Article
Multidisciplinary Sciences
Juan Diaz-Colunga, Nanxi Lu, Alicia Sanchez-Gorostiaga, Chang-Yu Chang, Helen S. Cai, Joshua E. Goldford, Mikhail Tikhonov, Alvaro Sanchez
Summary: Microbial communities frequently invade one another as a whole, a phenomenon known as community coalescence. This study provides direct evidence that collective invasions can lead to ecological coselection in microbial communities due to cross-feeding interactions at the community level.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yonatan Vanunu, Jared M. Hotaling, Mike E. Le Pelley, Ben R. Newell
Summary: The study shows that initial attention in risky choice is driven by perceptual properties of the stimulus, while subsequent choices are more influenced by goal-driven factors. Options with the highest values and largest font sizes have the greatest impact on choice, while distractors may attract attention but do not affect actual decision-making.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Automation & Control Systems
T. Burr, S. Croft, A. Favalli, T. Krieger, B. Weaver
Summary: This paper reviews progress and presents new results for uncertainty quantification in nuclear safeguards, focusing on data-driven choices in SD estimation, the use of approximate Bayesian computation, computational calibration, revisions to the GUM, and critique of a Unified Theory of Measurement Errors and Uncertainties.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Biology
Hajo Eicken, Finn Danielsen, Josephine-Mary Sam, Maryann Fidel, Noor Johnson, Michael K. Poulsen, Olivia A. Lee, Katie Spellman, Lisbeth Iversen, Peter Pulsifer, Martin Enghoff
Summary: Effective responses to rapid environmental change rely on observations to inform planning and decision-making. Comparing top-down, large-scale program driven approaches with bottom-up approaches initiated and steered at the community level can yield benefits, especially when connecting to Indigenous and local knowledge.
Article
Chemistry, Multidisciplinary
Gyurim Park, Dong Yeon Jeong, Seung Yeon Yu, Jong Jin Park, Jong H. Kim, Hoichang Yang, Youngmin You
Summary: This research demonstrates an advancement in the engineering of emitters with circularly polarized luminescence (CPL) properties. By utilizing a combined top-down and bottom-up strategy, the photoluminescence quantum yield and the luminescence dissymmetry factor were simultaneously amplified. The integration of chiral anions and the formation of helical assemblies of square-planar Pt(II) complexes played crucial roles in activating the CPL-active metal-metal-to-ligand charge transfer transition.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Environmental Sciences
Andreas Froemelt, Arne Geschke, Thomas Wiedmann
Summary: This article discusses a highly detailed, spatially-resolved modelling framework that quantifies local activities and analyzes system-wide environmental and economic effects of planned interventions. Two case studies were conducted to examine production-based greenhouse gas emissions, consumption-based carbon footprints, and regional differences in Switzerland. The importance of providing regionalized information along economic value chains and the potential benefits and drawbacks of detailed scenarios were highlighted.
ENVIRONMENTAL RESEARCH LETTERS
(2021)
Article
Environmental Sciences
Margarita Brandt, Isabel Silva-Romero, David Fernandez-Garnica, Esteban Agudo-Adriani, Colleen B. Bove, John F. Bruno
Summary: This study found that nutrient availability, temperature, and herbivory all have impacts on macroalgal biomass. Excluding herbivores significantly increased macroalgal biomass, regardless of season or nutrient availability. However, the interactive effects of nutrients and herbivores differed between the cool and warm seasons. The results suggest that nutrient availability, rather than temperature, modulates the effects of herbivory.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Ecology
Abby R. Gilson, Christopher Mcquaid
Summary: This study investigated the effects of grazing pressure, upwelling, and their interactions on the sessile invertebrate and macroalgal communities in a warm-temperate system. The results showed that the positive bottom-up effects of nutrient supply did not override top-down control, and had knock-on effects on invertebrates competing with macroalgae for space.
Article
Engineering, Environmental
Chen Zhang, Yuhong Zhou, Maria Spoljar, Jelena Fressl, Tea Tomljanovic, Valjbone Rama, Natalia Kuczynska-Kippen
Summary: Eutrophication leads to excessive algae growth and reduced water transparency, severely impacting water quality and ecosystem equilibrium, especially in shallow water bodies. Controlling the food chain by manipulating fish and macrophytes is an effective method to mitigate the effects of eutrophication. This study used a lake ecosystem model to predict the seasonal effects of biomanipulation on zooplankton in shallow water bodies, and the results were compared with mesocosm experiments.
Article
Chemistry, Analytical
Aldo Renato Couto, Felipe Rebello Lourenco
Summary: This paper aims to estimate the measurement uncertainty of the quantification of acetylsalicylic acid (ASA) and salicylic acid (SA) in ASA samples using a stability-indicating multivariate spectrophotometric procedure. The measurement uncertainties were estimated using both top-down and bottom-up approaches, considering various sources of uncertainty. The developed methodology allows for the estimation of measurement uncertainty in multivariate spectrophotometric analysis.
MICROCHEMICAL JOURNAL
(2023)
Article
Computer Science, Information Systems
Yingwei Pan, Yehao Li, Ting Yao, Tao Mei
Summary: This article discusses a technique for image captioning that utilizes a bottom-up and top-down attention mechanism to select and describe salient objects based on human subjective experience. The proposed approach uses the object sequence of interest as top-down signals to guide caption generation and incorporates an attention mechanism to integrate bottom-up and top-down signals. It also introduces a contrastive learning-based objective to ensure reliable and explainable cross-modal reasoning.
ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS
(2023)
Article
Computer Science, Information Systems
Meihui Li, Lingbing Peng, Tianfu Wu, Zhenming Peng
Summary: This paper proposes a bottom-up and top-down integration framework that combines short-term memory and long-term memory based trackers for online object tracking. Experimental results show that the method outperforms deep learning based trackers in a pre-training-free setting and the outputs from sparse coding are potentially useful for downstream tasks such as action recognition, multiple-object tracking, and object re-identification.
IEEE TRANSACTIONS ON MULTIMEDIA
(2021)
Review
Multidisciplinary Sciences
Deryn O. LeDuke, Matilde Borio, Raymundo Miranda, Kay M. Tye
Summary: The functional interaction between bottom-up and top-down processing allows individuals to respond appropriately to the changing environment. These processing modalities can be represented using a dynamical systems model of the brain. The transition between attractor states depends on stability, depth, neuromodulatory tone, and plasticity changes. In disease states like anxiety or depression, understanding the relationship between these states is crucial. This study examines bottom-up and top-down processing from Marr's computational perspective to understand depressive and anxious disease states, using examples of amygdala and prefrontal cortex signaling.
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2023)
Article
Physics, Particles & Fields
Karol Kampf
Summary: This work systematically studies the higher-derivative corrections of the non-linear Sigma model, focusing on ordered amplitudes of flavor scalars in massless limit. New S-matrix methods are applied to construct amplitudes and analyze tree-level amplitudes, with possible theoretical simplifications based on specific relations. Additionally, the comparison with the Z-function connected with string theory is also discussed in the same context.
JOURNAL OF HIGH ENERGY PHYSICS
(2021)
Article
Biochemical Research Methods
Diogo B. Lima, Mathieu Dupre, Magalie Duchateau, Quentin Giai Gianetto, Martial Rey, Mariette Matondo, Julia Chamot-Rooke
Summary: The software can integrate data from multiple experiments and search engines, enabling rapid and easy visualization, validation, and comparison of proteoform sequences with high performance. The effectiveness of the method was demonstrated on a large-scale Escherichia coli dataset, where ProteoCombiner accurately shortlisted proteoforms identified by multiple search engines.
Article
Biology
Marcelo Ardon, Lydia H. Zeglin, Ryan M. Utz, Scott D. Cooper, Walter K. Dodds, Rebecca J. Bixby, Ayesha S. Burdett, Jennifer Follstad Shah, Natalie A. Griffiths, Tamara K. Harms, Sherri L. Johnson, Jeremy B. Jones, John S. Kominoski, William H. McDowell, Amy D. Rosemond, Matt T. Trentman, David Van Horn, Amelia Ward
Summary: Anthropogenic increases in nitrogen and phosphorus concentrations can strongly affect the structure and function of lotic ecosystems, leading to increased organismal biomass and abundance, as well as rates of ecosystem processes across multiple trophic levels. Responses to nutrient enrichment vary depending on the nutrient added and experimental conditions, with effects higher in flume and whole-stream experiments. Overall, nutrient-enrichment effects are influenced by water temperature, light, and ambient concentrations of inorganic nutrients.
BIOLOGICAL REVIEWS
(2021)
Article
Geosciences, Multidisciplinary
John C. Hammond, Margaret Zimmer, Margaret Shanafield, Kendra Kaiser, Sarah E. Godsey, Meryl C. Mims, Samuel C. Zipper, Ryan M. Burrows, Stephanie K. Kampf, Walter Dodds, C. Nathan Jones, Corey A. Krabbenhoft, Kate S. Boersma, Thibault Datry, Julian D. Olden, George H. Allen, Adam N. Price, Katie Costigan, Rebecca Hale, Adam S. Ward, Daniel C. Allen
Summary: Analysis of nonperennial flow regimes in 540 U.S. Geological Survey watersheds revealed regional differences and the significant impact of aridity and human alterations on stream drying patterns. While aridity played a key role at a continental scale, unique combinations of drivers emerged at regional scales, highlighting the importance of climate change and land cover modifications in shaping future streamflow dynamics.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Ecology
Elizabeth A. LaRue, Jason Rohr, Jonathan Knott, Walter K. Dodds, Kyla M. Dahlin, James H. Thorp, Jeremy S. Johnson, Mayra Rodriguez Gonzalez, Brady S. Hardiman, Michael Keller, Robert T. Fahey, Jeff W. Atkins, Flavia Tromboni, Michael D. SanClements, Geoffrey Parker, Jianguo Liu, Songlin Fei
Summary: Macroecosystem biology (MSB) was developed to understand ecological patterns and processes within and across spatial and temporal scales during an era of unprecedented human impacts. The thematic composition of MSB articles since 2010 demonstrated a deep ecological root and a potential emergence as a new research frontier, with emphasis on large scales and human components. Further analysis with ecological studies confirmed that MSB has extended the knowledge space of ecology by examining large-scale patterns and processes alongside anthropogenic factors.
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT
(2021)
Article
Ecology
Flavia Tromboni, Jianguo Liu, Emanuele Ziaco, David D. Breshears, Kimberly L. Thompson, Walter K. Dodds, Kyla M. Dahlin, Elizabeth A. LaRue, James H. Thorp, Andres Vina, Marysa M. Lague, Alain Maasri, Hongbo Yang, Sudeep Chandra, Songlin Fei
Summary: Macrosystems, recognizing the interconnectedness of human-natural systems, should consider factors such as human-nature connectivity and multi-scale feedbacks. The metacoupling framework integrates ecological and socioeconomic dimensions to study interactions across different locations, showing how human activities impact systems on a global scale. This approach can lead to innovative discoveries and help address global challenges.
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT
(2021)
Article
Ecology
Walter K. Dodds, Kevin C. Rose, Songlin Fei, Sudeep Chandra
Summary: Macrosystems biology research has grown and become an important subdiscipline, integrating fields such as population and community ecology, biogeography, and global biogeochemistry. It has the potential to have increasing relevance to ecological science and practical applications in the future.
FRONTIERS IN ECOLOGY AND THE ENVIRONMENT
(2021)
Article
Ecology
James H. Thorp, Walter K. Dodds, Caleb J. Robbins, Alain Maasri, Emily R. Arsenault, Jackob A. Lutchen, Flavia Tromboni, Barbara Hayford, Mark Pyron, Gregory S. Mathews, Anne Schechner, Sudeep Chandra
Summary: This article analyzes the nature of research in freshwater macrosystem biology, focusing on lotic studies, from both conceptual and current research perspectives. It describes the boundaries of permanent and transitional lotic macrosystems across spatial extents, contrasts ecosystem vs. macrosystem research, and provides examples of aquatic macrosystems ecology projects in the USA. The article also recommends incorporating large-scale lotic concepts developed over the last 40 years as the basis for lotic macrosystem studies and suggests future research directions in areas of climate change and teleconnections among distant organisms and systems.
Article
Ecology
Julie C. Zinnert, Jesse B. Nippert, Jennifer A. Rudgers, Steven C. Pennings, Grizelle Gonzalez, Merryl Alber, Sara G. Baer, John M. Blair, Adrian Burd, Scott L. Collins, Christopher Craft, Daniela Di Iorio, Walter K. Dodds, Peter M. Groffman, Ellen Herbert, Christine Hladik, Fan Li, Marcy E. Litvak, Seth Newsome, John O'Donnell, William T. Pockman, John Schalles, Donald R. Young
Summary: Understanding complex and unpredictable ways ecosystems are changing and predicting future ecosystem states require coordinated, long-term research efforts. This paper reports on a US National Science Foundation funded Long Term Ecological Research network synthesis on anticipated changes in populations and communities. Common themes of state change, connectivity, resilience, time lags, and cascading effects are identified as key predictions across different ecosystems within the LTER network.
Article
Environmental Sciences
Davi Gasparini Fernandes Cunha, Nicolas Reinaldo Finkler, Marta Conde Lamparelli, Maria do Carmo Calijuri, Walter K. Dodds, Robert E. Carlson
Summary: The study found significant deviations among TSI components in tropical water bodies, which were related to turbidity, water temperature, and cyanobacterial biomass. TSItemp showed a more conservative approach in tropical reservoirs, with TSI values significantly different in relation to chlorophyll-a and total phosphorus.
ENVIRONMENTAL MANAGEMENT
(2021)
Article
Environmental Sciences
Samuel C. Zipper, John C. Hammond, Margaret Shanafield, Margaret Zimmer, Thibault Datry, C. Nathan Jones, Kendra E. Kaiser, Sarah E. Godsey, Ryan M. Burrows, Joanna R. Blaszczak, Michelle H. Busch, Adam N. Price, Kate S. Boersma, Adam S. Ward, Katie Costigan, George H. Allen, Corey A. Krabbenhoft, Walter K. Dodds, Meryl C. Mims, Julian D. Olden, Stephanie K. Kampf, Amy J. Burgin, Daniel C. Allen
Summary: The study investigated trends and drivers of intermittency signatures of non-perennial streams across the United States, revealing that half of the gages showed significant trends in at least one signature during a specific time period, with changes in no-flow duration being the most common. Regional patterns of change showed widespread drying in the southern US and wetting in the north.
ENVIRONMENTAL RESEARCH LETTERS
(2021)
Article
Environmental Sciences
Ricardo Gabriel Bandeira de Almeida, Marta Conde Lamparelli, Walter Kennedy Dodds, Davi Gasparini Fernandes Cunha
Summary: Water quality monitoring networks are crucial for providing data for management decisions, and this study analyzed and proposed improvements for the Sao Paulo State (Brazil) network to enhance its spatial representativeness.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Environmental Sciences
Adam S. Wymore, Penny J. Johnes, Susana Bernal, E. N. Jack Brookshire, Hannah M. Fazekas, Ashley M. Helton, Alba Argerich, Rebecca T. Barnes, Ashley A. Coble, Walter K. Dodds, Shahan Haq, Sherri L. Johnson, Jeremy B. Jones, Sujay S. Kaushal, Pirkko Kortelainen, Carla Lopez-Lloreda, Bianca M. Rodriguez-Cardona, Robert G. M. Spencer, Pamela L. Sullivan, Christopher A. Yates, William H. McDowell
Summary: A comprehensive assessment of nitrogen species in stream water reveals shifts in dissolved nitrogen pool composition from highly heterogeneous to primarily inorganic nitrogen under nutrient enrichment from human disturbances. With increasing total dissolved nitrogen concentrations, inorganic nitrogen dominates the pool while dissolved organic nitrogen decreases. These changes in stoichiometry may have significant implications for global biogeochemical cycles of carbon and nitrogen in freshwater ecosystems.
GLOBAL BIOGEOCHEMICAL CYCLES
(2021)
Article
Biodiversity Conservation
Bianca M. Rodriguez-Cardona, Adam S. Wymore, Alba Argerich, Rebecca T. Barnes, Susana Bernal, E. N. Jack Brookshire, Ashley A. Coble, Walter K. Dodds, Hannah M. Fazekas, Ashley M. Helton, Penny J. Johnes, Sherri L. Johnson, Jeremy B. Jones, Sujay S. Kaushal, Pirkko Kortelainen, Carla Lopez-Lloreda, Robert G. M. Spencer, William H. McDowell
Summary: DOC and DON concentrations in streams show different trends in various biomes and the DOC:DON molar ratios increase over time. The recovery from atmospheric acid deposition leads to fundamental changes in the DOM pool, affecting biogeochemical processes and food webs in streams.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Ecology
Walter K. Dodds, Gretchen Wichman, James P. Guinnip, Jessica R. Corman, John M. Blair
Summary: Riparian zones play a crucial role in transforming and retaining nutrients and sediment. This study investigates the direct influence of precipitation on material retention and transport in these zones. The findings suggest that vegetated riparian zones have a high capacity for retaining nitrate.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Ecology
Rachel M. Keen, Jesse B. Nippert, Pamela L. Sullivan, Zak Ratajczak, Brynn Ritchey, Kimberly O'Keefe, Walter K. Dodds
Summary: Woody encroachment has impacted grassland ecohydrology worldwide. In a tallgrass prairie in Kansas, USA, stream discharge has declined despite an increase in precipitation. Riparian vegetation, particularly woody species, primarily use deep soil water, leading to observed declines in stream flow.
Article
Green & Sustainable Science & Technology
Corey A. Krabbenhoft, George H. Allen, Peirong Lin, Sarah E. Godsey, Daniel C. Allen, Ryan M. Burrows, Amanda G. DelVecchia, Ken M. Fritz, Margaret Shanafield, Amy J. Burgin, Margaret A. Zimmer, Thibault Datry, Walter K. Dodds, C. Nathan Jones, Meryl C. Mims, Catherin Franklin, John C. Hammond, Sam Zipper, Adam S. Ward, Katie H. Costigan, Hylke E. Beck, Julian D. Olden
Summary: The global river gauge network is biased towards large, perennial rivers, neglecting other important areas for freshwater conservation and water security. This bias weakens our understanding of key hydrologic processes and our ability to make informed water-management and policy decisions.
NATURE SUSTAINABILITY
(2022)
