Stochastic Modeling of Reversible Biochemical Reaction-Diffusion Systems and High-Resolution Shock-Capturing Methods for Fluid Interfaces

Thesis (Ph.D.)--University of Washington, 2016-08

A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis

Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.

Rapid identification and differentiation of Mycobacterium avium subspecies paratuberculosis types by use of real-time PCR and high-resolution melt analysis of the MAP1506 locus

High-resolution melt (HRM) analysis can identify sequence polymorphisms by comparing the melting curves of amplicons generated by real-time PCR amplification. We describe the application of this technique to identify Mycobacterium avium subspecies paratuberculosis types I, II, and III. The HRM approach was based on type-specific nucleotide sequences in MAP1506, a member of the PPE (proline-proline-glutamic acid) gene family.

Self-serving biases: Evidence from a simulated labor relationship

Previous studies have found evidence of a self-serving bias in bargaining and dispute resolution. We use experimental data to test for this effect in a simulated labor relatonship. We finda consistent discrepancy between employer beliefs and employee actions that can only be attributed to self-serving biases. This discrepancy is evident through stated beliefs, revealed satisfaction, and actual actions. We present evidenceand discuss implications.

Mining in Developing Countries: A Case Study of Sustainability Challenges

Mining has severe impacts on its surrounding. Particularly in the developing countries it has degraded the environment and signigicantly altered the socio-economical dynamics of the hosts. Especially relocation disrupts people from their homes, livelihoods, cultures and social activities. Mining industry has failed to develop the local host and streghten its governance structures; instead it has further degraded the development of mineral rich third world countries, which are among the world poorest ones. Cash flows derived from mining companies have not benefitted the crass-root level that however, bears most of the detrimental impacts. Especially if the governance structure of the host is weak, the sudden wealth is likely to accelerate disparities, corruption and even fuel wars. Environmental degradation, miscommunication, mistrust and disputes over land use have created conflicts between the communities and a mining company in Obuasi, Ghana; a case study of this thesis. The disputes are deeply rooted and further fuelled by unrealistic expectations and broken promises. The relations with artisanal and illegal miners have been especially troublesome. Illegal activities, mainly encroachment of the land and assets of the mine, such as vandalising tailings pipes have resulted in profits losses, environmental degradation and security hazards. All challenges mentioned above have to be addressed locally with site-specific solutions. It is vital to increase two-way communication, initiate collaboration and build capacity of the stakeholders such as local communities, NGOs and governance authorities. The locals must be engaged to create livelihood opportunities that are designed with and for them. Capacity can also be strengthened through education and skills training, such as women’s literacy programs. In order to diminish the overdependence of locals to the mine, the activities have to be self -sufficient and able to survive without external financial and managerial inputs. Additionally adequate and fair compensation practises and dispute resolution methods that are understood and accepted by all parties have to be agreed on as early as possible.

Commercial management in project-based organisations

The term commercial management has been used for some time, similarly the job title commercial manager. However, as of yet, little emphasis has been placed on defining. This paper presents the findings from a two-year research initiative that has compared and contrasted the role of commercial managers from a range of organisations and across industry sectors, as a first step in developing a body of knowledge for commercial. It is argued that there are compelling arguments for considering commercial management, not solely as atask undertaken by commercial managers, but as a discipline in itself: a discipline that, arguably, bridges traditional project management and organisational theories. While the study has established differences in approach and application both between and within industry sectors, it has established sufficient similarity and synergy in practice to identify a specific role of commercial management in project-based organisations. These similarities encompass contract management and dispute resolution; the divergences include a greater involvement in financial and value management in construction and in bid management in defence/aerospace.

Responsiveness to change by standard-form contract drafters: A case study of the FIDIC White Book

Purpose – The purpose of this paper is to focus on the Fédération Internationale des Ingénieurs-Conseils (FIDIC) White Book standard form of building contract. It tracks the changes to this contract over its four editions, and seeks to identify their underlying causes. Design/methodology/approach – The changes made to the White Book are quantified using a specific type of quantitative content analysis. The amended clauses are then examined to understand the nature of the changes made. Findings – The length of the contract increased by 34 per cent between 1990 and 2006. A large proportion of the overall increase can be attributed to the clauses dealing with “conflict of interest/corruption” and “dispute resolution”. In both instances, the FIDIC drafting committees have responded to international developments to discourage corruption, and to encourage the use of alternative dispute resolution. Between 1998 and 2006, the average length of the sentences increased slightly, raising the question of whether long sentences are easily understood by users of contracts. Research limitations/implications – Quantification of text appears to be particularly useful for the analysis of documents which are regularly updated because changes can be clearly identified and the length of sentences can be determined, leading to conclusions about the readability of the text. However, caution is needed because changes of great relevance can be made to contract clauses without actually affecting their length. Practical implications – The paper will be instructive for contract drafters and informative for users of FIDIC's White Book. Originality/value – Quantifying text has been rarely used regarding standard-form contracts in the field of construction.

designing + (dis)assembling disputes: an ethnography of disputes & lawyers in the construction industry

The UK construction industry is notorious for the sheer amount of disputes which are likely to arise on each building and engineering project. Despite numerous creative attempts at “dispute avoidance” and “dispute resolution”, this industry is still plagued with these costly disputes. Whilst both academic literature and professional practices have investigated the causes of disputes and the mechanisms for avoidance/resolution of these disputes, neither has studied in any detail the nature of the construction disputes and why they develop as they do once a construction lawyer is engaged. Accordingly, this research explores the question of what influences the outcome of a construction dispute and to what extent do construction lawyers control or direct this outcome? The research approach was ethnographic. Fieldwork took place at a leading construction law firm in London over 18 months. The primary focus was participant observation in all of the firm’s activities. In addition, a database was compiled from the firm’s files and archives, thus providing information for quantitative analysis. The basis of the theoretical framework, and indeed the research method, was the Actor‐Network Theory (ANT). As such, this research viewed a dispute as a set of associations – an entity which takes form and acquires its attributes as a result of its relations with other entities. This viewpoint is aligned with relational contract theories, which in turn provides a unified platform for exploring the disputes. The research investigated the entities and events which appeared to influence the dispute’s identity, shape and outcome. With regard to a dispute’s trajectory, the research took as its starting point that a dispute follows the transformation of “naming, blaming, claiming…”, as identified by Felstiner, Abel and Sarat in 1980. The research found that construction disputes generally materialise and develop prior to any one of the parties approaching a lawyer. Once the lawyer is engaged, we see the reverse of the trajectory “naming, blaming, claiming…” this being: “claiming, blaming, naming…” The lawyers’ role is to identify or name (or rename) the dispute in the best possible light for their client in order to achieve the desired outcome – the development of which is akin to the design process. The transformation of a dispute and the reverse trajectory is by no means linear, but rather, iterative and spatial as it requires alliances, dependencies and contingencies to assemble and take the shape it does. The research concludes that construction disputes are rarely ever completely “resolved” as such. Whilst an independent third party may hand down a judgment, or the parties may reach a settlement agreement, this state is only temporal. Some construction disputes dissipate whist others reach a state of hibernation for a period of time only to pick up momentum and energy some years later. Accordingly, this research suggests that the concept of “dispute resolution” does not exist in the UK construction industry. The ultimate goal should be for parties to reach this ultimate and perpetual state of equilibrium as quickly and as cost effectively as possible: “dispute dissolution”, the slowing down of the dispute’s momentum. Rather than focusing on the design and assemblage of the dispute, the lawyers’ role therein is, or should be, to assist with the “disassembling” of the dispute.

Best practice in the training, appointment and remuneration of members of dispute boards for large infrastructure projects

This paper reports part of a qualitative study into evolving practice in the implementation of the Dispute Adjudication Board (DAB) construction dispute resolution technique, a variant of the Dispute Review Board (DRB) concept used in the US and Canada. Data was collected through a focus group interview of 20 highly experienced dispute resolution practitioners from engineering and the law. The group was assembled from members of FIDIC-NET with direct experience of project DABs. The part reported here concerns practice and procedure for establishing DABs. The main findings are that: constitution of the DABs is often delayed because of either project owners' ignorance of the DAB process or deterrence by the cost of the DABs; such owners also tend to insist on appointing DAB members from local engineers and lawyers without sufficient understanding of the DAB process; rates of remuneration of DAB members vary widely; the training provision for DAB membership and advocacy skills is inadequate; the process of selecting candidates for DAB membership and negotiating the tripartite agreement between each member and the contractual parties needs to be navigated with great care to avoid raising ethical problems. The research contribution is threefold. First, it highlights the importance of realistic fees for DAB members within a standard framework in achieving timely establishment of a board that works well as a team. Second, it illustrates the use of qualitative focus group interview to study the impact of new contract terms from multiple stakeholder perspectives. Finally, it identifies areas where further research is needed.

Bargaining efficiency and screening: An experimental investigation

This paper investigates whether information about fairness types canbe useful in lowering dispute costs and enhancing bargaining efficiency.An experiment was conducted in which subjects were first screened usinga dictator game, with the allocations chosen used to separate participantsinto two types. Mutually anonymous pairs of subjects then bargained, witha dispute cost structure imposed. Sorting with identification reducesdispute costs; there are also significant differences in bargainingefficiency across pairing types. Information about types is crucial forthese differences and also strongly affects the relative bargainingsuccess of the two types and the hypothetical optimal bargaining strategy.

Reforming the Iowa Civil Justice System, January 30, 2012

Executive Summary I. Survey The Task Force conducted a wide-ranging survey of more than 9,000 licensed Iowa attorneys and judges to obtain their input on a variety of civil justice system topics. The survey results helped inform the Task Force of problem areas in Iowa’s civil justice system. II. Two-Tier Justice System The Task Force recommends a pilot program based on a two-tier civil justice system. A two-tier system would streamline litigation processes—including rules of evidence and discovery disclosures—and reduce litigation costs of certain cases falling below a threshold dollar value. III. One Judge/One Case and Date Certain for Trial Some jurisdictions in Iowa have adopted one judge/one case and date certain for trial in certain cases. The assignment of one judge to each case for the life of the matter and the establishment of dates certain for civil trials could enhance Iowans’ access to the courts, improve judicial management, promote consistency and adherence to deadlines, and reduce discovery excesses. IV. Discovery Processes Reforms addressing inefficient discovery processes will reduce delays in and costs of litigation. Such measures include adopting an aspirational purpose for discovery rules to “secure the just, speedy, and inexpensive determination of every action,” holding discovery proportional to the size and nature of the case, requiring initial disclosures, limiting the number of expert witnesses, and enforcing existing rules. V. Expert Witness Fees The Task Force acknowledges the probable need to revisit the statutory additional daily compensation limit for expert witness fees. Leaving the compensation level to the discretion of the trial court is one potential solution. VI. Jurors Additions to the standard juror questionnaire would provide a better understanding of the potential jurors’ backgrounds and suitability for jury service. The Task Force encourages adoption of more modern juror educational materials and video. Rehabilitation of prospective jurors who express an unwillingness or inability to be fair should include a presumption of dismissal. VII. Video and Teleconferencing Options When court resources are constrained both by limited numbers of personnel and budget cuts, it is logical to look to video and teleconferencing technology to streamline the court process and reduce costs. The judicial branch should embrace technological developments in ways that will not compromise the fairness, dignity, solemnity, and decorum of judicial proceedings. VIII. Court-Annexed Alternative Dispute Resolution(ADR) Litigants and practitioners in Iowa are generally satisfied with the current use of private, voluntary ADR for civil cases. There is concern, however, that maintaining the status quo may have steep future costs. Court-annexed ADR is an important aspect of any justice system reform effort, and the Task Force perceives benefits and detriments to reforming this aspect of the Iowa civil justice system. IX. Relaxed Requirement of Findings of Fact and Conclusions of Law A rule authorizing parties to waive findings of fact and conclusions of law could expedite resolution of nonjury civil cases. X. Business (Specialty) Courts Specialty business courts have achieved widespread support across the country. In addition, specialty courts provide excellent vehicles for implementing or piloting other court innovations that may be useful in a broader court system context. A business specialty court should be and could be piloted in Iowa within the existing court system framework of the Iowa Judicial Branch. Appendix included as a separate document, is 176 pages.

High-resolution three-dimensional aortic magnetic resonance angiography and quantitative vessel wall characterization of different atherosclerotic stages in a rabbit model

PURPOSE: Atherosclerosis results in a considerable medical and socioeconomic impact on society. We sought to evaluate novel magnetic resonance imaging (MRI) angiography and vessel wall sequences to visualize and quantify different morphologic stages of atherosclerosis in a Watanabe hereditary hyperlipidemic (WHHL) rabbit model. MATERIAL AND METHODS: Aortic 3D steady-state free precession angiography and subrenal aortic 3D black-blood fast spin-echo vessel wall imaging pre- and post-Gadolinium (Gd) was performed in 14 WHHL rabbits (3 normal, 6 high-cholesterol diet, and 5 high-cholesterol diet plus endothelial denudation) on a commercial 1.5 T MR system. Angiographic lumen diameter, vessel wall thickness, signal-/contrast-to-noise analysis, total vessel area, lumen area, and vessel wall area were analyzed semiautomatically. RESULTS: Pre-Gd, both lumen and wall dimensions (total vessel area, lumen area, vessel wall area) of group 2 + 3 were significantly increased when compared with those of group 1 (all P < 0.01). Group 3 animals had significantly thicker vessel walls than groups 1 and 2 (P < 0.01), whereas angiographic lumen diameter was comparable among all groups. Post-Gd, only diseased animals of groups 2 + 3 showed a significant (>100%) signal-to-noise ratio and contrast-to-noise increase. CONCLUSIONS: A combination of novel 3D magnetic resonance angiography and high-resolution 3D vessel wall MRI enabled quantitative characterization of various atherosclerotic stages including positive arterial remodeling and Gd uptake in a WHHL rabbit model using a commercially available 1.5 T MRI system.

Physical access for persons with disabilities

For persons with disabilities, the activities that able-bodied people take for granted can be major, often insurmountable challenges. Attempting to enter a restaurant for lunch with friends can result in lengthy and adversarial litigation if the facility is not accessible to a person with a disability or other mobility impairment. This litigation would be initiated after the individual was effectively refused service; a refusal based on hislher personal physical characteristics. If a shopping mall is not equipped with "access amenities", then the disabled person may be excluded from shopping there and thus exercising consumer freedom. If workplaces are not equipped to accommodate the access needs of persons with disabilities, then those people are effectively barred from gainful employment there. If a municipal goveniment building is inaccessible to disabled persons, then they may be excluded from participating in council meetings. These are all activities that the majority of the population enjoys as a matter of course, in that they represent the functions of a free citizen in a free society. If a person is excluded from such activities because of some personal characteristic, then that person is subjected to differential or discr~minatory treatment. The guarantees provided in Canadian feden! and provincial rights legislation, are such that people are not to be discriminated againsL Where buildings and facilities othen\iise open to the public are not accessible for persens with disabilities, then those people are being discriminated against. To challenge these discriminatory practices, individuals initiate complaints through the administrative justice system. To address the extent to which this is a problem, many sources were consulted. Constitutional lawyers, tribunal members, advocates for the disabled and land use planners were interviewed. Case law and legislation were reviewed. Literature on citizenship theory, dispute resolution and dispute avoidance was compiled and assessed. And, the field of land use planning was analyzed (drawing on the WTiter's educational and experiential background) as a possible alternative method for effecting systemic access for persons with disabilities. The conclusion of this study is that there does exist a proactive method for assuring access, a method that can apply the systemic remedy needed to deal with this problem. The current method, which is an adversarial and piecemeal complaint process, has proven ineffective in remedying this discrimination problem~ Failure to provide an appropriate remedy means that persons with disabilities will not enjoy the degree of citizen status enjoyed by the able-bodied. This is the current circumstance, and since equity is the aim of rights legislation, and since such legislative and administrative frameworks have failed in that purpose, then an alternative method is necessary. An alternative model is the one in which land use planning is based. It has conflict avoidance and conflict minimization as underpinnings. And, most importantly, land use planning is already a proyen method of combatting discrimination.

Arbitrage en ligne et les litiges du commerce électronique

"Mémoire présenté à la Faculté des études supérieures en vue de l'obtention du grade de Maîtrise en droit (LLM)"

Challenges of Deliberation and Participation

The future of sustainability is tied to the future of our ability to manage interconnectedness and interdependence, and thus to our abilities to engage in cooperative, value-creating public deliberations and negotiations.To understand these issues,we need a better understanding of the micro-politics of planning and public participation, the relationships between our received theories and our practices, and in particular, the work of public dispute resolution and its implications for democratic deliberation and governance.We need better to understand the differences between dialogue, debate, and negotiation, as well as the corresponding work of facilitating a dialogue, moderating a debate, and mediating an actual negotiation. Contrasting processes and practical attitudes of dialogue, debate, and negotiation can teach us, in the context of creating a sustainable future, that we must devise discursive and conversational political processes and institutions that explore possible commitments so that we not only know the right things to do but actually bring ourselves and one another to do those right things.