References
Aboumatar, H., and R. A. Wise. 2019. “Notice of Retraction.
Aboumatar et al. Effect of a
Program Combining Transitional
Care and Long-term
Self-management Support on
Outcomes of Hospitalized Patients
With Chronic Obstructive
Pulmonary Disease: A
Randomized Clinical Trial.
JAMA.
2018;320(22):2335-2343.” JAMA 322 (14): 1417–18.
“Atlas-Based Whole Brain White Matter Analysis Using Large
Deformation Diffeomorphic Metric Mapping: Application to Normal Elderly
and Alzheimer’s Disease Participants.” 2009. Neuroimage
46 (2): 486–99. https://doi.org/10.1016/j.neuroimage.2009.01.002.
Aung T, Kromhout D, Halsey J. 2018. “Associations of Omega-3 Fatty
Acid Supplement Use with Cardiovascular Disease Risks: Meta-Analysis of
10 Trials Involving 77 917 Individuals.” Jama Cardiol,
March. https://doi.org/doi:
10.1001/jamacardio.2017.5205.
Balduzzi, Sara, Gerta Rücker, and Guido Schwarzer. 2019. “How to
Perform a Meta-Analysis with R: A Practical
Tutorial.” Evidence-Based Mental Health, no. 22: 153–60.
Beare, R., J. Chen, T. G. Phan, R. K. Lees, M. Ali, A. Alexandrov, P. M.
Bath, et al. 2015. “Googling
Stroke
ASPECTS
to Determine Disability:
Exploratory Analysis from
VISTA-Acute
Collaboration.” PLoS ONE 10 (5):
e0125687.
Berkhemer, O. A., P. S. Fransen, D. Beumer, L. A. van den Berg, H. F.
Lingsma, A. J. Yoo, W. J. Schonewille, et al. 2015. “A randomized trial of intraarterial
treatment for acute ischemic stroke.” N. Engl. J.
Med. 372 (1): 11–20.
BJ, Biggerstaff. 2000. “Comparing Diagnostic Tests: A Simple
Graphic Using Likelihood Ratios.” Stat Med 19 (March):
649–63. https://doi.org/10.1002/(sici)1097-0258(20000315)19:5<649::aid-sim371>3.0.co;2-h.
Brin, Sergey, and Lawrence Page. 1998. “The
Anatomy of a Large-Scale
Hypertextual Web Search
Engine.” Computer Networks and ISDN Systems
30 (1-7): 107–17. https://doi.org/10.1016/S0169-7552(98)00110-X.
Brunet, Jean-Philippe, Pablo Tamayo, Todd R. Golub, and Jill P. Mesirov.
2004. “Metagenes and Molecular Pattern Discovery Using Matrix
Factorization.” Proceedings of the National Academy of
Sciences 101 (12): 4164–69. https://doi.org/10.1073/pnas.0308531101.
Campbell, B. C., P. J. Mitchell, T. J. Kleinig, H. M. Dewey, L.
Churilov, N. Yassi, B. Yan, et al. 2015. “Endovascular therapy for ischemic stroke
with perfusion-imaging selection.” N. Engl. J.
Med. 372 (11): 1009–18.
Centor, Robert M., Rabih Geha, and Reza Manesh. 2019. “The Pursuit of Diagnostic Excellence.”
JAMA Network Open 2 (12): e1918040–40. https://doi.org/10.1001/jamanetworkopen.2019.18040.
Cohen, Jacob. 1977. “CHAPTER 6 - Differences Between
Proportions.” In Statistical Power Analysis for the
Behavioral Sciences, edited by Jacob Cohen, 179–213. Academic
Press. https://doi.org/https://doi.org/10.1016/B978-0-12-179060-8.50011-6.
D. S. Nagin, V. L. Passos, B. L. Jones, and R. E. Tremblay. 2018.
“Group-Based Multi-Trajectory Modeling.” Statistical
Methods in Medical Research 27: 2015–23. https://doi.org/10.1177/0962280216673085.
Decroocq, Méghane, Carole Frindel, Pierre Rougé, Makoto Ohta, and
Guillaume Lavoué. 2023. “Modeling and Hexahedral Meshing of
Cerebral Arterial Networks from Centerlines.” Medical Image
Analysis 89: 102912. https://doi.org/https://doi.org/10.1016/j.media.2023.102912.
Derek B Archer, Stephen A Coombes, David E Vaillancourt. 2018. “A
Template and Probabilistic Atlas of the Human Sensorimotor Tracts Using
Diffusion MRI.” Cerebral Cortex 28 (5): 1685--1699. https://doi.org/10.1093/cercor/bhx066.
Diamond, G. A. 1992. “What price
perfection? Calibration and discrimination of clinical
prediction models.” J Clin Epidemiol 45 (1):
85–89.
Durif, G., L. Modolo, J. Michaelsson, J. E. Mold, S. Lambert-Lacroix,
and F. Picard. 2018. “High
dimensional classification with combined adaptive sparse
PLS and logistic
regression.” Bioinformatics 34 (3): 485–93.
Fornito, Alex. 2016. “Graph Theoretic Analysis of Human Brain
Networks.” In Neuromethods, edited by Massimo Filippi,
2nd ed., 119:283–314. Neuromethods 119. United States of America: Humana
Press. https://doi.org/10.1007/978-1-4939-5611-1_10.
Fort, G., and S. Lambert-Lacroix. 2005. “Classification using partial least squares
with penalized logistic regression.”
Bioinformatics 21 (7): 1104–11.
Friedman, J. H., and C. B. Roosen. 1995. “An introduction to multivariate adaptive
regression splines.” Stat Methods Med Res 4 (3):
197–217.
Friston, K., J. Phillips, D. Chawla, and C. Buchel. 2000. “Nonlinear
PCA: characterizing interactions
between modes of brain activity.” Philos. Trans. R.
Soc. Lond., B, Biol. Sci. 355 (1393): 135–46.
Gopal, A. D., N. R. Desai, T. Tse, and J. S. Ross. 2015. “Reporting of noninferiority trials in
ClinicalTrials.gov and corresponding
publications.” JAMA 313 (11): 1163–65.
Graf E, Sauerbrei W, Schmoor C. 1999. “Assessment and Comparison
of Prognostic Classification Schemes for Survival Data.” Stat
Med 18 (September): 2529–45. https://doi.org/10.1002/(sici)1097-0258(19990915/30)18:17/18<2529::aid-sim274>3.0.co;2-5.
Grambsch, P. M., and T. M. Therneau. 1994. “Proportional hazards tests and diagnostics based on
weighted residuals.” Biometrika 81 (3): 515–26.
https://doi.org/10.1093/biomet/81.3.515.
Grinsztajn, Léo, Edouard Oyallon, and Gaël Varoquaux. 2022. “Why
Do Tree-Based Models Still Outperform Deep Learning on Tabular
Data?” ArXiv abs/2207.08815. https://doi.org/10.48550/arXiv.2207.08815.
Guo, Jingyi, and Andrea Riebler. 2015. “meta4diag: Bayesian Bivariate Meta-analysis of Diagnostic
Test Studies for Routine Practice.” arXiv
e-Prints, December, arXiv:1512.06220. https://arxiv.org/abs/1512.06220.
Harrell FE Jr, Pryor DB, Califf RM. 1982. “Evaluating the Yield of
Medical Tests.” JAMA 247 (May): 2543–46.
Hastie, Trevor, Robert Tibshirani, and Jerome Friedman. 2009. The
Elements of Statistical Learning: Data Mining, Inference and
Prediction. 2nd ed. Springer. http://www-stat.stanford.edu/~tibs/ElemStatLearn/.
Holmes CJ, Collins L, Hoge R. 1998. “Enhancement of MR Images
Using Registration for Signal Averaging.” J Comput Assist
Tomogr 22: 324–33. https://doi.org/10.1097/00004728-199803000-00032.
Hu, Hu, Y. 2019. “Marine Omega‐3 Supplementation and
Cardiovascular Disease: An Updated Meta‐analysis of 13 Randomized
Controlled Trials Involving 127 477 Participants.” JAHA,
September. https://doi.org/https://doi.org/10.1161/JAHA.119.013543.
Hubbard AE, Fleischer NL, Ahern J. 2010. “To GEE or Not to GEE:
Comparing Population Average and Mixed Models for Estimating the
Associations Between Neighborhood Risk Factors and Health.”
Epidemiology 21: 467–74. https://doi.org/10.1097/EDE.0b013e3181caeb9.
Ingall, Timothy John, William Michael O’Fallon, Kjell Asplund, Lewis
Robert Goldfrank, Vicki S. Hertzberg, Thomas Arthur Louis, and Teresa J.
Hengy Christianson. 2004. “Findings from the Reanalysis of the
NINDS Tissue Plasminogen Activator for Acute Ischemic Stroke Treatment
Trial.” Stroke 35 (10): 2418–24. https://doi.org/10.1161/01.STR.0000140891.70547.56.
J, Muschelli. 2020. “ROC and AUC with a Binary Predictor: A
Potentially Misleading Metric.” J Classif 37 (October):
696–708. https://doi.org/10.1007/s00357-019-09345-1.
Jaeschke, R., G. H. Guyatt, and D. L. Sackett. 1994. “Users’ guides to the medical literature.
III. How to use an
article about a diagnostic test. B. What are
the results and will they help me in caring for my patients?
The Evidence-Based
Medicine Working
Group.” JAMA 271 (9): 703–7.
Jamakovic, A., and Piet Van Mieghem. 2008. “On the Robustness of
Complex Networks by Using the Algebraic Connectivity.” In
Networking, edited by Amitabha Das, Hung Keng Pung, Francis
Bu-Sung Lee, and Lawrence Wai-Choong Wong, 4982:183–94. Lecture Notes in
Computer Science. Springer. http://dblp.uni-trier.de/db/conf/networking/networking2008.html#JamakovicM08.
K. Mehta, J. Ogden, B. Ljungquist, and G. A. Ascoli. 2023. “Online
Conversion of Reconstructed Neural Morphologies into Standardized SWC
Format.” Nature Communications 14: 7429. https://doi.org/10.1038/s41467-023-42931-x.
Kahan, Jairath, B. C. 2014. “The Risks and Rewards of Covariate
Adjustment in Randomized Trials: An Assessment of 12 Outcomes from 8
Studies.” Trials 15: 139. https://doi.org/10.1186/1745-6215-15-139.
Kaji, A. H., and R. J. Lewis. 2015. “Noninferiority Trials:
Is a New Treatment
Almost as Effective as
Another?” JAMA 313 (23): 2371–72.
Kempster, P. A., C. A. McLean, and T. G. Phan. 2016. “Ten year clinical experience with stroke and
cerebral vasculitis.” J Clin Neurosci 27 (May):
119–25.
Kleinbaum, David G, Lawrence L. Kupper, and Keith E. Muller. 1978.
“Applied Regression Analysis and Other Multivariable
Methods.” In.
Lee, Seung, D. 1999. “Learning the Parts of Objects by
Non-Negative Matrix Factorization.” Nature 401: 788–91.
https://doi.org/https://doi.org/10.1038/44565.
Leffondre K, Regeasse A, Abrahamowicz M. 2004. “Statistical
Measures Were Proposed for Identifying Longitudinal Patterns of Change
in Quantitative Health Indicators.” J Clin Epidemiol 57:
1049–62. https://doi.org/10.1016/j.jclinepi.2004.02.012.
Lim, Andy, Henry Ma, S. Claiborne Johnston, Shaloo Singhal, Subramanian
Muthusamy, Yongjun Wang, Yuesong Pan, et al. 2024. “Ninety‐day
Stroke Recurrence in Minor Stroke: Systematic Review and Meta‐analysis
of Trials and Observational Studies.” Journal of the American
Heart Association 13 (9): e032471. https://doi.org/10.1161/JAHA.123.032471.
Lim, Andy, Henry Ma, John Ly, Shaloo Singhal, Yuesong Pan, Yongjun Wang,
S. Claiborne Johnston, and Thanh G. Phan. 2024. “Comparison of
Dual Antiplatelet Therapies for Minor, Nondisabling, Acute Ischemic
Stroke: A Bayesian Network Meta-Analysis.” JAMA Network
Open 7 (5): e2411735–35. https://doi.org/10.1001/jamanetworkopen.2024.11735.
Longato, Enrico, Martina Vettoretti, and Barbara Di Camillo. 2020.
“A Practical Perspective on the Concordance Index for the
Evaluation and Selection of Prognostic Time-to-Event Models.”
Journal of Biomedical Informatics 108: 103496.
https://doi.org/https://doi.org/10.1016/j.jbi.2020.103496.
Ludwig, L., P. Darmon, and B Guerci. 2020. “Computing and interpreting the Number Needed to Treat for
Cardiovascular Outcomes Trials:Perspective on GLP-1 RA and SGLT-2i
therapies.” Cardiovasc Diabetol, May. https://doi.org/10.1186/s12933-020-01034-3.
Luo, Dehui, Xiang Wan, Jiming Liu, and Tiejun Tong. 2018.
“Optimally Estimating the Sample Mean from the Sample Size,
Median, Mid-Range, and/or Mid-Quartile Range.” Statistical
Methods in Medical Research 27 (6): 1785–805. https://doi.org/10.1177/0962280216669183.
Marx, Heiner C, Arthur. Bucher. 2003. “Numbers Needed to Treat
Derived from Meta-Analysis: A Word of Caution.” BMJ
Evidence-Based Medicine 8 (2): 36–37. https://doi.org/10.1136/ebm.8.2.36.
Mathur MB, Riddell CA, Ding P. 2018. “Web Site and r Package for
Computing e-Values.” Epidemiology, e45–47. https://doi.org/10.1097/EDE.0000000000000864.
Mazziotta J, Evans A, Toga A. 2001. “A Probabilistic Atlas and
Reference System for the Human Brain: International Consortium for Brain
Mapping (ICBM).” Philos Trans R Soc Lond B Biol Sci 356
(1412): 1293–1322. https://doi.org/10.1098/rstb.2001.0915.
McElfresh, Duncan C., Sujay Khandagale, Jonathan Valverde, C.
VishakPrasad, Ben Feuer, Chinmay Hegde, Ganesh Ramakrishnan, Micah
Goldblum, and Colin White. 2023. “When Do Neural Nets Outperform
Boosted Trees on Tabular Data?” ArXiv abs/2305.02997. https://doi.org/10.48550/arXiv.2305.02997.
McGrath, Sean, Stephan Katzenschlager, Alexander J. Zimmer, Alexander
Seitel, Russell J. Steele, and Andrea Benedetti. 2022. “Standard
Error Estimation in Meta-Analysis of Studies Reporting Medians.”
Statistical Methods in Medical Research 32: 373–88. https://doi.org/10.1177/09622802221139233.
McGrath, Sean, XiaoFei Zhao, Russell Steele, Brett D. Thombs, Andrea
Benedetti, the DEPRESsion Screening Data (DEPRESSD) Collaboration,
Brooke Levis, et al. 2020. “Estimating the Sample Mean and
Standard Deviation from Commonly Reported Quantiles in
Meta-Analysis.” Statistical Methods in Medical Research
29 (9): 2520–37. https://doi.org/10.1177/0962280219889080.
Molnar, Christoph, Bernd Bischl, and Giuseppe Casalicchio. 2018.
“Iml: An r Package for Interpretable Machine Learning.”
JOSS 3 (26): 786. https://doi.org/10.21105/joss.00786.
Moses, L. E., D. Shapiro, and B. Littenberg. 1993. “Combining independent studies of a
diagnostic test into a summary
ROC curve: data-analytic
approaches and some additional considerations.” Stat
Med 12 (14): 1293–1316.
Phan, T. G., J. Chen, G. Donnan, V. Srikanth, A. Wood, and D. C.
Reutens. 2010. “Development of a
new tool to correlate stroke outcome with infarct topography: a
proof-of-concept study.” Neuroimage 49 (1):
127–33.
Phan, T. G., J. Chen, S. Singhal, H. Ma, B. B. Clissold, J. Ly, and R.
Beare. 2018. “Exploratory
Use of Decision Tree
Analysis in Classification of
Outcome in Hypoxic-Ischemic
Brain Injury.” Front
Neurol 9: 126.
Phan, T. G., B. B. Clissold, H. Ma, J. V. Ly, and V. Srikanth. 2017.
“Predicting
Disability after Ischemic Stroke
Based on Comorbidity Index and
Stroke Severity-From the
Virtual International Stroke
Trials Archive-Acute
Collaboration.” Front Neurol 8: 192.
Phan, T. G., B. Clissold, J. Ly, H. Ma, C. Moran, V. Srikanth, K. R.
Lees, et al. 2016. “Stroke
Severity and Comorbidity Index
for Prediction of Mortality after
Ischemic Stroke from the Virtual
International Stroke Trials
Archive-Acute
Collaboration.” J Stroke Cerebrovasc
Dis 25 (4): 835–42.
Phan, T. G., A. Demchuk, V. Srikanth, B. Silver, S. C. Patel, P. A.
Barber, S. R. Levine, and M. D. Hill. 2013. “Proof of concept study: relating infarct
location to stroke disability in the
NINDS
rt-PA trial.” Cerebrovasc.
Dis. 35 (6): 560–65.
Phan, T. G., G. A. Donnan, S. M. Davis, and G. Byrnes. 2006.
“Proof-of-principle phase
II MRI
studies in stroke: sample size estimates from dichotomous and continuous
data.” Stroke 37 (10): 2521–25.
Phan, T. G., G. A. Donnan, M. Koga, L. A. Mitchell, M. Molan, G. Fitt,
W. Chong, M. Holt, and D. C. Reutens. 2006. “The
ASPECTS
template is weighted in favor of the striatocapsular
region.” Neuroimage 31 (2): 477–81.
Phan, T. G., T. Kooblal, C. Matley, S. Singhal, B. Clissold, J. Ly, A.
G. Thrift, V. Srikanth, and H. Ma. 2019. “Stroke Severity
Versus Dysphagia Screen as
Driver for Post-stroke
Pneumonia.” Front Neurol 10: 16.
Phan, T. G., N. Krishnadas, V. W. Y. Lai, M. Batt, L. A. Slater, R. V.
Chandra, V. Srikanth, and H. Ma. 2019. “Meta-Analysis of
Accuracy of the Spot Sign for
Predicting Hematoma Growth and
Clinical Outcomes.”
Stroke 50 (8): 2030–36.
Phan TG, Singhal S, Clissold B. 2021. “Network Mapping of Time to
Antithrombotic Therapy Among Patients with Ischemic Stroke and Transient
Ischemic Attack (TIA).” Front Neurol 12: 651869. https://doi.org/10.3389/fneur.2021.651869.
Reitsma, J. B., A. S. Glas, A. W. Rutjes, R. J. Scholten, P. M. Bossuyt,
and A. H. Zwinderman. 2005. “Bivariate analysis of sensitivity and
specificity produces informative summary measures in diagnostic
reviews.” J Clin Epidemiol 58 (10): 982–90.
Rodriguez-Linares, Leandro, Xose Vila, Maria Jose Lado, Arturo Mendez,
Abraham Otero, and Constantino Antonio Garcia. 2017. Heart Rate
Variability Analysis with the r Package RHRV. Use r! Springer.
https://doi.org/
10.1007/978-3-319-65355-6.
Royston, Parmar, P. 2013. “Restricted Mean Survival Time: An
Alternative to the Hazard Ratio for the Design and Analysis of
Randomized Trials with a Time-to-Event Outcome.” BMC Med Res
Methodol 13. https://doi.org/10.1186/1471-2288-13-152.
Salminen, P., H. Paajanen, T. Rautio, P. Nordstrom, M. Aarnio, T.
Rantanen, R. Tuominen, et al. 2015. “Antibiotic Therapy vs
Appendectomy for Treatment of
Uncomplicated Acute Appendicitis:
The
APPAC
Randomized Clinical
Trial.” JAMA 313 (23): 2340–48.
SD, Walter. 2002. “Properties of the Summary Receiver Operating
Characteristic (SROC) Curve for Diagnostic Test Data.” Stat
Med 21: 1237–56. https://doi.org/10.1002/sim.1099.
Seneviratne, U., Z. M. Low, Z. X. Low, A. Hehir, S. Paramaswaran, M.
Foong, H. Ma, and T. G. Phan. 2019. “Medical health care utilization cost of
patients presenting with psychogenic nonepileptic
seizures.” Epilepsia 60 (2): 349–57.
Shi, Jiandong, Dehui Luo, Xiang Wan, Yue Liu, Jiming Liu, Zhaoxiang
Bian, and Tiejun Tong. 2023. “Detecting the Skewness of Data from
the Five-Number Summary and Its Application in Meta-Analysis.”
Statistical Methods in Medical Research 32 (7): 1338–60. https://doi.org/10.1177/09622802231172043.
Signori, Alessio, Fabio Pellegrini, Francesca Bovis, Luca Carmisciano,
Carl de Moor, and Maria Pia Sormani. 2020. “Comparison of Placebos and Propensity Score Adjustment in
Multiple Sclerosis Nonrandomized Studies.” JAMA
Neurology, April. https://doi.org/10.1001/jamaneurol.2020.0678.
Singhal, Shaloo, Jian Chen, Richard Beare, Henry Ma, John Ly, and Thanh
G. Phan. 2012. “Application of Principal Component Analysis to
Study Topography of Hypoxic–Ischemic Brain Injury.”
NeuroImage 62 (1): 300–306. https://doi.org/https://doi.org/10.1016/j.neuroimage.2012.04.025.
Slater, Lee‐Anne, Nandhini Ravintharan, Stacy Goergen, Ronil Chandra,
Hamed Asadi, Julian Maingard, Ahilan Kuganesan, et al. 2024.
“<I>RapidAI</i> Compared with Human Readers of Acute
Stroke Imaging for Detection of Intracranial Vessel Occlusion.”
Stroke: Vascular and Interventional Neurology 4 (2): e001145.
https://doi.org/10.1161/SVIN.123.001145.
Smeeth, A. Ebrahim, L. Haines. 1999. “Numbers
needed to treat derived from meta-analyses–sometimes informative,
usually misleading.” BMJ 318: 1548–51. https://doi.org/10.1136/bmj.318.7197.1548.
Smith, Norman R. Draper. Harry. 1998. Applied Regression Analysis,
Third Edition. 3rd ed. Wiley Series in Probability and Statistics.
John Wiley & Sons, Inc.
Stensrud, M. J., and M. A. Hernan. 2020. “Why Test for
Proportional Hazards?”
JAMA, March.
TJ, Fagan. 1975. “Nomogram for Bayes’s Theorem.” N Engl
J Med 293 (July): 257. https://doi.org/10.1056/NEJM197507312930513.
Tzourio-Mazoyer N, Papathanassiou D, Landeau B. 2002. “Automated
Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical
Parcellation of the MNI MRI Single-Subject Brain.”
Neuroimage 15 (1): 273–89. https://doi.org/10.1006/nimg.2001.0978.
VanderWeele TJ, Ding P. 2017. “Sensitivity Analysis in
Observational Research: Introducing the e-Value.” Ann Intern
Med 167 (August): 268–74. https://doi.org/10.7326/M16-2607.
Viechtbauer, Wolfgang. 2010. “Conducting Meta-Analyses in r with
the Metafor Package.” Journal of Statistical Software 36
(3): 1–48. https://doi.org/10.18637/jss.v036.i03.
Wan, Wang, X. 2014. “Estimating the Sample Mean and Standard
Deviation from the Sample Size, Median, Range and/or Interquartile
Range.” BMC Med Res Methodol, December.
https://doi.org/https://doi.org/10.1186/1471-2288-14-135.
Wang, Rui, Stephen W. Lagakos, James H. Ware, David J. Hunter, and
Jeffrey M. Drazen. 2007. “Statistics in Medicine — Reporting of
Subgroup Analyses in Clinical Trials.” New England Journal of
Medicine 357 (21): 2189–94. https://doi.org/10.1056/NEJMsr077003.
Wickham, Hadley. 2016. Ggplot2: Elegant Graphics for Data
Analysis. Springer-Verlag New York. https://ggplot2.tidyverse.org.
———. 2019. 2nd ed. Chapman & Hall/CRC the r Series. Chapman;
Hall/CRC; 2 edition (May 30, 2019).