Alexandria Ogrey

Suitability of NFC for Medical Device Communication and Power Delivery

Near Field Communications (NFC) is a 13.56 MHz inductively coupled power delivery and communication protocol that extends the ISO 14443 RFID standard. Low cost NFC scanner subsystems are anticipated to be widely incorporated in coming generations of commodity cellular phones. We consider the potential of this emerging infrastructure to provide convenient and low cost power distribution and communication channels for a range of medical devices. For example, an NFC device within a cell phone could relay measurements collected from a defibrillator-pacemaker to a monitoring physician, remotely control an insulin pump, or activate an implanted neural simulation system. NFC devices pose similar bio-compatibility challenges to other implanted electronics without requiring the provisioning of battery power to support communication. Furthermore, an NFC communication subsystems power-independence provides a measure of defense against potential denial-of-service attacks that consume power in order to discharge a capacity-limited power source. The 13.56 MHz band has minimal interaction with human and animal tissues. We conducted several successful proof-of- concept experiments communicating with with ISO 14443 tags implanted at multiple locations within a human cadaver. Magnetic field strength decays with the cube of distance-to- antenna, limiting limits the range of potential eavesdroppers. At present, NFC protocols do not provide an appropriate set of privacy properties for implanted medical applications. However, NFC devices are implemented using embedded general purpose processors and thus only software modifications would be required to support protocol extensions with enhanced privacy.

MPCT: media propelled computational thinking

Media-Propelled Computational Thinking (MPCT - pronounced impact) is a course designed to introduce programming in the context of engaging problems in media computation, math, and physics. Programming concepts are introduced as incremental steps needed to solve pragmatic problems students already understand. The problems, graphical API, and hands-on program features are intended to expose fundamental concepts in mathematics and quantitative science. MPCT is offered in an entering students program for freshmen who plan to specialize in a variety of STEM (science, technology, engineering and math) and non-STEM subjects. The curriculum is intended to strengthen student intuition and interest in mathematical modeling and programming by engaging students in the direct manipulation of simple mathematical systems that model and display familiar physical phenomena. MPCT uses programs as concrete and manipulatable examples of fundamental concepts to engage a diverse range of students including women and underrepresented minorities. Variants of MPCT are being developed for high schools, and as a means to introduce computational science to upper division undergraduates studying non-computational STEM disciplines. This paper provides an overview of MPCT and representative problem studies including models of ballistics and resonant systems. The evaluation plan is described and very preliminary results are presented.

Prediction of G protein-coupled receptor encoding sequences from the synganglion transcriptome of the cattle tick, Rhipicephalus microplus

The cattle tick, Rhipicephalus (Boophilus) microplus, is a pest which causes multiple health complications in cattle. The G protein-coupled receptor (GPCR) super-family presents a candidate target for developing novel tick control methods. However, GPCRs share limited sequence similarity among orthologous family members, and there is no reference genome available for R. microplus. This limits the effectiveness of alignment-dependent methods such as BLAST and Pfam for identifying GPCRs from R. microplus. However, GPCRs share a common structure consisting of seven transmembrane helices. We present an analysis of the R. microplus synganglion transcriptome using a combination of structurally-based and alignment-free methods which supplement the identification of GPCRs by sequence similarity. TMHMM predicts the number of transmembrane helices in a protein sequence. GPCRpred is a support vector machine-based method developed to predict and classify GPCRs using the dipeptide composition of a query amino acid sequence. These two bioinformatic tools were applied to our transcriptome assembly of the cattle tick synganglion. Together, BLAST and Pfam identified 85 unique contigs as encoding partial or full length candidate cattle tick GPCRs. Collectively, TMHMM and GPCRpred identified 27 additional GPCR candidates that BLAST and Pfam missed. This demonstrates that the addition of structurally-based and alignment-free bioinformatic approaches to transcriptome annotation and analysis produces a greater collection of prospective GPCRs than an analysis based solely upon methodologies dependent upon sequence alignment and similarity.

Work in progress — Eliciting integrated understandings of high school STEM curricula through programming

We describe our early investigation of the integration of educational modules originally developed for a college-level entering students program (ESP) titled “Media Propelled Computational Thinking” (MPCT) into high school science, math, and engineering/technology courses. Primary objectives of MPCT include introducing students to imperative programming and reinforcement of foundational mathematical concepts. This report describes this evolving integration including early informal experiments and potential extensions using programming functions of ubiquitous graphing calculators.

Work in progress - initial evaluation of an introductory course in programming that assists in career choices

We present initial results from an effort to investigate the effectiveness of programming-centric computer literacy courses at the University of Texas at El Paso (UTEP). UTEP is an urban university serving a largely Hispanic student population principally drawn from the sister cities of El Paso, TX, USA, and Ciudad Juarez, Chihuahua, MX. This course is based on the creatively engaging ldquomedia programmingrdquo approach of Dr. Mark Guzdial of Georgia Tech. In this course, which was designed for Liberal Arts students, students are introduced to the Jython programming language. Class projects implement and extend algorithms that directly manipulate multimedia and expose students to digital representations of images and sounds in a sequence of aesthetically focused projects. We are investigating whether (1) there is value in modifying this curriculum to complement common occupational traits for student cohorts enrolled in engineering and computer-science programs and (2) such courses can assist students in career choices and improve long-term student success.

Work in progress - combined introduction of C and assembly with a focus on reduction of high-level language constructs

This paper describes the reform of a sophomore-level course in computer organization for the Computer Science BS curriculum at the University of Texas at El Paso, an urban minority-serving institution, where Java and integrated IDEs have been adopted as the only language and development environments used in the first three semesters of study. This effort was motivated by faculty observations and industry feedback indicating that upper-division students and graduates were failing to achieve mastery of non-garbage-collected, strictly imperative languages, such as C. The similarity of C variable semantics to the underlying machine model enables simultaneous mastery of both C and assembly-language programming and exposes implementation details that are difficult to teach independently, such as subroutine linkage and management of stack frame. An online lab manual has been developed for this course that is freely available for extension or use by other institutions. In this paper, we report on pedagogical techniques for facilitating student understanding of the relationships between high-level language constructs, such as algebraic expression syntax, block-structured control-flow structures, and composite data types, and their implementations in machine code.

A computational introduction to STEM studies

We report on the content and early evaluation of a new introductory programming course “Media Propelled Computational Thinking,” (abbreviated MPCT and pronounced iMPaCT). MPCT is integrated into a freshman-level program designed for under-prepared students with interests in a STEM discipline. It is intended to reduce attrition rates by fostering student intuition in, appreciation of, and confidence about basic pre-calculus concepts. The MPCT curriculum is problem-driven, with analytical challenge exercises that are intended to motivate inquiry and to illustrate the reasoning used in the STEM professions Preliminary evaluation results are encouraging — students from a wide range of academic majors found MPCT engaging, and report that the course conveyed insight, and decreased anxiety about foundational mathematical concepts.