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Surface geochemistry of the clay minerals.

Clay minerals are layer type aluminosilicates that figure in terrestrial biogeochemical cycles, in the buffering capacity of the oceans, and in the containment of toxic waste materials. They are also used as lubricants in petroleum extraction and as industrial catalysts for the synthesis of many organic compounds. These applications derive fundamentally from the colloidal size and permanent structural charge of clay mineral particles, which endow them with significant surface reactivity. Unraveling the surface geochemistry of hydrated clay minerals is an abiding, if difficult, topic in earth sciences research. Recent experimental and computational studies that take advantage of new methodologies and basic insights derived from the study of concentrated ionic solutions have begun to clarify the structure of electrical double layers formed on hydrated clay mineral surfaces, particularly those in the interlayer region of swelling 2:1 layer type clay minerals. One emerging trend is that the coordination of interlayer cations with water molecules and clay mineral surface oxygens is governed largely by cation size and charge, similarly to a concentrated ionic solution, but the location of structural charge within a clay layer and the existence of hydrophobic patches on its surface provide important modulations. The larger the interlayer cation, the greater the influence of clay mineral structure and hydrophobicity on the configurations of adsorbed water molecules. This picture extends readily to hydrophobic molecules adsorbed within an interlayer region, with important implications for clay-hydrocarbon interactions and the design of catalysts for organic synthesis.

Journal Article↗

Sequence alignment in molecular biology.

Molecular biology is becoming a computationally intense realm of contemporary science and faces some of the current grand scientific challenges. In its context, tools that identify, store, compare and analyze effectively large and growing numbers of bio-sequences are found of increasingly crucial importance. Biosequences are routinely compared or aligned, in a variety of ways, to infer common ancestry, to detect functional equivalence, or simply while searching for similar entries in a database. A considerable body of knowledge has accumulated on sequence alignment during the past few decades. Without pretending to be exhaustive, this paper attempts a survey of some criteria of wide use in sequence alignment and comparison problems, and of the corresponding solutions. The paper is based on presentations and literature given at the Workshop on Sequence Alignment held at Princeton, N.J., in November 1994, as part of the DIMACS Special Year on Mathematical Support for Molecular Biology.

Algorithms↗

Intelligent Systems for Molecular Biology: review of the first international conference.

This review provides a description of the background to the first international conference on Intelligent Systems for Molecular Biology and a problem-oriented overview of the papers presented. It focuses on genome analysis, gene identification, protein and RNA structure prediction and function, the modelling of biochemical pathways and data and knowledge bases. The range and quality of papers indicates that intelligent systems is emerging as an important sub-field of computational applications in the biological sciences.

Artificial Intelligence↗

DNA assembly using bis-peptide nucleic acids (bisPNAs).

DNA nanostructures are ordered oligonucleotide arrangements that have applications for DNA computers, crystallography, diagnostics and material sciences. Peptide nucleic acid (PNA) is a DNA/RNA mimic that offers many advantages for hybridization, but its potential for application in the field of DNA nanotechnology has yet to be thoroughly examined. We report the synthesis and characterization of tethered PNA molecules (bisPNAs) designed to assemble two individual DNA molecules through Watson-Crick base pairing. The spacer regions linking the PNAs were varied in length and contained amino acids with different electrostatic properties. We observed that bisPNAs effectively assembled oligonucleotides that were either the exact length of the PNA or that contained overhanging regions that projected outwards. In contrast, DNA assembly was much less efficient if the oligonucleotides contained overhanging regions that projected inwards. Surprisingly, the length of the spacer region between the PNA sequences did not greatly affect the efficiency of DNA assembly. Reasons for inefficient assembly of inward projecting DNA oligonucleotides include non-sequence-specific intramolecular interactions between the overhanging region of the bisPNA and steric conflicts that complicate simultaneous binding of two inward projecting strands. These results suggest that bisPNA molecules can be used for self-assembling DNA nanostructures provided that the arrangement of the hybridizing DNA oligonucleotides does not interfere with simultaneous hybridization to the bisPNA molecule.

Chromatography, High Pressure Liquid↗

Forensic analysis of nonlinear collusion attacks for multimedia fingerprinting.

Digital fingerprinting is a technology for tracing the distribution of multimedia content and protecting them from unauthorized redistribution. Unique identification information is embedded into each distributed copy of multimedia signal and serves as a digital fingerprint. Collusion attack is a cost-effective attack against digital fingerprinting, where colluders combine several copies with the same content but different fingerprints to remove or attenuate the original fingerprints. In this paper, we investigate the average collusion attack and several basic nonlinear collusions on independent Gaussian fingerprints, and study their effectiveness and the impact on the perceptual quality. With unbounded Gaussian fingerprints, perceivable distortion may exist in the fingerprinted copies as well as the copies after the collusion attacks. In order to remove this perceptual distortion, we introduce bounded Gaussian-like fingerprints and study their performance under collusion attacks. We also study several commonly used detection statistics and analyze their performance under collusion attacks. We further propose a preprocessing technique of the extracted fingerprints specifically for collusion scenarios to improve the detection performance.

Algorithms↗

The Rosetta Stone of stability.

A number of proposals to augment the classical theory of natural selection turn on the need to consider the role of neutral genetic modifications, as well as on the role of patterns of physicochemically stable substructures. There are similarities between this opposition and that within cognitive science, where the dynamic and computational approaches emphasize complementary aspects of perceptual-motor development. This paper summarizes the relevant arguments of the various schools of evolutionary and cognitive theory, as well as the various calls that have been made for unification or complementarity of explanations. An extended concept of stability is then proposed, which bridges the gap between thermodynamic equilibrium and semantic closure.

Biological Evolution↗

SPECT functional brain imaging. Technical considerations.

The technical aspects of functional brain single-photon emission computed tomography (SPECT) imaging, referring primarily to the most common SPECT brain function measure--regional cerebral blood flow--are reviewed. SPECT images of regional cerebral blood flow are influenced by a number of factors unrelated to pathology, including tomographic quality, radiopharmaceuticals, environmental conditions at the time of radiotracer administration, characteristics of the subject (e.g., age, sex), image presentation, and image processing techniques. Modern SPECT scans yield excellent image quality, and instrumentation continues to improve. The armamentarium of regional cerebral blood flow and receptor radiopharmaceuticals is rapidly expanding. Standards regarding the environment for patient imaging and image presentation are emerging. However, there is still much to learn about the circumstances for performances and evaluation of SPECT functional brain imaging. Challenge tests, primarily established in cerebrovascular disease (i.e., the acetazolamide test), offer great promise in defining the extent and nature of disease, as well as predicting therapeutic responses. Clearly, SPECT brain imaging is a powerful clinical and research tool. However, SPECT will only achieve its full potential in the management of patients with cerebral pathology through close cooperation among members of the nuclear medicine, neurology, psychiatry, neurosurgery, and internal medicine specialties.

Brain↗

The origins of informatics.

This article summarizes the origins of informatics, which is based on the science, engineering, and technology of computer hardware, software, and communications. In just four decades, from the 1950s to the 1990s, computer technology has progressed from slow, first-generation vacuum tubes, through the invention of the transistor and its incorporation into microprocessor chips, and ultimately, to fast, fourth-generation very-large-scale-integrated silicon chips. Programming has undergone a parallel transformation, from cumbersome, first-generation, machine languages to efficient, fourth-generation application-oriented languages. Communication has evolved from simple copper wires to complex fiberoptic cables in computer-linked networks. The digital computer has profound implications for the development and practice of clinical medicine.

Computer Communication Networks↗

Trends in rates of occupational fatal injuries in the United States (1983-92).

OBJECTIVES: An updated version of a national surveillance system of traumatic occupational fatalities was used to explore adjusted and unadjusted trends in rates of fatal injury. METHODS: Data from the national traumatic occupational fatalities surveillance system were combined with data on employment from the United States Bureau of Labor Statistics. Poisson regression was then used to examine trends in rates of occupational fatality injuries while controlling for demographic and workplace characteristics. RESULTS: Adjusted annual changes in rates of fatal injuries ranged from a decline of 6.2% for workers in technical and administrative support occupations--for example, health, science, and engineering technicians, pilots, computer programmers--to an increase of 1.6% in machine operators, assemblers, and inspectors. For industries, annual changes ranged from a decline of 5.3% for workers in public administration--for example, justice, public order, and safety workers--to an increase of 2.6% for workers in the wholesale trade. By comparison, the annual decline over all industries and occupations was 3.1%. In many industries and occupations, an effect modification of annual trends by the age of the worker was also found with the oldest workers experiencing either no decline or a significant increase in rates of fatal injuries. CONCLUSIONS: This general pattern of decline, adjusted for the effects of demographic characteristics of the worker population, is encouraging; however, increases in rates of fatal injuries found in particular industries and occupations, suggest appropriate targets for increased injury prevention efforts.

Accidents, Occupational↗

The road to Yellowstone--and beyond.

This memoir describes the professional life and times of Thomas D. Brock, with an emphasis on those aspects of his career relating to research in microbial ecology, and how this work led to field research in Yellowstone. The first discovery of extremely thermophilic bacteria is described, followed by a discussion of some of the consequences of this discovery for biotechnology and microbiology. Also covered briefly in this memoir are Brock's activities in textbook writing, publishing, computers, and the history of science.

Bacteria↗

Student Assistant for Learning from Text (SALT): a hypermedia reading aid.

Student Assistant for Learning from Text (SALT) is a software system for developing hypermedia versions of textbooks designed to help students with learning disabilities and other low-achieving students to compensate for their reading difficulties. In the present study, 10 students with learning disabilities (3 young women and 7 young men ages 15 to 17) in Grades 9 and 10 read passages from a science textbook using a basic computer version and an enhanced computer version. The basic version included the components found in the printed textbook (text, graphics, outline, and questions) and a notebook. The enhanced version added speech synthesis, an on-line glossary, links between questions and text, highlighting of main ideas, and supplementary explanations that summarized important ideas. Students received significantly higher comprehension scores using the enhanced version. Furthermore, students preferred the enhanced version and thought it helped them learn the material better.

Adolescent↗

Electrocorticographic and histological findings in a Shetland sheepdog with intractable epilepsy.

A Shetland sheepdog with epilepsy refractory to antiepileptic drugs was brought to the division of Veterinary Radiology at Nippon Veterinary and Animal Science University. Scalp electroencephalography and computed tomography was performed, but no abnormality was detected in either examination. To obtain detailed information, electrodes were implanted on the dura mater, and the electrocorticogram (ECoG) was recorded. In the ECoG, sporadic spikes were detected in the left parietal region, suggesting the presence of the epileptic focus in this region. After the dog's death, abnormalities of gyri were found in the region where spikes were detected in the ECoG. On histopathological examination, laminar malacia of the cingulate gyrus was observed. Furthermore, in the hippocampus, neuronal loss of pyramidal cells was observed.

Animals↗

Applying the transtheoretical model to pregnancy and STD prevention: a review of the literature.

PURPOSE: To conduct a systematic review of the peer-reviewed literature on the Transtheoretical Model (TTM) and pregnancy and STD prevention. DATA SOURCES: Computer database search (Applied Social Science Index and Abstracts [ASSIA], Biological Abstracts, Criminal Justice Abstracts, CINAHL-Allied Health, Current Contents, Current Index to Journals in Education, Education Index, ERIC, Excerpta Medica, Family Index, Index Medicus, Medline, Multicultural Education Abstracts, PsychInfo, Psychological Abstracts, Research Alert, Social Science Citation Index, Social Work Abstracts, and Sociological Abstracts), and manual journal search. STUDY INCLUSION AND EXCLUSION CRITERIA: All English, peer-reviewed, original articles on the TTM as it relates to pregnancy and STD prevention published prior to December 31, 2001, were included. Editorials, commentaries, thesis/dissertations, unpublished studies, technical reports, and books were not included. DATA EXTRACTION METHODS: Articles were categorized as Intervention, Population (stage distribution), or Validation studies. Within each category, articles were subdivided into groups, summarized, and analyzed. DATA SYNTHESIS: The 32 articles reviewed included 9 intervention studies, 11 population studies, and 12 validation studies. Studies represented a variety of U.S. populations of a broad demographic range. Evidence both for and against criterion-related and construct validity of the TTM was found. MAJOR CONCLUSIONS: Age, partner type, gender, reasons for engaging in safer sex behaviors (i.e., pregnancy vs. disease prevention), self-efficacy, sexual assertiveness, and perceived advantages and disadvantages of condom use were related to stage of change. The use of the TTM to reduce risk of pregnancy and STDs is a relatively new, but important, area of research. However, because of the wide-ranging differences in methodologies and samples, no strong conclusions about its effectiveness can yet be made.

Algorithms↗

Where does informatics fit in health care organizations?

Why is medical informatics important to health care leaders? As an emerging science, informatics focuses on applying computing and communication technology to decision making for clinicians and managers. It enhances the understanding of how information and communication systems can impact the work health care managers must accomplish. As the cost of technology for digital information management continues to decline, organizations and individuals will look for ways to offset the human costs of managing and conveying information. The way of the paper medical record is being replaced by the less expensive and more efficient digital information systems. Leaders of health care organizations need to look for every opportunity to deploy networks and computers to reduce the labor costs of data collection, storage, retrieval, and analysis.

Computer Communication Networks↗

Dental characteristics of a large military population useful for identification.

The number and complexity of dental restorations has decreased for younger Americans. Since the presence and extent of restorations are important data for forensic science identification purposes, the Computer-Assisted Postmortem Identification (CAPMI) system was used to assess the practical effect of the decreased selectivity expected as a result of improved dental health. Dental examination data from 7030 soldiers were recorded on optical mark read forms and entered into a database. The data were reorganized and analyzed to generate summary statistics about the incidence of each type of restoration (divided into 16 categories) for both anterior, posterior, upper, lower, and combined segments. Patients' ages ranged from 17 to 49 with a mean of 24 years 5 months. Sixty percent were from 18 to 25 years old. A characteristic is defined as any situation other than a virgin tooth; for example, extracted, missing, unerupted, or restored. The average subject had 7 dental characteristics with approximately 75% having 4 or more. Within the entire population, 9% had 32 unrestored teeth. 3.6% had only one characteristic. To test the selectivity and uniqueness of various combinations of dental characteristics, 363 simulations using the CAPMI system were made against the entire 7030 subject database. Sample records (33 per group) with 2, 3, 4, 5, 6, 7, 8, 9-11, 12-14, 15-18, and 19+ characteristics were chosen at random from the database and searches were made.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

[An innovative program for teaching social medicine at the Medical School for Hygiene at Charles University].

The author makes readers familiar with the programme of innovation of training in social medicine at the Medical Faculty of Hygiene, Charles University. In his opinion the demands on rationalization and intensification of health services call for enlargement of undergraduate training in social medicine by findings from the science on systems, management and computers, and last not least economics of the health services.

Czechoslovakia↗

CINAHL list of subject headings: a nursing thesaurus revised.

The rationale and methods for revising the thesaurus of one of the major health sciences indexing tools are discussed. Computer production of the Cumulative Index to Nursing & Allied Health Literature and the possibility of online access mandated a revision of the list of subject headings. CINAHL has maintained a policy of responding to user needs and to changes in the nursing and allied health literature, and user input was encouraged during revision of the thesaurus. The methods of structural revision are described, and major changes in the thesaurus are detailed. Modification of the thesaurus is expected to have a far-reaching impact on the retrieval of information in nursing and allied health. Nursing and Allied Health (CINAHL) is now available online through DIALOG (file 218) and BRS (access code NAHL).

Abstracting and Indexing↗

Parallel numerical simulation of the ultrasonic waves in a prestressed formation.

Formation stress prediction plays an important role in petroleum production. Understanding ultrasonic wave propagation in a stress-induced anisotropic formation will help us to find an efficient method to correctly predict formation stress or formation pore pressure. In this work, a parallel 3D finite-difference time domain (FDTD) method is developed to simulate elastic wave propagation in pre-stressed formations. A perfectly matched layer (PML) is used as an absorbing boundary condition. The acceleration ration of total CPU computation time and the lasting time of the program run in the super computer-ShenTeng 6800 in the Super Computation Center of Chinese Academy of Science (CAS) are tested. It shows that the acceleration factor of the parallel FDTD program is considerably high even if the domain is only divided in one direction. When the total computation model size fixed, the acceleration factor of 8 CPU and 64 CPU is 3.0 and 13.8, respectively. The velocities under various static stresses are obtained by processing the array data calculated with the FDTD using Prony's method. The linear relation between velocity and the applied pre-stress is in agreement with that predicted by the acoustoelasticity theory. Results from the numerical simulation confirm the reciprocity principle and the superposition principle.

Journal Article↗