Ameet Soni

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Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is(More)
MOTIVATION One bottleneck in high-throughput protein crystallography is interpreting an electron-density map, that is, fitting a molecular model to the 3D picture crystallography produces. Previously, we developed ACMI (Automatic Crystallographic Map Interpreter), an algorithm that uses a probabilistic model to infer an accurate protein backbone layout.(More)
An important problem in high-throughput protein crystallography is constructing a protein model from an electron-density map. Previous work by some of this pa-per's authors [1] describes an automated approach to this otherwise time-consuming process. An important step in the previous method requires searching the density map for many small template(More)
In line with institutions across the United States, the Computer Science Department at Swarthmore College has faced the challenge of maintaining a demographic composition of students that matches the student body as a whole. To combat this trend, our department has made a concerted effort to revamp our introductory course sequence to both attract and retain(More)
Several methods for automatically constructing a protein model from an electron-density map require searching for many small protein-fragment templates in the density. We propose to use the spherical-harmonic decomposition of the template and the maps density to speed this matching. Unlike other template-matching approaches, this allows us to eliminate(More)
We present a comparison of weak and distant supervision methods for producing proxy examples for supervised relation extraction. We find that knowledge-based weak supervision tends to outperform popular distance supervision techniques, providing a higher yield of positive examples and more accurate models.
A major bottleneck in high-throughput protein crystallography is producing protein-structure models from an electron-density map. In previous work, we developed Acmi, a probabilistic framework for sampling all-atom protein-structure models. Acmi uses a fully connected, pairwise Markov random field to model the 3D location of each non-hydrogen atom in a(More)
BACKGROUND AND RATIONALE Medical professionals' attitude towards homosexuals affects health care offered to such patients with a different sexual orientation. There is absence of literature that explores the attitudes of Indian medical students or physicians towards homosexuality. AIM This study aimed to evaluate Indian medical students and interns'(More)
We consider the task of KBP slot filling – extracting relation information from newswire documents for knowledge base construction. We present our pipeline, which employs Relational Dependency Networks (RDNs) to learn linguistic patterns for relation extraction. Additionally , we demonstrate how several components such as weak supervision , word2vec(More)