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Full Access(LTS Version) https://www.academia.edu/104236887/Using_ACO_Algorithm_to_Improve_Performance_for_Container_based_Scientific_Workflows https://orcid.org/0000-0003-3729-6290

Medical scientists are encouraged to use GitHub for software development, but without training, they might leak protected health information (PHI) by inadvertently including data in what should be software repositories. During the fall of 2016, we attempted to identify obvious breaches of PHI on GitHub as part of an ongoing interest in patient privacy. Searching GitHub for keywords patient, dob, and ssn uncovered hundreds of repositories, which were further scanned for sensitive information (names, organizations, phone numbers, street addresses, credit cards, IPs, SSNs, and emails) using Python's common regex module and the Stanford Natural Language Toolkit. Manual investigation of the results uncovered three repositories that exposed patient information. A popular health care provider exposed approximately 4000 patient names. On Dec 1, we were able to track down the healthcare provider from both the repository name and doctor names in the repository files. We contacted the organization and those repositories were taken down within the day of contact. A health collection agency’s repository led to the exposure of social security numbers, dates of birth, home addresses, email addresses, and insurance and billing information of roughly 30,000 patients. After we contacted the repository owner, the data and the repository were removed from GitHub some six months after the data had first been exposed. A crisis center’s long-term breach of PHI was discovered in August 2016, and from the repository dates, it had been up for at least three years. The original repository managed the medical records application developed for the crisis center. We contacted that organization and the repository was taken down within a few days. A contractor for a health insurance wellness program leaked some patient data with names, social security numbers, addresses, and health measures such as blood pressure, etc. This organization was contacted by our hospital compliance office and the GitHub repository was removed. Our talk will cover the discovery of these PHI breaches, and how we handled them with GitHub, our compliance office, and the organizations involved.

{"references": ["Tsokos GC. Systemic lupus erythematosus. N Engl J Med. 2011;365(22):2110-21. doi: 10.1056/NEJMra1100359. PubMed PMID: 22129255", "Bradley SJ, Suarez-Fueyo A, Moss DR, Kyttaris VC, Tsokos GC. T Cell Transcriptomes Describe Patient Subtypes in Systemic Lupus Erythematosus. PLoS One. 2015;10(11):e0141171. doi: 10.1371/journal.pone.0141171. PubMed PMID: 26544975; PubMed Central PMCID: PMCPMC4636226", "Koga T, Hedrich CM, Mizui M, Yoshida N, Otomo K, Lieberman LA, et al. CaMK4-dependent activation of AKT/mTOR and CREM-alpha underlies autoimmunity-associated Th17 imbalance. J Clin Invest. 2014;124(5):2234-45. doi: 10.1172/JCI73411. PubMed PMID: 24667640; PubMed Central PMCID: PMCPMC4001553.", "Kis-Toth K, Tsokos GC. Engagement of SLAMF2/CD48 prolongs the time frame of effective T cell activation by supporting mature dendritic cell survival. J Immunol. 2014;192(9):4436-42. doi: 10.4049/jimmunol.1302909. PubMed PMID: 24670806; PubMed Central PMCID: PMCPMC4017928.", "Mizui M, Koga T, Lieberman LA, Beltran J, Yoshida N, Johnson MC, et al. IL-2 protects lupus-prone mice from multiple end-organ damage by limiting CD4-CD8- IL-17-producing T cells. J Immunol. 2014;193(5):2168-77. doi: 10.4049/jimmunol.1400977. PubMed PMID: 25063876; PubMed Central PMCID: PMCPMC4135016.", "Almlof JC, Alexsson A, Imgenberg-Kreuz J, Sylwan L, Backlin C, Leonard D, et al. Novel risk genes for systemic lupus erythematosus predicted by random forest classification. Sci Rep. 2017;7(1):6236. doi: 10.1038/s41598-017-06516-1. PubMed PMID: 28740209; PubMed Central PMCID: PMCPMC5524838", "Tan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF, et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 1982;25(11):1271-7. PubMed PMID: 7138600.", "Lawrence JS, Martins CL, Drake GL. A family survey of lupus erythematosus. 1. Heritability. J Rheumatol. 1987;14(5):913-21. PubMed PMID: 3430520.", "Morris DL, Sheng Y, Zhang Y, Wang YF, Zhu Z, Tombleson P, et al. Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus. Nat Genet. 2016;48(8):940-6. doi: 10.1038/ng.3603. PubMed PMID: 27399966; PubMed Central PMCID: PMCPMC4966635.", "Moser KL, Kelly JA, Lessard CJ, Harley JB. Recent insights into the genetic basis of systemic lupus erythematosus. Genes and Immunity. 2009;10(5):373-9. doi: 10.1038/gene.2009.39. PubMed PMID: WOS:000268168800001.", "Dai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM. Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage. Curr Opin Immunol. 2014;31:87-96. doi: 10.1016/j.coi.2014.10.004. PubMed PMID: 25458999; PubMed Central PMCID: PMCPMC4274270.", "Kariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, et al. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun. 2015;16(1):15-23. doi: 10.1038/gene.2014.57. PubMed PMID: 25338677; PubMed Central PMCID: PMCPMC4305028.", "Tsokos GC, Lo MS, Reis PC, Sullivan KE. New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol. 2016;12(12):716-30. doi: 10.1038/nrrheum.2016.186. PubMed PMID: WOS:000389219600006.", "Harley JB, Moser KL, Gaffney PM, Behrens TW. The genetics of human systemic lupus erythematosus. Curr Opin Immunol. 1998;10(6):690-6. PubMed PMID: 9914226.", "Galante PAF, Sakabe NJ, Kirschbaum-Slager N, De Souza SJ. Detection and evaluation of intron retention events in the human transcriptome. Rna. 2004;10(5):757-65. doi: 10.1261/rna.5123504. PubMed PMID: WOS:000221072500001.", "Wang ET, Sandberg R, Luo SJ, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456(7221):470-6. doi: 10.1038/nature07509. PubMed PMID: WOS:000261170500031.", "Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463(7280):457-63. doi: 10.1038/nature08909. PubMed PMID: WOS:000273981100037.", "Boutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Gene Dev. 2015;29(1):63-80. doi: 10.1101/gad.247361.114. PubMed PMID: WOS:000347372100006.", "Wong JJL, Ritchie W, Ebner OA, Selbach M, Wong JWH, Huang YZ, et al. Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation. Cell. 2013;154(3):583-95. doi: 10.1016/j.cell.2013.06.052. PubMed PMID: WOS:000322629900012.", "Dvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015;7. doi: ARTN 45 10.1186/s13073-015-0168-9. PubMed PMID: WOS:000357021700001.", "Yap K, Lim ZQ, Khandelia P, Friedman B, Makeyev EV. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Gene Dev. 2012;26(11):1209-23. doi: 10.1101/gad.188037.112. PubMed PMID: WOS:000304767000008.", "Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2016;44(2):838-51. doi: 10.1093/nar/gkv1168. PubMed PMID: 26531823; PubMed Central PMCID: PMCPMC4737145.", "Ni T, Yang W, Han M, Zhang Y, Shen T, Nie H, et al. Global intron retention mediated gene regulation during CD4+ T cell activation. Nucleic Acids Res. 2016;44(14):6817-29. doi: 10.1093/nar/gkw591. PubMed PMID: 27369383; PubMed Central PMCID: PMCPMC5001615.", "Chen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol. 2014;24:141-9. doi: 10.1016/j.sbi.2014.01.009. PubMed PMID: 24530854; PubMed Central PMCID: PMCPMC3987960.", "Scotti MM, Swanson MS. RNA mis-splicing in disease. Nat Rev Genet. 2016;17(1):19-32. doi: 10.1038/nrg.2015.3. PubMed PMID: 26593421; PubMed Central PMCID: PMCPMC5993438.", "Evsyukova I, Somarelli JA, Gregory SG, Garcia-Blanco MA. Alternative splicing in multiple sclerosis and other autoimmune diseases. RNA Biol. 2010;7(4):462-73. PubMed PMID: 20639696; PubMed Central PMCID: PMCPMC3070910.", "Bombardier C, Gladman DD, Urowitz MB, Caron D, Chang CH. Derivation of the SLEDAI. A disease activity index for lupus patients. The Committee on Prognosis Studies in SLE. Arthritis Rheum. 1992;35(6):630-40. PubMed PMID: 1599520.", "Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. PubMed PMID: 19289445; PubMed Central PMCID: PMCPMC2672628.", "Shi X, Ran L, Liu Y, Zhong SH, Zhou PP, Liao MX, et al. Knockdown of hnRNP A2/B1 inhibits cell proliferation, invasion and cell cycle triggering apoptosis in cervical cancer via PI3K/AKT signaling pathway. Oncol Rep. 2018;39(3):939-50. doi: 10.3892/or.2018.6195. PubMed PMID: 29328485; PubMed Central PMCID: PMCPMC5802035.", "Li D, Tang Q, Tan L, Zhao M, Liang GP, Yang Y, et al. Ten-Eleven Translocation 2 Protein Down-Regulates DNA Methylation of Interleukin-17A Promoter and Induces Its Expression in CD4(+)t Cells of Patients with Systemic Lupus Erythematosus. Arthritis Rheumatol. 2014;66:S1175-S. PubMed PMID: WOS:000344384905362.", "1.\tTsokos GC. Systemic lupus erythematosus. N Engl J Med. 2011;365(22):2110-21. doi: 10.1056/NEJMra1100359. PubMed PMID: 22129255. 2.\tBradley SJ, Suarez-Fueyo A, Moss DR, Kyttaris VC, Tsokos GC. T Cell Transcriptomes Describe Patient Subtypes in Systemic Lupus Erythematosus. PLoS One. 2015;10(11):e0141171. doi: 10.1371/journal.pone.0141171. PubMed PMID: 26544975; PubMed Central PMCID: PMCPMC4636226. 3.\tKoga T, Hedrich CM, Mizui M, Yoshida N, Otomo K, Lieberman LA, et al. CaMK4-dependent activation of AKT/mTOR and CREM-alpha underlies autoimmunity-associated Th17 imbalance. J Clin Invest. 2014;124(5):2234-45. doi: 10.1172/JCI73411. PubMed PMID: 24667640; PubMed Central PMCID: PMCPMC4001553. 4.\tKis-Toth K, Tsokos GC. Engagement of SLAMF2/CD48 prolongs the time frame of effective T cell activation by supporting mature dendritic cell survival. J Immunol. 2014;192(9):4436-42. doi: 10.4049/jimmunol.1302909. PubMed PMID: 24670806; PubMed Central PMCID: PMCPMC4017928. 5.\tMizui M, Koga T, Lieberman LA, Beltran J, Yoshida N, Johnson MC, et al. IL-2 protects lupus-prone mice from multiple end-organ damage by limiting CD4-CD8- IL-17-producing T cells. J Immunol. 2014;193(5):2168-77. doi: 10.4049/jimmunol.1400977. PubMed PMID: 25063876; PubMed Central PMCID: PMCPMC4135016. 6.\tAlmlof JC, Alexsson A, Imgenberg-Kreuz J, Sylwan L, Backlin C, Leonard D, et al. Novel risk genes for systemic lupus erythematosus predicted by random forest classification. Sci Rep. 2017;7(1):6236. doi: 10.1038/s41598-017-06516-1. PubMed PMID: 28740209; PubMed Central PMCID: PMCPMC5524838. 7.\tTan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF, et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 1982;25(11):1271-7. PubMed PMID: 7138600. 8.\tLawrence JS, Martins CL, Drake GL. A family survey of lupus erythematosus. 1. Heritability. J Rheumatol. 1987;14(5):913-21. PubMed PMID: 3430520. 9.\tMorris DL, Sheng Y, Zhang Y, Wang YF, Zhu Z, Tombleson P, et al. Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus. Nat Genet. 2016;48(8):940-6. doi: 10.1038/ng.3603. PubMed PMID: 27399966; PubMed Central PMCID: PMCPMC4966635. 10.\tMoser KL, Kelly JA, Lessard CJ, Harley JB. Recent insights into the genetic basis of systemic lupus erythematosus. Genes and Immunity. 2009;10(5):373-9. doi: 10.1038/gene.2009.39. PubMed PMID: WOS:000268168800001. 11.\tDai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM. Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage. Curr Opin Immunol. 2014;31:87-96. doi: 10.1016/j.coi.2014.10.004. PubMed PMID: 25458999; PubMed Central PMCID: PMCPMC4274270. 12.\tKariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, et al. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun. 2015;16(1):15-23. doi: 10.1038/gene.2014.57. PubMed PMID: 25338677; PubMed Central PMCID: PMCPMC4305028. 13.\tTsokos GC, Lo MS, Reis PC, Sullivan KE. New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol. 2016;12(12):716-30. doi: 10.1038/nrrheum.2016.186. PubMed PMID: WOS:000389219600006. 14.\tHarley JB, Moser KL, Gaffney PM, Behrens TW. The genetics of human systemic lupus erythematosus. Curr Opin Immunol. 1998;10(6):690-6. PubMed PMID: 9914226. 15.\tGalante PAF, Sakabe NJ, Kirschbaum-Slager N, De Souza SJ. Detection and evaluation of intron retention events in the human transcriptome. Rna. 2004;10(5):757-65. doi: 10.1261/rna.5123504. PubMed PMID: WOS:000221072500001. 16.\tWang ET, Sandberg R, Luo SJ, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456(7221):470-6. doi: 10.1038/nature07509. PubMed PMID: WOS:000261170500031. 17.\tNilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463(7280):457-63. doi: 10.1038/nature08909. PubMed PMID: WOS:000273981100037. 18.\tBoutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Gene Dev. 2015;29(1):63-80. doi: 10.1101/gad.247361.114. PubMed PMID: WOS:000347372100006. 19.\tWong JJL, Ritchie W, Ebner OA, Selbach M, Wong JWH, Huang YZ, et al. Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation. Cell. 2013;154(3):583-95. doi: 10.1016/j.cell.2013.06.052. PubMed PMID: WOS:000322629900012. 20.\tDvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015;7. doi: ARTN 45 10.1186/s13073-015-0168-9. PubMed PMID: WOS:000357021700001. 21.\tYap K, Lim ZQ, Khandelia P, Friedman B, Makeyev EV. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Gene Dev. 2012;26(11):1209-23. doi: 10.1101/gad.188037.112. PubMed PMID: WOS:000304767000008. 22.\tPimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2016;44(2):838-51. doi: 10.1093/nar/gkv1168. PubMed PMID: 26531823; PubMed Central PMCID: PMCPMC4737145. 23.\tNi T, Yang W, Han M, Zhang Y, Shen T, Nie H, et al. Global intron retention mediated gene regulation during CD4+ T cell activation. Nucleic Acids Res. 2016;44(14):6817-29. doi: 10.1093/nar/gkw591. PubMed PMID: 27369383; PubMed Central PMCID: PMCPMC5001615. 24.\tChen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol. 2014;24:141-9. doi: 10.1016/j.sbi.2014.01.009. PubMed PMID: 24530854; PubMed Central PMCID: PMCPMC3987960. 25.\tScotti MM, Swanson MS. RNA mis-splicing in disease. Nat Rev Genet. 2016;17(1):19-32. doi: 10.1038/nrg.2015.3. PubMed PMID: 26593421; PubMed Central PMCID: PMCPMC5993438. 26.\tEvsyukova I, Somarelli JA, Gregory SG, Garcia-Blanco MA. Alternative splicing in multiple sclerosis and other autoimmune diseases. RNA Biol. 2010;7(4):462-73. PubMed PMID: 20639696; PubMed Central PMCID: PMCPMC3070910. 27.\tBombardier C, Gladman DD, Urowitz MB, Caron D, Chang CH. Derivation of the SLEDAI. A disease activity index for lupus patients. The Committee on Prognosis Studies in SLE. Arthritis Rheum. 1992;35(6):630-40. PubMed PMID: 1599520. 28.\tTrapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. PubMed PMID: 19289445; PubMed Central PMCID: PMCPMC2672628. 29.\tShi X, Ran L, Liu Y, Zhong SH, Zhou PP, Liao MX, et al. Knockdown of hnRNP A2/B1 inhibits cell proliferation, invasion and cell cycle triggering apoptosis in cervical cancer via PI3K/AKT signaling pathway. Oncol Rep. 2018;39(3):939-50. doi: 10.3892/or.2018.6195. PubMed PMID: 29328485; PubMed Central PMCID: PMCPMC5802035. 30.\tLi D, Tang Q, Tan L, Zhao M, Liang GP, Yang Y, et al. Ten-Eleven Translocation 2 Protein Down-Regulates DNA Methylation of Interleukin-17A Promoter and Induces Its Expression in CD4(+)t Cells of Patients with Systemic Lupus Erythematosus. Arthritis Rheumatol. 2014;66:S1175-S. PubMed PMID: WOS:000344384905362. 31.\tWu H, Huang X, Qiu H, Zhao M, Lu Q. 16 High salt promotes systemic lupus erythematosus by TET2-induced dna demethylation and driving the differentiation of TFH cells. Archives of Disease in childhood; 2017."]} Abstract: SLE is a complex autoimmune disease and its cause is unclear. Given the autoimmune nature of SLE and the newly-recognizedrole of intron retention (IR) played in global gene regulation, we studied the global gene expression and intron retention pattern of lupus patients.

This is the replication package for our ESEC/FSE 2021 paper A Large-Scale Empirical Study on Java Library Migrations: Prevalence, Trends, and Rationales. It can be used to replicate all three research questions in the paper using our preprocessed and manually labeled data. Please refer to this GitHub repository (https://github.com/hehao98/LibraryMigration) or the git repository archive (gitrepo.zip) in this package for detailed documentation about how to use this replication package. It consists of the following files: cache.zip: This file contains some most important datasets used in this paper, including the GitHub repositories and Maven libraries used, the set of all dependency changes, and the migration graph. Data related to thematic analysis can be found in the git repository. dbdata.tar.xz: This file contains the raw MongoDB data folder that will be used if you choose to install the required environment using Docker. dbdump.zip: This file contains the MongoDB data dump which will be used if you choose to manually install the required environment. gitrepo.zip: A git repository archive for the scripts, notebooks, and spreadsheets we used for this paper. Note that this archive may be somewhat older than the GitHub repository (https://github.com/hehao98/LibraryMigration). We recommend referring to the latest version at GitHub and only resort to this archive if the GitHub repository becomes unavailable in the unforeseeable future. We hope the provided scripts and dataset can be used to facilitate further research.

This is the Artifact for paper FTTN: Feature-Targeted Testing for Numerical Properties of NVIDIA & AMD Matrix Accelerators

We consider global models of communicating agents specified as transition systems labelled by interactions in which multiple senders and receivers can participate. A realisation of such a model is a set of local transition systems—one per agent—which are executed concurrently using synchronous communication. Our core challenge is how to check whether a global model is realisable and, if it is, how to synthesise a realisation. We identify and compare two variants to realise global interaction models, both relying on bisimulation equivalence. Then we investigate, for both variants, realisability conditions to be checked on global models. We propose a synthesis method for the construction of realisations by grouping locally indistinguishable states. The paper is accompanied by a tool that implements realisability checks and synthesises realisations. This document extends a publication accepted at the International Colloquium on Theoretical Aspects of Computing 2023 (ICTAC 2023), including the proofs of all results, more examples, and a more detailed explanation of the companion prototype tool.

This repository contains the code and data necessary to reproduce the figures and tables in "How research programs come apart: the case of supersymmetry and the disunity of physics"

This document contains the vision statement of PlasmaPy.