Browsing by Subject "Error Correction"

Brain-computer interfaces (BCI) have the potential to restore communication or control abilities in individuals with severe neuromuscular limitations, such as those with amyotrophic lateral sclerosis (ALS). The role of a BCI is to extract and decode relevant information that conveys a user's intent directly from brain electro-physiological signals and translate this information into executable commands to control external devices. However, the BCI decision-making process is error-prone due to noisy electro-physiological data, representing the classic problem of efficiently transmitting and receiving information via a noisy communication channel.

This research focuses on P300-based BCIs which rely predominantly on event-related potentials (ERP) that are elicited as a function of a user's uncertainty regarding stimulus events, in either an acoustic or a visual oddball recognition task. The P300-based BCI system enables users to communicate messages from a set of choices by selecting a target character or icon that conveys a desired intent or action. P300-based BCIs have been widely researched as a communication alternative, especially in individuals with ALS who represent a target BCI user population. For the P300-based BCI, repeated data measurements are required to enhance the low signal-to-noise ratio of the elicited ERPs embedded in electroencephalography (EEG) data, in order to improve the accuracy of the target character estimation process. As a result, BCIs have relatively slower speeds when compared to other commercial assistive communication devices, and this limits BCI adoption by their target user population. The goal of this research is to develop algorithms that take into account the physical limitations of the target BCI population to improve the efficiency of ERP-based spellers for real-world communication.

In this work, it is hypothesised that building adaptive capabilities into the BCI framework can potentially give the BCI system the flexibility to improve performance by adjusting system parameters in response to changing user inputs. The research in this work addresses three potential areas for improvement within the P300 speller framework: information optimisation, target character estimation and error correction. The visual interface and its operation control the method by which the ERPs are elicited through the presentation of stimulus events. The parameters of the stimulus presentation paradigm can be modified to modulate and enhance the elicited ERPs. A new stimulus presentation paradigm is developed in order to maximise the information content that is presented to the user by tuning stimulus paradigm parameters to positively affect performance. Internally, the BCI system determines the amount of data to collect and the method by which these data are processed to estimate the user's target character. Algorithms that exploit language information are developed to enhance the target character estimation process and to correct erroneous BCI selections. In addition, a new model-based method to predict BCI performance is developed, an approach which is independent of stimulus presentation paradigm and accounts for dynamic data collection. The studies presented in this work provide evidence that the proposed methods for incorporating adaptive strategies in the three areas have the potential to significantly improve BCI communication rates, and the proposed method for predicting BCI performance provides a reliable means to pre-assess BCI performance without extensive online testing.

Promising applications in the design of various biological systems hold critical implications as heralded in the rising field of synthetic biology. But, to achieve these goals, the ability to synthesize and screen in situ DNA constructs of any size or sequence rapidly, accurately and economically is crucial. Today, the process of DNA oligonucleotide synthesis has been automated but the overall development of gene and genome synthesis and error correction technology has far lagged behind that of gene and genome sequencing. What even lagged behind is the capability of screening a large population of information on a single cell, protein or gene level. Compartmentalization of single cells in water-in-oil emulsion droplets provides an opportunity to screen vast numbers of individual assays with quantitative readouts. However these single-emulsion droplets are incompatible with aqueous phase analysis and are not controllable through molecule transports.

This thesis presents the development of a multi-tool ensemble platform targeted at high-throughput gene synthesis, error correction and screening. An inkjet oligonucleotide synthesizer is constructed to synthesize oligonucleotides as sub-arrays onto patterned and functionalized thermoplastic microchips. The arrays are married to microfluidic wells that provide a chamber to for enzymatic amplification and assembly of the DNA from the microarrays into a larger construct. Harvested product is then amplified off-chip and error corrected using a mismatch endonuclease-based reaction. Bacterial cells baring individual synthetic gene variants are encapsulated as single cells into double-emulsion droplets where cell populations are enriched by up to 1000 times within several hours of proliferation. Permeation of Isopropyl-D-1-thiogalactopyranoside (IPTG) molecules from the external solution allows induction of target gene expression. The induced expression of the synthetic fluorescent proteins from at least ~100 bacteria per droplet generates clearly distinguishable fluorescent signals that enable droplets sorting through fluorescence-activated cell sorting (FACS) technique. The integration of oligo synthesis and gene assembly on the same microchip facilitates automation and miniaturization, which leads to cost reduction and increases in throughput. The capacity of double emulsion system (millions discrete compartments in 1ml solution) combined with high-throughput sorting by FACS provide the basis for screening complex gene libraries for different functionality and activity, significantly reducing the cost and turn-around time.