My Bibliography

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Li C, Xu W, Cohen T, Pakhomov S. Useful blunders: Can automated speech recognition errors improve downstream dementia classification?. J Biomed Inform. 2024 Feb;150:104598. doi: 10.1016/j.jbi.2024.104598. Epub 2024 Jan 20. PubMed PMID: 38253228; PubMed Central PMCID: PMC10922372.

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Guo Y, Qiu W, Leroy G, Wang S, Cohen T. Retrieval augmentation of large language models for lay language generation. J Biomed Inform. 2024 Jan;149:104580. doi: 10.1016/j.jbi.2023.104580. Epub 2023 Dec 30. PubMed PMID: 38163514; PubMed Central PMCID: PMC10874606.

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Ding X, Sheng Z, Hur B, Chen F, Pakhomov S. Enhancing Robustness of Foundation Model Representations under Provenance-related Distribution Shifts. Version: 1. arxiv [preprint]. 2023 December. 2312.05435[15 pages]. Available from: https://arxiv.org/abs/2312.05435. doi: https://doi.org/10.48550/arXiv.2312.05435.

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Ding X, Sheng Z, Yetisgen M, Pakhomov S. Backdoor adjustment of confounding by provenance for robust text classification of multi-institutional clinical notes. Version: 1. arxiv [preprint]. 2023 October. 2310.02451[10 pages]. Available from: https://arxiv.org/abs/2310.02451. doi: https://doi.org/10.48550/arXiv.2310.02451.

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Buck B, Wingerson M, Tauscher JS, Enkema M, Wang W, Campbell AT, Ben-Zeev D. Using Smartphones to Identify Momentary Characteristics of Persecutory Ideation Associated With Functional Disability. Schizophr Bull Open. 2023 Jan;4(1):sgad021. doi: 10.1093/schizbullopen/sgad021. eCollection 2023 Jan. PubMed PMID: 37601285; PubMed Central PMCID: PMC10439515.

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Curtis JR, Lee RY, Brumback LC, Kross EK, Downey L, Torrence J, LeDuc N, Mallon Andrews K, Im J, Heywood J, Brown CE, Sibley J, Lober WB, Cohen T, Weiner BJ, Khandelwal N, Abedini NC, Engelberg RA. Intervention to Promote Communication About Goals of Care for Hospitalized Patients With Serious Illness: A Randomized Clinical Trial. JAMA. 2023 Jun 20;329(23):2028-2037. doi: 10.1001/jama.2023.8812. PubMed PMID: 37210665; PubMed Central PMCID: PMC10201405.

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Li C, Xu W, Cohen T, Michalowski M, Pakhomov S. TRESTLE: Toolkit for Reproducible Execution of Speech, Text and Language Experiments. AMIA Jt Summits Transl Sci Proc. 2023;2023:360-369. eCollection 2023. PubMed PMID: 37350929; PubMed Central PMCID: PMC10283131.

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Burkhardt HA, Ding X, Kerbrat A, Comtois KA, Cohen T. From benchmark to bedside: transfer learning from social media to patient-provider text messages for suicide risk prediction. J Am Med Inform Assoc. 2023 May 19;30(6):1068-1078. doi: 10.1093/jamia/ocad062. PubMed PMID: 37043748; PubMed Central PMCID: PMC10198538.

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Burkhardt HA, Laine M, Kerbrat A, Cohen T, Comtois KA, Hartzler A. Identifying opportunities for informatics-supported suicide prevention: the case of Caring Contacts. AMIA Annu Symp Proc. 2022;2022:309-318. eCollection 2022. PubMed PMID: 37128371; PubMed Central PMCID: PMC10148379.

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Wu Y, Mower J, Ding X, Li O, Subramanian D, Cohen T. Predicting Drug Blood-Brain Barrier Penetration with Adverse Event Report Embeddings. AMIA Annu Symp Proc. 2022;2022:1163-1172. eCollection 2022. PubMed PMID: 37128462; PubMed Central PMCID: PMC10148361.

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Singh T, Roberts K, Cohen T, Cobb N, Franklin A, Myneni S. Discerning conversational context in online health communities for personalized digital behavior change solutions using Pragmatics to Reveal Intent in Social Media (PRISM) framework. J Biomed Inform. 2023 Apr;140:104324. doi: 10.1016/j.jbi.2023.104324. Epub 2023 Feb 24. PubMed PMID: 36842490; PubMed Central PMCID: PMC10206862.

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Tauscher JS, Lybarger K, Ding X, Chander A, Hudenko WJ, Cohen T, Ben-Zeev D. Automated Detection of Cognitive Distortions in Text Exchanges Between Clinicians and People With Serious Mental Illness. Psychiatr Serv. 2023 Apr 1;74(4):407-410. doi: 10.1176/appi.ps.202100692. Epub 2022 Sep 27. PubMed PMID: 36164769.

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Lee RY, Kross EK, Torrence J, Li KS, Sibley J, Cohen T, Lober WB, Engelberg RA, Curtis JR. Assessment of Natural Language Processing of Electronic Health Records to Measure Goals-of-Care Discussions as a Clinical Trial Outcome. JAMA Netw Open. 2023 Mar 1;6(3):e231204. doi: 10.1001/jamanetworkopen.2023.1204. PubMed PMID: 36862411; PubMed Central PMCID: PMC9982698.

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Uyeda AM, Lee RY, Pollack LR, Paul SR, Downey L, Brumback LC, Engelberg RA, Sibley J, Lober WB, Cohen T, Torrence J, Kross EK, Curtis JR. Predictors of Documented Goals-of-Care Discussion for Hospitalized Patients With Chronic Illness. J Pain Symptom Manage. 2023 Mar;65(3):233-241. doi: 10.1016/j.jpainsymman.2022.11.012. Epub 2022 Nov 22. PubMed PMID: 36423800; PubMed Central PMCID: PMC9928787.

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Myneni S, Cuccaro P, Montgomery S, Pakanati V, Tang J, Singh T, Dominguez O, Cohen T, Reininger B, Savas LS, Fernandez ME. Lessons Learned From Interdisciplinary Efforts to Combat COVID-19 Misinformation: Development of Agile Integrative Methods From Behavioral Science, Data Science, and Implementation Science. JMIR Infodemiology. 2023;3:e40156. doi: 10.2196/40156. eCollection 2023. PubMed PMID: 37113378; PubMed Central PMCID: PMC9987191.

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Jujjavarapu C, Suri P, Pejaver V, Friedly J, Gold LS, Meier E, Cohen T, Mooney SD, Heagerty PJ, Jarvik JG. Predicting decompression surgery by applying multimodal deep learning to patients' structured and unstructured health data. BMC Med Inform Decis Mak. 2023 Jan 6;23(1):2. doi: 10.1186/s12911-022-02096-x. PubMed PMID: 36609379; PubMed Central PMCID: PMC9824905.

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Guo Y, Qiu W, Leroy G, Wang S, Cohen T. CELLS: A Parallel Corpus for Biomedical Lay Language Generation. Version: 1. arxiv [preprint]. 2022 November. arXiv.2211.03818[14 pages]. Available from: https://arxiv.org/abs/2211.03818. doi: https://doi.org/10.48550/arXiv.2211.03818.

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Uyeda AM, Curtis JR, Engelberg RA, Brumback LC, Guo Y, Sibley J, Lober WB, Cohen T, Torrence J, Heywood J, Paul SR, Kross EK, Lee RY. Mixed-methods evaluation of three natural language processing modeling approaches for measuring documented goals-of-care discussions in the electronic health record. J Pain Symptom Manage. 2022 Jun;63(6):e713-e723. doi: 10.1016/j.jpainsymman.2022.02.006. Epub 2022 Feb 16. PubMed PMID: 35182715; PubMed Central PMCID: PMC9124686.

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Mower J, Bernstam E, Xu H, Myneni S, Subramanian D, Cohen T. Improving Pharmacovigilance Signal Detection from Clinical Notes with Locality Sensitive Neural Concept Embeddings. AMIA Jt Summits Transl Sci Proc. 2022;2022:349-358. eCollection 2022. PubMed PMID: 35854716; PubMed Central PMCID: PMC9285153.

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Jujjavarapu C, Pejaver V, Cohen TA, Mooney SD, Heagerty PJ, Jarvik JG. A Comparison of Natural Language Processing Methods for the Classification of Lumbar Spine Imaging Findings Related to Lower Back Pain. Acad Radiol. 2022 Mar;29 Suppl 3(Suppl 3):S188-S200. doi: 10.1016/j.acra.2021.09.005. Epub 2021 Dec 1. PubMed PMID: 34862122; PubMed Central PMCID: PMC8917985.

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Xu W, Wang W, Portanova J, Chander A, Campbell A, Pakhomov S, Ben-Zeev D, Cohen T. Fully automated detection of formal thought disorder with Time-series Augmented Representations for Detection of Incoherent Speech (TARDIS). J Biomed Inform. 2022 Feb;126:103998. doi: 10.1016/j.jbi.2022.103998. Epub 2022 Jan 19. PubMed PMID: 35063668; PubMed Central PMCID: PMC8844699.

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Singh T, Olivares S, Cohen T, Cobb N, Wang J, Franklin A, Myneni S. Pragmatics to Reveal Intent in Social Media Peer Interactions: Mixed Methods Study. J Med Internet Res. 2021 Nov 17;23(11):e32167. doi: 10.2196/32167. PubMed PMID: 34787578; PubMed Central PMCID: PMC8663565.

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Burkhardt HA, Alexopoulos GS, Pullmann MD, Hull TD, Areán PA, Cohen T. Behavioral Activation and Depression Symptomatology: Longitudinal Assessment of Linguistic Indicators in Text-Based Therapy Sessions. J Med Internet Res. 2021 Jul 14;23(7):e28244. doi: 10.2196/28244. PubMed PMID: 34259637; PubMed Central PMCID: PMC8319778.

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Ding X, Mower J, Subramanian D, Cohen T. Augmenting aer2vec: Enriching distributed representations of adverse event report data with orthographic and lexical information. J Biomed Inform. 2021 Jul;119:103833. doi: 10.1016/j.jbi.2021.103833. Epub 2021 Jun 8. PubMed PMID: 34111555; PubMed Central PMCID: PMC8260467.

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Singh T, Cobb N, Cohen T, Myneni S. Transitions Between Electronic and Combustible Cigarettes: A Mixed Methods Analysis of Peer Interactions in an Online Community for Tobacco Cessation. Stud Health Technol Inform. 2021 May 27;281:1004-1008. doi: 10.3233/SHTI210329. PubMed PMID: 34042824; PubMed Central PMCID: PMC9134573.

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Areán PA, Pratap A, Hsin H, Huppert TK, Hendricks KE, Heagerty PJ, Cohen T, Bagge C, Comtois KA. Perceived Utility and Characterization of Personal Google Search Histories to Detect Data Patterns Proximal to a Suicide Attempt in Individuals Who Previously Attempted Suicide: Pilot Cohort Study. J Med Internet Res. 2021 May 6;23(5):e27918. doi: 10.2196/27918. PubMed PMID: 33955838; PubMed Central PMCID: PMC8138707.

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Malec SA, Wei P, Bernstam EV, Boyce RD, Cohen T. Using computable knowledge mined from the literature to elucidate confounders for EHR-based pharmacovigilance. J Biomed Inform. 2021 May;117:103719. doi: 10.1016/j.jbi.2021.103719. Epub 2021 Mar 11. PubMed PMID: 33716168; PubMed Central PMCID: PMC8559730.

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Guo Y, Li C, Roan C, Pakhomov S, Cohen T. Crossing the “Cookie Theft” Corpus Chasm: Applying What BERT Learns From Outside Data to the ADReSS Challenge Dementia Detection Task. Front. Comput. Sci.. 2021 April. doi: https://doi.org/10.3389/fcomp.2021.642517.

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Xu W, Portanova J, Chander A, Ben-Zeev D, Cohen T. The Centroid Cannot Hold: Comparing Sequential and Global Estimates of Coherence as Indicators of Formal Thought Disorder. AMIA Annu Symp Proc. 2020;2020:1315-1324. eCollection 2020. PubMed PMID: 33936508; PubMed Central PMCID: PMC8075468.

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Ding X, Cohen T. Retrofitting Vector Representations of Adverse Event Reporting Data to Structured Knowledge to Improve Pharmacovigilance Signal Detection. AMIA Annu Symp Proc. 2020;2020:383-392. eCollection 2020. PubMed PMID: 33936411; PubMed Central PMCID: PMC8075473.

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Singh T, Roberts K, Cohen T, Cobb N, Wang J, Fujimoto K, Myneni S. Social Media as a Research Tool (SMaaRT) for Risky Behavior Analytics: Methodological Review. JMIR Public Health Surveill. 2020 Nov 30;6(4):e21660. doi: 10.2196/21660. Review. PubMed PMID: 33252345; PubMed Central PMCID: PMC7735906.

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Ben-Zeev D, Buck B, Chander A, Brian R, Wang W, Atkins D, Brenner CJ, Cohen T, Campbell A, Munson J. Mobile RDoC: Using Smartphones to Understand the Relationship Between Auditory Verbal Hallucinations and Need for Care. Schizophr Bull Open. 2020 Jan;1(1):sgaa060. doi: 10.1093/schizbullopen/sgaa060. eCollection 2020 Jan. PubMed PMID: 33937774; PubMed Central PMCID: PMC8061119.

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Raisaro JL, Marino F, Troncoso-Pastoriza J, Beau-Lejdstrom R, Bellazzi R, Murphy R, Bernstam EV, Wang H, Bucalo M, Chen Y, Gottlieb A, Harmanci A, Kim M, Kim Y, Klann J, Klersy C, Malin BA, Méan M, Prasser F, Scudeller L, Torkamani A, Vaucher J, Puppala M, Wong STC, Frenkel-Morgenstern M, Xu H, Musa BM, Habib AG, Cohen T, Wilcox A, Salihu HM, Sofia H, Jiang X, Hubaux JP. SCOR: A secure international informatics infrastructure to investigate COVID-19. J Am Med Inform Assoc. 2020 Nov 1;27(11):1721-1726. doi: 10.1093/jamia/ocaa172. PubMed PMID: 32918447; PubMed Central PMCID: PMC7454652.

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Portanova J, Murray N, Mower J, Subramanian D, Cohen T. aer2vec: Distributed Representations of Adverse Event Reporting System Data as a Means to Identify Drug/Side-Effect Associations. AMIA Annu Symp Proc. 2019;2019:717-726. eCollection 2019. PubMed PMID: 32308867; PubMed Central PMCID: PMC7153155.

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Burkhardt HA, Subramanian D, Mower J, Cohen T. Predicting Adverse Drug-Drug Interactions with Neural Embedding of Semantic Predications. AMIA Annu Symp Proc. 2019;2019:992-1001. eCollection 2019. PubMed PMID: 32308896; PubMed Central PMCID: PMC7153048.

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Mower J, Cohen T, Subramanian D. Complementing Observational Signals with Literature-Derived Distributed Representations for Post-Marketing Drug Surveillance. Drug Saf. 2020 Jan;43(1):67-77. doi: 10.1007/s40264-019-00872-9. PubMed PMID: 31646442; PubMed Central PMCID: PMC7243821.

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Amith M, Cohen T, Cunningham R, Savas LS, Smith N, Cuccaro P, Gabay E, Boom J, Schvaneveldt R, Tao C. Mining HPV Vaccine Knowledge Structures of Young Adults From Reddit Using Distributional Semantics and Pathfinder Networks. Cancer Control. 2020 Jan-Dec;27(1):1073274819891442. doi: 10.1177/1073274819891442. PubMed PMID: 31912742; PubMed Central PMCID: PMC6950556.

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Cohen T, Pakhomov S. A Tale of Two Perplexities: Sensitivity of Neural Language Models to Lexical Retrieval Deficits in Dementia of the Alzheimer’s Type. In: (to appear) Proceedings of the Annual Meeting of the Association for Computational Linguistics (ACL 2020) Virtual conference, July 2020.: ACL; 2020.

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Paullada A, Percha B, Cohen T. Improving Biomedical Analogical Retrieval with Embedding of Structural Dependencies. In: Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing [Internet] 2020 ed. Online: Association for Computational Linguistics; 2020. 38–48p. Available from: https://aclanthology.org/2020.bionlp-1.4.

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Wei Q, Chen Y, Salimi M, Denny JC, Mei Q, Lasko TA, Chen Q, Wu S, Franklin A, Cohen T, Xu H. Cost-aware active learning for named entity recognition in clinical text. J Am Med Inform Assoc. 2019 Nov 1;26(11):1314-1322. doi: 10.1093/jamia/ocz102. PubMed PMID: 31294792; PubMed Central PMCID: PMC6798575.

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Ji Z, Wei Q, Franklin A, Cohen T, Xu H. Cost-sensitive Active Learning for Phenotyping of Electronic Health Records. AMIA Jt Summits Transl Sci Proc. 2019;2019:829-838. eCollection 2019. PubMed PMID: 31259040; PubMed Central PMCID: PMC6568101.

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Fathiamini S, Johnson AM, Zeng J, Holla V, Sanchez NS, Meric-Bernstam F, Bernstam EV, Cohen T. Rapamycin - mTOR + BRAF = ? Using relational similarity to find therapeutically relevant drug-gene relationships in unstructured text. J Biomed Inform. 2019 Feb;90:103094. doi: 10.1016/j.jbi.2019.103094. Epub 2019 Jan 4. PubMed PMID: 30615938; PubMed Central PMCID: PMC6386529.

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Portanova J, Murray N, Mower J, Subramanian D, Cohen T. aer2vec: Distributed Representations of Adverse Event Reporting System Data as a Means to Identify Drug/Side-Effect Associations.. In: (to appear) Proc AMIA Annu Symp 2019 Washington, DC: AMIA; 2019.

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Burkhardt H, Subramanian D, Mower J, Cohen T. Predicting Adverse Drug-Drug Interactions with Neural Embedding of Semantic Predications.. In: (to appear) Proc AMIA Annu Symp 2019 Washington, DC: AMIA; 2019.

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Wei Q, Franklin A, Cohen T, Xu H. Clinical text annotation - what factors are associated with the cost of time?. AMIA Annu Symp Proc. 2018;2018:1552-1560. eCollection 2018. PubMed PMID: 30815201; PubMed Central PMCID: PMC6371268.

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Mower J, Subramanian D, Cohen T. Learning predictive models of drug side-effect relationships from distributed representations of literature-derived semantic predications. J Am Med Inform Assoc. 2018 Oct 1;25(10):1339-1350. doi: 10.1093/jamia/ocy077. PubMed PMID: 30010902; PubMed Central PMCID: PMC6454491.

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Zhang Y, Li HJ, Wang J, Cohen T, Roberts K, Xu H. Adapting Word Embeddings from Multiple Domains to Symptom Recognition from Psychiatric Notes. AMIA Jt Summits Transl Sci Proc. 2018;2017:281-289. eCollection 2018. PubMed PMID: 29888086; PubMed Central PMCID: PMC5961810.

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Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H. DataMed - an open source discovery index for finding biomedical datasets. J Am Med Inform Assoc. 2018 Mar 1;25(3):300-308. doi: 10.1093/jamia/ocx121. PubMed PMID: 29346583; PubMed Central PMCID: PMC7378878.

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Cohen T, Widdows D. Bringing Order to Neural Word Embeddings with Embeddings Augmented by Random Permutations (EARP). In: Proceedings of the 22nd Conference on Computational Natural Language Learning (CoNLL 2018) aclweb.org: Association of Computational Linguistics; 2018. p.465-475.

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Amith M, Cunningham R, Savas LS, Boom J, Schvaneveldt R, Tao C, Cohen T. Using Pathfinder networks to discover alignment between expert and consumer conceptual knowledge from online vaccine content. J Biomed Inform. 2017 Oct;74:33-45. doi: 10.1016/j.jbi.2017.08.007. Epub 2017 Aug 18. PubMed PMID: 28823922; PubMed Central PMCID: PMC5641252.