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Shanmugan S, Seidlitz J, Cui Z, Adebimpe A, Bassett DS, Bertolero MA, Davatzikos C, Fair DA, Gur RE, Gur RC, Larsen B, Li H, Pines A, Raznahan A, Roalf DR, Shinohara RT, Vogel J, Wolf DH, Fan Y, Alexander-Bloch A, Satterthwaite TD. Sex differences in the functional topography of association networks in youth. Proc Natl Acad Sci U S A 2022; 119:e2110416119. [PMID: 35939696 PMCID: PMC9388107 DOI: 10.1073/pnas.2110416119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/15/2022] [Indexed: 01/16/2023] Open
Abstract
Prior work has shown that there is substantial interindividual variation in the spatial distribution of functional networks across the cerebral cortex, or functional topography. However, it remains unknown whether there are sex differences in the topography of individualized networks in youth. Here, we leveraged an advanced machine learning method (sparsity-regularized non-negative matrix factorization) to define individualized functional networks in 693 youth (ages 8 to 23 y) who underwent functional MRI as part of the Philadelphia Neurodevelopmental Cohort. Multivariate pattern analysis using support vector machines classified participant sex based on functional topography with 82.9% accuracy (P < 0.0001). Brain regions most effective in classifying participant sex belonged to association networks, including the ventral attention, default mode, and frontoparietal networks. Mass univariate analyses using generalized additive models with penalized splines provided convergent results. Furthermore, transcriptomic data from the Allen Human Brain Atlas revealed that sex differences in multivariate patterns of functional topography were spatially correlated with the expression of genes on the X chromosome. These results highlight the role of sex as a biological variable in shaping functional topography.
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Affiliation(s)
- Sheila Shanmugan
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Jakob Seidlitz
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Zaixu Cui
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
- Chinese Institute for Brain Research, Beijing,102206, China
| | - Azeez Adebimpe
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Danielle S. Bassett
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104
- Santa Fe Institute, Santa Fe, NM 87501
| | - Maxwell A. Bertolero
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Christos Davatzikos
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
| | - Damien A. Fair
- Department of Behavioral Neuroscience, Department of Psychiatry, Advanced Imaging Research Center, Oregon Health and Science University, Portland, OR 97239
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
| | - Ruben C. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
| | - Bart Larsen
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Hongming Li
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
| | - Adam Pines
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Armin Raznahan
- Section on Developmental Neurogenomics Unit, Intramural Research Program, National Institutes of Mental Health, Bethesda, MD 20892
| | - David R. Roalf
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Russell T. Shinohara
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104
| | - Jacob Vogel
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Daniel H. Wolf
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
| | - Yong Fan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Theodore D. Satterthwaite
- Penn Lifespan Informatics and Neuroimaging Center, University of Pennsylvania, Philadelphia, PA 19104
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104
- Penn-Children's Hospital of Philadelphia Lifespan Brain Institute, University of Pennsylvania, Philadelphia, PA 19104
- Center for Biomedical Image Computation and Analytics, University of Pennsylvania, Philadelphia, PA 19104
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Huang M, Chai L, Jiang D, Zhang M, Jia W, Huang Y, Zhou J. Dissolved organic matter (DOM) quality drives biogeographic patterns of soil bacterial communities and their association networks in semi-arid regions. FEMS Microbiol Ecol 2021; 97:6307509. [PMID: 34156067 DOI: 10.1093/femsec/fiab083] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
It is of great interest to elucidate the biogeographic patterns of soil microorganisms and their driving forces, which is fundamental to predicting alterations in microbial-mediated functions arising from environment changes. Although dissolved organic matter (DOM) represents an important resource for soil microorganisms, knowledge of how its quality affects microbial biogeography is limited. Here, we characterized soil bacterial communities and DOM quality in 45 soil samples collected from a 1500-km sampling transect through semi-arid regions in northern China which are currently suffering great pressure from climate change, using Illumina Miseq sequencing and fluorescence spectroscopy, respectively. We found that DOM quality (i.e. the source of DOM and the humification degree of DOM) had profound shaping influence on the biogeographic patterns exhibited by bacterial diversity, community composition and association networks. Specifically, the composition of bacteria community closely associated with DOM quality. Plant-derived DOM sustained higher bacterial diversity relative to microbial-derived DOM. Meanwhile, bacterial diversity linearly increased with increasing humification degree of DOM. Additionally, plant-derived DOM was observed to foster more complex bacterial association networks with less competition. Together, our work contributes to the factors underlying biogeographic patterns not only of bacterial diversity, community composition but also of their association networks and reports previously undocumented important role of DOM quality in shaping these patterns.
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Affiliation(s)
- Muke Huang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Liwei Chai
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Dalin Jiang
- Gradute School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Mengjun Zhang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Weiqian Jia
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yi Huang
- College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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van Tilborg D, Saccenti E. Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. Cancers (Basel) 2021; 13:393. [PMID: 33494351 DOI: 10.3390/cancers13030393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Changes in metabolism are a well-known characteristic of cancer cells. Different cancer types are unique in their genetic aspects, but also in their metabolism, which is in turn, governed by genetics. The aim of our study was to find these differences in metabolic behavior across different cancer types and uncovering intersections between gene expression and metabolic deregulations. We scoured the public domain for metabolomics and transcriptomics data from clinical profiling studies to perform a comprehensive comparison study. By combining evidence from both the genetic and the metabolic aspects, we described the most prominently aberrated pathways across eight different cancer types together with their metabolomic and transcriptomics similarities. Abstract One of the major hallmarks of cancer is the derailment of a cell’s metabolism. The multifaceted nature of cancer and different cancer types is transduced by both its transcriptomic and metabolomic landscapes. In this study, we re-purposed the publicly available transcriptomic and metabolomics data of eight cancer types (breast, lung, gastric, renal, liver, colorectal, prostate, and multiple myeloma) to find and investigate differences and commonalities on a pathway level among different cancer types. Topological analysis of inferred graphical Gaussian association networks showed that cancer was strongly defined in genetic networks, but not in metabolic networks. Using different statistical approaches to find significant differences between cancer and control cases, we highlighted the difficulties of high-level data-merging and in using statistical association networks. Cancer transcriptomics and metabolomics and landscapes were characterized by changed macro-molecule production, however, only major metabolic deregulations with highly impacted pathways were found in liver cancer. Cell cycle was enriched in breast, liver, and colorectal cancer, while breast and lung cancer were distinguished by highly enriched oncogene signaling pathways. A strong inflammatory response was observed in lung cancer and, to some extent, renal cancer. This study highlights the necessity of combining different omics levels to obtain a better description of cancer characteristics.
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Mena C, Reglero P, Balbín R, Martín M, Santiago R, Sintes E. Seasonal Niche Partitioning of Surface Temperate Open Ocean Prokaryotic Communities. Front Microbiol 2020; 11:1749. [PMID: 32849378 PMCID: PMC7399227 DOI: 10.3389/fmicb.2020.01749] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 07/03/2020] [Indexed: 12/20/2022] Open
Abstract
Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche.
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Affiliation(s)
- Catalina Mena
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Patricia Reglero
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Rosa Balbín
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Melissa Martín
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Rocío Santiago
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
| | - Eva Sintes
- Instituto Español de Oceanografía (IEO), Centre Oceanogràfic de les Balears, Ecosystem Oceanography Group (GRECO), Palma, Spain
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Dover Y, Moore Z. Using free association networks to extract characteristic patterns of affect dynamics. Proc Math Phys Eng Sci 2020; 476:20190647. [PMID: 32398929 PMCID: PMC7209140 DOI: 10.1098/rspa.2019.0647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/04/2020] [Indexed: 11/12/2022] Open
Abstract
The dynamics of human affect in day-to-day life are an intrinsic part of human behaviour. Yet, it is difficult to observe and objectively measure how affect evolves over time with sufficient resolution. Here, we suggest an approach that combines free association networks with affect mapping, to gain insight into basic patterns of affect dynamics. This approach exploits the established connection in the literature between association networks and behaviour. Using extant rich data, we find consistent patterns of the dynamics of the valence and arousal dimensions of affect. First, we find that the individuals represented by the data tend to feel a constant pull towards an affect-neutral global equilibrium point in the valence-arousal space. The farther the affect is from that point, the stronger the pull. We find that the drift of affect exhibits high inertia, i.e. is slow-changing, but with occasional discontinuous jumps of valence. We further find that, under certain conditions, another metastable equilibrium point emerges on the network, but one which represents a much more negative and agitated state of affect. Finally, we demonstrate how the affect-coded association network can be used to identify useful or harmful trajectories of associative thoughts that otherwise are hard to extract.
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Affiliation(s)
- Yaniv Dover
- Federmann Center for the Study of Rationality, Hebrew University, Jerusalem, Israel
- The Jerusalem Business School, Hebrew University, Jerusalem, Israel
| | - Zohar Moore
- The Jerusalem Business School, Hebrew University, Jerusalem, Israel
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