Review
Plant Sciences
Benjamin W. Lee, Liesl C. Oeller, David W. Crowder
Summary: Insect vectors interact with both host-vector-pathogen and other species in food webs, influencing virus transmission. However, studies on these interactions are limited, hindering the development of models that capture community-level effects on virus prevalence.
Article
Ecology
Lyndsie S. Wszola, Zachary S. Feiner, John P. Delong
Summary: The study found that simpler and less restrictive fishing regulations perform better in conserving the population of walleye and overall population abundance while still allowing for large harvests. Moderate regulations can achieve conservation objectives when considering the interaction between regulatory policy, human behavior, and animal life history.
ECOLOGICAL MODELLING
(2023)
Article
Public, Environmental & Occupational Health
Min Shi, Clarice R. Weinberg
Summary: This study proposes a generalized linear model based on the inverse link, which can be used for data analysis in time-to-pregnancy studies without requiring constancy assumptions. Simulation results show that this approach can maintain the nominal confidence interval coverage and does not rely on hard-to-verify constancy assumptions.
Article
Ecology
James Reed, Koen Kusters, Jos Barlow, Michael Balinga, Joli Rumi Borah, Rachel Carmenta, Colas Chervier, Houria Djoudi, Davison Gumbo, Yves Laumonier, Kaala B. Moombe, Elizabeth L. Yuliani, Terry Sunderland
Summary: ILAs that aim to balance conservation and development need to incorporate ecological factors and consider potential trade-offs. Re-integrating ecology into ILAs will not only improve ecological understanding, but also generate insights into local and traditional knowledge. Better incorporation of the ecological dimension requires engaging relevant stakeholders using participatory methods.
Article
Limnology
Celyn L. L. Khoo, Rachel E. Sipler, Sally J. M. Faulkner, Sean G. Boyd, Maryam Beheshti Foroutani, Colleen E. McBride, Susan E. Ziegler
Summary: Observed and predicted hydrological changes in C-rich boreal ecosystems have the potential to impact the transport trajectory of biogeochemical components from land to coastal systems. In this study, we assessed the biogeochemical constituents in two adjacent small systems in the boreal zone and found that dissolved iron and its ratio with dissolved organic carbon are sensitive indicators of heterogeneity in small catchments. The study also highlights the importance of the summer-to-fall transition period for investigating the linkages between biogeochemical parameters and coastal ecosystem functioning.
LIMNOLOGY AND OCEANOGRAPHY
(2023)
Review
Cell Biology
Bum-Kyu Lee, Jonghwan Kim
Summary: Understanding the molecular mechanisms of early human placenta development is crucial for maternal and fetal health. Recent advancements in human trophoblast models offer new opportunities, but the application of high-throughput omics tools in this field remains limited. Integration of omics approaches with human in vitro model systems has the potential to enhance our understanding of placental development and associated complications.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Genetics & Heredity
Haotian Wu, Christina M. M. Eckhardt, Andrea A. A. Baccarelli
Summary: A substantial proportion of disease risk for common complex disorders is attributable to environmental exposures and pollutants. Recent research has shown the impact of environmental pollutants on the human genome and epigenome through epigenetic modifications. Furthermore, other molecular processes, such as the production of extracellular vesicles, epitranscriptomic changes, and mitochondrial changes, have also been identified as mechanisms through which the environment can exert its effects.
NATURE REVIEWS GENETICS
(2023)
Article
Plant Sciences
Advyth Ramachandran, Jared D. Huxley, Shane McFaul, Lisa Schauer, Jeff Diez, Rohan Boone, Tesa Madsen-Hepp, Erin McCann, Janet Franklin, Danielle Logan, M. Brooke Rose, Marko J. Spasojevic
Summary: Many studies have shown that assembly mechanisms may differ between life stages, and ontogenetic dependency plays an important role in determining the composition of different life stages. In this study conducted in a forest dynamics plot in California, it was found that adult plant diversity was mainly influenced by spatial factors, while seedling diversity was mainly explained by ontogenetic dependency.
JOURNAL OF ECOLOGY
(2023)
Article
Ecology
Bruce A. Menge
Summary: This study evaluated the empirical support for environmental stress models (ESMs) and found that consumer pressure on prey typically decreases with increasing environmental stress (consumer stress model; CSM), while prey pressure on consumers (prey stress model; PSM) occurs less frequently. This contrasts with a prior survey, suggesting that consumers are generally more suppressed by stress than prey. Therefore, increased climate change-induced environmental stress is likely to reduce the impacts of consumers on prey more often than the reverse.
Editorial Material
Chemistry, Physical
Julia Tomei, Bernard Tembo, Mulima Nyambe-Mubanga
Summary: Delivering efficient energy transitions in sub-Saharan Africa requires careful planning and consideration of diverse objectives. While Baker et al. provide a useful method for eliciting stakeholder preferences in Ghana, they do not show how this evidence can be integrated into quantitative energy models.
Article
Energy & Fuels
Tsisilile Igogo, Kwame Awuah-Offei, Alexandra Newman, Travis Lowder, Jill Engel-Cox
Summary: Mining is one of the most energy-intensive industries worldwide, with increasing demand for raw materials due to population growth and economic development. Despite numerous opportunities, there are still technical issues to be addressed in integrating renewable energy technologies into the mining industry.
Article
Engineering, Marine
Ying Yang, Ran Yan, Shuaian Wang
Summary: Maritime transportation is crucial in international trade and the global supply chain. To improve safety and minimize pollution, international organizations have proposed regulations and conventions. Maritime surveillance has gained increasing attention to ensure compliance with these regulations. This study proposes a new approach that integrates computer vision and domain knowledge to accurately recognize ships, enhancing maritime surveillance.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Review
Development Studies
Nessa Winston
Summary: The paper presents a new definition and conceptualisation of sustainable communities, emphasizing the importance of addressing both social and environmental needs. Social sustainability is defined as meeting basic human needs and ensuring sufficiency within planetary boundaries. By integrating social and environmental aspects, regeneration programmes targeting housing can effectively address various social and environmental challenges, contributing to progress on multiple dimensions of sustainable development and the UN SD goals.
SUSTAINABLE DEVELOPMENT
(2022)
Article
Critical Care Medicine
Juan C. Rojas, John Fahrenbach, Sonya Makhni, Scott C. Cook, James S. Williams, Craig A. Umscheid, Marshall H. Chin
Summary: Predictive analytic models powered by machine learning are increasingly important in healthcare organizations, but they can be biased and harmful. We propose a strategy to evaluate and mitigate biases in these models, ensuring their safe and effective use in healthcare.
Review
Environmental Sciences
Lauren Jarvis, Jordan Rosenfeld, Pedro C. Gonzalez-Espinosa, Eva C. Enders
Summary: This article provides a process framework for integrating stressor-response (SR) functions into cumulative effects (CE) models, highlighting the importance of selecting appropriate stressors and responses, and dealing with stressor interactions. It emphasizes the need for adaptive management and confirms suspected interaction presence through targeted stressor manipulations.
SCIENCE OF THE TOTAL ENVIRONMENT
(2024)
Article
Toxicology
Lyle D. Burgoon, Claudio Fuentes, Christopher J. Borgert
Summary: This paper introduces a new method for calculating the kinetically derived maximal dose (KMD) based on Bayesian methods and the Kneedle algorithm. The new approach converts toxicokinetic data to the Michaelis-Menten curve using Bayesian methods and uses the Kneedle algorithm to find the point at which the curve begins to taper off. This reshapes the KMD methodology and places it within the Michaelis-Menten framework, leveraging existing biochemical and pharmacological concepts.
ARCHIVES OF TOXICOLOGY
(2022)
Article
Virology
Justin T. Reese, Ben Coleman, Lauren Chan, Hannah Blau, Tiffany J. Callahan, Luca Cappelletti, Tommaso Fontana, Katie Rebecca Bradwell, Nomi L. Harris, Elena Casiraghi, Giorgio Valentini, Guy Karlebach, Rachel Deer, Julie A. McMurry, Melissa A. Haendel, Christopher G. Chute, Emily Pfaff, Richard Moffitt, Heidi Spratt, Jasvinder Singh, Christopher J. Mungall, Andrew E. Williams, Peter N. Robinson
Summary: This study found that the use of non-steroidal anti-inflammatory drugs (NSAIDs) is not associated with increased severity or other adverse outcomes in COVID-19 inpatients. The results confirm and extend the findings of previous observational studies and provide evidence against the initial concerns raised about the use of NSAIDs in COVID-19 patients.
Letter
Psychiatry
Ben Coleman, Elena Casiraghi, Hannah Blau, Lauren Chan, Melissa A. Haendel, Bryan Laraway, Tiffany J. Callahan, Rachel R. Deer, Kenneth J. Wilkins, Justin Reese, Peter N. Robinson
Letter
Biotechnology & Applied Microbiology
Julius O. B. Jacobsen, Michael Baudis, Gareth S. Baynam, Jacques S. Beckmann, Sergi Beltran, Orion J. Buske, Tiffany J. Callahan, Christopher G. Chute, Melanie Courtot, Daniel Danis, Olivier Elemento, Andrea Essenwanger, Robert R. Freimuth, Michael A. Gargano, Tudor Groza, Ada Hamosh, Nomi L. Harris, Rajaram Kaliyaperumal, Kevin C. Kent Lloyd, Aly Khalifa, Peter M. Krawitz, Sebastian Koeler, Brian J. Laraway, Heikki Lehvaslaiho, Leslie Matalonga, Julie A. McMurry, Alejandro Metke-Jimenez, Christopher J. Mungall, Monica C. Munoz-Torres, Soichi Ogishima, Anastasios Papakonstantinou, Davide Piscia, Nikolas Pontikos, Nuria Queralt-Rosinach, Marco Roos, Julian Sass, Paul N. Schofield, Dominik Seelow, Anastasios Siapos, Damian Smedley, Lindsay D. Smith, Robin Steinhaus, Jagadish Chandrabose Sundaramurthi, Emilia M. Swietlik, Sylvia Thun, Nicole A. Vasilevsky, Alex H. Wagner, Jeremy L. Warner, Claus Weiland, Melissa A. Haendel, Peter N. Robinson
NATURE BIOTECHNOLOGY
(2022)
Article
Computer Science, Interdisciplinary Applications
Elena Casiraghi, Rachel Wong, Margaret Hall, Ben Coleman, Marco Notaro, Michael D. Evans, Jena S. Tronieri, Hannah Blau, Bryan Laraway, Tiffany J. Callahan, Lauren E. Chan, Carolyn T. Bramante, John B. Buse, Richard A. Moffitt, Til Sturmer, Steven G. Johnson, Yu Raymond Shao, Justin Reese, Peter N. Robinson, Alberto Paccanaro, Giorgio Valentini, Jared D. Huling, Kenneth J. Wilkins
Summary: Healthcare datasets from Electronic Health Records are valuable for assessing associations between patients' predictors and outcomes. However, missing values are common in these datasets, and removing them may introduce bias. Multiple imputation algorithms have been proposed to recover missing information, but there is no consensus on which algorithm works best. Choosing algorithm parameters and data-related modeling choices is also challenging.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Multidisciplinary Sciences
Charles Tapley Hoyt, Meghan Balk, Tiffany J. Callahan, Daniel Domingo-Fernandez, Melissa A. Haendel, Harshad B. Hegde, Daniel S. Himmelstein, Klas Karis, John Kunze, Tiago Lubiana, Nicolas Matentzoglu, Julie McMurry, Sierra Moxon, Christopher J. Mungall, Adriano Rutz, Deepak R. Unni, Egon Willighagen, Donald Winston, Benjamin M. Gyori
Summary: The standardized identification of biomedical entities is important for interoperability and data integration in the life sciences. The Bioregistry is an integrative and open metaregistry that expands upon existing registries to address the evolving needs of researchers. By leveraging public infrastructure and automation, and employing an open code and open data governance model, the Bioregistry promotes interoperability and reuse of data and scientific literature.
Article
Computer Science, Interdisciplinary Applications
Sanya B. Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
Summary: The study constructed a knowledge graph (KG) for pharmacokinetic natural product-drug interactions (NPDIs), which can be used to discover plausible mechanistic explanations and guide scientific research.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Computer Science, Interdisciplinary Applications
Scott A. Malec, Sanya B. Taneja, Steven M. Albert, C. Elizabeth Shaaban, Helmet T. Karim, Arthur S. Levine, Paul Munro, Tiffany J. Callahan, Richard D. Boyce
Summary: Traditional methods of identifying confounders rely on content-matter expertise and literature review, but these methods have limitations. To overcome these challenges, researchers propose a novel method based on knowledge graph, which combines computable literature-derived knowledge with biomedical ontologies for better causal feature selection. The application of this method identifies potential confounders and highlights the need for standardized databases of causal variables.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Health Care Sciences & Services
Tiffany J. Callahan, Adrianne L. Stefanski, Jordan M. Wyrwa, Chenjie Zeng, Anna Ostropolets, Juan M. Banda, William A. Baumgartner, Richard D. Boyce, Elena Casiraghi, Ben D. Coleman, Janine H. Collins, Sara J. Deakyne Davies, James A. Feinstein, Asiyah Y. Lin, Blake Martin, Nicolas A. Matentzoglu, Daniella Meeker, Justin Reese, Jessica Sinclair, Sanya B. Taneja, Katy E. Trinkley, Nicole A. Vasilevsky, Andrew E. Williams, Xingmin A. Zhang, Joshua C. Denny, Patrick B. Ryan, George Hripcsak, Tellen D. Bennett, Melissa A. Haendel, Peter N. Robinson, Lawrence E. Hunter, Michael G. Kahn
Summary: Common data models address standardization challenges in EHR data, but fail to integrate all resources for deep phenotyping. OBO ontologies provide computable representations of biological knowledge, but mapping EHR data to OBO ontologies requires manual curation. OMOP2OBO is an algorithm that maps OMOP vocabularies to OBO ontologies, enabling deep phenotyping and identification of undiagnosed patients.
NPJ DIGITAL MEDICINE
(2023)
Article
Health Care Sciences & Services
Matthew Spotnitz, Nripendra Acharya, James J. Cimino, Shawn Murphy, Bahram Namjou, Nancy Crimmins, Theresa Walunas, Cong Liu, David Crosslin, Barbara Benoit, Elisabeth Rosenthal, Jennifer A. Pacheco, Anna Ostropolets, Harry Reyes Nieva, Jason S. Patterson, Lauren R. Richter, Tiffany J. Callahan, Ahmed Elhussein, Chao Pang, Krzysztof Kiryluk, Jordan Nestor, Atlas Khan, Sumit Mohan, Evan Minty, Wendy Chung, Wei-Qi Wei, Karthik Natarajan, Chunhua Weng
Summary: This study develops a comprehensive metadata framework for defining computational clinical phenotypes. The framework was positively evaluated by more than 90% of the survey respondents in terms of phenotype definition and validation methods and metrics. The strengths of the framework include explicit descriptions, compliance with data standards, and comprehensive validation methods.
Article
Computer Science, Interdisciplinary Applications
Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. J. Callahan, Carlos Cano, Marcin P. P. Joachimiak, Christopher J. J. Mungall, Peter N. N. Robinson, Justin Reese, Giorgio Valentini
Summary: GRAPE is a software resource for graph processing and embedding that can scale with big graphs, showing substantial improvements in space and time complexity compared to existing resources. It offers efficient graph-processing utilities, node embedding methods, and inference models, making it a valuable tool for graph representation learning. GRAPE is capable of handling millions of nodes and billions of edges, enabling large-graph analysis in various real-world applications.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Medicine, General & Internal
Justin T. Reese, Hannah Blau, Elena Casiraghi, Timothy Bergquist, Johanna J. Loomba, Tiffany J. Callahan, Bryan Laraway, Corneliu Antonescu, Ben Coleman, Michael Gargano, Kenneth J. Wilkins, Luca Cappelletti, Tommaso Fontana, Nariman Ammar, Blessy Antony, T. M. Murali, J. Harry Caufield, Guy Karlebach, Julie A. McMurry, Andrew Williams, Richard Moffitt, Jineta Banerjee, Anthony E. Solomonides, Hannah Davis, Kristin Kostka, Giorgio Valentini, David Sahner, Christopher G. Chute, Charisse Madlock-Brown, Melissa A. Haendel, Peter N. Robinson
Summary: By computationally modelling PASC phenotype data and assessing semantic similarity, we identified six distinct clusters of PASC patients with different clinical features and severity, including diverse manifestations. This semantic phenotypic clustering approach provides a foundation for stratifying and studying PASC patients for natural history or therapy studies.
Article
Mathematical & Computational Biology
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M. Gyori, Melissa Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad B. Hegde, Amelia L. Hoyt, Charles T. Hoyt, Dazhi Jiao, Ernesto Jimenez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim Putman, Nuria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H. Wagner, Christopher J. Mungall
Summary: This paper introduces the "Simple Standard for Sharing Ontological Mappings (SSSOM)" standard, which addresses issues in mapping different representations of objects in different databases by enhancing readability of metadata, defining an easy-to-use table-based format, and implementing open collaborative workflows. The standard provides reference tools and software libraries for handling mappings.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Mathematical & Computational Biology
Federica Quaglia, Rama Balakrishnan, Susan M. Bello, Nicole Vasilevsky
Summary: The International Society for Biocuration (ISB) aims to promote the field of biocuration through annual international conferences and provide a platform for information exchange and networking. Due to the ongoing pandemic, this year's ISB conference was held virtually, covering topics such as the future of biocuration, career paths, and equity and inclusion.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)