Articles — Recent

This is a poster presenting DeCAF – Discrimination, Comparison, Alignment algorithm for small molecules.

Utkarsh Raj's Internship Résumé

This paper presents a new entropy minimization criterion and corresponding algorithms that are used for both symbol timing and carrier frequency recovery for underwater acoustic receivers. It relies on the entropy estimation of the eye diagram and the constellation diagram of the received signal. During the parameter search, when perfect synchronization is achieved, the entropy will reach a global minimum, indicating the least intersymbol interference or a restored constellation diagram. Unlike other synchronization methods, this unified criterion can be used to build an all-in-one synchronizer with high accuracy. The feasibility of this method is proven using a theoretical analysis and supported by sea trial measurement data.

Recent work on information extraction has suggested that fast, interactive tools can be highly effective; however, creating a usable system is challenging, and few publically available tools exist. In this paper we present IKE, a new extraction tool that performs fast, interactive bootstrapping to develop high-quality extraction patterns for targeted relations, and provides novel solutions to these usability concerns. In particular, it uses a novel query language that is expressive, easy to understand, and fast to execute - essential requirements for a practical system - and is the first interactive extraction tool to seamlessly integrate symbolic and distributional methods for search. An initial evaluation suggests that relation tables can be populated substantially faster than by manual pattern authoring or using fully automated tools, while retaining accuracy, an important step towards practical knowledge-base construction.

Odilia Almeida's CV

NIJE GOTOVO

Bacterial cells can have DNA damage due to transcriptional error, or through the effect of an antibiotic. The SOS response is a bacterial cell program for coping with DNA damage, in which the cell cycle is arrested, and DNA repair is induced. The repairs have high probability in leading to mutagenesis in the bacteria, which can lead to antibiotic resistance. The RecA protein in bacteria is responsible for the activation of the SOS response; therefore, making it a target for inhibition. I elected to use the ubiquitination system, natively used for apoptosis, as a means of targeted degradation of the RecA protein in bacteria prone to mutations. Polyubiquitination of misfolded proteins leads to the breaking down of the protein with the aid of proteasomes, which break down unnecessary proteins through a chemical reaction known as proteolysis. Using random forest-predictors, I determined a statistically high likelihood of ubiquitination of the RecA protein in MRSA, Tuberculosis, and other high risk bacterial infections. I hypothesized that I could foster ubiquitin-tagging on RecA by forcing the protein to misfold. Chaperones are proteins which interact with each other to prevent specific sets of proteins from misfolding. CHIP (C terminus of HSC70-Interacting Protein) is a biomolecule that inhibits interactions between the chaperones of RecA. Adding CHIP, ubiquitin, and 26s proteasomes into the bacterial system, should theoretically lead to the degradation of the RecA protein inside the bacteria. I tested my hypothesis by conducting an assay for monitoring CHIP-mediated ubiquitination, and conducted analysis on the assay using SDS- Page gel electrophoresis, and Western-blotting. The resulting data showed signs of polyubiquitination on the RecA protein, with chains of five or more ubiquitin, showing high drug potential. Adding an antibody drug conjugate, containing all the necessary components of a CHIP-mediated ubiquitination reaction, to common antibiotics can lead to the inhibition of bacterial mutagenesis, and higher antibiotic drug potency.

This investigation explores the conditions under which an object, moving through a liquid in high speed, has the greatest deceleration. The conditions focused on are the mass of the object, its initial velocity and its entry angle into the liquid. This is achieved through shooting pellets of varied masses and energies out of two different soft guns at a water container, recording them with a high speed camera and mapping their motion with a tracking program. The results of the experiment indicate that the lesser the mass of the object, the greater its deceleration in the fluid. The initial velocity and the entry angle of the object do not influence the rate of its speed loss. It is further explored that as the density of the fluid becomes greater, so does the deceleration of the object. The investigation is intended to deepen the understanding of the high speed motion through a medium.

An experiment investigating full wave rectification, for the purposes of producing a steady DC output. This is implemented using every half-cycle input from the supply voltage instead of every other half, this is known as a full wave rectifier.