Deceiving the Ear: Recontextualization, Key Association, and Auxiliary Cadence in Two Songs by Hugo Wolf

Analysis of Hugo Wolf's "An den Schlaf" and "Lebe wohl

Range Segmentation Using Visibility Constraints

Visibility constraints can aid the segmentation of foreground objects observed with multiple range images. In our approach, points are defined as foreground if they can be determined to occlude some {em empty space} in the scene. We present an efficient algorithm to estimate foreground points in each range view using explicit epipolar search. In cases where the background pattern is stationary, we show how visibility constraints from other views can generate virtual background values at points with no valid depth in the primary view. We demonstrate the performance of both algorithms for detecting people in indoor office environments

Coping with uncertain dynamics in visual tracking : redundant state models and discrete search methods

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 133-142).A model of the world dynamics is a vital part of any tracking algorithm. The observed world can exhibit multiple complex dynamics at different spatio-temporal scales. Faithfully modeling all motion constraints in a computationally efficient manner may be too complicated or completely impossible. Resorting to use of approximate motion models complicates tracking by making it less robust to unmodeled noise and increasing running times. We propose two complimentary approaches to tracking with approximate dynamic models in a probabilistic setting. The Redundant State Multi-Chain Model formalism described in the first part of the thesis allows combining multiple weak motion models, each representing a particular aspect of overall dynamic, in a cooperative manner to improve state estimates. This is applicable, in particular, to hierarchical machine vision systems that combine trackers at several spatio-temporal scales. In the second part of the dissertation, we propose supplementing exploration of the continuous likelihood surface with the discrete search in a fixed set of points distributed through the state space. We demonstrate the utility of these approaches on a range of machine vision problems: adaptive background subtraction, structure from motion estimation, and articulated body tracking.by Leonid Taycher.Ph.D

Redeeming the Betrayer: Elgar's Portrayal of Judas in 'The Apostles'

Despite its generally agreed importance, very little has been written about 'The Apostles.' Even among the extant publications that address 'The Apostles,' scholars have focused on its history and development, its reception, or analytical descriptions of its surface themes. The aim of this study will therefore be to provide neither a biography of Elgar, nor an account of the genesis of the work, but to analyze 'The Apostles' in a manner that will achieve a deeper understanding of the oratorio. Chapter 1 explores the complexities that surround Judas and the different ways in which he was perceived throughout history. Then, through my analysis of the surface motives in Chapter 2 and their significance in relation to the large-scale harmonic structure in Chapter 3, I will suggest that Elgar does not denigrate Judas as the betrayer of Christ in 'The Apostles,' but rather depicts him as a tragic yet crucial figure in achieving the redemption of mankind, and through this Judas himself is redeemed

A novel approach to sequence validating protein expression clones with automated decision making

<p>Abstract</p> <p>Background</p> <p>Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation.</p> <p>Results</p> <p>We have developed an Automated Clone Evaluation (ACE) system – the first comprehensive, multi-platform, web-based plasmid sequence verification software package. ACE automates the clone verification process by defining each clone sequence as a list of multidimensional discrepancy objects, each describing a difference between the clone and its expected sequence including the resulting polypeptide consequences. To evaluate clones automatically, this list can be compared against user acceptance criteria that specify the allowable number of discrepancies of each type. This strategy allows users to re-evaluate the same set of clones against different acceptance criteria as needed for use in other experiments. ACE manages the entire sequence validation process including contig management, identifying and annotating discrepancies, determining if discrepancies correspond to polymorphisms and clone finishing. Designed to manage thousands of clones simultaneously, ACE maintains a relational database to store information about clones at various completion stages, project processing parameters and acceptance criteria. In a direct comparison, the automated analysis by ACE took less time and was more accurate than a manual analysis of a 93 gene clone set.</p> <p>Conclusion</p> <p>ACE was designed to facilitate high throughput clone sequence verification projects. The software has been used successfully to evaluate more than 55,000 clones at the Harvard Institute of Proteomics. The software dramatically reduced the amount of time and labor required to evaluate clone sequences and decreased the number of missed sequence discrepancies, which commonly occur during manual evaluation. In addition, ACE helped to reduce the number of sequencing reads needed to achieve adequate coverage for making decisions on clones.</p

Avoiding the "streetlight effect": tracking by exploring likelihood modes

Classic methods for Bayesian inference effectively constrain search to lie within regions of significant probability of the temporal prior. This is efficient with an accurate dynamics model, but otherwise is prone to ignore significant peaks in the true posterior. A more accurate posterior estimate can be obtained by explicitly finding modes of the likelihood function and combining them with a weak temporal prior. In our approach modes are found using efficient example-based matching followed by local refinement to find peaks and estimate peak bandwidth. By reweighting these peaks according to the temporal prior we obtain an estimate of the full posterior model. We show comparative results on real and synthetic images in a high degree of freedom articulated tracking task. 1

Generalizing the Wythoff Array and other Fibonacci Facts to Tribonacci Numbers

In this paper, we generalize a lot of facts from John Conway and Alex Ryba's paper, \textit{The extra Fibonacci series and the Empire State Building}, where we replace the Fibonacci sequence with the Tribonacci sequence. We study the Tribonacci array, which we also call \textit{the Trithoff array} to emphasize the connection to the Wythoff array. We describe 13 new sequences.Comment: 28 pages, 5 table

A Full-Genomic Sequence-Verified Protein-Coding Gene Collection for Francisella tularensis

The rapid development of new technologies for the high throughput (HT) study of proteins has increased the demand for comprehensive plasmid clone resources that support protein expression. These clones must be full-length, sequence-verified and in a flexible format. The generation of these resources requires automated pipelines supported by software management systems. Although the availability of clone resources is growing, current collections are either not complete or not fully sequence-verified. We report an automated pipeline, supported by several software applications that enabled the construction of the first comprehensive sequence-verified plasmid clone resource for more than 96% of protein coding sequences of the genome of F. tularensis, a highly virulent human pathogen and the causative agent of tularemia. This clone resource was applied to a HT protein purification pipeline successfully producing recombinant proteins for 72% of the genes. These methods and resources represent significant technological steps towards exploiting the genomic information of F. tularensis in discovery applications

A Biomedically Enriched Collection of 7000 Human ORF Clones

We report the production and availability of over 7000 fully sequence verified plasmid ORF clones representing over 3400 unique human genes. These ORF clones were derived using the human MGC collection as template and were produced in two formats: with and without stop codons. Thus, this collection supports the production of either native protein or proteins with fusion tags added to either or both ends. The template clones used to generate this collection were enriched in three ways. First, gene redundancy was removed. Second, clones were selected to represent the best available GenBank reference sequence. Finally, a literature-based software tool was used to evaluate the list of target genes to ensure that it broadly reflected biomedical research interests. The target gene list was compared with 4000 human diseases and over 8500 biological and chemical MeSH classes in ∼15 Million publications recorded in PubMed at the time of analysis. The outcome of this analysis revealed that relative to the genome and the MGC collection, this collection is enriched for the presence of genes with published associations with a wide range of diseases and biomedical terms without displaying a particular bias towards any single disease or concept. Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery