Black-robes, or, Sketches of missions and ministers in the wilderness and on the border.

http://www.archive.org/details/blackrobesorsket00nevirich

Integration of relational and hierarchical network information for protein function prediction

BACKGROUND:In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO) database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions.RESULTS:We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing.CONCLUSION:A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor) and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased positive predictive value), and that this increase is consistent uniformly with GO-term depth. Additional in silico validation on a collection of new annotations recently added to GO confirms the advantages suggested by the cross-validation study. Taken as a whole, our results show that a hierarchical approach to network-based protein function prediction, that exploits the ontological structure of protein annotation databases in a principled manner, can offer substantial advantages over the successive application of 'flat' network-based methods.

Singing Through Struggle: Music as a Mode of Cultural Exchange in African American Border City Churches After Emancipation, 1862-1890

This project investigates how religious music, invested with symbolic and cultural meaning, provided African Americans in border city churches with a way to negotiate conflict, assert individual values, and establish a collective identity in the post- emancipation era. In order to focus on the encounter between former slaves and free Blacks, the dissertation examines black churches that received large numbers of southern migrants during and after the Civil War. Primarily a work of history, the study also employs insights and conceptual frameworks from other disciplines including anthropology and ritual studies, African American studies, aesthetic theory, and musicology. It is a work of historical reconstruction in the tradition of scholarship that some have called "lived religion." Chapter 1 introduces the dissertation topic and explains how it contributes to scholarship. Chapter 2 examines social and religious conditions African Americans faced in Baltimore, MD, Philadelphia, PA, and Washington, DC to show why the Black Church played a key role in African Americans' adjustment to post-emancipation life. Chapter 3 compares religious slave music and free black church music to identify differences and continuities between them, as well as their functions in religious settings. Chapters 4, 5, and 6 present case studies on Bethel African Methodist Episcopal Church (Baltimore), Zoar Methodist Episcopal Church (Philadelphia), and St. Luke’s Protestant Episcopal Church (Washington, DC), respectively. Informed by fresh archival materials, the dissertation shows how each congregation used its musical life to uphold values like education and community, to come to terms with a shared experience, and to confront or avert authority when cultural priorities were threatened. By arguing over musical choices or performance practices, or agreeing on mutually appealing musical forms like the gospel songs of the Sunday school movement, African Americans forged lively faith communities and distinctive cultures in otherwise adverse environments. The study concludes that religious music was a crucial form of African American discourse and expression in the post-emancipation era. In the Black Church, it nurtured an atmosphere of exchange, gave structure and voice to conflict, helped create a public sphere, and upheld the values of black people.

Neural Models of Motion Integration, Segmentation, and Probablistic Decision-Making

When brain mechanism carry out motion integration and segmentation processes that compute unambiguous global motion percepts from ambiguous local motion signals? Consider, for example, a deer running at variable speeds behind forest cover. The forest cover is an occluder that creates apertures through which fragments of the deer's motion signals are intermittently experienced. The brain coherently groups these fragments into a trackable percept of the deer in its trajectory. Form and motion processes are needed to accomplish this using feedforward and feedback interactions both within and across cortical processing streams. All the cortical areas V1, V2, MT, and MST are involved in these interactions. Figure-ground processes in the form stream through V2, such as the seperation of occluding boundaries of the forest cover from the boundaries of the deer, select the motion signals which determine global object motion percepts in the motion stream through MT. Sparse, but unambiguous, feauture tracking signals are amplified before they propogate across position and are intergrated with far more numerous ambiguous motion signals. Figure-ground and integration processes together determine the global percept. A neural model predicts the processing stages that embody these form and motion interactions. Model concepts and data are summarized about motion grouping across apertures in response to a wide variety of displays, and probabilistic decision making in parietal cortex in response to random dot displays.