The complex problem of food safety : Applying agent-based modeling to the policy process

Many problems facing policymakers are complex and cannot be understood by reducing them to their component parts. However, many of the policy responses to complex problems continue to be based on simple, reductionist methods. Agent-based modeling (ABM) is one alternative method for informing policy that is well-suited to analyzing complex problems. ABM has practical implications for different stages of the policy process, such as testing alternatives, assisting with evaluation by setting up a counterfactual, and agenda setting. The objective of the research presented in this dissertation is to explore the opportunity for using ABM to examine complex problems of relevance for policy. To do so, three separate models were developed to investigate different aspects of food safety inspection systems. Complex problems involve interrelated feedback loops, many actors, exponential growth, asymmetric information, and uncertainty in outcomes and data, and food safety exhibits these traits, providing an interesting case study for the use of ABM. The first model explores three inspection scenarios incorporating access to information. The main finding was that the number of sick consumers is greatly reduced by giving consumers and inspectors more information about whether a retail outlet is contaminated, even if that information may be uncertain. The second model incorporated theories on risk and the role of transparency in encouraging consumer trust by giving consumers access to inspection scores. Overall, the findings were more nuanced: having access to restaurant inspection scores results in a slightly higher mean number of sick consumers, but less variation overall in the number of sick consumers. As well, a greater number of compliant restaurants results in fewer sick consumers. Rather than investigating the structure of the inspection system, the third model examines the potential for mobile technology to crowdsource information about suspected foodborne illness. This model illustrates the potential for health-oriented mobile technologies to improve the surveillance system for foodborne illness. Overall, the findings from the three models support using stylized ABMs to study various aspects of food safety inspection systems, and show that these models can be used to generate insight for policy choices and evidence-based decision making in this area

On the lag phase in amyloid fibril formation.

The formation of nanoscale amyloid fibrils from normally soluble peptides and proteins is a common form of self-assembly phenomenon that has fundamental connections with biological functions and human diseases. The kinetics of this process has been widely studied and exhibits on a macroscopic level three characteristic stages: a lag phase, a growth phase and a final plateau regime. The question of which molecular events take place during each one of these phases has been a central element in the quest for a mechanism of amyloid formation. In this review, we discuss the nature and molecular origin of the lag-phase in amyloid formation by making use of tools and concepts from physical chemistry, in particular from chemical reaction kinetics. We discuss how, in macroscopic samples, it has become apparent that the lag-phase is not a waiting time for nuclei to form. Rather, multiple parallel processes exist and typically millions of primary nuclei form during the lag phase from monomers in solution. Thus, the lag-time represents a time that is required for the nuclei that are formed early on in the reaction to grow and proliferate in order to reach an aggregate concentration that is readily detected in bulk assays. In many cases, this proliferation takes place through secondary nucleation, where fibrils may present a catalytic surface for the formation of new aggregates. Fibrils may also break (fragmentation) and thereby provide new ends for elongation. Thus, at least two - primary nucleation and elongation - and in many systems at least four - primary nucleation, elongation, secondary nucleation and fragmentation - microscopic processes occur during the lag phase. Moreover, these same processes occur during all three phases of the macroscopic aggregation process, albeit at different rates as governed by rate constants and by the concentration of reacting species at each point in time.This work was supported by the Swedish Research Council (SL) and its Linneus Centre Organizing Molecular Matter for CD spectrometer, plate readers (SL), the Alzheimer Foundation Sweden (SL), the Frances and Augustus Newman Foundation (TPJK), the BBSRC (TPJK), and the Marie Curie fellowship scheme for career development (PA).This is the final version of the article. It first appeared from RSC via http://dx.doi.org/10.1039/C4CP05563

Indirect measurement of dysfunctional attitudes in bipolar affective disorder

Objective. The present study uses an indirect measure to explore whether dysfunctional attitudes are characteristic of all phases of bipolar disorder. Previous studies with bipolar patients using indirect measurements have uncovered depression-like responses that were otherwise undetected. Design. A cross-sectional study design was adopted to explore the presence of dysfunctional attitudes within each phase of the illness. Method. Manic patients, depressed bipolar patients, remitted bipolar patients, and healthy controls were compared on a sentence stem completion task designed to implicitly assess dysfunctional attitudes. Results. The manic, depressed, and remitted patients all exceeded the controls on implicit measures of dysfunctional attitudes. Conclusions. The findings are consistent with the hypothesis that all phases of bipolar disorder are associated with depressogenic dysfunctional attitudes. © 2009 The British Psychological Society

Collaboration and the Generation of New Knowledge in Networked Innovation Systems: A Bibliometric Analysis

AbstractCanola, a high-value, export-oriented agricultural commodity, was developed in Canada over the course of 40 years in public institutions, driven by imported technology and imported research scientists. The evolution of canola R&D closely mirrors the evolution of the Triple Helix Models of innovation. Through the application of longitudinal citation analysis, using five-year intervals, publications from Canadian public institutions involved in canola R&D have been analyzed. In the most recent five- year interval, the relative citation rates of public sector research increased by 60% compared to the global average. A unique fixed-effect negative binomial regression model is used to demonstrate the critical relationship between the institutional arrangement that governs collaboration and the production of knowledge that underscores technological innovation

Physical determinants of the self-replication of protein fibrils

The ability of biological molecules to replicate themselves, achieved with the aid of a complex cellular machinery, is the foundation of life. However, a range of aberrant processes involve the selfreplication of pathological protein structures without any additional factors. A dramatic example is the autocatalytic replication of pathological protein aggregates, including amyloid fibrils and prions, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can only take place in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer’s disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.We acknowledge support from the Human Frontier Science Program and Emmanuel College (A.Š), Leverhulme Trust and Magdalene College (A.K.B), St. John’s College (T.C.T.M), the Biotechnology and Biological Sciences Research Council (T.P.J.K. and C. M. D.), the Frances and Augustus Newman Foundation (T.P.J.K.), the European Research Council (T.P.J.K., S.L. and D.F), and the Engineering and Physical Sciences Research Council (D.F.).This is the author accepted manuscript. The final version is available from Nature Publishing Group via https://doi.org/10.1038/nphys382

On-chip label-free protein analysis with downstream electrodes for direct removal of electrolysis products.

The ability to apply highly controlled electric fields within microfluidic devices is valuable as a basis for preparative and analytical processes. A challenge encountered in the context of such approaches in conductive media, including aqueous buffers, is the generation of electrolysis products at the electrode/liquid interface which can lead to contamination, perturb fluid flows and generally interfere with the measurement process. Here, we address this challenge by designing a single layer microfluidic device architecture where the electric potential is applied outside and downstream of the microfluidic device while the field is propagated back to the chip via the use of a co-flowing highly conductive electrolyte solution that forms a stable interface at the separation region of the device. The co-flowing electrolyte ensures that all the generated electrolysis products, including Joule heat and gaseous products, are flowed away from the chip without coming into contact with the analytes while the single layer fabrication process where all the structures are defined lithographically allows producing the devices in a simple yet highly reproducible manner. We demonstrate that by allowing stable and effective application of electric fields in excess of 100 V cm-1, the described platform provides the basis for rapid separation of heterogeneous mixtures of proteins and protein complexes directly in their native buffers as well as for the simultaneous quantification of their charge states. We illustrate this by probing the interactions in a mixture of an amyloid forming protein, amyloid-β, and a molecular chaperone, Brichos, known to inhibit the process of amyloid formation. The availability of a platform for applying stable electric fields and its compatibility with single-layer soft-lithography processes opens up the possibility of separating and analysing a wide range of molecules on chip, including those with similar electrophoretic mobilities

Autocatalytic amplification of Alzheimer-associated Aβ42 peptide aggregation in human cerebrospinal fluid

Funder: Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation); doi: https://doi.org/10.13039/501100004063Funder: Alzheimerfonden; doi: https://doi.org/10.13039/501100008599Abstract: Alzheimer’s disease is linked to amyloid β (Aβ) peptide aggregation in the brain, and a detailed understanding of the molecular mechanism of Aβ aggregation may lead to improved diagnostics and therapeutics. While previous studies have been performed in pure buffer, we approach the mechanism in vivo using cerebrospinal fluid (CSF). We investigated the aggregation mechanism of Aβ42 in human CSF through kinetic experiments at several Aβ42 monomer concentrations (0.8–10 µM). The data were subjected to global kinetic analysis and found consistent with an aggregation mechanism involving secondary nucleation of monomers on the fibril surface. A mechanism only including primary nucleation was ruled out. We find that the aggregation process is composed of the same microscopic steps in CSF as in pure buffer, but the rate constant of secondary nucleation is decreased. Most importantly, the autocatalytic amplification of aggregate number through catalysis on the fibril surface is prevalent also in CSF

Feasibility and acceptability of web-based enhanced relapse prevention for bipolar disorder (ERPonline):trial protocol

BACKGROUND: Relapse prevention interventions for Bipolar Disorder are effective but implementation in routine clinical services is poor. Web-based approaches offer a way to offer easily accessible access to evidence based interventions at low cost, and have been shown to be effective for other mood disorders. METHODS/DESIGN: This protocol describes the development and feasibility testing of the ERPonline web-based intervention using a single blind randomised controlled trial. Data will include the extent to which the site was used, detailed feedback from users about their experiences of the site, reported benefits and costs to mental health and wellbeing of users, and costs and savings to health services. We will gain an estimate of the likely effect size of ERPonline on a range of important outcomes including mood, functioning, quality of life and recovery. We will explore potential mechanisms of change, giving us a greater understanding of the underlying processes of change, and consequently how the site could be made more effective. We will be able to determine rates of recruitment and retention, and identify what factors could improve these rates. DISCUSSION: The findings will be used to improve the site in accordance with user needs, and inform the design of a large scale evaluation of the clinical and cost effectiveness of ERPonline. They will further contribute to the growing evidence base for web-based interventions designed to support people with mental health problems