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Binois Y, Renaudier M, Dumas F, Youssfi Y, Beganton F, Jost D, Lamhaut L, Marijon E, Jouven X, Cariou A, Bougouin W. Factors associated with circulatory death after out-of-hospital cardiac arrest: a population-based cluster analysis. Ann Intensive Care 2023; 13:49. [PMID: 37294400 DOI: 10.1186/s13613-023-01143-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
BACKGROUND Out-of-hospital cardiac arrest (OHCA) is a common cause of death. Early circulatory failure is the most common reason for death within the first 48 h. This study in intensive care unit (ICU) patients with OHCA was designed to identify and characterize clusters based on clinical features and to determine the frequency of death from refractory postresuscitation shock (RPRS) in each cluster. METHODS We retrospectively identified adults admitted alive to ICUs after OHCA in 2011-2018 and recorded in a prospective registry for the Paris region (France). We identified patient clusters by performing an unsupervised hierarchical cluster analysis (without mode of death among the variables) based on Utstein clinical and laboratory variables. For each cluster, we estimated the hazard ratio (HRs) for RPRS. RESULTS Of the 4445 included patients, 1468 (33%) were discharged alive from the ICU and 2977 (67%) died in the ICU. We identified four clusters: initial shockable rhythm with short low-flow time (cluster 1), initial non-shockable rhythm with usual absence of ST-segment elevation (cluster 2), initial non-shockable rhythm with long no-flow time (cluster 3), and long low-flow time with high epinephrine dose (cluster 4). RPRS was significantly associated with this last cluster (HR, 5.51; 95% confidence interval 4.51-6.74). CONCLUSIONS We identified patient clusters based on Utstein criteria, and one cluster was strongly associated with RPRS. This result may help to make decisions about using specific treatments after OHCA.
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Affiliation(s)
- Yannick Binois
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
| | - Marie Renaudier
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
| | - Florence Dumas
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
- Emergency Department, AP-HP, Cochin-Hotel-Dieu Hospital, 75014, Paris, France
| | - Younès Youssfi
- Paris Sudden Death Expertise Center, 75015, Paris, France
- Center for Research in Economics and Statistics, 91120, Palaiseau, France
| | - Frankie Beganton
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
| | - Daniel Jost
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
- BSPP (Paris Fire-Brigade Emergency-Medicine Department), 1 Place Jules Renard, 75017, Paris, France
| | - Lionel Lamhaut
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
- Intensive Care Unit and SAMU 75, Necker Enfants-Malades Hospital, 75014, Paris, France
| | - Eloi Marijon
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
- Cardiology Department, AP-HP, European Georges Pompidou Hospital, 75015, Paris, France
| | - Xavier Jouven
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
- Cardiology Department, AP-HP, European Georges Pompidou Hospital, 75015, Paris, France
| | - Alain Cariou
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France
- Medical Intensive Care Unit, AP-HP, Cochin Hospital, 75014, Paris, France
- Paris Sudden Death Expertise Center, 75015, Paris, France
- AfterROSC network, Paris, France
| | - Wulfran Bougouin
- Université de Paris, INSERM U970, Paris Cardiovascular Research Center (PARCC), European Georges Pompidou Hospital, 75015, Paris, France.
- Paris Sudden Death Expertise Center, 75015, Paris, France.
- Medical Intensive Care Unit, Ramsay Générale de Santé, Hôpital Privé Jacques Cartier, 6 Avenue du Noyer Lambert, 91300, Massy, France.
- AfterROSC network, Paris, France.
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2
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An ensemble algorithm using quantum evolutionary optimization of weighted type-II fuzzy system and staged Pegasos Quantum Support Vector Classifier with multi-criteria decision making system for diagnosis and grading of breast cancer. Soft comput 2023. [DOI: 10.1007/s00500-023-07939-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2023]
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3
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Bhandari N, Walambe R, Kotecha K, Khare SP. A comprehensive survey on computational learning methods for analysis of gene expression data. Front Mol Biosci 2022; 9:907150. [PMID: 36458095 PMCID: PMC9706412 DOI: 10.3389/fmolb.2022.907150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/28/2022] [Indexed: 09/19/2023] Open
Abstract
Computational analysis methods including machine learning have a significant impact in the fields of genomics and medicine. High-throughput gene expression analysis methods such as microarray technology and RNA sequencing produce enormous amounts of data. Traditionally, statistical methods are used for comparative analysis of gene expression data. However, more complex analysis for classification of sample observations, or discovery of feature genes requires sophisticated computational approaches. In this review, we compile various statistical and computational tools used in analysis of expression microarray data. Even though the methods are discussed in the context of expression microarrays, they can also be applied for the analysis of RNA sequencing and quantitative proteomics datasets. We discuss the types of missing values, and the methods and approaches usually employed in their imputation. We also discuss methods of data normalization, feature selection, and feature extraction. Lastly, methods of classification and class discovery along with their evaluation parameters are described in detail. We believe that this detailed review will help the users to select appropriate methods for preprocessing and analysis of their data based on the expected outcome.
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Affiliation(s)
- Nikita Bhandari
- Computer Science Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, India
| | - Rahee Walambe
- Electronics and Telecommunication Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, India
- Symbiosis Center for Applied AI (SCAAI), Symbiosis International (Deemed University), Pune, India
| | - Ketan Kotecha
- Computer Science Department, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, India
- Symbiosis Center for Applied AI (SCAAI), Symbiosis International (Deemed University), Pune, India
| | - Satyajeet P. Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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4
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An ensemble algorithm integrating consensus-clustering with feature weighting based ranking and probabilistic fuzzy logic-multilayer perceptron classifier for diagnosis and staging of breast cancer using heterogeneous datasets. APPL INTELL 2022. [DOI: 10.1007/s10489-022-04157-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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5
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Lidströmer N, Davids J, Sood HS, Ashrafian H. AIM in Primary Healthcare. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Flores AM, Schuler A, Eberhard AV, Olin JW, Cooke JP, Leeper NJ, Shah NH, Ross EG. Unsupervised Learning for Automated Detection of Coronary Artery Disease Subgroups. J Am Heart Assoc 2021; 10:e021976. [PMID: 34845917 PMCID: PMC9075403 DOI: 10.1161/jaha.121.021976] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/14/2021] [Indexed: 12/24/2022]
Abstract
Background The promise of precision population health includes the ability to use robust patient data to tailor prevention and care to specific groups. Advanced analytics may allow for automated detection of clinically informative subgroups that account for clinical, genetic, and environmental variability. This study sought to evaluate whether unsupervised machine learning approaches could interpret heterogeneous and missing clinical data to discover clinically important coronary artery disease subgroups. Methods and Results The Genetic Determinants of Peripheral Arterial Disease study is a prospective cohort that includes individuals with newly diagnosed and/or symptomatic coronary artery disease. We applied generalized low rank modeling and K-means cluster analysis using 155 phenotypic and genetic variables from 1329 participants. Cox proportional hazard models were used to examine associations between clusters and major adverse cardiovascular and cerebrovascular events and all-cause mortality. We then compared performance of risk stratification based on clusters and the American College of Cardiology/American Heart Association pooled cohort equations. Unsupervised analysis identified 4 phenotypically and prognostically distinct clusters. All-cause mortality was highest in cluster 1 (oldest/most comorbid; 26%), whereas major adverse cardiovascular and cerebrovascular event rates were highest in cluster 2 (youngest/multiethnic; 41%). Cluster 4 (middle-aged/healthiest behaviors) experienced more incident major adverse cardiovascular and cerebrovascular events (30%) than cluster 3 (middle-aged/lowest medication adherence; 23%), despite apparently similar risk factor and lifestyle profiles. In comparison with the pooled cohort equations, cluster membership was more informative for risk assessment of myocardial infarction, stroke, and mortality. Conclusions Unsupervised clustering identified 4 unique coronary artery disease subgroups with distinct clinical trajectories. Flexible unsupervised machine learning algorithms offer the ability to meaningfully process heterogeneous patient data and provide sharper insights into disease characterization and risk assessment. Registration URL: https://www.clinicaltrials.gov; Unique identifier: NCT00380185.
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Affiliation(s)
- Alyssa M. Flores
- Division of Vascular SurgeryDepartment of SurgeryStanford University School of MedicineStanfordCA
| | - Alejandro Schuler
- Center for Biomedical Informatics ResearchStanford UniversityStanfordCA
| | - Anne Verena Eberhard
- Division of Vascular SurgeryDepartment of SurgeryStanford University School of MedicineStanfordCA
| | - Jeffrey W. Olin
- Zena and Michael A. Wiener Cardiovascular InstituteMarie‐Josée and Henry R. Kravis Center for Cardiovascular HealthIcahn School of Medicine at Mount SinaiNew YorkNY
| | - John P. Cooke
- Department of Cardiovascular SciencesHouston Methodist Research InstituteHoustonTX
| | - Nicholas J. Leeper
- Division of Vascular SurgeryDepartment of SurgeryStanford University School of MedicineStanfordCA
- Division of Cardiovascular MedicineDepartment of MedicineStanford University School of MedicineStanfordCA
- Stanford Cardiovascular InstituteStanfordCA
| | - Nigam H. Shah
- Center for Biomedical Informatics ResearchStanford UniversityStanfordCA
| | - Elsie G. Ross
- Division of Vascular SurgeryDepartment of SurgeryStanford University School of MedicineStanfordCA
- Center for Biomedical Informatics ResearchStanford UniversityStanfordCA
- Stanford Cardiovascular InstituteStanfordCA
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7
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Deraz O, Rangé H, Boutouyrie P, Chatzopoulou E, Asselin A, Guibout C, Van Sloten T, Bougouin W, Andrieu M, Vedié B, Thomas F, Danchin N, Jouven X, Bouchard P, Empana JP. Oral Condition and Incident Coronary Heart Disease: A Clustering Analysis. J Dent Res 2021; 101:526-533. [PMID: 34875909 DOI: 10.1177/00220345211052507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Poor oral health has been linked to coronary heart disease (CHD). Clustering clinical oral conditions routinely recorded in adults may identify their CHD risk profile. Participants from the Paris Prospective Study 3 received, between 2008 and 2012, a baseline routine full-mouth clinical examination and an extensive physical examination and were thereafter followed up every 2 y until September 2020. Three axes defined oral health conditions: 1) healthy, missing, filled, and decayed teeth; 2) masticatory capacity denoted by functional masticatory units; and 3) gingival inflammation and dental plaque. Hierarchical cluster analysis was performed with multivariate Cox proportional hazards regression models and adjusted for age, sex, smoking, body mass index, education, deprivation (EPICES score; Evaluation of Deprivation and Inequalities in Health Examination Centres), hypertension, type 2 diabetes, LDL and HDL serum cholesterol (low- and high-density lipoprotein), triglycerides, lipid-lowering medications, NT-proBNP and IL-6 serum level. A sample of 5,294 participants (age, 50 to 75 y; 37.10% women) were included in the study. Cluster analysis identified 3,688 (69.66%) participants with optimal oral health and preserved masticatory capacity (cluster 1), 1,356 (25.61%) with moderate oral health and moderately impaired masticatory capacity (cluster 2), and 250 (4.72%) with poor oral health and severely impaired masticatory capacity (cluster 3). After a median follow-up of 8.32 y (interquartile range, 8.00 to 10.05), 128 nonfatal incident CHD events occurred. As compared with cluster 1, the risk of CHD progressively increased from cluster 2 (hazard ratio, 1.45; 95% CI, 0.98 to 2.15) to cluster 3 (hazard ratio, 2.47; 95% CI, 1.34 to 4.57; P < 0.05 for trend). To conclude, middle-aged individuals with poor oral health and severely impaired masticatory capacity have more than twice the risk of incident CHD than those with optimal oral health and preserved masticatory capacity (ClinicalTrials.gov NCT00741728).
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Affiliation(s)
- O Deraz
- Université de Paris, INSERM U970, Integrative Epidemiology of Cardiovascular Disease, Paris, France.,Université de Paris, UFR of Odontology, Department of Periodontology, Paris, France
| | - H Rangé
- Université de Paris, UFR of Odontology, Department of Periodontology, Paris, France.,AP-HP, Rothschild Hospital, Department of Odontology, Paris, France.,Université de Paris, URP 2496, Paris, France
| | - P Boutouyrie
- Université de Paris, INSERM U970, Cellular, Molecular and Pathophysiological Mechanisms of Heart Failure, Paris, France
| | - E Chatzopoulou
- Université de Paris, UFR of Odontology, Department of Periodontology, Paris, France.,AP-HP, Rothschild Hospital, Department of Odontology, Paris, France.,Université de Paris, URP 2496, Paris, France
| | - A Asselin
- Université de Paris, INSERM U970, Integrative Epidemiology of Cardiovascular Disease, Paris, France
| | - C Guibout
- Université de Paris, INSERM U970, Integrative Epidemiology of Cardiovascular Disease, Paris, France
| | - T Van Sloten
- Maastricht University Medical Centre, Cardiovascular Research Institute Maastricht and Department of Internal Medicine, Maastricht, The Netherlands
| | - W Bougouin
- Université de Paris, INSERM U970, Integrative Epidemiology of Cardiovascular Disease, Paris, France
| | - M Andrieu
- Université de Paris, Cochin Institute, Platform CYBIO, INSERM U1016, Paris, France
| | - B Vedié
- AP-HP, Georges Pompidou European Hospital, Department of Biochemistry, Tissue and Blood Samples Biobank, Paris, France
| | - F Thomas
- Preventive and Clinical Investigation Center, Paris, France
| | - N Danchin
- Preventive and Clinical Investigation Center, Paris, France
| | - X Jouven
- Université de Paris, INSERM U970, Integrative Epidemiology of Cardiovascular Disease, Paris, France.,AP-HP, Georges Pompidou European Hospital, Department of Cardiology, Paris, France
| | - P Bouchard
- Université de Paris, UFR of Odontology, Department of Periodontology, Paris, France.,AP-HP, Rothschild Hospital, Department of Odontology, Paris, France.,Université de Paris, URP 2496, Paris, France
| | - J P Empana
- Université de Paris, INSERM U970, Integrative Epidemiology of Cardiovascular Disease, Paris, France
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8
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9
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Szurman-Zubrzycka M, Chwiałkowska K, Niemira M, Kwaśniewski M, Nawrot M, Gajecka M, Larsen PB, Szarejko I. Aluminum or Low pH - Which Is the Bigger Enemy of Barley? Transcriptome Analysis of Barley Root Meristem Under Al and Low pH Stress. Front Genet 2021; 12:675260. [PMID: 34220949 PMCID: PMC8244595 DOI: 10.3389/fgene.2021.675260] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/13/2021] [Indexed: 11/13/2022] Open
Abstract
Aluminum (Al) toxicity is considered to be the most harmful abiotic stress in acidic soils that today comprise more than 50% of the world’s arable lands. Barley belongs to a group of crops that are most sensitive to Al in low pH soils. We present the RNA-seq analysis of root meristems of barley seedlings grown in hydroponics at optimal pH (6.0), low pH (4.0), and low pH with Al (10 μM of bioavailable Al3+ ions). Two independent experiments were conducted: with short-term (24 h) and long-term (7 days) Al treatment. In the short-term experiment, more genes were differentially expressed (DEGs) between root meristems grown at pH = 6.0 and pH = 4.0, than between those grown at pH = 4.0 with and without Al treatment. The genes upregulated by low pH were associated mainly with response to oxidative stress, cell wall organization, and iron ion binding. Among genes upregulated by Al, overrepresented were those related to response to stress condition and calcium ion binding. In the long-term experiment, the number of DEGs between hydroponics at pH = 4.0 and 6.0 were lower than in the short-term experiment, which suggests that plants partially adapted to the low pH. Interestingly, 7 days Al treatment caused massive changes in the transcriptome profile. Over 4,000 genes were upregulated and almost 2,000 genes were downregulated by long-term Al stress. These DEGs were related to stress response, cell wall development and metal ion transport. Based on our results we can assume that both, Al3+ ions and low pH are harmful to barley plants. Additionally, we phenotyped the root system of barley seedlings grown in the same hydroponic conditions for 7 days at pH = 6.0, pH = 4.0, and pH = 4.0 with Al. The results correspond to transcriptomic data and show that low pH itself is a stress factor that causes a significant reduction of root growth and the addition of aluminum further increases this reduction. It should be noted that in acidic arable lands, plants are exposed simultaneously to both of these stresses. The presented transcriptome analysis may help to find potential targets for breeding barley plants that are more tolerant to such conditions.
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Affiliation(s)
- Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Nawrot
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Monika Gajecka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paul B Larsen
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Lidströmer N, Davids J, Sood HS, Ashrafian H. AIM in Primary Healthcare. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Abstract
The delineation of precipitation regions is to identify homogeneous zones in which the characteristics of the process are statistically similar. The regionalization process has three main components: (i) delineation of regions using clustering algorithms, (ii) determining the optimal number of regions using cluster validity indices (CVIs), and (iii) validation of regions for homogeneity using L-moments ratio test. The identification of the optimal number of clusters will significantly affect the homogeneity of the regions. The objective of this study is to investigate the performance of the various CVIs in identifying the optimal number of clusters, which maximizes the homogeneity of the precipitation regions. The k-means clustering algorithm is adopted to delineate the regions using location-based attributes for two large areas from Canada, namely, the Prairies and the Great Lakes-St Lawrence lowlands (GL-SL) region. The seasonal precipitation data for 55 years (1951–2005) is derived using high-resolution ANUSPLIN gridded point data for Canada. The results indicate that the optimal number of clusters and the regional homogeneity depends on the CVI adopted. Among 42 cluster indices considered, 15 of them outperform in identifying the homogeneous precipitation regions. The Dunn, D e t _ r a t i o and Trace( W − 1 B ) indices found to be the best for all seasons in both the regions.
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12
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Hambarde P, Talbar SN, Sable N, Mahajan A, Chavan SS, Thakur M. Radiomics for peripheral zone and intra-prostatic urethra segmentation in MR imaging. Biomed Signal Process Control 2019. [DOI: 10.1016/j.bspc.2019.01.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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13
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Noureen N, Fazal S, Qadir MA, Afzal MT. HCVS: Pinpointing Chromatin States Through Hierarchical Clustering and Visualization Scheme. Curr Bioinform 2019. [DOI: 10.2174/1574893613666180402141107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Specific combinations of Histone Modifications (HMs) contributing towards
histone code hypothesis lead to various biological functions. HMs combinations have been utilized by
various studies to divide the genome into different regions. These study regions have been classified as
chromatin states. Mostly Hidden Markov Model (HMM) based techniques have been utilized for this
purpose. In case of chromatin studies, data from Next Generation Sequencing (NGS) platforms is being
used. Chromatin states based on histone modification combinatorics are annotated by mapping them to
functional regions of the genome. The number of states being predicted so far by the HMM tools have
been justified biologically till now.
Objective:
The present study aimed at providing a computational scheme to identify the underlying
hidden states in the data under consideration.
</P><P>
Methods: We proposed a computational scheme HCVS based on hierarchical clustering and
visualization strategy in order to achieve the objective of study.
Results:
We tested our proposed scheme on a real data set of nine cell types comprising of nine
chromatin marks. The approach successfully identified the state numbers for various possibilities. The
results have been compared with one of the existing models as well which showed quite good
correlation.
Conclusion:
The HCVS model not only helps in deciding the optimal state numbers for a particular data
but it also justifies the results biologically thereby correlating the computational and biological aspects.
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Affiliation(s)
- Nighat Noureen
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Sahar Fazal
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Abdul Qadir
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Tanvir Afzal
- Department of Computer Science, Faculty of Computing, Capital University of Science and Technology, Islamabad, Pakistan
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Dalton LA, Benalcázar ME, Dougherty ER. Optimal clustering under uncertainty. PLoS One 2018; 13:e0204627. [PMID: 30278063 PMCID: PMC6168142 DOI: 10.1371/journal.pone.0204627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/11/2018] [Indexed: 11/18/2022] Open
Abstract
Classical clustering algorithms typically either lack an underlying probability framework to make them predictive or focus on parameter estimation rather than defining and minimizing a notion of error. Recent work addresses these issues by developing a probabilistic framework based on the theory of random labeled point processes and characterizing a Bayes clusterer that minimizes the number of misclustered points. The Bayes clusterer is analogous to the Bayes classifier. Whereas determining a Bayes classifier requires full knowledge of the feature-label distribution, deriving a Bayes clusterer requires full knowledge of the point process. When uncertain of the point process, one would like to find a robust clusterer that is optimal over the uncertainty, just as one may find optimal robust classifiers with uncertain feature-label distributions. Herein, we derive an optimal robust clusterer by first finding an effective random point process that incorporates all randomness within its own probabilistic structure and from which a Bayes clusterer can be derived that provides an optimal robust clusterer relative to the uncertainty. This is analogous to the use of effective class-conditional distributions in robust classification. After evaluating the performance of robust clusterers in synthetic mixtures of Gaussians models, we apply the framework to granular imaging, where we make use of the asymptotic granulometric moment theory for granular images to relate robust clustering theory to the application.
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Affiliation(s)
- Lori A. Dalton
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, United States of America
- * E-mail:
| | - Marco E. Benalcázar
- Departamento de Informática y Ciencias de la Computación, Facultad de Ingeniería de Sistemas, Escuela Politécnica Nacional, Quito, Ecuador
| | - Edward R. Dougherty
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, United States of America
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15
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Group communication analysis: A computational linguistics approach for detecting sociocognitive roles in multiparty interactions. Behav Res Methods 2018; 51:1007-1041. [DOI: 10.3758/s13428-018-1102-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Wielek T, Lechinger J, Wislowska M, Blume C, Ott P, Wegenkittl S, del Giudice R, Heib DPJ, Mayer HA, Laureys S, Pichler G, Schabus M. Sleep in patients with disorders of consciousness characterized by means of machine learning. PLoS One 2018; 13:e0190458. [PMID: 29293607 PMCID: PMC5749793 DOI: 10.1371/journal.pone.0190458] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022] Open
Abstract
Sleep has been proposed to indicate preserved residual brain functioning in patients suffering from disorders of consciousness (DOC) after awakening from coma. However, a reliable characterization of sleep patterns in this clinical population continues to be challenging given severely altered brain oscillations, frequent and extended artifacts in clinical recordings and the absence of established staging criteria. In the present study, we try to address these issues and investigate the usefulness of a multivariate machine learning technique based on permutation entropy, a complexity measure. Specifically, we used long-term polysomnography (PSG), along with video recordings in day and night periods in a sample of 23 DOC; 12 patients were diagnosed as Unresponsive Wakefulness Syndrome (UWS) and 11 were diagnosed as Minimally Conscious State (MCS). Eight hour PSG recordings of healthy sleepers (N = 26) were additionally used for training and setting parameters of supervised and unsupervised model, respectively. In DOC, the supervised classification (wake, N1, N2, N3 or REM) was validated using simultaneous videos which identified periods with prolonged eye opening or eye closure.The supervised classification revealed that out of the 23 subjects, 11 patients (5 MCS and 6 UWS) yielded highly accurate classification with an average F1-score of 0.87 representing high overlap between the classifier predicting sleep (i.e. one of the 4 sleep stages) and closed eyes. Furthermore, the unsupervised approach revealed a more complex pattern of sleep-wake stages during the night period in the MCS group, as evidenced by the presence of several distinct clusters. In contrast, in UWS patients no such clustering was found. Altogether, we present a novel data-driven method, based on machine learning that can be used to gain new and unambiguous insights into sleep organization and residual brain functioning of patients with DOC.
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Affiliation(s)
- Tomasz Wielek
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
| | - Julia Lechinger
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
| | - Malgorzata Wislowska
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
| | - Christine Blume
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
| | - Peter Ott
- ITS Informationstechnik & System-Management, Salzburg University of Applied Sciences, Salzburg, Austria
| | - Stefan Wegenkittl
- ITS Informationstechnik & System-Management, Salzburg University of Applied Sciences, Salzburg, Austria
| | - Renata del Giudice
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
| | - Dominik P. J. Heib
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
| | - Helmut A. Mayer
- Department of Computer Sciences, University of Salzburg, Salzburg, Austria
| | - Steven Laureys
- Coma Science Group, Cyclotron Research Centre and Neurology Department, University and University Hospital of Liège, Liège, Belgium
| | - Gerald Pichler
- Apallic Care Unit, Neurological Division, Albert Schweitzer Hospital Graz, Graz, Austria
| | - Manuel Schabus
- Laboratory for Sleep, Cognition and Consciousness, & Centre for Cognitive Neuroscience (CCNS), University of Salzburg, Salzburg, Austria
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Pagnuco IA, Pastore JI, Abras G, Brun M, Ballarin VL. Analysis of genetic association using hierarchical clustering and cluster validation indices. Genomics 2017; 109:438-445. [PMID: 28694080 DOI: 10.1016/j.ygeno.2017.06.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/24/2017] [Accepted: 06/28/2017] [Indexed: 11/28/2022]
Abstract
It is usually assumed that co-expressed genes suggest co-regulation in the underlying regulatory network. Determining sets of co-expressed genes is an important task, based on some criteria of similarity. This task is usually performed by clustering algorithms, where the genes are clustered into meaningful groups based on their expression values in a set of experiment. In this work, we propose a method to find sets of co-expressed genes, based on cluster validation indices as a measure of similarity for individual gene groups, and a combination of variants of hierarchical clustering to generate the candidate groups. We evaluated its ability to retrieve significant sets on simulated correlated and real genomics data, where the performance is measured based on its detection ability of co-regulated sets against a full search. Additionally, we analyzed the quality of the best ranked groups using an online bioinformatics tool that provides network information for the selected genes.
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Affiliation(s)
- Inti A Pagnuco
- Digital Image Processing Lab., ICyTE, UNMdP, Argentina; Department of Mathematics, School of Engineering, UNMdP, Argentina; CONICET, Argentina.
| | - Juan I Pastore
- Digital Image Processing Lab., ICyTE, UNMdP, Argentina; Department of Mathematics, School of Engineering, UNMdP, Argentina; CONICET, Argentina
| | - Guillermo Abras
- Digital Image Processing Lab., ICyTE, UNMdP, Argentina; Department of Mathematics, School of Engineering, UNMdP, Argentina
| | - Marcel Brun
- Digital Image Processing Lab., ICyTE, UNMdP, Argentina; Department of Mathematics, School of Engineering, UNMdP, Argentina.
| | - Virginia L Ballarin
- Digital Image Processing Lab., ICyTE, UNMdP, Argentina; Department of Mathematics, School of Engineering, UNMdP, Argentina
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18
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Shankar-Hari M, Rubenfeld GD. The use of enrichment to reduce statistically indeterminate or negative trials in critical care. Anaesthesia 2017; 72:560-565. [PMID: 28317096 DOI: 10.1111/anae.13870] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- M Shankar-Hari
- Department of Intensive Care Medicine, Guy's and St Thomas' NHS Foundation Trust, London, UK.,Division of Asthma, Allergy and Lung Biology, Kings College, London, UK
| | - G D Rubenfeld
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Chief, Program in Trauma, Emergency and Critical Care, Sunnybrook Health Sciences Center, Toronto, Canada
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19
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Bruse JL, Zuluaga MA, Khushnood A, McLeod K, Ntsinjana HN, Hsia TY, Sermesant M, Pennec X, Taylor AM, Schievano S. Detecting Clinically Meaningful Shape Clusters in Medical Image Data: Metrics Analysis for Hierarchical Clustering Applied to Healthy and Pathological Aortic Arches. IEEE Trans Biomed Eng 2017; 64:2373-2383. [PMID: 28221991 DOI: 10.1109/tbme.2017.2655364] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Today's growing medical image databases call for novel processing tools to structure the bulk of data and extract clinically relevant information. Unsupervised hierarchical clustering may reveal clusters within anatomical shape data of patient populations as required for modern precision medicine strategies. Few studies have applied hierarchical clustering techniques to three-dimensional patient shape data and results depend heavily on the chosen clustering distance metrics and linkage functions. In this study, we sought to assess clustering classification performance of various distance/linkage combinations and of different types of input data to obtain clinically meaningful shape clusters. METHODS We present a processing pipeline combining automatic segmentation, statistical shape modeling, and agglomerative hierarchical clustering to automatically subdivide a set of 60 aortic arch anatomical models into healthy controls, two groups affected by congenital heart disease, and their respective subgroups as defined by clinical diagnosis. Results were compared with traditional morphometrics and principal component analysis of shape features. RESULTS Our pipeline achieved automatic division of input shape data according to primary clinical diagnosis with high F-score (0.902 ± 0.042) and Matthews correlation coefficient (0.851 ± 0.064) using the correlation/weighted distance/linkage combination. Meaningful subgroups within the three patient groups were obtained and benchmark scores for automatic segmentation and classification performance are reported. CONCLUSION Clustering results vary depending on the distance/linkage combination used to divide the data. Yet, clinically relevant shape clusters and subgroups could be found with high specificity and low misclassification rates. SIGNIFICANCE Detecting disease-specific clusters within medical image data could improve image-based risk assessment, treatment planning, and medical device development in complex disease.
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20
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Jaeger PA, Lucin KM, Britschgi M, Vardarajan B, Huang RP, Kirby ED, Abbey R, Boeve BF, Boxer AL, Farrer LA, Finch N, Graff-Radford NR, Head E, Hofree M, Huang R, Johns H, Karydas A, Knopman DS, Loboda A, Masliah E, Narasimhan R, Petersen RC, Podtelezhnikov A, Pradhan S, Rademakers R, Sun CH, Younkin SG, Miller BL, Ideker T, Wyss-Coray T. Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. Mol Neurodegener 2016; 11:31. [PMID: 27112350 PMCID: PMC4845325 DOI: 10.1186/s13024-016-0095-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/08/2016] [Indexed: 12/17/2022] Open
Abstract
Background Biological pathways that significantly contribute to sporadic Alzheimer’s disease are largely unknown and cannot be observed directly. Cognitive symptoms appear only decades after the molecular disease onset, further complicating analyses. As a consequence, molecular research is often restricted to late-stage post-mortem studies of brain tissue. However, the disease process is expected to trigger numerous cellular signaling pathways and modulate the local and systemic environment, and resulting changes in secreted signaling molecules carry information about otherwise inaccessible pathological processes. Results To access this information we probed relative levels of close to 600 secreted signaling proteins from patients’ blood samples using antibody microarrays and mapped disease-specific molecular networks. Using these networks as seeds we then employed independent genome and transcriptome data sets to corroborate potential pathogenic pathways. Conclusions We identified Growth-Differentiation Factor (GDF) signaling as a novel Alzheimer’s disease-relevant pathway supported by in vivo and in vitro follow-up experiments, demonstrating the existence of a highly informative link between cellular pathology and changes in circulatory signaling proteins. Electronic supplementary material The online version of this article (doi:10.1186/s13024-016-0095-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Philipp A Jaeger
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany. .,Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Kurt M Lucin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Present address: Biology Department, Eastern Connecticut State University, Willimantic, CT, USA
| | - Markus Britschgi
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Present address: Roche Pharma Research and Early Development, NORD DTA, Roche Innovation, Center Basel, Basel, Switzerland
| | - Badri Vardarajan
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine, Boston, MA, USA
| | - Ruo-Pan Huang
- RayBiotech, Guangzhou, China.,RayBiotech, Norcrosse, GA, USA
| | - Elizabeth D Kirby
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachelle Abbey
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Adam L Boxer
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University Schools of Medicine, Boston, MA, USA.,Departments of Neurology, Ophthalmology, Genetics and Genomics, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - NiCole Finch
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | | | - Elizabeth Head
- Departments of Pharmacology and Nutritional Sciences and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Matan Hofree
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Ruochun Huang
- RayBiotech, Guangzhou, China.,RayBiotech, Norcrosse, GA, USA
| | - Hudson Johns
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Karydas
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | | | - Andrey Loboda
- Genetics and Pharmacogenomics, Merck Research Laboratories, West Point, PA, USA
| | - Eliezer Masliah
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Ramya Narasimhan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Suraj Pradhan
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Chung-Huan Sun
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Bruce L Miller
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Trey Ideker
- Departments of Bioengineering and Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Tissue Regeneration, Repair and Restoration, VA Palo Alto Health Care System, Palo Alto, CA, USA.
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Fang Y. Compound annotation with real time cellular activity profiles to improve drug discovery. Expert Opin Drug Discov 2016; 11:269-80. [PMID: 26787137 DOI: 10.1517/17460441.2016.1143460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION In the past decade, a range of innovative strategies have been developed to improve the productivity of pharmaceutical research and development. In particular, compound annotation, combined with informatics, has provided unprecedented opportunities for drug discovery. AREAS COVERED In this review, a literature search from 2000 to 2015 was conducted to provide an overview of the compound annotation approaches currently used in drug discovery. Based on this, a framework related to a compound annotation approach using real-time cellular activity profiles for probe, drug, and biology discovery is proposed. EXPERT OPINION Compound annotation with chemical structure, drug-like properties, bioactivities, genome-wide effects, clinical phenotypes, and textural abstracts has received significant attention in early drug discovery. However, these annotations are mostly associated with endpoint results. Advances in assay techniques have made it possible to obtain real-time cellular activity profiles of drug molecules under different phenotypes, so it is possible to generate compound annotation with real-time cellular activity profiles. Combining compound annotation with informatics, such as similarity analysis, presents a good opportunity to improve the rate of discovery of novel drugs and probes, and enhance our understanding of the underlying biology.
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Affiliation(s)
- Ye Fang
- a Biochemical Technologies, Science and Technology Division , Corning Incorporated , Corning , NY , USA
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22
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Al-Najdi A, Pasquier N, Precioso F. Frequent Closed Patterns Based Multiple Consensus Clustering. ARTIFICIAL INTELLIGENCE AND SOFT COMPUTING 2016. [DOI: 10.1007/978-3-319-39384-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Linking Genes to Cardiovascular Diseases: Gene Action and Gene-Environment Interactions. J Cardiovasc Transl Res 2015; 8:506-27. [PMID: 26545598 DOI: 10.1007/s12265-015-9658-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/08/2015] [Indexed: 01/22/2023]
Abstract
A unique myocardial characteristic is its ability to grow/remodel in order to adapt; this is determined partly by genes and partly by the environment and the milieu intérieur. In the "post-genomic" era, a need is emerging to elucidate the physiologic functions of myocardial genes, as well as potential adaptive and maladaptive modulations induced by environmental/epigenetic factors. Genome sequencing and analysis advances have become exponential lately, with escalation of our knowledge concerning sometimes controversial genetic underpinnings of cardiovascular diseases. Current technologies can identify candidate genes variously involved in diverse normal/abnormal morphomechanical phenotypes, and offer insights into multiple genetic factors implicated in complex cardiovascular syndromes. The expression profiles of thousands of genes are regularly ascertained under diverse conditions. Global analyses of gene expression levels are useful for cataloging genes and correlated phenotypes, and for elucidating the role of genes in maladies. Comparative expression of gene networks coupled to complex disorders can contribute insights as to how "modifier genes" influence the expressed phenotypes. Increasingly, a more comprehensive and detailed systematic understanding of genetic abnormalities underlying, for example, various genetic cardiomyopathies is emerging. Implementing genomic findings in cardiology practice may well lead directly to better diagnosing and therapeutics. There is currently evolving a strong appreciation for the value of studying gene anomalies, and doing so in a non-disjointed, cohesive manner. However, it is challenging for many-practitioners and investigators-to comprehend, interpret, and utilize the clinically increasingly accessible and affordable cardiovascular genomics studies. This survey addresses the need for fundamental understanding in this vital area.
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Reeb PD, Bramardi SJ, Steibel JP. Assessing Dissimilarity Measures for Sample-Based Hierarchical Clustering of RNA Sequencing Data Using Plasmode Datasets. PLoS One 2015; 10:e0132310. [PMID: 26162080 PMCID: PMC4498680 DOI: 10.1371/journal.pone.0132310] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 06/11/2015] [Indexed: 01/03/2023] Open
Abstract
Sample- and gene- based hierarchical cluster analyses have been widely adopted as tools for exploring gene expression data in high-throughput experiments. Gene expression values (read counts) generated by RNA sequencing technology (RNA-seq) are discrete variables with special statistical properties, such as over-dispersion and right-skewness. Additionally, read counts are subject to technology artifacts as differences in sequencing depth. This possesses a challenge to finding distance measures suitable for hierarchical clustering. Normalization and transformation procedures have been proposed to favor the use of Euclidean and correlation based distances. Additionally, novel model-based dissimilarities that account for RNA-seq data characteristics have also been proposed. Adequacy of dissimilarity measures has been assessed using parametric simulations or exemplar datasets that may limit the scope of the conclusions. Here, we propose the simulation of realistic conditions through creation of plasmode datasets, to assess the adequacy of dissimilarity measures for sample-based hierarchical clustering of RNA-seq data. Consistent results were obtained using plasmode datasets based on RNA-seq experiments conducted under widely different conditions. Dissimilarity measures based on Euclidean distance that only considered data normalization or data standardization were not reliable to represent the expected hierarchical structure. Conversely, using either a Poisson-based dissimilarity or a rank correlation based dissimilarity or an appropriate data transformation, resulted in dendrograms that resemble the expected hierarchical structure. Plasmode datasets can be generated for a wide range of scenarios upon which dissimilarity measures can be evaluated for sample-based hierarchical clustering analysis. We showed different ways of generating such plasmodes and applied them to the problem of selecting a suitable dissimilarity measure. We report several measures that are satisfactory and the choice of a particular measure may rely on the availability on the software pipeline of preference.
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Affiliation(s)
- Pablo D. Reeb
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
- Department of Statistics, Universidad Nacional del Comahue, Cinco Saltos, Rio Negro, Argentina
| | - Sergio J. Bramardi
- Department of Statistics, Universidad Nacional del Comahue, Cinco Saltos, Rio Negro, Argentina
- College of Agricultural and Forest Sciences, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Juan P. Steibel
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, United States of America
- Department of Animal Science, Michigan State University, East Lansing, Michigan, United States of America
- * E-mail:
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A general framework for a reliable multivariate analysis and pattern recognition in high-dimensional epidemiological data, based on cluster robustness: a tutorial to enrich the epidemiologists' toolkit. Rev Epidemiol Sante Publique 2015; 63:9-19. [PMID: 25604830 DOI: 10.1016/j.respe.2014.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 12/01/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In an epidemiologist's toolbox, three main types of statistical tools can be found: means and proportions comparisons, linear or logistic regression models and Cox-type regression models. All these techniques have their own multivariate formulations, so that biases can be accounted for. Nonetheless, there is an entire set of natively massive multivariate techniques, which are based on weaker assumptions than classical statistical techniques are, and which seem to be underestimated or remain unknown to most epidemiologists. These techniques are used for pattern recognition or clustering – that is, for retrieving homogeneous groups in data without any a priori about these groups. They are widely used in connex domains such as genetics or biomolecular studies. METHODS Most clustering techniques require tuning specific parameters so that groups can be identified in data. A critical parameter to set is the number of groups the technique needs to discover. Different approaches to find the optimal number of groups are available, such as the silhouette approach and the robustness approach. This article presents the key aspects of clustering techniques (how proximity between observations is defined and how to find the number of groups), two archetypal techniques (namely the k-means and PAM algorithms) and how they relate to more classical statistical approaches. RESULTS Through a theoretical, simple example and a real data application, we provide a complete framework within which classical epidemiological concerns can be reconsidered. We show how to (i) identify whether distinct groups exist in data, (ii) identify the optimal number of groups in data, (iii) label each observation according to its own group and (iv) analyze the groups identified according to separate and explicative data. In addition, how to achieve consistent results while removing sensitivity to initial conditions is explained. CONCLUSIONS Clustering techniques, in conjunction with methods for parameter tuning, provide the epidemiologist with substantial additional tools. They differ from the usual approaches based on hypothesis-testing because no assumptions are made on the data and these clustering techniques are natively multivariate.
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Applying multivariate clustering techniques to health data: the 4 types of healthcare utilization in the Paris metropolitan area. PLoS One 2014; 9:e115064. [PMID: 25506916 PMCID: PMC4266672 DOI: 10.1371/journal.pone.0115064] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 11/11/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Cost containment policies and the need to satisfy patients' health needs and care expectations provide major challenges to healthcare systems. Identification of homogeneous groups in terms of healthcare utilisation could lead to a better understanding of how to adjust healthcare provision to society and patient needs. METHODS This study used data from the third wave of the SIRS cohort study, a representative, population-based, socio-epidemiological study set up in 2005 in the Paris metropolitan area, France. The data were analysed using a cross-sectional design. In 2010, 3000 individuals were interviewed in their homes. Non-conventional multivariate clustering techniques were used to determine homogeneous user groups in data. Multinomial models assessed a wide range of potential associations between user characteristics and their pattern of healthcare utilisation. RESULTS We identified four distinct patterns of healthcare use. Patterns of consumption and the socio-demographic characteristics of users differed qualitatively and quantitatively between these four profiles. Extensive and intensive use by older, wealthier and unhealthier people contrasted with narrow and parsimonious use by younger, socially deprived people and immigrants. Rare, intermittent use by young healthy men contrasted with regular targeted use by healthy and wealthy women. CONCLUSION The use of an original technique of massive multivariate analysis allowed us to characterise different types of healthcare users, both in terms of resource utilisation and socio-demographic variables. This method would merit replication in different populations and healthcare systems.
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Hammac GK, Pierlé SA, Cheng X, Scoles GA, Brayton KA. Global transcriptional analysis reveals surface remodeling of Anaplasma marginale in the tick vector. Parasit Vectors 2014; 7:193. [PMID: 24751137 PMCID: PMC4022386 DOI: 10.1186/1756-3305-7-193] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/08/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Pathogens dependent upon vectors for transmission to new hosts undergo environment specific changes in gene transcription dependent on whether they are replicating in the vector or the mammalian host. Differential gene transcription, especially of potential vaccine candidates, is of interest in Anaplasma marginale, the tick-borne causative agent of bovine anaplasmosis. METHODS RNA-seq technology allowed a comprehensive analysis of the transcriptional status of A. marginale genes in two conditions: bovine host blood and tick derived cell culture, a model for the tick vector. Quantitative PCR was used to assess transcription of a set of genes in A. marginale infected tick midguts and salivary glands at two time points during the transmission cycle. RESULTS Genes belonging to fourteen pathways or component groups were found to be differentially transcribed in A. marginale in the bovine host versus the tick vector. One of the most significantly altered groups was composed of surface proteins. Of the 56 genes included in the surface protein group, eight were up regulated and 26 were down regulated. The down regulated surface protein encoding genes include several that are well studied due to their immunogenicity and function. Quantitative PCR of a set of genes demonstrated that transcription in tick cell culture most closely approximates transcription in salivary glands of recently infected ticks. CONCLUSIONS The ISE6 tick cell culture line is an acceptable model for early infection in tick salivary glands, and reveals disproportionate down regulation of surface protein genes in the tick. Transcriptional profiling in other cell lines may help us simulate additional microenvironments. Understanding vector-specific alteration of gene transcription, especially of surface protein encoding genes, may aid in the development of vaccines or transmission blocking therapies.
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Affiliation(s)
| | | | | | | | - Kelly A Brayton
- Program in Genomics, Department of Veterinary Microbiology and Pathology, Paul G, Allen School for Global Animal Health, Washington State University, Pullman, WA 99164-7040, USA.
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Abstract
Background Cell survival and development are orchestrated by complex interlocking programs of gene activation and repression. Understanding how this gene regulatory network (GRN) functions in normal states, and is altered in cancers subtypes, offers fundamental insight into oncogenesis and disease progression, and holds great promise for guiding clinical decisions. Inferring a GRN from empirical microarray gene expression data is a challenging task in cancer systems biology. In recent years, module-based approaches for GRN inference have been proposed to address this challenge. Despite the demonstrated success of module-based approaches in uncovering biologically meaningful regulatory interactions, their application remains limited a single condition, without supporting the comparison of multiple disease subtypes/conditions. Also, their use remains unnecessarily restricted to computational biologists, as accurate inference of modules and their regulators requires integration of diverse tools and heterogeneous data sources, which in turn requires scripting skills, data infrastructure and powerful computational facilities. New analytical frameworks are required to make module-based GRN inference approach more generally useful to the research community. Results We present the RMaNI (Regulatory Module Network Inference) framework, which supports cancer subtype-specific or condition specific GRN inference and differential network analysis. It combines both transcriptomic as well as genomic data sources, and integrates heterogeneous knowledge resources and a set of complementary bioinformatic methods for automated inference of modules, their condition specific regulators and facilitates downstream network analyses and data visualization. To demonstrate its utility, we applied RMaNI to a hepatocellular microarray data containing normal and three disease conditions. We demonstrate that how RMaNI can be employed to understand the genetic architecture underlying three disease conditions. RMaNI is freely available at http://inspect.braembl.org.au/bi/inspect/rmani Conclusion RMaNI makes available a workflow with comprehensive set of tools that would otherwise be challenging for non-expert users to install and apply. The framework presented in this paper is flexible and can be easily extended to analyse any dataset with multiple disease conditions.
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Dimitrakopoulou K, Vrahatis AG, Wilk E, Tsakalidis AK, Bezerianos A. OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2013; 111:650-661. [PMID: 23796450 DOI: 10.1016/j.cmpb.2013.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/07/2013] [Accepted: 05/30/2013] [Indexed: 06/02/2023]
Abstract
The increasing flow of short time series microarray experiments for the study of dynamic cellular processes poses the need for efficient clustering tools. These tools must deal with three primary issues: first, to consider the multi-functionality of genes; second, to evaluate the similarity of the relative change of amplitude in the time domain rather than the absolute values; third, to cope with the constraints of conventional clustering algorithms such as the assignment of the appropriate cluster number. To address these, we propose OLYMPUS, a novel unsupervised clustering algorithm that integrates Differential Evolution (DE) method into Fuzzy Short Time Series (FSTS) algorithm with the scope to utilize efficiently the information of population of the first and enhance the performance of the latter. Our hybrid approach provides sets of genes that enable the deciphering of distinct phases in dynamic cellular processes. We proved the efficiency of OLYMPUS on synthetic as well as on experimental data. The discriminative power of OLYMPUS provided clusters, which refined the so far perspective of the dynamics of host response mechanisms to Influenza A (H1N1). Our kinetic model sets a timeline for several pathways and cell populations, implicated to participate in host response; yet no timeline was assigned to them (e.g. cell cycle, homeostasis). Regarding the activity of B cells, our approach revealed that some antibody-related mechanisms remain activated until day 60 post infection. The Matlab codes for implementing OLYMPUS, as well as example datasets, are freely accessible via the Web (http://biosignal.med.upatras.gr/wordpress/biosignal/).
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Exploiting identifiability and intergene correlation for improved detection of differential expression. ISRN BIOINFORMATICS 2013; 2013:404717. [PMID: 25937946 PMCID: PMC4393076 DOI: 10.1155/2013/404717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 11/19/2012] [Indexed: 11/23/2022]
Abstract
Accurate differential analysis of microarray data strongly depends on effective treatment of intergene correlation. Such dependence is ordinarily accounted for in terms of its effect on significance cutoffs. In this paper, it is shown that correlation can, in fact, be exploited to share information across tests and reorder expression differentials for increased statistical power, regardless of the threshold. Significantly improved differential analysis is the result of two simple measures: (i) adjusting test statistics to exploit information from identifiable genes (the large subset of genes represented on a microarray that can be classified a priori as nondifferential with very high confidence], but (ii) doing so in a way that accounts for linear dependencies among identifiable and nonidentifiable genes. A method is developed that builds upon the widely used two-sample t-statistic approach and uses analysis in Hilbert space to decompose the nonidentified gene vector into two components that are correlated and uncorrelated with the identified set. In the application to data derived from a widely studied prostate cancer database, the proposed method outperforms some of the most highly regarded approaches published to date. Algorithms in MATLAB and in R are available for public download.
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Deller JR, Radha H, McCormick JJ, Wang H. Nonlinear dependence in the discovery of differentially expressed genes. ISRN BIOINFORMATICS 2012; 2012:564715. [PMID: 25937940 PMCID: PMC4393074 DOI: 10.5402/2012/564715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 11/09/2011] [Indexed: 11/23/2022]
Abstract
Microarray data are used to determine which genes are active in response to a changing cell environment. Genes are “discovered” when they are significantly differentially expressed in the microarray data collected under the differing conditions. In one prevalent approach, all genes are assumed to satisfy a null hypothesis, ℍ0, of no difference in expression. A false discovery (type
1 error) occurs when ℍ0 is incorrectly rejected. The quality of a detection algorithm is assessed by estimating its number of false
discoveries, 𝔉. Work involving the second-moment modeling of the z-value histogram (representing gene expression differentials) has
shown significantly deleterious effects of intergene expression correlation on the estimate of 𝔉. This paper suggests that nonlinear
dependencies could likewise be important. With an applied emphasis, this paper extends the “moment framework” by including
third-moment skewness corrections in an estimator of 𝔉. This estimator combines observed correlation (corrected for sampling
fluctuations) with the information from easily identifiable null cases. Nonlinear-dependence modeling reduces the estimation error
relative to that of linear estimation. Third-moment calculations involve empirical densities of 3 × 3 covariance matrices estimated using very few samples. The principle of entropy maximization is employed to connect estimated moments to 𝔉 inference. Model results are tested with BRCA and HIV data sets and with carefully constructed simulations.
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Affiliation(s)
- J R Deller
- Department of Electrical and Computer Engineering, Michigan State University, 2120 EB, East Lansing, MI 48824, USA
| | - Hayder Radha
- Department of Electrical and Computer Engineering, Michigan State University, 2120 EB, East Lansing, MI 48824, USA
| | - J Justin McCormick
- Carcinogenesis Laboratory, Department of Molecular Biology and Biochemistry, Michigan State University, 341 FST, East Lansing, MI 48824, USA
| | - Huiyan Wang
- College of Computer Science and Information Engineering, Zhejiang Gongshang University, 18 Xuezheng Street, Zhejiang Province Hangzhou, 310018, China
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Fontanillo C, Nogales-Cadenas R, Pascual-Montano A, De Las Rivas J. Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PLoS One 2011; 6:e24289. [PMID: 21949701 PMCID: PMC3174934 DOI: 10.1371/journal.pone.0024289] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 08/03/2011] [Indexed: 11/30/2022] Open
Abstract
Functional analysis of large sets of genes and proteins is becoming more and more necessary with the increase of experimental biomolecular data at omic-scale. Enrichment analysis is by far the most popular available methodology to derive functional implications of sets of cooperating genes. The problem with these techniques relies in the redundancy of resulting information, that in most cases generate lots of trivial results with high risk to mask the reality of key biological events. We present and describe a computational method, called GeneTerm Linker, that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. The algorithm is tested with a small set of well known interacting proteins from yeast and with a large collection of reference sets from three heterogeneous resources: multiprotein complexes (CORUM), cellular pathways (SGD) and human diseases (OMIM). Statistical Precision, Recall and balanced F-score are calculated showing robust results, even when different levels of random noise are included in the test sets. Although we could not find an equivalent method, we present a comparative analysis with a widely used method that combines enrichment and functional annotation clustering. A web application to use the method here proposed is provided at http://gtlinker.cnb.csic.es.
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Affiliation(s)
- Celia Fontanillo
- Cancer Research Center (CiC-IBMCC, CSIC/USAL), Campus Miguel de Unamuno, Salamanca, Spain
| | - Ruben Nogales-Cadenas
- National Center of Biotechnology (CNB, CSIC), Campus de Cantoblanco UAM, Madrid, Spain
| | | | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL), Campus Miguel de Unamuno, Salamanca, Spain
- * E-mail:
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Libeau P, Durandet M, Granier F, Marquis C, Berthomé R, Renou JP, Taconnat-Soubirou L, Horlow C. Gene expression profiling of Arabidopsis meiocytes. PLANT BIOLOGY (STUTTGART, GERMANY) 2011; 13:784-93. [PMID: 21815983 DOI: 10.1111/j.1438-8677.2010.00435.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is a special type of cell division present in all organisms that reproduce by sexual reproduction. It ensures the transition between the sporophytic and gametophytic state and allows gamete production through meiotic recombination and chromosome number reduction. In this paper, we describe a technique for the isolation of Arabidopsis thaliana male meiocytes. From this cellular material, it was then possible to develop large-scale transcriptome studies using CATMA microarrays and thus to obtain an overview of genes expressed during Arabidopsis meiosis. The expression profiles were studied with either stringent statistical criteria or by performing clustering. Both methods resulted in gene clusters enriched in meiosis-specific genes (from 14- to 55-fold). Analysis of these data provided a unique set of genes that will be pivotal to further analysis aimed at understanding the meiotic process.
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Affiliation(s)
- P Libeau
- Institut Jean-Pierre Bourgin, INRA de Versailles, INRA-AgroParisTech, Versailles, France
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George S, Xia T, Rallo R, Zhao Y, Ji Z, Lin S, Wang X, Zhang H, France B, Schoenfeld D, Damoiseaux R, Liu R, Lin S, Bradley KA, Cohen Y, Nel AE. Use of a high-throughput screening approach coupled with in vivo zebrafish embryo screening to develop hazard ranking for engineered nanomaterials. ACS NANO 2011; 5:1805-17. [PMID: 21323332 PMCID: PMC3896549 DOI: 10.1021/nn102734s] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Because of concerns about the safety of a growing number of engineered nanomaterials (ENM), it is necessary to develop high-throughput screening and in silico data transformation tools that can speed up in vitro hazard ranking. Here, we report the use of a multiparametric, automated screening assay that incorporates sublethal and lethal cellular injury responses to perform high-throughput analysis of a batch of commercial metal/metal oxide nanoparticles (NP) with the inclusion of a quantum dot (QD1). The responses chosen for tracking cellular injury through automated epifluorescence microscopy included ROS production, intracellular calcium flux, mitochondrial depolarization, and plasma membrane permeability. The z-score transformed high volume data set was used to construct heat maps for in vitro hazard ranking as well as showing the similarity patterns of NPs and response parameters through the use of self-organizing maps (SOM). Among the materials analyzed, QD1 and nano-ZnO showed the most prominent lethality, while Pt, Ag, SiO2, Al2O3, and Au triggered sublethal effects but without cytotoxicity. In order to compare the in vitro with the in vivo response outcomes in zebrafish embryos, NPs were used to assess their impact on mortality rate, hatching rate, cardiac rate, and morphological defects. While QDs, ZnO, and Ag induced morphological abnormalities or interfered in embryo hatching, Pt and Ag exerted inhibitory effects on cardiac rate. Ag toxicity in zebrafish differed from the in vitro results, which is congruent with this material's designation as extremely dangerous in the environment. Interestingly, while toxicity in the initially selected QD formulation was due to a solvent (toluene), supplementary testing of additional QDs selections yielded in vitro hazard profiling that reflect the release of chalcogenides. In conclusion, the use of a high-throughput screening, in silico data handling and zebrafish testing may constitute a paradigm for rapid and integrated ENM toxicological screening.
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Affiliation(s)
- Saji George
- Department of Medicine, Division of NanoMedicine; University of California, Los Angeles, CA, USA
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
| | - Tian Xia
- Department of Medicine, Division of NanoMedicine; University of California, Los Angeles, CA, USA
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
| | - Robert Rallo
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | - Yan Zhao
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Zhaoxia Ji
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
| | - Sijie Lin
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
| | - Xiang Wang
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
| | - Haiyuan Zhang
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
| | - Bryan France
- Molecular Shared Screening Resources, University of California, Los Angeles, CA, USA
| | - David Schoenfeld
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Robert Damoiseaux
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Molecular Shared Screening Resources, University of California, Los Angeles, CA, USA
| | - Rong Liu
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | - Shuo Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Kenneth A Bradley
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology and Mol Genetics, University of California, Los Angeles, CA, USA
| | - Yoram Cohen
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA
| | - André E Nel
- Department of Medicine, Division of NanoMedicine; University of California, Los Angeles, CA, USA
- Center for Environmental Implications of Nanotechnology, California NanoSystems Institute; University of California, Los Angeles, CA, USA
- Address correspondence to
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