Authors Website Research Articles

Quantitative linking hypotheses for infant eye movements.

The study of cognitive development hinges, largely, on the analysis of infant looking. But analyses of eye gaze data require the adoption of linking hypotheses: assumptions about the relationship between observed eye movements and underlying cognitive processes. We develop a general framework for constructing, testing, and comparing these hypotheses, and thus for producing new insights into early cognitive development. We first introduce the general framework – applicable to any infant gaze experiment – and then demonstrate its utility by analyzing data from a set of experiments investigating the role of attentional cues in infant learning. The new analysis uncovers significantly more structure in these data, finding evidence of learning that was not found in standard analyses and showing an unexpected relationship between cue use and learning rate. Finally, we discuss general implications for the construction and testing of quantitative linking hypotheses. MATLAB code for sample linking hypotheses can be found on the first author's website.

Latent Curve Models and Latent Change Score Models Estimated in R

In recent years the use of the latent curve model (LCM) among researchers in social sciences has increased noticeably, probably thanks to contemporary software developments and the availability of specialized literature. Extensions of the LCM, like the the latent change score model (LCSM), have also increased in popularity. At the same time, the R statistical language and environment, which is open source and runs on several operating systems, is becoming a leading software for applied statistics. We show how to estimate both the LCM and LCSM with the sem, lavaan, and OpenMx packages of the R software. We also illustrate how to read in, summarize, and plot data prior to analyses. Examples are provided on data previously illustrated by Ferrer, Hamagami, and McArdle (2004). The data and all scripts used here are available on the first author's Web site.

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB

Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use the UniProt Knowledgebase (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations.Results: By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality.Availability: Source code is available at the authors website: http://homepages.cs.ncl.ac.uk/m.j.bell1/annotation.Contact: phillip.lord@newcastle.ac.uk

Fast Simulation of Levy Processes

We present a robust method for simulating an increment of a Levy process, based on decomposing the jump part of the process into the sum of its positive and negative jump components. The characteristic exponent of a spectrally one-sided Levy process has excellent analytic properties, which we exploit to design a fast and accurate algorithm for calculating the cumulative distribution function of an increment of such a process. That algorithm is based on the parabolic inverse Fourier transform method introduced by S. Boyarchenko and S. Levendorskii, while the method of simulating a random variable using the values of its cumulative distribution function goes back to the work of P. Glasserman and Z. Liu.C code based on the simulation algorithm described in this article is available on the author's website for Levy processes of class KoBoL (a.k.a. the CGMY model). It can be used as a building block of any Monte-Carlo program for pricing derivative securities under a KoBoL process. Our method typically performs faster than the CGMY simulation method introduced by Madan and Yor by a factor of 10--100, and sometimes even higher, depending on the type of the option.

Two atlases of abstract chiral polytopes for small groups

We construct chiral abstract polytopes in two different ways. Firstly we seek them as quotients of regular polytopes arising from the Atlas of Small Regular Polytopes ( http://www.abstract-polytopes.com/atlas/ ); the resulting atlas of chiral polytopes atlas is available on the website http://www.abstract-polytopes.com/chiral/ . Secondly, for each almost simple group Γ such that S ≤ Γ ≤ Aut( S ) where S is a simple group and Γ is a group of order less than 900,000 listed in the Atlas of Finite Groups, we give, up to isomorphism, the number of abstract chiral polytopes on which Γ acts regularly. The results have been obtained using a series of Magma programs. All these polytopes are made available on the third author's website, at http://math.auckland.ac.nz/~dleemans/CHIRAL/ .

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.

A Guide to Conducting a Systematic Literature Review of Information Systems Research

This working paper has been thoroughly revised and superseded by two distinct articles. The first is a revised and peer-reviewed version of the original article: Okoli, Chitu (2015), A Guide to Conducting a Standalone Systematic Literature Review. Communications of the Association for Information Systems (37:43), November 2015, pp. 879-910. This article presents a methodology for conducting a systematic literature review with many examples from IS research and references to guides with further helpful details. The article is available from Google Scholar or from the author's website. The second extension article focuses on developing theory with literature reviews: Okoli, Chitu (2015), The View from Giants’ Shoulders: Developing Theory with Theory-Mining Systematic Literature Reviews. SSRN Working Paper Series, December 8, 2015. This article identifies theory-mining reviews, which are literature reviews that extract and synthesize theoretical concepts from the source primary studies. The article demonstrates by citation analysis that, in information systems research, this kind of literature review is more highly cited than other kinds of literature review. The article provides detailed guidelines to writing a high-quality theory-mining review.

Clustering with position-specific constraints on variance: Applying redescending M-estimators to label-free LC-MS data analysis

BackgroundClustering is a widely applicable pattern recognition method for discovering groups of similar observations in data. While there are a large variety of clustering algorithms, very few of these can enforce constraints on the variation of attributes for data points included in a given cluster. In particular, a clustering algorithm that can limit variation within a cluster according to that cluster's position (centroid location) can produce effective and optimal results in many important applications ranging from clustering of silicon pixels or calorimeter cells in high-energy physics to label-free liquid chromatography based mass spectrometry (LC-MS) data analysis in proteomics and metabolomics.ResultsWe present MEDEA (M-Estimator with DEterministic Annealing), an M-estimator based, new unsupervised algorithm that is designed to enforce position-specific constraints on variance during the clustering process. The utility of MEDEA is demonstrated by applying it to the problem of "peak matching"--identifying the common LC-MS peaks across multiple samples--in proteomic biomarker discovery. Using real-life datasets, we show that MEDEA not only outperforms current state-of-the-art model-based clustering methods, but also results in an implementation that is significantly more efficient, and hence applicable to much larger LC-MS data sets.ConclusionsMEDEA is an effective and efficient solution to the problem of peak matching in label-free LC-MS data. The program implementing the MEDEA algorithm, including datasets, clustering results, and supplementary information is available from the author website at http://www.hephy.at/user/fru/medea/.

A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues

Monoclonal antibodies (mAbs) are among the most powerful and important tools in biology and medicine. MAb development is of great significance to many research and clinical applications. Therefore, objective mAb classification is essential for categorizing and comparing mAb panels based on their reactivity patterns in different cellular species. However, typical flow cytometric mAb profiles present unique modeling challenges with their non-Gaussian features and intersample variations. It makes accurate mAb classification difficult to do with the currently used kernel-based or hierarchical clustering techniques. To address these challenges, in the present study we developed a formal two-step framework called mAbprofiler for systematic, parametric characterization of mAb profiles. Further, we measured the reactivity of hundreds of new antibodies in diverse tissues using flow cytometry, which we successfully classified using mAbprofiler. First, mAbprofiler fits a mAb's flow cytometric histogram with a finite mixture model of skew t distributions that is robust against non-Gaussian features, and constructs a precise, smooth and mathematically rigorous profile. Then it performs novel curve clustering of the fitted mAb profiles using a skew t mixture of non-linear regression model that can handle intersample variation. Thus, mAbprofiler provides a new framework for identifying robust mAb classes, all well defined by distinct parametric templates, which can be used for classifying new mAb samples. We validated our classification results both computationally and empirically using mAb profiles of known classification. A demonstration code in R is available at the journal website. The R code implementing the full framework is available from the author website - http://amath.nchu.edu.tw/www/teacher/tilin/software saumyadipta_pyne@dfci.harvard.edu Supplementary data are available at Bioinformatics online.

Essentials of Paleomagnetism

This book lives up to its title and does so in a manner that authors of modern science textbooks should seek to emulate. The book is produced as an affordable paperback and an even more affordable e‐book. It contains 16 chapters, several appendices, and more than 250 high‐quality illustrations. As a bonus, a considerable amount of related material that parallels the book is made freely available from the author's Web site (http://magician.ucsd.edu/~ltauxe), including the companion PmagPy software package, which is used throughout the book for hands‐on problem solving.

Data Preparation 101: How To Use Query-By-Example To Get Your Research Dataset Ready For Primetime

Researchers are often distressed to discover that the data they wanted to use in their landmark study is not configured in a way that is usable by a Statistical Analysis Software Package (SASP). For example, the data needed may come from two or more sources and it may not be clear to the researcher how to get them combined into one analyzable dataset. Fortunately, there is hope. The query facility within database management software (DBMS), such as Microsoft Access, is particularly well-equipped to do the data reconfigurations necessary to get datasets ready for a SASP. Unfortunately, most researchers have either never been exposed to a DBMS or are unaware of the powerful data-transforming queries that they can perform. The purpose of this paper is to introduce researchers to some very helpful and relatively easy to learn techniques for solving common dataset misconfiguration problems. It is presented in three sets of hands-on examples: (1) how to import a dataset from an electronic spreadsheet into a database table, (2) how to use an easy-to-learn DBMS facility called Query-By-Example (QBE) to perform specific data reconfiguration tasks, and (3) how to import the reconfigured dataset from the DBMS into a SASP. The software used is MS Excel, MS Access, and SPSS (originally called Statistical Package for the Social Sciences). The examples are presented step-by-step so that the reader can follow along using files downloadable from the authors website

Flexible, reliable software: using patterns and agile development

Flexible, Reliable Software: Using Patterns and Agile Development guidesstudents through the software development process. By describing practical stories, explaining the design and programming process in detail, and using projects as a learning context, the text helpsreaders understand why a given technique is required and why techniques must be combined to overcome the challenges facing software developers. The presentation is pedagogically organized as a realistic development story in which customer requests require introducing new techniques to combat ever-increasing software complexity. After an overview and introduction of basic terminology, the book presents the core practices, concepts, tools, and analytic skills for designing flexible and reliable software, including test-driven development, refactoring, design patterns, test doubles, and responsibility driven and compositional design. It then provides a collection of design patterns leading to a thorough discussion of frameworks, exemplified by a graphical user interface frramework (MiniDraw). The author also discusses the important topics of configuration management and systematic testing. In the last chapter, projects lead students to design and implement their own frameworks, resulting in a reliable and usable implementation of a large and complex software system complete with a graphical user interface. This textteacheshow to design, program, and maintain flexible and reliable software. Installation guides, source code for the examples, exercises, and projects can be found on the authors website.

4. Bayesian Propensity Score Estimators: Incorporating Uncertainties in Propensity Scores into Causal Inference

Despite their popularity, conventional propensity score estimators (PSEs) do not take into account uncertainties in propensity scores. This paper develops Bayesian propensity score estimators (BPSEs) to model the joint likelihood of both propensity score and outcome in one step, which naturally incorporates such uncertainties into causal inference. Simulations show that PSEs using estimated propensity scores tend to overestimate variations in the estimates of treatment effects—that is, too often they provide larger than necessary standard errors and lead to overly conservative inference—whereas BPSEs provide correct standard errors for the estimates of treatment effects and valid inference. Compared with other variance adjustment methods, BPSEs are guaranteed to provide positive standard errors, more reliable in small samples, can be readily employed to draw inference on individual treatment effects, etc. To illustrate the proposed methods, BPSEs are applied to evaluating a job training program. Accompanying software is available on the author's website.

Algorithms in bioinformatics: a practical introduction

This text focuses on using algorithms and discrete mathematics to solve biological problems. It systematically describes biological applications, the corresponding mathematical/computational problems, and various algorithmic solutions. The author also discusses the practical use of many algorithmic methods and describes what algorithms should be used in different situations. Each chapter contains an overview of the biological problem, a precise definition of the computational problem, a description of various methods, practical issues and further research, references to further reading, and a set of knowledge-testing exercises. Instruction and data for practical exercises are provided on the authors website.

Relevance ratings and salience categorizations for objects in a set of 80 pictures

In this study, we provide normative data for objects in a set of 80 digital color pictures (e.g., nature scenes, human activities, cartoon characters, magazine covers). In Experiment 1, four objects in each picture were rated by 48 observers on a 6-point Likert scale for their relevance to the overall meaning of the scene. In Experiment 2, Salience Toolbox software (Walther & Koch, 2006) provided additional information about whether the four relevance-rated objects were located in areas that were high or low in visual salience. Brief descriptions of the four objects, their locations in the picture, their categorizations as high or low in salience, the means and standard deviations of their relevance ratings, and statistical analyses specifying which pairs of objects in a picture differed significantly on their relevance to the meaning of the scene are given in the Appendix. An example is provided of how the pictures could be used to create stimuli for a change blindness task in which detection of item onset versus offset is contrasted for low-relevance and high-relevance features. The 80 pictures are accessible as jpg files from the first author's Web site at http://marcellm.people.cofc.edu/research.htm.

Periodicity Detection Method for Small-Sample Time Series Datasets

Time series of gene expression often exhibit periodic behavior under the influence of multiple signal pathways, and are represented by a model that incorporates multiple harmonics and noise. Most of these data, which are observed using DNA microarrays, consist of few sampling points in time, but most periodicity detection methods require a relatively large number of sampling points. We have previously developed a detection algorithm based on the discrete Fourier transform and Akaike’s information criterion. Here we demonstrate the performance of the algorithm for small-sample time series data through a comparison with conventional and newly proposed periodicity detection methods based on a statistical analysis of the power of harmonics.We show that this method has higher sensitivity for data consisting of multiple harmonics, and is more robust against noise than other methods. Although “combinatorial explosion” occurs for large datasets, the computational time is not a problem for small-sample datasets. The MATLAB/GNU Octave script of the algorithm is available on the author’s web site: http://www.cbrc.jp/%7Etominaga/piccolo/.

Standardized mixed language programming for Fortran and C

Programmers have long practiced the matter of mixed language procedure calls. This is particularly true for the programming languages C and Fortran. The use of the alternate language often results in efficient running time or the effective use of human or other resources. Prior to the Fortran 2003 standard there was silence about how the two languages interoperated. Before this release there existed a set of differing ad hoc methods for making the inter-language calls. These typically depended on the Fortran and C compilers. The newer Fortran standard provides an intrinsic module, iso_c_binding, that permits the languages to interoperate. There remain restrictions regarding interoperable data types. This paper illustrates several programs that contain core exercises likely to be encountered by programmers. The source code is available from the first author's web site. Included is an illustration of a "trap" based on use of the ad hoc methods: A call from a C to a Fortran 2003 routine that passes a character in C to a character variable in Fortran results in a run-time error.

Optimizing substitution matrix choice and gap parameters for sequence alignment

BackgroundWhile substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or approximately optimal gap penalties. It is also not well understood which substitution matrices are the most effective when alignment accuracy is the goal rather than homolog recognition. Here a new parameter optimization procedure, POP, is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments.ResultsPOP is compared to a recent method due to Kim and Kececioglu and found to achieve from 0.2% to 1.3% higher accuracies on pair-wise benchmarks extracted from BALIBASE. The VTML matrix series is shown to be the most accurate on several global pair-wise alignment benchmarks, with VTML200 giving best or close to the best performance in all tests. BLOSUM matrices are found to be slightly inferior, even with the marginal improvements in the bug-fixed RBLOSUM series. The PAM series is significantly worse, giving accuracies typically 2% less than VTML. Integer rounding is found to cause slight degradations in accuracy. No evidence is found that selecting a matrix based on sequence divergence improves accuracy, suggesting that the use of this heuristic in CLUSTALW may be ineffective. Using VTML200 is found to improve the accuracy of CLUSTALW by 8% on BALIBASE and 5% on PREFAB.ConclusionThe hypothesis that more accurate alignments of distantly related sequences may be achieved using low-identity matrices is shown to be false for commonly used matrix types. Source code and test data is freely available from the author's web site at http://www.drive5.com/pop.

Integrating Literature to Support Mathematics Learning in Middle School

Supporting all students' learning is a challenge for middle grades mathematics teachers. One approach that holds promise is integrating mathematics and literacy, a practice consistent with middle school philosophy. While reading and language arts are typically easy to integrate with other subjects, some have cautioned that integrating mathematics with other subjects may be difficult to do in ways that lead to deep understanding of mathematics content (Klein, 1996; Shanahan, 1997) In particular, new research supports integrative approaches that use literature with mathematical themes to support and extend the conceptual understanding of complex mathematical development (Austin, Thompson, & Beckman, 2005; Bean, 2000). This is because familiar contexts allow students to draw on their prior knowledge to bring meaning to the mathematics (Miller, 1998; Murphy, 1999; Whitin, Mills, & O'Keefe, 1990; Whitin & Wilde, 1992). Integrating mathematics and literacy creates opportunities to introduce new vocabulary, make connections among abstract concepts, and showcase ways that mathematics applies across curriculum (Whitin & Wilde, 1992). In addition, integrating multicultural literature in the mathematics classroom can provide familiar contexts for culturally diverse students and it can present content from various viewpoints. This can help students develop cultural awareness and sensitivity as it strengthens their mathematical content knowledge and literacy skills (Bean, 2000). One possible reason teachers have difficulty integrating mathematics and literacy is the perceived lack of materials recommended and readily available to middle grades teachers. In this article, we identify a wealth of short stories, novels, and texts that not only represent rich language but also complex mathematical thought. For the purpose of this article, we focus on literature that could be easily integrated into mathematics classrooms. We developed a framework for classifying texts based on the complexity of the mathematics content, and we have organized our discussion according to this framework. Reviewing texts The authors searched extensively to find novels and short stories with mathematical content. Using advanced searching mechanisms and keywords such as math or numbers, we examined online book warehouses (e.g., Amazon.com) and literature databases (e.g., Children's Literature Comprehensive Database). These resources provided all types of literature; however, for the purposes of this article, we limit our discussion to only young adult literature. The second author's website features a complete list of titles, including a brief synopsis of each (http://ksuweb.kennesaw.edu/~fwallac1/). We used national standards for teaching middle grades mathematics to determine the type of mathematical content within these young adult texts (see Figure 1). Broad categories of content in middle grades mathematics classrooms include numbers and operations, algebra, geometry, measurement, data analysis and probability, and problem solving. As we read each text and identified the mathematical content, we found that the potential for using the books to support integrated instruction varied in relation to the complexity of the mathematics. Consequently, we developed categories related to the potential opportunities to teach rich mathematics. In other words, the higher the level of mathematical complexity within a story, the greater the number of opportunities for using integration to support the development of rich mathematical ideas for students. To develop the categories, we compared each new text read with each previously read text and asked questions such as: How does the story support the development of mathematical ideas? What is the purpose of the mathematical content within the story? How is the mathematical content presented? and How are solutions to mathematical problems described? Integrating mathematics and literature Our examination of literature found that middle school mathematical concepts found in the national standards are represented in young adult literature and offer possibilities for integration. …

The Origins, Aims and Future of The Franciscan Authors Website

The Origins, Aims and Future of The Franciscan Authors Website