Article
Multidisciplinary Sciences
Sung Yong Park, Sonia Ter-Saakyan, Gina Faraci, Ha Youn Lee
Summary: Single cell RNA sequencing is crucial for immune profiling, disease marker identification, and therapeutic target gene suggestion. However, accurate cell type assignment is challenging due to gene expression heterogeneity. In this study, we present ImmunIC, a robust tool that combines marker genes with machine learning to achieve 98% accuracy in immune cell identification and 92% accuracy in categorizing into ten immune cell types.
SCIENTIFIC REPORTS
(2023)
Article
Materials Science, Multidisciplinary
Amit Jamadagni, Hendrik Weimer
Summary: The lack of comprehensive understanding of topological order can be interpreted as the ability of a system to perform topological error correction. This operational approach lays the conceptual foundations for previous classifications of topological order and has also led to successful classification in the case of topological order in open quantum systems. The viability of topological order in nonequilibrium quantum systems substantially broadens the scope of possible technological applications.
Article
Biotechnology & Applied Microbiology
Marek Bartosovic, Mukund Kabbe, Goncalo Castelo-Branco
Summary: An improved method for single-cell analysis of histone modifications was applied to the mouse brain, combining CUT&Tag technology with droplet-based single-cell library preparation to produce high-quality data. The results provided unique insights into epigenomic landscapes in the central nervous system at single-cell resolution, highlighting the potential of this method for studying chromatin modifications and transcription factor occupancy.
NATURE BIOTECHNOLOGY
(2021)
Review
Microbiology
Abhyudai Singh, Michael Saint-Antoine
Summary: The stochasticity of gene product levels can cause individual cells in a population to have different phenotypic states. The dynamic nature of this intercellular variation makes it challenging to characterize. This review focuses on the use of the Luria-Delbruck experiment to understand the transient heritability of cellular states and discusses modeling approaches for capturing dynamic state transitions in cell populations.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Qianying Hu, Zhen Zhan, Huiying Cui, Yalei Zhang, Feng Jin, Xuan Zhao, Mingjie Zhang, Zhichuan Wang, Qingming Zhang, Kenji Watanabe, Takashi Taniguchi, Xuewei Cao, Wu-Ming Liu, Fengcheng Wu, Shengjun Yuan, Yang Xu
Summary: Researchers demonstrate the spatial confinement and manipulation of Rydberg moire excitons through two-dimensional moire superlattices, indicating their potential for quantum technologies.
Article
Biology
Susan Eliazer, Xuefeng Sun, Emilie Barruet, Andrew S. Brack
Summary: The muscle fiber maintains a continuum of quiescent states through a gradient of Notch ligand, Dll4, which is captured by QSCs. The abundance of Dll4 captured by the QSC correlates with the protein levels of the stem cell identity marker, Pax7. Niche-specific loss of Dll4 decreases QSC diversity and shifts the continuum to cell states that are biased toward more proliferative and committed fates.
Article
Engineering, Electrical & Electronic
Yuxing Zhou, Wei Zhang, En Ma, Volker L. Deringer
Summary: This study presents a machine-learning-based potential model that can simulate phase-change materials, including germanium-antimony-tellurium compositions, under realistic device conditions. The model's speed allows for atomistic simulations of multiple thermal cycles and complex operations, making it potentially valuable for neuro-inspired computing.
NATURE ELECTRONICS
(2023)
Article
Engineering, Electrical & Electronic
Yuxing Zhou, Wei Zhang, En Ma, Volker L. Deringer
Summary: Computer simulations are important for understanding phase-change materials and developing memory technologies, but there are limitations in directly simulating with quantum mechanics. In this study, a machine-learning-based potential model was trained using quantum-mechanical data to simulate a range of compositions of phase-change materials under realistic device conditions. The model allows for atomistic simulations of multiple thermal cycles and delicate operations for neuro-inspired computing.
NATURE ELECTRONICS
(2023)
Article
Optics
Thomas Pieter van Swieten, Jesse Merlijn Steenhoff, Auke Vlasblom, Ravi de Berg, Sam Pieter Mattern, Freddy Teunis Rabouw, Markus Suta, Andries Meijerink
Summary: Lanthanide-doped (nano)crystals play a crucial role in luminescence thermometry. By shifting the onset temperature of thermal equilibrium, the dynamic range of Boltzmann thermometers can be extended.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Physics, Multidisciplinary
Andrew T. Pierce, Yonglong Xie, Jeong Min Park, Eslam Khalaf, Seung Hwan Lee, Yuan Cao, Daniel E. Parker, Patrick R. Forrester, Shaowen Chen, Kenji Watanabe, Takashi Taniguchi, Ashvin Vishwanath, Pablo Jarillo-Herrero, Amir Yacoby
Summary: The discovery of unexpected incompressible states in MATBG, with Chern numbers incompatible with the simple sequential band filling assumption, can be understood as a consequence of broken translation symmetry that doubles the moire unit cell and splits each flavour band in two. These unusual incompressible phases expand the known phase diagram of MATBG and shed light on the close competition between different correlated phases in the system.
Article
Multidisciplinary Sciences
Masayuki Ohashi, Takuya Yoda, Norio Imai, Toshihide Fujii, Kei Watanabe, Hideki Tashi, Yohei Shibuya, Jin Watanabe, Naoto Endo
Summary: This study analyzed the 5-year natural course of frailty status assessed using the KCL in community-dwelling elderly adults, finding that the prevalence of frailty increased by 4.3% over this period. Maintaining optimal physical activity is recommended to prevent transition towards frailty.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Srivatsan Raghavan, Peter S. Winter, Andrew W. Navia, Hannah L. Williams, Alan DenAdel, Kristen E. Lowder, Jennyfer Galvez-Reyes, Radha L. Kalekar, Nolawit Mulugeta, Kevin S. Kapner, Manisha S. Raghavan, Ashir A. Borah, Nuo Liu, Sara A. Vayrynen, Andressa Dias Costa, Raymond W. S. Ng, Junning Wang, Emma K. Hill, Dorisanne Y. Ragon, Lauren K. Brais, Alex M. Jaeger, Liam F. Spurr, Yvonne Y. Li, Andrew D. Cherniack, Matthew A. Booker, Elizabeth F. Cohen, Michael Y. Tolstorukov, Isaac Wakiro, Asaf Rotem, Bruce E. Johnson, James M. McFarland, Ewa T. Sicinska, Tyler E. Jacks, Ryan J. Sullivan, Geoffrey Shapiro, Thomas E. Clancy, Kimberly Perez, Douglas A. Rubinson, Kimmie Ng, James M. Cleary, Lorin Crawford, Scott R. Manalis, Jonathan A. Nowak, Brian M. Wolpin, William C. Hahn, Andrew J. Aguirre, Alex K. Shalek
Summary: Prognostically relevant RNA expression states exist in pancreatic ductal adenocarcinoma (PDAC), with strong culture-specific biases in cancer cell transcriptional state representation and non-genetic modulation of cell state strongly influencing drug responses. This study provides a framework for aligning cell states across in vivo and ex vivo settings, identifying drivers of transcriptional plasticity, and manipulating cell state to target associated vulnerabilities.
Review
Psychiatry
Brett T. Hagman, Daniel Falk, Raye Litten, George F. Koob
Summary: The main aim of this article is to provide an operational definition of recovery from alcohol use disorder (AUD) in order to facilitate research consistency and stimulate further studies. The authors identified limitations in current recovery definitions and proposed a newly developed definition by NIAAA to enhance understanding of recovery and facilitate the recovery process.
AMERICAN JOURNAL OF PSYCHIATRY
(2022)
Article
Physics, Multidisciplinary
Taras Verkholyak, Jozef Strecka
Summary: This study uses a novel type of many-body perturbation theory to investigate the Spin-1/2 Heisenberg model on the Shastry-Sutherland lattice. The study reveals the occurrence of specific magnetization plateaux and a possible quantum phase of bound triplons for moderate values of the interdimer coupling.
Article
Oncology
Navin R. Mahadevan, Erik H. Knelson, Jacquelyn O. Wolff, Amir Vajdi, Maria Saigi, Marco Campisi, Deli Hong, Tran C. Thai, Brandon Piel, Saemi Han, Bruce B. Reinhold, Jonathan S. Duke-Cohan, Michael J. Poitras, Luke J. Taus, Patrick H. Lizotte, Andrew Portell, Victor Quadros, Alison D. Santucci, Takahiko Murayama, Israel Canadas, Shunsuke Kitajima, Aoi Akitsu, Maya Fridrikh, Hideo Watanabe, Brendan Reardon, Prafulla C. Gokhale, Cloud P. Paweletz, Mark M. Awad, Eliezer M. Van Allen, Ana Lako, Xi-Tao Wang, Benjamin Chen, Fangxin Hong, Lynette M. Sholl, Michael Y. Tolstorukov, Kathleen Pfaff, Pasi A. Janne, Evisa Gjini, Robin Edwards, Scott Rodig, Ellis L. Reinherz, Matthew G. Oser, David A. Barbie
Summary: A subset of SCLC patients exhibit durable response to immune checkpoint blockade by upregulating MHC I after losing neuroendocrine differentiation, which can be enhanced through EZH2 inhibition and STING agonism, leading to immune rejection of SCLC in preclinical models.
Article
Multidisciplinary Sciences
Isma Bennabi, Flora Crozet, Elvira Nikalayevich, Agathe Chaigne, Gaelle Letort, Marion Manil-Segalen, Clement Campillo, Clotilde Cadart, Alice Othmani, Rafaele Attia, Auguste Genovesio, Marie-Helene Verlhac, Marie-Emilie Terret
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Andrea Dimitracopoulos, Pragya Srivastava, Agathe Chaigne, Zaw Win, Roie Shlomovitz, Oscar M. Lancaster, Mael Le Berre, Matthieu Piel, Kristian Franze, Guillaume Salbreux, Buzz Baum
Review
Cell & Tissue Engineering
Eszter Posfai, Fredrik Lanner, Carla Mulas, Harry G. Leitch
Summary: Studying embryos provides a mechanistic understanding of development with relevance to human disease. In vitro cultured stem cell models offer an alternative for studying embryo development, but their usefulness depends on how accurately they reflect in vivo embryonic development.
Article
Cell Biology
Agathe Chaigne, Matthew B. Smith, Rocio Lopez Cavestany, Edouard Hannezo, Kevin J. Chalut, Ewa K. Paluch
Summary: This study investigates the control of cell division in three-dimensional environments, finding that at the periphery of 3D colonies, embryonic stem cells exhibit high spindle mobility and asymmetric division. The research suggests that in 3D contexts, both the shape of the cell and its interactions with neighboring cells play key roles in regulating division orientation and symmetry.
JOURNAL OF CELL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Celine Labouesse, Bao Xiu Tan, Chibeza C. Agley, Moritz Hofer, Alexander K. Winkel, Giuliano G. Stirparo, Hannah T. Stuart, Christophe M. Verstreken, Carla Mulas, William Mansfield, Paul Bertone, Kristian Franze, Jose C. R. Silva, Kevin J. Chalut
Summary: The study explores the independent control of substrate stiffness and extracellular matrix tethering by developing StemBond hydrogels. The hydrogels are validated to provide an optimal system for culturing mouse and human pluripotent stem cells, and they modulate stem cell function, partly through stiffness-sensitive ERK signaling. Ultimately, the findings emphasize the importance of optimizing the complete mechanical microenvironment for greater control over stem cell fate specification.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Agathe Chaigne, Thibaut Brunet
Summary: The traditional view of cell division ending with abscission, which is the final separation of daughter cells, is challenged by the presence of cytoplasmic bridges in various cell types of multicellular organisms. This review explores the distribution, function, and formation of cytoplasmic bridges across different lineages of eukaryotes and suggests that they have played a pivotal role in the evolution of multicellularity by facilitating nutrient exchange and intercellular communication.
Review
Cell Biology
Henry De Belly, Ewa K. Paluch, Kevin J. Chalut
Summary: This article reviews the importance of mechanical signalling in development and adult organisms, and discusses the regulation of biological processes by outside-in mechanical signalling and cell surface mechanics. The interaction between mechanosensing, intracellular signalling, and cell surface mechanics has a significant impact on stem cell fate and development.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Review
Developmental Biology
Yekaterina A. Miroshnikova, Marta N. Shahbazi, Jose Negrete, Kevin J. Chalut, Austin Smith
Summary: The Company of Biologists' 2022 workshop on 'Cell State Transitions: Approaches, Experimental Systems and Models' gathered an international and interdisciplinary team of investigators from various fields to study how cells navigate between different identities dynamically. This workshop is the second edition following a successful virtual workshop on the same topic in 2021.
Article
Biochemical Research Methods
Snjezana Kodba, Agathe Chaigne
Summary: This article introduces a method for immunofluorescent labeling of endogenous proteins and presents a simplified, cost-effective, user-friendly, and reproducible protocol specifically designed for mouse embryonic stem cells (mESCs). The protocol allows for fast visualization of the target proteins and includes specific tips for stem cell culture.
Review
Cell Biology
Snjezana Kodba, Agathe Chaigne
Summary: Cell division involves separating the genetic material and cytoplasm of a mother cell into two daughter cells. The last step of cell division, abscission, consists of cutting the cytoplasmic bridge, a microtubule-rich membranous tube connecting the two cells, which contains the midbody, a dense proteinaceous structure. Canonically, abscission occurs 1-3 h after anaphase.
JOURNAL OF CELL SCIENCE
(2023)
Article
Biochemical Research Methods
Carla Mulas, Andrew C. Hodgson, Timo N. Kohler, Chibeza C. Agley, Peter Humphreys, Hans Kleine-Bruggeney, Florian Hollfelder, Austin Smith, Kevin J. Chalut