Browsing by Author "Wang, Kai"
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Item Advancing Active Authentication for User Privacy and Revocability with BioCapsules(ACM, 2023-10) Sanchez, Edwin; Weyer, Anthony; Palackal, Joseph; Wang, Kai; Philips, Tyler; Zou, Xukai; Computer Science, Luddy School of Informatics, Computing, and EngineeringBiometric Facial Authentication has become a pervasive mode of authentication in recent years. With this surge in popularity, concerns over the security and privacy of biometrics-based systems have grown. Therefore, there is a need for a system that can address security and privacy issues while remaining user-friendly and practical. The BioCapsule scheme is a flexible solution that can be embedded in existing biometrics systems in order to provide robust security and privacy protections. While BioCapsules have been evaluated for their static face authentication capabilities, this paper extends the scheme to Active Authentication, where a user is continuously authenticated throughout a session. We use the MOBIO dataset, which contains video recordings of 150 individuals using mobile devices over several sessions, in order to evaluate the BioCapsule scheme within the domain of Active Authentication. We find that the BioCapsule scheme not only performs comparably to baseline, unsecured system performance, but in some cases exceeds baseline performance in terms of False Acceptance Rate, False Rejection Rate, and Equal Error Rate. Through our experiments, we demonstrate that the BioCapsule scheme is a powerful and practical addition to existing biometrics-based Active Authentication systems to provide robust security and privacy protections.Item Characterization of Chronic Gastritis in Lynch Syndrome Patients With Gastric Adenocarcinoma(Elmer Press, 2021-02) Saulino, David; Chen, Rong; Wang, Kai; Shen, Minqian; Zhang, Xuefeng; Westerhoff, Maria; Cheng, Jerome; Lin, Jingmei; Zhang, Xuchen; Feely, Michael; Liu, Xiuli; Pathology and Laboratory Medicine, School of MedicineBackground: Gastric cancer is one of the Lynch syndrome (LS)-associated malignancies. Previous studies have suggested that LS patients with gastric cancer also had chronic atrophic gastritis in the background mucosa, but further histologic characterization was not attempted. This study aims to understand the histologic features of background chronic gastritis in LS patients with gastric adenocarcinoma. Methods: Eleven LS-associated gastric cancer cases were collected from five institutions. Demographics and clinical features were retrieved by review of medical charts. Pathological material was reviewed for tumor location and histologic type. In addition, non-neoplastic gastric mucosa was assessed for inflammation (chronic and active), atrophy, intestinal metaplasia (IM) in the antrum and body, as well as pyloric gland metaplasia and enterochromaffin-like (ECL) cell hyperplasia in the body. Results: Eleven LS patients with gastric cancer (four male and seven female) with a mean age of 63 years (range: 23 - 83) were included. Ten (90.9%) had personal cancer histories; however none of the patients had family history of gastric cancer. Eight (72.7%) patients underwent gastrectomy and three had endoscopic resection. Nine (81.8%) patients had tumor in the fundus and/or body and two had tumor present in the antrum. Seven (63.6%) cases were intestinal type or mixed type carcinoma, and the remaining four were signet ring cell carcinoma. Eight (of 11, 72.7%) patients had chronic gastritis, five (45.4%) had atrophy, and four (36.3%) had intestinal metaplasia. Four of five patients with both antrum and body mucosa available for evaluation (80%), demonstrated body-predominant chronic gastritis. Four patients had germline MLH1 alterations and all of these patients had chronic gastritis, including one Helicobacter pylori (H. pylori) gastritis and three H. pylori-negative gastritis. Conclusions: None of LS patients with gastric cancer in our cohort had a family history of gastric cancer. Gastric adenocarcinomas in LS patients were primarily located in the fundus and/or body. Two-thirds of these tumors were of intestinal type and had a background chronic, H. pylori-negative gastritis. These results support a chronic atrophic gastritis with intestinal metaplasia-dysplasia-carcinoma sequence in LS-related gastric tumorigenesis, particularly in MLH1-mutated LS patients.Item Circulating microRNAs and life expectancy among identical twins(Wiley, 2016-09) Wu, Shenghui; Kim, Taek-Kyun; Wu, Xiaogang; Scherler, Kelsey; Baxter, David; Wang, Kai; Krasnow, Ruth E.; Reed, Terry; Dai, Jun; Department of Medical & Molecular Genetics, IU School of MedicineHuman life expectancy is influenced not only by longevity assurance mechanisms and disease susceptibility loci but also by the environment, gene–environment interactions, and chance. MicroRNAs (miRNAs) are a class of small noncoding RNAs closely related to genes. Circulating miRNAs have been shown as promising noninvasive biomarkers in the development of many pathophysiological conditions. However, the concentration of miRNA in the circulation may also be affected by environmental factors. We used a next-generation sequencing platform to assess the association of circulating miRNA with life expectancy, for which deaths are due to all causes independent of genes. In addition, we showed that miRNAs are present in 41-year archived plasma samples, which may be useful for both life expectancy and all-cause mortality risk assessment. Plasma miRNAs from nine identical male twins were profiled using next-generation sequencing. The average absolute difference in the minimum life expectancy was 9.68 years. Intraclass correlation coefficients were above 0.4 for 50% of miRNAs. Comparing deceased twins with their alive co-twin brothers, the concentrations were increased for 34 but decreased for 30 miRNAs. Identical twins discordant in life expectancy were dissimilar in the majority of miRNAs, suggesting that environmental factors are pivotal in miRNAs related to life expectancy.Item Correction to: The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases(BMC, 2020) Zhao, Zhongming; Dai, Yulin; Zhang, Chi; Mathé, Ewy; Wei, Lai; Wang, Kai; Medical and Molecular Genetics, School of MedicineAfter publication of this supplement article [1], it is requested the grant ID in the Funding section should be corrected from NSF grant IIS-7811367 to NSF grant IIS-1902617. Therefore, the correct 'Funding' section in this article should read: We thank the National Science Foundation (NSF grant IIS-1902617) for the financial support of ICIBM 2019. This article has not received sponsorship for publication.Item Correction to: The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomic(BMJ Publishing Group, 2020-05-06) Mathé, Ewy; Zhang, Chi; Wang, Kai; Ning, Xia; Guo, Yan; Zhao, Zhongming; Medical and Molecular Genetics, School of MedicineAfter publication of this supplement article [1], it is requested the grant ID in the Funding section should be corrected from NSF grant IIS-7811367 to NSF grant IIS-1902617. Therefore, the correct ‘Funding’ section in this article should read: This article has not received sponsorship for publication. We thank the National Science Foundation (NSF grant IIS-1902617) and the Data Science and Informatics Core for Cancer Research (CPRIT grant RP170668) for the financial support of ICIBM 2019, as well as the support from Cancer Prevention and Research Institute of Texas (RP180734).Item Correction to: The International Conference on Intelligent Biology and Medicine 2019: computational methods for drug interactions(BMC, 2020) Ning, Xia; Zhang, Chi; Wang, Kai; Zhao, Zhongming; Mathé, Ewy; Medical and Molecular Genetics, School of MedicineAfter publication of this supplement article [1], it is requested the grant ID in the Funding section should be corrected from NSF grant IIS-7811367 to NSF grant IIS-1902617.Item Genomic Profiling of Advanced-Stage, Metaplastic Breast Carcinoma by Next-Generation Sequencing Reveals Frequent, Targetable Genomic Abnormalities and Potential New Treatment Options(2015-05) Ross, Jeffrey S.; Badve, Sunil; Wang, Kai; Sheehan, Christine E.; Boguniewicz, Ann B.; Otto, Geoff A.; Yelensky, Roman; Lipson, Doron; Ali, Siraj; Morosini, Deborah; Chliemlecki, Juliann; Elvin, Julia A.; Miller, Vincent A.; Stephens, Philip J.; Department of Pathology and Laboratory Medicine, IU School of MedicineContext.— Metastatic metaplastic breast carcinoma (MPBC) is an uncommon, but aggressive, tumor resistant to conventional chemotherapy. Objective.— To learn whether next-generation sequencing could identify potential targets of therapy for patients with relapsed and metastatic MPBC. Design.— Hybridization capture of 3769 exons from 236 cancer-related genes and 47 introns of 19 genes commonly rearranged in cancer was applied to a minimum of 50 ng of DNA extracted from 20 MPBC formalin-fixed, paraffin-embedded specimens and sequenced to high uniform coverage. Results.— The 20 patients with MPBC had a median age of 62 years (range, 42–86 years). There were 9 squamous (45%), 9 chondroid (45%), and 2 spindle cell (10%) MPBCs, all of which were high grade. Ninety-three genomic alterations were identified, (range, 1–11) with 19 of the 20 cases (95%) harboring an alteration that could potentially lead to a targeted treatment option. The most-common alterations were in TP53 (n = 69; 75%), PIK3CA (n = 37; 40%), MYC (n = 28; 30%), MLL2 (n = 28; 30%), PTEN (n = 23; 25%), CDKN2A/B (n = 19; 20%), CCND3 (n = 14; 15%), CCNE1 (n = 9; 10%), EGFR (n = 9; 10%), and KDM6A (n = 9; 10%); AKT3, CCND1, CCND2, CDK4, FBXW7, FGFR1, HRAS, NF1, PIK3R1, and SRC were each altered in a single case. All 16 MPBCs (100%) that were negative for ERBB2 (HER2) overexpression by immunohistochemistry and/or ERBB2 (HER2) amplification by fluorescence in situ hybridization were also uniformly (100%) negative for ERBB2 amplification by next-generation sequencing–based copy-number assessment. Conclusions.— Our results indicate that genomic profiling using next-generation sequencing can identify clinically meaningful alterations that have the potential to guide targeted treatment decisions in most patients with metastatic MPBC.Item Genomic Profiling of T-Cell Neoplasms Reveals Frequent JAK1 and JAK3 Mutations With Clonal Evasion From Targeted Therapies(American Society of Clinical Oncology, 2018) Greenplate, Allison; Wang, Kai; Tripathi, Rati M.; Palma, Norma; Ali, Siraj M.; Stephens, Phil J.; Miller, Vincent A.; Shyr, Yu; Guo, Yan; Reddy, Nishitha M.; Kozhaya, Lina; Unutmaz, Derya; Chen, Xueyan; Irish, Jonathan M.; Davé, Utpal P.; Medicine, School of MedicinePurpose: The promise of precision oncology is that identification of genomic alterations will direct the rational use of molecularly targeted therapy. This approach is particularly applicable to neoplasms that are resistant to standard cytotoxic chemotherapy, like T-cell leukemias and lymphomas. In this study, we tested the feasibility of targeted next-generation sequencing in profiles of diverse T-cell neoplasms and focused on the therapeutic utility of targeting activated JAK1 and JAK3 in an index case. Patients and Methods: Using Foundation One and Foundation One Heme assays, we performed genomic profiling on 91 consecutive T-cell neoplasms for alterations in 405 genes. The samples were sequenced to high uniform coverage with an Illumina HiSeq and averaged a coverage depth of greater than 500× for DNA and more than 8M total pairs for RNA. An index case of T-cell prolymphocytic leukemia (T-PLL), which was analyzed by targeted next-generation sequencing, is presented. T-PLL cells were analyzed by RNA-seq, in vitro drug testing, mass cytometry, and phospho-flow. Results: One third of the samples had genomic aberrations in the JAK-STAT pathway, most often composed of JAK1 and JAK3 gain-of-function mutations. We present an index case of a patient with T-PLL with a clonal JAK1 V658F mutation that responded to ruxolitinib therapy. After relapse developed, an expanded clone that harbored mutant JAK3 M511I and downregulation of the phosphatase, CD45, was identified. We demonstrate that the JAK missense mutations were activating, caused pathway hyperactivation, and conferred cytokine hypersensitivity. Conclusion: These results underscore the utility of profiling occurrences of resistance to standard regimens and support JAK enzymes as rational therapeutic targets for T-cell leukemias and lymphomas.Item Innovating Computational Biology and Intelligent Medicine: ICIBM 2019 Special Issue(MDPI, 2020-04-17) Guo, Yan; Ning, Xia; Mathé, Ewy; Wang, Kai; Li, Lang; Zhang, Chi; Zhao, Zhongming; Medical and Molecular Genetics, School of MedicineThe International Association for Intelligent Biology and Medicine (IAIBM) is a nonprofit organization that promotes intelligent biology and medical science. It hosts an annual International Conference on Intelligent Biology and Medicine (ICIBM), which was established in 2012. The ICIBM 2019 was held from 9 to 11 June 2019 in Columbus, Ohio, USA. Out of the 105 original research manuscripts submitted to the conference, 18 were selected for publication in a Special Issue in Genes. The topics of the selected manuscripts cover a wide range of current topics in biomedical research including cancer informatics, transcriptomic, computational algorithms, visualization and tools, deep learning, and microbiome research. In this editorial, we briefly introduce each of the manuscripts and discuss their contribution to the advance of science and technology.Item The International Conference on Intelligent Biology and Medicine (ICIBM) 2018: genomics with bigger data and wider applications(Biomed Central, 2019-02-04) Wu, Zhijin; Yan, Jingwen; Wang, Kai; Liu, Xiaoming; Guo, Yan; Zhi, Degui; Ruan, Jianhua; Zhao, Zhongming; BioHealth Informatics, School of Informatics and ComputingThe sixth International Conference on Intelligent Biology and Medicine (ICIBM) took place in Los Angeles, California, USA on June 10-12, 2018. This conference featured eleven regular scientific sessions, four tutorials, one poster session, four keynote talks, and four eminent scholar talks. The scientific program covered a wide range of topics from bench to bedside, including 3D Genome Organization, reconstruction of large scale evolution of genomes and gene functions, artificial intelligence in biological and biomedical fields, and precision medicine. Both method development and application in genomic research continued to be a main component in the conference, including studies on genetic variants, regulation of transcription, genetic-epigenetic interaction at both single cell and tissue level and artificial intelligence. Here, we write a summary of the conference and also briefly introduce the four high quality papers selected to be published in BMC Genomics that cover novel methodology development or innovative data analysis.