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  • 1
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    Late 20 th Century Indian Ocean Heat Content Gain Masked by Wind Forcing (2020)
    American Geophysical Union
    Details
    Publication Date: 2020-10-26
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by American Geophysical Union
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  • 2
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    UDSMProt: universal deep sequence models for protein classification (2020)
    Oxford University Press
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    Publication Date: 2020-01-08
    Description: Motivation Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step. Results We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies. Availability and implementation Source code is available under https://github.com/nstrodt/UDSMProt. Supplementary information Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 3
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    Late 20th century Indian Ocean heat content gain masked by wind forcing (2021)
    American Geophysical Union
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2020. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 47(22), (2020): e2020GL088692, doi:10.1029/2020GL088692.
    Description: Rapid increases in upper 700‐m Indian Ocean heat content (IOHC) since the 2000s have focused attention on its role during the recent global surface warming hiatus. Here, we use ocean model simulations to assess distinct multidecadal IOHC variations since the 1960s and explore the relative contributions from wind stress and buoyancy forcing regionally and with depth. Multidecadal wind forcing counteracted IOHC increases due to buoyancy forcing from the 1960s to the 1990s. Wind and buoyancy forcing contribute positively since the mid‐2000s, accounting for the drastic IOHC change. Distinct timing and structure of upper ocean temperature changes in the eastern and western Indian Ocean are linked to the pathway how multidecadal wind forcing associated with the Interdecadal Pacific Oscillation is transmitted and affects IOHC through local and remote winds. Progressive shoaling of the equatorial thermocline—of importance for low‐frequency variations in Indian Ocean Dipole occurrence—appears to be dominated by multidecadal variations in wind forcing.
    Description: This work was supported by the Alexander von Humboldt Foundation (CCU and SR), The Investment in Science Fund given primarily by WHOI Trustee and Corporation Members (CCU), James E. and Barbara V. Moltz Fellowship for climate‐related research (CCU), the ARC Centre of Excellence for Climate Extremes (CE170100023; CCU and MHE), ARC DP150101331 (CCU and MHE), and PW was supported through grant IndoArchipel from the Deutsche Forschungsgemeinschaft (DFG) as part of the Special Priority Program (SPP)‐1889”Regional Sea Level Change and Society” (SeaLevel).
    Description: 2021-04-26
    Keywords: Decadal variability ; Hiatus ; Indian Ocean ; Ocean heat content ; Ocean models ; Pacific Ocean
    Repository Name: Woods Hole Open Access Server
    Type: Article
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