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PubMed2003

Finding extraterrestrial organisms living on thermosynthesis.

During thermal cycling, organisms could live on thermosynthesis, a theoretical mechanism applicable to the origin of life and the early evolution of biological energy conversion. All extraterrestrial ice may be a repository for frozen dead or dormant organisms from earlier stages of evolution. In the presence of a thermal gradient within the ice, organisms might still be harvesting energy from thermosynthesis. Possible habitats for thermosynthesizers can be found throughout the Solar System, particularly in the cold traps on Mercury and the Moon, convecting waters on Mars, the oceans on moons in the outer Solar System, and smaller bodies rotating in the sunlight such as cosmic dust, meteorites, asteroids, and comets. A general strategy for detecting thermosynthetic organisms on Earth is offered, and highlights of current and upcoming robotic exploratory missions relevant to the detection of thermosynthesis are reviewed.

Environment↗
PubMed2003

BioSPICE: access to the most current computational tools for biologists.

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

Computational Biology↗
PubMed2004

Collaborative design for automated DNA storage that allows for rapid, accurate, large-scale studies.

Genomics Collaborative, Inc., a division of Sera Care Life Sciences, Inc. (Cambridge, MA), is among the first commercial entities in the world to enable genetic research on an industrial scale via its Large Scale Global Repository, a biobank of human specimens collected for research purposes. With the demand for large-scale DNA studies increasing, decisions about the strategic direction of sample storage and collection must be made to create a sound plan to support continued demands for drug discovery. Reported here is the approach used by Genomics Collaborative to automate its DNA processing, storage, and retrieval.

Automation↗
PubMed1995

Preparation and characterization of human HIV type 1 neutralizing reference sera.

Reference neutralizing antibody (NA) reagents are needed for laboratories to be able to compare results of neutralization assays that will be used to monitor HIV-1 vaccine recipients. In an effort to establish such reference reagents two asymptomatic, seropositive patients were identified with medium to high amounts of cross-reactive NA activity against a number of HIV-1 strains. Sera obtained from each individual at three or four sequential phlebotomies were pooled, and the two pools were each distributed in > 3000 aliquots into glass ampoules and lyophilized, and the ampoules were flame sealed. An HIV-1 antibody-negative reference serum was prepared in a similar fashion after pooling serum from four individuals. Ampoules were tested for uniformity of fill, sterility, moisture content, residual oxygen, stability, infectivity, and presence of antibody. An international collaborative study was conducted to determine the potency of the samples in six laboratories, each using their own neutralization assays and reagents. The results indicated reasonable consistency between laboratories and that both sera have sufficient titers against a variety of strains for use as reference reagents. These reference sera have been included in the World Health Organization (WHO) AIDS Reagent Project and are available through the three AIDS reagent repositories.

AIDS Vaccines↗
PubMed2006

With a grain of salt: what halite has to offer to discussions on the origin of life.

This experimental study investigated how the dynamics of the crystallization of the evaporite mineral halite could affect the accumulation and preservation of organic macromolecules present in the crystallizing solution. Halite was grown under controlled conditions in the presence of polymer nanoparticles that acted as an analog to protocellular material. Optical microscopy, atomic force microscopy, and laser scanning confocal fluorescence microscopy were used to trace the localization of the nanoparticles during and after growth of halite crystals. The present study revealed that the organic nanoparticles were not regularly incorporated within the halite, but were very concentrated on its surfaces. Their distribution was controlled dominantly by the morphologic surface features of the mineral rather than by specific molecular interactions with an atomic plane of the mineral. This means that the distribution of organic molecules was controlled by surfaces like those of halite's evaporitic growth forms. The experiments with halite also demonstrated that a mineral need not continuously incorporate organic molecules during its crystallization to preserve those molecules: After rejection by (non-incorporation into) the crystallizing halite, the organic nanoparticles increased in concentration in the evaporating brine. They ultimately either adsorbed in rectilinear patterns onto the hopper-enhanced surfaces and along discontinuities within the crystals, or they were encapsulated within fluid inclusions. Of additional importance in origin-of-life considerations is the fact that halite in the natural environment rapidly can change its role from that of a protective repository (in the absence of water) to that of a source of organic particles (as soon as water is present) when the mineral dissolves.

Crystallization↗
PubMed1995

The PLDD registry.

The rapid acceptance of minimally invasive surgery in the United States has largely occurred without statistical proof of its superiority over traditional methods. All players in the healthcare field now see the need for valid outcome studies supporting the efficacy of new treatment techniques. Percutaneous laser disc decompression (PLDD) will gain wide acceptance only if it is statistically shown to be a safe and effective alternative treatment of a lumbar disc herniation. To that end, a central PLDD registry has been developed and implemented into clinical practice at several centers. This article reviews healthcare trends that motivated the creation of this data repository and discusses the history of its development. The currently used PLDD evaluation form is outlined and its utility is discussed. Most importantly, preliminary PLDD results and complications based on the data received are presented and analyzed.

Diskectomy, Percutaneous↗
PubMed2004

Adaptive interface for personalizing information seeking.

An adaptive interface autonomously adjusts its display and available actions to current goals and abilities of the user by assessing user status, system task, and the context. Knowledge content adaptability is needed for knowledge acquisition and refinement tasks. In the case of knowledge content adaptability, the requirements of interface design focus on the elicitation of information from the user and the refinement of information based on patterns of interaction. In such cases, the emphasis on adaptability is on facilitating information search and knowledge discovery. In this article, we present research on adaptive interfaces that facilitates personalized information seeking from a large data warehouse. The resulting proof-of-concept system, called source recommendation system (SRS), assists users in locating and navigating data sources in the repository. Based on the initial user query and an analysis of the content of the search results, the SRS system generates a profile of the user tailored to the individual's context during information seeking. The user profiles are refined successively and are used in progressively guiding the user to the appropriate set of sources within the knowledge base. The SRS system is implemented as an Internet browser plug-in to provide a seamless and unobtrusive, personalized experience to the users during the information search process. The rationale behind our approach, system design, empirical evaluation, and implications for research on adaptive interfaces are described in this paper.

Data Display↗
PubMed2005

Website review: diabetes insight--www.diabetes-insight.info.

In previous Diabetes Information Technology & WebWatch columns some different diabetes Websites have been highlighted. In this issue we focus on one particular site and use this to illustrate how such Internet-based repositories of information can provide important and useful resources for people with diabetes and their carers. Diabetes is perhaps unique in the fact that much of the day-to-day responsibility for care rests with individuals themselves. Successful therapy demands considerable understanding of the condition by the person with diabetes, or his or her carer, and this can only be made possible with access to appropriate information. Provision of information via a Website is now recognised to be cost-effective and convenient, available 24 hours a day, 365 days a year-and access to the Internet by the general public has grown rapidly in recent years. The increasing way in which the Internet is being used to supply individuals with tools and information for their self-care is exemplified by the Diabetes Insight Website (at: www.diabetes-insight.info).

Computer User Training↗
PubMed2004

Tele-diagnostic and therapeutic guidance in urology.

PURPOSE: To design a Web-based network for diagnostic and therapeutic guidance in urology. MATERIALS AND METHODS: We designed an architectural model of a low-cost multimedia Web platform that runs on a collection of distributed collaborative network nodes to provide a set of urologist-oriented Web-enabled services. Any node of the platform was able to share patient-oriented data via automated processes with appropriate authorization, confidentiality, and high-security protocols. The urologist can show the details of the records of patients and additionally enrich the world experience with his or her own cases. Video clips maintained locally at the nodes will be accessible by clinicians in a trouble-free way with MS Windows Media player and a relatively small amount of source code. RESULTS AND CONCLUSIONS: The primary advantage of this architectural model is that it provides Web-enabled integrated urologic services while using a distributed storage scheme for urological video files (AVI format) and a global repository of laboratory results using Extensible Markup Language (XML) and Data Grid technologies. In addition, this model provides decision-support services (knowledge from a global database and predefined procedures). The architecture model is based entirely on HTTP, XML, GRID-like environment and DotNet technologies. Finally, the platform provides extensibility and scalability targeted to large-scale Web-enabled global urologic databases.

Decision Support Techniques↗
PubMed2005

Palliative care needs of cancer patients in U.S. nursing homes.

BACKGROUND: Increasingly, nursing homes are the place of care for older Americans with cancer. Yet, few studies has characterized the quality of care for this growing population. OBJECTIVE: Characterize the scope and quality of cancer care in U.S. nursing homes. DESIGN: Secondary analysis of the national repository of the Minimum Data Set (MDS) SETTING AND SUBJECTS: Nursing home residents noted to have cancer diagnosis on the MDS. RESULTS: Of the 190,769 New Hampshire residents (8.8%) with a cancer diagnosis, 1 in 4 had weight loss (23.4%), received intravenous medications (27.7%), or used oxygen (25.4%). Overall, 45.3% had a do-not-resuscitate (DNR) order, with state variations ranging from 17.8% (New Jersey) to 70.5% (Wisconsin). More than 1 in 10 (12.0%) were defined as terminally ill, although only 29.3% of these received hospice services. Among patients with pain, half of those who survived to a second assessment had persistent, severe pain (51.3%), which also varied by state, ranging from 43.3% (Iowa) to 65.8% (Nevada). Active treatment was rare; less than 5% received chemotherapy or radiotherapy. However, 15.5% had parenteral and/or tube feedings for nutrition. Approximately, 1 in 10 New Hampshire residents had advanced cancer. CONCLUSION: Our findings suggest important opportunities to improve the quality of cancer care for older adults.

Adolescent↗
PubMed2006

Comparative microarray analysis.

Microarrays enable high-throughput parallel gene expression analysis, and their use has grown exponentially during the past decade. We are now in a position where individual experiments could benefit from using the swelling public data repositories to allow microarrays to progress from being a hypothesis-generating tool to a powerful resource that can be used to test hypothesis about biology. Comparative microarray analysis could better distinguish phenotypes from associated phenotypes; identify valid differentially expressed genes by combining many studies; test new hypothesis; and discover fundamental patterns of gene regulation. This review aims to describe the additional methodology needed for such comparative microarray analysis, and we identify and discuss a number of problems such as loss of published data, lack of annotations, and variable array quality, which need to be solved before comparative microarray analysis can be used in a more systematic and powerful manner.

Animals↗
PubMed2015

Clostridium difficile Infections after Blunt Trauma: A Different Patient Population?

BACKGROUND: The epidemiology of Clostridium difficile-associated infection (CDI) has changed, and it is evident that susceptibility is related not only to exposures and bacterial potency, but host factors as well. Several small studies have suggested that CDI after trauma is associated with a different patient phenotype. The purpose of this study was to examine and describe the epidemiologic factors associated with C. difficile in blunt trauma patients without traumatic brain injury using the Trauma-Related Database as a part of the "Inflammation and Host Response to Injury" (Glue Grant) and the University of Florida Integrated Data Repository. METHODS: Previously recorded baseline characteristics, clinical data, and outcomes were compared between groups (67 C. difficile and 384 uncomplicated, 813 intermediate, and 761 complicated non-C. difficile patients) as defined by the Glue Grant on admission and at days seven and 14. RESULTS: The majority of CDI patients experienced complicated or intermediate clinical courses. The mean ages of all cohorts were less than 65 y and CDI patients were significantly older than uncomplicated patients without CDI. The CDI patients had increased days in the hospital and on the ventilator, as well as significantly higher new injury severity scores (NISS), and a greater percentage of patients with NISS >34 points compared with non-CDI patients. They also had greater Marshall and Denver multiple organ dysfunction scores than non-CDI uncomplicated patients, and greater creatinine, alkaline phosphatase, neutrophil count, lactic acid, and PiO2:FiO2 compared with all non-CDI cohorts on admission. In addition, the CDI patients had higher glucose concentrations and base deficit from uncomplicated patients and greater leukocytosis than complicated patients on admission. Several of these changes persisted to days seven and 14. CONCLUSION: Analysis of severe blunt trauma patients with C. difficile, as compared with non-CDI patients, reveals evidence of increased inflammation, immunosuppression, worse acute kidney injury, higher NISS, greater days in the hospital and on the ventilator, higher organ injury scores, and prolonged clinical courses. This supports reports of an increased prevalence of CDI in a younger population not believed previously to be at risk. This unique population may have specific genomic or inflammation-related risk factors that may play more important roles in disease susceptibility. Prospective analysis may allow early identification of at-risk patients, creation of novel therapeutics, and improved understanding of how and why C. difficile colonization transforms into infection after severe blunt trauma.

Adolescent↗
PubMed1984

Report of a planning conference concerning an international network of food data systems (INFOODS).

A small international planning conference on the topic of "An International Network of Food Data Systems" was held on January 30 to February 5, 1983, at the Rockefeller Conference and Study Center, in Bellagio, Italy. It was sponsored through the Food, Nutrition and Poverty Subprogramme of the United Nations University and supported by various US government agencies, private foundations, and the food industry. Participants included representatives from FAO, WHO, IUNS, and IUFoST. The purpose was to explore the needs for, and current limitations of, food composition data bases, especially in the international context, and to propose what was needed. The conference focused on the design and scope of an organization to be called INFOODS (International Network of Food Data Systems) which would promote international participation and cooperation in the acquisition and interchange of quality data on the nutrient composition of foods, beverages, and their ingredients in forms appropriate to meet the needs of government agencies; nutrition scientists; health and agriculture professionals; policy makers and planners; food producers, processors, and retailers; consumers. The conference identified the more important aspects of INFOODS to include: 1) a network of regional data centers; 2) an organizational/administrative framework for various expert task forces; 3) the generator and repository of special international data bases; 4) the stimulator of national data base programs; 5) a general and specific resource for persons and organizations interested in food composition data on a worldwide basis.(ABSTRACT TRUNCATED AT 250 WORDS)

Computers↗
PubMed1991

Frozen sections of cellular lymphoid proliferations provide adequate DNA for routine gene rearrangement analysis.

Optimal use of frozen tissue procured as part of a thorough diagnostic workup of suspected lymphoma is important, and conservation of similar samples is a prerequisite for maintaining a large and varied frozen archive repository. The authors have evaluated a simple tissue-conserving method for the preparation of cellular lymphoid specimens for immunoglobulin and T-cell receptor gene rearrangement analysis. Initially, 16-microns-thick frozen tonsil sections were examined to determine adequacy for DNA extraction. Specimens containing three, six, and nine sections each were evaluated separately. DNA quantitation disclosed yields ranging from 84 to 204 micrograms (mean, 156 micrograms). The authors have used this technique on 24 cellular lymphoid proliferations from their frozen archives. Six to ten 16-microns sections were used, depending on tissue size. DNA quantitation ranged from 0 to 520 micrograms (mean, 135 micrograms). Twenty-one of 24 cases yielded adequate DNA for analysis; each showed appropriate germline or rear-ranged bands with respect to the particular morphologic diagnosis. Attempts to obtain adequate DNA with the use of this technique on skin biopsy specimens with lymphoid infiltrates resulted in overall poor yields; this may be because of dermal collagen or small sample size. This method of sample preparation provides adequate DNA for routine Southern blot hybridization analysis of cellular lymphoid tissues and offers the additional advantage of allowing preservation of frozen tissue for future study.

Blotting, Southern↗
PubMed1987

The Multicenter AIDS Cohort Study: rationale, organization, and selected characteristics of the participants.

The Multicenter AIDS Cohort Study was designed to elucidate the natural history of the infection causing acquired immunodeficiency syndrome (AIDS), identify risk factors for occurrence and clinical expression of the infection, and establish a repository of biologic specimens for future study. A variety of recruitment techniques, including special assurance of confidentiality, were used to enroll participants. Nearly 5,000 homosexual men volunteered for semiannual interview, physical examination, and laboratory testing in four metropolitan areas. A significant majority of these men in each center (69-83%) reported having 50 or more lifetime sexual partners, and over 80% had engaged in receptive anal intercourse with at least some of their partners in the previous two years. By the time of the participants' initial evaluation (April 1984-April 1985), infection with the human immunodeficiency virus (HIV) had occurred in higher proportions of men in Los Angeles (51%) and Chicago (43%) than in Baltimore/Washington, DC (31%) and Pittsburgh (21%), presumably as a result of the higher number of partners and proportion with whom these men had engaged in high-risk practices (e.g., receptive anal intercourse). Follow-up evaluations are underway in this comprehensive longitudinal investigation of HIV infection.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Building a better online formulary.

The history of and improvements made to the University of Michigan Health System (UMHS) inpatient online formulary are described. The current formulary at UMHS is the third version of the Web-based formulary. The original effort in 1997 consisted of converting word-processing documents to HTML format and exporting this information to the university's intranet. There was no mechanism to search for formulary items, no therapeutic class cross-referencing, and no cost information. Documents and their conversion had to be manually maintained. The second version incorporated a series of automatic daily computer downloads from the inpatient pharmacy computer system. Web pages were built to dynamically display the formulary information from the database based on users' requests. The formulary enabled searching by brand or generic names, provided therapeutic category cross-references, listed the location of products within automated dispensing cabinets, provided accurate cost information, and was always up-to-date. Maintenance efforts drastically decreased. The current version has incorporated additional logic to meet users' needs. If no matches are found, the system expands its search by automatically linking to UMHS's inpatient pharmacy system repository of all drugs, finding matches to what the user entered, and then returning the names of therapeutically similar formulary agents to the user. A cross-index feature allows the system to return all the drugs that fall under the searched therapeutic category. Dramatic improvements have been made to UMHS's inpatient online formulary in the past two years. The current formulary provides a very low-cost, easily maintainable, and effective means to access the formulary and clinically relevant and timely information specific to each medication.

Computers↗
PubMed2006

Genetic diversity and structure of managed and semi-natural populations of cocoa (Theobroma cacao) in the Huallaga and Ucayali Valleys of Peru.

BACKGROUND AND AIMS: Cocoa (Theobroma cacao) is indigenous to the Amazon region of South America, and it is well known that the Peruvian Amazon harbours a large number of diverse cocoa populations. A small fraction of the diversity has been collected and maintained as an ex-situ germplasm repository in Peru. However, incorrect labelling of accessions and lack of information on genetic diversity have hindered efficient conservation and use of this germplasm. This study targeted assessment of genetic diversity and population structure in a managed and a semi-natural population. METHODS: Using a capillary electrophoresis genotyping system, 105 cocoa accessions collected from the Huallaga and Ucayali valleys of Peru were fingerprinted. Based on 15 loci SSR profiles, genetic identity was examined for each accession and duplicates identified, population structure assessed and genetic diversity analysed in these two populations. KEY RESULTS: Ten synonymous mislabelled groups were identified among the 105 accessions. The germplasm group in the Huallaga valley was clearly separated from the group in Ucayali valley by the Bayesian assignment test. The Huallaga group has lower genetic diversity, both in terms of allelic richness and of gene diversity, than the Ucayali group. Analysis of molecular variance suggested genetic substructure in the Ucayali group. Significant spatial correlation between genetic distance and geographical distances was detected in the Ucayali group by Mantel tests. CONCLUSIONS: These results substantiate the hypothesis that the Peruvian Amazon hosts a high level of cocoa genetic diversity, and the diversity has a spatial structure. The introduction of exotic seed populations into the Peruvian Amazon is changing the cocoa germplasm spectrum in this region. The spatial structure of cocoa diversity recorded here highlights the need for additional collecting and conservation measures for natural and semi-natural cocoa populations.

Cacao↗
PubMed2002

Emerging bioinformatics for the metabolome.

Metabolic profiling applied to functional genomics (metabolomics) is in an early stage of development. Here, the technologies used for metabolite profiling are briefly covered, illustrated by a few pioneering studies. Issues related to bioinformatics, namely data analysis, visualisation and archival, are the main focus of this review. Arguably there is already a need for databases containing metabolite profiles specific for a single organism, and a generic repository containing all metabolite profiling results, regardless of species. Data analyses and visualisations that combine the biological context with chemistry details are suggested as being the most promising.

Animals↗