Browsing by Subject "FDR"
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Item Reincarnation of the good neighbor : Nixon and the creation of Latin American policy(2015-05) Martin, James Ralph; Suri, Jeremi; Lawrence, Mark AMuch of the research on President Richard Nixon and his Latin American policy offers an overly simplistic portrayal of his attitudes and polices toward Latin America. This report explores the creation of President Richard Nixon's Latin American policy in the first year of his administration. After a brief overview of key events early in the administration, such as the U.S. government's response to the brief war between El Salvador and Honduras known colloquially as the "Soccer War", the body of the report will explore two discrete events. The first event was the ill-fated Operation Intercept, an attempt by the Nixon administration to stem the flow of marijuana across the Mexican border. Operation Intercept, the largest peacetime search and seizure operation in U.S. history up to that point, highlighted many of the sources of friction between U.S. government agencies. Additionally, the operation provides an example of the growing importance of the NSC in government decision making and the ability of the Nixon administration to learn from past mistakes. This incident also provides an example of the agency of the Mexican government, the other half of the foreign policy equation. The other event this report will highlight is Nixon's one major speech on Latin America, which he gave on October 31, 1969. This speech was the culmination of almost a year’s worth of events, meetings, and reports that morphed into the White House's strategic vision toward the region. This report concludes with a comparison of Nixon and Franklin Delano Roosevelt's Latin American policies. Both president's approaches were remarkably similar in substance including an increased focus on hemispheric trade and close relations with unsavory dictators that advanced U.S. interests. The differences in policy outcomes were ultimately due to changing cultures in both the United States and Latin America, but also to fundamental differences in how both men approached the presidency.Item Statistical Methods for the Analysis of Mass Spectrometry-based Proteomics Data(2012-07-16) Wang, XuanProteomics serves an important role at the systems-level in understanding of biological functioning. Mass spectrometry proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. In the most widely used bottom-up approach to MS-based high-throughput quantitative proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical properties and then analyzed using a mass spectrometer. The three fundamental challenges in the analysis of bottom-up MS-based proteomics are as follows: (i) Identifying the proteins that are present in a sample, (ii) Aligning different samples on elution (retention) time, mass, peak area (intensity) and etc, (iii) Quantifying the abundance levels of the identified proteins after alignment. Each of these challenges requires knowledge of the biological and technological context that give rise to the observed data, as well as the application of sound statistical principles for estimation and inference. In this dissertation, we present a set of statistical methods in bottom-up proteomics towards protein identification, alignment and quantification. We describe a fully Bayesian hierarchical modeling approach to peptide and protein identification on the basis of MS/MS fragmentation patterns in a unified framework. Our major contribution is to allow for dependence among the list of top candidate PSMs, which we accomplish with a Bayesian multiple component mixture model incorporating decoy search results and joint estimation of the accuracy of a list of peptide identifications for each MS/MS fragmentation spectrum. We also propose an objective criteria for the evaluation of the False Discovery Rate (FDR) associated with a list of identifications at both peptide level, which results in more accurate FDR estimates than existing methods like PeptideProphet. Several alignment algorithms have been developed using different warping functions. However, all the existing alignment approaches suffer from a useful metric for scoring an alignment between two data sets and hence lack a quantitative score for how good an alignment is. Our alignment approach uses "Anchor points" found to align all the individual scan in the target sample and provides a framework to quantify the alignment, that is, assigning a p-value to a set of aligned LC-MS runs to assess the correctness of alignment. After alignment using our algorithm, the p-values from Wilcoxon signed-rank test on elution (retention) time, M/Z, peak area successfully turn into non-significant values. Quantitative mass spectrometry-based proteomics involves statistical inference on protein abundance, based on the intensities of each protein's associated spectral peaks. However, typical mass spectrometry-based proteomics data sets have substantial proportions of missing observations, due at least in part to censoring of low intensities. This complicates intensity-based differential expression analysis. We outline a statistical method for protein differential expression, based on a simple Binomial likelihood. By modeling peak intensities as binary, in terms of "presence / absence", we enable the selection of proteins not typically amendable to quantitative analysis; e.g., "one-state" proteins that are present in one condition but absent in another. In addition, we present an analysis protocol that combines quantitative and presence / absence analysis of a given data set in a principled way, resulting in a single list of selected proteins with a single associated FDR.Item Unity, Justice and Protection: The Colored Trainmen of America's Struggle to End Jim Crow in the American Railroad Industry [and Elsewhere](2012-10-19) James, ErvinThe Colored Trainmen of America (CTA) actively challenged Jim Crow policies on the job and in the public sphere between the 1930s and 1950s. In response to lingering questions concerning the relationship between early black labor activism and civil rights protest, this study goes beyond both local lure and cursory research. This study examines the Colored Trainmen's major contributions to the advancement of African Americans. It also provides context for some of the organization's shortcomings in both realms. On the job the African American railroad workers belonging to the CTA fought valiantly to receive the same opportunities for professional growth and development as whites working in the operating trades of the railroad industry. In the public sphere, these men collectively protested second-class services and accommodations both on and off the clock. Neither their agenda, the scope of their activities, nor their influence was limited to the railroad lines the members of the CTA operated within the Gulf Coast region. The CTA belonged to a progressive coalition comprised of four other powerful independent African American labor unions committed to unyielding labor activism and the toppling of Jim Crow. Together, they all worked to effectuate meaningful social change in partnership with national civil rights attorney Charles H. Houston. Houston's experience and direction, coupled with the CTA's dedicated membership and willingness to challenge authority, created considerable momentum in movements aimed at toppling racial inequality in the workplace and elsewhere. Like most of their predecessors, the CTA's struggle for advancement fits within a continuum of successive challenges to economic exploitation and racial inequality. No single person or organization can take full credit for ending segregation or achieving equality. Many who remain nameless and faceless contributed and sacrificed. This study not only chronicles the contribution of a relatively unsung African American labor organization that waged war against Jim Crow on two different fronts, it also pays homage to a few more individuals who made a difference in the lives of an entire race of people during the course of a bitterly contested, never-ending struggle for racial equality in the United States of America during the twentieth century.