Article
Astronomy & Astrophysics
Till Sawala, Stuart McAlpine, Jens Jasche, Guilhem Lavaux, Adrian Jenkins, Peter H. Johansson, Carlos S. Frenk
Summary: The study introduces a simulation method that connects the Local Group to its cosmic environment, showing that introducing small-scale perturbations to a density field constrained on large scales is an efficient way to explore LG analogues. It identifies that LG characteristics are largely determined by modes above 1.6 comoving Mpc in the primordial density field, with smaller scale variations mainly manifesting as perturbations to the MW-M31 orbit.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2022)
Article
Multidisciplinary Sciences
George Dimas, Eirini Cholopoulou, Dimitris K. Iakovidis
Summary: This paper proposes a novel and interpretable framework for convolutional neural network (CNN) models, called E pluribus unum interpretable CNN (EPU-CNN). The EPU-CNN model is capable of providing explanations for inputs based on different perceptual features, while maintaining good performance. Experimental results demonstrate that EPU-CNN models achieve comparable or better classification performance than other CNN architectures, while providing interpretable results that are perceptible to humans.
SCIENTIFIC REPORTS
(2023)
Article
Area Studies
Nguh Nwei Asanga Fon
Summary: Since independence, the identities of Anglophone and Francophone have been dominant in Cameroon, but the cohabitation of these linguistic and cultural identities faces incompatibilities. The current cohabitation model has significant challenges and is believed to have a negative impact on national integration, hence the need for a new alternative.
NATIONALITIES PAPERS-THE JOURNAL OF NATIONALISM AND ETHNICITY
(2023)
Article
Economics
Massimo Antonini, David Fielding, Jacinta Pires
Summary: The extent of deviations from the Law of One Price across cities is influenced by various factors such as language differences, distance, and correlates of trade costs. In the USA, political differences between cities are shown to also play a significant role in these deviations, with cities being more in line with LOP if they share strong Democrat or Republican tendencies. These political differences are found to be comparable in impact to distance, indicating that they can act as a substantial barrier to competition.
OXFORD ECONOMIC PAPERS-NEW SERIES
(2022)
Article
Political Science
Melissa M. . Lee, Nan Zhang, Tilmann Herchenroeder
Summary: Contestation over the structure and location of final sovereign authority, historically settled by war, now relies on the recognition of the governed. This study examines the impact of warfare on imagined sovereignty in the United States during the American Civil War. Using textual analysis of newspapers and congressional speeches, the findings show that war shapes imagined sovereignty, particularly in the Northern states where the debate over competing visions of sovereignty was prominent.
AMERICAN POLITICAL SCIENCE REVIEW
(2023)
Article
Political Science
Andrew Frankel, Jacob Bennett, Mathew Robinson, Walt Heinecke
Summary: This manuscript aims to explore the use of linguistic devices in critiquing the moral and political frameworks surrounding the United Nations Declaration of the Rights of Indigenous Peoples (UNDRIP). By analyzing the press release outlining the US government's position against the adoption of UNDRIP and President Obama's speech reversing this position, the authors reveal the extent to which power is exercised within the endorsement of UNDRIP as a statement of state-centered goals.
CRITICAL POLICY STUDIES
(2023)
Article
Psychology, Experimental
Anita Keshmirian, Ophelia Deroy, Bahador Bahrami
Summary: Moral judgments are influenced by social interactions, with collective judgments tending to be more utilitarian than individual judgments. This is likely because group deliberation and consensus reduce the emotional burden of norm violation.
Article
Chemistry, Multidisciplinary
Gregory J. O. Beran, Isaac J. Sugden, Chandler Greenwell, David H. Bowskill, Constantinos C. Pantelides, Claire S. Adjiman
Summary: With 12 crystal forms, 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecabonitrile (ROY) has the largest number of fully characterized organic crystal polymorphs. The study reveals that the seven most stable ROY polymorphs and nine of the twelve lowest-energy forms have already been discovered experimentally. Future discovery of new polymorphs may require specialized crystallization techniques, while high-pressure experiments are predicted to reveal a new, more stable crystal form.
Article
Physics, Multidisciplinary
Jonathan A. Gross, Carlton M. Caves
Summary: It is challenging to establish achievable sensitivity bounds for quantum multiparameter estimation. In a special case where many parameters of a process are unknown, estimating a specific linear combination of these parameters without control is superficially similar to single-parameter estimation but retains genuinely multiparameter aspects. Geometric reasoning demonstrates the necessary and sufficient conditions for saturating the fundamental and attainable quantum-process bound in this context.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Philosophy
Thomas Meier
Summary: This paper discusses the methodology of mathematical philosophy and argues for using a variety of formal and mathematical methods. It highlights how other types of philosophy fail to provide the rigor needed for clarity, objectivity, and interdisciplinary success. Multiple examples of mathematized philosophy are mentioned, including the concept of epistemic utility theory. The paper advocates for an interdisciplinary approach and the integration of philosophy with unified science.
Article
Humanities, Multidisciplinary
Nick Baxter-Moore, Munroe Eagles
Summary: Lipset argues that there is a 'continental divide' separating political value systems in Canada and the United States, due to their differing foundational experiences. Critics suggest that this difference is largely influenced by the uniqueness of the American South and Quebec, with Canadians and Americans outside these regions forming a single, homogeneous cultural unit. Advocates of the 'borderlands thesis' propose a convergence of values among populations living near the Canada-US border.
BRITISH JOURNAL OF CANADIAN STUDIES
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Diana Lin, Kareem A. Wahid, Benjamin E. Nelms, Renjie He, Mohammed A. Naser, Simon Duke, Michael V. Sherer, John P. Christodouleas, Abdallah S. R. Mohamed, Michael Cislo, James D. Murphy, Clifton D. Fuller, Erin F. Gillespie
Summary: The C3RO project is a collaborative effort in radiation oncology that involves crowdsourcing and challenges radiation oncologists across different expertise levels in segmentation. The study found that aggregate segmentations generated from multiple nonexperts can meet or even exceed expert agreement. This suggests that nonexpert segmentations can be a cost-effective choice for artificial intelligence inputs.
JOURNAL OF MEDICAL IMAGING
(2023)
Article
Geosciences, Multidisciplinary
Noel Cressie, Michael Bertolacci, Andrew Zammit-Mangion
Summary: A Model Intercomparison Project (MIP) consists of teams estimating the same underlying quantity and offers a way to obtain a weighted consensus estimate through statistical analysis.
GEOPHYSICAL RESEARCH LETTERS
(2022)
Review
Biochemistry & Molecular Biology
Michael Palmgren
Summary: P-type ATPases are a large ancient super-family of primary active pumps with diverse substrate specificities. They play a significant role in biology, but there is still much to be learned.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
C. Satheesan Babu, Carmay Lim
Summary: The study found that solution ionic strengths can affect the conformation of the protein M20 loop, with higher ionic strengths favoring closed/occluded conformations. This suggests caution should be exercised in linking M20 loop conformations derived from crystal structures solved at ionic strengths beyond that tolerated by E. coli to the function of ecDHFR.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Vijay Jayaraman, D. John Lee, Nadav Elad, Shay Vimer, Michal Sharon, James S. Fraser, Dan S. Tawfik
Summary: This study discovered a 1.6 megadalton multi-enzyme complex made up of glutamate synthase and glutamate dehydrogenase, which have opposite functions, in Bacillus subtilis. The complex inhibits the activity of glutamate dehydrogenase and is essential for cell growth under fluctuating glutamate concentrations.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kaitlyn Tsai, Vanja Stojkovic, D. John Lee, Iris D. Young, Teresa Szal, Dorota Klepacki, Nora Vazquez-Laslop, Alexander S. Mankin, James S. Fraser, Danica Galonic Fujimori
Summary: Linezolid and radezolid are oxazolidinone antibiotics that inhibit bacterial ribosome translation by binding to the peptidyl transferase center in a context-specific manner, leading to stalling when alanine occupies the penultimate position in the nascent chain.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Physics, Multidisciplinary
Matthew P. Leighton, David A. Sivak
Summary: The article investigates the motor-driven intracellular transport of organelles, vesicles, and other molecular cargo. It explores the properties of these systems and provides analytic solutions for the dependence on the number of motors. The study also examines the trade-offs between performance metrics and the variation in the number of motors, offering insights into matching different numbers of motors to different contexts.
NEW JOURNAL OF PHYSICS
(2022)
Article
Multidisciplinary Sciences
Eric W. Jones, Jean M. Carlson, David A. Sivak, William B. Ludington
Summary: Observational studies show significant variability in microbiome composition among individuals, with interactions between bacteria affecting the microbiome assembly process. In experiments with germ-free flies fed known bacterial species at high concentrations, it was found that some species colonize more frequently than others. The presence of context-dependent interactions between bacterial species can substantially improve the performance of models in predicting colonization outcomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Miranda D. Louwerse, David A. Sivak
Summary: By using minimum-work protocols in multidimensional control-parameter space, we can efficiently manipulate the configurational state of a system and reduce resistance and work.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Cody Krivacic, Kale Kundert, Xingjie Pan, Roland A. Pache, Lin Liu, Shane O. Conchuir, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Michael C. Thompson, James S. Fraser, Tanja Kortemme
Summary: The article introduces two computational methods (FKIC and LHKIC) capable of generating and predicting new local protein geometries. These methods were used to create a design protocol (PIP) to position functionally important side chains in proteins, resulting in the engineering of new protein functions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Stephanie A. Wankowicz, Saulo H. de Oliveira, Daniel W. Hogan, Henry van den Bedem, James S. Fraser
Summary: This study measured conformational heterogeneity in a large number of crystallographic datasets and found that binding site residues become more rigid upon ligand binding, while distant residues become more flexible, especially in non-solvent-exposed regions. Additionally, protein flexibility was observed to increase as the number of hydrogen bonds decreases and relative hydrophobicity increases.
Editorial Material
Biotechnology & Applied Microbiology
Jennifer M. Michaud, Ali Madani, James S. Fraser
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
David C. Wych, Phillip C. Aoto, Lily Vu, Alexander M. Wolff, David L. Mobley, James S. Fraser, Susan S. Taylor, Michael E. Wall
Summary: This article investigates the use of molecular-dynamics (MD) simulations to improve macromolecular crystallography (MX) studies. By combining MD simulations with conventional modeling and refinement tools, the authors were able to improve the interpretation of ambiguous density in protein crystals, leading to more accurate protein models and mechanistic insights into enzyme interactions.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Physics, Multidisciplinary
Steven Blaber, David A. Sivak
Summary: We review recent progress in optimal control in stochastic thermodynamics, focusing on minimum-dissipation control and its theoretical advances. Exact solutions provide insight into the properties of minimum-dissipation control, which are reproduced by approximate methods. Connections between optimal-transport theory and minimum-dissipation protocols under full control give deep insight into the properties of optimal control and place bounds on the dissipation of thermodynamic processes.
JOURNAL OF PHYSICS COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Do-Hyun Kim, Yilin Wang, Haerin Jung, Rachael L. Field, Xinya Zhang, Ta-Chiang Liu, Changqing Ma, James S. Fraser, Jonathan R. Brestoff, Steven J. Van Dyken
Summary: This study describes a mammalian adaptation to dietary chitin through gastric immune activation and acidic mammalian chitinase, which facilitates chitin digestion. This adaptation is preserved in germ-free mice and leads to enhanced metabolic health and resistance to obesity.
Article
Physics, Fluids & Plasmas
Miranda D. Louwerse, David A. Sivak
Summary: This paper investigates the correspondence between driving protocols and spontaneous transition mechanisms in a system undergoing metastable configurations. The study shows that even though control parameters cannot fully reproduce the detailed features of spontaneous mechanisms, the general order of spin flips during the transition remains preserved. The external control parameters provide energy to the system components to compensate for changes in internal energy during a minimum-work protocol, highlighting the importance of tuning control parameters to counteract underlying energetic features.
Article
Physics, Fluids & Plasmas
Steven Blaber, David A. Sivak
Summary: Quadratic trapping potentials are widely used in experiments to study biopolymers and molecular machines. A multidimensional trapping protocol has been designed to minimize dissipation, which can be easily applied to various systems. This approximation is valid for any duration, as long as the trapping potential is sufficiently strong.
Meeting Abstract
Biophysics
Matthew P. Leighton, David A. Sivak
BIOPHYSICAL JOURNAL
(2022)
Article
Physics, Fluids & Plasmas
Emma Lathouwers, David A. Sivak
Summary: Researchers are investigating the general design principles for effective energy conversion in microscopic biological systems. Using a model of two strongly coupled stochastic rotary motors, they found that intermediate coupling strength leads to prominent thermodynamic characteristics, such as maximum power and information transfer, as well as equal subsystem entropy production rates.