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Bulygin I, Shatov V, Rykachevskiy A, Raiko A, Bernstein A, Burnaev E, Gelfand MS. Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods. PeerJ 2023; 11:e15838. [PMID: 37701837 PMCID: PMC10494839 DOI: 10.7717/peerj.15838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/12/2023] [Indexed: 09/14/2023] Open
Abstract
Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.
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Affiliation(s)
- Ivan Bulygin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | | | - Arsenii Raiko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Evgeny Burnaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Artificial Intelligence Research Institute (AIRI), Moscow, Russia
| | - Mikhail S. Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems, Moscow, Russia
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2
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Zhang F, Wang W, Nie Y, Li J, He X. From microbial technology to microbiota medicine as a clinical discipline: Sustainable development goal. Microb Biotechnol 2023; 16:1705-1708. [PMID: 37452703 PMCID: PMC10443319 DOI: 10.1111/1751-7915.14317] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/03/2023] [Indexed: 07/18/2023] Open
Affiliation(s)
- Faming Zhang
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Weihong Wang
- Department of Microbiota Medicine & Medical Center for Digestive DiseasesThe Second Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive DiseasesXijing Hospital, Air Force Medical UniversityXi'anChina
| | - Jingnan Li
- Department of Gastroenterology, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xingxiang He
- Department of GastroenterologyThe First Affiliated Hospital of Guangdong Pharmaceutical UniversityGuangzhouChina
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Yang P, Zhu X, Ning K. Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship. Commun Biol 2023; 6:391. [PMID: 37037946 PMCID: PMC10085995 DOI: 10.1038/s42003-023-04753-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/24/2023] [Indexed: 04/12/2023] Open
Abstract
Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
- Institute of Medical Genomics, Biomedical Sciences College, Shandong First Medical University, Shandong, 250117, China
| | - Xue Zhu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center of AI Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Institute of Medical Genomics, Biomedical Sciences College, Shandong First Medical University, Shandong, 250117, China.
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Mostafaei H, Salehi-Pourmehr H, Rahnama’i MS, Mostafaei H, Shariat SF, Hajebrahimi S. Microbiome in Lower Urinary Tract Symptoms (LUTSs): Mapping the State of the Art with Bibliometric Analysis. Life (Basel) 2023; 13:life13020552. [PMID: 36836909 PMCID: PMC9964026 DOI: 10.3390/life13020552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/15/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND The main objective of this study is to provide the first characterization of the current research field of the clinical microbiome in LUTSs. METHODS First-of-its-kind scientometric insight into the historical development and structural state of the discipline is provided by a field analysis, mapping, and sub-analysis of articles for future research. On 22 December 2022, the entire Scopus database was searched without language or date restrictions. Search terms included "Chronic prostatitis", OR "Interstitial cystitis", OR "Lower urinary tract symptoms", OR "Lower urinary tract dysfunction", OR "Overactive bladder", OR "Incontinence", OR "Urolithiasis", OR "Urothelium", OR "Urine", OR "Urology", OR "urinary disorder", OR "Pathophysiology", OR "Benign prostatic hyperplasia", OR "Benign prostatic enlargement", AND "Microbiota", OR "Microbiome", OR "Urobio-ma", OR "Urobiota; microflora". The author and institutional data were transformed using the analytical tool Biblioshiny (a Shiny app for Bibliometrix), which took into account variations in author spelling as well as institutional naming and subgroups. RESULTS The specified search strategy was able to locate 529 documents from 267 sources published from 1981 to 2022. The average number of years from publication was 4.59 years. The authors with the most publications were Wolfe AJ and Brubaker I. The top three most collaborative networks were Loyola University Chicago, Loyola University Medical Center, and the University of California San Diego. The most frequently occurring words among the 50 nodes were: human, humans, nonhuman, female, adult, article, microbiology, microflora, microbiota, and controlled study. Frontiers in Cellular and Infection Microbiology and the International Urogynecology Journal, followed by Nature Reviews Urology, were the top three most relevant sources in microbiome research in urology. CONCLUSIONS One of the most crucial requirements for developing research policies and anticipating the scientific requirements of researchers is paying attention to the evolution of various scientific fields. Understanding research gaps and future needs in microbiome research in urology can be effectively understood by paying attention to the models, maps, and visualizations used in this research, which are the results of systematic analysis of scientific products in the most esteemed scientific journals in the world.
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Affiliation(s)
- Hadi Mostafaei
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Hanieh Salehi-Pourmehr
- Research Center for Evidence-Based Medicine, Iranian EBM Center, A Joanna Briggs Institute Center of Excellence, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
- Correspondence: or (H.S.-P.); or (S.H.); Tel./Fax: +98-41333-42219 (H.S.-P.)
| | | | - Helia Mostafaei
- Research Center for Evidence-Based Medicine, Iranian EBM Center, A Joanna Briggs Institute Center of Excellence, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Shahrokh F. Shariat
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Sakineh Hajebrahimi
- Research Center for Evidence-Based Medicine, Iranian EBM Center, A Joanna Briggs Institute Center of Excellence, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
- Correspondence: or (H.S.-P.); or (S.H.); Tel./Fax: +98-41333-42219 (H.S.-P.)
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Abstract
The term “microbiome” is currently applied predominantly to assemblages of organisms with 16S rRNA genes. In this context, “microbiome” is a misnomer that has been conferred a wide-ranging primacy over terms for community members lacking such genes, e.g., mycobiome, eukaryome, and virome, yet these are also important subsets of microbial communities. Widespread convenient and affordable 16S rRNA sequencing pipelines have accelerated continued use of such a “microbiome”, but at what intellectual and practical costs? Here we show that the use of “microbiome” in ribosomal gene-based studies has been egregiously misapplied, and discuss potential impacts. We argue that the current focus of “microbiome” research, predominantly on only ‘bacteria’, presents a dangerous narrowing of scope which encourages dismissal and even ignorance of other organisms’ contributions to microbial diversity, sensu stricto, and as etiologic agents; we put this in context by discussing cases in both marine microbial diversity and the role of pathogens in global amphibian decline. Fortunately, the solution is simple. We must use descriptive nouns that strictly reflect the outcomes attainable by the methods used. “Microbiome”, as a descriptive noun, should only be used when diversity in the three recognized domains is explored.
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Baudoin L, Sapinho D, Maddi A, Miotti L. Scientometric analysis of the term 'microbiota' in research publications (1999-2017): a second youth of a century-old concept. FEMS Microbiol Lett 2020; 366:5523130. [PMID: 31240301 DOI: 10.1093/femsle/fnz138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022] Open
Abstract
Great progress in microbiota research during last decades resulted in a growing corpus of publications mentioning the term 'microbiota'. Specifically, the human microbiota increasingly recognised nowadays as one of the most important health challenges is becoming an emerging research front. By examining over 28 000 microbiota-related papers from the Web of Science database, our study aims to characterise the evolution of publication patterns in this field between 1999 and 2017. The corpus is first analysed in terms of breakdown by journal subject categories, then an additional insight in the structuring of the microbiota research into different topics is provided by means of topic modelling. Our results demonstrate that over time (i) a substantial increase in the publications number is accompanied by a broad diversification of associated journal subject categories; (ii) the research focus moved outside from its primary research field showing successive shifts from dentistry and ecologically centred areas, through agri-food applied topics, towards the most recent clinical applications. The trends in thematic structure of the field presented from a historical perspective suggest that the current systemic approach to host-microbiota relationship inherited from the ecological background of the concept of microbiota has opened up a number of new research directions and perspectives.
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Affiliation(s)
- Lesya Baudoin
- Observatoire des Sciences et Techniques, Hcéres, 2 Rue Albert Einstein, Paris, 75013 France
| | - David Sapinho
- Observatoire des Sciences et Techniques, Hcéres, 2 Rue Albert Einstein, Paris, 75013 France
| | - Abdelghani Maddi
- Observatoire des Sciences et Techniques, Hcéres, 2 Rue Albert Einstein, Paris, 75013 France.,CEPN, UMR-CNRS 723, Université Paris 13, Villetaneuse, 93430 France
| | - Luis Miotti
- Observatoire des Sciences et Techniques, Hcéres, 2 Rue Albert Einstein, Paris, 75013 France.,CEPN, UMR-CNRS 723, Université Paris 13, Villetaneuse, 93430 France
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7
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Morar N, Bohannan BJM. The Conceptual Ecology of the Human Microbiome. QUARTERLY REVIEW OF BIOLOGY 2019. [DOI: 10.1086/703582] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kohl KD. An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology. Integr Comp Biol 2018; 57:674-681. [PMID: 28985331 DOI: 10.1093/icb/icx013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
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O’Malley MA, Skillings DJ. Methodological Strategies in Microbiome Research and their Explanatory Implications. ACTA ACUST UNITED AC 2018. [DOI: 10.1162/posc_a_00274] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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O'Malley MA. From endosymbiosis to holobionts: Evaluating a conceptual legacy. J Theor Biol 2017; 434:34-41. [PMID: 28302492 DOI: 10.1016/j.jtbi.2017.03.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 03/03/2017] [Accepted: 03/09/2017] [Indexed: 02/07/2023]
Abstract
In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term 'holobiont' to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system. My analysis will track how Margulis came to propose the term, its current use in microbiome research, and how those applications link back to Margulis. I then evaluate what contemporary use says about Margulis's legacy for microbiome research.
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Pellegatta T, Saler M, Bonfanti V, Nicoletti G, Faga A. Novel perspectives on the role of the human microbiota in regenerative medicine and surgery. Biomed Rep 2016; 5:519-524. [PMID: 27882211 PMCID: PMC5103662 DOI: 10.3892/br.2016.778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/21/2016] [Indexed: 12/19/2022] Open
Abstract
Plastic surgery is transitioning from a fine craftsmanship to a regenerative science. In wound healing, the role of microorganisms is no longer considered to be just counteracting, but also promoting. Furthermore, host-microbe interactions are essential for numerous aspects of normal mammalian physiology, from metabolic activity to immune homeostasis. Each area of the human body hosts a unique microbial community, and the composition of microbiota is dependent on the host, age and the anatomical area, and it changes according to the characteristics of the microenvironment. Every squared centimeter of skin contains ~1 billion bacteria. The majority of microorganisms of the skin are commensal or temporary passing members. Skin flora mechanisms interacting or influencing the human physical skin barrier are not well defined. Resident skin bacteria provide the first line of defence against potentially dangerous pathogens and produce small molecules that influence their microbial neighbours. Furthermore, the microbiota activates and assists innate immunity and influences adaptive immunity. Various types of immune and non-immune cells contribute to wound healing. The proliferative phase of wound healing is inversely proportional to the extent of the post-traumatic inflammatory reaction. Topical bacterial lipopolysaccharide application markedly affects wound healing by accelerating the resolution of inflammation, increasing macrophage infiltration, enhancing collagen synthesis and altering the secretion of mediators involved in skin regeneration. Various studies have investigated the biological contents of thermal spring waters, and their anti-inflammatory and immune protective roles. In addition, the regenerative properties of thermal spring waters were analysed in an experimental animal wound model. The areas treated with thermal water healed faster than the areas treated with conventional dressings, and exhibited a collagen and elastic fiber network comparable with the normal skin. Thus, the microbial environment may be considered as a potential tool in regenerative medicine and surgery.
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Affiliation(s)
- Tommaso Pellegatta
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Plastic Surgery Unit, University of Pavia, Pavia, I-27100 Lombardy, Italy
| | - Marco Saler
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Plastic Surgery Unit, University of Pavia, Pavia, I-27100 Lombardy, Italy
| | - Viola Bonfanti
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Plastic Surgery Unit, University of Pavia, Pavia, I-27100 Lombardy, Italy
| | - Giovanni Nicoletti
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Plastic Surgery Unit, University of Pavia, Pavia, I-27100 Lombardy, Italy
- Plastic and Reconstructive Surgery Unit, Salvatore Maugeri Research and Care Institute, Pavia, I-27100 Lombardy, Italy
| | - Angela Faga
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Plastic Surgery Unit, University of Pavia, Pavia, I-27100 Lombardy, Italy
- Plastic and Reconstructive Surgery Unit, Salvatore Maugeri Research and Care Institute, Pavia, I-27100 Lombardy, Italy
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Adami AJ, Bracken SJ. Breathing Better Through Bugs: Asthma and the Microbiome. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:309-324. [PMID: 27698615 PMCID: PMC5045140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Asthma is a highly heterogeneous disease characterized by inflammation of the airways, which invokes symptoms such as wheeze, dyspnea, and chest tightness. Asthma is the product of multiple interconnected immunological processes and represents a constellation of related, but distinct, disease phenotypes. The prevalence of asthma has more than doubled since the 1980s, and efforts to understand this increase have inspired consideration of the microbiome as a key player in the pathophysiology and regulation of this disease. While recent years have seen an explosion of new research in this area, researchers are only beginning to untangle to mechanisms by which the microbiome may influence asthma. This review will focus on the relationship between the microbiome and the immune system and how this influences development of asthma. This review will also highlight evidence that may point the way toward new therapies and potential cures for this ancient respiratory foe.
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Affiliation(s)
- Alexander J. Adami
- To whom all correspondence should be addressed: Alexander J. Adami, MD/PhD Student, University of Connecticut Health Center, Department of Immunology, 263 Farmington Avenue, MC 1319, Farmington, CT 06030, , Phone: 1-860-679-1995, Fax: 1-860-679-1047
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Abstract
How effectively communities of scientists come together and co-operate is crucial both to the quality of research outputs and to the extent to which such outputs integrate insights, data and methods from a variety of fields, laboratories and locations around the globe. This essay focuses on the ensemble of material and social conditions that makes it possible for a short-term collaboration, set up to accomplish a specific task, to give rise to relatively stable communities of researchers. We refer to these distinctive features as repertoires, and investigate their development and implementation across three examples of collaborative research in the life sciences. We conclude that whether a particular project ends up fostering the emergence of a resilient research community is partly determined by the degree of attention and care devoted by researchers to material and social elements beyond the specific research questions under consideration.
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Affiliation(s)
- Sabina Leonelli
- Department of Sociology, Philosophy and Anthropology & Exeter Centre for the Study of the Life Sciences (Egenis), University of Exeter, Byrne House, St Germans Road, EX4 4PJ Exeter, UK;
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Individuality as a Theoretical Scheme. I. Formal and Material Concepts of Individuality. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s13752-014-0192-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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