bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling of Continental Normal Fault Earthquakes
Authors: Muldashev Iskander A. , Pérez‐Gussinyé Marta , Sobolev Stephan V. 
Published: November 2022

AbstractThe magnitude of earthquakes on continental normal faults rarely exceeds 7.0 Mw. However, because of their vicinity to large population centers they can be highly destructive. Long recurrence time, relatively small deformations, and limited observations hinder our understanding of the deformation patterns and mechanisms controlling the magnitude of events. Here, this problem is addressed with 2D thermomechanical modeling of normal fault seismic cycles. The 2020 Samos, Greece Mw7.0 earthquake is used as an example as it is one of the largest and most studied continental normal fault earthquakes. The modeling approach employs visco‐elasto‐plastic rheology, compressibility, free surface, and a rate‐and‐state friction law for the fault. Modeling of the Samos earthquake suggests the pore fluid pressure ratio on the fault ranges from 0 to 0.7. The model demonstrates that most of the deformation during interseismic and coseismic periods, besides on the fault, occurs in the hanging wall and footwall below the seismogenic part of the fault. The largest vertical surface displacement during the earthquake is the subsidence of the hanging wall in the vicinity of the fault, while the uplift of the footwall and remote part of the hanging wall is significantly smaller. Modeling of the seismic cycles on normal faults with different setups shows the dependency of the magnitude on the thermal profile and dipping angle of the fault; low heat flow and low dipping angle are favorable conditions for the largest events, while steep normal faults in the areas of high heat flow tend to have the smallest magnitudes.
Characterization of SARS-CoV-2 antibodies in human milk from 21 women with confirmed COVID-19 infection
Authors: Bode Lars , Bertrand Kerri , Najera Julia A. , Furst Annalee , Honerkamp-Smith Gordon , Shandling Adam D. , Chambers Christina D. , Camerini David , Campo Joseph J. 
Published: November 2022

AbstractBackgroundOne potential mechanism for protection from SARS-CoV-2 in children is through passive immunity via breast milk from a mother infected with the novel coronavirus. The primary objectives of this study were to establish the presence of SARS-CoV-2-specific IgA and IgG and to characterize the antigenic regions of SARS-CoV-2 proteins that were reactive with antibodies in breast milk.MethodsBetween March 2020 and September 2020, 21 women with confirmed SARS-CoV-2 infection were enrolled in Mommy’s Milk. Participants donated serial breast milk samples around their time of illness. Breast milk samples were used to probe a multi-coronavirus protein microarray containing full-length and variable-length overlapping fragments of SARS-CoV-2 proteins. Samples were also tested against S and N proteins by electrochemiluminescence assay.ResultsThe breast milk samples contained IgA reactive with a variety of SARS-CoV-2 antigens. The most IgA-reactive SARS-CoV-2 proteins were N (42.9% of women responded to ≥1 N fragment) and S proteins (23.9% responded to ≥1 fragment of S1 or S2). IgG responses were similar. A striking observation was the dissimilarity between mothers in antibody recognition, giving distinct antibody reactivity and kinetic profiles.ConclusionsIndividual COVID-19 cases had diverse and unique milk IgA profiles following the onset of symptoms.ImpactIn this observational longitudinal case series of 21 women with confirmed SARS-CoV-2 infection, IgA binding to SARS-CoV-2 proteins detected by orthologous proteome microarray and electrochemiluminescence assays was observed in >75% of women, but there was heterogeneity in which antigens and how many were reactive between women.Immunological profiles of protein regions recognized by each woman were distinct.Diverse repertoires of mucosal breast milk antibody to SARS-CoV-2 reflect heterogeneous passive transfer of maternal antibody to exposed breastfeeding infants.
The ColR/S two-component system is a conserved determinant of host association across Pseudomonas species
Authors: Wiesmann Christina L , Zhang Yue , Alford Morgan , Hamilton Corri D , Dosanjh Manisha , Thoms David , Dostert Melanie , Wilson Andrew , Pletzer Daniel , Hancock Robert E W , Haney Cara H 
Published: November 2022

Abstract
Members of the bacterial genus Pseudomonas form mutualistic, commensal, and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system, part of the Pseudomonas core genome, is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens. Using plant rhizosphere colonization and virulence in a murine abscess model, we show that colR is required for commensalism with plants and virulence in animals. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not host-specific, requirements for ColR-dependent genes. Collectively, our results suggest that ColR/S allows Pseudomonas to sense and respond to a host, but that the ColR-regulon has diverged between Pseudomonas strains with distinct lifestyles. This suggests that conservation of two-component systems, coupled with life-style dependent diversification of the regulon, may play a role in host association and lifestyle transitions.
Translational readthrough of nonsense mutant TP53 by mRNA incorporation of 5-Fluorouridine
Authors: Palomar-Siles Mireia , Heldin Angelos , Zhang Meiqiongzi , Strandgren Charlotte , Yurevych Viktor , van Dinter Jip T. , Engels Sem A. G. , Hofman Damon A. , Öhlin Susanne , Meineke Birthe , Bykov Vladimir J. N. , van Heesch Sebastiaan , Wiman Klas G. 
Published: November 2022

AbstractTP53 nonsense mutations in cancer produce truncated inactive p53 protein. We show that 5-FU metabolite 5-Fluorouridine (FUr) induces full-length p53 in human tumor cells carrying R213X nonsense mutant TP53. Ribosome profiling visualized translational readthrough at the R213X premature stop codon and demonstrated that FUr-induced readthrough is less permissive for canonical stop codon readthrough compared to aminoglycoside G418. FUr is incorporated into mRNA and can potentially base-pair with guanine, allowing insertion of Arg tRNA at the TP53 R213X UGA premature stop codon and translation of full-length wild-type p53. We confirmed that full-length p53 rescued by FUr triggers tumor cell death by apoptosis. FUr also restored full-length p53 in TP53 R213X mutant human tumor xenografts in vivo. Thus, we demonstrate a novel strategy for therapeutic rescue of nonsense mutant TP53 and suggest that FUr should be explored for treatment of patients with TP53 nonsense mutant tumors.
Amyloid fibril structure from the vascular variant of systemic AA amyloidosis
Authors: Banerjee Sambhasan , Baur Julian , Daniel Christoph , Pfeiffer Peter Benedikt , Hitzenberger Manuel , Kuhn Lukas , Wiese Sebastian , Bijzet Johan , Haupt Christian , Amann Kerstin U. , Zacharias Martin , Hazenberg Bouke P. C. , Westermark Gunilla T. , Schmidt Matthias , Fändrich Marcus 
Published: November 2022

AbstractSystemic AA amyloidosis is a debilitating protein misfolding disease in humans and animals. In humans, it occurs in two variants that are called ‘vascular’ and ‘glomerular’, depending on the main amyloid deposition site in the kidneys. Using cryo electron microscopy, we here show the amyloid fibril structure underlying the vascular disease variant. Fibrils purified from the tissue of such patients are mainly left-hand twisted and contain two non-equal stacks of fibril proteins. They contrast in these properties to the fibrils from the glomerular disease variant which are right-hand twisted and consist of two structurally equal stacks of fibril proteins. Our data demonstrate that the different disease variants in systemic AA amyloidosis are associated with different fibril morphologies.
Measurement of the transition frequency from 2S1/2, F = 0 to 2P1/2, F = 1 states in Muonium
Authors: Janka Gianluca , Ohayon Ben , Cortinovis Irene , Burkley Zak , de Sousa Borges Lucas , Depero Emilio , Golovizin Artem , Ni Xiaojie , Salman Zaher , Suter Andreas , Prokscha Thomas , Crivelli Paolo 
Published: November 2022

AbstractMuons are puzzling physicists since their discovery when they were first thought to be the meson predicted by Yukawa to mediate the strong force. The recent result at Fermilab on the muon g-2 anomaly puts the muonic sector once more under the spotlight and calls for further measurements with this particle. Here, we present the results of the measurement of the 2S1/2, F = 0 → 2P1/2, F = 1 transition in Muonium. The measured value of 580.6(6.8) MHz is in agreement with the theoretical calculations. A value of the Lamb shift of 1045.5(6.8) MHz is extracted, compatible with previous experiments. We also determine the 2S hyperfine splitting in Muonium to be 559.6(7.2) MHz. The measured transition being isolated from the other hyperfine levels holds the promise to provide an improved determination of the Muonium Lamb shift at a level where bound state QED recoil corrections not accessible in hydrogen could be tested. This result would be sensitive to new physics in the muonic sector, e.g., to new bosons which might provide an explanation of the g-2 muon anomaly and allow to test Lorentz and CPT violation. We also present the observation of Muonium in the n = 3 excited state opening up the possibility of additional precise microwave measurements.
Path sampling of recurrent neural networks by incorporating known physics
Authors: Tsai Sun-Ting , Fields Eric , Xu Yijia , Kuo En-Jui , Tiwary Pratyush 
Published: November 2022

AbstractRecurrent neural networks have seen widespread use in modeling dynamical systems in varied domains such as weather prediction, text prediction and several others. Often one wishes to supplement the experimentally observed dynamics with prior knowledge or intuition about the system. While the recurrent nature of these networks allows them to model arbitrarily long memories in the time series used in training, it makes it harder to impose prior knowledge or intuition through generic constraints. In this work, we present a path sampling approach based on principle of Maximum Caliber that allows us to include generic thermodynamic or kinetic constraints into recurrent neural networks. We show the method here for a widely used type of recurrent neural network known as long short-term memory network in the context of supplementing time series collected from different application domains. These include classical Molecular Dynamics of a protein and Monte Carlo simulations of an open quantum system continuously losing photons to the environment and displaying Rabi oscillations. Our method can be easily generalized to other generative artificial intelligence models and to generic time series in different areas of physical and social sciences, where one wishes to supplement limited data with intuition or theory based corrections.
Effect of current density on the solid electrolyte interphase formation at the lithium∣Li6PS5Cl interface
Authors: Narayanan Sudarshan , Ulissi Ulderico , Gibson Joshua S. , Chart Yvonne A. , Weatherup Robert S. , Pasta Mauro 
Published: November 2022

AbstractUnderstanding the chemical composition and morphological evolution of the solid electrolyte interphase (SEI) formed at the interface between the lithium metal electrode and an inorganic solid-state electrolyte is crucial for developing reliable all-solid-state lithium batteries. To better understand the interaction between these cell components, we carry out X-ray photoemission spectroscopy (XPS) measurements during lithium plating on the surface of a Li6PS5Cl solid-state electrolyte pellet using an electron beam. The analyses of the XPS data highlight the role of Li plating current density on the evolution of a uniform and ionically conductive (i.e., Li3P-rich) SEI capable of decreasing the electrode∣solid electrolyte interfacial resistance. The XPS findings are validated via electrochemical impedance spectrsocopy measurements of all-solid-state lithium-based cells.
High-throughput screening of caterpillars as a platform to study host–microbe interactions and enteric immunity
Authors: Windfelder Anton G. , Müller Frank H. H. , Mc Larney Benedict , Hentschel Michael , Böhringer Anna Christina , von Bredow Christoph-Rüdiger , Leinberger Florian H. , Kampschulte Marian , Maier Lorenz , von Bredow Yvette M. , Flocke Vera , Merzendorfer Hans , Krombach Gabriele A. , Vilcinskas Andreas , Grimm Jan , Trenczek Tina E. , Flögel Ulrich 
Published: November 2022

AbstractMammalian models of human disease are expensive and subject to ethical restrictions. Here, we present an independent platform for high-throughput screening, using larvae of the tobacco hornworm Manduca sexta, combining diagnostic imaging modalities for a comprehensive characterization of aberrant phenotypes. For validation, we use bacterial/chemical-induced gut inflammation to generate a colitis-like phenotype and identify significant alterations in morphology, tissue properties, and intermediary metabolism, which aggravate with disease progression and can be rescued by antimicrobial treatment. In independent experiments, activation of the highly conserved NADPH oxidase DUOX, a key mediator of gut inflammation, leads to similar, dose-dependent alterations, which can be attenuated by pharmacological interventions. Furthermore, the developed platform could differentiate pathogens from mutualistic gastrointestinal bacteria broadening the scope of applications also to microbiomics and host-pathogen interactions. Overall, larvae-based screening can complement mammals in preclinical studies to explore innate immunity and host-pathogen interactions, thus representing a substantial contribution to improve mammalian welfare.
Discovery of LaAlO3 as an efficient catalyst for two-electron water electrolysis towards hydrogen peroxide
Authors: Baek Jihyun , Jin Qiu , Johnson Nathan Scott , Jiang Yue , Ning Rui , Mehta Apurva , Siahrostami Samira , Zheng Xiaolin 
Published: November 2022

AbstractElectrochemical two-electron water oxidation reaction (2e-WOR) has drawn significant attention as a promising process to achieve the continuous on-site production of hydrogen peroxide (H2O2). However, compared to the cathodic H2O2 generation, the anodic 2e-WOR is more challenging to establish catalysts due to the severe oxidizing environment. In this study, we combine density functional theory (DFT) calculations with experiments to discover a stable and efficient perovskite catalyst for the anodic 2e-WOR. Our theoretical screening efforts identify LaAlO3 perovskite as a stable, active, and selective candidate for catalyzing 2e-WOR. Our experimental results verify that LaAlO3 achieves an overpotential of 510 mV at 10 mA cm−2 in 4 M K2CO3/KHCO3, lower than those of many reported metal oxide catalysts. In addition, LaAlO3 maintains a stable H2O2 Faradaic efficiency with only a 3% decrease after 3 h at 2.7 V vs. RHE. This computation-experiment synergistic approach introduces another effective direction to discover promising catalysts for the harsh anodic 2e-WOR towards H2O2.
Genomic disparities between cancers in adolescent and young adults and in older adults
Authors: Wang Xiaojing , Langevin Anne-Marie , Houghton Peter J. , Zheng Siyuan 
Published: November 2022

AbstractCancers cause significant mortality and morbidity in adolescents and young adults (AYAs), but their biological underpinnings are incompletely understood. Here, we analyze clinical and genomic disparities between AYAs and older adults (OAs) in more than 100,000 cancer patients. We find significant differences in clinical presentation between AYAs and OAs, including sex, metastasis rates, race and ethnicity, and cancer histology. In most cancer types, AYA tumors show lower mutation burden and less genome instability. Accordingly, most cancer genes show less mutations and copy number changes in AYAs, including the noncodingTERTpromoter mutations. However,CTNNB1andBRAFmutations are consistently overrepresented in AYAs across multiple cancer types. AYA tumors also exhibit more driver gene fusions that are frequently observed in pediatric cancers. We find that histology is an important contributor to genetic disparities between AYAs and OAs. Mutational signature analysis of hypermutators shows stronger endogenous mutational processes such as MMR-deficiency but weaker exogenous processes such as tobacco exposure in AYAs. Finally, we demonstrate a panoramic view of clinically actionable genetic events in AYA tumors.
A topological nonlinear parametric amplifier
Authors: Sohn Byoung-Uk , Huang Yue-Xin , Choi Ju Won , Chen George F. R. , Ng Doris K. T. , Yang Shengyuan A. , Tan Dawn T. H. 
Published: November 2022

AbstractTopological boundary states are well localized eigenstates at the boundary between two different bulk topologies. As long as bulk topology is preserved, the topological boundary mode will endure. Here, we report topological nonlinear parametric amplification of light in a dimerized coupled waveguide system based on the Su-Schrieffer-Heeger model with a domain wall. The good linear transmission properties of the topological waveguide arising from the strong localization of light to the topological boundary is demonstrated through successful high-speed transmission of 30 Gb/s non-return-to-zero and 56 Gb/s pulse amplitude 4-level data. The strong localization of a co-propagating pump and probe to the boundary waveguide is harnessed for efficient, low power optical parametric amplification and wavelength conversion. A nonlinear tuning mechanism is shown to induce chiral symmetry breaking in the topological waveguide, demonstrating a pathway in which Kerr nonlinearities may be applied to tune the topological boundary mode and control the transition to bulk states.
Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine
Authors: Moen Jack M. , Mohler Kyle , Rogulina Svetlana , Shi Xiaojian , Shen Hongying , Rinehart Jesse 
Published: November 2022

AbstractProtein phosphorylation is a ubiquitous post-translational modification used to regulate cellular processes and proteome architecture by modulating protein-protein interactions. The identification of phosphorylation events through proteomic surveillance has dramatically outpaced our capacity for functional assignment using traditional strategies, which often require knowledge of the upstream kinase a priori. The development of phospho-amino-acid-specific orthogonal translation systems, evolutionarily divergent aminoacyl-tRNA synthetase and tRNA pairs that enable co-translational insertion of a phospho-amino acids, has rapidly improved our ability to assess the physiological function of phosphorylation by providing kinase-independent methods of phosphoprotein production. Despite this utility, broad deployment has been hindered by technical limitations and an inability to reconstruct complex phopho-regulatory networks. Here, we address these challenges by optimizing genetically encoded phosphothreonine translation to characterize phospho-dependent kinase activation mechanisms and, subsequently, develop a multi-level protein interaction platform to directly assess the overlap of kinase and phospho-binding protein substrate networks with phosphosite-level resolution.
Varying strength of selection contributes to the intragenomic diversity of rRNA genes
Authors: Sultanov Daniel , Hochwagen Andreas 
Published: November 2022

AbstractRibosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA). The multiple copies of rRNA genes are thought to have low sequence diversity within one species. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this view. We show that rDNA copies in this yeast are heterogeneous, both among and within isolates, and that many variants avoided fixation or elimination over evolutionary time. The sequence diversity landscape across the rDNA shows clear functional stratification, suggesting different copy-number thresholds for selection that contribute to rDNA diversity. Notably, nucleotide variants in the most conserved rDNA regions are sufficiently deleterious to exhibit signatures of purifying selection even when present in only a small fraction of rRNA gene copies. Our results portray a complex evolutionary landscape that shapes rDNA sequence diversity within a single species and reveal unexpectedly strong purifying selection of multi-copy genes.
Examining the influence of turbulence on viscosity measurements of molten germanium under reduced gravity
Authors: Bracker G. P. , Luo Y. , Damaschke B. , Samwer K. , Hyers R. W. 
Published: November 2022

AbstractThe thermophysical properties of liquid germanium were recently measured both in parabolic flight experiments and on the ISS in the ISS-EML facility. The viscosity measurements differed between the reduced gravity experiments and the literature values. Since the oscillating drop method has been widely used in EML, further exploration into this phenomenon was of interest. Models of the magnetohydrodynamic flow indicated that turbulence was present during the measurement in the ISS-EML facility, which accounts for the observed difference.
Examining the source of increased bipolar disorder and major depressive disorder common risk variation burden in multiplex schizophrenia families
Authors: Ahangari Mohammad , Kirkpatrick Robert , Nguyen Tan-Hoang , Gillespie Nathan , Kendler Kenneth S. , Bacanu Silviu-Alin , Webb Bradley T. , Verrelli Brian C. , Riley Brien P. 
Published: November 2022

AbstractPsychotic and affective disorders often aggregate in the relatives of probands with schizophrenia, and genetic studies show substantial genetic correlation among schizophrenia, bipolar disorder, and major depressive disorder. In this study, we examined the polygenic risk burden of bipolar disorder and major depressive disorder in 257 multiplex schizophrenia families (N = 1005) from the Irish Study of High-Density Multiplex Schizophrenia Families versus 2205 ancestry-matched controls. Our results indicate that members of multiplex schizophrenia families have an increased polygenic risk for bipolar disorder and major depressive disorder compared to population controls. However, this observation is largely attributable to the part of the genetic risk that bipolar disorder or major depressive disorder share with schizophrenia due to genetic correlation, rather than the affective portion of the genetic risk unique to them. These findings suggest that a complete interpretation of cross-disorder polygenic risks in multiplex families requires an assessment of the relative contribution of shared versus unique genetic factors to account for genetic correlations across psychiatric disorders.