Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method

Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA) and compared it to two other methods, a simpler label free method known as spectral counting and the isotope coded affinity tag (ICAT) method. Data analysis by these methods of a standard mixture containing proteins of known, but varying, concentrations showed that they performed similarly with a mean squared error of 0.09. Additionally, complex bacterial protein mixtures spiked with known concentrations of standard proteins were analyzed using the PICA label-free method. These results indicated that the PICA method detected all levels of standard spiked proteins at the 90% confidence level in this complex biological sample. This finding confirms that label-free methods, based on direct measurement of the area under a single ion current trace, performed as well as the standard ICAT method. Given the fact that the label-free methods provide ease in experimental design well beyond pair-wise comparison, label-free methods such as our PICA method are well suited for proteomic expression profiling of large numbers of samples as is needed in clinical analysis

Global Journalist: How oil production affects the world economy

In this May 8, 2003 episode of Global Journalist, host Byron Scott and four journalists from Venezuela, Saudi Arabia, Nigeria and Russia discuss about how the oil market in OPEC member countries and allies impacts the world economy, and what is the future of oil and OPEC from these countries' perspectives

Team-focused implementation strategies to improve implementation of mental health screening and referral in rural Children\u27s Advocacy Centers: Study protocol for a pilot cluster randomized hybrid type 2 trial

BACKGROUND: Children\u27s Advocacy Centers (CACs) use multidisciplinary teams to investigate and respond to maltreatment allegations. CACs play a critical role in connecting children with mental health needs to evidence-based mental health treatment, especially in low-resourced rural areas. Standardized mental health screening and referral protocols can improve CACs\u27 capacity to identify children with mental health needs and encourage treatment engagement. In the team-based context of CACs, teamwork quality is likely to influence implementation processes and outcomes. Implementation strategies that target teams and apply the science of team effectiveness may enhance implementation outcomes in team-based settings. METHODS: We will use Implementation Mapping to develop team-focused implementation strategies to support the implementation of the Care Process Model for Pediatric Traumatic Stress (CPM-PTS), a standardized screening and referral protocol. Team-focused strategies will integrate activities from effective team development interventions. We will pilot team-focused implementation in a cluster-randomized hybrid type 2 effectiveness-implementation trial. Four rural CACs will implement the CPM-PTS after being randomized to either team-focused implementation (n = 2 CACs) or standard implementation (n = 2 CACs). We will assess the feasibility of team-focused implementation and explore between-group differences in hypothesized team-level mechanisms of change and implementation outcomes (implementation aim). We will use a within-group pre-post design to test the effectiveness of the CPM-PTS in increasing caregivers\u27 understanding of their child\u27s mental health needs and caregivers\u27 intentions to initiate mental health services (effectiveness aim). CONCLUSIONS: Targeting multidisciplinary teams is an innovative approach to improving implementation outcomes. This study will be one of the first to test team-focused implementation strategies that integrate effective team development interventions. Results will inform efforts to implement evidence-based practices in team-based service settings. TRIAL REGISTRATION: Clinicaltrials.gov, NCT05679154 . Registered on January 10, 2023

A Bayesian comparative effectiveness trial in action: developing a platform for multisite study adaptive randomization

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author's publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Background In the last few decades, the number of trials using Bayesian methods has grown rapidly. Publications prior to 1990 included only three clinical trials that used Bayesian methods, but that number quickly jumped to 19 in the 1990s and to 99 from 2000 to 2012. While this literature provides many examples of Bayesian Adaptive Designs (BAD), none of the papers that are available walks the reader through the detailed process of conducting a BAD. This paper fills that gap by describing the BAD process used for one comparative effectiveness trial (Patient Assisted Intervention for Neuropathy: Comparison of Treatment in Real Life Situations) that can be generalized for use by others. A BAD was chosen with efficiency in mind. Response-adaptive randomization allows the potential for substantially smaller sample sizes, and can provide faster conclusions about which treatment or treatments are most effective. An Internet-based electronic data capture tool, which features a randomization module, facilitated data capture across study sites and an in-house computation software program was developed to implement the response-adaptive randomization. Results A process for adapting randomization with minimal interruption to study sites was developed. A new randomization table can be generated quickly and can be seamlessly integrated in the data capture tool with minimal interruption to study sites. Conclusion This manuscript is the first to detail the technical process used to evaluate a multisite comparative effectiveness trial using adaptive randomization. An important opportunity for the application of Bayesian trials is in comparative effectiveness trials. The specific case study presented in this paper can be used as a model for conducting future clinical trials using a combination of statistical software and a web-based application. Trial registration ClinicalTrials.gov Identifier: NCT02260388, registered on 6 October 201

T-CaST: an implementation theory comparison and selection tool

Abstract Background Theories, models, and frameworks (TMF) are foundational for generalizing implementation efforts and research findings. However, TMF and the criteria used to select them are not often described in published articles, perhaps due in part to the challenge of selecting from among the many TMF that exist in the field. The objective of this international study was to develop a user-friendly tool to help scientists and practitioners select appropriate TMF to guide their implementation projects. Methods Implementation scientists across the USA, the UK, and Canada identified and rated conceptually distinct categories of criteria in a concept mapping exercise. We then used the concept mapping results to develop a tool to help users select appropriate TMF for their projects. We assessed the tool’s usefulness through expert consensus and cognitive and semi-structured interviews with implementation scientists. Results Thirty-seven implementation scientists (19 researchers and 18 practitioners) identified four criteria domains: usability, testability, applicability, and familiarity. We then developed a prototype of the tool that included a list of 25 criteria organized by domain, definitions of the criteria, and a case example illustrating an application of the tool. Results of cognitive and semi-structured interviews highlighted the need for the tool to (1) be as succinct as possible; (2) have separate versions to meet the unique needs of researchers versus practitioners; (3) include easily understood terms; (4) include an introduction that clearly describes the tool’s purpose and benefits; (5) provide space for noting project information, comparing and scoring TMF, and accommodating contributions from multiple team members; and (6) include more case examples illustrating its application. Interview participants agreed that the tool (1) offered them a way to select from among candidate TMF, (2) helped them be explicit about the criteria that they used to select a TMF, and (3) enabled them to compare, select from among, and/or consider the usefulness of combining multiple TMF. These revisions resulted in the Theory Comparison and Selection Tool (T-CaST), a paper and web-enabled tool that includes 16 specific criteria that can be used to consider and justify the selection of TMF for a given project. Criteria are organized within four categories: applicability, usability, testability, and acceptability. Conclusions T-CaST is a user-friendly tool to help scientists and practitioners select appropriate TMF to guide implementation projects. Additionally, T-CaST has the potential to promote transparent reporting of criteria used to select TMF within and beyond the field of implementation science

Foot and ankle surgery in Australia: a descriptive analysis of the Medicare Benefits Schedule database, 1997–2006

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Tradable Pollution Permits and the Regulatory Game

This paper analyzes polluters\u27 incentives to move from a traditional command and control (CAC) environmental regulatory regime to a tradable permits (TPP) regime. Existing work in environmental economics does not model how firms contest and bargain over actual regulatory implementation in CAC regimes, and therefore fail to compare TPP regimes with any CAC regime that is actually observed. This paper models CAC environmental regulation as a bargaining game over pollution entitlements. Using a reduced form model of the regulatory contest, it shows that CAC regulatory bargaining likely generates a regulatory status quo under which firms with the highest compliance costs bargain for the smallest pollution reductions, or even no reduction at all. As for a tradable permits regime, it is shown that all firms are better off under such a regime than they would be under an idealized CAC regime that set and enforced a uniform pollution standard, but permit sellers (low compliance cost firms) may actually be better off under a TPP regime with relaxed aggregate pollution levels. Most importantly, because high cost firms (or facilities) are the most weakly regulated in the equilibrium under negotiated or bargained CAC regimes, they may be net losers in a proposed move to a TPP regime. When equilibrium costs under a TPP regime are compared with equilibrium costs under a status quo CAC regime, several otherwise paradoxical aspects of firm attitudes toward TPP type reforms can be explained. In particular, the otherwise paradoxical pattern of allowances awarded under Phase II of the 1990 Clean Air Act\u27s acid rain program, a pattern tending to favor (in Phase II) cleaner, newer generating units, is explained by the fact that under the status quo regime, a kind of bargained CAC, it was the newer cleaner units that were regulated, and which therefore had higher marginal control costs than did the largely unregulated older, plants. As a normative matter, the analysis here implies that the proper baseline for evaluating TPP regimes such as those contained in the Bush Administration\u27s recent Clear Skies initiative is not idealized, but nonexistent CAC regulatory outcomes, but rather the outcomes that have resulted from the bargaining game set up by CAC laws and regulations