Colony size measurement of the yeast gene deletion strains for functional genomics

BACKGROUND: Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences. RESULTS: Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research. CONCLUSION: GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations

Validating an infrared thermal switch as a novel access technology

<p>Abstract</p> <p>Background</p> <p>Recently, a novel single-switch access technology based on infrared thermography was proposed. The technology exploits the temperature differences between the inside and surrounding areas of the mouth as a switch trigger, thereby allowing voluntary switch activation upon mouth opening. However, for this technology to be clinically viable, it must be validated against a gold standard switch, such as a chin switch, that taps into the same voluntary motion.</p> <p>Methods</p> <p>In this study, we report an experiment designed to gauge the concurrent validity of the infrared thermal switch. Ten able-bodied adults participated in a series of 3 test sessions where they simultaneously used both an infrared thermal and conventional chin switch to perform multiple trials of a number identification task with visual, auditory and audiovisual stimuli. Participants also provided qualitative feedback about switch use. User performance with the two switches was quantified using an efficiency measure based on mutual information.</p> <p>Results</p> <p>User performance (p = 0.16) and response time (p = 0.25) with the infrared thermal switch were comparable to those of the gold standard. Users reported preference for the infrared thermal switch given its non-contact nature and robustness to changes in user posture.</p> <p>Conclusions</p> <p>Thermal infrared access technology appears to be a valid single switch alternative for individuals with disabilities who retain voluntary mouth opening and closing.</p

A Novel Access Technology Based on Infrared Thermography for People with Severe Motor Impairments

Many individuals with severe motor impairments are cognitively capable, but because of their physical impairments, unable to express their intention through conventional means of communication. Access technologies are devices that attempt to translate the intention of these individuals into functional activity by harnessing their residual physical or physiological abilities. The primary objective of this thesis was to design and develop a novel non-invasive and non-contact access technology based on infrared thermal imaging. This access technology translates the local temperature change associated with voluntary mouth opening to activation of a binary switch such as a mouse click or key press. To this end, an algorithm based on motion and temperature analyses, and morphological and anthropometric filters was designed to detect mouth opening activity in thermal video in real-time. The secondary objective of this thesis was to introduce a mutual information measure for objective assessment of binary switch users’ performance. A model was suggested, in which combination of cognitive and physical abilities of the human user of a binary access switch constitute a communication channel. The proposed mutual information measure estimates the rate of information transmission in the ‘human communication channel’ during stimulus response tasks. Using this measure, in a study with ten able-bodied participants, the infrared thermal switch was validated against a conventional chin switch. Impairments in body functions and structures that may contraindicate the use of the infrared thermal switch were explored in a study with seven clients, with severe disabilities. Potential hard and soft technological solutions to mitigate the effect of these impairments on infrared thermal switch use were recommended. Finally the infrared thermal switch was tailored to meet the needs of a young man with severe spastic quadriplegic cerebral palsy, who had no other means of physical access.Ph

Infrared thermography as an access pathway for individuals with severe motor impairments

Abstract Background People with severe motor impairments often require an alternative access pathway, such as a binary switch, to communicate and to interact with their environment. A wide range of access pathways have been developed from simple mechanical switches to sophisticated physiological ones. In this manuscript we report the inaugural investigation of infrared thermography as a non-invasive and non-contact access pathway by which individuals with disabilities can interact and perhaps eventually communicate. Methods Our method exploits the local temperature changes associated with mouth opening/closing to enable a highly sensitive and specific binary switch. Ten participants (two with severe disabilities) provided examples of mouth opening and closing. Thermographic videos of each participant were recorded with an infrared thermal camera and processed using a computerized algorithm. The algorithm detected a mouth open-close pattern using a combination of adaptive thermal intensity filtering, motion tracking and morphological analysis. Results High detection sensitivity and low error rate were achieved for the majority of the participants (mean sensitivity of all participants: 88.5% ± 11.3; mean specificity of all participants: 99.4% ± 0.7). The algorithm performance was robust against participant motion and changes in the background scene. Conclusion Our findings suggest that further research on the infrared thermographic access pathway is warranted. Flexible camera location, convenience of use and robustness to ambient lighting levels, changes in background scene and extraneous body movements make this a potential new access modality that can be used night or day in unconstrained environments

Quantitative analysis of structural neuroimaging of mesial temporal lobe epilepsy.

Mesial temporal lobe epilepsy (MTLE) is the most common of the surgically remediable drug-resistant epilepsies. MRI is the primary diagnostic tool to detect anatomical abnormalities and, when combined with EEG, can more accurately identify an epileptogenic lesion, which is often hippocampal sclerosis in cases of MTLE. As structural imaging technology has advanced the surgical treatment of MTLE and other lesional epilepsies, so too have the analysis techniques that are used to measure different structural attributes of the brain. These techniques, which are reviewed here and have been used chiefly in basic research of epilepsy and in studies of MTLE, have identified different types and the extent of anatomical abnormalities that can extend beyond the affected hippocampus. These results suggest that structural imaging and sophisticated imaging analysis could provide important information to identify networks capable of generating spontaneous seizures and ultimately help guide surgical therapy that improves postsurgical seizure-freedom outcomes