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Gap Filling in the Plant Kingdom---Trait Prediction Using Hierarchical Probabilistic Matrix Factorization [article]

Hanhuai Shan, Jens Kattge (Max Planck Institute for Biogeochemistry), Peter Reich , Arindam Banerjee, Franziska Schrodt (University of Minnesota), Markus Reichstein
2012 arXiv   pre-print
We propose hierarchical probabilistic matrix factorization (HPMF), which effectively uses hierarchical phylogenetic information for trait prediction.  ...  Meanwhile, the trait data is characterized by the hierarchical phylogenetic structure of the plant kingdom.  ...  Acknowledgments The research was supported by NSF grants IIS-0812183, IIS-0916750, IIS-1029711, IIS-1017647, and NSF CAREER award IIS-0953274.  ... 
arXiv:1206.6439v1 fatcat:ybleoqd5zjau7aq2qx5t3rqviq

BHPMF - a hierarchical Bayesian approach to gap-filling and trait prediction for macroecology and functional biogeography

Franziska Schrodt, Jens Kattge, Hanhuai Shan, Farideh Fazayeli, Julia Joswig, Arindam Banerjee, Markus Reichstein, Gerhard Bönisch, Sandra Díaz, John Dickie, Andy Gillison, Anuj Karpatne (+6 others)
2015 Global Ecology and Biogeography  
We propose the application of probabilistic models which, for the first time, utilize all three characteristics to fill gaps in trait databases and predict trait values at larger spatial scales.  ...  Innovation For this purpose we introduce BHPMF, a hierarchical Bayesian extension of probabilistic matrix factorization (PMF).  ...  This study has been performed with support by the TRY initiative on plant traits (https://www.try-db.org).  ... 
doi:10.1111/geb.12335 fatcat:rqvq3ikrtzgknlyednfui4sb2u

Approaches to Macroevolution: 2. Sorting of Variation, Some Overarching Issues, and General Conclusions

David Jablonski
2017 Evolutionary biology  
Some overarching issues relating to both the origin and sorting of clades and phenotypes include the macroevolutionary role of mass extinctions, the potential differences between plant and animal macroevolution  ...  A novel approach to diversity-disparity analysis shows that taxonomic diversifications can lag behind, occur in concert with, or precede, increases in disparity.  ...  Acknowledgements This pair of papers had its start in a much  ... 
doi:10.1007/s11692-017-9434-7 pmid:29142334 pmcid:PMC5661022 fatcat:6fbmslwvqrhftg2kanjyv6p25q

Conference program and abstracts. International Biogeography Society 7th Biennial Meeting. 8–12 January 2015, Bayreuth, Germany. Frontiers of Biogeography Vol. 6, suppl. 1. International Biogeography Society, 246 pp

Daniel Gavin, Carl Beierkuhnlein, Stefan Holzheu, Birgit Thies, Karen Faller, Rosemary Gillespie, Joaquín Hortal
2014 Frontiers of Biogeography  
Approx. 70% of the most frequent species are represented by at least one trait in the global trait database TRY and gap-filled data will become available for the most common traits.  ...  However, the use of large database about host-parasite relationship associated with "macroscopic" geographical range can be an elegant solution to throw foundations to fill this gap.  ...  We are using amphibians to test these predictions (A or B) using next generation sequencing methods (RAD-seq) and species distribution models.  ... 
doi:10.21425/f56525118 fatcat:3puoxcjd4bcublj6adlg2nzczq

29th Conference of European Vegetation Survey: Revegetating Europe – Contributions of the EVS to the UN Decade on Ecological Restoration. Online conference, 6–7 September 2021. Abstracts [article]

European Vegetation Survey
2021 Zenodo  
Book of Abstracts of the 29th Conference of European Vegetation Survey  ...  Plant functional traits can be used in assessing the succession dynamics of vegetation. Jan Roleček*, P. Dřevojan, D. Iakushenko, M.  ...  NFVDT fills an important gap in continental and global vegetation-plot databases. Its content is already included in the European Vegetation Archive (EVA), and future updates are planned.  ... 
doi:10.5281/zenodo.5171736 fatcat:msqmubro7bdt3fww2otdg6mdgq

Conference program and abstracts. International Biogeography Society 6th Biennial Meeting – 9-13 January 2013, Miami, Florida, USA

Joaquín Hortal, Karen Faller, Kenneth Feeley, Richard Field, Catherine Graham, François Guilhaumon, Daniel Gavin
2012 Frontiers of Biogeography  
The geography of divergence and disparity: how landscapes help understand the decoupling of genetic structure and phenotypic diversity. 43A Assembly of plant communities in climate space Benjamin Blonder  ...  We tested the ability of trait-based models to predict plant distribution change across seven geographic regions (Flanders and six regions in Britain) that varied in terms of land-cover and species composition  ...  host plant abundance or its reproductive output; rather canopy cover was amongst the most important factors predicting specialist herbivory rates between landscapes.  ... 
doi:10.21425/f5fbg15702 fatcat:lwyauz5kbvcwbmimvei4iota3a

Sponsored Collection | Hangzhou Normal University: Serving China through world-class research and education

2018 Science  
The study in the Cong laboratory was supported by grants from the National Natural Science Foundation of China (31730020, 31371398, and 315714090) and the National Basic Research Program of China (2012CB911203  ...  Acknowledgments We gratefully acknowledge the National Natural Science Acknowledgments The authors wish to thank the Science and Technology Development Program of Hangzhou (20170533B09) and the Natural  ...  These studies highlight the importance of phylogenetic analysis in testing relationships between plant functional traits and environmental factors.  ... 
doi:10.1126/science.360.6387.454-b fatcat:s6ypk6lvl5dmzhfom3vokgx7f4

DNATagger, colors for codons

N.M. Scherer, D.M. Basso
2008 Genetics and Molecular Research  
In the next step, the curated datasets were used to estimate the phylogeny of each family, and subsequently to infer the strength of natural selection acting on these proteins.  ...  The main objective of this thesis was to investigate and characterize all PR-families from an evolutionary point of view, using the genetic data available in public databases, to gain insights into the  ...  The location of the deletions is conserved throughout the whole plant kingdom.  ... 
doi:10.4238/vol7-3x-meeting003 fatcat:3erb3dubpjgzjnogoyjctwsla4

Cognitive Constructivism and the Epistemic Significance of Sharp Statistical Hypotheses in Natural Sciences [article]

J.M. Stern
2020 arXiv   pre-print
This book presents our case in defense of a constructivist epistemological framework and the use of compatible statistical theory and inference tools.  ...  This metaphor has proven to be very useful, leading the development of Bayesian statistics since its XX-th century revival, rooted on the work of de Finetti, Savage and others.  ...  A factorization (or ellimination) resulting in no fill in is called perfect.  ... 
arXiv:1006.5471v8 fatcat:v375ybolz5bkbe6ordmjnnulhi

Modelling the dynamic pattern of surface area in basketball and its effects on team performance

Rodolfo Metulini, Marica Manisera, Paola Zuccolotto
2018 Journal of Quantitative Analysis in Sports (JQAS)  
We carry out the proposed procedure using real data and, in the analyzed case studies, we find that structural changes are strongly associated to offensive and defensive game phases and that there is some  ...  Because of the advent of GPS techniques, a wide range of scientific literature on Sport Science is nowadays devoted to the analysis of players' movement in relation to team performance in the context of  ...  Secondly, a C++ and an R implementation of the proposed method are provided, which fills in the existing gap in statistical software.  ... 
doi:10.1515/jqas-2018-0041 fatcat:b3qwsi7tqjg2vdo7gbjtiorv6m

Chromosome-scale assembly of the coral endosymbiont Symbiodinium microadriaticum genome provides insight into the unique biology of dinoflagellate chromosomes [article]

Ankita Nand, Ye Zhan, Octavio R. Salazar, Manuel Aranda, Christian R. Voolstra, Job Dekker
2020 biorxiv/medrxiv   pre-print
Here we used Hi-C to order short read-based sub-scaffolds into 94 chromosome-scale scaffolds of the genome of the coral endosymbiont Symbiodinium microadriaticum.  ...  Dinoflagellates are major primary producers in the world's oceans, the cause of harmful algal blooms, and endosymbionts of marine invertebrates.  ...  This work was supported by the Howard Hughes Medical Institute, an endowment by the Byrne family in support of the Joseph J. Byrne Chair in Biomedical Research held by J.D., and by baseline funding  ... 
doi:10.1101/2020.07.01.182477 fatcat:xb2ndjv4bbcupdea3jn5ifrvvu

EMBnet.journal 18 Suppl. A

EMBnet Journal
2012 EMBnet journal  
, the second one in filling the gap between them.  ...  only the contigs consisting of paired reads whose gap has been successfully filled.  ...  PostErs 101 the seed region of each miRNA, while micro-RNA.org target prediction incorporates current knowledge on target rules and on the use of a compendium of mammalian miRNAs.  ... 
doi:10.14806/ej.18.a.497 fatcat:2aexioifkfgfnipbo3btxqwvia

Theatre presentations

2011 Advances in Animal Biosciences  
We are grateful for funding for the project from the Royal College of Veterinary Surgeons. Acknowledgements We thank the owners for allowing their dogs to be used in this study.  ...  In: Bioengineering of the skin: water and the stratum corneum. Eds: P. Elsner, E. Berardesca, H.I. Maibach. C.R.C Press, Florida, 13-22.  ...  Introduction In the United Kingdom, Home Office requirements ensure the welfare of animals used in research.  ... 
doi:10.1017/s2040470011000045 fatcat:bvlod4wzyzfrnnq4nfctvrocvu

Behavioural responses to human disturbance in an alpine bird

Cristina Vallino, Enrico Caprio, Fabrizio Genco, Dan Chamberlain, Claudia Palestrini, Angela Roggero, Massimo Bocca, Antonio Rolando
2019 Journal of Ornithology  
The use of large non-excavated holes by tawny owls and other forest vertebrates in oak forest Yehor Yatsiuk PP-85, p. 197 Evolution of the Satchinez Marshland avifauna in the past two decades and a half  ...  patterns in a Mediterranean urban bird community  ...  We aim to fill this knowledge gap by investigating the interactions between wood warblers Phylloscopus sibilatrix breeding in unenclosed nests on the forest floor, and the invertebrate fauna colonising  ... 
doi:10.1007/s10336-019-01660-z fatcat:cproziwtgrdkhnini27xqchwpy

Engineering, Technology & Applied Science Research (ETASR), Vol. 11, No. 4, pp. 7291-7530

Various
2021 Zenodo  
The journal was first published in February 2011. ISSN: 1792-8036 and 2241-4487.  ...  ETASR is indexed in the Web of Science Core Collection (former Web of Science/Thomson Reuters Master Journal List), through the Emerging Sources Citation Index, is a Crossref member (DOI prefix: 10.48084  ...  .ூ ೠ . (14 a-b) where ݇ ௨ is the filled factor of the windings in the magnetic window and ‫ܬ‬ is the electric current density.  ... 
doi:10.5281/zenodo.5506592 fatcat:73sj5nawgndeffb26wh6wnux4a
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