Article
Mechanics
Gabriel Regnault, Alexander A. Doinikov, Cyril Mauger, Philippe Blanc-Benon, Claude Inserra
Summary: We experimentally investigate the attraction between two closely spaced, oscillating microbubbles. Above a certain value of the applied acoustic field, the bubbles jump to a new equilibrium location, separated by a thin fluid layer much smaller than the bubble radii. The sign reversal of the radiation interaction force between the bubbles, caused by multiple rescattering effects of the emitted waves, leads to this new equilibrium. Theoretical investigation reveals the presence of a new stable equilibrium at short distances, resulting in a quasi-contacting bubble pair.
Review
Microbiology
Daniela Rothschild-Rodriguez, Morgen Hedges, Merve Kaplan, Sercan Karav, Franklin L. Nobrega
Summary: The interaction between the gut mucosa and the bacterial component of the microbiota in the human gastrointestinal tract plays a crucial role in digestion, immune regulation, and overall health. Gut bacteria residing in the mucus layer can influence the integrity of the mucosal barrier, affecting health or disease progression. The viral members, particularly bacteriophages, also have the potential to interact with gut mucus, but their effects remain largely unexplored. This review discusses the role of bacteriophages in influencing mucosal integrity and their potential impact on health and disease states.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biology
Leo van Iersel, Remie Janssen, Mark Jones, Yukihiro Murakami
Summary: Orchard phylogenetic networks were introduced for computational benefits and can be interpreted as trees with additional horizontal arcs, closely related to tree-based networks.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Physics, Fluids & Plasmas
Martin van Hecke
Summary: The interactions between hysterons have a significant impact on pathways and memory, with three interacting hysterons generating over 15,000 transition graphs, most of which violate return point memory. This exploration opens up possibilities for designer pathways and information processing in complex matter.
Article
Multidisciplinary Sciences
Bin Li, Jue Liang, Hamid R. Baniasadi, Margaret A. Phillips, Anthony J. Michael
Summary: Viruses manipulate host cells' metabolic and replication systems to produce more viruses. They acquire metabolic genes from ancestral hosts and use the encoded enzymes to subvert host metabolism. This study identified and characterized various phage and virus-encoded polyamine metabolic enzymes and pathways, supporting the important role of spermidine in virus biology on a global scale.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Agriculture, Dairy & Animal Science
Ziqiang Bao, Cheng Li, Cheng Guo, Zuofu Xiang
Summary: The study reveals that Himalayan marmots have adapted to high-altitude environments partly through convergent evolution of the ND3 protein with other plateau animals, indicating it is not the sole strategy for adaptation to high altitudes.
Article
Cell Biology
Fei Meng, Gilman Kit-Hang Siu, Bobo Wing-Yee Mok, Jiahong Sun, Kitty S. C. Fung, Jimmy Yiu-Wing Lam, Nonthaphat Kent Wong, Lealem Gedefaw, Shumeng Luo, Thomas M. H. Lee, Shea Ping Yip, Chien-Ling Huang
Summary: The study identified SARS-CoV-2 viral miRNAs and found that v-miRNA-N is positively associated with viral load in COVID-19 patients. Through deep sequencing and analysis, novel functional targets and associations with cellular metabolism and biosynthesis were revealed for these viral miRNAs.
Article
Plant Sciences
Xun Liao, Xiao-Jie Li, Guan-Tao Zheng, Feng-Rui Chang, Lin Fang, Hang Yu, Jun Huang, Ya-Feng Zhang
Summary: Mitochondrion-encoded circRNAs are widespread and translatable in plants, and a newly developed computational pipeline efficiently identifies them, demonstrating their prevalence and translation in plants.
Article
Physics, Fluids & Plasmas
Yu Feng, Nicolas Brunel
Summary: Attractor neural networks are the leading theoretical frameworks for memory formation and retrieval in biological neuron networks. This paper studies the storage capacity of fully connected and sparsely connected networks using a binarized Hebbian rule. The results show that discrete synapses have a similar storage capacity as continuous synapses, and that sparse coding can approach the optimal capacity. The study also reveals that networks with Hebbian learning rules have slow convergence to optimal capacity at low coding levels, and that sparse binary connectivity matrices can store information more efficiently.
Article
Computer Science, Information Systems
Michele Coscia
Summary: Estimating the distance covered by a spreading event on a network can provide insights into epidemics, economic growth, and human behavior. This study proposes a novel algorithm, called Multi Layer Generalized Euclidean (MLGE), to solve the Node Vector Distance (NVD) problem in multilayer networks. The MLGE algorithm incorporates the graph's topology using the pseudoinverse of its Laplacian and demonstrates good performance in recovering infection parameters. The algorithm has a high time complexity but can cache computationally heavy parts for efficient solving of NVD problems on the same network.
ACM TRANSACTIONS ON KNOWLEDGE DISCOVERY FROM DATA
(2022)
Article
Biology
Kiri Choi, Won Kyu Kim, Changbong Hyeon
Summary: Reconstructed from electron microscope images, the projection neurons of the Drosophila olfactory system provide a detailed view of neuronal anatomy and shed light on the relationship between neuronal organization and odor perception.
Article
Nanoscience & Nanotechnology
Y. -h. Peng, S. K. Hsiao, K. Gupta, A. Ruland, G. K. Auernhammer, M. F. Maitz, S. Boye, J. Lattner, C. Gerri, A. Honigmann, C. Werner, E. Krieg
Summary: This study reports on a fully synthetic hydrogel based on DNA that can be used for three-dimensional cell and organoid cultures. The hydrogel self-assembles to form a dynamic DNA-crosslinked matrix, allowing control over its viscoelasticity, thermodynamic and kinetic parameters. It can tune stress-relaxation times, recapitulating mechanical characteristics of living tissues.
NATURE NANOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lei Shi, Ke Wang, Lipu Du, Yuxia Song, Huihui Li, Xingguo Ye
Summary: The WOX family is a group of plant-specific transcription factors that regulate plant growth and development. In Triticeae species, WOX genes are conserved and play a role in tissue-specific expression, with TaWOX9 potentially being closely related to the regulation of the regeneration process in wheat. This study provides a foundation for the evolution, functional investigation, and practical application of WOX family genes in Triticeae species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Mathematics, Interdisciplinary Applications
Padraig MacCarron, Shane Mannion, Thierry Platini
Summary: In this work, the researchers explore the degree assortativity in complex networks and propose an extended definition beyond nearest neighbors. They apply this definition to model networks and present a rewiring algorithm to induce assortativity. The results are compared to real networks, revealing that social networks tend to be assortatively mixed by degree. However, after one step, these positive correlations diminish, including in most empirical networks analyzed. Other properties, such as the number of papers in scientific coauthorship networks, also show no correlations beyond nearest neighbors. Additionally, there is a tendency for disassortativity between nodes three steps away, indicating that distant nodes are more likely to be different than similar.
JOURNAL OF COMPLEX NETWORKS
(2023)
Review
Biochemistry & Molecular Biology
Hai Nguyen, Perrin Guyer, Ruth A. Ettinger, Eddie A. James
Summary: Islet antigen reactive T cells are crucial in promoting beta cell destruction in type 1 diabetes. New classes of non-genetically encoded epitopes may play a significant role in the progression of islet autoimmunity.
Article
Genetics & Heredity
Laura Grange, Jean-Francois Bureau, Iryna Nikolayeva, Richard Paul, Kristel Van Steen, Benno Schwikowski, Anavaj Sakuntabhai
Article
Immunology
Xiaoyi Chen, Milena Hasan, Valentina Libri, Alejandro Urrutia, Benoit Beitz, Vincent Rouilly, Darragh Duffy, Etienne Patin, Bernard Chalmond, Lars Rogge, Lluis Quintana-Murci, Matthew L. Albert, Benno Schwikowski
CLINICAL IMMUNOLOGY
(2015)
Article
Immunology
Juliane Lippmann, Frederik Gwinner, Camille Rey, Uyanga Tamir, Helen K. W. Law, Benno Schwikowski, Jost Enninga
INFECTION AND IMMUNITY
(2015)
Article
Biochemical Research Methods
Frederik Gwinner, Gwenola Boulday, Claire Vandiedonck, Minh Arnould, Cecile Cardoso, Iryna Nikolayeva, Oriol Guitart-Pla, Cecile V. Denis, Olivier D. Christophe, Johann Beghain, Elisabeth Tournier-Lasserve, Benno Schwikowski
Article
Biochemical Research Methods
Cheikh Loucoubar, Audrey V. Grant, Jean-Francois Bureau, Isabelle Casademont, Ndjido Ardo Bar, Avner Bar-Hen, Mamadou Diop, Joseph Faye, Fatoumata Diene Sarr, Abdoulaye Badiane, Adama Tall, Jean-Francois Trape, Freddy Cliquet, Benno Schwikowski, Mark Lathrop, Richard Edward Paul, Anavaj Sakuntabhai
BRIEFINGS IN BIOINFORMATICS
(2017)
Review
Environmental Sciences
Beate I. Escher, Joerg Hackermuller, Tobias Polte, Stefan Scholz, Achim Aigner, Rolf Altenburger, Alexander Boehme, Stephanie K. Bopp, Werner Brack, Wibke Busch, Marc Chadeau-Hyam, Adrian Covaci, Adolf Eisentraeger, James J. Galligan, Natalia Garcia-Reyero, Thomas Hartung, Michaela Hein, Gunda Herberth, Annika Jahnke, Jos Kleinjans, Nils Kluever, Martin Krauss, Marja Lamoree, Irina Lehmann, Till Luckenbach, Gary W. Miller, Andrea Mueller, David H. Phillips, Thorsten Reemtsma, Ulrike Rolle-Kampczyk, Gerrit Schueuermann, Benno Schwikowski, Yu-Mei Tan, Saskia Trump, Susanne Walter-Rohde, John F. Wambaugh
ENVIRONMENT INTERNATIONAL
(2017)
Article
Biochemical Research Methods
Iryna Nikolayeva, Oriol Guitart Pla, Benno Schwikowski
Article
Biochemical Research Methods
Oriol Guitart-Pla, Manjunath Kustagi, Frank Ruegheimer, Andrea Califano, Benno Schwikowski
Article
Multidisciplinary Sciences
Sjouke Piersma, Emma L. Denham, Samuel Drulhe, Rudi H. J. Tonk, Benno Schwikowski, Jan Maarten van Dijl
Article
Multidisciplinary Sciences
Laura L. Elo, Benno Schwikowski
Article
Biochemistry & Molecular Biology
Raul Y. Sanchez David, Chantal Combredet, Valerie Najburg, Gael A. Millot, Guillaume Beauclair, Benno Schwikowski, Thibaut Leger, Jean-Michel Camadro, Yves Jacob, Jacques Bellalou, Nolwenn Jouvenet, Frederic Tangy, Anastassia V. Komarova
Review
Biochemical Research Methods
Farzaneh Firoozbakht, Behnam Yousefi, Benno Schwikowski
Summary: This article provides a comprehensive review of the literature on monotherapy drug response prediction, offering a systematic classification and description of over 70 machine learning methods. It introduces ML experts to the biological problem and how ML methods can be applied, while also providing basic principles of ML methods for biologists and biomedical researchers.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Neurosciences
Mor Kenigsbuch, Pierre Bost, Shahar Halevi, Yuzhou Chang, Shuo Chen, Qin Ma, Renana Hajbi, Benno Schwikowski, Bernd Bodenmiller, Hongjun Fu, Michal Schwartz, Ido Amit
Summary: This study identifies a shared signature of oligodendrocytes in central nervous system pathologies. The researchers discovered a specific oligodendrocyte state, termed disease-associated oligodendrocytes (DOLs), that increased with brain pathology. DOLs were found in various neurodegenerative and inflammatory conditions, indicating a common response to severe pathological conditions.
NATURE NEUROSCIENCE
(2022)
Correction
Neurosciences
Mor Kenigsbuch, Pierre Bost, Shahar Halevi, Yuzhou Chang, Shuo Chen, Qin Ma, Renana Hajbi, Benno Schwikowski, Bernd Bodenmiller, Hongjun Fu, Michal Schwartz, Ido Amit
NATURE NEUROSCIENCE
(2023)
Article
Rheumatology
Renaud Felten, Tao Ye, Cedric Schleiss, Benno Schwikowski, Jean Sibilia, Fanny Monneaux, Helene Dumortier, Roland Jonsson, Christopher Lessard, Fai Ng, Tsutomu Takeuchi, Xavier Mariette, Jacques-Eric Gottenberg
Summary: This study analyzed the gene expression differences between pSS patients and healthy controls and identified 11 potential candidate drugs, including histone deacetylases and PI3K inhibitors. Additionally, 12 genes with a pSS-like profile and 23 genes with a pSS-revert profile were identified, most of which were interferon-regulated.