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1.  Genome Sequence of the Oleaginous Yeast Rhodotorula glutinis ATCC 204091 
Genome Announcements  2014;2(1):e00046-14.
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.
doi:10.1128/genomeA.00046-14
PMCID: PMC3924368  PMID: 24526636
2.  PACS Bypass: A Semi-automated Routing Solution to Enable Filmless Operations When PACS Fails 
Journal of Digital Imaging  2011;25(4):466-470.
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.
doi:10.1007/s10278-011-9446-2
PMCID: PMC3389085  PMID: 22193756
Computer hardware; Computer networks; Computers in medicine
3.  Using an Open-Source PACS Virtual Machine for a Digital Angiography Unit: Methods and Initial Impressions 
Journal of Digital Imaging  2011;25(1):81-90.
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.
doi:10.1007/s10278-011-9401-2
PMCID: PMC3264707  PMID: 21748411
PACS; Open-source; Software; Digital subtraction angiography
4.  Virtual Machine Performance Benchmarking 
Journal of Digital Imaging  2011;24(5):883-889.
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.
doi:10.1007/s10278-010-9358-6
PMCID: PMC3180542  PMID: 21207096
Computer hardware; Computer systems; Computers in medicine
5.  Tracking PACS Usage with Open Source Tools 
Journal of Digital Imaging  2010;24(4):719-723.
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.
doi:10.1007/s10278-010-9337-y
PMCID: PMC3138942  PMID: 20830501
Clinical use determination; Computer systems; Cost savings; Data mining
6.  TCP/IP Optimization over Wide Area Networks: Implications for Teleradiology 
Journal of Digital Imaging  2010;24(2):314-321.
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.
doi:10.1007/s10278-010-9309-2
PMCID: PMC3056981  PMID: 20544373
Enterprise PACS; wide area network (WAN); teleradiology
7.  DCMTB: A Virtual Appliance DICOM Toolbox 
Journal of Digital Imaging  2009;23(6):681-688.
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.
doi:10.1007/s10278-009-9230-8
PMCID: PMC3046693  PMID: 19705204
DICOM; HL7; virtualization
8.  Proteome and Membrane Fatty Acid Analyses on Oligotropha carboxidovorans OM5 Grown under Chemolithoautotrophic and Heterotrophic Conditions 
PLoS ONE  2011;6(2):e17111.
Oligotropha carboxidovorans OM5 T. (DSM 1227, ATCC 49405) is a chemolithoautotrophic bacterium able to utilize CO and H2 to derive energy for fixation of CO2. Thus, it is capable of growth using syngas, which is a mixture of varying amounts of CO and H2 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 H2 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.
doi:10.1371/journal.pone.0017111
PMCID: PMC3046131  PMID: 21386900

Results 1-8 (8)