Article
Ecology
Marguerite V. Langwig, Valerie De Anda, Nina Dombrowski, Kiley W. Seitz, Ian M. Rambo, Chris Greening, Andreas P. Teske, Brett J. Baker
Summary: Deltaproteobacteria, proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. A genomic catalog of 1,792 genomes, including 402 newly reconstructed metagenome-assembled genomes, reveals previously unrecognized metabolic abilities and expands our understanding of the diversity and ecological roles of these bacteria.
Article
Ecology
Yuval Werber, Hadar Sextin, Yossi Yovel, Nir Sapir
Summary: Bat movement and behavior are not well-studied due to the difficulties in visual identification caused by their high-altitude and nocturnal activity. This study presents a bat classifier called BATScan, which uses radar data to identify and characterize bat movements. The classifier was constructed using data from 10 radar deployments over a 7-year period and achieved high accuracy and precision through ecological validations.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Environmental Sciences
Sonke Dangendorf, Thomas Frederikse, Leon Chafik, John M. Klinck, Tal Ezer, Benjamin D. Hamlington
Summary: Research on historical and projected coastal sea-level change reveals that ocean dynamics, including density fluctuations, have a significant impact. By analyzing global tide-gauge records, a reconstruction of coastal sea-level budget over nine regions is possible, indicating that ocean circulation has been a dominant factor in sea-level variability since 1960.
NATURE CLIMATE CHANGE
(2021)
Article
Biodiversity Conservation
H. Patrick Roberts, Michael T. Jones, Lisabeth L. Willey, Thomas S. B. Akre, Paul R. Sievert, Phillip DeMaynadier, Katharine D. Gipe, Glenn Johnson, John Kleopfer, Michael Marchand, Joshua Megyesy, Steven Parren, Edward Thompson, Chris Urban, Derek Yorks, Brian Zarate, Lori Erb, Angelena M. Ross, Jeffrey Dragon, Lori Johnson, Ellery Lassiter, Elliot Lassiter
Summary: Freshwater turtles and tortoises are facing a worldwide decline, with collaborative monitoring efforts revealing that mature forest cover positively impacts population demographics, while agriculture and road traffic have negative effects. Effective conservation strategies for demographically robust turtle populations require consideration of multiple spatial scales.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Computer Science, Interdisciplinary Applications
Jialin Liu, Hongkan Chen, Zhibo Liu, Yi Bu, Weiye Gu
Summary: This paper defines and calculates five indicators of references and investigates their relations with the citation impact of the focal publication using articles published in 2005 covered by Microsoft Academic Graph. The results show non-linear relationships in all the five indicators, with two types of patterns, inverted-L and inverted-U, both presenting the existence of critical points. The paper further explores the discipline-level differences of such a relationship and how it relates to the characteristics of the discipline itself.
JOURNAL OF INFORMETRICS
(2022)
Article
Computer Science, Information Systems
Yi Bu, Wei Lu, Yifei Wu, Hongkan Chen, Yong Huang
Summary: The study focuses on understanding the width of citation impact of scientific publications through ego-centered citation networks. It finds that as the number of citations of publications rises, the number and size of connected components also increase, with differences observed in Arts and Humanities publications compared to other disciplines, Natural Sciences showing greater values. These findings have implications on research assessment practices and literature searching.
INFORMATION PROCESSING & MANAGEMENT
(2021)
Article
Biodiversity Conservation
Miika Kotila, Kati M. M. Suominen, Ville V. V. Vasko, Anna S. S. Blomberg, Aleksi Lehikoinen, Tommi Andersson, Jouni Aspi, Tony Cederberg, Jari Haenninen, Jasmin Inkinen, Janne Koskinen, Goeran Lundberg, Katja Makinen, Markku Rontti, Martin Snickars, Jostein Solbakken, Janne Sundell, Ilkka Syvanpera, Silja Vuorenmaa, Jari Ylonen, Eero J. J. Vesterinen, Thomas M. M. Lilley
Summary: The distribution ranges and spatio-temporal patterns of boreal bats are poorly known. In this study, a passive-acoustic sampling setup was established in Finland to investigate the effect of latitude on bat species composition and activity patterns in northern Europe. Bat calls were identified and seasonal activity patterns were modeled for three target species across seven sampling years. The results indicate an increase in activity for E. nilssonii and Myotis spp. since 2015, with significant latitude-dependent seasonal patterns. The passive-acoustic monitoring network proved to be an effective and cost-efficient method for studying bat activity and analyzing spatio-temporal patterns.
Article
Chemistry, Analytical
Ricardo Munoz-Cancino, Sebastian A. Rios, Manuel Grana
Summary: The impact of micro-level people's activities on urban macro-level indicators is a complex question that has garnered much interest. Individual activities, such as transportation preferences and consumption habits, can significantly influence large-scale urban characteristics, such as innovation potential. Understanding the interdependence between micro- and macro-level factors is crucial for effective public policies.
Article
Mechanics
Sk Zeeshan Ali, Subhasish Dey
Summary: This paper investigates the instability of large-scale riverbed patterns through a linear stability analysis of zero-pressure gradient free-surface flow. By developing a depth-averaged flow model and relevant equations, the mechanism of large-scale patterns formation is explored.
Article
Meteorology & Atmospheric Sciences
Catalin-Constantin Roibu, Viorica Nagavciuc, Monica Ionita, Ionel Popa, Sergiu-Andrei Horodnic, Andrei Mursa, Ulf Buentgen
Summary: The study presents a new beech tree-ring width composite chronology from eastern Romania, reflecting hydroclimate variability and its correlation with atmospheric circulation patterns and sea surface temperatures. The reconstructed hydroclimatic extremes back to 1768 CE are confirmed by documentary evidences, providing insights into regional hydroclimate variation and large-scale teleconnection patterns.
Article
Multidisciplinary Sciences
Lucas J. Ustick, Alyse A. Larkin, Catherine A. Garcia, Nathan S. Garcia, Melissa L. Brock, Jenna A. Lee, Nicola A. Wiseman, J. Keith Moore, Adam C. Martiny
Summary: Nutrient supply affects phytoplankton activity, but understanding of global nutrient limitation and co-limitation is limited. Prochlorococcus adapt to local environments through gene gains and losses, with genomic changes indicating adaptation to nutrient stress. Regional transitions in stress type and severity, as well as widespread co-stress, were found, with correlations between Prochlorococcus stress genes, bottle experiments, and Earth system model predictions. The biogeography of multinutrient stress is linked through controls on nitrogen fixation, providing a detailed description of nutrient stress in the global ocean based on omics data.
Article
Engineering, Electrical & Electronic
Alireza Haqiqatnejad, Farbod Kayhan, Bjorn Ottersten
Summary: This study tackles the symbol-level precoding design problem in a multiuser millimeter wave MIMO wireless system using a hybrid analog-digital architecture, aiming to minimize the Euclidean distance, achieve power savings in precoding, and substantially improve energy efficiency through phase shifter selection.
IEEE TRANSACTIONS ON COMMUNICATIONS
(2021)
Article
Neurosciences
Pierre Baldi, Wedad Alhassen, Siwei Chen, Henry Nguyen, Mohammad Khoudari, Amal Alachkar
Summary: Cilia are dynamic subcellular systems with circadian rhythmic gene expression observed in various primate brain areas, suggesting a potential role in the physiology of the basal ganglia-cortical circuit and motor control. Study of coordinated cilia rhythmicity may provide insights into the regulation of movement and other behaviors.
JOURNAL OF NEUROSCIENCE RESEARCH
(2021)
Article
Geosciences, Multidisciplinary
R. Roded, P. Szymczak, R. Holtzman
Summary: The dynamics of wormholing in anisotropic media are significantly influenced by anisotropy, controlling competition and spacing between wormholes, as well as affecting their shapes and flow. In media with low transverse pore conductivities, wormhole distribution is no longer scale-invariant and pronounced side branches develop.
GEOPHYSICAL RESEARCH LETTERS
(2021)
Article
Biology
Karim Karimi, Duy Ngoc Do, Jingy Wang, John Easley, Shima Borzouie, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Younes Miar
Summary: This study successfully achieved a high-quality chromosome-level genome assembly for American mink and explored its relationships with other related genomes, providing support for the development of breeding strategies and conservation programs for American mink.
COMMUNICATIONS BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Luiz G. A. Alves, Alberto Aleta, Francisco A. Rodrigues, Yamir Moreno, Luis A. Nunes Amaral
NEW JOURNAL OF PHYSICS
(2020)
Article
Multidisciplinary Sciences
Luis A. Nunes Amaral, Joao A. G. Moreira, Murielle L. Dunand, Heliodoro Tejedor Navarro, Hyojun Ada Lee
Editorial Material
Multidisciplinary Sciences
Adam R. Pah, David L. Schwartz, Sarath Sanga, Zachary D. Clopton, Peter DiCola, Rachel Davis Mersey, Charlotte S. Alexander, Kristian J. Hammond, Luis A. Nunes Amaral
Article
Biochemistry & Molecular Biology
Jenny Liu, Luis A. Nunes Amaral, Sinan Keten
Summary: Allosteric regulation of conformational states plays a key role in catch-bond behavior in adhesive proteins like FimH. By studying the molecular dynamics of the lectin domain in different states, such as the HL mutant, researchers gain insight into the transmission of allosteric information across protein domains. This information could potentially guide drug development efforts to prevent infections by inhibiting FimH adhesion.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biology
Thomas Stoeger, Luis A. Nunes Amaral
Article
Mathematics, Interdisciplinary Applications
Charles C. Hyland, Yuanming Tao, Lamiae Azizi, Martin Gerlach, Tiago P. Peixoto, Eduardo G. Altmann
Summary: The method proposed in the study is based on Multilayer Networks and Stochastic Block Models, applying the same non-parametric probabilistic framework to different types of datasets to tackle the challenge of clustering documents and finding topics. By taking into account multiple types of information, it provides a more nuanced view on topic- and document-clusters and increases the ability to predict missing links.
Article
Computer Science, Artificial Intelligence
Adam R. Pah, David L. Schwartz, Sarath Sanga, Charlotte S. Alexander, Kristian J. Hammond, Luis A. N. Amaral
Summary: To craft effective public policy, governments need to gather data on performance and public responses. While federal administrative agencies and the Congress do this and make the data accessible, the judicial branch is an outlier, as court records are effectively out of reach behind a paywall and technical obstacles. The SCALES OKN aims to address this by transforming the transparency and accessibility of court records, facilitating the development of new AI solutions for the benefit of the judiciary, legal scholars, and the public.
Article
Health Care Sciences & Services
Meagan Bechel, Adam R. Pah, Stephen D. Persell, Curtis H. Weiss, Luis A. Nunes Amaral
Summary: This study proposes a data-driven metric for clinician disease recognition that takes into account the variability in patient disease severity and institutional standards. By evaluating ventilatory management in patients with acute respiratory distress syndrome (ARDS), it was found that training background was associated with physician recognition, with non-PCCM physicians recognizing ARDS cases less frequently but expressing greater satisfaction with obtaining diagnostic information.
BMC MEDICAL RESEARCH METHODOLOGY
(2022)
Article
Multidisciplinary Sciences
Weihua Lei, Luiz G. A. Alves, Luis A. Nunes Amaral
Summary: The authors propose a machine learning framework for predicting connections removal in transportation networks and investigate the dynamics of edge removal in the Brazilian domestic bus transportation network and the U.S. domestic air transportation network. They find that machine learning models can accurately predict edge removals on a monthly time scale and even in the presence of external shocks. The authors also demonstrate the usefulness of their approach by forecasting the impact of a hypothetical reduction in the scale of the U.S. air transportation network due to CO2 emissions reduction policies. This forecasting approach could be valuable for future infrastructure planning.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jenny Liu, Luis A. N. Amaral, Sinan Keten
Summary: A promising approach to study protein dynamics is to represent it using networks and take advantage of well-established methods from network science. Most studies construct protein dynamics networks using correlation measures, which are only applicable under specific conditions. In this study, the researchers applied an inverse approach to build networks based on protein dihedral angles, resulting in physically interpretable and robust networks. By using this method, dynamical differences were identified for proteins with structural similarity. The study demonstrates the importance of using the inverse approach to extract networks from protein dynamics.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Computer Science, Information Systems
Tiziano Piccardi, Martin Gerlach, Akhil Arora, Robert West
Summary: This article presents the first large-scale analysis of how readers navigate Wikipedia, using billions of page requests from the server logs. The study finds that navigation behavior is highly diverse, with the depth and shape of paths varying systematically with topic, device type, and time of day. The research also reveals that Wikipedia navigation paths often intersect with external pages and differ from targeted navigation in lab-based settings. Additionally, the results suggest that navigation is abandoned when readers encounter low-quality pages. These insights contribute to a better understanding of readers' information needs and can help improve their experience on Wikipedia and the Web in general.
ACM TRANSACTIONS ON THE WEB
(2023)
Article
Cell Biology
Thomas Stoeger, Rogan A. Grant, Alexandra C. McQuattie-Pimentel, Kishore R. Anekalla, Sophia S. Liu, Heliodoro Tejedor-Navarro, Benjamin D. Singer, Hiam Abdala-Valencia, Michael Schwake, Marie-Pier Tetreault, Harris Perlman, William E. Balch, Navdeep S. Chandel, Karen M. Ridge, Jacob Sznajder, Richard Morimoto, Alexander Misharin, G. R. Scott Budinger, Luis A. Nunes Amaral
Summary: The length of transcripts explains the majority of transcriptional changes observed during aging in mice and humans. The relative abundance of long transcripts is lower in aging, and antiaging interventions can counter this length association. Genes with the longest transcripts are associated with lifespan extension, while genes with the shortest transcripts are associated with lifespan shortening.
Proceedings Paper
Computer Science, Artificial Intelligence
Akhil Arora, Martin Gerlach, Tiziano Piccardi, Alberto Garcia-Duran, Robert West
Summary: This study examines the navigation behaviors of Wikipedia readers using clickstream data. It finds that clickstream data can effectively approximate the real navigation sequences, providing a useful resource for practical applications relying on reader data.
WSDM'22: PROCEEDINGS OF THE FIFTEENTH ACM INTERNATIONAL CONFERENCE ON WEB SEARCH AND DATA MINING
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Isaac Johnson, Martin Gerlach, Diego Saez-Trumper
Summary: Analyzing Wikipedia dynamics poses a challenge in grouping articles into coherent topics. Past approaches have been limited in coverage, but a new language-agnostic method proposed in this paper shows promising results in simplifying classification while increasing coverage.
WEB CONFERENCE 2021: COMPANION OF THE WORLD WIDE WEB CONFERENCE (WWW 2021)
(2021)
Article
Physics, Fluids & Plasmas
Hyojun A. Lee, Luiz G. A. Alves, Luis A. Nunes Amaral
Summary: This study compares transmission dynamics between temporal multipartite networks and their time-aggregated unipartite projections, and finds significant differences on three levels. The ratio of the number of nodes to the number of active edges over the time-aggregation scale determines the ability of projected networks to capture the dynamics on multipartite networks.
