A graph-theory method for pattern identification in geographical epidemiology - a preliminary application to deprivation and mortality

Background: Graph theoretical methods are extensively used in the field of computational chemistry to search datasets of compounds to see if they contain particular molecular substructures or patterns. We describe a preliminary application of a graph theoretical method, developed in computational chemistry, to geographical epidemiology in relation to testing a prior hypothesis. We tested the methodology on the hypothesis that if a socioeconomically deprived neighbourhood is situated in a wider deprived area, then that neighbourhood would experience greater adverse effects on mortality compared with a similarly deprived neighbourhood which is situated in a wider area with generally less deprivation. Methods: We used the Trent Region Health Authority area for this study, which contained 10,665 census enumeration districts (CED). Graphs are mathematical representations of objects and their relationships and within the context of this study, nodes represented CEDs and edges were determined by whether or not CEDs were neighbours (shared a common boundary). The overall area in this study was represented by one large graph comprising all CEDs in the region, along with their adjacency information. We used mortality data from 1988-1998, CED level population estimates and the Townsend Material Deprivation Index as an indicator of neighbourhood level deprivation. We defined deprived CEDs as those in the top 20% most deprived in the Region. We then set out to classify these deprived CEDs into seven groups defined by increasing deprivation levels in the neighbouring CEDs. 506 (24.2%) of the deprived CEDs had five adjacent CEDs and we limited pattern development and searching to these CEDs. We developed seven query patterns and used the RASCAL (Rapid Similarity Calculator) program to carry out the search for each of the query patterns. This program used a maximum common subgraph isomorphism method which was modified to handle geographical data. Results: Of the 506 deprived CEDs, 10 were not identified as belonging to any of the seven groups because they were adjacent to a CED with a missing deprivation category quintile, and none fell within query Group 1 (a deprived CED for which all five adjacent CEDs were affluent). Only four CEDs fell within Group 2, which was defined as having four affluent adjacent CEDs and one non-affluent adjacent CED. The numbers of CEDs in Groups 3-7 were 17, 214, 95, 81 and 85 respectively. Age and sex adjusted mortality rate ratios showed a non-significant trend towards increasing mortality risk across Groups (Chi-square = 3.26, df = 1, p = 0.07). Conclusion: Graph theoretical methods developed in computational chemistry may be a useful addition to the current GIS based methods available for geographical epidemiology but further developmental work is required. An important requirement will be the development of methods for specifying multiple complex search patterns. Further work is also required to examine the utility of using distance, as opposed to adjacency, to describe edges in graphs, and to examine methods for pattern specification when the nodes have multiple attributes attached to them

Subjectivity in personal storytelling with visualization

In this article we explore visualization for personal storytelling and investigate techniques for communicating subjective experiences in personal visual narratives. Personal stories are often subjective and storytellers omit, make up, or embellish details to craft engaging stories or to communicate a perspective. As growing personal data collections allow individuals to leverage visualizations, we explore how personal visual narratives can express subjectivity. From an analysis of personal visualizations created by data enthusiasts, designers and artists, we collect techniques for deliberately expressing subjectivity during data collection, processing, visual encoding, and presentation. Our results prompt a discussion about the role and potential of subjectivity in personal visual storytelling

Rapid Quantification of Molecular Diversity for Selective Database Acquisition

There is an increasing need to expand the structural diversity of the molecules investigated in lead-discovery programs. One way in which this can be achieved is by acquiring external datasets that will enhance an existing database. This paper describes a rapid procedure for the selection of external datasets using a measure of structural diversity that is calculated from sums of pairwise intermolecular structural similarities

Stream bank erosion rates of small Missouri streams

Paper presented at the 11th North American Agroforesty Conference, which was held May 31-June 3, 2009 in Columbia, Missouri.In Gold, M.A. and M.M. Hall, eds. Agroforestry Comes of Age: Putting Science into Practice. Proceedings, 11th North American Agroforestry Conference, Columbia, Mo., May 31-June 3, 2009.Sedimentation of surface waters in the United States is a significant environmental concern. Investigating land use impacts on stream bank erosion rates is intended to lead to the development of improved management practices and provide the basis for targeting the placement of management practices to mitigate this problem. The overall objective of this research was to determine the effect of stream order, adjacent land use, and season on stream bank erosion rates. Study sites were established in 2007 and 2008 within Crooked and Otter Creek watersheds, two claypan watersheds located in northeast Missouri. Detailed site information was recorded, including eroded stream bank length, soil descriptions, gullies, debris dams, cattle access areas, and point bars. A factorial experimental design was implemented with four land uses (cropped, forest, pasture, and riparian forest) and three stream orders (1st, 2nd, 3rd). Each treatment was replicated three times for each stream order, except for the cropped 3rd order treatment as only one suitable treatment could be found. Erosion pins were installed based on bank height and length at each site to measure bank erosion/deposition rates. The effect of different seasons was assessed by measuring the length of the exposed pins three times per year (March, July, and November). Statistical analyses were performed to determine the effect of stream order, land use, and season on erosion rates. The results showed that the seasonal effect was highly significant, with much greater erosion rates in the winter of 2008 compared to the other seasons. Land use was significant when low magnitude deposition was observed and was not significant in any of the seasons in which erosion occurred.C.C. Willett (1), S.A. Berges (2), R.N. Lerch (3), and R.C. Schultz (2) ; 1. Department of Soil, Environmental and Atmospheric Sciences, University of Missouri. 2. Department of Natural Resource, Ecology and Management, Iowa State University. 3. USDA-Agricultural Research Service, Cropping Systems and Water Quality Research Unit, Columbia, MO.Includes bibliographical references

A Fermi Fluid Description of the Half-Filled Landau Level

We present a many-body approach to calculate the ground state properties of a system of electrons in a half-filled Landau level. Our starting point is a simplified version of the recently proposed trial wave function where one includes the antisymmetrization operator to the bosonic Laughlin state. Using the classical plasma analogy, we calculate the pair-correlation function, the static structure function and the ground state energy in the thermodynamic limit. These results are in good agreement with the expected behavior at $\nu=\frac12$.Comment: 4 pages, REVTEX, and 4 .ps file

Open access megajournals: The publisher perspective (Part 2: Operational realities)

This paper is the second of two Learned Publishing articles in which we report the results of a series of interviews, with senior publishers and editors exploring open access megajournals (OAMJs). Megajournals (of which PLoS One is the best known example) represent a relatively new approach to scholarly communication and can be characterized as large, broad-scope, open access journals, which take an innovative approach to peer review, basing acceptance decisions solely on the technical or scientific soundness of the article. Based on interviews with 31 publishers and editors, this paper reports the perceived cultural, operational, and technical challenges associated with launching, growing, and maintaining a megajournal. We find that overcoming these challenges while delivering the societal benefits associated with OAMJs is seen to require significant investment in people and systems, as well as an ongoing commitment to the model

Open-access mega-journals

Purpose: Open-access mega-journals (OAMJs) represent an increasingly important part of the scholarly communication landscape. OAMJs, such as PLOS ONE, are large scale, broad scope journals that operate an open access business model (normally based on article-processing charges), and which employ a novel form of peer review, focusing on scientific ‘soundness’ and eschewing judgment of novelty or importance. This paper examines the discourses relating to OAMJs, and their place within scholarly publishing, and considers attitudes towards mega-journals within the academic community. Design/methodology/approach: This paper presents a review of the literature of OAMJs structured around four defining characteristics: scale, disciplinary scope, peer review policy and economic model. The existing scholarly literature was augmented by searches of more informal outputs, such as blogs and email discussion lists, to capture the debate in its entirety. Findings: While the academic literature relating specifically to OAMJs is relatively sparse, discussion in other fora is detailed and animated, with debates ranging from the sustainability and ethics of the mega-journal model, to the impact of soundness-only peer review on article quality and discoverability, and the potential for OAMJs to represent a paradigm-shifting development in scholarly publishing. Originality/value: This article represents the first comprehensive review of the mega-journal phenomenon, drawing not only on the published academic literature, but also grey, professional and informal sources. The paper advances a number of ways in which the role of OAMJs in the scholarly communication environment can be conceptualised

Open access megajournals: The publisher perspective (Part 1: Motivations)

This paper is the first of two Learned Publishing articles in which we report the results of a series of interviews with senior publishers and editors exploring open access megajournals (OAMJs). Megajournals (of which PLoS One is the best known example) represent a relatively new approach to scholarly communication and can be characterized as large, broad-scope, open access journals that take an innovative approach to peer review, basing acceptance decisions solely on the technical or scientific soundness of the article. This model is often said to support the broader goals of the open science movement. Based on in-depth interviews with 31 publishers and editors representing 16 different organizations (10 of which publish a megajournal), this paper reports how the term ‘megajournal’ is understood and publishers’ rationale and motivations for launching (or not launching) an OAMJ. We find that while there is general agreement on the common characteristics of megajournals, there is not yet a consensus on their relative importance. We also find seven motivating factors that were said to drive the launch of an OAMJ and link each of these factors to potential societal and business benefits. These results suggest that the often polarized debate surrounding OAMJs is a consequence of the extent to which observers perceive publishers to be motivated by these societal or business benefits

Transitioning from a Conventional to a ‘Mega’ Journal: A Bibliometric Case Study of the Journal Medicine

Open-Access Mega-Journals (OAMJs) are a relatively new and increasingly important publishing phenomenon. The journal Medicine is in the unique position of having transitioned in 2014 from being a ‘traditional’ highly-selective journal to the OAMJ model. This study compares the bibliometric profile of the journal Medicine before and after its transition to the OAMJ model. Three standard modes of bibliometric analysis are employed, based on data from Web of Science: journal output volume, author characteristics, and citation analysis. The journal’s article output is seen to have grown hugely since its conversion to an OAMJ, a rise driven in large part by authors from China. Articles published since 2015 have fewer citations, and are cited by lower impact journals than articles published before the OAMJ transition. The adoption of the OAMJ model has completely changed the bibliometric profile of the journal, raising questions about the impact of OAMJ peer-review practices. In many respects, the post-2014 version of Medicine is best viewed as a new journal rather than a continuation of the original title

“Let the community decide”? The vision and reality of soundness-only peer review in open-access mega-journals

Purpose: The aim of this research is to better understand the theory and practice of peer review in open-access mega-journals (OAMJs). Mega-journals typically operate a “soundness only” review policy aiming to evaluate only the rigour of an article, not the novelty or significance of the research or its relevance to a particular community, with these elements being left for “the community to decide” post-publication. Design/methodology/approach: The paper reports the results of interviews with 31 senior publishers and editors representing 16 different organisations, including 10 that publish an OAMJ. Thematic Analysis was carried out on the data and an analytical model developed to explicate their significance. Findings: Findings suggest that in reality criteria beyond technical or scientific soundness can and do influence editorial decisions. Deviations from the original OAMJ model are both publisher-supported (in the form of requirements for an article to be ‘worthy’ of publication) and practice-driven (in the form of some reviewers and editors applying traditional peer review criteria to mega-journal submissions). Also publishers believe post-publication evaluation of novelty, significance, and relevance remains problematic. Originality/value: The study is based on unprecedented access to senior publishers and editors, allowing insight into their strategic and operational priorities. The paper is the first to report in-depth qualitative data relating specifically to soundness-only peer review for OAMJs, shedding new light on the mega-journal phenomenon, and helping inform discussion on its future role in scholarly communication. The paper proposes a new model for understanding the mega-journal approach to quality assurance, and how it is different from traditional peer review