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Undergraduate Summer Research Projects

Jump To: PROJECT S141, PROJECT S142, PROJECT S143, PROJECT S144, PROJECT S145, PROJECT S146 

Instructions for potential undergraduate students:

  1. Review the ISS Training Program and its goal.
  2. Review the projects below for projects which match your experience and interest.
  3. Contact the Project Supervisor to discuss working in their laboratory for the Summer; (or other term)
  4. Complete the ISS Application Form, listing your preferred projects

If you already have a Supervisor & Project and wish to participate in the Training Activities:

  1. Review the ISS Program with your supervisor
  2. Ensure your supervisor submitted the project description to the ISS Program by January 6, 2013 and that it was accepted.
  3. Complete  the ISS Application Form listing only your project number in the preferences section.

By Friday, February 21, 2014 submit to the ISS Office:

  1. Completed ISS Application Form
  2. Copies of your unofficial university transcripts
  3. Your updated CV
  4. One reference letter

2013 Summer* Undergraduate Research Projects (apply now!)

Project S141: A Stand-Alone Self-Powered Microfluidic Cartridge for Nucleic Acid Amplification-Based Diagnostics of Infectious Diseases

Supervisor:  Prof David Juncker

Biomedical Engineering, McGill University and Genome Quebec Innovation Center, McGill University
740 Dr. Penfield Avenue Room 6206, Montréal (Québec) Canada, H3A 0G1
Tel:  1 514 398-7676
Website: http://wikisites.mcgill.ca/djgroup
Contact Instructions:  Any

McGill University and Genome Quebec Innovation Center, 

740 Dr. Penfield Avenue, Montréal (Québec)

Possible Project Terms: Summer 2014

Introduction:

Infectious diseases are among the most critical health problems for people living in both the developed and developing world. Emerging pathogens, from viral infections such as HIV/AIDS, SARS, and avian influenza, to bacterial infections such as Cholera and Tuberculosis (TB) are a constant and rapidly evolving threat. Nucleic acid amplification-based tests (NATs) such as polymerase chain reaction (PCR) have been considered as a gold standard method for detection of such diseases due to high accuracy and sensitivity. In DJ Group, we are developing a novel

electricity free PCR device that consists of a thermal cycler and a microfluidic cartridge. Our device will be used in low resource settings for detection of tuberculosis from sputum samples in less than 30 minutes. The microfluidic cartridge is an important component of our system as it enables us to preload the small amounts of reagents, facilitates performing multiple assays and is low cost. In this project, we seek students who are interested in developing the microfluidic cartridge that mixes different reagents with the sample without using an external power and

withstands high temperatures up to 100 C. This cartridge will be subsequently deployed in low resource settings.

Student's role:

The proposed project is aimed at developing a self-powered and low-cost microfluidic cartridge that will be used our electricity-free thermal cycler. The student role in this project is to design, and fabricate a microfluidic cartridge that primarily contains 5 reaction chambers, each has 1 μL volume. Sample will be loaded in an inlet port and will be distributed in the chambers to hydrate the preloaded lyophilized reagents by capillary force. The cartridge will be tested on our thermal cycler to detect the traces of a specific antigen in the samples. The combination of this cartridge and the thermal cycler would make a powerful detection system, which will improve the quality of people’s life, especially in poor resource settings. The main tasks for the student are:

· Design and fabricate a microfluidic assay cartridge and assess the functionality of the devise in terms of proper liquid handling within the cartridge, pre-loading the chip with lyophilized reagents, delivery of the sample to all chambers and hydrate the reagents, and proper packaging of the cartridge to avoid leakage and evaporation during 40 cycles of heating between 55-94 C (months 1-2).

· Assess the functionality and performance of the cartridge by conducting a complete PCR cycle using commercially available thermal cyclers and control samples (months 3-4).

This project requires basic knowledge of fluid mechanics, heat transfer, microfabrication techniques, microscopy, and biomolecular analysis. This is an exciting multidisciplinary project and the student will actively interact with researchers in DJ group as well as Harvard Medical

School and will gain real world experience by learning different experimental techniques. We are currently collaborating with an institute in India to use our device for detecting pulmonary tuberculosis.

PROJECT S142—Sensor Database

Supervisor:  Marcelo M. Wanderley

Music Technology

McGill University

Montreal, Canada

0.1 Problem Statement

Currently, there is no stable tool or protocol to create and manage a database suitable for sensor data. A sensor database requires the storage, management and visualization of sensor measure- ments, sensor calibration, processed data, subject/specimen data, measurement session informa- tion etc. Also, it's essential to a sensor database to present APIs for the most common program- ming language used on data treatment and analysis, like C++, SQL, Matlab/Octave, Python and R. Nowadays, specially in collaborative projects, users have di
erent preferences concerning OS platform. Therefore, a sensor database should not be restricted to a single OS.

0.2 Solution Requirements

We propose as solution a DB based on JAVA, HTML5 and/or WebSQL, therefore accessible by multiple OSs. The implementation would start from scratch, including server and client setup. The database can be relational (PostGreSQL) or NO-SQL (Redis). The solution should accomplish the following requirements:

database security: internal network only, access control: password and IP, encryption, back- ups etc;

functions:

{ upload: sensor measurements, sensor calibration data; sensor data check: check and warn about missing samples, saturated data and other hazards;

{ edition of subject/specimen measurements, measurement session information, sensor node information;

{ multisensor synchronization ticks; multiple measuring system filename relation;

{ creation of measurement sessions, subject/specimen, sensor node information;

2

{ safe removal or update of any data (optional);

{ simple data visualization (for raw and processed data);

{ metadata catalog management and multiple concurrent queries;

{ API or similar to C++, Matlab and Python: script can access the data in the database.

ideally, it might be able to write in the database as well.

user friendly front end (might be done in collaboration with another student);

everything you can imagine to make it e
ective, user-friendly and safe.

0.3 Outreach and work format

The student will be free to choose the tools to perform this challenge, as long as it it’s the requirements. His/her work will contribute to Carolina Brum Medeiros thesis (visit her website), so she will be glad on mentoring the student. Carolina works with sensor fusion for gesture analysis of musicians and baseball players.

In the end of the project, the student should be able to:

deliver a functional prototype;

deliver a report documenting your implementation, stating its advantages and the limitations. Considering the limitations, you might suggest techniques to overcome them;

post your work at www.idmil.org;

ideally, publish your work in case it is applicable.

 

Finally, we will be glad to have you working with us.

PROJECT S143—An optofluidic probe combining precise reagent delivery and integrated fluorescence sensing

Supervisor:  Prof Thomas Gervais

Prof Thomas Gervais
Engineering Physics, Ecole Polytechnique de Montreal
Room 8582.2 - Pavilion principal, Ecole Polytechnique de Montreal, 2500 Ch. de Ia Polytechnique, Montreal, H3T 1J4
Tel: 514-340-4711 ext 3752
Website:  none
Contact Instructions:  Please contact by email

Engineering Physics, Ecole Polytechnique de Montreal

Possible Project terms:  Summer 2014

Title: An optofluidic probe combining precise reagent delivery and integrated fluorescence sensing

Microfluidic probes (MFPs) are a class of channel-free microfluidics systems able to create confined flow patterns by injecting and

withdrawing fluids from the tip of a pen-like probe located on top of a flat surface. Recently, they have been used to produce sharp,

highly-tunable floating concentration gradients [1) for surface processing and to study adherent cell motility. Other groups have used similar probes to perform fluorescence immunohistochemistry on tissue slices [2].

Currently, all microfluidic probes must operate strictly on flat, transparent surfaces on top of an inverted microscope to allow for probe positioning and fluorescence readout. This is an important limitation to extend the use of these devices to process non-transparent surfaces or to operate without the need of a microscopy environment.

To circumvent this limitation, we propose to integrate a fiber optic directly in the device as an optical probe channel surrounded by fluidic channels, thus creating and optofluidic probe (OFP). The 500 micron-diameter bundle, consisting of over a thousand fused fiber optics, will be position directly at the center of a quadrupolar probe. It will allow for direct sensing of the surface located directly under the probe in bright field and fluorescence mode without the need for a microscope. Our goal is to use the optofluidic probe to locally expose freshly cut tumor tissue slices to chemotherapeutics and image their chemoresponse locally, which will be done in a subsequent project.

The student working in team will be responsible for microfabricating a quadrupolar probe incorporating the fiber optics sensors in the design. Close collaboration with tile Juncker lab (McGill), the Laboratoire des fibres optiques (Poly, Prof. Nicolas Godbout), and the Laboratoire d'optique et d'imagerie medicale (Poly, prof. Caroline Boudoux) be required to achieve the fluidic/optic integration. Prof. Frederic Leblond (Poly) will provide expertise in image reconstruction from the sensor signal. Prof. Thomas Gervais will provide the background expertise for probe design, operation and application. A strong synergy exists between this project and the other ISS project we proposed titled : " On-chip chemoresponse assessment of live microtumor samples with an integrated fluorescence imaging system".

Students working on either projects are expect to collaborate with each other to develop the required expertise in microfabrication, optics and imaging required for their success. The device will be tested by comparing the images acquired through the fibers with those acquired by fluorel;cence microscopy using conventional methods. Students with interest in microfluidics, optics and microfabrication are welcome to apply. The interest to work in interdisciplinary teams is essential.

 

(1] Qasaimeh, M. a, Gervais, T., & Juncker, D. (2011j. Microfluidic quadrupole and floating concentration gradient. Nature

communications, 2(May), 464. doi :10.1038/ncomms1471

(2) Lovchik, R. D., Kaigala, G. V, Georgiadis, M., & Delamarche, E. (2012). Micro-immunohistochemistry using a microfluidic probe. Lab

on a chip, 12(6), 1040-3. doi:10.1039/c21c21016a

  

PROJECT S144—On chip chemoresponse assessment of live microtumor samples with an integrated fluorescence imaging system

Supervisor:  Prof Thomas Gervais

Prof Thomas Gervais
Engineering Physics, Ecole Polytechnique de Montreal
Room 8582.2 - Pavilion principal, Ecole Polytechnique de Montreal, 2500 Ch. de Ia Polytechnique, Montreal, H3T 1J4
Tel: 514-340-4711 ext 3752
Contact Instructions:  Please contact by email

Engineering Physics, Ecole Polytechnique de Montreal

Possible Project terms:  Summer 2014

In ovarian cancer patients, empirical chemosensitivity assays are currently performed mostly on 2D cell cultures of primary cell lines. Although proven high throughput techniques exist to perform these assays, they are inherently limited because the information pertaining to the 3D nature of real tumors is lost and so they are ultimately poor predictors of drug efficiency. One step our lab has taken, in collaboration with the CHUM Research Center researcher Dr Anne-Marie Mes Masson, was to cut sub-millimeter 3D tumor pellets from mouse tumor xenografts and load them on a microfluidic chip designed to selectively expose each tumor sample to a different drug concentration (and/or drug type). Cell viability within the tumor was subsequently assayed using confocal fluorescence microscopy. However, this last step is expensive, time consuming and limits cell death monitoring to a few discrete measurements over the course of several days. The goal of this project is to design and fabricate a micro fluidic chip integrating a miniature fluorescence imaging system, eliminating the need of confocal microscopy to assess the viability of the tumor samples marke  with two different viability fluorophores. An ISS project following the same general objective was conducted last year. Students were able to obtain the fluorescence spectra of Cell Tracker Green (CTG) and Propidium Iodide (PI) stained spheroids, a 3D cell culture model similar to micro tumors. The spheroids were placed in a custom designed microfluidic platform with integrated optical fibers. This year's project will focus on the imaging system needed to analyse the viability of tumor samples. An optic fiber bundle will be integrated on chip to obtain spatial fluorescence measurements, leading to imaging. Fluorescence spectra will then be acquired with the use of a laser and a spectrometer controlled by custom Labview coding. Spectra will then be deconvoluted and compared with calibration measurements in order to calculate the concentration of each viability marker in the tumor samples.

This technique will allow cell death monitoring in tissue samples providing us with important information relating to drug concentration including cell death kinetics, onset time, and IC50 values for various drugs and flow conditions. A longer-term objective of the project will be the development of a platform where multiple samples can be analyzed under different conditions with multiple fluorophores. The fiber optics design proposed here will also be expanded in order to allow mathematical algorithms to be used in order to retrieve 3D spatial information on cell death beyond what can be provided by confocal scanners. The student(s) will be responsible for the integration of an optical fiber bundle on a microfluidic chip and the necessary redesign and microfabrication of a new microfluidic chip. A Labview-controlled large spectrum laser and spectrometer will be used as a light source and detector. Students will be required to write the necessary code to be able to record a white light and a fluorescence spectrum. Calibration measurements will then be performed on the resulting imaging system to be able to quantify the fluorescence of the two viability markers. Briefly, spectra measurements will be carried on phantoms with varying fluorophores concentration, absorption coefficient and scattering coefficient. These extensive measurements will allow spectra to be corrected for inter-specimen variation in absorption, scattering and shape. Integration on chip and alignment of the optical fiber bundle on chip will also be the responsibility of the student. He or she will perform preliminary measurements on tumor samples provided by the collaborators at CHUM and then compare the results to those obtained by the gold standard of conventional fluorescence microscopy. The project will involve close collaboration with Prof. Frederic Leblond's and Prof. Caroline Boudoux's laboratories at Polytechnique. Fin.al testing of the device will be performed at the CHUM in Dr Anne-Marie Mes-Masson's laboratory. Students with interest in optics, microfabrication, and cancer biology are welcome to apply. Up to two students can take part in this challenging project.

References: 1. T. Das, L. Meunier, L. Barbe, D. Provencher, 0. Guenat, T. Gervais, and A.-M. Mes-Masson, "Empirical

chemosensitivity testing in a spheroid model of ovarian cancer using a microfluidics-based multiplex

platform," Biomicrofluidics, vol. 7, no. 1, pp. 011805 1 15, 2013.

2. M. Astolfi, S. Fartoumi, S. Kataria, M.-H. Faille, W. Sanger, 0. Morin, B. Peant, J. Kendall-Dupont, D.

Provencher, A.-M. Mes-Masson, and T. Gervais, "On-chip trapping and viability assessment of submicroliter

primary tissues for personalized treatment of ovarian cancer," in MicroTAS, 2013, poster.

  

PROJECT S145—Data acquisition/treatment for mechatronics characterization of molding of composites

Supervisor:  Prof Sofiane Achiche

Collaborator information: Professor Edu Ruiz

edu [dot] ruiz [at] polymtl [dot] ca

Email: sofiane [dot] achiche [at] polymtl [dot] ca

Telephone: 514-340-4711 #4317

École Polytechnique Montréal

2500 Chemin Polytechnique, MTL, H3T 1J4

Available: Summer 2014

Introduction:

The manufacturing of polymer matrix composites consists in impregnating a ceramic fiber with a polymer in a liquid state. Then with the aid of heat, the polymer resin undergoes into a chemical reaction during the molding process known as cure which gives to the piece the mechanical properties and the final part shape. With a growing necessity for composites the aerospatial, automotive and sport industries are demanding improvements in the molding process to produce high quality parts at higher production rates. This task is only possible knowing the changes of the constituent materials during the cure of the composite part.

The long term aim of this project is to provide an intelligent device capable of tracking and measuring the cure kinetics of the polymer. The short term objective of the project proposed here deals with the data acquisition device for the purpose of condition monitoring of the composite parts

The development of the described mechatronics device involves a multidisciplinary knowledge in chemistry, mechanics, electronics, materials and software development sciences. For this reason the student will have the opportunity to interact in a multidisciplinary engineering team, in which the communication and leadership skills are challenged in an industrial environment. The student will have the opportunity of share his/her own ideas, fulfill assigned objectives to contribute in his/her role in the data acquisition module, always supported by staff with several years of experience in the field.

Student's role:

The student(s) will be engaged in the data acquisition team to work with engineers and doctoral students, who share the responsibility of developing the data acquisition and data conditioner module of the global intelligent device. In particular, the student will review the existing sensors to measure the needed physical properties (pressure, temperature, displacement, heat flux, speed, torque, etc) together with their data conditioning to better read and interpret the collected data. Then, with well-defined selection criteria (repeatability, linearity and costs) the student have to support his/her selection.

Once the sensor(s) performance is well set and selected, tests will be made to obtain their range capabilities.

Finally, the student will implement strategies to noise and error reduction in the measurement and define the protocols of communication to store the measured data.

Prior knowledge of semiconductors, electronics and programming languages are helpful but not required. Enthusiasm, the ability to learn quickly and the capacity to search for new information and team work performance are highly required. This research project require of manual work to setup the experiment giving the opportunity to the student to learn the industrial molding process of composites structures.

  PROJECT S146—Smart Textiles Based Wearable Health Monitoring System

Supervisor: Vamsy Chodavarapu

Office: 3480 University St., Room 642

Montreal, Quebec, Canada H3A 0E9

Website: http://www.ece.mcgill.ca/~vchod

Telephone: 514 398 3118

3480 University St., Room 210

Montreal, Quebec, Canada H3A 0E9

Collaborator: Sharp Microsystems 7640 Rue Lima, Brossard, QC J4Y0H7

Available: Summer 2014

Obstructive Sleep Apnea (OSA) is a common chronic condition and a significant public health problem. The

diagnosis of OSA is typically made after a hospital/clinic polysomnography (PSG) study which requires an

overnight stay in a sleep laboratory. Portable at-home monitoring using a limited number of bioparameters has

been suggested as an alternative to PSG for the diagnosis of OSA. This project is to develop a “smart vest” to

allow diagnosis and monitoring of this condition at night while patients are at home sleeping comfortably with

non-invasive equipment that leverages mobile technology and sensor telemetry. The smart vest system will

include an accelerometer sensor to measure breathing rate and breathing effort, ECG electrodes to monitor heart

rate, and a pulse oximeter. The obtained data from the vest can be collected using a smartphone device or

logged at an internet website.

There are several portable devices commercially available which may be useful for at-home diagnosis of OSA

including SleepStrip from Accutest Inc. which is approved by US Food and Drug Agency. However, each

device utilizes different diagnosis numbers and types of physiological measurements and in the unattended

setting there is always the problem of data loss. The proposed system overcomes the above issues by monitoring

various biometrics that are commonly used in a PSG study and allowing real-time data logging in a smartphone

or internet website. The proposed project fits well with the ongoing mobile/internet revolution wherein the use of

wearable technologies for health and wellness applications has attracted attention from a number of companies

and university labs. The proposed project will enable our group to be the first to develop such wearable

technology to diagnose OSA.

The student role would include working with iOS operating system to create a functional application suitable for

iTunes distribution. The student would also work on integration of sensor devices with bluetooth enable

microcontroller interface.

 

Links

The ISS Training Program is funded in part by Funded in part by the National Science & Engineering Research Council of Canada and by the Participating Universities:  

  Training program activities hosted by McGill University     ISS hosted in concert with Universite de Sherbrooke          ISS hosted in concert with Ecole Polytechnique       ISS hosted in concert with INRS