Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects

Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used, significant challenges remain, and there are many opportunities for statisticians to make important contributions. In the most widely used "bottom-up" approach to proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical properties and analyzed using a mass spectrometer. The two fundamental challenges in the analysis of bottom-up MS-based proteomics are: (1) Identifying the proteins that are present in a sample, and (2) Quantifying the abundance levels of the identified proteins. Both of these challenges require knowledge of the biological and technological context that gives rise to observed data, as well as the application of sound statistical principles for estimation and inference. We present an overview of bottom-up proteomics and outline the key statistical issues that arise in protein identification and quantification.     

THE POWER AND SIZE OF NONPARAMETRIC TESTS FOR COMMON DISTRIBUTIONAL CHARACTERISTICS

This paper considers the power and size properties of some well known nonparametric linear rank tests for location and scale as well as the Kolmogorov-Smirnov omnibus test and proposed alternatives to it. Independence between some classes of linear rank tests is established facilitating their joint application. Monte Carlo study confirms the asymptotic power properties of the linear rank tests but raises concerns about their application in more general and practically relevant circumstances. It also indicates that the new omnibus tests constitute viable alternatives with superior properties to the Kolmogorov-Smirnov test in certain circumstances.     

Micro-Political Strategies and Their Implications for Participative Decision Making

Drawing on both organizational behaviour and employee relations perspectives,the paper defines participation as `opportunity to influence decisions,' andconsiders the impact of the micro-political behaviour of organization membersin pursuit of their interests on the development of genuine participation.Three types of micro-political strategy are identified and their implicationsdiscussed: information control, flexibility, and stage-craft. The discussionis illustrated with findings from an international study of decision making,and brief comment is made on international cultural differences as acomplicating factor. It is suggested that the role of participation in enhancing the knowledge baseof the organization has been neglected. If genuine participation is to beinstituted, decision making will become more complex, requiring negotiation,not only of competing interests but also of what is to be accepted as`knowledge' in the organization. This in turn will place greater demands onthe intellectual skills and personal behaviour of participants.     

Payoff Effects in Information Cascade Experiments

Error rates are estimated using data from "information cascade" experiments. The econometric estimation assumes a logistic error structure and error rates are compared across three experimental treatments that differ only with respect to payoff structure. In a "no payoff" treatment subjects receive a fixed payment for participating in the experiment and earnings do not vary with decisions. In "payoff" and "double payoff" treatments earnings depend on each subject's decisions. The results indicate that rewarding correct decisions reduces the amount of decision error. However, increasing the payment for a correct decision does not reduce errors over the range of payoffs considered.     

Housing Conditions of Nuclear and Extended Households in the Miami-Fort Lauderdale Area

Arrivals of new immigrants into the south Florida area have put increased pressure on housing markets and fostered renewed efforts to provide more affordable housing. Many view household extension largely as a response to the lack of a sufficient amount of affordable housing. This paper examines the nature, proportion and housing condition of nuclear and extended households in the Miami-Fort Lauderdale area. The study also investigates how the incidence and housing situation of extended households has changed during the period from 1986 to 1990. This study illustrates that extended families in the Miami-Fort Lauderdale area are not uniformly worse off than nuclear families, given ethnicity and income level. While the area's housing problems require attention, some of that attention should be focused on removing institutional barriers to household extension and to providing broader housing choices for minority ethnic groups.     

Principles of Good Practice for the Use of Monte Carlo Techniques in Human Health and Ecological Risk Assessments

We propose 14 principles of good practice to assist people in performing and reviewing probabilistic or Monte Carlo risk assessments, especially in the context of the federal and state statutes concerning chemicals in the environment. Monte Carlo risk assessments for hazardous waste sites that follow these principles will be easier to understand, will explicitly distinguish assumptions from data, and will consider and quantify effects that could otherwise lead to misinterpretation of the results. The proposed principles are neither mutually exclusive nor collectively exhaustive. We think and hope that these principles will evolve as new ideas arise and come into practice.     

Open Access Mandates and Policies: The Basics

Abstract

Universities can afford to subscribe to only a small percentage of available scholarly journals. Consequently, researchers do not have access to all articles in journals pertinent to their fields of study. The Open Access (OA) movement began in response to wanting to find a solution to this “serials crisis” and the availability of the Internet to disseminate scholarly research in new and innovative ways to a larger, worldwide audience. OA mandates are policies adopted by research institutions, universities, or funders that require researchers to provide free, unrestricted access to their published research by publishing in OA journals, depositing their articles in an OA repository or both. This edition of “In Lay Terms” provides basic information about OA mandates and policies, gives an overview of university and funder OA mandates, discusses geographic differences in policies and compliance rates, and reviews United States federal funding agencies’ OA policies and Plan S.