Target prediction and a statistical sampling algorithm for RNA-RNA interaction

It has been proven that the accessibility of the target sites has a critical influence for miRNA and siRNA. In this paper, we present a program, rip2.0, not only the energetically most favorable targets site based on the hybrid-probability, but also a statistical sampling structure to illustrate the statistical characterization and representation of the Boltzmann ensemble of RNA-RNA interaction structures. The outputs are retrieved via backtracing an improved dynamic programming solution for the partition function based on the approach of Huang et al. (Bioinformatics). The $O(N^6)$ time and $O(N^4)$ space algorithm is implemented in C (available from \url{http://www.combinatorics.cn/cbpc/rip2.html})Comment: 7 pages, 10 figure

Best Practices for Test Driven Development

In his award-winning book, Test-driven Development By Example, Kent Beck wrote, Clean code that works...is the goal of Test-driven Development (TDD). TDD is a style of software development that first begins with the creation of tests and then makes use short, iterative development cycles until all test requirements are fulfilled. In order to provide the reader with sufficient background to understand the concepts discussed, this thesis begins by presenting a detailed description of this style of development. TDD is then contrasted with other popular styles, with a focus toward highlighting the many benefits this style offers over the others. This thesis then offers the reader a series of concrete and practical best practices that can be used in conjunction with TDD. It is the hope of the author that these lessons learned will aid those considering the adoption of this style of development avoid a number of pitfalls

Microfluidic Based Hydrate Permeability System: Design and Construction

Methane hydrates represent a vast and untapped fossil fuel resource underlying large portions of the world\u27s artic continental surfaces and sub-sea continental shelves. These hydrates are crystalline solids that consist of methane molecules surrounded by cages of interacting water molecules, similar to ice. Methane hydrates occur naturally, where temperature and pressure conditions favor their formation. In order to utilize these resources, methods must be developed to determine the conditions most favorable to hydrate extraction. One important condition is permeability and how it is affected by hydrates. Due to the difficulty and cost of field studies, the study of laboratory-synthesized hydrates is favored. The purpose of this research is to develop a microfluidic-chip-based model to study the formation and dissociation of methane hydrates. The chosen microfluidic chip mimics a porous media, allowing permeability studies to be performed. This use of a microfluidic chip also allows real-time visualization of hydrate formation, and accurate analysis to determine hydrate saturation levels generated in the model. Peltier plates and PID controllers add temperature control to the model to allow for profiling of hydrate formation and permeability under different experimental conditions. This model is unique in that it allows for a simultaneous correlation between permeability and hydrate saturation levels, a feature not previously available in laboratory-based hydrate models

Revisiting the Foundations of International Law: A Close Analysis of the Peace of Westphalia

Historians have generally accepted that the Peace of Westphalia (1648), which concluded the Thirty Years’ War (1618-48), was the moment when the concept of sovereign equality, a concept that recognizes that states have jurisdiction over their own territory and are all equal before international law, became an internationally recognized principle in diplomatic negotiations. However, recently, some scholars have begun to reevaluate this assumption, claiming that the Peace did not actually (formally or officially) establish the principle of sovereign equality throughout Europe. This reopening of a question long considered answered has proved fruitful and has encouraged this project’s exploration of both the Peace itself and of how subsequent politicians and diplomats actually deployed the Peace in their negotiations. This paper argues that, in international treaty negotiations, it may have mattered less to negotiators what the Peace actually said or what it formally established, than what negotiators argued it said and how they wielded it in their discussions. A close reading of the text of the Peace itself, as well as of subsequent negotiations between the 17th and 20th centuries, reveals when and how diplomats wielded the Peace in their negotiations and to what effect. This project applies a close, contextual reading of the texts of treaties and the various interpretations of them over time. It looks for specific references to the Peace of Westphalia in later peace treaties, analyzes what diplomats meant when they invoked it, and considers whether the treaties themselves resulted in outcomes that were consistent with the intent of the negotiators. Finally, it considers whether or not the Peace exercised the influence on international relations that some past scholars have claimed. This project has three sections. First, it analyzes the context for the Peace of Westphalia including the wider debates circulating at the time that influenced negotiations. It reads the texts of the treaties that comprised the Peace and it considers the immediate interpretations associated with it. Second, it explores if and how it was invoked in subsequent peace treaties and organizations up to the United Nations Charter (1948). A careful examination of the texts and debates from the time frame indicates that diplomats and politicians invoked the Peace of Westphalia during negotiations that concluded the following wars: The War of Spanish Succession with its Treaty of Utrecht (1715), the War of Austrian Succession with its Treaty of Aix-la-Chapelle (1748), The Napoleonic Wars with the Congress of Vienna (1814), and World War I and the Treaty of Versailles (1919). This paper will also examine the United Nations Charter because it is the focus of several influential sources. Finally, it places this history in conversation with the current scholarly arguments about the importance of the Peace for international relations

Freedom Triumphant: Embracing Joyful Freedom but Facing an Uncertain, Perilous Future

The newly freed slaves had almost nothing—no money, no education, and no strong social institutions, including marriage which had often been prohibited, rarely supported by slaveholders. Discrimination was rampant and government was often the worst discriminator. Yet, somehow, they triumphed. They built marriages that were actually slightly more stable than those of white families. The newly free went from virtually zero literacy to at least 50% literacy in a generation. They worked incredibly hard and increased their income about one third faster than white workers. The newly free, anchored in their strong faith, were amazingly forgiving and optimistic. Economics Professor Thomas Tacker tells their inspiring story in a lively, non-technical style. Along the way Professor Tacker demolishes the myths that were told to justify slavery and racism. This is the exciting saga of the spectacularly successful, such as George Washington Carver and Madam C.J. Walker, but also of typical families, every-day champions. In the end, these newly free people overcame seemingly insurmountable obstacles and emerged as heroes and heroines. They were, indeed, our other greatest generation

Yangians, finite W-algebras and the Non Linear Schrodinger hierarchy

We show an algebra morphism between Yangians and some finite W-algebras. This correspondence is nicely illustrated in the framework of the Non Linear Schrodinger hierarchy. For such a purpose, we give an explicit realization of the Yangian generators in terms of deformed oscillators.Comment: LaTeX2e, 10 pages, Talk presented by E. Ragoucy at ACTP-Nankai Symposium on Yang-Baxter systems, non linear models and their applications, Seoul (Korea) October 20-23, 199

Sharing Behaviors of Saudi Students in an Intensive English Environment

For more than three semesters, the Saudi students of the Intensive English Center (IEC) have had what could be viewed as interesting kinds of sharing behaviors, manifesting themselves in ways that teachers have started to notice. These behaviors have gone on for some time and they seem to have increased with the number of Saudi students coming to the IEC over the past 2 years. The students have been observed helping each other on tests, forging homework, and plagiarizing. What makes this situation difficult is that the students are not American, so they cannot clearly be judged under a set of rules that they have no knowledge of. Some could say since they are here, they must learn how to be American. The problem with this is that while they can be shown the path, only they can choose to walk it. This paper attempts to explore this issue in depth and seeks to identify if there is a primary cultural reason for the behaviors, or if there another explanation for it. The study was completed in the spring term of 2006 during the month of April. The study followed the classroom lives of the Saudi Arabian students in the Intensive English program. The methods used to find data during the study were participant observation in the anthropological/ethnographic sense, as well as interviews with the students and surveys given to the teachers of the students. The research brought to life a concept of bonding or friendship among the Saudi Arabian students within their own group and also other students of Arab background. What was observed is that they worked together on homework outside of school, as well inside of school, and helped each other on tests during class. They could be seen copying each others homework, speaking in Arabic during tests, and generally disregarding any concept of individual work. This disregard, however, is not seen as misplaced in their home Arab culture as it is couched in friendship. This friendship may mean doing things that you know are not necessarily right to keep the group together for example: lying or cheating. This working together strengthened the bonds between them and also gave them a leg up in facing the outside forces put on each of them. In this way it created a difference in comparison to American culture. For Americans it is usually each individual against the system, for the Saudi Arabian students, it was the group against the system: The betterment of all rather than the one. For all of the Saudi students, various factors contributed to the friendships and bonding between them. For example, scholarships required that they must maintain good grades or be sent home. A mistake in school leading to expulsion, loss of scholarship or worse could mean shame and dishonor for the family which could reflect badly on those around them, family and friends alike. At the end of the research, the most clearly defining reason for the sharing behaviors of the Saudi Arabian students was their own ideas of friendship brought over from their home country. Other important but less significant reasoning for the behavior was that it was seen as clever for them to do such things or their cultural based definitions are different from U.S. academic ones: for example, plagiarism. The last question asked and one of the most important is to figure out: Are they really learning anything at all when they share all the work? It is not answered here, but one way to potentially stop the behaviors could be to have more intimate friendship based relations in the classroom and perhaps students in the same friendship based situations would start to do work more individually

Rethinking Consumer Protection: Escaping Death by Regulation

This book is designed to appeal to anyone who is at all interested in topics related to making life better and safer—for all us consumers. Our current approach to consumer protection is extremely flawed; sometimes costing lives rather than saving them. There are better ways to protect ourselves and the people we love

Chance and Necessity in Evolution: Lessons from RNA

The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are realized much more frequently than others), (2) the notion of shape space covering (that all typical shapes are realized in a small neighborhood of any random sequence), and (3) the notion of a neutral network (that sequences folding into the same typical shape form networks that percolate through sequence space). Neutral networks loosen the requirements on the mutation rate for selection to remain effective. The original (genotypic) error threshold has to be reformulated in terms of a phenotypic error threshold. With regard to adaptation, neutrality has two seemingly contradictory effects: It acts as a buffer against mutations ensuring that a phenotype is preserved. Yet it is deeply enabling, because it permits evolutionary change to occur by allowing the sequence context to vary silently until a single point mutation can become phenotypically consequential. Neutrality also influences predictability of adaptive trajectories in seemingly contradictory ways. On the one hand it increases the uncertainty of their genotypic trace. At the same time neutrality structures the access from one shape to another, thereby inducing a topology among RNA shapes which permits a distinction between continuous and discontinuous shape transformations. To the extent that adaptive trajectories must undergo such transformations, their phenotypic trace becomes more predictable.Comment: 37 pages, 14 figures; 1998 CNLS conference; high quality figures at http://www.santafe.edu/~walte

Writing a Scientific Paper Prior to the Research

The traditional approach to preparing a research report for publication is to begin writing after the study has been completed. We propose another approach- to write a zeroth draft before the study is begun. This approach helps to focus the investigator\u27s attention during the planning stage on critical aspects of the study. The discipline of writing down the rationale, the methods, and the variety of possible outcomes and their significance helps to clarify the logic on which the study is based. If these are acceptable to all authors and colleagues in the zeroth draft, it is likely that the research questions posed will be answered in a definitive way and that the final draft will be scientifically sound. The notion of writing a paper before doing the research may raise concerns of prejudice, preconception, or even academic dishonesty. How could one possibly know what to write until after the study is completed? However, if one considers the actual content of a scientific paper or research report, it becomes clear that most of the report can be drafted before the first data are collected. The process is in many ways similar to that of preparing a formal proposal to a funding agency. Indeed, a grant application may borrow heavily from the zeroth draft of the paper, and vice versa. The content of the zeroth draft is only the first of a series of approximations to the final form. Yet, it can be a very useful beginning. Authors often procrastinate when faced with writing up the results of completed research projects and may find it much easier to write at the beginning of a project when enthusiasm is at its peak. Most importantly, there may be no better way to prepare the mind, anticipate pitfalls, and avoid wasted time, effort, and money than to write a zeroth draft