More Like this

1. CoralCache: a virtual coral core repository for transparent and reproducible annual growth rate analyses

   https://doi.org/10.5194/essd-2025-598  

   DeCarlo, Thomas M; Jasnos, Oliwia; Strange, Avi; Andersson, Andreas; Bautista_VII, Angel T; Bloomer, Sierra; Bolden, Isaiah W; Bosman, Maartje; Brachert, Thomas C; Braz, Giulia B; et al (December 2025, Earth System Science Data)

   Abstract. As science fields enter the Big Data revolution, open-access repositories are essential for addressing larger-scale questions than are possible for single researchers by making data findable, accessible, interoperable, and reusable (FAIR). Furthermore, transparent data and code are increasingly important for reproducible research, especially for data types that inherently require subjective human interpretations. These ideas are applicable to coral sclerochronology, as the field has long been characterized by individual researchers collecting and analyzing coral skeletal cores from their study sites without substantial data sharing or archiving of the core images to meet FAIR principles. Here, we present CoralCache, a virtual coral core repository that not only archives image datasets (i.e., digitized X-rays and computed tomography scans), but also observer interpretations of the density banding patterns. CoralCache is linked to a graphical user interface, CoralCT, which together offer a way forward for coral growth rate analysis that is reproducible and collaborative. The data organization systems presented here could also be readily applied to related archives such as tree rings or bivalve shells. 

   more » « less
2. The next generation U.S. National Science Foundation Ice Core Facility: supporting state-of-the-art science

   https://doi.org/10.5194/egusphere-egu23-1684  

   Powers, L.; Kurbatov, A.; Kershaw, C.; Hargreaves, G.; Labombard, C.; Fudge, T. J. (April 2023, EGU General Assembly 2023, Vienna, Austria, 24–28 Apr 2023)

   The National Science Foundation Ice Core Facility (NSF-ICF, fka NICL) is in the process of building a new facility including freezer and scientist support space. The facility is being designed to minimize environmental impacts while maximizing ice core curation and science support. In preparation for the new facility, we are updating research equipment and integrating ice core data collection and processing by assigning International Generic Sample Numbers (IGSN) to advance the “FAIR”ness and establish clear provenance of samples, fostering the next generation of linked research data products. The NSF-ICF team, in collaboration with the US ice core science community, has established a metadata schema for the assignment of IGSNs to ice cores and samples. In addition, in close coordination with the US ice core community, we are adding equipment modules that expand traditional sets of physical property, visual stratigraphy, and electrical conductance ice core measurements. One such module is an ice core hyperspectral imaging (HSI) system. Adapted for the cold laboratory settings, the SPECIM SisuSCS HSI system can collect up to 224 bands using a continuous line-scanning mode in the visible and near-infrared (VNIR) 400-1000 nm spectral region. A modular system design allows expansion of spectral properties in the future. The second module is an updated multitrack electrical conductance system. These new data will guide real time optimization of sampling for planned analyses during ice core processing, especially for ice with deformed or highly compressed layering. The aim is to facilitate the collection of robust, long-term, and FAIR data archives for every future ice core section processed at NSF-ICF. The NSF-ICF is fully funded by the National Science Foundation and operated by the U.S. Geological Survey. 

   more » « less
3. A comparison of neuroelectrophysiology databases

   https://doi.org/10.1038/s41597-023-02614-0  

   Subash, Priyanka; Gray, Alex; Boswell, Misque; Cohen, Samantha L.; Garner, Rachael; Salehi, Sana; Fisher, Calvary; Hobel, Samuel; Ghosh, Satrajit; Halchenko, Yaroslav; et al (December 2023, Scientific Data)

   Abstract As data sharing has become more prevalent, three pillars - archives, standards, and analysis tools - have emerged as critical components in facilitating effective data sharing and collaboration. This paper compares four freely available intracranial neuroelectrophysiology data repositories: Data Archive for the BRAIN Initiative (DABI), Distributed Archives for Neurophysiology Data Integration (DANDI), OpenNeuro, and Brain-CODE. The aim of this review is to describe archives that provide researchers with tools to store, share, and reanalyze both human and non-human neurophysiology data based on criteria that are of interest to the neuroscientific community. The Brain Imaging Data Structure (BIDS) and Neurodata Without Borders (NWB) are utilized by these archives to make data more accessible to researchers by implementing a common standard. As the necessity for integrating large-scale analysis into data repository platforms continues to grow within the neuroscientific community, this article will highlight the various analytical and customizable tools developed within the chosen archives that may advance the field of neuroinformatics. 

   more » « less
4. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics

   https://doi.org/10.3389/fmicb.2022.1007877  

   Silva, Denise P.; Epstein, Hannah E.; Vega Thurber, Rebecca L. (February 2023, Frontiers in Microbiology)

   Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade. 

   more » « less
5. Climate Model Teleconnection Patterns Govern the Niño-3.4 Response to Early Nineteenth-Century Volcanism in Coral-Based Data Assimilation Reconstructions

   https://doi.org/10.1175/JCLI-D-20-0549.1  

   Sanchez, Sara C.; Hakim, Gregory J.; Saenger, Casey P. (March 2021, Journal of Climate)

   null (Ed.)

   Abstract Scientific understanding of low-frequency tropical Pacific variability, especially responses to perturbations in radiative forcing, suffers from short observational records, sparse proxy networks, and bias in model simulations. Here, we combine the strengths of proxies and models through coral-based paleoclimate data assimilation. We combine coral archives ( δ 18 O, Sr/Ca) with the dynamics, spatial teleconnections, and intervariable relationships of the CMIP5/PMIP3 Past1000 experiments using the Last Millennium Reanalysis data assimilation framework. This analysis creates skillful reconstructions of tropical Pacific temperatures over the observational era. However, during the period of intense volcanism in the early nineteenth century, southwestern Pacific corals produce El Niño–Southern Oscillation (ENSO) reconstructions that are of opposite sign from those from eastern Pacific corals and tree ring records. We systematically evaluate the source of this discrepancy using 1) single-proxy experiments, 2) varied proxy system models (PSMs), and 3) diverse covariance patterns from the Past1000 simulations. We find that individual proxy records and coral PSMs do not significantly contribute to the discrepancy. However, following major eruptions, the southwestern Pacific corals locally record more persistent cold anomalies than found in the Past1000 experiments and canonical ENSO teleconnections to the southwest Pacific strongly control the reconstruction response. Furthermore, using covariance patterns independent of ENSO yields reconstructions consistent with coral archives across the Pacific. These results show that model bias can strongly affect how proxy information is processed in paleoclimate data assimilation. As we illustrate here, model bias influences the magnitude and persistence of the response of the tropical Pacific to volcanic eruptions. 

   more » « less