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Nam IC, Park JO, Kim CS, Park SJ, Lee DH, Kim HB, Han K, Joo YH. Association of smoking status, duration and amount with the risk of head and neck cancer subtypes: a national population-based study. Am J Cancer Res 2022; 12:4815-4824. [PMID: 36381316 PMCID: PMC9641393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023] Open
Abstract
Smoking is positively associated with multiple cancer types including head and neck cancer (HNC). We sought to confirm the effect of smoking in HNC and subtypes through big data analysis. All data used in this study originated from the Korean National Health Insurance Service database. We analyzed subjects who had undergone health check-ups in 2009 with follow-up until 2018 (n=10,585,852). We collected data on smoking and other variables that could affect the risk of HNC. The overall incidence of HNC was highest in current smokers (HR: 1.822, 95% CI: 1.729-1.920), followed by ex-smokers (HR: 1.242, 95% CI: 1.172-1.317). Laryngeal cancer, hypopharynx cancer, oral cancer, oropharyngeal cancer, and salivary gland cancer showed increasing incidence rates from ex-smokers to current smokers. Smoking duration and amount showed a dose-dependent relationship with the occurrence of HNC. However, the incidence of HNC did not increase significantly when smoking duration was less than 10 years, or when the smoking amount was less than 10 pack-years in ex-smokers. Smoking is associated with the risk of HNC. Smoking cessation before 10 years or 10 pack-years can prevent the development of HNC.
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Affiliation(s)
- Inn-Chul Nam
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of KoreaSeoul, Republic of Korea
| | - Jun-Ook Park
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of KoreaSeoul, Republic of Korea
| | - Choung-Soo Kim
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of KoreaSeoul, Republic of Korea
| | - Sung Joon Park
- Department of Otolaryngology-Head and Neck Surgery, Gwangmyeong Hospital, College of Medicine, Chung-Ang UniversitySeoul, Republic of Korea
| | - Dong-Hyun Lee
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of KoreaSeoul, Republic of Korea
| | - Hyun-Bum Kim
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of KoreaSeoul, Republic of Korea
| | - Kyungdo Han
- Department of Statistics and Actuarial Science, Soongsil UniversitySeoul, Republic of Korea
| | - Young-Hoon Joo
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, The Catholic University of KoreaSeoul, Republic of Korea
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Lee C, Lin J, Prokop A, Gopalakrishnan V, Hanna RN, Papa E, Freeman A, Patel S, Yu W, Huhn M, Sheikh AS, Tan K, Sellman BR, Cohen T, Mangion J, Khan FM, Gusev Y, Shameer K. StarGazer: A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit. Front Genet 2022; 13:868015. [PMID: 35711912 PMCID: PMC9197487 DOI: 10.3389/fgene.2022.868015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/29/2022] [Indexed: 01/26/2023] Open
Abstract
Target prioritization is essential for drug discovery and repositioning. Applying computational methods to analyze and process multi-omics data to find new drug targets is a practical approach for achieving this. Despite an increasing number of methods for generating datasets such as genomics, phenomics, and proteomics, attempts to integrate and mine such datasets remain limited in scope. Developing hybrid intelligence solutions that combine human intelligence in the scientific domain and disease biology with the ability to mine multiple databases simultaneously may help augment drug target discovery and identify novel drug-indication associations. We believe that integrating different data sources using a singular numerical scoring system in a hybrid intelligent framework could help to bridge these different omics layers and facilitate rapid drug target prioritization for studies in drug discovery, development or repositioning. Herein, we describe our prototype of the StarGazer pipeline which combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits, and is available via https://github.com/AstraZeneca/StarGazer.
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Affiliation(s)
- Chiyun Lee
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Junxia Lin
- Georgetown University, Washington, DC, United States
| | | | | | - Richard N. Hanna
- Early Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Eliseo Papa
- Research Data and Analytics, R&D IT, AstraZeneca, Cambridge, United Kingdom
| | - Adrian Freeman
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Saleha Patel
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Wen Yu
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Monika Huhn
- Biometrics and Information Sciences, BioPharmaceuticals R&D, AstraZeneca, Mölndal, Sweden
| | - Abdul-Saboor Sheikh
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Keith Tan
- Neuroscience, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Bret R. Sellman
- Discovery Microbiome, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Taylor Cohen
- Discovery Microbiome, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Jonathan Mangion
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Faisal M. Khan
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States
| | - Yuriy Gusev
- Georgetown University, Washington, DC, United States
| | - Khader Shameer
- Data Science and Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States,*Correspondence: Khader Shameer,
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Saadoun A, Schein A, Péan V, Legrand P, Aho Glélé LS, Bozorg Grayeli A. Frequency Fitting Optimization Using Evolutionary Algorithm in Cochlear Implant Users with Bimodal Binaural Hearing. Brain Sci 2022; 12:brainsci12020253. [PMID: 35204015 PMCID: PMC8870060 DOI: 10.3390/brainsci12020253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 02/04/2023] Open
Abstract
Optimizing hearing in patients with a unilateral cochlear implant (CI) and contralateral acoustic hearing is a challenge. Evolutionary algorithms (EA) can explore a large set of potential solutions in a stochastic manner to approach the optimum of a minimization problem. The objective of this study was to develop and evaluate an EA-based protocol to modify the default frequency settings of a MAP (fMAP) of the CI in patients with bimodal hearing. Methods: This monocentric prospective study included 27 adult CI users (with post-lingual deafness and contralateral functional hearing). A fitting program based on EA was developed to approach the best fMAP. Generated fMAPs were tested by speech recognition (word recognition score, WRS) in noise and free-field-like conditions. By combining these first fMAPs and adding some random changes, a total of 13 fMAPs over 3 generations were produced. Participants were evaluated before and 45 to 60 days after the fitting by WRS in noise and questionnaires on global sound quality and music perception in bimodal binaural conditions. Results: WRS in noise improved with the EA-based fitting in comparison to the default fMAP (41.67 ± 9.70% versus 64.63 ± 16.34%, respectively, p = 0.0001, signed-rank test). The global sound quality and music perception were also improved, as judged by ratings on questionnaires and scales. Finally, most patients chose to keep the new fitting definitively. Conclusions: By modifying the default fMAPs, the EA improved the speech discrimination in noise and the sound quality in bimodal binaural conditions.
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Affiliation(s)
- Alexis Saadoun
- Department of Otolaryngology—Head and Neck Surgery, Dijon University Hospital, 21000 Dijon, France; (A.S.); (A.S.)
| | - Antoine Schein
- Department of Otolaryngology—Head and Neck Surgery, Dijon University Hospital, 21000 Dijon, France; (A.S.); (A.S.)
| | - Vincent Péan
- Clinical Support Department, MED-EL, 75012 Paris, France;
| | - Pierrick Legrand
- Institute of Mathematics of Bordeaux, UMR CNRS 5251, ASTRAL Team, Inria Bordeaux Sud-Ouest, University of Bordeaux, 33405 Talence, France;
| | - Ludwig Serge Aho Glélé
- Department of Hospital Epidemiology and Infection Control, Dijon University Hospital, 21000 Dijon, France;
| | - Alexis Bozorg Grayeli
- Department of Otolaryngology—Head and Neck Surgery, Dijon University Hospital, 21000 Dijon, France; (A.S.); (A.S.)
- ImVia Research Laboratory, Bourgogne-Franche Comté University, 21000 Dijon, France
- Correspondence:
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Cheng S, Ma L, Lu H, Lei X, Shi Y. Evolutionary computation for solving search-based data analytics problems. Artif Intell Rev 2020. [DOI: 10.1007/s10462-020-09882-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Resteghini C, Trama A, Borgonovi E, Hosni H, Corrao G, Orlandi E, Calareso G, De Cecco L, Piazza C, Mainardi L, Licitra L. Big Data in Head and Neck Cancer. Curr Treat Options Oncol 2018; 19:62. [DOI: 10.1007/s11864-018-0585-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Inference of Biochemical S-Systems via Mixed-Variable Multiobjective Evolutionary Optimization. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:3020326. [PMID: 28607576 PMCID: PMC5457779 DOI: 10.1155/2017/3020326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 12/18/2022]
Abstract
Inference of the biochemical systems (BSs) via experimental data is important for understanding how biochemical components in vivo interact with each other. However, it is not a trivial task because BSs usually function with complex and nonlinear dynamics. As a popular ordinary equation (ODE) model, the S-System describes the dynamical properties of BSs by incorporating the power rule of biochemical reactions but behaves as a challenge because it has a lot of parameters to be confirmed. This work is dedicated to proposing a general method for inference of S-Systems by experimental data, using a biobjective optimization (BOO) model and a specially mixed-variable multiobjective evolutionary algorithm (mv-MOEA). Regarding that BSs are sparse in common sense, we introduce binary variables indicating network connections to eliminate the difficulty of threshold presetting and take data fitting error and the L0-norm as two objectives to be minimized in the BOO model. Then, a selection procedure that automatically runs tradeoff between two objectives is employed to choose final inference results from the obtained nondominated solutions of the mv-MOEA. Inference results of the investigated networks demonstrate that our method can identify their dynamical properties well, although the automatic selection procedure sometimes ignores some weak connections in BSs.
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An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria. mSystems 2016; 1:mSystems00028-15. [PMID: 27822535 PMCID: PMC5069768 DOI: 10.1128/msystems.00028-15] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 04/01/2016] [Indexed: 11/20/2022] Open
Abstract
Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of chemicals. The approach allowed us to identify new antibiotics and their associated biosynthetic pathways. Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting.
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Maansson M, Vynne NG, Klitgaard A, Nybo JL, Melchiorsen J, Nguyen DD, Sanchez LM, Ziemert N, Dorrestein PC, Andersen MR, Gram L. An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria. mSystems 2016. [PMID: 27822535 DOI: 10.1128/msystems.00038-00016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023] Open
Abstract
Microorganisms are a rich source of bioactives; however, chemical identification is a major bottleneck. Strategies that can prioritize the most prolific microbial strains and novel compounds are of great interest. Here, we present an integrated approach to evaluate the biosynthetic richness in bacteria and mine the associated chemical diversity. Thirteen strains closely related to Pseudoalteromonas luteoviolacea isolated from all over the Earth were analyzed using an untargeted metabolomics strategy, and metabolomic profiles were correlated with whole-genome sequences of the strains. We found considerable diversity: only 2% of the chemical features and 7% of the biosynthetic genes were common to all strains, while 30% of all features and 24% of the genes were unique to single strains. The list of chemical features was reduced to 50 discriminating features using a genetic algorithm and support vector machines. Features were dereplicated by tandem mass spectrometry (MS/MS) networking to identify molecular families of the same biosynthetic origin, and the associated pathways were probed using comparative genomics. Most of the discriminating features were related to antibacterial compounds, including the thiomarinols that were reported from P. luteoviolacea here for the first time. By comparative genomics, we identified the biosynthetic cluster responsible for the production of the antibiotic indolmycin, which could not be predicted with standard methods. In conclusion, we present an efficient, integrative strategy for elucidating the chemical richness of a given set of bacteria and link the chemistry to biosynthetic genes. IMPORTANCE We here combine chemical analysis and genomics to probe for new bioactive secondary metabolites based on their pattern of distribution within bacterial species. We demonstrate the usefulness of this combined approach in a group of marine Gram-negative bacteria closely related to Pseudoalteromonas luteoviolacea, which is a species known to produce a broad spectrum of chemicals. The approach allowed us to identify new antibiotics and their associated biosynthetic pathways. Combining chemical analysis and genetics is an efficient "mining" workflow for identifying diverse pharmaceutical candidates in a broad range of microorganisms and therefore of great use in bioprospecting.
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Affiliation(s)
- Maria Maansson
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Nikolaj G Vynne
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas Klitgaard
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jane L Nybo
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jette Melchiorsen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Don D Nguyen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
| | - Laura M Sanchez
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany; Collaborative Mass Spectrometry Innovation Center, University of California at San Diego, La Jolla, California, USA
| | - Nadine Ziemert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA; Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Pieter C Dorrestein
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA; Collaborative Mass Spectrometry Innovation Center, University of California at San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
| | - Mikael R Andersen
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lone Gram
- Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Toward a Literature-Driven Definition of Big Data in Healthcare. BIOMED RESEARCH INTERNATIONAL 2015; 2015:639021. [PMID: 26137488 PMCID: PMC4468280 DOI: 10.1155/2015/639021] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/04/2015] [Indexed: 11/17/2022]
Abstract
Objective. The aim of this study was to provide a definition of big data in healthcare. Methods. A systematic search of PubMed literature published until May 9, 2014, was conducted. We noted the number of statistical individuals (n) and the number of variables (p) for all papers describing a dataset. These papers were classified into fields of study. Characteristics attributed to big data by authors were also considered. Based on this analysis, a definition of big data was proposed. Results. A total of 196 papers were included. Big data can be defined as datasets with Log(n∗p) ≥ 7. Properties of big data are its great variety and high velocity. Big data raises challenges on veracity, on all aspects of the workflow, on extracting meaningful information, and on sharing information. Big data requires new computational methods that optimize data management. Related concepts are data reuse, false knowledge discovery, and privacy issues. Conclusion. Big data is defined by volume. Big data should not be confused with data reuse: data can be big without being reused for another purpose, for example, in omics. Inversely, data can be reused without being necessarily big, for example, secondary use of Electronic Medical Records (EMR) data.
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