Caesar is an interactive graphic editor that is used to generate layouts for VLSI circuits. It runs on a VAX-11 /780 under the UNIX operating system with Berkeley extensions. Caesar has a unique and simple user interface. Phled is an enhanced version of Caesar that runs on a M68000-based engineering...
MicroRNAs are a highly conserved class of small endogenous RNA, about ~22nt in length, involved in post-transcriptional gene silencing and have prominent roles in disease and development. Though the process of microRNA discovery was once an arduous task, the advent of high throughput sequencing technology has resulted in novel microRNAs...
Throughout Europe, Northern Africa, and the Near East, hundreds of Roman ruins lie scattered about. Many Roman aqueducts, bridges, roads, and even buildings remain standing over two thousand years after their construction, as functional as the day they were built. In the modern United States, however, many public works projects...
All life depends on the reliable translation of RNA to protein according to complex interactions between translation machinery and RNA sequence features. While ribosomal occupancy and codon frequencies vary across coding regions, well-established metrics for computing coding potential of RNA do not capture such positional dependence. Here, we investigate position-dependent...
Our goal is to build a system to model the RNA sequences that reveals their structural information by using efficient dynamic programming algorithms and deep learning approaches. We aim to 1) achieve linear-time for RNA secondary structure prediction based on existing minimum free energy models; 2) utilize deep neural networks...
Profile Hidden Markov Models utilize the information stored in a multiple sequence alignment such as its residues and conserved regions to assign probabilities at each column. This indicates areas in the sequences where similar functionality is observed. These probability weights are then combined to assign a sequence score, which is...
The Pacific Islander diaspora in the Pacific Northwest United States is a unique community characterized by diverse cultures, experiences, and motivations for migration. This study aimed to explore the narratives of individuals from different Pacific Islander backgrounds residing in Oregon, shedding light on their reasons for migration and the impact...
State-of-the-art personal robots need to perform complex manipulation tasks to be viable in complex scenarios. However, many of these robots, like the PR2, use manipulators with high degrees of freedom. High degrees of freedom are desirable from a functionality standpoint, but make the learning task more difficult by adding a...
In this research, we have captured, in pattern form, key elements of programming and design in four programming paradigms (imperative, object-oriented, functional and logical) as well as multiparadigm programming. These pattern sets have formed a foundation upon which we were able to build a deeper understanding of multiparadigm programming and...
This study compares three approaches in the design of an autonomous machine listening agent that predicts harbor porpoise ultrasonic echolocation clicks in diverse noise environments. Considering the temporal variations of noisy coastal ocean soundscapes which the harbor porpoises inhabit, we propose a leave-one-day-out (LODO) cross-validation strategy in the training of...