Dissolved organic carbon thresholds affect mercury bioaccumulation in Arctic lakes.

Dissolved organic carbon (DOC) is known to affect the Hg cycle in aquatic environments due to its overriding influence on complexation, photochemical, and microbial processes, but its role as a mediating factor in the bioaccumulation of Hg in aquatic biota has remained enigmatic. Here, we examined 26 tundra lakes in Canada's western Arctic that span a large gradient of DOC concentrations to show that total Hg (HgT) and methyl mercury (MeHg) accumulation by aquatic invertebrates is defined by a threshold response to Hg-DOC binding. Our results showed that DOC promotes HgT and MeHg bioaccumulation in tundra lakes having low DOC (<8.6 - 8.8 mg C L(-1); DOC threshold concentration, TC) whereas DOC inhibits HgT and MeHg bioaccumulation in lakes having high DOC (>DOC TC), consistent with bioaccumulation results in a companion paper (this issue) using a microbial bioreporter. Chemical equilibrium modeling showed that Hg bioaccumulation factors were elevated when Hg was associated mainly to fulvic acids, but became dramatically reduced when DOC was >8.5 mg C L(-1), at which point Hg was associated primarily with strong binding sites on larger, less bioaccessible humic acids. This study demonstrates that the biological uptake of Hg in lakes is determined by binding thresholds on DOC, a water quality variable predicted to change markedly with future environmental change.

Genome Sequence of the Oleaginous Yeast Rhodotorula glutinis ATCC 204091.

Rhodotorula glutinis ATCC 204091 is an oleaginous oxidative red yeast that can accumulate lipids to >50% of its biomass when grown with appropriate carbon and nitrogen ratios. It produces a red pigment consisting of useful antioxidants, such as carotenoids, torulene, and torularhodin, when cultivated under carbon-deficient conditions.

DEWEY: the DICOM-enabled workflow engine system.

Workflow is a widely used term to describe the sequence of steps to accomplish a task. The use of workflow technology in medicine and medical imaging in particular is limited. In this article, we describe the application of a workflow engine to improve workflow in a radiology department. We implemented a DICOM-enabled workflow engine system in our department. We designed it in a way to allow for scalability, reliability, and flexibility. We implemented several workflows, including one that replaced an existing manual workflow and measured the number of examinations prepared in time without and with the workflow system. The system significantly increased the number of examinations prepared in time for clinical review compared to human effort. It also met the design goals defined at its outset. Workflow engines appear to have value as ways to efficiently assure that complex workflows are completed in a timely fashion.

Biocrude production by activated sludge microbial cultures using pulp and paper wastewaters as fermentation substrate.

Municipal wastewater activated sludge contains a mixed microbial community, which can be manipulated to produce biocrude, a lipid feedstock for biodiesel production. In this study, the potential of biocrude production by activated sludge microorganisms grown in three different types of pulp and paper mill wastewaters was investigated. A 20% (v/v) activated sludge was inoculated into pulp and paper wastewater, supplemented with glucose (60 g/L) and nutrients (nitrogen and phosphorus) to obtain a high carbon to nitrogen ratio (70:1). The culture was incubated aerobically for seven days. The results showed that the activated sludge microorganisms were able to grow and accumulate lipids when cultivated in amended wastewaters. Microorganisms growing in anaerobic settling pond effluent water showed the highest lipid accumulation of up to 40.6% cell dry weight (CDW) after five days of cultivation compared with pulp wash wastewater (PuWW) (11.7% CDW) and mixed wastewater (MWW) (8.2% CDW) after seven days of cultivation. The lipids mostly contained C16-C18 fatty acids groups with oleic acid and palmitic acid being the dominant fatty acids. The maximum biodiesel yield was about 6-8% CDW for all the wastewaters. The results showed the potential of utilizing pulp and paper mill effluents and other waste streams, such as activated sludge for the sustainable production of lipids for biofuel production.

Electronic cameras for low-light microscopy.

This chapter introduces to electronic cameras, discusses the various parameters considered for evaluating their performance, and describes some of the key features of different camera formats. The chapter also presents the basic understanding of functioning of the electronic cameras and how these properties can be exploited to optimize image quality under low-light conditions. Although there are many types of cameras available for microscopy, the most reliable type is the charge-coupled device (CCD) camera, which remains preferred for high-performance systems. If time resolution and frame rate are of no concern, slow-scan CCDs certainly offer the best available performance, both in terms of the signal-to-noise ratio and their spatial resolution. Slow-scan cameras are thus the first choice for experiments using fixed specimens such as measurements using immune fluorescence and fluorescence in situ hybridization. However, if video rate imaging is required, one need not evaluate slow-scan CCD cameras. A very basic video CCD may suffice if samples are heavily labeled or are not perturbed by high intensity illumination. When video rate imaging is required for very dim specimens, the electron multiplying CCD camera is probably the most appropriate at this technological stage. Intensified CCDs provide a unique tool for applications in which high-speed gating is required. The variable integration time video cameras are very attractive options if one needs to acquire images at video rate acquisition, as well as with longer integration times for less bright samples. This flexibility can facilitate many diverse applications with highly varied light levels.

Using an open-source PACS virtual machine for a digital angiography unit: methods and initial impressions.

The productivity gains, diagnostic benefit, and enhanced data availability to clinicians enabled by picture archiving and communication systems (PACS) are no longer in doubt. However, commercial PACS offerings are often extremely expensive initially and require ongoing support contracts with vendors to maintain them. Recently, several open-source offerings have become available that put PACS within reach of more users. However, they can be resource-intensive to install and assure that they have room for future growth--both for computational and storage capacity. An alternate approach, which we describe herein, is to use PACS built on virtual machines which can be moved from smaller to larger hardware as needed in a just-in-time manner. This leverages the cost benefits of Moore's Law for both storage and compute costs. We describe the approach and current results in this paper.

PACS bypass: a semi-automated routing solution to enable filmless operations when PACS fails.

In the filmless imaging department, an integrated imaging and reporting system is only as strong as its weakest link. An outage or downtime of a key segment, such as the Picture Archive Communications System (PACS), is a significant threat to efficient workflow, quality of image interpretation, ordering clinician's review, and ultimately patient care. A multidisciplinary team (including physicists, technologists, radiologists, operations, and IT) developed a backup system to provide business continuity (i.e., quality control, interpretation, reporting, and clinician access) during an extended outage of the main departmental PACS.

Proteome and membrane fatty acid analyses on Oligotropha carboxidovorans OM5 grown under chemolithoautotrophic and heterotrophic conditions.

Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H(2) to derive energy for fixation of CO(2). Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H(2) generated by organic waste gasification. O. carboxidovorans is capable also of heterotrophic growth in standard bacteriologic media. Here we characterize how the O. carboxidovorans proteome adapts to different lifestyles of chemolithoautotrophy and heterotrophy. Fatty acid methyl ester (FAME) analysis of O. carboxidovorans grown with acetate or with syngas showed that the bacterium changes membrane fatty acid composition. Quantitative shotgun proteomic analysis of O. carboxidovorans grown in the presence of acetate and syngas showed production of proteins encoded on the megaplasmid for assimilating CO and H(2) as well as proteins encoded on the chromosome that might have contributed to fatty acid and acetate metabolism. We found that adaptation to chemolithoautotrophic growth involved adaptations in cell envelope, oxidative homeostasis, and metabolic pathways such as glyoxylate shunt and amino acid/cofactor biosynthetic enzymes.

Virtual machine performance benchmarking.

The attractions of virtual computing are many: reduced costs, reduced resources and simplified maintenance. Any one of these would be compelling for a medical imaging professional attempting to support a complex practice on limited resources in an era of ever tightened reimbursement. In particular, the ability to run multiple operating systems optimized for different tasks (computational image processing on Linux versus office tasks on Microsoft operating systems) on a single physical machine is compelling. However, there are also potential drawbacks. High performance requirements need to be carefully considered if they are to be executed in an environment where the running software has to execute through multiple layers of device drivers before reaching the real disk or network interface. Our lab has attempted to gain insight into the impact of virtualization on performance by benchmarking the following metrics on both physical and virtual platforms: local memory and disk bandwidth, network bandwidth, and integer and floating point performance. The virtual performance metrics are compared to baseline performance on "bare metal." The results are complex, and indeed somewhat surprising.

Tracking PACS usage with open source tools.

A typical choice faced by Picture Archiving and Communication System (PACS) administrators is deciding how many PACS workstations are needed and where they should be sited. Oftentimes, the social consequences of having too few are severe enough to encourage oversupply and underutilization. This is costly, at best in terms of hardware and electricity, and at worst (depending on the PACS licensing and support model) in capital costs and maintenance fees. The PACS administrator needs tools to asses accurately the use to which her fleet is being subjected, and thus make informed choices before buying more workstations. Lacking a vended solution for this challenge, we developed our own.

TCP/IP optimization over wide area networks: implications for teleradiology.

Radiology examinations are large. The advent of fast volume imaging is making that statement truer every year. PACS are based on the assumption of fast local networking and just-in-time image pull to the desktop. On the other hand, teleradiology has been developed on a push model to accommodate the challenges of moderate bandwidth, high-latency wide area networks (WANs). Our group faced the challenging task of creating a PACS environment that felt local, while pulling images across a 3,000-mile roundtrip WAN link. Initial tests showed WAN performance lagging local area network (LAN) performance by a factor of 30 times. A 16-month journey of explorations pulled the WAN value down to only 1.5 times slower than the LAN.

DCMTB: a virtual appliance DICOM toolbox.

Medical Imaging has been fortunate to see an avalanche of free and open source software become available in the last several years. Applications have been written to enable image viewing/storage/analysis/processing, DICOM and HL7 message parsing, results aggregation, anonymization, and more. While robust, many of these packages are difficult to install and configure. Our group desired an approach that would mitigate the efforts required to use these packages across different projects. We found such a solution in the context of using virtual machines.

Biodiesel production by in situ transesterification of municipal primary and secondary sludges.

The potential of using municipal wastewater sludges as a lipid feedstock for biodiesel production was investigated. Primary and secondary sludge samples obtained from a municipal wastewater treatment plant in Tuscaloosa, AL were freeze-dried and subjected to an acid-catalyzed insitu transesterification process. Experiments were conducted to determine the effects of temperature, sulfuric acid concentration, and mass ratio of methanol to sludge on the yield of fatty acid methyl esters (FAMEs). Results indicated a significant interactive effect between temperature, acid concentration, and methanol to sludge mass ratio on the FAME yield for the insitu transesterification of primary sludge, while the FAME yield for secondary sludge was significantly affected by the independent effects of the three factors investigated. The maximum FAME yields were obtained at 75 degrees C, 5% (v/v) H(2)SO(4), and 12:1 methanol to sludge mass ratio and were 14.5% and 2.5% for primary and secondary sludge, respectively. Gas chromatography (GC) analysis of the FAMEs revealed a similar fatty acid composition for both primary and secondary sludge. An economic analysis estimated the cost of $3.23/gallon for a neat biodiesel obtained from this process at an assumed yield of 10% FAMEs/dry weight of sludge.

Performance validation for microplate fluorimeters.

As the sophistication of instruments that make fluorimetric measurements on samples in microplates has increased, so has the need for methods to validate instrumental performance. This paper describes a solid-state validation microplate that tests multiple aspects of fluorescence performance, including signal linearity, gain, noise, sensitivity, wavelength accuracy, and polarization stability. Both the operating principles and the validation of the validation microplate are discussed.