Research papers

The systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models

Michael Hucka, Andrew Finney, Herbert M. Sauro, Hamid Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, B. Bornstein, D…

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Adaptive background mixture models for real-time tracking

Chris Stauffer, W. Eric L. Grimson

A common method for real-time segmentation of moving regions in image sequences involves "background subtraction", or thresholding the error between an estimate of the image without moving objects and the current image. The numerous approaches to this problem differ in the type of background model used and the procedure used to update the model. This paper discusses modeling each pixel as a mixture of Gaussians and using an on-line approximation to update the model. The Gaussian, distributions of the adaptive mixture model are then evaluated to determine which are most likely to result from a background process. Each pixel is classified based on whether the Gaussian distribution which represents it most effectively is considered part of the background model. This results in a stable, real-time outdoor tracker which reliably deals with lighting changes, repetitive motions from clutter, and long-term scene changes. This system has been run almost continuously for 16 months, 24 hours a day, through rain and snow.

Common method biases in behavioral research: A critical review of the literature and recommended remedies.

Philip M. Podsakoff, Scott MacKenzie, Jeong Yeon Lee, Nathan P. Podsakoff

Interest in the problem of method biases has a long history in the behavioral sciences. Despite this, a comprehensive summary of the potential sources of method biases and how to control for them does not exist. Therefore, the purpose of this article is to examine the extent to which method biases influence behavioral research results, identify potential sources of method biases, discuss the cognitive processes through which method biases influence responses to measures, evaluate the many different procedural and statistical techniques that can be used to control method biases, and provide recommendations for how to select appropriate procedural and statistical remedies for different types of research settings.

The concept of allostasis in biology and biomedicine

Bruce S. McEwen, John C. Wingfield

Mathematical Biology

J. D. Murray

The Biology of Wahoo (Acanthocybium solandri) in the Western Central Atlantic

Hazel A. Oxenford, P.A. Murray, Brian E. Luckhurst

This contribution summarizes aspects of the biology of the wahoo, Acanthocybium solandri (Scombridae), that are pertinent to assessment and management of this species in the western central Atlantic (WCA). In this region wahoo is a target species for both commercial and recreational fisheries, and annual landings appear to have increased steadily over the last 30 years to in excess of 2000 mt. Wahoo is believed to be migratory, but little is known of the migration patterns. Significant seasonal variation in catches within the region indicates that it is seasonally abundant in most locations. Periods of peak abundance occur from the fall through spring in the southeastern and northern Caribbean islands, and are restricted to the warmer months (late spring through early fall) in the more northerly locations (northern Gulf of Mexico, North Carolina, and Bermuda). Wahoo exhibits early sexual maturity (within the first year) and a spawning season that extends from at least May to October. Females are multiple batch spawners and are highly fecund. Limited age and growth studies indicate that it is a relatively fast-growing species, has high mortality, and probably lives for 5-6 years. Wahoo is primarily piscivorous, although some invertebrates including squids are eaten. A relatively small number of parasite species have been associated with it. There is no evidence of more than a single shared stock of wahoo in the WCA, and recent genetic studies, using RAPD markers, suggest that stock boundaries may extend beyond this region. The status of the wahoo resource in the WCA remains unclear. Reliable wahoo catch and fishing effort data from the entire WCA, improved knowledge of migration patterns, reproductive characteristics and critical habitat (e.g., preferred spawning areas), validation of age, growth and mortality estimates, and a more comprehensive analysis of stock structure for the entire Atlantic are needed for informed wahoo stock assessment and management.

The DSSAT cropping system model

J. W. Jones, Gerrit Hoogenboom, Cheryl Porter, Kenneth J. Boote, William D. Batchelor, L. A. Hunt, Paul W. Wilkens, Udaya P.…

Relationship between STS approach, scientific literacy, and achievement in biology

N. M. Mbajiorgu, Anthony Ali

Abstract This study set out to investigate the relationship between STS approach, scientific literacy (SL), and achievement in biology. A quasi‐experimental design of the nonequivalent group was employed. Four secondary schools, eight teachers, and 246 students from Nigeria were involved in the study. Two classes were randomly selected from each school and assigned to either the experimental or control group. Two instruments were used to collect data: an Achievement Test on Reproduction and Family Planning and a SL Scale. Results showed that there is no relationship between SL and achievement in biology. The split‐wise posttest regression showed a weak positive relationship between SL and achievement in biology for the experimental group and a no relationship for the control group. However, STS approach mediated between SL and achievement to effect a slightly stronger significant positive relationship. The slope of SL was greater when we controlled for instruction showing that the relationship between SL and achievement is not spurious when instruction is taken into account. We therefore conclude that STS approach might be affecting other variables in the science classroom that in turn affect achievement in the sciences. © 2002 Wiley Periodicals, Inc. Sci Ed 87: 31–39, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/sce.10012

Estimation of Average Treatment Effects Based on Propensity Scores

Sascha O. Becker, Andrea Ichino

In this paper, we give a short overview of some propensity score matching estimators suggested in the evaluation literature, and we provide a set of Stata programs, which we illustrate using the National Supported Work (NSW) demonstration widely known in labor economics.

Particle swarm optimization

James Kennedy, R.C. Eberhart

A concept for the optimization of nonlinear functions using particle swarm methodology is introduced. The evolution of several paradigms is outlined, and an implementation of one of the paradigms is discussed. Benchmark testing of the paradigm is described, and applications, including nonlinear function optimization and neural network training, are proposed. The relationships between particle swarm optimization and both artificial life and genetic algorithms are described.

The world report on violence and health

Etienne Krug, James A. Mercy, Linda L. Dahlberg, Anthony B. Zwi

k-ANONYMITY: A MODEL FOR PROTECTING PRIVACY

Latanya Sweeney

Consider a data holder, such as a hospital or a bank, that has a privately held collection of person-specific, field structured data. Suppose the data holder wants to share a version of the data with researchers. How can a data holder release a version of its private data with scientific guarantees that the individuals who are the subjects of the data cannot be re-identified while the data remain practically useful? The solution provided in this paper includes a formal protection model named k-anonymity and a set of accompanying policies for deployment. A release provides k-anonymity protection if the information for each person contained in the release cannot be distinguished from at least k-1 individuals whose information also appears in the release. This paper also examines re-identification attacks that can be realized on releases that adhere to k-anonymity unless accompanying policies are respected. The k-anonymity protection model is important because it forms the basis on which the real-world systems known as Datafly, μ-Argus and k-Similar provide guarantees of privacy protection.

The Biology of Terrestrial Molluscs

Alan N. Hodgson

"The Biology of Terrestrial Molluscs." African Zoology, 37(2), p. 259

American Association of Colleges of Nursing

Edward L. Beard

Edward L. Beard, Jr, MSN, RN, CNAA, is vice president of Patient Care Services at Catawba Memorial Hospital in Hickory, NC. He is a member of the editorial advisory board of JONA’s Healthcare Law, Ethics, and Regulation.

Proliferation in African Breast Cancer: Biology and Prognostication in Nigerian Breast Cancer Material

Offiong F. Ikpatt, Teijo Kuopio, Yrjö Collan

Three hundred cases of invasive breast carcinoma from the University of Calabar Teaching Hospital, Nigeria were subjected to evaluation of proliferative activity by mitotic counts. The prognostic significance and association with other prognostic factors were evaluated. The mitotic activity was expressed as mitotic activity index (MAI), and standardized mitotic index (SMI). Pearson's correlation and univariate and multivariate Cox's regression were used. The mean follow-up time was 25.9 months. The mean values of SMI and MAI were 42.6 mitotic figures per square millimeter and 30.5 mitotic figures per 10 high-power fields, respectively, and these were much higher than values reported for Europe or other Western countries. The SMI had a positive correlation with tumor size (r = 0.31, P <.0001), histologic grade (r = 0.68, P <.0001), nuclear area (r = 0.45, P <.0001), and negative correlation with fraction of fields with tubular differentiation (FTD; r = -0.56, P = <0.0001). There was no statistically significant difference in the mitotic activity between the postmenopausal and the premenopausal patients. Also, lymph node-positive patients had higher counts than did lymph node-negative patients. Earlier determined grading associated decision thresholds divided the patients into groups of favorable and unfavorable prognosis. However, the statistically optimal thresholds for Nigerian material were different (32 and 92 mitotic figures per square millimeter for SMI). Tumor size of 5 cm, SMI, and MAI were independent prognostic factors. Nigerian breast cancers are high-grade, high-stage, and high-proliferating cancers occurring in a younger population than those of the Western countries. Proliferation is also more active. Evaluation of SMI or MAI can improve the distinction between aggressive and less aggressive variants of breast cancer.

Real-time forecasting of ICME shock arrivals at L1 during the &amp;quot;April Fool’s Day&amp;quot; epoch: 28 March – 21 April 2001

W. Sun, M. Dryer, C. D. Fry, C. S. Deehr, Z. Smith, S.‐I. Akasofu, М. Д. Карталев, K. G. Grigorov

Abstract. The Sun was extremely active during the "April Fool’s Day" epoch of 2001. We chose this period between a solar flare on 28 March 2001 to a final shock arrival at Earth on 21 April 2001. The activity consisted of two presumed helmet-streamer blowouts, seven M-class flares, and nine X-class flares, the last of which was behind the west limb. We have been experimenting since February 1997 with real-time, end-to-end forecasting of interplanetary coronal mass ejection (ICME) shock arrival times. Since August 1998, these forecasts have been distributed in real-time by e-mail to a list of interested scientists and operational USAF and NOAA forecasters. They are made using three different solar wind models. We describe here the solar events observed during the April Fool’s 2001 epoch, along with the predicted and actual shock arrival times, and the ex post facto correction to the real-time coronal shock speed observations. It appears that the initial estimates of coronal shock speeds from Type II radio burst observations and coronal mass ejections were too high by as much as 30%. We conclude that a 3-dimensional coronal density model should be developed for application to observations of solar flares and their Type II radio burst observations.Key words. Interplanetary physics (flare and stream dynamics; interplanetary shocks) – Magnetosheric physics (storms and substorms)

Physics and Applications of Microfluidics in Biology

David J. Beebe, Glennys Mensing, Glenn M. Walker

Fluid flow at the microscale exhibits unique phenomena that can be leveraged to fabricate devices and components capable of performing functions useful for biological studies. The physics of importance to microfluidics are reviewed. Common methods of fabricating microfluidic devices and systems are described. Components, including valves, mixers, and pumps, capable of controlling fluid flow by utilizing the physics of the microscale are presented. Techniques for sensing flow characteristics are described and examples of devices and systems that perform bioanalysis are presented. The focus of this review is microscale phenomena and the use of the physics of the scale to create devices and systems that provide functionality useful to the life sciences.

Ancient Integrals and Modern Numerics - Where's the Physics?

Colin Britcher

It is proposed that engineering educators should carefully consider the use of modern numerical solution techniques as outright replacements for traditional analytical solutions in many applications. Examples are given from the field of aerodynamics, specifically thin airfoil and finite wing theory. It is shown that an arguably more useful solution can be obtained more easily, and with a more direct connection to the underlying physics of the problem, using numerical approaches.

The Structure of Haplotype Blocks in the Human Genome

Stacey Gabriel, S. F. Schaffner, Huy Nguyen, Jamie Moore, Jessica Roy, Brendan Blumenstiel, John M. Higgins, Matthew DeFelic…

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease.

SMOTE: Synthetic Minority Over-sampling Technique

Nitesh V. Chawla, Kevin W. Bowyer, Lawrence Hall, W. Philip Kegelmeyer

An approach to the construction of classifiers from imbalanced datasets is described. A dataset is imbalanced if the classification categories are not approximately equally represented. Often real-world data sets are predominately composed of ``normal'' examples with only a small percentage of ``abnormal'' or ``interesting'' examples. It is also the case that the cost of misclassifying an abnormal (interesting) example as a normal example is often much higher than the cost of the reverse error. Under-sampling of the majority (normal) class has been proposed as a good means of increasing the sensitivity of a classifier to the minority class. This paper shows that a combination of our method of over-sampling the minority (abnormal) class and under-sampling the majority (normal) class can achieve better classifier performance (in ROC space) than only under-sampling the majority class. This paper also shows that a combination of our method of over-sampling the minority class and under-sampling the majority class can achieve better classifier performance (in ROC space) than varying the loss ratios in Ripper or class priors in Naive Bayes. Our method of over-sampling the minority class involves creating synthetic minority class examples. Experiments are performed using C4.5, Ripper and a Naive Bayes classifier. The method is evaluated using the area under the Receiver Operating Characteristic curve (AUC) and the ROC convex hull strategy.

The Cambridge Grammar of the English Language

Rodney Huddleston, Geoffrey K. Pullum

This book presents a new and comprehensive descriptive grammar of English, written by the principal authors in collaboration with an international research team of a dozen linguists in five countries. It represents a major advance over previous grammars by virtue of drawing systematically on the linguistic research carried out on English during the last forty years. It incorporates insights from the theoretical literature but presents them in a way that is accessible to readers without formal training in linguistics. It is based on a sounder and more consistent descriptive framework than previous large-scale grammars, and includes much more explanation of grammatical terms and concepts, together with justification for the ways in which the analysis differs from traditional grammar. The book contains twenty chapters and a guide to further reading. Its usefulness is enhanced by diagrams of sentence structure, cross-references between sections, a comprehensive index, and user-friendly design and typography throughout.

The Entity Relationship Model — Toward a Unified View of Data

Peter Pin-Shan Chen

Mathematical Biology

J. D. Murray

Women in Physics in Ghana: A Situational Analysis

Aba A.B. Andam