cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.

MOTIVATION: Many bioinformatics areas require us to assign domain matches onto stretches of a query protein. Starting with a set of candidate matches, we want to identify the optimal subset that has limited/no overlap between matches. This may be further complicated by discontinuous domains in the input data. Existing tools are increasingly facing very large data-sets for which they require prohibitive amounts of CPU-time and memory. RESULTS: We present cath-resolve-hits (CRH), a new tool that uses a dynamic-programming algorithm implemented in open-source C++ to handle large datasets quickly (up to ∼1 million hits/second) and in reasonable amounts of memory. It accepts multiple input formats and provides its output in plain text, JSON or graphical HTML. We describe a benchmark against an existing algorithm, which shows CRH delivers very similar or slightly improved results and very much improved CPU/memory performance on large datasets. AVAILABILITY AND IMPLEMENTATION: CRH is available at https://github.com/UCLOrengoGroup/cath-tools; documentation is available at http://cath-tools.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The ecological effects of trichloroacetic acid in the environment.

Trichloroacetic acid (TCAA) is a member of the family of compounds known as chloroacetic acids, which includes mono-, di- and trichloroacetic acid. The significant property these compounds share is that they are all phytotoxic. TCAA once was widely used as a potent herbicide. However, long after TCAA's use as a herbicide was discontinued, its presence is still detected in the environment in various compartments. Methods for quantifying TCAA in aqueous and solid samples are summarized. Concentrations in various environmental compartments are presented, with a discussion of the possible formation of TCAA through natural processes. Concentrations of TCAA found to be toxic to aquatic and terrestrial organisms in laboratory and field studies were compiled and used to estimate risk quotients for soil and surface waters. TCAA levels in most water bodies not directly affected by point sources appear to be well below toxicity levels for the most sensitive aquatic organisms. Given the phytotoxicity of TCAA, aquatic plants and phytoplankton would be the aquatic species to monitor for potential effects. Given the concentrations of TCAA measured in various soils, there appears to be a risk to terrestrial organisms. Soil uptake of TCAA by plants has been shown to be rapid. Also, combined uptake of TCAA from soil and directly from the atmosphere has been shown. Therefore, risk quotients derived from soil exposure may underestimate the risk TCAA poses to plants. Moreover, TCE and TCA have been shown to be taken up by plants and converted to TCAA, thus leading to an additional exposure route. Mono- and di-chloroacetic acids can co-occur with TCAA in the atmosphere and soil and are more phytotoxic than TCAA. The cumulative effects of TCAA and compounds with similar toxic effects found in air and soil must be considered in subsequent terrestrial ecosystem risk assessments.

Potential of thraustochytrids to partially replace fish oil in Atlantic salmon feeds.

The replacement of fish oil with a dried product made from thraustochytrid culture, a marine microorganism, in canola-oil-based diets for Atlantic salmon was investigated. Salmon (37 g) were fed for 51 days on diets containing only canola oil, canola oil and fish oil, or canola oil and the thraustochytrid. There were no significant differences in final weight (106.1 +/- 1.1 g), weight gain (69.6 +/- 1.1 g), feed consumption (16.5 +/- 0.2 mg dry matter g(-1) d(-1)), feed efficiency ratio (1.15 +/- 0.03 g (g-1)), or productive protein value (51.2% +/- 1.7%) between the diets. Nor were there any significant differences in whole-body chemical composition, organ somatic indices, or measures of immune function. However, following transfer to seawater and 2 challenges with Vibrio anguillarum, cumulative mortality was significantly lower in fish fed some fish oil than in those fed the 2 diets containing no fish oil. In conclusion, the thraustochytrid had no detrimental effects on the performance of salmon but, at the current inclusion of 10%, failed to confer the same effect as fish oil under challenging conditions.

Sterol and squalene content of a docosahexaenoic-acid-producing thraustochytrid: influence of culture age, temperature, and dissolved oxygen.

Thraustochytrid strain ACEM 6063, rich in omega-3 polyunsaturated fatty acids, was cultured at 15 degrees C and 20 degrees C in high (>40%) and low (<5%) dissolved oxygen (DO), and at 25 degrees C in low-DO media. Samples were taken 4, 2, and 0 days before each culture reached peak biomass (T(-4), T(-2), and T(p), respectively). Twenty sterols, 13 of which were identified, were detected. Predominant were cholest-5-en-3 beta-ol, 24-ethylcholesta-5,22E-dien-3 beta-ol, 24-methylcholesta-5,22E-dien-3 beta-ol, and 2 coeluting sterols, one of which was 24-ethylcholesta-5,7,22-trien-3 beta-ol. These 4 sterols comprised 50% to 90% of total sterols. Cultures grown at high DO had simpler sterol profiles than those grown at low DO. Only the 4 sterols mentioned above were present at more than 3% of total sterols in high-DO cultures. In low-DO cultures, up to 6 additional sterols were present at more than 3% of total sterols. Culture age, temperature, and DO influenced squalene and sterol content. Total sterols (as a proportion of total lipids) decreased with increasing culture age. If organisms such as ACEM 6063 are to be used for commercial production of lipid products for human consumption, both their sterol content and factors influencing sterol production need to be characterized thoroughly.

Interfacing the PACS and the HIS: results of a 5-year implementation.

An interface was created between the Department of Defense's hospital information system (HIS) and its two picture archiving and communication system (PACS)-based radiology information systems (RISs). The HIS is called the Composite Healthcare Computer System (CHCS), and the RISs are called the Medical Diagnostic Imaging System (MDIS) and the Digital Imaging Network (DIN)-PACS. Extensive mapping between dissimilar data protocols was required to translate data from the HIS into both RISs. The CHCS uses a Health Level 7 (HL7) protocol, whereas the MDIS uses the American College of Radiology-National Electrical Manufacturers Association 2.0 protocol and the DIN-PACS uses the Digital Imaging and Communications in Medicine (DICOM) 3.0 protocol. An interface engine was required to change some data formats, as well as to address some nonstandard HL7 data being output from the CHCS. In addition, there are differences in terminology between fields and segments in all three protocols. This interface is in use at 20 military facilities throughout the world. The interface reduces the amount of manual entry into more than one automated system to the smallest level possible. Data mapping during installation saved time, improved productivity, and increased user acceptance during PACS implementation. It also resulted in more standardized database entries in both the HIS (CHCS) and the RIS (PACS).

Reengineering the picture archiving and communication system (PACS) process for digital imaging networks PACS.

Prior to June 1997, military picture archiving and communications systems (PACS) were planned, procured, and installed with key decisions on the system, equipment, and even funding sources made through a research and development office called Medical Diagnostic Imaging Systems (MDIS). Beginning in June 1997, the Joint Imaging Technology Project Office (JITPO) initiated a collaborative and consultative process for planning and implementing PACS into military treatment facilities through a new Department of Defense (DoD) contract vehicle called digital imaging networks (DIN)-PACS. The JITPO reengineered this process incorporating multiple organizations and politics. The reengineered PACS process administered through the JITPO transformed the decision process and accountability from a single office to a consultative method that increased end-user knowledge, responsibility, and ownership in PACS. The JITPO continues to provide information and services that assist multiple groups and users in rendering PACS planning and implementation decisions. Local site project managers are involved from the outset and this end-user collaboration has made the sometimes difficult transition to PACS an easier and more acceptable process for all involved. Corporately, this process saved DoD sites millions by having PACS plans developed within the government and proposed to vendors second, and then having vendors respond specifically to those plans. The integrity and efficiency of the process have reduced the opportunity for implementing nonstandard systems while sharing resources and reducing wasted government dollars. This presentation will describe the chronology of changes, encountered obstacles, and lessons learned within the reengineering of the PACS process for DIN-PACS.

Acceptance testing of integrated picture archiving and communications systems.

An integrated picture archiving and communication system (PACS) is a large investment in both money and resources. With all of the components and systems contained in the PACS, a methodical set of protocols and procedures must be developed to test all aspects of the PACS within the short time allocated for contract compliance. For the Department of Defense (DoD), acceptance testing (AT) sets the protocols and procedures. Broken down into modules and test procedures that group like components and systems, the AT protocol maximizes the efficiency and thoroughness of testing all aspects of an integrated PACS. A standardized and methodical protocol reduces the probability of functionality or performance limitations being overlooked. The AT protocol allows complete PACS testing within the 30 days allocated by the digital imaging network (DIN)-PACS contract. AT shortcomings identified during the testing phase properly allows for resolution before complete acceptance of the system. This presentation will describe the evolution of the process, the components of the DoD AT protocol, the benefits of the AT process, and its significance to the successful implementation of a PACS. This is a US government work. There are no restrictions on its use.

An accelerated schedule for tick-borne encephalitis vaccine: the American Military experience in Bosnia.

Tick-borne encephalitis (TBE) is a viral illness endemic to the Balkan region. United States military forces were deployed to Bosnia in early 1996 as part of Operation Joint Endeavor, a U.S.-led multinational peace-keeping operation. To counteract the TBE threat, an inactivated, parenteral vaccine (FSME-Immun Inject; Immuno AG, Vienna, Austria) was offered to soldiers at high risk on a volunteer basis in an accelerated, 3-dose schedule (0, 7, and 28 days). Passive adverse reaction surveillance was conducted on 3,981 vaccinated personnel. Paired sera from a randomly selected group of 1,913 deployed personnel (954 who received vaccine and 959 who were unvaccinated) were tested for antibodies to TBE by an ELISA. Three-dose recipients demonstrated an 80% seroconversion rate (4-fold or greater increase in anti-TBE titers). By comparison, the TBE infection rate in the unvaccinated cohort was found to be only 0.42% (4 of 959). Only 0.18% of vaccinees reported self-limited symptoms. An accelerated immunization schedule appears to be an acceptable option for military personnel or travelers on short-term notice to TBE-endemic areas.

Laboratory diagnosis of acute dengue fever during the United Nations Mission in Haiti, 1995-1996.

We evaluated laboratory methods to confirm a clinical diagnosis of dengue. Acute sera were collected from personnel (n = 414) supporting the United Nations Mission in Haiti and presenting with febrile illness consistent with dengue fever or no apparent underlying cause. Dengue virus was recovered from 161 of 379 acute sera by inoculation into C6/36 cell culture. While 93 of 414 acute sera had detectable IgM antibodies, the IgM capture ELISA (MAC ELISA) had a sensitivity of only 13% compared with the virus isolation gold standard. If presumptive dengue fever cases were identified by both virus isolation and the presence of IgM, virus isolation and the MAC ELISA had clinical sensitivities of 69% and 40%, respectively. This study suggests that a combination of laboratory methods that target virus or subviral components as well as anti-viral IgM antibodies may be necessary for sensitive laboratory diagnosis with acute sera.

Soil sampling and analysis for volatile organic compounds.

Concerns over data quality have raised many questions related to sampling soils for volatile organic compounds (VOCs). This paper was prepared in response to some of these questions and concerns expressed by Remedial Project Managers (RPMs) and On-Scene Coordinators (OSCs). The following questions are frequently asked: 1. Is there a specific device suggested for sampling soils for VOCs? 2. Are there significant losses of VOCs when transferring a soil sample from a sampling device (e.g., split spoon) into the sample container? 3. What is the best method for getting the sample from the split spoon (or other device) into the sample container? 4. Are there smaller devices such as subcore samplers available for collecting aliquots from the larger core and efficiently transferring the sample into the sample container? 5. Are certain containers better than others for shipping and storing soil samples for VOC analysis? 6. Are there any reliable preservation procedures for reducing VOC losses from soil samples and for extending holding times? Guidance is provided for selecting the most effective sampling device for collecting samples from soil matrices. The techniques for sample collection, sample handling, containerizing, shipment, and storage described in this paper reduce VOC losses and generally provide more representative samples for volatile organic analyses (VOA) than techniques in current use. For a discussion on the proper use of sampling equipment the reader should refer to other sources (Acker, 1974; U.S. EPA, 1983; U.S. EPA, 1986a).Soil, as referred to in this report, encompasses the mass (surface and subsurface) of unconsolidated mantle of weathered rock and loose material lying above solid rock. Further, a distinction must be made as to what fraction of the unconsolidated material is soil and what fraction is not. The soil component here is defined as all mineral and naturally occurring organic material that is 2 mm or less in size. This is the size normally used to differentiate between soils (consisting of sands, silts, and clays) and gravels.Although numerous sampling situations may be encountered, this paper focuses on three broad categories of sites that might be sampled for VOCs: 1. Open test pit or trench. 2. Surface soils (<5 ft in depth). 3. Subsurface soils (>5 ft in depth).

Activation of the mouse heart adenosine 5',5"'-P1-P4-tetraphosphate receptor.

We have previously demonstrated that mouse brain membrane fractions have a specific, saturable receptor for diadenylated nucleotides. Binding is specific for two adenosines, and the length of the phosphate bridge is critical, with four phosphates being optimal [Hilderman et al. (1991) J. Biol. Chem. 266, 6915-6918]. In this report, we demonstrate that adenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) binding to its receptor is dependent upon an activation step that requires divalent cations and a serine protease. Monoclonal antibodies (Mabs) are identified that inhibit Ap4A binding to its membrane receptor. These antibodies recognize a 212-kDa membrane protein. However, SDS-PAGE analysis of Ap4A cross-linked to membrane fractions reveals that Ap4A is not attached to the 212-kDa peptide but to a 30-kDa polypeptide. Appearance of the 30-kDa polypeptide is dependent on the activation step, and one of the inhibitory antibodies blocks its appearance. We suggest that the protease-dependent processing step involves cleavage of the 212-kDa component with the appearance of an active 30-kDa receptor.

A prospective field evaluation of an enzyme immunoassay: detection of eastern equine encephalomyelitis virus antigen in pools of Culiseta melanura.

A prospective field study was conducted to determine the sensitivity and specificity of an enzyme immunoassay (EIA) compared to virus isolation in cell culture for the detection of eastern equine encephalomyelitis (EEE) virus in naturally infected mosquitoes. A total of 10,811 adult female Culiseta melanura were collected in light traps during 1985 from four locations in Maryland. Eastern equine encephalomyelitis virus was isolated from 5 of 495 mosquito pools in African green monkey kidney and baby hamster kidney cell cultures. All five virus-infected pools were detected by the EIA, and all 490 uninfected pools were correctly scored as not containing virus. The EIA did not produce false positive or false negative results. Results support the assertion of previous researchers that the antigen detection EIA is a rapid, sensitive, specific, and simple alternative to traditional bioassays for the detection of EEE virus in mosquitoes.

The bacterial biota on crustose (nonarticulated) coralline algae from Tasmanian waters.

The bacterial biota associated with the cuticle surface of healthy benthic samples of crustose nonarticulated coralline algae from the east coast of Tasmania (Australia) was examined by bacteriological cultivation and electron microscopy. In 32 samples studied, the viable count on Zobell's marine agar (supplemented with vitamins) was 3.3×10(6) bacteria g(-1) wet wt. (range 2.9×10(4)-2.7×10(7)). Of 732 strains isolated from 16 out of 32 samples and identified to genus level,Moraxella was the predominant genus (66%). In contrast,Moraxella comprised only 11% of 217 strains isolated from benthic seawater samples collected at the same time as coralline algae. In 22 out of 32 algal samples examined by scanning electron microscopy, the total count was 1.6 × 10(7) bacteria g(-1) wet wt. (range 5.1× 10(6)-3.8×107); the major morphotype was cocco-bacilli (80%). Several environmental factors did not significantly influence the viable count or generic distribution, or the total count or morphotypic distribution of bacteria on the cuticle. These factors included geographical site, season, storage of samples in aquarium conditions, and the presence or absence of abalone from shells that the coralline algae encrusted. The microbiota, consisting mostly of the nonmotile bacterial genusMoraxella, appeared to be highly adapted to its calcerous plant host.

Du pont chambers works - integrated site waste disposal system

At the Du Pont Chambers Works, continuing efforts are being made to reduce the generation of waste materials. At the same time, recognizing the inevitable continuation of need for adequate treatment and disposal, we are working tomake our waste management system as efficient and reliable as possible by applying new technology as it becomes available (AU)