in the peritoneal cavity in women. Most WDPMs are benign, and the histologic features that indicate a more aggressive course are controversial. We report 20 cases of WDPM, which contained invasive foci. Thirteen cases arose in the peritoneal cavity, 1 in a hernia sac, 3 in the pleural cavity, and 3 in hydroceles. The female:male ratio was 16:4, and age range was 7 to 74 years. Tumor was multifocal in 15 cases. Some tumors showed back-to-back papillae, a pattern mimicking invasion but discernible on pan-keratin stain as compressive crowding. True invasive patterns ranged from simple bland-appearing glands invading the stalks of the papillae to solid foci of invasive tumor of higher cytologic grade than the original WDPM. All 5 tested cases were negative for p16 deletion by fluorescence in situ hybridization, but 2/3 had abnormal karyotypes. Recurrences were seen in 8 patients, and in 4 multiple recurrences were documented. Of 16 patients with follow-up, 14 are alive from periods of 6 months to 6 years (average 3.5 y), and 2 have known recurrent disease. One patient died of disseminated tumor at 8 years but without histologic confirmation of the nature of the tumor. We conclude that WDPM with invasive foci in the papillae appear to be prone to multifocality and recurrence, but that they rarely give rise to life-threatening disease. We suggest that these lesions be called WDPM with invasive foci to alert clinicians to the possibility of recurrence

First application of dynamic oxygen-17 magnetic resonance imaging at 7 Tesla in a patient with early subacute stroke.

Dynamic oxygen-17 (17O) magnetic resonance imaging (MRI) is an imaging method that enables a direct and non-invasive assessment of cerebral oxygen metabolism and thus potentially the distinction between viable and non-viable tissue employing a three-phase inhalation experiment. The purpose of this investigation was the first application of dynamic 17O MRI at 7 Tesla (T) in a patient with stroke. In this proof-of-concept experiment, dynamic 17O MRI was applied during 17O inhalation in a patient with early subacute stroke. The analysis of the relative 17O water (H217O) signal for the affected stroke region compared to the healthy contralateral side revealed no significant difference. However, the technical feasibility of 17O MRI has been demonstrated paving the way for future investigations in neurovascular diseases

Science in the Supply Chain: Collaboration Opportunities for Advancing Sustainable Agriculture in the United States

Consumers and corporations are increasingly interested in understanding the sustainability of agricultural supply chains and reducing the environmental impacts of food, fiber, feed, and fuel production. This emerging need to quantify environmental impacts from agricultural production creates an opportunity for collaboration with the scientific community. Without such collaboration, sustainability efforts risk failure by adopting unrealistic goals or misguided approaches. This commentary explores the role of science in Field to Market, a nonprofit organization developing a sustainability program for US commodity crops, and highlights opportunities to address emerging science challenges. We evaluate changes over the past 35 years in key environmental impacts of crop production used to inform land managers as well as companies that are committed to improvements. Achieving improvements will only be possible if three key gaps are addressed regarding available simulation models and data, scale of implementation and uncertainty, and effectiveness of conservation practices. Filling these gaps presents an opportunity for dialogue between scientists, farmers, and private-sector stakeholders to advance scientific knowledge and promote the common objective of sustainable agriculture