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  1. Article ; Online: Reply to Amundson: Time to go to work.

    Northrup, Daniel L / Basso, Bruno / Wang, Michael Q / Morgan, Cristine L S / Benfey, Philip N

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 12, Page(s) e2122842119

    MeSH term(s) Agriculture ; Crop Production ; Technology
    Language English
    Publishing date 2022-03-18
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2122842119
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    Zs.A 1148: Show issues Location:
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  2. Article ; Online: Introduction to The Plant Phenome Journal special section on belowground phenotyping

    Tracy, Saoirse R. / Northrup, Daniel L.

    The Plant Phenome Journal. 2022, v. 5, no. 1 p.e20059-

    2022  

    Abstract: The Plant Phenome Journal is excited to present 10 papers that were submitted in a special section on belowground phenotyping. Plant roots and their environment are important for crop resilience and resource efficiency. To meet growing productivity ... ...

    Abstract The Plant Phenome Journal is excited to present 10 papers that were submitted in a special section on belowground phenotyping. Plant roots and their environment are important for crop resilience and resource efficiency. To meet growing productivity challenges, breeders will benefit from tools that are developed to optimize belowground traits.
    Keywords crops ; introduced plants ; journals ; paper ; phenotype ; planting ; roots ; wills
    Language English
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ISSN 2578-2703
    DOI 10.1002/ppj2.20059
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Fragmentation effects on an endangered species across a gradient from the interior to edge of its range.

    Valente, Jonathon J / Rivers, James W / Yang, Zhiqiang / Nelson, S Kim / Northrup, Joseph M / Roby, Daniel D / Meyer, Carolyn B / Betts, Matthew G

    Conservation biology : the journal of the Society for Conservation Biology

    2023  Volume 37, Issue 5, Page(s) e14091

    Abstract: Understanding how habitat fragmentation affects individual species is complicated by challenges associated with quantifying species-specific habitat and spatial variability in fragmentation effects within a species' range. We aggregated a 29-year ... ...

    Abstract Understanding how habitat fragmentation affects individual species is complicated by challenges associated with quantifying species-specific habitat and spatial variability in fragmentation effects within a species' range. We aggregated a 29-year breeding survey data set for the endangered marbled murrelet (Brachyramphus marmoratus) from >42,000 forest sites throughout the Pacific Northwest (Oregon, Washington, and northern California) of the United States. We built a species distribution model (SDM) in which occupied sites were linked with Landsat imagery to quantify murrelet-specific habitat and then used occupancy models to test the hypotheses that fragmentation negatively affects murrelet breeding distribution and that these effects are amplified with distance from the marine foraging habitat toward the edge of the species' nesting range. Murrelet habitat declined in the Pacific Northwest by 20% since 1988, whereas the proportion of habitat comprising edges increased by 17%, indicating increased fragmentation. Furthermore, fragmentation of murrelet habitat at landscape scales (within 2 km of survey stations) negatively affected occupancy of potential breeding sites, and these effects were amplified near the range edge. On the coast, the odds of occupancy decreased by 37% (95% confidence interval [CI] -54 to 12) for each 10% increase in edge habitat (i.e., fragmentation), but at the range edge (88 km inland) these odds decreased by 99% (95% CI 98 to 99). Conversely, odds of murrelet occupancy increased by 31% (95% CI 14 to 52) for each 10% increase in local edge habitat (within 100 m of survey stations). Avoidance of fragmentation at broad scales but use of locally fragmented habitat with reduced quality may help explain the lack of murrelet population recovery. Further, our results emphasize that fragmentation effects can be nuanced, scale dependent, and geographically variable. Awareness of these nuances is critical for developing landscape-level conservation strategies for species experiencing broad-scale habitat loss and fragmentation.
    MeSH term(s) Animals ; Endangered Species ; Conservation of Natural Resources ; Ecosystem ; Forests ; Washington
    Language English
    Publishing date 2023-05-25
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
    ZDB-ID 58735-7
    ISSN 1523-1739 ; 0888-8892
    ISSN (online) 1523-1739
    ISSN 0888-8892
    DOI 10.1111/cobi.14091
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  4. Article ; Online: Novel technologies for emission reduction complement conservation agriculture to achieve negative emissions from row-crop production.

    Northrup, Daniel L / Basso, Bruno / Wang, Michael Q / Morgan, Cristine L S / Benfey, Philip N

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 28

    Abstract: Plants remove carbon dioxide from the atmosphere through photosynthesis. Because agriculture's productivity is based on this process, a combination of technologies to reduce emissions and enhance soil carbon storage can allow this sector to achieve net ... ...

    Abstract Plants remove carbon dioxide from the atmosphere through photosynthesis. Because agriculture's productivity is based on this process, a combination of technologies to reduce emissions and enhance soil carbon storage can allow this sector to achieve net negative emissions while maintaining high productivity. Unfortunately, current row-crop agricultural practice generates about 5% of greenhouse gas emissions in the United States and European Union. To reduce these emissions, significant effort has been focused on changing farm management practices to maximize soil carbon. In contrast, the potential to reduce emissions has largely been neglected. Through a combination of innovations in digital agriculture, crop and microbial genetics, and electrification, we estimate that a 71% (1,744 kg CO
    MeSH term(s) Agriculture/methods ; Ammonia/metabolism ; Carbon Dioxide/analysis ; Conservation of Natural Resources ; Crop Production ; Crops, Agricultural/genetics ; Technology
    Chemical Substances Carbon Dioxide (142M471B3J) ; Ammonia (7664-41-7)
    Language English
    Publishing date 2021-06-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2022666118
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    In stock of ZB MED Cologne/Königswinter

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  5. Book ; Online: Generating Synthetic Multispectral Satellite Imagery from Sentinel-2

    Mohandoss, Tharun / Kulkarni, Aditya / Northrup, Daniel / Mwebaze, Ernest / Alemohammad, Hamed

    2020  

    Abstract: Multi-spectral satellite imagery provides valuable data at global scale for many environmental and socio-economic applications. Building supervised machine learning models based on these imagery, however, may require ground reference labels which are not ...

    Abstract Multi-spectral satellite imagery provides valuable data at global scale for many environmental and socio-economic applications. Building supervised machine learning models based on these imagery, however, may require ground reference labels which are not available at global scale. Here, we propose a generative model to produce multi-resolution multi-spectral imagery based on Sentinel-2 data. The resulting synthetic images are indistinguishable from real ones by humans. This technique paves the road for future work to generate labeled synthetic imagery that can be used for data augmentation in data scarce regions and applications.

    Comment: Presented at the AI for Earth Sciences Workshop at NeurIPS 2020
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing
    Publishing date 2020-12-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  6. Book ; Online: Semantic Segmentation of Medium-Resolution Satellite Imagery using Conditional Generative Adversarial Networks

    Kulkarni, Aditya / Mohandoss, Tharun / Northrup, Daniel / Mwebaze, Ernest / Alemohammad, Hamed

    2020  

    Abstract: Semantic segmentation of satellite imagery is a common approach to identify patterns and detect changes around the planet. Most of the state-of-the-art semantic segmentation models are trained in a fully supervised way using Convolutional Neural Network ( ...

    Abstract Semantic segmentation of satellite imagery is a common approach to identify patterns and detect changes around the planet. Most of the state-of-the-art semantic segmentation models are trained in a fully supervised way using Convolutional Neural Network (CNN). The generalization property of CNN is poor for satellite imagery because the data can be very diverse in terms of landscape types, image resolutions, and scarcity of labels for different geographies and seasons. Hence, the performance of CNN doesn't translate well to images from unseen regions or seasons. Inspired by Conditional Generative Adversarial Networks (CGAN) based approach of image-to-image translation for high-resolution satellite imagery, we propose a CGAN framework for land cover classification using medium-resolution Sentinel-2 imagery. We find that the CGAN model outperforms the CNN model of similar complexity by a significant margin on an unseen imbalanced test dataset.

    Comment: Presented at the AI for Earth Sciences Workshop at NeurIPS 2020
    Keywords Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Machine Learning ; Electrical Engineering and Systems Science - Image and Video Processing
    Subject code 006
    Publishing date 2020-12-05
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Subglacial precipitates record Antarctic ice sheet response to late Pleistocene millennial climate cycles.

    Piccione, Gavin / Blackburn, Terrence / Tulaczyk, Slawek / Rasbury, E Troy / Hain, Mathis P / Ibarra, Daniel E / Methner, Katharina / Tinglof, Chloe / Cheney, Brandon / Northrup, Paul / Licht, Kathy

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 5428

    Abstract: Ice cores and offshore sedimentary records demonstrate enhanced ice loss along Antarctic coastal margins during millennial-scale warm intervals within the last glacial termination. However, the distal location and short temporal coverage of these records ...

    Abstract Ice cores and offshore sedimentary records demonstrate enhanced ice loss along Antarctic coastal margins during millennial-scale warm intervals within the last glacial termination. However, the distal location and short temporal coverage of these records leads to uncertainty in both the spatial footprint of ice loss, and whether millennial-scale ice response occurs outside of glacial terminations. Here we present a >100kyr archive of periodic transitions in subglacial precipitate mineralogy that are synchronous with Late Pleistocene millennial-scale climate cycles. Geochemical and geochronologic data provide evidence for opal formation during cold periods via cryoconcentration of subglacial brine, and calcite formation during warm periods through the addition of subglacial meltwater originating from the ice sheet interior. These freeze-flush cycles represent cyclic changes in subglacial hydrologic-connectivity driven by ice sheet velocity fluctuations. Our findings imply that oscillating Southern Ocean temperatures drive a dynamic response in the Antarctic ice sheet on millennial timescales, regardless of the background climate state.
    Language English
    Publishing date 2022-09-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-33009-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A Chemical Approach for Programmable Protein Outputs Based on Engineered Cell Interactions.

    Jacome, Daniel A / Northrup, Justin D / Ruff, Andrew J / Reilly, Sean W / Lee, Iris K / Blizard, Gabrielle S / Sellmyer, Mark A

    ACS chemical biology

    2020  Volume 16, Issue 1, Page(s) 52–57

    Abstract: Cell-cell interactions and communication are crucial to the proper function of complex mammalian physiology including neurocognitive and immune system functions. While many tools are available for observing and perturbing intracellular processes, ... ...

    Abstract Cell-cell interactions and communication are crucial to the proper function of complex mammalian physiology including neurocognitive and immune system functions. While many tools are available for observing and perturbing intracellular processes, relatively few exist to probe intercellular processes. Current techniques for studying interactions often rely on direct protein contact, and few can manipulate diverse, functional outputs with tunable protein expression. To address these limitations, we have developed a small-molecule approach based on a trimethoprim prodrug-enzyme pair capable of reporting the presence of two different engineered cell populations with programmable protein outputs. The approach relies on bacterial nitroreductase enzyme catalysis, which is orthogonal to normal mammalian biology, and diffusion of trimethoprim from "activator" cells to "receiver" cells. We test this strategy, which can theoretically regulate many different types of proteins, using biochemical and
    MeSH term(s) Animals ; Cell Communication ; Cell Engineering ; Coculture Techniques ; Dose-Response Relationship, Drug ; Luciferases, Firefly/chemistry ; Prodrugs/chemistry ; Proteins/chemistry ; Small Molecule Libraries/chemistry ; Trimethoprim/chemistry
    Chemical Substances Prodrugs ; Proteins ; Small Molecule Libraries ; Trimethoprim (AN164J8Y0X) ; Luciferases, Firefly (EC 1.13.12.7)
    Language English
    Publishing date 2020-12-22
    Publishing country United States
    Document type Journal Article
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.0c00935
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  9. Article: Frequency, Progression, and Current Management: Report of 16 New Cases of Nonfunctional Pancreatic Neuroendocrine Tumors in Tuberous Sclerosis Complex and Comparison With Previous Reports.

    Mowrey, Kate / Northrup, Hope / Rougeau, Peyton / Hashmi, S Shahrukh / Krueger, Darcy A / Ebrahimi-Fakhari, Daniel / Towbin, Alexander J / Trout, Andrew T / Capal, Jamie K / Franz, David Neal / Rodriguez-Buritica, David

    Frontiers in neurology

    2021  Volume 12, Page(s) 627672

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2021-04-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2564214-5
    ISSN 1664-2295
    ISSN 1664-2295
    DOI 10.3389/fneur.2021.627672
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  10. Article ; Online: Application of ChIP-Seq and related techniques to the study of immune function.

    Northrup, Daniel L / Zhao, Keji

    Immunity

    2011  Volume 34, Issue 6, Page(s) 830–842

    Abstract: Behaviors observed at the cellular level such as development and acquisition of effector functions by immune cells result from transcriptional changes. The biochemical mediators of transcription are sequence-specific transcription factors (TFs), ... ...

    Abstract Behaviors observed at the cellular level such as development and acquisition of effector functions by immune cells result from transcriptional changes. The biochemical mediators of transcription are sequence-specific transcription factors (TFs), chromatin modifying enzymes, and chromatin, the complex of DNA and histone proteins. Covalent modification of DNA and histones, also termed epigenetic modification, influences the accessibility of target sequences for transcription factors on chromatin and the expression of linked genes required for immune functions. Genome-wide techniques such as ChIP-Seq have described the entire "cistrome" of transcription factors involved in specific developmental steps of B and T cells and started to define specific immune responses in terms of the binding profiles of critical effectors and epigenetic modification patterns. Current data suggest that both promoters and enhancers are prepared for action at different stages of activation by epigenetic modification through distinct transcription factors in different cells.
    MeSH term(s) Animals ; Chromatin Immunoprecipitation/methods ; Epigenesis, Genetic ; Genome ; Humans ; Promoter Regions, Genetic ; Sequence Analysis, DNA/methods ; Transcription Factors/genetics ; Transcription Factors/immunology
    Chemical Substances Transcription Factors
    Language English
    Publishing date 2011-04-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Review
    ZDB-ID 1217235-2
    ISSN 1097-4180 ; 1074-7613
    ISSN (online) 1097-4180
    ISSN 1074-7613
    DOI 10.1016/j.immuni.2011.06.002
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