Predicting transcription factor binding sites (TFBS) from sequence is one of the most challenging problems in computational biology. The development of (semi-)automated computer-assisted prediction methods are needed to find TFBS over an entire genome, which is a first step in reconstructing mechanisms that controls gene activity. Bioinformatics journals continue to publish diverse methods for predicting TFBS on a monthly basis. To help practitioners in deciding which method to use to predict for a particular TFBS, we provide a platform to assess the quality and applicability of the available methods. Assessment tools allow researchers to determine how methods can be expected to perform on specific organisms or on specific transcription factor families. This chapter introduces the TFBS detection problem and reviews current strategies for evaluating algorithm effectiveness. In this chapter, a novel and robust assessment tool, the Motif Tool Assessment Platform (MTAP) is introduced and discussed.

As our dependence on the cyber infrastructure grows more complex and more distributed, the systems that compose it become more prone to failures and exploitation. Intelligence refers to discrete or private information, which possess currency and relevance. The ability to abstract, evaluate, and understand such information underlies its accuracy and true value. The collection, analysis and utilization of information constitutes a business-, sociopolitical-, military-intelligence activity that ultimately poses significant advantages and liabilities to the survivability of "our" society. The aim of this workshop (www.csiir.ornl.gov/csiirw) was to discuss (and publish) novel theoretical and empirical research focused on the many different aspects of cyber security and information intelligence. The scope will vary from methodologies and tools to systems and applications to more precise definition of the various problems and impacts. Topics include: Scalable trustworthy systems Enterprise-level metrics Coping with insider and life-cycle threats Coping with malware and polymorphism Phishing/whaling, spam and cyber crime High assurance system survivability Cyber security for the Smart Grid Digital provenance and data integrity Privacy-aware security and usable security Social networking models for managing trust and security A principle goal of the workshop was to foster discussions and dialog among the 150 registered attendees from North America, Europe, …

Fungi and yeast have been characterized as important components in the bioremediation of organic contaminants in soil and water including polyaromatic hydrocarbons (PAHs); however, research into their ability to metabolize these compounds in extreme environments has been limited. In this work forty-three fungi and yeasts were isolated from a PAH-contaminated sludge waste lagoon in Poland. The lagoon was part of a monitored natural attenuation (MNA) study where natural reduction of PAHs and associated toxicity over time in non-disturbed areas of the sludge lagoon indicated MNA activity. The microorganisms were initially isolated on minimal medium containing naphthalene as the sole carbon and energy source. Fungal isolates were then maintained on MEA and identified based on microscopic examination and BIOLOG{reg_sign}. The analysis identified several of the fungal isolates as belonging to the genera Penicillium, Paecilomyces, Aspergillus, and Eupenicillium. Yeasts included Candida parapsilosis and C. fluvialitis. Further microbial characterization revealed that several isolates were capable of rowing on acidified media of pH 4, 3, and 2.5. Over twenty percent of the fungi demonstrated growth as low as pH 2.5. Of the 43 isolates examined, 24 isolates exhibited growth at 5 C. Nine of the fungal isolates exhibiting growth at 5 C were then …

Environmental health focus with training conducted as part of the United Negro College Fund Special Programs Corporation/National Library of Medicine HBCU ACCESS Project at Winston-Salem State University, NC on November 10, 2010.

Prokaryotic life on earth is manifested by its diversity and omnipresence. These microbes serve as natural sources of a large variety of compounds with the potential to serve the ever growing, medicinal, chemical and transportation needs of the human population. However, commercially viable production of these compounds can be realized only through significant improvement of the native production capacity of natural isolates. The most favorable way to achieve this goal is through the genetic manipulation of metabolic pathways that direct the production of these molecules. While random mutagenesis and screening have dominated the industrial production of such compounds in the past our increased understanding of microbial physiology over the last five decades has shifted this trend towards rational approaches for metabolic design. Major drivers of this trend include recombinant DNA technology, high throughput characterization of macromolecular cellular components, quantitative modeling for metabolic engine ring, targeted combinatorial engineering and synthetic biology. In this chapter we track the evolution of microbial engineering technologies from the black box era of random mutagenesis to the science and engineering-driven era of metabolic design.

The National Library of Medicine's Environmental Health and Toxicology Portal provides access to numerous databases that can help you explore environmental chemicals and risks. TOXNET and Beyond: Using NLM's Environmental Health and Toxicology Portal conveys the fundamentals of searching the NLM's TOXNET system of databases in chemistry, toxicology, environmental health, and related fields. In addition to TOXNET, the course will highlight various resources available through the Environmental Health and Toxicology Portal.

As the treatment and management of HIV/AIDS continues to evolve with new scientific breakthroughs, treatment discoveries, and management challenges, it is difficult for people living with HIV/AIDS and those who care for them to keep up with the latest information on HIV/AIDS screening and testing, prevention, treatment, and research. The National Library of Medicine (NLM), of the National Institutes of Health, has a wealth of health information resources freely available on the Internet to address these needs.

Developing a predictive understanding of subsurface flow and transport is complicated by the disparity of scales across which controlling hydrological properties and processes span. Conventional techniques for characterizing hydrogeological properties (such as pumping, slug, and flowmeter tests) typically rely on borehole access to the subsurface. Because their spatial extent is commonly limited to the vicinity near the wellbores, these methods often can not provide sufficient information to describe key controls on subsurface flow and transport. The field of hydrogeophysics has evolved in recent years to explore the potential that geophysical methods hold for improving the quantification of subsurface properties and processes relevant for hydrological investigations. This chapter is intended to familiarize hydrogeologists and water resource professionals with the state-of-the-art as well as existing challenges associated with hydrogeophysics. We provide a review of the key components of hydrogeophysical studies, which include: geophysical methods commonly used for shallow subsurface characterization; petrophysical relationships used to link the geophysical properties to hydrological properties and state variables; and estimation or inversion methods used to integrate hydrological and geophysical measurements in a consistent manner. We demonstrate the use of these different geophysical methods, petrophysical relationships, and estimation approaches through several field-scale case studies. Among other applications, …

Laser interactions with materials have unique advantages to explore the rapid synthesis, processing, and in situ characterization of high quality and novel nanoparticles, nanotubes and nanowires. For example, laser vaporization of solids into background gases provides a wide range of processing conditions for the formation of nanomaterials by both catalyst-free and catalyst-assisted growth processes. Laser interactions with the growing nanomaterials provide remote in situ characterization of their size, structure, and composition with unprecedented temporal resolution. In this article, laser interactions involved in the synthesis of primarily carbon nanostructures are reviewed, including the catalyst-free synthesis of single-walled carbon nanohorns and quantum dots, to the catalyst-assisted growth of single and multi-walled carbon nanotubes.

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Training update with Environmental a health focus. Training conducted as part of the United Negro College Fund Special Programs Corporation/National Library of Medicine - HBCU ACCESS Project at the University of the District of Columbia, Washington, DC on November 2, 2010.

Enzymes catalyze biochemical reactions with remarkable specificity and efficiency, usually under physiological conditions. Computer simulation is a powerful tool for understanding enzyme catalytic mechanisms, particularly in cases where standard experimental techniques may be of limited utility. Here, we present an overview of the application of computer simulation techniques to understanding enzyme catalytic mechanisms. Examples using quantum chemical methods, as well as combined quantum mechanical/classical mechanical approaches, are provided.

The purpose of this training is to familiarize participants with reliable online environmental health and toxicology information, from the National Library of Medicine and other reliable sources. Skills and knowledge acquired in this training class will enable participants to access, utilize, and refer others to environmental health and toxicology information.

Familiarize students affiliated with the Student National Medical Association with the National Library of Medicine's online resources that address medical conditions, health disparities, and public health preparedness needs.

The gastrointestinal (GI) tract is teeming with an extremely abundant and diverse microbial community. The members of this community have coevolved along with their hosts over millennia. Until recently, the gut ecosystem was viewed as black box with little knowledge of who or what was there or their specific functions. Over the past decade, however, this ecosystem has become one of fastest growing research areas of focus in microbial ecology and human and animal physiology. This increased interest is largely in response to studies tying microbes in the gut to important diseases afflicting modern society, including obesity, allergies, inflammatory bowel diseases, and diabetes. Although the importance of a resident community of microorganisms in health was first hypothesized by Pasteur over a century ago (Sears, 2005), the multiplicity of physiological changes induced by commensal bacteria has only recently been recognized (Hooper et al., 2001). The term 'ecological development' was recently coined to support the idea that development of the GI tract is a product of the genetics of the host and the host's interactions with resident microbes (Hooper, 2004). The search for new therapeutic targets and disease biomarkers has escalated the need to understand the identities and functions of the microorganisms …

Training Manual updated for United Negro College Fund Special Programs Corporation/National Library of Medicine - HBCU ACCESS Project for Alcorn State University, Natchez, Mississippi, November 12, 2010

Training conducted as a part of the United Negro College Fund Special Programs/National Library of Medicine -HBCU ACCESS Project at Howard University, Washington, DC on November 20, 2010.

The workshop titled, National Library of Medicine: Evidence-based Information At Your Fingertips, is a computer training class designed to meet the needs of nurses who require access to information on specific medical topics and on the adverse health effects of exposure to hazardous substances. The Specialized Information Services Division of the National Library of Medicine (NLM) is sponsoring this workshop for the National Black Nurses Association to increase the awareness of health professionals of the availability and value of the free NLM medical, environmental health, and toxicology databases.

Proceedings of the Environmental Health Information Partnership (EnHIP) Meeting March 25-26, 2010

The HIV/AIDS Information Resources from the National Library of Medicine training is designed specifically for the UNCFSP HBCU Screening, Testing, Outreach, and Prevention (STOP) HIV/AIDS Program project members to provide valuable health information resources from the National Library of Medicine and other reliable sources to increase awareness of the wealth of treatment information and educational materials that are available on the Internet and to improve prevention and treatment education for their clients. These resources will also meet the needs of community-based organizations

This chapter will address some of the many issues associated with the identification of signatures based on genomic DNA/RNA, which can be used to identify and characterize pathogens for biodefense and microbial forensic goals. For the purposes of this chapter, we define a signature as one or more strings of contiguous genomic DNA or RNA bases that are sufficient to identify a pathogenic target of interest at the desired resolution and which could be instantiated with particular detection chemistry on a particular platform. The target may be a whole organism, an individual functional mechanism (e.g., a toxin gene), or simply a nucleic acid indicative of the organism. The desired resolution will vary with each program's goals but could easily range from family to genus to species to strain to isolate. The resolution may not be taxonomically based but rather pan-mechanistic in nature: detecting virulence or antibiotic-resistance genes shared by multiple microbes. Entire industries exist around different detection chemistries and instrument platforms for identification of pathogens, and we will only briefly mention a few of the techniques that we have used at Lawrence Livermore National Laboratory (LLNL) to support our biosecurity-related work since 2000. Most nucleic acid based detection chemistries involve …

This chapter describes the current status of evaluated nuclear data for nuclear technology applications. We start with evaluation procedures for neutron-induced reactions focusing on incident energies from the thermal energy up to 20 MeV, though higher energies are also mentioned. This is followed by examining the status of evaluated neutron data for actinides that play dominant role in most of the applications, followed by coolants/moderators, structural materials and fission products. We then discuss neutron covariance data that characterize uncertainties and correlations. We explain how modern nuclear evaluated data libraries are validated against an extensive set of integral benchmark experiments. Afterwards, we briefly examine other data of importance for nuclear technology, including fission yields, thermal neutron scattering and decay data. A description of three major evaluated nuclear data libraries is provided, including the latest version of the US library ENDF/B-VII.0, European JEFF-3.1 and Japanese JENDL-3.3. A brief introduction is made to current web retrieval systems that allow easy access to a vast amount of up-to-date evaluated nuclear data for nuclear technology applications.

Thermochemical processes are being developed to provide global-scale quantities of hydrogen. A variant on sulfur-based thermochemical cycles is the Hybrid Sulfur (HyS) Process, which uses a sulfur dioxide depolarized electrolyzer (SDE) to produce the hydrogen. In the HyS Process, sulfur dioxide is oxidized in the presence of water at the electrolyzer anode to produce sulfuric acid and protons. The protons are transported through a cation-exchange membrane electrolyte to the cathode and are reduced to form hydrogen. In the second stage of the process, the sulfuric acid by-product from the electrolyzer is thermally decomposed at high temperature to produce sulfur dioxide and oxygen. The two gases are separated and the sulfur dioxide recycled to the electrolyzer for oxidation. The Savannah River National Laboratory (SRNL) has been exploring a fuel-cell design concept for the SDE using an anolyte feed comprised of concentrated sulfuric acid saturated with sulfur dioxide. The advantages of this design concept include high electrochemical efficiency and small footprint compared to a parallel-plate electrolyzer design. This paper will provide a summary of recent advances in the development of the SDE for the HyS process.

Nuclear fission, nuclear fusion, and renewable energy (including biofuels) are the only energy sources capable of satisfying the Earth's need for power for the next century and beyond without the negative environmental impacts of fossil fuels. Substantially increasing the use of nuclear fission and renewable energy now could help reduce dependency on fossil fuels, but nuclear fusion has the potential of becoming the ultimate base-load energy source. Fusion is an attractive fuel source because it is virtually inexhaustible, widely available, and lacks proliferation concerns. It also has a greatly reduced waste impact, and no danger of runaway reactions or meltdowns. The substantial environmental, commercial, and security benefits of fusion continue to motivate the research needed to make fusion power a reality. Replicating the fusion reactions that power the sun and stars to meet Earth's energy needs has been a long-sought scientific and engineering challenge. In fact, this technological challenge is arguably the most difficult ever undertaken. Even after roughly 60 years of worldwide research, much more remains to be learned. the magnitude of the task has caused some to declare that fusion is 20 years away, and always will be. This glib criticism ignores the enormous progress that has occurred …