Better primer design for metagenomics applications by increasing taxonomic distinguishability

Current methods of understanding microbiome composition and structure rely on accurately estimating the number of distinct species and their relative abundance. Most of these methods require an efficient PCR whose forward and reverse primers bind well to the same, large number of identifiable species, and produce amplicons that are unique. It is therefore not surprising that currently used universal primers designed many years ago are not as efficient and fail to bind to recently cataloged species. We propose an automated general method of designing PCR primer pairs that abide by primer design rules and uses current sequence database as input. Since the method is automated, primers can be designed for targeted microbial species or updated as species are added or deleted from the database. In silico experiments and laboratory experiments confirm the efficacy of the newly designed primers for metagenomics applications.

A quantitative approach to the organizational design problem

The span of control is the most discussed single concept in classical and modern management theory. In specifying conditions for organizational effectiveness, the span of control has generally been regarded as a critical factor. Existing research work has focused mainly on qualitative methods to analyze this concept, for example heuristic rules based on experiences and/or intuition. This research takes a quantitative approach to this problem and formulates it as a binary integer model, which is used as a tool to study the organizational design issue. This model considers a range of requirements affecting management and supervision of a given set of jobs in a company. These decision variables include allocation of jobs to workers, considering complexity and compatibility of each job with respect to workers, and the requirement of management for planning, execution, training, and control activities in a hierarchical organization. The objective of the model is minimal operations cost, which is the sum of supervision costs at each level of the hierarchy, and the costs of workers assigned to jobs. The model is intended for application in the make-to-order industries as a design tool. It could also be applied to make-to-stock companies as an evaluation tool, to assess the optimality of their current organizational structure. Extensive experiments were conducted to validate the model, to study its behavior, and to evaluate the impact of changing parameters with practical problems. This research proposes a meta-heuristic approach to solving large-size problems, based on the concept of greedy algorithms and the Meta-RaPS algorithm. The proposed heuristic was evaluated with two measures of performance: solution quality and computational speed. The quality is assessed by comparing the obtained objective function value to the one achieved by the optimal solution. The computational efficiency is assessed by comparing the computer time used by the proposed heuristic to the time taken by a commercial software system. Test results show the proposed heuristic procedure generates good solutions in a time-efficient manner.

Electoral rules and elite recruitment: A comparative analysis of the Bundestag and the U.S. House of Representatives

In this research, I analyze the effects of candidate nomination rules and campaign financing rules on elite recruitment into the national legislatures of Germany and the United States. This dissertation is both theory-driven and constitutes exploratory research, too. While the effects of electoral rules are frequently studied in political science, the emphasis is thereby on electoral rules that are set post-election. My focus, in contrast, is on electoral rules that have an effect prior to the election. Furthermore, my dissertation is comparative by design.^ The research question is twofold. Do electoral rules have an effect on elite recruitment, and does it matter? To answer these question, I create a large-N original data set, in which I code the behavior and recruitment paths and patterns of members of the American House of Representatives and the German Bundestag. Furthermore, I include interviews with members of the said two national legislatures. Both the statistical analyses and the interviews provide affirmative evidence for my working hypothesis that differences in electoral rules lead to a different type of elite recruitment. To that end, I use the active-politician concept, through which I dichotomously distinguish the economic behavior of politicians.^ Thanks to the exploratory nature of my research, I also discover the phenomenon of differential valence of local and state political office for entrance into national office in comparative perspective. By statistically identifying this hitherto unknown paradox, as well as evidencing the effects of electoral rules, I show that besides ideology and culture, institutional rules are key in shaping the ruling elite. The way institutional rules are set up, in particular electoral rules, does not only affect how the electorate will vote and how seats will be distributed, but it will also affect what type of people will end up in elected office.^