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Abstract
The shape of phylogenetic trees can be used to gain evolutionary insights. A tree’s shape specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic distance between branching events; well-known measures of tree shape include the Colless and Sackin imbalance, which describe the asymmetry of a tree. In other contexts, network science has become an important paradigm for describing structural features of networks and using them to understand complex systems, ranging from protein interactions to social systems. Network science is thus a potential source of many novel ways to characterize tree shape, as trees are also networks. Here, we tailor tools from network science, including diameter, average path length, and betweenness, closeness, and eigenvector centrality, to summarize phylogenetic tree shapes. We thereby propose tree shape summaries that are complementary to both asymmetry and the frequencies of small configurations. These new statistics can be computed in linear time and scale well to describe the shapes of large trees. We apply these statistics, alongside some conventional tree statistics, to phylogenetic trees from three very different viruses (HIV, dengue fever and measles), from the same virus in different epidemiological scenarios (influenza A and HIV) and from simulation models known to produce trees with different shapes. Using mutual information and supervised learning algorithms, we find that the statistics adapted from network science perform as well as or better than conventional statistics. We describe their distributions and prove some basic results about their extreme values in a tree. We conclude that network science-based tree shape summaries are a promising addition to the toolkit of tree shape features. All our shape summaries, as well as functions to select the most discriminating ones for two sets of trees, are freely available as an R package at http://github.com/Leonardini/treeCentrality.
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Affiliation(s)
- Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
- * E-mail:
| | - Maryam Hayati
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Art F. Y. Poon
- Department of Pathology & Laboratory Medicine, University of Western Ontario, London, ON, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
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2
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Wilkins D, Tong X, Leung MHY, Mason CE, Lee PKH. Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching. Microbiome 2021; 9:129. [PMID: 34090519 PMCID: PMC8180031 DOI: 10.1186/s40168-021-01082-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/21/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days. RESULTS Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied. CONCLUSIONS These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.
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Affiliation(s)
- David Wilkins
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
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3
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Medley JK, Teo J, Woo SS, Hellerstein J, Sarpeshkar R, Sauro HM. A compiler for biological networks on silicon chips. PLoS Comput Biol 2020; 16:e1008063. [PMID: 32966274 PMCID: PMC7535129 DOI: 10.1371/journal.pcbi.1008063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 10/05/2020] [Accepted: 06/16/2020] [Indexed: 12/18/2022] Open
Abstract
The explosive growth in semiconductor integrated circuits was made possible in large part by design automation software. The design and/or analysis of synthetic and natural circuits in living cells could be made more scalable using the same approach. We present a compiler which converts standard representations of chemical reaction networks and circuits into hardware configurations that can be used to simulate the network on specialized cytomorphic hardware. The compiler also creates circuit–level models of the target configuration, which enhances the versatility of the compiler and enables the validation of its functionality without physical experimentation with the hardware. We show that this compiler can translate networks comprised of mass–action kinetics, classic enzyme kinetics (Michaelis–Menten, Briggs–Haldane, and Botts–Morales formalisms), and genetic repressor kinetics, thereby allowing a large class of models to be transformed into a hardware representation. Rule–based models are particularly well–suited to this approach, as we demonstrate by compiling a MAP kinase model. Development of specialized hardware and software for simulating biological networks has the potential to enable the simulation of larger kinetic models than are currently feasible or allow the parallel simulation of many smaller networks with better performance than current simulation software. We present a “silicon compiler” that is capable of translating biochemical models encoded in the SBML standard into specialized analog cytomorphic hardware and transfer function–level simulations of such hardware. We show how the compiler and hardware address challenges in analog computing: 1) We ensure that the integration of errors due to the mismatch between analog circuit parameters does not become infinite over time but always remains finite via the use of total variables (the solution of the “divergence problem”); 2) We describe the compilation process through a series of examples using building blocks of biological networks, and show the results of compiling two SBML models from the literature: the Elowitz repressilator model and a rule–based model of a MAP kinase cascade. Source code for the compiler is available at https://doi.org/10.5281/zenodo.3948393.
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Affiliation(s)
- J. Kyle Medley
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Jonathan Teo
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Sung Sik Woo
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, United States of America
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Joseph Hellerstein
- eScience Institute, University of Washington, Seattle, Washington, United States of America
| | - Rahul Sarpeshkar
- Departments of Engineering, Microbiology & Immunology, Physics, and Molecular and Systems Biology, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
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Cheng W, Ramachandran S, Crawford L. Estimation of non-null SNP effect size distributions enables the detection of enriched genes underlying complex traits. PLoS Genet 2020; 16:e1008855. [PMID: 32542026 PMCID: PMC7316356 DOI: 10.1371/journal.pgen.1008855] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 06/25/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022] Open
Abstract
Traditional univariate genome-wide association studies generate false positives and negatives due to difficulties distinguishing associated variants from variants with spurious nonzero effects that do not directly influence the trait. Recent efforts have been directed at identifying genes or signaling pathways enriched for mutations in quantitative traits or case-control studies, but these can be computationally costly and hampered by strict model assumptions. Here, we present gene-ε, a new approach for identifying statistical associations between sets of variants and quantitative traits. Our key insight is that enrichment studies on the gene-level are improved when we reformulate the genome-wide SNP-level null hypothesis to identify spurious small-to-intermediate SNP effects and classify them as non-causal. gene-ε efficiently identifies enriched genes under a variety of simulated genetic architectures, achieving greater than a 90% true positive rate at 1% false positive rate for polygenic traits. Lastly, we apply gene-ε to summary statistics derived from six quantitative traits using European-ancestry individuals in the UK Biobank, and identify enriched genes that are in biologically relevant pathways.
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Affiliation(s)
- Wei Cheng
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Sohini Ramachandran
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- Department of Biostatistics, Brown University, Providence, Rhode Island, United States of America
- Center for Statistical Sciences, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (SR); (LC)
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5
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Abstract
Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed to investigate the shape of a phylogenetic tree. Tree shape statistics are a common approach to quantifying the shape of a phylogenetic tree by encoding it with a single number. In this article, we propose a new resolution function to evaluate the power of different tree shape statistics to distinguish between dissimilar trees. We show that the new resolution function requires less time and space in comparison with the previously proposed resolution function for tree shape statistics. We also introduce a new class of tree shape statistics, which are linear combinations of two existing statistics that are optimal with respect to a resolution function, and show evidence that the statistics in this class converge to a limiting linear combination as the size of the tree increases. Our implementation is freely available at https://github.com/WGS-TB/TreeShapeStats.
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Affiliation(s)
- Maryam Hayati
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Bita Shadgar
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
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Prussin AJ, Torres PJ, Shimashita J, Head SR, Bibby KJ, Kelley ST, Marr LC. Seasonal dynamics of DNA and RNA viral bioaerosol communities in a daycare center. Microbiome 2019; 7:53. [PMID: 30935423 PMCID: PMC6444849 DOI: 10.1186/s40168-019-0672-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/22/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Viruses play an important role in ecosystems, including the built environment (BE). While numerous studies have characterized bacterial and fungal microbiomes in the BE, few have focused on the viral microbiome (virome). Longitudinal microbiome studies provide insight into the stability and dynamics of microbial communities; however, few such studies exist for the microbiome of the BE, and most have focused on bacteria. Here, we present a longitudinal, metagenomic-based analysis of the airborne DNA and RNA virome of a children's daycare center. Specifically, we investigate how the airborne virome varies as a function of season and human occupancy, and we identify possible sources of the viruses and their hosts, mainly humans, animals, plants, and insects. RESULTS Season strongly influenced the airborne viral community composition, and a single sample collected when the daycare center was unoccupied suggested that occupancy also influenced the community. The pattern of influence differed between DNA and RNA viromes. Human-associated viruses were much more diverse and dominant in the winter, while the summertime virome contained a high relative proportion and diversity of plant-associated viruses. CONCLUSIONS This airborne microbiome in this building exhibited seasonality in its viral community but not its bacterial community. Human occupancy influenced both types of communities. By adding new data about the viral microbiome to complement burgeoning information about the bacterial and fungal microbiomes, this study contributes to a more complete understanding of the airborne microbiome.
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Affiliation(s)
- Aaron J. Prussin
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
| | - Pedro J. Torres
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - John Shimashita
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Steven R. Head
- Next Generation Sequencing and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Kyle J. Bibby
- Department of Civil and Environmental Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Scott T. Kelley
- Department of Biology, San Diego State University, San Diego, CA 92182 USA
| | - Linsey C. Marr
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061 USA
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Olm MR, West PT, Brooks B, Firek BA, Baker R, Morowitz MJ, Banfield JF. Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms. Microbiome 2019; 7:26. [PMID: 30770768 PMCID: PMC6377789 DOI: 10.1186/s40168-019-0638-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/29/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Fungal infections are a significant cause of mortality and morbidity in hospitalized preterm infants, yet little is known about eukaryotic colonization of infants and of the neonatal intensive care unit as a possible source of colonizing strains. This is partly because microbiome studies often utilize bacterial 16S rRNA marker gene sequencing, a technique that is blind to eukaryotic organisms. Knowledge gaps exist regarding the phylogeny and microdiversity of eukaryotes that colonize hospitalized infants, as well as potential reservoirs of eukaryotes in the hospital room built environment. RESULTS Genome-resolved analysis of 1174 time-series fecal metagenomes from 161 premature infants revealed fungal colonization of 10 infants. Relative abundance levels reached as high as 97% and were significantly higher in the first weeks of life (p = 0.004). When fungal colonization occurred, multiple species were present more often than expected by random chance (p = 0.008). Twenty-four metagenomic samples were analyzed from hospital rooms of six different infants. Compared to floor and surface samples, hospital sinks hosted diverse and highly variable communities containing genomically novel species, including from Diptera (fly) and Rhabditida (worm) for which genomes were assembled. With the exception of Diptera and two other organisms, zygosity of the newly assembled diploid eukaryote genomes was low. Interestingly, Malassezia and Candida species were present in both room and infant gut samples. CONCLUSIONS Increased levels of fungal co-colonization may reflect synergistic interactions or differences in infant susceptibility to fungal colonization. Discovery of eukaryotic organisms that have not been sequenced previously highlights the benefit of genome-resolved analyses, and low zygosity of assembled genomes could reflect inbreeding or strong selection imposed by room conditions.
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Affiliation(s)
- Matthew R. Olm
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Patrick T. West
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Brandon Brooks
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
- Present address: Kaleido Biosciences, Bedford, MA USA
| | - Brian A. Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Robyn Baker
- Division of Newborn Medicine, Magee-Womens Hospital of UPMC, Pittsburgh, PA USA
| | - Michael J. Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA USA
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA USA
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8
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Silverman JD, Durand HK, Bloom RJ, Mukherjee S, David LA. Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome 2018; 6:202. [PMID: 30419949 PMCID: PMC6233358 DOI: 10.1186/s40168-018-0584-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/23/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Artificial gut models provide unique opportunities to study human-associated microbiota. Outstanding questions for these models' fundamental biology include the timescales on which microbiota vary and the factors that drive such change. Answering these questions though requires overcoming analytical obstacles like estimating the effects of technical variation on observed microbiota dynamics, as well as the lack of appropriate benchmark datasets. RESULTS To address these obstacles, we created a modeling framework based on multinomial logistic-normal dynamic linear models (MALLARDs) and performed dense longitudinal sampling of four replicate artificial human guts over the course of 1 month. The resulting analyses revealed how the ratio of biological variation to technical variation from sample processing depends on sampling frequency. In particular, we find that at hourly sampling frequencies, 76% of observed variation could be ascribed to technical sources, which could also skew the observed covariation between taxa. We also found that the artificial guts demonstrated replicable trajectories even after a recovery from a transient feed disruption. Additionally, we observed irregular sub-daily oscillatory dynamics associated with the bacterial family Enterobacteriaceae within all four replicate vessels. CONCLUSIONS Our analyses suggest that, beyond variation due to sequence counting, technical variation from sample processing can obscure temporal variation from biological sources in artificial gut studies. Our analyses also supported hypotheses that human gut microbiota fluctuates on sub-daily timescales in the absence of a host and that microbiota can follow replicable trajectories in the presence of environmental driving forces. Finally, multiple aspects of our approach are generalizable and could ultimately be used to facilitate the design and analysis of longitudinal microbiota studies in vivo.
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Affiliation(s)
- Justin D. Silverman
- Program in Computational Biology and Bioinformatics, Duke University, CIEMAS, Room 2171, 101 Science Drive, Box 3382, Durham, NC 27708 USA
- Medical Scientist Training Program, Duke University, Durham, NC 27708 USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA
| | - Heather K. Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708 USA
| | - Rachael J. Bloom
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708 USA
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke University, CIEMAS, Room 2171, 101 Science Drive, Box 3382, Durham, NC 27708 USA
- Departments of Statistical Science, Mathematics, Computer Science, Biostatistics & Bioinformatics, Duke University, Durham, NC 27708 USA
| | - Lawrence A. David
- Program in Computational Biology and Bioinformatics, Duke University, CIEMAS, Room 2171, 101 Science Drive, Box 3382, Durham, NC 27708 USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27708 USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708 USA
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9
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Abstract
Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare off-target effects. We present a method, CRISPhieRmix, that resolves these issues by using a hierarchical mixture model with a broad-tailed null distribution. We show that CRISPhieRmix allows for more accurate and powerful inferences in large-scale pooled CRISPRi/a screens. We discuss key issues in the analysis and design of screens, particularly the number of guides needed for faithful full discovery.
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Affiliation(s)
- Timothy P. Daley
- Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305 USA
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
| | - Zhixiang Lin
- Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305 USA
- Present Address: Department of Statistics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Xueqiu Lin
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
| | - Yanxia Liu
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, 450 Serra Mall, Stanford, 94305 USA
- Department of Biomedical Data Science, Stanford University, 1265 Welch Road, Stanford, 94305 USA
| | - Lei S. Qi
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, 94305 USA
- Department of Chemical and Systems Biology, Stanford University, 443 Via Ortega, Stanford, 94305 USA
- ChEM-H Institute, Stanford University, 443 Via Ortega, Stanford, 94305 USA
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Honey CJ, Newman EL, Schapiro AC. Switching between internal and external modes: A multiscale learning principle. Netw Neurosci 2017; 1:339-356. [PMID: 30090870 PMCID: PMC6063714 DOI: 10.1162/netn_a_00024] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/18/2017] [Indexed: 01/21/2023] Open
Abstract
Brains construct internal models that support perception, prediction, and action in the external world. Individual circuits within a brain also learn internal models of the local world of input they receive, in order to facilitate efficient and robust representation. How are these internal models learned? We propose that learning is facilitated by continual switching between internally biased and externally biased modes of processing. We review computational evidence that this mode-switching can produce an error signal to drive learning. We then consider empirical evidence for the instantiation of mode-switching in diverse neural systems, ranging from subsecond fluctuations in the hippocampus to wake-sleep alternations across the whole brain. We hypothesize that these internal/external switching processes, which occur at multiple scales, can drive learning at each scale. This framework predicts that (a) slower mode-switching should be associated with learning of more temporally extended input features and (b) disruption of switching should impair the integration of new information with prior information.
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Affiliation(s)
- Christopher J. Honey
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Ehren L. Newman
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Anna C. Schapiro
- Department of Psychiatry, Beth Israel Deaconess Medical Center / Harvard Medical School, Boston, MA, USA
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Jayaprakash B, Adams RI, Kirjavainen P, Karvonen A, Vepsäläinen A, Valkonen M, Järvi K, Sulyok M, Pekkanen J, Hyvärinen A, Täubel M. Indoor microbiota in severely moisture damaged homes and the impact of interventions. Microbiome 2017; 5:138. [PMID: 29029638 PMCID: PMC5640920 DOI: 10.1186/s40168-017-0356-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 09/27/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The limited understanding of microbial characteristics in moisture-damaged buildings impedes efforts to clarify which adverse health effects in the occupants are associated with the damage and to develop effective building intervention strategies. The objectives of this current study were (i) to characterize fungal and bacterial microbiota in house dust of severely moisture-damaged residences, (ii) to identify microbial taxa associated with moisture damage renovations, and (iii) to test whether the associations between the identified taxa and moisture damage are replicable in another cohort of homes. We applied bacterial 16S rRNA gene and fungal ITS amplicon sequencing complemented with quantitative PCR and chemical-analytical approaches to samples of house dust, and also performed traditional cultivation of bacteria and fungi from building material samples. RESULTS Active microbial growth on building materials had significant though small influence on the house dust bacterial and fungal communities. Moisture damage interventions-including actual renovation of damaged homes and cases where families moved to another home-had only a subtle effect on bacterial community structure, seen as shifts in abundance weighted bacterial profiles after intervention. While bacterial and fungal species richness were reduced in homes that were renovated, they were not reduced for families that moved houses. Using different discriminant analysis tools, we were able identify taxa that were significantly reduced in relative abundance during renovation of moisture damage. For bacteria, the majority of candidates belonged to different families within the Actinomycetales order. Results for fungi were overall less consistent. A replication study in approximately 400 homes highlighted some of the identified taxa, confirming associations with observations of moisture damage and mold. CONCLUSIONS The present study is one of the first studies to analyze changes in microbiota due to moisture damage interventions using high-throughput sequencing. Our results suggest that effects of moisture damage and moisture damage interventions may appear as changes in the abundance of individual, less common, and especially bacterial taxa, rather than in overall community structure.
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Affiliation(s)
| | - Rachel I. Adams
- Plant and Microbial Biology, University of California, Berkeley, California USA
- California Department of Public Health, Richmond, California USA
| | - Pirkka Kirjavainen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Anne Karvonen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Asko Vepsäläinen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Maria Valkonen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Kati Järvi
- School of Engineering, Aalto University, Espoo, Finland
| | - Michael Sulyok
- Department for Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, (BOKU), Vienna, Tulln Austria
| | - Juha Pekkanen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, Helsinki University, Helsinki, Finland
| | - Anne Hyvärinen
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
| | - Martin Täubel
- Environmental Health Unit, National Institute for Health and Welfare, Kuopio, Finland
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12
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Wu X, Tan LZ, Shen X, Hu T, Miyata K, Trinh MT, Li R, Coffee R, Liu S, Egger DA, Makasyuk I, Zheng Q, Fry A, Robinson JS, Smith MD, Guzelturk B, Karunadasa HI, Wang X, Zhu X, Kronik L, Rappe AM, Lindenberg AM. Light-induced picosecond rotational disordering of the inorganic sublattice in hybrid perovskites. Sci Adv 2017; 3:e1602388. [PMID: 28782016 PMCID: PMC5529057 DOI: 10.1126/sciadv.1602388] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/22/2017] [Indexed: 05/19/2023]
Abstract
Femtosecond resolution electron scattering techniques are applied to resolve the first atomic-scale steps following absorption of a photon in the prototypical hybrid perovskite methylammonium lead iodide. Following above-gap photoexcitation, we directly resolve the transfer of energy from hot carriers to the lattice by recording changes in the mean square atomic displacements on 10-ps time scales. Measurements of the time-dependent pair distribution function show an unexpected broadening of the iodine-iodine correlation function while preserving the Pb-I distance. This indicates the formation of a rotationally disordered halide octahedral structure developing on picosecond time scales. This work shows the important role of light-induced structural deformations within the inorganic sublattice in elucidating the unique optoelectronic functionality exhibited by hybrid perovskites and provides new understanding of hot carrier-lattice interactions, which fundamentally determine solar cell efficiencies.
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Affiliation(s)
- Xiaoxi Wu
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Liang Z. Tan
- The Makineni Theoretical Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323, USA
| | - Xiaozhe Shen
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Te Hu
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
| | - Kiyoshi Miyata
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - M. Tuan Trinh
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Renkai Li
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ryan Coffee
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Shi Liu
- Extreme Materials Initiative, Geophysical Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - David A. Egger
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Igor Makasyuk
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Qiang Zheng
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Alan Fry
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Matthew D. Smith
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Burak Guzelturk
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Xijie Wang
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Xiaoyang Zhu
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Leeor Kronik
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovoth 76100, Israel
| | - Andrew M. Rappe
- The Makineni Theoretical Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104–6323, USA
| | - Aaron M. Lindenberg
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA
- PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Corresponding author.
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13
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Abstract
Neuroprosthetic brain-computer interfaces function via an algorithm which decodes neural activity of the user into movements of an end effector, such as a cursor or robotic arm. In practice, the decoder is often learned by updating its parameters while the user performs a task. When the user's intention is not directly observable, recent methods have demonstrated value in training the decoder against a surrogate for the user's intended movement. Here we show that training a decoder in this way is a novel variant of an imitation learning problem, where an oracle or expert is employed for supervised training in lieu of direct observations, which are not available. Specifically, we describe how a generic imitation learning meta-algorithm, dataset aggregation (DAgger), can be adapted to train a generic brain-computer interface. By deriving existing learning algorithms for brain-computer interfaces in this framework, we provide a novel analysis of regret (an important metric of learning efficacy) for brain-computer interfaces. This analysis allows us to characterize the space of algorithmic variants and bounds on their regret rates. Existing approaches for decoder learning have been performed in the cursor control setting, but the available design principles for these decoders are such that it has been impossible to scale them to naturalistic settings. Leveraging our findings, we then offer an algorithm that combines imitation learning with optimal control, which should allow for training of arbitrary effectors for which optimal control can generate goal-oriented control. We demonstrate this novel and general BCI algorithm with simulated neuroprosthetic control of a 26 degree-of-freedom model of an arm, a sophisticated and realistic end effector.
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Affiliation(s)
- Josh Merel
- Neurobiology and Behavior program, Columbia University, New York, New York, United States of America
- Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
| | - David Carlson
- Department of Statistics, Columbia University, New York, New York, United States of America
- Grossman Center for the Statistics of Mind, Columbia University, New York, New York, United States of America
| | - Liam Paninski
- Neurobiology and Behavior program, Columbia University, New York, New York, United States of America
- Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
- Grossman Center for the Statistics of Mind, Columbia University, New York, New York, United States of America
| | - John P. Cunningham
- Neurobiology and Behavior program, Columbia University, New York, New York, United States of America
- Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
- Grossman Center for the Statistics of Mind, Columbia University, New York, New York, United States of America
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14
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Abstract
Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the built environment is characterizing the various sources of airborne microorganisms and the relative contribution of each. We have identified the following eight major categories of sources of airborne bacteria, viruses, and fungi in the built environment: humans; pets; plants; plumbing systems; heating, ventilation, and air-conditioning systems; mold; dust resuspension; and the outdoor environment. Certain species are associated with certain sources, but the full potential of source characterization and source apportionment has not yet been realized. Ideally, future studies will quantify detailed emission rates of microorganisms from each source and will identify the relative contribution of each source to the indoor air microbiome. This information could then be used to probe fundamental relationships between specific sources and human health, to design interventions to improve building health and human health, or even to provide evidence for forensic investigations.
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Affiliation(s)
- Aaron J Prussin
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Linsey C Marr
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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15
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Miletto M, Lindow SE. Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences. Microbiome 2015; 3:61. [PMID: 26653310 PMCID: PMC4674937 DOI: 10.1186/s40168-015-0128-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 10/29/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that determine their assembly. We investigated the source-sink relationships of airborne bacteria in 29 homes in the San Francisco Bay Area. Samples taken in the sites expected to be source habitats for indoor air microbes were analyzed by 16S rRNA-based pyrosequencing and quantitative PCR. The community composition was related to the characteristics of the household collected at the time of sampling, including the number of residents and pets, activity levels, frequency of cooking and vacuum cleaning, extent of natural ventilation, and abundance and type of vegetation surrounding the building. RESULTS Indoor air harbored a diverse bacterial community dominated by Diaphorobacter sp., Propionibacterium sp., Sphingomonas sp., and Alicyclobacillus sp. Source-sink analysis suggested that outdoor air was the primary source of indoor air microbes in most homes. Bacterial phylogenetic diversity and relative abundance in indoor air did not differ statistically from that in outdoor air. Moreover, the abundance of bacteria in outdoor air was positively correlated with that in indoor air, as would be expected if outdoor air was the main contributor to the bacterial community in indoor bioaerosols. The number of residents, presence of pets, and local tap water also influenced the diversity and size of indoor air microbes. The bacterial load in air increased with the number of residents, activity, and frequency of natural ventilation, and the proportion of bacteria putatively derived from skin increased with the number of residents. Vacuum cleaning increased the signature of pet- and floor-derived bacteria in indoor air, while the frequency of natural ventilation decreased the relative abundance of tap water-derived microorganisms in air. CONCLUSIONS Indoor air in residences harbors a diverse bacterial community originating from both outdoor and indoor sources and is strongly influenced by household characteristics.
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Affiliation(s)
- Marzia Miletto
- Plant & Microbial Biology, University of California Berkeley, 331 Koshland Hall, Berkeley, CA, 94720, USA.
| | - Steven E Lindow
- Plant & Microbial Biology, University of California Berkeley, 331 Koshland Hall, Berkeley, CA, 94720, USA.
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