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Srivastava R, Singh K, Abouhashem AS, Kumar M, Kacar S, Verma SS, Mohanty SK, Sinha M, Ghatak S, Xuan Y, Sen CK. Human fetal dermal fibroblast-myeloid cell diversity is characterized by dominance of pro-healing Annexin1-FPR1 signaling. iScience 2023; 26:107533. [PMID: 37636079 PMCID: PMC10450526 DOI: 10.1016/j.isci.2023.107533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/06/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
Fetal skin achieves scarless wound repair. Dermal fibroblasts play a central role in extracellular matrix deposition and scarring outcomes. Both fetal and gingival wound repair share minimal scarring outcomes. We tested the hypothesis that compared to adult skin fibroblasts, human fetal skin fibroblast diversity is unique and partly overlaps with gingival skin fibroblasts. Human fetal skin (FS, n = 3), gingiva (HGG, n = 13), and mature skin (MS, n = 13) were compared at single-cell resolution. Dermal fibroblasts, the most abundant cluster, were examined to establish a connectome with other skin cells. Annexin1-FPR1 signaling pathway was dominant in both FS as well as HGG fibroblasts and related myeloid cells while scanty in MS fibroblasts. Myeloid-specific FPR1-ORF delivered in murine wound edge using tissue nanotransfection (TNT) technology significantly enhanced the quality of healing. Pseudotime analyses identified the co-existence of an HGG fibroblast subset with FPR1high myeloid cells of fetal origin indicating common underlying biological processes.
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Affiliation(s)
- Rajneesh Srivastava
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kanhaiya Singh
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ahmed S. Abouhashem
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
- Sharkia Clinical Research Department, Ministry of Health, Zagazig, Egypt
| | - Manishekhar Kumar
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sedat Kacar
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sumit S. Verma
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sujit K. Mohanty
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mithun Sinha
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Subhadip Ghatak
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yi Xuan
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chandan K. Sen
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Indiana Center for Regenerative Medicine and Engineering, Indiana University Health Comprehensive Wound Center, Indiana University School of Medicine, Indianapolis, IN, USA
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2
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Sarkar A, Das T, Das G, Ghosh Z. MicroRNA mediated gene regulatory circuits leads to machine learning based preliminary detection of Acute Myeloid Leukemia. Comput Biol Chem 2023; 104:107859. [PMID: 37031648 DOI: 10.1016/j.compbiolchem.2023.107859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Acute Myeloid Leukemia (AML) can be detected based on morphology, cytochemistry, immunological markers, and cytogenetics. MicroRNAs (miRNAs) influence key biological pathways in multiple haematological malignancies including AML. In this work, we have analysed the miRNome and the transcriptome of normal and AML samples and have identified the significant set of miRNA-target mRNA pairs present within AML- Peripheral Blood and AML- Bone Marrow samples from both tissue and cell lines. The miRNA target genes are further filtered based on their functional significance in AML system. These filtered genes constitute the set of selected miRNA target features, which have been finally used for developing machine learning based prediction tool, 'TbAMLPred' for preliminary detection of AML. This model implements both unsupervised clustering and supervised classification algorithms that would increase the reliability of prediction. Our results show that the selected miRNA target-based features can separate the control and disease samples linearly. Overall, we put forward 'TbAMLPred' for a non-invasive mode of preliminary AML diagnosis in future. Github link for accessing TbAMLPred: https://github.com/zglabDIB/TbAMLPred.
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Affiliation(s)
- Arijita Sarkar
- Division of Bioinformatics, Bose Institute, P-1/12, C.I.T. Scheme-VII M, Kolkata 700 054, India; Present Affiliation: Department of Orthopaedic Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Troyee Das
- Division of Bioinformatics, Bose Institute, P-1/12, C.I.T. Scheme-VII M, Kolkata 700 054, India
| | - Gourab Das
- Division of Bioinformatics, Bose Institute, P-1/12, C.I.T. Scheme-VII M, Kolkata 700 054, India
| | - Zhumur Ghosh
- Division of Bioinformatics, Bose Institute, P-1/12, C.I.T. Scheme-VII M, Kolkata 700 054, India.
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3
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Clink DJ, Kier I, Ahmad AH, Klinck H. A workflow for the automated detection and classification of female gibbon calls from long-term acoustic recordings. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1071640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
Passive acoustic monitoring (PAM) allows for the study of vocal animals on temporal and spatial scales difficult to achieve using only human observers. Recent improvements in recording technology, data storage, and battery capacity have led to increased use of PAM. One of the main obstacles in implementing wide-scale PAM programs is the lack of open-source programs that efficiently process terabytes of sound recordings and do not require large amounts of training data. Here we describe a workflow for detecting, classifying, and visualizing female Northern grey gibbon calls in Sabah, Malaysia. Our approach detects sound events using band-limited energy summation and does binary classification of these events (gibbon female or not) using machine learning algorithms (support vector machine and random forest). We then applied an unsupervised approach (affinity propagation clustering) to see if we could further differentiate between true and false positives or the number of gibbon females in our dataset. We used this workflow to address three questions: (1) does this automated approach provide reliable estimates of temporal patterns of gibbon calling activity; (2) can unsupervised approaches be applied as a post-processing step to improve the performance of the system; and (3) can unsupervised approaches be used to estimate how many female individuals (or clusters) there are in our study area? We found that performance plateaued with >160 clips of training data for each of our two classes. Using optimized settings, our automated approach achieved a satisfactory performance (F1 score ~ 80%). The unsupervised approach did not effectively differentiate between true and false positives or return clusters that appear to correspond to the number of females in our study area. Our results indicate that more work needs to be done before unsupervised approaches can be reliably used to estimate the number of individual animals occupying an area from PAM data. Future work applying these methods across sites and different gibbon species and comparisons to deep learning approaches will be crucial for future gibbon conservation initiatives across Southeast Asia.
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4
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Zhang K, Feng W, Wang P. Identification of spatially variable genes with graph cuts. Nat Commun 2022; 13:5488. [PMID: 36123336 PMCID: PMC9485129 DOI: 10.1038/s41467-022-33182-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 09/07/2022] [Indexed: 11/08/2022] Open
Abstract
Single-cell gene expression data with positional information is critical to dissect mechanisms and architectures of multicellular organisms, but the potential is limited by the scalability of current data analysis strategies. Here, we present scGCO, a method based on fast optimization of hidden Markov Random Fields with graph cuts to identify spatially variable genes. Comparing to existing methods, scGCO delivers a superior performance with lower false positive rate and improved specificity, while demonstrates a more robust performance in the presence of noises. Critically, scGCO scales near linearly with inputs and demonstrates orders of magnitude better running time and memory requirement than existing methods, and could represent a valuable solution when spatial transcriptomics data grows into millions of data points and beyond.
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Affiliation(s)
- Ke Zhang
- National Genomics Data Center, CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wanwan Feng
- National Genomics Data Center, CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peng Wang
- National Genomics Data Center, CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Faculty of Health Science, University of Macau, Macau, China.
- Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau, China.
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5
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Sun Y, Zhang Z, Zhang C, Zhang N, Wang P, Chu Y, Chard Dunmall LS, Lemoine NR, Wang Y. An effective therapeutic regime for treatment of glioma using oncolytic vaccinia virus expressing IL-21 in combination with immune checkpoint inhibition. Mol Ther Oncolytics 2022; 26:105-119. [PMID: 35795092 PMCID: PMC9233193 DOI: 10.1016/j.omto.2022.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 05/13/2022] [Indexed: 12/24/2022] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant tumor in the brain, accounting for 51.4% of all primary brain tumors. GBM has a highly immunosuppressive tumor microenvironment (TME) and, as such, responses to immunotherapeutic strategies are poor. Vaccinia virus (VV) is an oncolytic virus that has shown tremendous therapeutic effect in various tumor types. In addition to its directly lytic effect on tumor cells, it has an ability to enhance immune cell infiltration into the TME allowing for improved immune control over the tumor. Here, we used a new generation of VV expressing the therapeutic payload interleukin-21 to treat murine GL261 glioma models. After both intratumoral and intravenous delivery, virus treatment induced remodeling of the TME to promote a robust anti-tumor immune response that resulted in control over tumor growth and long-term survival in both subcutaneous and orthotopic mouse models. Treatment efficacy was significantly improved in combination with systemic α-PD1 therapy, which is ineffective as a standalone treatment but synergizes with oncolytic VV to enhance therapeutic outcomes. Importantly, this study also revealed the upregulation of stem cell memory T cell populations after the virus treatment that exert strong and durable anti-tumor activity.
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Affiliation(s)
- Yijie Sun
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Zhe Zhang
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Chenglin Zhang
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Na Zhang
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Pengju Wang
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Yongchao Chu
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Louisa S. Chard Dunmall
- Centre for Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Nicholas R. Lemoine
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
- Centre for Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Yaohe Wang
- National Centre for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
- Centre for Cancer Biomarkers & Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
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6
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Comella I, Tasirin JS, Klinck H, Johnson LM, Clink DJ. Investigating note repertoires and acoustic tradeoffs in the duet contributions of a basal haplorrhine primate. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.910121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Acoustic communication serves a crucial role in the social interactions of vocal animals. Duetting—the coordinated singing among pairs of animals—has evolved independently multiple times across diverse taxonomic groups including insects, frogs, birds, and mammals. A crucial first step for understanding how information is encoded and transferred in duets is through quantifying the acoustic repertoire, which can reveal differences and similarities on multiple levels of analysis and provides the groundwork necessary for further studies of the vocal communication patterns of the focal species. Investigating acoustic tradeoffs, such as the tradeoff between the rate of syllable repetition and note bandwidth, can also provide important insights into the evolution of duets, as these tradeoffs may represent the physical and mechanical limits on signal design. In addition, identifying which sex initiates the duet can provide insights into the function of the duets. We have three main goals in the current study: (1) provide a descriptive, fine-scale analysis of Gursky’s spectral tarsier (Tarsius spectrumgurskyae) duets; (2) use unsupervised approaches to investigate sex-specific note repertoires; and (3) test for evidence of acoustic tradeoffs in the rate of note repetition and bandwidth of tarsier duet contributions. We found that both sexes were equally likely to initiate the duets and that pairs differed substantially in the duration of their duets. Our unsupervised clustering analyses indicate that both sexes have highly graded note repertoires. We also found evidence for acoustic tradeoffs in both male and female duet contributions, but the relationship in females was much more pronounced. The prevalence of this tradeoff across diverse taxonomic groups including birds, bats, and primates indicates the constraints that limit the production of rapidly repeating broadband notes may be one of the few ‘universals’ in vocal communication. Future carefully designed playback studies that investigate the behavioral response, and therefore potential information transmitted in duets to conspecifics, will be highly informative.
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7
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Milošević D, Medeiros AS, Stojković Piperac M, Cvijanović D, Soininen J, Milosavljević A, Predić B. The application of Uniform Manifold Approximation and Projection (UMAP) for unconstrained ordination and classification of biological indicators in aquatic ecology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152365. [PMID: 34963591 DOI: 10.1016/j.scitotenv.2021.152365] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The analysis of community structure in studies of freshwater ecology often requires the application of dimensionality reduction to process multivariate data. A high number of dimensions (number of taxa/environmental parameters × number of samples), nonlinear relationships, outliers, and high variability usually hinder the visualization and interpretation of multivariate datasets. Here, we proposed a new statistical design using Uniform Manifold Approximation and Projection (UMAP), and community partitioning using Louvain algorithms, to ordinate and classify the structure of aquatic biota in two-dimensional space. We present this approach with a demonstration of five previously published datasets for diatoms, macrophytes, chironomids (larval and subfossil), and fish. Principal Component Analysis (PCA) and Ward's clustering were also used to assess the comparability of the UMAP approach compared to traditional approaches for ordination and classification. The ordination of sampling sites in 2-dimensional space showed a much denser, and easier to interpret, grouping using the UMAP approach in comparison to PCA. The classification of community structure using the Louvain algorithm in UMAP ordinal space showed a high classification strength for data with a high number of dimensions than the cluster patterns obtained with the use of a Ward's algorithm in PCA. Environmental gradients, presented via heat maps, were overlayed with the ordination patterns of aquatic communities, confirming that the ordinations obtained by UMAP were ecologically meaningful. This is the first study that has applied a UMAP approach with classification using Louvain algorithms on ecological datasets. We show that the performance of local and global structures, as well as the number of clusters determined by the algorithm, make this approach more powerful than traditional approaches.
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Affiliation(s)
- Djuradj Milošević
- University of Niš, Faculty of Sciences and Mathematics, Department of Biology and Ecology, Višegradska 33, 18000 Niš, Serbia.
| | - Andrew S Medeiros
- School for Resource and Environmental Studies, Dalhousie University, Halifax, Canada
| | - Milica Stojković Piperac
- University of Niš, Faculty of Sciences and Mathematics, Department of Biology and Ecology, Višegradska 33, 18000 Niš, Serbia
| | - Dušanka Cvijanović
- University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Janne Soininen
- Department of Geosciences and Geography, University of Helsinki, Finland
| | - Aleksandar Milosavljević
- University of Niš, Faculty of Electronic Engineering, Aleksandra Medvedeva 14, 18000 Niš, Serbia
| | - Bratislav Predić
- University of Niš, Faculty of Electronic Engineering, Aleksandra Medvedeva 14, 18000 Niš, Serbia
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8
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Clink DJ, Zafar M, Ahmad AH, Lau AR. Limited Evidence for Individual Signatures or Site-Level Patterns of Variation in Male Northern Gray Gibbon (Hylobates funereus) Duet Codas. INT J PRIMATOL 2021. [DOI: 10.1007/s10764-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Mai ND, Lee BG, Chung WY. Affective Computing on Machine Learning-Based Emotion Recognition Using a Self-Made EEG Device. SENSORS (BASEL, SWITZERLAND) 2021; 21:5135. [PMID: 34372370 PMCID: PMC8348417 DOI: 10.3390/s21155135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022]
Abstract
In this research, we develop an affective computing method based on machine learning for emotion recognition using a wireless protocol and a wearable electroencephalography (EEG) custom-designed device. The system collects EEG signals using an eight-electrode placement on the scalp; two of these electrodes were placed in the frontal lobe, and the other six electrodes were placed in the temporal lobe. We performed experiments on eight subjects while they watched emotive videos. Six entropy measures were employed for extracting suitable features from the EEG signals. Next, we evaluated our proposed models using three popular classifiers: a support vector machine (SVM), multi-layer perceptron (MLP), and one-dimensional convolutional neural network (1D-CNN) for emotion classification; both subject-dependent and subject-independent strategies were used. Our experiment results showed that the highest average accuracies achieved in the subject-dependent and subject-independent cases were 85.81% and 78.52%, respectively; these accuracies were achieved using a combination of the sample entropy measure and 1D-CNN. Moreover, our study investigates the T8 position (above the right ear) in the temporal lobe as the most critical channel among the proposed measurement positions for emotion classification through electrode selection. Our results prove the feasibility and efficiency of our proposed EEG-based affective computing method for emotion recognition in real-world applications.
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Affiliation(s)
- Ngoc-Dau Mai
- Department of Artificial Intelligence Convergence, Pukyong National University, Busan 48513, Korea;
| | - Boon-Giin Lee
- School of Computer Science, The University of Nottingham Ningbo China, Ningbo 315100, China;
| | - Wan-Young Chung
- Department of Artificial Intelligence Convergence, Pukyong National University, Busan 48513, Korea;
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10
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Odom KJ, Araya-Salas M, Morano JL, Ligon RA, Leighton GM, Taff CC, Dalziell AH, Billings AC, Germain RR, Pardo M, de Andrade LG, Hedwig D, Keen SC, Shiu Y, Charif RA, Webster MS, Rice AN. Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa. Biol Rev Camb Philos Soc 2021; 96:1135-1159. [PMID: 33652499 DOI: 10.1111/brv.12695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
Animals produce a wide array of sounds with highly variable acoustic structures. It is possible to understand the causes and consequences of this variation across taxa with phylogenetic comparative analyses. Acoustic and evolutionary analyses are rapidly increasing in sophistication such that choosing appropriate acoustic and evolutionary approaches is increasingly difficult. However, the correct choice of analysis can have profound effects on output and evolutionary inferences. Here, we identify and address some of the challenges for this growing field by providing a roadmap for quantifying and comparing sound in a phylogenetic context for researchers with a broad range of scientific backgrounds. Sound, as a continuous, multidimensional trait can be particularly challenging to measure because it can be hard to identify variables that can be compared across taxa and it is also no small feat to process and analyse the resulting high-dimensional acoustic data using approaches that are appropriate for subsequent evolutionary analysis. Additionally, terminological inconsistencies and the role of learning in the development of acoustic traits need to be considered. Phylogenetic comparative analyses also have their own sets of caveats to consider. We provide a set of recommendations for delimiting acoustic signals into discrete, comparable acoustic units. We also present a three-stage workflow for extracting relevant acoustic data, including options for multivariate analyses and dimensionality reduction that is compatible with phylogenetic comparative analysis. We then summarize available phylogenetic comparative approaches and how they have been used in comparative bioacoustics, and address the limitations of comparative analyses with behavioural data. Lastly, we recommend how to apply these methods to acoustic data across a range of study systems. In this way, we provide an integrated framework to aid in quantitative analysis of cross-taxa variation in animal sounds for comparative phylogenetic analysis. In addition, we advocate the standardization of acoustic terminology across disciplines and taxa, adoption of automated methods for acoustic feature extraction, and establishment of strong data archival practices for acoustic recordings and data analyses. Combining such practices with our proposed workflow will greatly advance the reproducibility, biological interpretation, and longevity of comparative bioacoustic studies.
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Affiliation(s)
- Karan J Odom
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Marcelo Araya-Salas
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Sede del Sur, Universidad de Costa Rica, Golfito, 60701, Costa Rica
| | - Janelle L Morano
- Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Russell A Ligon
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Gavin M Leighton
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Department of Biology, SUNY Buffalo State, Buffalo, NY, 14222, U.S.A
| | - Conor C Taff
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, U.S.A
| | - Anastasia H Dalziell
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Centre for Sustainable Ecosystem Solutions, University of Wollongong, Northfields Ave, Wollongong, NSW, 2522, Australia
| | - Alexis C Billings
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, U.S.A.,Department of Environmental, Science, Policy and Management, University of California, Berkeley, Berkeley, CA, 94709, U.S.A
| | - Ryan R Germain
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, DK-2100, Denmark
| | - Michael Pardo
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, 80523, U.S.A
| | - Luciana Guimarães de Andrade
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, U.S.A.,Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Daniela Hedwig
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Sara C Keen
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A.,Department of Geological Sciences, Stanford University, Stanford, CA, 94305, U.S.A
| | - Yu Shiu
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Russell A Charif
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Michael S Webster
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, 14853, U.S.A.,Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
| | - Aaron N Rice
- Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, 14850, U.S.A
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11
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Clink DJ, Klinck H. Unsupervised acoustic classification of individual gibbon females and the implications for passive acoustic monitoring. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Dena J. Clink
- Center for Conservation Bioacoustics Cornell Laboratory of Ornithology Cornell University Ithaca NY USA
| | - Holger Klinck
- Center for Conservation Bioacoustics Cornell Laboratory of Ornithology Cornell University Ithaca NY USA
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