Search

Your search keyword '"Lo, Christine"' showing total 322 results
Start Over Author "Lo, Christine"
322 results on '"Lo, Christine"'

1. Dynamic Changes in Circulating Tumor Fraction as a Predictor of Real-World Clinical Outcomes in Solid Tumor Malignancy Patients Treated with Immunotherapy

Author

Gentzler, Ryan D., Guittar, John, Mitra, Akash, Iams, Wade T., Driessen, Terri, Schwind, Regina, Stein, Michelle M., Kaneva, Kristiyana, Hyun, Seung Won, Liu, Yan, Dugan, Adam J., Vibat, Cecile Rose T., Sangli, Chithra, Freaney, Jonathan, Rivers, Zachary, Feliciano, Josephine L., Lo, Christine, Sasser, Kate, Ben-Shachar, Rotem, Nimeiri, Halla, Patel, Jyoti D., and Chaudhuri, Aadel A.

Published
2024
Full Text
View/download PDF

3. Automated Movement Detection with Dirichlet Process Mixture Models and Electromyography

Author

Cooray, Navin, Li, Zhenglin, Wang, Jinzhuo, Lo, Christine, Arvaneh, Mahnaz, Symmonds, Mkael, Hu, Michele, De Vos, Maarten, and Mihaylova, Lyudmila S

Subjects
Quantitative Biology - Quantitative Methods, Electrical Engineering and Systems Science - Signal Processing
Abstract

Numerous sleep disorders are characterised by movement during sleep, these include rapid-eye movement sleep behaviour disorder (RBD) and periodic limb movement disorder. The process of diagnosing movement related sleep disorders requires laborious and time-consuming visual analysis of sleep recordings. This process involves sleep clinicians visually inspecting electromyogram (EMG) signals to identify abnormal movements. The distribution of characteristics that represent movement can be diverse and varied, ranging from brief moments of tensing to violent outbursts. This study proposes a framework for automated limb-movement detection by fusing data from two EMG sensors (from the left and right limb) through a Dirichlet process mixture model. Several features are extracted from 10 second mini-epochs, where each mini-epoch has been classified as 'leg-movement' or 'no leg-movement' based on annotations of movement from sleep clinicians. The distributions of the features from each category can be estimated accurately using Gaussian mixture models with the Dirichlet process as a prior. The available dataset includes 36 participants that have all been diagnosed with RBD. The performance of this framework was evaluated by a 10-fold cross validation scheme (participant independent). The study was compared to a random forest model and outperformed it with a mean accuracy, sensitivity, and specificity of 94\%, 48\%, and 95\%, respectively. These results demonstrate the ability of this framework to automate the detection of limb movement for the potential application of assisting clinical diagnosis and decision-making.

Published
2023
Full Text
View/download PDF

4. Abnormal Exertional Breathlessness on Cardiopulmonary Cycle Exercise Testing in Relation to Self-Reported and Physiologic Responses in Chronic Airflow Limitation

Author

Bourbeau, Jean, Tan, Wan C., FitzGerald, J. Mark, Sin, Don D., Marciniuk, Darcy D., O’Donnell, Denis E., Hernandez, Paul, Chapman, Kenneth R., Walker, Brandie, Aaron, Shawn, Maltais, François, Samet, Jonathon, Puhan, Milo, Hamid, Qutayba, Hogg, James C., Doiron, Dany, Mancino, Palmina, Li, Pei Zhi, Jensen, Dennis, Baglole, Carolyn, Fortier, Yvan, Sin, Don, Yang, Julia, Road, Jeremy, Comeau, Joe, Png, Adrian, Johnson, Kyle, Coxson, Harvey, Leipsic, Jonathon, Hague, Cameron, Kirby, Miranda, Sadatsafavi, Mohsen, To, Teresa, Gershon, Andrea, Li, Pei-Zhi, Song, Zhi, Benedetti, Andrea, Lo, Christine, Cheng, Sarah, Un, Elena, Fung, Cynthia, Wang, Wen Tiang, Zheng, Liyun, Faroon, Faize, Radivojevic, Olga, Chung, Sally, Zou, Carl, Baril, Jacinthe, Labonte, Laura, Chapman, Kenneth, McClean, Patricia, Audisho, Nadeen, Dumonceaux, Curtis, Machado, Lisette, Fulton, Scott, Osterling, Kristen, Wigerius, Denise, Vandemheen, Kathy, Pratt, Gay, Bergeron, Amanda, O’Donnell, Denis, McNeil, Matthew, Whelan, Kate, Brouillard, Cynthia, Marciniuk, Darcy, Clemens, Ron, Baran, Janet, Leuschen, Candice, Ekström, Magnus, and Lewthwaite, Hayley

Published
2024
Full Text
View/download PDF

5. Impaired Spirometry and COPD Increase the Risk of Cardiovascular Disease: A Canadian Cohort Study

Author

FitzGerald, J. Mark, Sin, Don D., Marciniuk, Darcy D., O’Donnell, Denis E., Hernandez, Paul, Chapman, Kenneth R., Walker, Brandie, Aaron, Shawn, Maltais, François, Doiron, Dany, Mancino, Palmina, Li, Pei Zhi, Jensen, Dennis, Baglole, Carolyn, Fortier, Yvan, Sin, Don, Yang, Julia, Road, Jeremy, Comeau, Joe, Png, Adrian, Johnson, Kyle, Coxson, Harvey, Leipsic, Jonathon, Hague, Cameron, Kirby, Miranda, Song, Zhi, Benedetti, Andrea, Lo, Christine, Cheng, Sarah, Un, Elena, Fung, Cynthia, Wang, Wen Tiang, Zheng, Liyun, Faroon, Faize, Radivojevic, Olga, Chung, Sally, Zou, Carl, Bourbeau, Jean, Baril, Jacinthe, Labonte, Laura, Chapman, Kenneth, McClean, Patricia, Audisho, Nadeen, Dumonceaux, Curtis, Machado, Lisette, Fulton, Scott, Osterling, Kristen, Wigerius, Denise, Vandemheen, Kathy, Pratt, Gay, Bergeron, Amanda, O’Donnell, Denis, McNeil, Matthew, Whelan, Kate, Brouillard, Cynthia, Marciniuk, Darcy, Clemens, Ron, Baran, Janet, Leuschen, Candace, Krishnan, Suurya, Tan, Wan C., Farias, Raquel, and Aaron, Shawn D.

Published
2023
Full Text
View/download PDF

6. A data driven approach towards understanding deficits in olfactory and motor function and identifying applications of smartphone motor testing in prodromal and manifest Parkinson's

Author

Lo, Christine, Hu, Michele, Arora, Siddharth, and De Vos, Maarten

Subjects
Medicine, Parkinson's disease, Rapid eye movement sleep
Abstract

Background: Significant disease heterogeneity in Parkinson's means that identifying ways of applying observations made at a group level, to specific individuals, remains challenging. Standardised clinical assessments, critical for capturing the scientific evidence that informs clinical practice, are rarely used outside of research due to the time required for their administration. Methods: Since 2010, the Oxford Discovery longitudinal cohort study has recruited over 1600 individuals with Parkinson's, Rapid Eye Movement Sleep Behaviour disorder (RBD) (a condition associated with a high risk of developing Parkinson's or another neurodegenerative disorder) and controls. Detailed clinical assessments, including clinical tests of olfactory and motor function and smartphone motor testing, were performed at 18-month intervals. Machine learning algorithms (chiefly random forests) were used to predict clinical scores and outcomes using clinical data or smartphone motor testing data alone. Results: The use of three Sniffin' sticks (Anise, Liquorice, Banana) allowed the identification of individuals with a poor sense of smell (ordinarily requiring assessment with all 16 sticks) with excellent accuracy (area under the curve (AUCs) values of over 0.90 in development and validation cohorts). Summation of scores from 6 tasks of the Movement Disorders Society Unified Parkinson's Disease Rating Scale (MDS-UPDRS) motor examination: repetitive hand movements, finger tapping, pronation/supination, leg movements, constancy of rest tremor and bradykinesia, yielded an abbreviated score whose correlation coefficient with the total 18 task score was high at 0.91. Three approaches to using smartphone motor testing to quantify motor impairment were explored. Smartphone motor testing was also used to predict dopaminergic deficit in RBD with AUCs > 0.73 and the new future onset of motor, cognitive and functional disability in Parkinson's with AUCs > 0.75. Conclusion: A data-driven approach can be used to promote understanding of existing clinical tests in prodromal and manifest Parkinson's, and to drive their refinement. Smartphone motor testing can be used to quantify motor impairment and provide individual estimates of risk; however, both are likely to benefit from further evaluation within the context of clinical trials and routine clinical practice.

Published
2020

7. Development and validation of risk prediction models for COVID-19 positivity in a hospital setting

Author

Ng, Ming-Yen, Wan, Eric Yuk Fai, Wong, Ho Yuen Frank, Leung, Siu Ting, Lee, Jonan Chun Yin, Chin, Thomas Wing-Yan, Lo, Christine Shing Yen, Lui, Macy Mei-Sze, Chan, Edward Hung Tat, Fong, Ambrose Ho-Tung, Fung, Sau Yung, Ching, On Hang, Chiu, Keith Wan-Hang, Chung, Tom Wai Hin, Vardhanbhuti, Varut, Lam, Hiu Yin Sonia, To, Kelvin Kai Wang, Chiu, Jeffrey Long Fung, Lam, Tina Poy Wing, Khong, Pek Lan, Liu, Raymond Wai To, Chan, Johnny Wai Man, Wu, Alan Ka Lun, Lung, Kwok-Cheung, Hung, Ivan Fan Ngai, Lau, Chak Sing, Kuo, Michael D, and Ip, Mary Sau-Man

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, 4.2 Evaluation of markers and technologies, Detection, screening and diagnosis, Good Health and Well Being, Adult, Aged, Aged, 80 and over, Area Under Curve, COVID-19, Female, Hospitals, Humans, Logistic Models, Male, Middle Aged, Nomograms, Probability, SARS-CoV-2, Chest x-ray, Nomogram, Prediction model, White cell count, Microbiology, Medical Microbiology, Public Health and Health Services, Clinical sciences, Epidemiology, Public health
Abstract

ObjectivesTo develop: (1) two validated risk prediction models for coronavirus disease-2019 (COVID-19) positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation.MethodsPatients with and without COVID-19 were included from 4 Hong Kong hospitals. The database was randomly split into 2:1: for model development database (n = 895) and validation database (n = 435). Multivariable logistic regression was utilised for model creation and validated with the Hosmer-Lemeshow (H-L) test and calibration plot. Nomograms and probabilities set at 0.1, 0.2, 0.4 and 0.6 were calculated to determine sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV).ResultsA total of 1330 patients (mean age 58.2 ± 24.5 years; 50.7% males; 296 COVID-19 positive) were recruited. The first prediction model developed had age, total white blood cell count, chest x-ray appearances and contact history as significant predictors (AUC = 0.911 [CI = 0.880-0.941]). The second model developed has the same variables except contact history (AUC = 0.880 [CI = 0.844-0.916]). Both were externally validated on the H-L test (p = 0.781 and 0.155, respectively) and calibration plot. Models were converted to nomograms. Lower probabilities give higher sensitivity and NPV; higher probabilities give higher specificity and PPV.ConclusionTwo simple-to-use validated nomograms were developed with excellent AUCs based on readily available parameters and can be considered for clinical utilisation.

Published
2020

8. Screening for REM Sleep Behaviour Disorder with Minimal Sensors

Author

Cooray, Navin, Andreotti, Fernando, Lo, Christine, Symmonds, Mkael, Hu, Michele T. M., and De Vos, Maarten

Subjects
Quantitative Biology - Quantitative Methods, Electrical Engineering and Systems Science - Signal Processing
Abstract

Rapid-Eye-Movement (REM) sleep behaviour disorder (RBD) is an early predictor of Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. This study investigates a minimal set of sensors to achieve effective screening for RBD in the population, integrating automated sleep staging (three state) followed by RBD detection without the need for cumbersome electroencephalogram (EEG) sensors. Polysomnography signals from 50 participants with RBD and 50 age-matched healthy controls were used to evaluate this study. Three stage sleep classification was achieved using a Random Forest (RF) classifier and features derived from a combination of cost-effective and easy to use sensors, namely electrocardiogram (ECG), electrooculogram (EOG), and electromyogram (EMG) channels. Subsequently, RBD detection was achieved using established and new metrics derived from ECG and EMG metrics. The EOG and EMG combination provided the best minimalist fully automated performance, achieving $0.57\pm0.19$ kappa (3 stage) for sleep staging and an RBD detection accuracy of $0.90\pm0.11$, (sensitivity, and specificity $0.88\pm0.13$, and $0.92\pm0.098$). A single ECG sensor allowed three state sleep staging with $0.28\pm0.06$ kappa and RBD detection accuracy of $0.62\pm0.10$. This study demonstrated the feasibility of using signals from a single EOG and EMG sensor to detect RBD using fully-automated techniques. This study proposes a cost-effective, practical, and simple RBD identification support tool using only two sensors (EMG and EOG), ideal for screening purposes., Comment: 21 pages, 6 figures, and 6 tables. arXiv admin note: text overlap with arXiv:1811.04662

Published
2019

9. Detection of REM Sleep Behaviour Disorder by Automated Polysomnography Analysis

Author

Cooray, Navin, Andreotti, Fernando, Lo, Christine, Symmonds, Mkael, Hu, Michele T. M., and De Vos, Maarten

Subjects
Computer Science - Machine Learning, Electrical Engineering and Systems Science - Signal Processing, Quantitative Biology - Neurons and Cognition, Statistics - Machine Learning
Abstract

Evidence suggests Rapid-Eye-Movement (REM) Sleep Behaviour Disorder (RBD) is an early predictor of Parkinson's disease. This study proposes a fully-automated framework for RBD detection consisting of automated sleep staging followed by RBD identification. Analysis was assessed using a limited polysomnography montage from 53 participants with RBD and 53 age-matched healthy controls. Sleep stage classification was achieved using a Random Forest (RF) classifier and 156 features extracted from electroencephalogram (EEG), electrooculogram (EOG) and electromyogram (EMG) channels. For RBD detection, a RF classifier was trained combining established techniques to quantify muscle atonia with additional features that incorporate sleep architecture and the EMG fractal exponent. Automated multi-state sleep staging achieved a 0.62 Cohen's Kappa score. RBD detection accuracy improved by 10% to 96% (compared to individual established metrics) when using manually annotated sleep staging. Accuracy remained high (92%) when using automated sleep staging. This study outperforms established metrics and demonstrates that incorporating sleep architecture and sleep stage transitions can benefit RBD detection. This study also achieved automated sleep staging with a level of accuracy comparable to manual annotation. This study validates a tractable, fully-automated, and sensitive pipeline for RBD identification that could be translated to wearable take-home technology., Comment: 20 pages, 3 figures

Published
2018

10. Impaired Sleep Quality in COPD Is Associated With Exacerbations The CanCOLD Cohort Study

Author

Shorofsky, Matthew, Bourbeau, Jean, Kimoff, John, Jen, Rachel, Malhotra, Atul, Ayas, Najib, Tan, Wan C, Aaron, Shawn D, Sin, Don D, Road, Jeremy, Chapman, Kenneth R, O’Donnell, Denis E, Maltais, François, Hernandez, Paul, Walker, Brandie L, Marciniuk, Darcy, Kaminska, Marta, FitzGerald, J Mark, Sin, DD, Marciniuk, DD, O'Donnell, DE, Cowie, Robert, Aaron, Shawn, Maltais, F, Samet, Jonathon, Puhan, Milo, Hamid, Qutayba, Hogg, James C, Baglole, Carole, Jabet, Carole, Mancino, Palmina, Fortier, Yvan, Sin, Don, Tam, Sheena, Comeau, Joe, Png, Adrian, Coxson, Harvey, Kirby, Miranda, Leipsic, Jonathon, Hague, Cameron, Sadatsafavi, Mohsen, Gershon, Andrea, Li, Pei-Zhi, Duquette, Jean-Francois, Benedetti, Andrea, Jensen, Denis, O'Donnell, Denis, Lo, Christine, Cheng, Sarah, Fung, Cindy, Ferguson, Nancy, Haynes, Nancy, Chuang, Li, Licong, Bayat, Selva, Wong, Amanda, Alavi, Zoe, Peng, Catherine, Zhao, Bin, Scott-Hsiung, Nathalie, Nadirshaw, Tasha, Latreille, David, Baril, Jacinthe, Labonte, Laura, Chapman, Kenneth, McClean, Patricia, Audisho, Nadeen, Walker, Brandie, Cowie, Ann, Dumonceaux, Curtis, Machado, Lisette, Fulton, Scott, Osterling, Kristen, Vandemheen, Kathy, Pratt, Gay, Bergeron, Amanda, McNeil, Matthew, Whelan, Kate, Maltais, Francois, Brouillard, Cynthia, and Clemens, Ron

Subjects
Biomedical and Clinical Sciences, Cardiovascular Medicine and Haematology, Clinical Sciences, Sleep Research, Lung, Behavioral and Social Science, Clinical Research, Chronic Obstructive Pulmonary Disease, Respiratory, Aged, Cohort Studies, Disease Progression, Dyspnea, Female, Health Services, Humans, Male, Middle Aged, Proportional Hazards Models, Prospective Studies, Pulmonary Disease, Chronic Obstructive, Sleep, Sleep Wake Disorders, Sputum, Time Factors, acute exacerbation of chronic bronchitis, COPD, sleep medicine, Canadian Respiratory Research Network, CanCOLD Collaborative Research group, Respiratory System, Cardiovascular medicine and haematology, Clinical sciences
Abstract

BackgroundCOPD increases susceptibility to sleep disturbances, which may in turn predispose to increased respiratory symptoms. The objective of this study was to evaluate, in a population-based sample, the relationship between subjective sleep quality and risk of COPD exacerbations.MethodsData were obtained from the Canadian Cohort Obstructive Lung Disease (CanCOLD) study. Participants with COPD who had completed 18 months of follow-up were included. Sleep quality was measured with the Pittsburgh Sleep Quality Index (PSQI) and a three-factor analysis. Symptom-based (dyspnea or sputum change ≥ 48 h) and event-based (symptoms plus medication or unscheduled health services use) exacerbations were assessed. Association of PSQI with exacerbation rate was assessed by using negative binomial regression. Exacerbation-free survival was also assessed.ResultsA total of 480 participants with COPD were studied, including 185 with one or more exacerbations during follow-up and 203 with poor baseline sleep quality (PSQI score > 5). Participants with subsequent symptom-based exacerbations had higher median baseline PSQI scores than those without (6.0 [interquartile range, 3.0-8.0] vs 5.0 [interquartile range, 2.0-7.0]; P = .01), and they were more likely to have baseline PSQI scores > 5 (50.3% vs 37.3%; P = .01). Higher PSQI scores were associated with increased symptom-based exacerbation risk (adjusted rate ratio, 1.09; 95% CI, 1.01-1.18; P = .02) and event-based exacerbation risk (adjusted rate ratio, 1.10; 95% CI, 1.00-1.21; P = .048). The association occurred mainly in those with undiagnosed COPD. Strongest associations were with Factor 3 (sleep disturbances and daytime dysfunction). Time to symptom-based exacerbation was shorter in participants with poor sleep quality (adjusted hazard ratio, 1.49; 95% CI, 1.09-2.03).ConclusionsHigher baseline PSQI scores were associated with increased risk of COPD exacerbation over 18 months' prospective follow-up.

Published
2019

12. Biomarkers of conversion to α-synucleinopathy in isolated rapid-eye-movement sleep behaviour disorder

Author

Miglis, Mitchell G, Adler, Charles H, Antelmi, Elena, Arnaldi, Dario, Baldelli, Luca, Boeve, Bradley F, Cesari, Matteo, Dall'Antonia, Irene, Diederich, Nico J, Doppler, Kathrin, Dušek, Petr, Ferri, Raffaele, Gagnon, Jean-François, Gan-Or, Ziv, Hermann, Wiebke, Högl, Birgit, Hu, Michele T, Iranzo, Alex, Janzen, Annette, Kuzkina, Anastasia, Lee, Jee-Young, Leenders, Klaus L, Lewis, Simon J G, Liguori, Claudio, Liu, Jun, Lo, Christine, Ehgoetz Martens, Kaylena A, Nepozitek, Jiri, Plazzi, Giuseppe, Provini, Federica, Puligheddu, Monica, Rolinski, Michal, Rusz, Jan, Stefani, Ambra, Summers, Rebekah L S, Yoo, Dallah, Zitser, Jennifer, and Oertel, Wolfgang H

Published
2021
Full Text
View/download PDF

16. Predicting recurrence using a tumor-uninformed ctDNA assay detecting MRD in patients with resected stage II or III colorectal cancer: Subset analysis from the GALAXY study in CIRCULATE-Japan.

Author

Nakamura, Yoshiaki, primary, Kaneva, Kristiyana, additional, Lo, Christine, additional, Neems, Daniel, additional, Freaney, Jonathan, additional, Boulos, Hala, additional, Hyun, Seung Won, additional, Oki, Eiji, additional, Kotani, Daisuke, additional, Wantanabe, Jun, additional, Kotaka, Masahito, additional, Bando, Hideaki, additional, Yamazaki, Kentaro, additional, Takemasa, Ichiro, additional, Kato, Takeshi, additional, Sangli, Chithra, additional, Blidner, Richard, additional, Sasser, Kate, additional, Nimeiri, Halla, additional, and Yoshino, Takayuki, additional

Published
2024
Full Text
View/download PDF

17. Normative Reference Equations for Breathlessness Intensity during Incremental Cardiopulmonary Cycle Exercise Testing

Author

Ekström, Magnus, primary, Li, Pei Zhi, additional, Lewthwaite, Hayley, additional, Bourbeau, Jean, additional, Tan, Wan C., additional, Schiöler, Linus, additional, Brotto, Andrew, additional, Stickland, Michael K., additional, Jensen, Dennis, additional, FitzGerald, J. Mark, additional, Sin, Don D., additional, Marciniuk, Darcy D., additional, O’Donnell, Denis E., additional, Hernandez, Paul, additional, Chapman, Kenneth R., additional, Walker, Brandie, additional, Aaron, Shawn, additional, Maltais, François, additional, Samet, Jonathon, additional, Puhan, Milo, additional, Hamid, Qutayba, additional, Hogg, James C., additional, Doiron, Dany, additional, Mancino, Palmina, additional, Baglole, Carolyn, additional, Fortier, Yvan, additional, Yang, Julia, additional, Road, Jeremy, additional, Comeau, Joe, additional, Png, Adrian, additional, Johnson, Kyle, additional, Coxson, Harvey, additional, Leipsic, Jonathon, additional, Hague, Cameron, additional, Kirby, Miranda, additional, Sadatsafavi, Mohsen, additional, To, Teresa, additional, Gershon, Andrea, additional, Song, Zhi, additional, Benedetti, Andrea, additional, Lo, Christine, additional, Cheng, Sarah, additional, Un, Elena, additional, Fung, Cynthia, additional, Wang, Wen Tiang, additional, Zheng, Liyun, additional, Faroon, Faize, additional, Radivojevic, Olga, additional, Chung, Sally, additional, Zou, Carl, additional, Baril, Jacinthe, additional, Labonte, Laura, additional, McClean, Patricia, additional, Audisho, Nadeen, additional, Dumonceaux, Curtis, additional, Machado, Lisette, additional, Fulton, Scott, additional, Osterling, Kristen, additional, Wigerius, Denise, additional, Vandemheen, Kathy, additional, Pratt, Gay, additional, Bergeron, Amanda, additional, McNeil, Matthew, additional, Whelan, Kate, additional, Brouillard, Cynthia, additional, Clemens, Ron, additional, Baran, Janet, additional, and Leuschen, Candice, additional

Published
2024
Full Text
View/download PDF

18. Machine learning application for the prediction of SARS-CoV-2 infection using blood tests and chest radiograph

Author

Du, Richard, Tsougenis, Efstratios D., Ho, Joshua W. K., Chan, Joyce K. Y., Chiu, Keith W. H., Fang, Benjamin X. H., Ng, Ming Yen, Leung, Siu-Ting, Lo, Christine S. Y., Wong, Ho-Yuen F., Lam, Hiu-Yin S., Chiu, Long-Fung J., So, Tiffany Y, Wong, Ka Tak, Wong, Yiu Chung I., Yu, Kevin, Yeung, Yiu-Cheong, Chik, Thomas, Pang, Joanna W. K., Wai, Abraham Ka-chung, Kuo, Michael D., Lam, Tina P. W., Khong, Pek-Lan, Cheung, Ngai-Tseung, and Vardhanabhuti, Varut

Published
2021
Full Text
View/download PDF

20. Impaired Sleep Quality in COPD Is Associated With Exacerbations: The CanCOLD Cohort Study

Author

Bourbeau, Jean, Tan, Wan C., FitzGerald, J. Mark, Sin, D.D., Marciniuk, D.D., O'Donnell, D.E., Hernandez, Paul, Chapman, Kenneth R., Cowie, Robert, Aaron, Shawn, Maltais, F., Samet, Jonathon, Puhan, Milo, Hamid, Qutayba, Hogg, James C., Baglole, Carole, Jabet, Carole, Mancino, Palmina, Fortier, Yvan, Sin, Don, Tam, Sheena, Road, Jeremy, Comeau, Joe, Png, Adrian, Coxson, Harvey, Kirby, Miranda, Leipsic, Jonathon, Hague, Cameron, Sadatsafavi, Mohsen, Gershon, Andrea, Li, Pei-Zhi, Duquette, Jean-Francois, Benedetti, Andrea, Jensen, Denis, O'Donnell, Denis, Lo, Christine, Cheng, Sarah, Fung, Cindy, Ferguson, Nancy, Haynes, Nancy, Chuang, Junior, Li, Licong, Bayat, Selva, Wong, Amanda, Alavi, Zoe, Peng, Catherine, Zhao, Bin, Scott-Hsiung, Nathalie, Nadirshaw, Tasha, Latreille, David, Baril, Jacinthe, Labonte, Laura, Chapman, Kenneth, McClean, Patricia, Audisho, Nadeen, Walker, Brandie, Cowie, Ann, Dumonceaux, Curtis, Machado, Lisette, Fulton, Scott, Osterling, Kristen, Vandemheen, Kathy, Pratt, Gay, Bergeron, Amanda, McNeil, Matthew, Whelan, Kate, Maltais, Francois, Brouillard, Cynthia, Marciniuk, Darcy, Clemens, Ron, Baran, Janet, Shorofsky, Matthew, Kimoff, John, Jen, Rachel, Malhotra, Atul, Ayas, Najib, Aaron, Shawn D., Sin, Don D., O’Donnell, Denis E., Maltais, François, Walker, Brandie L., and Kaminska, Marta

Published
2019
Full Text
View/download PDF

22. SeeSite: Efficiently Finding Co-occurring Splice Sites and Exon Splicing Enhancers

Author

Lo, Christine, Kakaradov, Boyko, Lokshtanov, Daniel, and Boucher, Christina

Subjects
Quantitative Biology - Quantitative Methods, Quantitative Biology - Genomics
Abstract

The problem of identifying splice sites consists of two sub-problems: finding their boundaries, and characterizing their sequence markers. Other splicing elements---including, enhancers and silencers---that occur in the intronic and exonic regions play an important role in splicing activity. Existing methods for detecting splicing elements are limited to finding either splice sites or enhancers and silencers, even though these elements are well-known to co-occur. We introduce SeeSite, an efficient and accurate tool for detecting splice sites and their complementary exon splicing enhancers (ESEs). SeeSite has three stages: graph construction, finding dense subgraphs, and recovering splice sites and ESEs along with their consensus. The third step involves solving Consensus Sequence with Outliers, an NP-complete string clustering problem. We prove that our algorithm for this problem outputs near-optimal solutions in polynomial time. Using SeeSite we demonstrate that ESEs are preferentially associated with weaker splice sites, and splice sites of a certain canonical form co-occur with specific ESEs.

Published
2012

23. Outlier Detection for DNA Fragment Assembly

Author

Boucher, Christina, Lo, Christine, and Lokshtanov, Daniel

Subjects
Computer Science - Data Structures and Algorithms
Abstract

Given $n$ length-$\ell$ strings $S =\{s_1, ..., s_n\}$ over a constant size alphabet $\Sigma$ together with parameters $d$ and $k$, the objective in the {\em Consensus String with Outliers} problem is to find a subset $S^*$ of $S$ of size $n-k$ and a string $s$ such that $\sum_{s_i \in S^*} d(s_i, s) \leq d$. Here $d(x, y)$ denotes the Hamming distance between the two strings $x$ and $y$. We prove 1. a variant of {\em Consensus String with Outliers} where the number of outliers $k$ is fixed and the objective is to minimize the total distance $\sum_{s_i \in S^*} d(s_i, s)$ admits a simple PTAS. (ii) Under the natural assumption that the number of outliers $k$ is small, the PTAS for the distance minimization version of {\em Consensus String with Outliers} performs well. In particular, as long as $k\leq cn$ for a fixed constant $c < 1$, the algorithm provides a $(1+\epsilon)$-approximate solution in time $f(1/\epsilon)(n\ell)^{O(1)}$ and thus, is an EPTAS. 2. In order to improve the PTAS for {\em Consensus String with Outliers} to an EPTAS, the assumption that $k$ is small is necessary. Specifically, when $k$ is allowed to be arbitrary the {\em Consensus String with Outliers} problem does not admit an EPTAS unless FPT=W[1]. This hardness result holds even for binary alphabets. 3. The decision version of {\em Consensus String with Outliers} is fixed parameter tractable when parameterized by $\frac{d}{n-k}$. and thus, also when parameterized by just $d$. To the best of our knowledge, {\em Consensus String with Outliers} is the first problem that admits a PTAS, and is fixed parameter tractable when parameterized by the value of the objective function but does not admit an EPTAS under plausible complexity assumptions., Comment: 29 pages, 1 figure

Published
2011

24. 34 Association of a novel circulating tumor fraction DNA biomarker of treatment response monitoring and clinical outcomes in a real-world, diverse pan-cancer cohort treated with immunotherapy

Author

Guittar, John, primary, Gentzler, Ryan, additional, Mitra, Akash, additional, Stein, Michelle M, additional, Lo, Christine, additional, Zhu, Wei, additional, Driessen, Terri, additional, Guinney, Justin, additional, Nimeiri, Halla, additional, Ben-Shachar, Rotem, additional, and Patel, Jyoti, additional

Published
2023
Full Text
View/download PDF

25. Detection of COVID-19 Using Deep Learning Algorithms on Chest Radiographs

Author

Chiu, Wan Hang Keith, Vardhanabhuti, Varut, Poplavskiy, Dmytro, Yu, Philip Leung Ho, Du, Richard, Yap, Alistair Yun Hee, Zhang, Sailong, Fong, Ambrose Ho-Tung, Chin, Thomas Wing-Yan, Lee, Jonan Chun Yin, Leung, Siu Ting, Lo, Christine Shing Yen, Lui, Macy Mei-Sze, Fang, Benjamin Xin Hao, Ng, Ming-Yen, and Kuo, Michael D.

Published
2020
Full Text
View/download PDF

26. On the design of clone-based haplotyping

Author

Lo, Christine, Liu, Rui, Lee, Jehyuk, Robasky, Kimberly, Byrne, Susan, Lucchesi, Carolina, Aach, John, Church, George, Bafna, Vineet, and Zhang, Kun

Abstract

Abstract Background Haplotypes are important for assessing genealogy and disease susceptibility of individual genomes, but are difficult to obtain with routine sequencing approaches. Experimental haplotype reconstruction based on assembling fragments of individual chromosomes is promising, but with variable yields due to incompletely understood parameter choices. Results We parameterize the clone-based haplotyping problem in order to provide theoretical and empirical assessments of the impact of different parameters on haplotype assembly. We confirm the intuition that long clones help link together heterozygous variants and thus improve haplotype length. Furthermore, given the length of the clones, we address how to choose the other parameters, including number of pools, clone coverage and sequencing coverage, so as to maximize haplotype length. We model the problem theoretically and show empirically the benefits of using larger clones with moderate number of pools and sequencing coverage. In particular, using 140 kb BAC clones, we construct haplotypes for a personal genome and assemble haplotypes with N50 values greater than 2.6 Mb. These assembled haplotypes are longer and at least as accurate as haplotypes of existing clone-based strategies, whether in vivo or in vitro. Conclusions Our results provide practical guidelines for the development and design of clone-based methods to achieve long range, high-resolution and accurate haplotypes.

Published
2013

27. Evaluating genome architecture of a complex region via generalized bipartite matching

Author

Lo, Christine, Kim, Sangwoo, Zakov, Shay, and Bafna, Vineet

Abstract

Abstract With the remarkable development in inexpensive sequencing technologies and supporting computational tools, we have the promise of medicine being personalized by knowledge of the individual genome. Current technologies provide high throughput, but short reads. Reconstruction of the donor genome is based either on de novo assembly of the (short) reads, or on mapping donor reads to a standard reference. While such techniques demonstrate high success rates for inferring 'simple' genomic segments, they are confounded by segments with complex duplication patterns, including regions of direct medical relevance, like the HLA and the KIR regions. In this work, we address this problem with a method for assessing the quality of a predicted genome sequence for complex regions of the genome. This method combines two natural types of evidence: sequence similarity of the mapped reads to the predicted donor genome, and distribution of reads across the predicted genome. We define a new scoring function for read-to-genome matchings, which penalizes for sequence dissimilarities and deviations from expected read location distribution, and present an efficient algorithm for finding matchings that minimize the penalty. The algorithm is based on a formal problem, first defined in this paper, called Coverage Sensitive many-to-many min-cost bipartite Matching (CSM). This new problem variant generalizes the standard (one-to-one) weighted bipartite matching problem, and can be solved using network flows. The resulting Java-based tool, called SAGE (Scoring function for Assembled GEnomes), is freely available upon request. We demonstrate over simulated data that SAGE can be used to infer correct haplotypes of the highly repetitive KIR region on the Human chromosome 19.

Published
2013

28. Strobe sequence design for Haplotype assembly

Author

Lo, Christine, Bashir, Ali, Bansal, Vikas, and Bafna, Vineet

Abstract

Abstract Background Humans are diploid, carrying two copies of each chromosome, one from each parent. Separating the paternal and maternal chromosomes is an important component of genetic analyses such as determining genetic association, inferring evolutionary scenarios, computing recombination rates, and detecting cis-regulatory events. As the pair of chromosomes are mostly identical to each other, linking together of alleles at heterozygous sites is sufficient to phase, or separate the two chromosomes. In Haplotype Assembly, the linking is done by sequenced fragments that overlap two heterozygous sites. While there has been a lot of research on correcting errors to achieve accurate haplotypes via assembly, relatively little work has been done on designing sequencing experiments to get long haplotypes. Here, we describe the different design parameters that can be adjusted with next generation and upcoming sequencing technologies, and study the impact of design choice on the length of the haplotype. Results We show that a number of parameters influence haplotype length, with the most significant one being the advance length (distance between two fragments of a clone). Given technologies like strobe sequencing that allow for large variations in advance lengths, we design and implement a simulated annealing algorithm to sample a large space of distributions over advance-lengths. Extensive simulations on individual genomic sequences suggest that a non-trivial distribution over advance lengths results a 1-2 order of magnitude improvement in median haplotype length. Conclusions Our results suggest that haplotyping of large, biologically important genomic regions is feasible with current technologies.

Published
2011

32. Consensus Patterns (Probably) Has no EPTAS

Author

Boucher, Christina, Lo, Christine, Lokshantov, Daniel, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bansal, Nikhil, editor, and Finocchi, Irene, editor

Published
2015
Full Text
View/download PDF

33. Impaired Spirometry and COPD Increase the Risk of Cardiovascular Disease

Author

Krishnan, Suurya, primary, Tan, Wan C., additional, Farias, Raquel, additional, Aaron, Shawn D., additional, Benedetti, Andrea, additional, Chapman, Kenneth R., additional, Hernandez, Paul, additional, Maltais, François, additional, Marciniuk, Darcy D., additional, O’Donnell, Denis E., additional, Sin, Don D., additional, Walker, Brandie, additional, Bourbeau, Jean, additional, FitzGerald, J. Mark, additional, Aaron, Shawn, additional, Doiron, Dany, additional, Mancino, Palmina, additional, Li, Pei Zhi, additional, Jensen, Dennis, additional, Baglole, Carolyn, additional, Fortier, Yvan, additional, Sin, Don, additional, Yang, Julia, additional, Road, Jeremy, additional, Comeau, Joe, additional, Png, Adrian, additional, Johnson, Kyle, additional, Coxson, Harvey, additional, Leipsic, Jonathon, additional, Hague, Cameron, additional, Kirby, Miranda, additional, Song, Zhi, additional, Lo, Christine, additional, Cheng, Sarah, additional, Un, Elena, additional, Fung, Cynthia, additional, Wang, Wen Tiang, additional, Zheng, Liyun, additional, Faroon, Faize, additional, Radivojevic, Olga, additional, Chung, Sally, additional, Zou, Carl, additional, Baril, Jacinthe, additional, Labonte, Laura, additional, Chapman, Kenneth, additional, McClean, Patricia, additional, Audisho, Nadeen, additional, Dumonceaux, Curtis, additional, Machado, Lisette, additional, Fulton, Scott, additional, Osterling, Kristen, additional, Wigerius, Denise, additional, Vandemheen, Kathy, additional, Pratt, Gay, additional, Bergeron, Amanda, additional, O’Donnell, Denis, additional, McNeil, Matthew, additional, Whelan, Kate, additional, Brouillard, Cynthia, additional, Marciniuk, Darcy, additional, Clemens, Ron, additional, Baran, Janet, additional, and Leuschen, Candace, additional

Published
2023
Full Text
View/download PDF

34. The COPD Assessment Test: Can It Discriminate Across COPD Subpopulations?

Author

Bourbeau, Jean, Tan, Wan C., FitzGerald, J. Mark, Sin, D.D., Marciniuk, D.D., O'Donnell, D.E., Hernandez, Paul, Chapman, Kenneth R., Cowie, Robert, Aaron, Shawn, Maltais, F., Samet, Jonathon, Puhan, Milo, Hamid, Qutayba, Hogg, James C., Baglole, Carole, Jabet, Carole, Mancino, Palmina, Fortier, Yvan, Sin, Don, Tam, Sheena, Road, Jeremy, Comeau, Joe, Png, Adrian, Coxson, Harvey, Kirby, Miranda, Leipsic, Jonathon, Hague, Cameron, Sadatsafavi, Mohsen, To, Teresa, Gershon, Andrea, Li, Pei-Zhi, Duquette, Jean-Francois, Benedetti, Andrea, Jensen, Denis, O'Donnell, Denis, Lo, Christine, Cheng, Sarah, Fung, Cindy, Haynes, Nancy, Chuang, Junior, Zheng, Liyun, Latreille, David, Baril, Jacinthe, Labonte, Laura, Chapman, Kenneth, McClean, Patricia, Audisho, Nadeen, Cowie, Ann, Dumonceaux, Curtis, Machado, Lisette, Fulton, Scott, Osterling, Kristen, Vandemheen, Kathy, Pratt, Gay, Bergeron, Amanda, McNeil, Matthew, Whelan, Kate, Maltais, Francois, Brouillard, Cynthia, Marciniuk, Darcy, Clemens, Ron, Baran, Janet, Gupta, Nisha, Pinto, Lancelot, Li, Pei Zhi, Aaron, Shawn D., Marciniuk, Darcy D., Maltais, François, O'Donnell, Denis E., and Walker, Brandie L.

Published
2016
Full Text
View/download PDF

43. Ambient Air Pollution and Dysanapsis: Associations with Lung Function and Chronic Obstructive Pulmonary Disease in the Canadian Cohort Obstructive Lung Disease Study

Author

Bourbeau, Jean, primary, Doiron, Dany, additional, Biswas, Sharmistha, additional, Smith, Benjamin M., additional, Benedetti, Andrea, additional, Brook, Jeffrey R., additional, Aaron, Shawn D., additional, Chapman, Kenneth R., additional, Hernandez, Paul, additional, Maltais, François, additional, Marciniuk, Darcy D., additional, O’Donnell, Denis, additional, Sin, Don D., additional, Walker, Brandie, additional, Dsilva, Liesel, additional, Nadeau, Gilbert, additional, Coats, Valérie, additional, Compton, Chris, additional, Miller, Bruce E., additional, Tan, Wan C., additional, Bourbeau, Jean, additional, FitzGerald, J. Mark, additional, O’Donnell, Denis E., additional, Aaron, Shawn, additional, Samet, Jonathon, additional, Puhan, Milo, additional, Hamid, Qutayba, additional, Hogg, James C., additional, Mancino, Palmina, additional, Li, Pei Zhi, additional, Jensen, Dennis, additional, Baglole, Carolyn, additional, Fortier, Yvan, additional, Yang, Julia, additional, Road, Jeremy, additional, Comeau, Joe, additional, Png, Adrian, additional, Johnson, Kyle, additional, Coxson, Harvey, additional, Kirby, Miranda, additional, Leipsic, Jonathon, additional, Hague, Cameron, additional, Sadatsafavi, Mohsen, additional, To, Teresa, additional, Gershon, Andrea, additional, Song, Zhi, additional, Lo, Christine, additional, Cheng, Sarah, additional, Un, Elena, additional, Fung, Cynthia, additional, Wang, Wen Tiang, additional, Zheng, Liyun, additional, Faroon, Faize, additional, Radivojevic, Olga, additional, Chung, Sally, additional, Zou, Carl, additional, Baril, Jacinthe, additional, Labonté, Laura, additional, McClean, Patricia, additional, Audisho, Nadeen, additional, Dumonceaux, Curtis, additional, Machado, Lisette, additional, Fulton, Scott, additional, Osterling, Kristen, additional, Wigerius, Denise, additional, Vandemheen, Kathy, additional, Pratt, Gay, additional, Bergeron, Amanda, additional, Vincent, Sandra, additional, McNeil, Matthew, additional, Whelan, Kate, additional, Brouillard, Cynthia, additional, Clemens, Ron, additional, Baran, Janet, additional, and Leuschen, Candice, additional

Published
2022
Full Text
View/download PDF

44. Impaired Ventilatory Efficiency, Dyspnea, and Exercise Intolerance in Chronic Obstructive Pulmonary Disease: Results from the CanCOLD Study

Author

Phillips, Devin B., primary, Elbehairy, Amany F., additional, James, Matthew D., additional, Vincent, Sandra G., additional, Milne, Kathryn M., additional, de-Torres, Juan P., additional, Neder, J. Alberto, additional, Kirby, Miranda, additional, Jensen, Dennis, additional, Stickland, Michael K., additional, Guenette, Jordan A., additional, Smith, Benjamin M., additional, Aaron, Shawn D., additional, Tan, Wan C., additional, Bourbeau, Jean, additional, O’Donnell, Denis E., additional, Samet, Jonathon, additional, Puhan, Milo, additional, Hogg, James C., additional, Hamid, Qutayba, additional, Doiron, Dany, additional, Mancino, Palmina, additional, Li, Pei-Zhi, additional, Song, Zhi, additional, Fortier, Yvan, additional, Chapman, Kenneth, additional, McClean, Patricia, additional, Duke, Jane, additional, Gershon, Andrea S., additional, Toh, Teresa, additional, Sadatsafavi, Mohsen, additional, Sin, Don, additional, Fitzgerald, J. Mark, additional, Road, Jeremy, additional, Lo, Christine, additional, Cheng, Sarah, additional, Un, Elena, additional, Cheng, Michael, additional, Fung, Cynthia, additional, Faroon, Faize, additional, Radivojevic, Olga, additional, Chung, Sally, additional, Zou, Carl, additional, Choi, Rena, additional, Comeau, Joe, additional, Coxson, Harvey, additional, Leipsic, Jonathon, additional, Hague, Cameron, additional, Walker, Brandie, additional, Dumonceaux, Curtis, additional, Hernandez, Paul, additional, Fulton, Scott, additional, Vandemheen, Kathy, additional, McNeil, Matthew, additional, Whelan, Kate, additional, Maltais, Francois, additional, Brouillard, Cynthia, additional, Marciniuk, Darcy, additional, Clemens, Ron, additional, and Baran, Janet, additional

Published
2022
Full Text
View/download PDF

45. Exploration of whether socioeconomic factors affect the results of priority setting partnerships: updating the top 10 research priorities for the management of Parkinson’s in an international setting

Author

Bowring, Francesca, primary, Welch, Jessica, additional, Woodward, Charlotte, additional, Lo, Christine, additional, Lawton, Michael, additional, Sulzer, Patricia, additional, Hanff, Anne-Marie, additional, Kruger, Rejko, additional, Liepelt-Scarfone, Inga, additional, and Hu, Michele T, additional

Published
2022
Full Text
View/download PDF

47. The effects of ginger (Zingiber officinale) rhizome extract on ethanol-induced behaviors in C. elegans

Author

Vincent Mercado Manalo,, Rafael, primary, Louise C. Lapuz, Bianca, additional, K. Lim, Krisha, additional, Edelwina Y. Legaspi, Katelyn, additional, Marie M. Lota, Patricia, additional, Melissa B, Francine, additional, Abdelaziz N. Maldisa, Lucas, additional, C. Malipot, Vinson, additional, Bernadette O. Lo, Christine, additional, Khriztofer P. Lichauco, Allen, additional, and Mark Baco Medina, Paul, additional

Published
2022
Full Text
View/download PDF

50. Colaboradores

Author

Adrada, Beatriz, Aminololama-Shakeri, Shadi, Ataya, Dana, Bennett, Debbie L., Bhole, Sonya, Chung, Maggie, Eby, Peter R., Eghtedari, Mohammad, Fowler, Amy M., Friedewald, Sarah, Funaro, Kimberly, Ghate, Sujata V., Gibbons, Julie, Greenwood, Heather Ilana, Guirguis, Mary S., Hoyt, Anne C., Ikeda, Debra M., Joe, Bonnie N., Kozlov, Andrew Nicholas, Lee, Amie Y., Lo, Christine S., Luo, Jing, Mainprize, James Gordon, McDonald, Elizabeth S., Milch, Hannah S., Miyake, Kanae Kawai, Moy, Linda, Muhar, Ramanjyot K., Niell, Bethany Lynn, Ojeda-Fournier, Haydee, Orvedal, Dakota, Peterson, Molly, Rahbar, Habib, Rapelyea, Jocelyn, Rauch, Gaiane M., Ray, Kimberly M., and Zuckerman, Samantha P.

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results