Article
Multidisciplinary Sciences
Anna L. C. Wood, Kathryn R. Kirby, Carol R. Ember, Stella Silbert, Sam Passmore, Hideo Daikoku, John McBride, Forrestine Paulay, Michael J. Flory, John Szinger, Gideon D'Arcangelo, Karen Kohn Bradley, Marco Guarino, Maisa Atayeva, Jesse Rifkin, Violet Baron, Miriam El Hajli, Martin Szinger, Patrick E. Savage
Summary: Standardized cross-cultural databases of the arts are crucial for a balanced scientific understanding of performing arts and their role in society. The Global Jukebox serves as a resource for comparative and cross-cultural study, providing an extensive and detailed database that enhances our understanding of cultural diversity.
Article
Physics, Multidisciplinary
Marco Alberto Javarone
Summary: Complex systems study natural and societal phenomena, involving emergent behaviors, interaction patterns, and resource requirements. This review examines methods for studying complexity across various topics, revealing interesting relationships between complexity and distance in different systems, from phase transitions to black hole evolution. Implications and examples beyond Physics further support the validity of these relationships.
Article
Computer Science, Artificial Intelligence
Giuseppe De Giacomo, Xavier Oriol, Riccardo Rosati, Domenico Fabio Savo
Summary: This paper studies instance-level update in DL-LiteA and shows that it has a first-order rewritability property. Updates can be reformulated into insertion and deletion instructions computable through a non-recursive Datalog program. Experiments demonstrate the effectiveness of this approach in practice.
JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH
(2021)
Article
Computer Science, Artificial Intelligence
Frits de Nijs, Erwin Walraven, Mathijs M. de Weerdt, Matthijs T. J. Spaan
Summary: This survey explores the uncertainty in multiagent planning problems, establishes a generic problem class based on Markov decision processes, compares the conditions for applying different algorithms, discusses the advantages and disadvantages of these algorithms, and identifies unresolved issues related to the conceptualized domains and adjacent research areas.
JOURNAL OF ARTIFICIAL INTELLIGENCE RESEARCH
(2021)
Article
Biology
Yuanxiao Gao, Hye Jin Park, Arne Traulsen, Yuriy Pichugin
Summary: The article discusses the emergence of irreversible somatic differentiation in complex animals, as well as the differences in cell differentiation and separation of reproductive tasks between primitive species and complex animals. The study found that costly cell differentiation, vegetative cells that can significantly improve organism performance even in small numbers, and large enough organism size are necessary components for the evolution of irreversible somatic differentiation.
Article
Computer Science, Information Systems
Peng Su, Meihua Chen, Yanfei Wang
Summary: This article introduces the application of agent-based model in the field of Library and Information Science and emphasizes the advantages of ABM as a research tool.
JOURNAL OF INFORMATION SCIENCE
(2022)
Article
Psychology, Biological
Joyce F. Benenson, Christine E. Webb, Richard W. Wrangham
Summary: This paper discusses the adaptive strategy of increasing self-protection investment among females and proposes an expanded explanation by integrating modern theories, in order to understand different lifestyle strategies.
BEHAVIORAL AND BRAIN SCIENCES
(2022)
Article
Multidisciplinary Sciences
Paulo Roberto de Melo Barros Junior, Kianny Lopes Bunge, Vitor Hugo Serravalle Reis Rodrigues, Michell Thompson Ferreira Santiago, Euler Bentes dos Santos Marinho, Jose Luis Lima de Jesus Silva
Summary: Complex systems in various fields possess emergent properties that can be understood by analyzing cross-correlations. We propose a systematic approach, MF-DCCHM, that utilizes heatmaps to map relationships between signal fluctuations on different scales and regimes. Our results demonstrate cross-correlated patterns and cyclical patterns, including hidden high-intensity cycles.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Dinah R. Davison, Richard E. Michod
Summary: This paper examines how the stages of biological evolutionary transitions in individuality could be applied to the evolution of human culture. It uses the example of the evolution of multicellularity in volvocine algae to illustrate these stages and applies them to the cultural transition involving integrated groups of cultural traditions and hominins. The analysis highlights important similarities and differences between biological and cultural evolutionary transitions.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Correction
Biology
Axel H. Newton, Andrew J. Pask
Summary: The correction to this paper has been published.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemical Research Methods
Dominik Deffner, Anne Kandler, Laurel Fogarty
Summary: The importance of population size for cultural diversity and complexity is examined in this study. The authors highlight the concept of effective population size for culturally evolving traits and show how it depends on various factors such as the way traits are learned, population connectedness, and social network structure. The results provide insights into understanding cultural evolution and emphasize the need for a careful definition of effective population size in cultural systems.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Physics, Multidisciplinary
David B. Saakian
Summary: The researchers aim to uncover the generative principles for complex biological systems, drawing analogies between decision-making properties in quantum physics and reflections in biological systems. They highlight the importance of reflection as a mapping mechanism from microscopic to macroscopic scales, and discuss the concept of self-reflection in phenomena such as cognition and information transfer. The study proposes that systems with similar reflection structures can be described using similar mathematical tools and introduces the concept of a complexity engine for the emergence of life.
CHINESE JOURNAL OF PHYSICS
(2021)
Article
Biology
David Gil, Yeshayahu Shen
Summary: Metaphors, a common feature in human language, reflect mappings between different conceptual domains. The unidirectionality of metaphors is a result of various asymmetries in grammatical structures. Through an experiment comparing Hebrew and Abui, it was found that Hebrew has significantly higher metaphor unidirectionality than Abui, suggesting a evolutionary journey from bidirectionality to unidirectionality in metaphorical expressions.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Adam B. Roddy, David Alvarez-Ponce, Scott W. Roy
Summary: Genome size in mammals is not significantly correlated with population size, suggesting that the Drift-Barrier Hypothesis may be considered provisional.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Chemistry, Multidisciplinary
Jianing Xie, Axel Pahl, Adrian Krzyzanowski, Anna Krupp, Jie Liu, Sandra Koska, Beate Schoelermann, Ruirui Zhang, Jana Bonowski, Sonja Sievers, Carsten Strohmann, Slava Ziegler, Michael Grigalunas, Herbert Waldmann
Summary: Monoterpene indole alkaloids (MIAs) exhibit high structural and spatial complexity, along with diverse biological activities. A pseudo-natural product (pseudo-NP) collection has been designed and synthesized by combining MIA fragments through complexity-generating transformations, occupying a unique chemical space with high spatial complexity-density similar to MIAs and showing bioactivities inhibiting DNA synthesis and tubulin modulation. These findings suggest potential novel bioactive compounds inspired by MIAs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Nicholas Heitman, Rachel Sennett, Ka-Wai Mok, Nivedita Saxena, Devika Srivastava, Pieter Martino, Laura Grisanti, Zichen Wang, Avi Ma'ayan, Panteleimon Rompolas, Michael Rendl
Article
Immunology
Jens Eberlein, Bennett Davenport, Tom T. Nguyen, Francisco Victorino, Kevin Jhun, Verena van der Heide, Maxim Kuleshov, Avi Ma'ayan, Ross Kedl, Dirk Homann
JOURNAL OF IMMUNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Minji Jeon, Kathleen M. Jagodnik, Eryk Kropiwnicki, Daniel J. Stein, Avi Ma'ayan
Summary: While many genes are associated with pain, the molecular mechanisms are largely unknown. A machine learning model was trained to predict new pain targets, showing promising results for identifying novel drug targets and pathways. This approach provides a foundation for future experimental exploration in developing safer and more effective analgesics.
Article
Multidisciplinary Sciences
Evan Austin, Eugene Koo, Alexander Merleev, Denis Torre, Alina Marusina, Guillaume Luxardi, Andrew Mamalis, Roslyn Rivkah Isseroff, Avi Ma'ayan, Emanual Maverakis, Jared Jagdeo
Summary: Red light phototherapy can improve skin fibrosis by regulating extracellular matrices, proliferation, and cellular responses to oxygen-containing compounds. The study found that red light therapy may have anti-fibrotic effects by increasing the expression of MMP1 and PRSS35.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Maxim Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan
Summary: KEA3 is a webserver application used to predict upstream kinases and analyze data from proteomics and phosphoproteomics studies. The background database of KEA3 contains measured and predicted kinase-substrate interactions. Studies show that integrating kinase-substrate and kinase-protein interactions across data sources improves the recovery of the expected kinase.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan
Summary: This paper introduces an algorithm called blitzGSEA, which significantly improves gene set enrichment analysis. Compared to previous methods, blitzGSEA allows for faster calculations and more accurate estimation of small P-values.
Article
Biochemical Research Methods
Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
Summary: DrugShot is a web-based server application that provides ranked lists of drugs and small molecules relevant to biomedical search terms. By integrating PubMed abstracts and LINCS L1000 signatures, DrugShot can predict additional drugs and small molecules associated with the search term.
BMC BIOINFORMATICS
(2022)
Article
Dermatology
Alexandros Onoufriadis, Laura E. Proudfoot, Chrysanthi Ainali, Denis Torre, Maria Papanikolaou, Tuntas Rayinda, Ellie Rashidghamat, Retno Danarti, Jemima E. Mellerio, Avi Ma'ayan, John A. McGrath
Summary: This study identified gene expression profiles and pathways in RDEB wounds, identifying potential drugs or compounds to restore wound healing. The findings highlight the clinical value of reverse transcriptomics data analysis in RDEB and the potential of this approach in discovering or repurposing drugs for other diseases.
EXPERIMENTAL DERMATOLOGY
(2022)
Article
Cell Biology
Edmund Charles Jenkins, Mrittika Chattopadhyay, Maria Gomez, Denis Torre, Avi Ma'ayan, Miguel Torres-Martin, Daniela Sia, Doris Germain
Summary: A major limitation in breast cancer research using mouse models is that most mice develop estrogen receptor-alpha (ER alpha)-negative mammary tumors, while in humans, the majority of breast cancers are ER alpha-positive. However, a new study using an inducible mouse model revealed that mammary tumors in young mice are ER alpha-negative, while they are ER alpha-positive in aged mice. The study also identified genes involved in the activation of ER alpha axis and the regulation of UPR stress responses in aged female-derived mammary tumors. These findings suggest that aging alters the oncogenic trajectory towards ER alpha-positive breast cancer subtype.
Article
Cell Biology
J. B. Daniel Clarke, W. Alison Rebman, Jinshui Fan, J. Mark Soloski, N. John Aucott, Avi Ma'ayan
Summary: This study analyzed differential gene expression in peripheral blood cells of patients with acute Lyme disease and post-treatment Lyme disease using RNA sequencing, revealing an inflammatory signature in post-treatment patients distinct from those with acute disease. By extracting gene sets and analyzing feature importance, a potential biomarker set was identified for distinguishing healthy individuals from those with acute or post-treatment Lyme disease.
CELL REPORTS MEDICINE
(2022)
Article
Cell Biology
Eden Z. Deng, Reid H. Fleishman, Zhuorui Xie, Giacomo B. Marino, Daniel J. B. Clarke, Avi Ma'ayan
Summary: To identify potential targets for selective identification and removal of senescent cells, gene expression signatures of senescent cells were compared to normal human tissues and cell types. A gene set called SenoRanger, composed of 301 genes, was established based on consensus analysis. Pathway analysis confirmed the potential role of SenoRanger genes in aging and senescence-related processes. Overall, SenoRanger provides solid hypotheses for identifying and removing senescent cells.
Article
Biochemistry & Molecular Biology
Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan
Summary: GeneRanger is a web server that integrates data from multiple atlases to provide information about gene and protein expression in normal human cells, tissues, and cell lines. TargetRanger, on the other hand, compares uploaded RNA-seq data to expression levels across atlases to identify highly expressed genes in the input that are lowly expressed in normal human cells and tissues. Both servers offer visualization through box and scatter plots, as well as interactive tables.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan
Summary: Enrichr-KG is a knowledge graph database and web-server application that integrates gene set libraries from Enrichr for comprehensive enrichment analysis and visualization. The graphical representation of cross-library results allows users to uncover hidden associations between genes and annotated enriched terms from different datasets and resources. Enrichr-KG currently offers 26 gene set libraries from various categories including transcription, pathways, ontologies, diseases/drugs, and cell types.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan
Summary: lncHUB2 is a web server database that provides extensive information about the function and regulation of human and mouse lncRNAs, including secondary structure fold, related publications, correlated coding genes and lncRNAs, visualized gene network, predicted phenotypes, participation in biological processes and pathways, predicted transcription factors, disease associations, subcellular localization information, expression patterns, and predicted regulators. Overall, lncHUB2 is a valuable resource for hypothesis generation in future studies.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Cardiac & Cardiovascular Systems
Jonathan J. Edwards, Andrew D. Rouillard, Nicolas F. Fernandez, Zichen Wang, Alexander Lachmann, Sunita S. Shankaran, Brent W. Bisgrove, Bradley Demarest, Nahid Turan, Deepak Srivastava, Daniel Bernstein, John Deanfield, Alessandro Giardini, George Porter, Richard Kim, Amy E. Roberts, Jane W. Newburger, Elizabeth Goldmuntz, Martina Brueckner, Richard P. Lifton, Christine E. Seidman, Wendy K. Chung, Martin Tristani-Firouzi, H. Joseph Yost, Avi Ma'ayan, Bruce D. Gelb
JACC-BASIC TO TRANSLATIONAL SCIENCE
(2020)
