Bayesian analysis of directed graphs data with applications to social networks

Summary.  A fully Bayesian analysis of directed graphs, with particular emphasis on applica- tions in social networks, is explored. The model is capable of incorporating the effects of covariates, within and between block ties and multiple responses. Inference is straightforward by using software that is based on Markov chain Monte Carlo methods. Examples are provided which highlight the variety of data sets that can be entertained and the ease with which they can be analysed.     

D-efficient window experimental designs

In the paper we present a new method of calculating sampling intervals, so-called windows, allowing an experimenter some flexibility in timing the sample collection, while a minimum required design efficiency for parameter estimation is assured. The method is based on the Equivalence Theorem for D-optimality what makes the length of each window related to the parameter sensitivities. An example of calculating the windows in a pharmacokinetic study is presented. Some other methods of calculating efficient sampling windows are briefly discussed.     

Adaptive Management: A Paradigm for Remediation of Public Facilities Following a Terrorist Attack

Terrorist actions are aimed at maximizing harm (health, psychological, economical, and political) through the combined physical impacts of the act and fear. Immediate and effective response to a terrorist act is critical to limit human and environmental harm, effectively restore facility function, and maintain public confidence. Though there have been terrorist attacks in public facilities that we have learned from, overall our experiences in restoration of public facilities following a terrorist attack are limited. Restoration of public facilities following a release of a hazardous material is inherently far more complex than in industrial settings and has many unique technical, economic, social, and political challenges. For example, there may be a great need to quickly restore the facility to full operation and allow public access even though it was not designed for easy or rapid restoration, and critical information is needed for quantitative risk assessment and effective restoration must be anticipated to be incomplete and uncertain. Whereas present planning documents have substantial linearity in their organization, the “adaptive management” paradigm provides a constructive parallel paradigm for restoration of public facilities that anticipates and plans for uncertainty, inefficiencies, and stakeholder participation. Adaptive management grew out of the need to manage and restore natural resources in highly complex and changing environments with limited knowledge about causal relationships and responses to restoration actions. Similarities between natural resource management and restoration of a public facility after a terrorist attack suggest that integration of adaptive management principles explicitly into restoration processes will result in substantially enhanced and flexible responses necessary to meet the uncertainties of potential terrorist attacks.     

Mission,money, and merit: Strategic decision making by nonprofit managers

Public and nonprofit organizations need to make strategic choices about where to invest their resources. They also need to expose hidden managerial assumptions and lack of adequate knowledge that prevent the attainment of consensus in strategic decision making. The approach we developed and tested in the field used a dynamic, three‐dimensional model that tracks individual programs in an organization's portfolio on their contribution to mission, money, and merit. The first dimension measures whether the organization is doing the right things; the second, whether it is doing things right financially; and the third, whether it doing things right in terms of quality. Senior managers provide their own evaluations of the organization's programs. Both the consensus view and the variation in individual assessments contribute to an improved managerial understanding of the organization's current situation and to richer discussions in strategic decision making. In field tests, this visual model proved to be a useful and powerful tool for illuminating underlying assumptions and variations in knowledge among managers facing the complex, multidimensional tradeoffs needed in strategic decision making.     

The Access/Impact Problem and the Green and Gold Roads to Open Access

The research access/impact problem arises because journal articles are not accessible to all of their would-be users; hence, they are losing potential research impact. The solution is to make all articles Open Access (OA; i.e., accessible online, free for all). OA articles have significantly higher citation impact than non-OA articles. There are two roads to OA: the “golden” road (publish your article in an OA journal) and the “green” road (publish your article in a non-OA journal but also self-archive it in an OA archive). Only 5% of journals are gold, but over 90% are already green (i.e., they have given their authors the green light to self-archive); yet only about 10–20% of articles have been self-archived. To reach 100% OA, self-archiving needs to be mandated by researchers' employers and funders, as the United Kingdom and the United States have recently recommended, and universities need to implement that mandate.     

Bayesian inference for a discretely observed stochastic kinetic model

The ability to infer parameters of gene regulatory networks is emerging as a key problem in systems biology. The biochemical data are intrinsically stochastic and tend to be observed by means of discrete-time sampling systems, which are often limited in their completeness. In this paper we explore how to make Bayesian inference for the kinetic rate constants of regulatory networks, using the stochastic kinetic Lotka-Volterra system as a model. This simple model describes behaviour typical of many biochemical networks which exhibit auto-regulatory behaviour. Various MCMC algorithms are described and their performance evaluated in several data-poor scenarios. An algorithm based on an approximating process is shown to be particularly efficient.     

Optimal scaling of Metropolis algorithms: Heading toward general target distributions

The authors provide an overview of optimal scaling results for the Metropolis algorithm with Gaussian proposal distribution. They address in more depth the case of high‐dimensional target distributions formed of independent, but not identically distributed components. They attempt to give an intuitive explanation as to why the well‐known optimal acceptance rate of 0.234 is not always suitable. They show how to find the asymptotically optimal acceptance rate when needed, and they explain why it is sometimes necessary to turn to inhomogeneous proposal distributions. Their results are illustrated with a simple example.     

Ecocultural Attributes: Evaluating Ecological Degradation in Terms of Ecological Goods and Services Versus Subsistence and Tribal Values

It is becoming increasingly clear that scientists, managers, lawyers, public policymakers, and the public must decide how to value what is provided by, and is a consequence of, natural resources. While “Western” scientists have clear definitions for the goods and services that ecosystems provide, we contend that these categories do not encompass the full totality of the values provided by natural resources. Partly the confusion results from a limited view of natural resources derived from the need to monetize the value of ecosystems and their component parts. Partly it derives from the “Western” way of separating natural resources from cultural resources or values, and partly it derives from the false dichotomy of assuming that ecosystems are natural, and anything constructed by man is not natural. In this article, we explore the previous assumptions, and suggest that because cultural resources often derive from, and indeed require, intact and unspoiled natural ecosystems or settings, that these values are rightly part of natural resources. The distinction is not trivial because of the current emphasis on cleaning up chemically and radiologically contaminated sites, on restoration of damaged ecosystems, on natural resource damage assessments, and on long‐term stewardship goals. All of these processes depend upon defining natural resources appropriately. Several laws, regulations, and protocols depend upon natural resource trustees to protect natural resources on trust lands, which could lead to the circular definition that natural resources are those resources that the trustees feel they are responsible for. Where subsistence or tribal peoples are involved, the definition of natural resources should be broadened to include those ecocultural attributes that are dependent upon, and have incorporated, natural resources. For example, a traditional hunting and fishing ground is less valued by subsistence peoples if it is despoiled by contamination or physical ecosystem degradation; an Indian sacred ground is tarnished if the surrounding natural environment is degraded; a traditional homeland is less valued if the land itself is contaminated. Our argument is that intact natural resources are essential elements of many cultural resources, and this aspect requires and demands adequate consideration (and may therefore require compensation).