bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patterned crystal growth and heat wave generation in hydrogels
Authors: Schroeder Thomas B. H. , Aizenberg Joanna 
Published: January 2022

AbstractThe crystallization of metastable liquid phase change materials releases stored energy as latent heat upon nucleation and may therefore provide a triggerable means of activating downstream processes that respond to changes in temperature. In this work, we describe a strategy for controlling the fast, exothermic crystallization of sodium acetate from a metastable aqueous solution into trihydrate crystals within a polyacrylamide hydrogel whose polymerization state has been patterned using photomasks. A comprehensive experimental study of crystal shapes, crystal growth front velocities and evolving thermal profiles showed that rapid growth of long needle-like crystals through unpolymerized solutions produced peak temperatures of up to 45˚C, while slower-crystallizing polymerized solutions produced polycrystalline composites and peaked at 30˚C due to lower rates of heat release relative to dissipation in these regions. This temperature difference in the propagating heat waves, which we describe using a proposed analytical model, enables the use of this strategy to selectively activate thermoresponsive processes in predefined areas.
molBV reveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history
Authors: Usyk Mykhaylo , Schlecht Nicolas F. , Pickering Sarah , Williams LaShanda , Sollecito Christopher C. , Gradissimo Ana , Porras Carolina , Safaeian Mahboobeh , Pinto Ligia , Herrero Rolando , Strickler Howard D. , Viswanathan Shankar , Nucci-Sack Anne , Diaz Angela ,   Costa Rica HPV Vaccine Trial (CVT) Group, Cortés Bernal , González Paula , Jiménez Silvia E. , Rodríguez Ana Cecilia , Hildesheim Allan , Kreimer Aimée R. , Lowy Douglas R. , Schiffman Mark , Schiller John T. , Sherman Mark , Wacholder Sholom , Kemp Troy J. , Sidawy Mary K. , Quint Wim , van Doorn Leen-Jan , Struijk Linda , Palefsky Joel M. , Darragh Teresa M. , Stoler Mark H. , Burk Robert D. 
Published: January 2022

AbstractBacterial vaginosis (BV) is a highly prevalent condition that is associated with adverse health outcomes. It has been proposed that BV’s role as a pathogenic condition is mediated via bacteria-induced inflammation. However, the complex interplay between vaginal microbes and host immune factors has yet to be clearly elucidated. Here, we develop molBV, a 16 S rRNA gene amplicon-based classification pipeline that generates a molecular score and diagnoses BV with the same accuracy as the current gold standard method (i.e., Nugent score). Using 3 confirmatory cohorts we show that molBV is independent of the 16 S rRNA region and generalizable across populations. We use the score in a cohort without clinical BV states, but with measures of HPV infection history and immune markers, to reveal that BV-associated increases in the IL-1β/IP-10 cytokine ratio directly predicts clearance of incident high-risk HPV infection (HR = 1.86, 95% CI: 1.19-2.9). Furthermore, we identify an alternate inflammatory BV signature characterized by elevated TNF-α/MIP-1β ratio that is prospectively associated with progression of incident infections to CIN2 + (OR = 2.81, 95% CI: 1.62-5.42). Thus, BV is a heterogeneous condition that activates different arms of the immune response, which in turn are independent risk factors for HR-HPV clearance and progression. Clinical Trial registration number: The CVT trial has been registered under: NCT00128661.
The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis
Authors: Zhou Ming , Coruh Ceyda , Xu Guanghui , Martins Laura M. , Bourbousse Clara , Lambolez Alice , Law Julie A. 
Published: January 2022

AbstractDNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As is evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation, also control tissue-specific methylation patterns, with the most striking pattern observed in ovules where CLSY3 and CLSY4 control DNA methylation at loci with a highly conserved DNA motif. On a more global scale, we demonstrate that specific clsy mutants are sufficient to shift the epigenetic landscape between tissues. Together, these findings reveal substantial epigenetic diversity between tissues and assign these changes to specific CLSY proteins, elucidating how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.
Boundary conductance in macroscopic bismuth crystals
Authors: Kang Woun , Spathelf Felix , Fauqué Benoît , Fuseya Yuki , Behnia Kamran 
Published: January 2022

AbstractThe interface between a solid and vacuum can become electronically distinct from the bulk. This feature, encountered in the case of quantum Hall effect, has a manifestation in insulators with topologically protected metallic surface states. Non-trivial Berry curvature of the Bloch waves or periodically driven perturbation are known to generate it. Here, by studying the angle-dependent magnetoresistance in prismatic bismuth crystals of different shapes, we detect a robust surface contribution to electric conductivity when the magnetic field is aligned parallel to a two-dimensional boundary between the three-dimensional crystal and vacuum. The effect is absent in antimony, which has an identical crystal symmetry, a similar Fermi surface structure and equally ballistic carriers, but an inverted band symmetry and a topological invariant of opposite sign. Our observation confirms that the boundary interrupting the cyclotron orbits remains metallic in bismuth, which is in agreement with what was predicted by Azbel decades ago. However, the absence of the effect in antimony indicates an intimate link between band symmetry and this boundary conductance.
Transglutaminase 3 crosslinks the secreted gel-forming mucus component Mucin-2 and stabilizes the colonic mucus layer
Authors: Sharpen Jack D. A. , Dolan Brendan , Nyström Elisabeth E. L. , Birchenough George M. H. , Arike Liisa , Martinez-Abad Beatriz , Johansson Malin E. V. , Hansson Gunnar C. , Recktenwald Christian V. 
Published: January 2022

AbstractThe colonic mucus layer is organized as a two-layered system providing a physical barrier against pathogens and simultaneously harboring the commensal flora. The factors contributing to the organization of this gel network are not well understood. In this study, the impact of transglutaminase activity on this architecture was analyzed. Here, we show that transglutaminase TGM3 is the major transglutaminase-isoform expressed and synthesized in the colon. Furthermore, intrinsic extracellular transglutaminase activity in the secreted mucus was demonstrated in vitro and ex vivo. Absence of this acyl-transferase activity resulted in faster degradation of the major mucus component the MUC2 mucin and changed the biochemical properties of mucus. Finally, TGM3-deficient mice showed an early increased susceptibility to Dextran Sodium Sulfate-induced colitis. Here, we report that natural isopeptide cross-linking by TGM3 is important for mucus homeostasis and protection of the colon from inflammation, reducing the risk of colitis.
A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control
Authors: Schroeder Griffin M. , Cavender Chapin E. , Blau Maya E. , Jenkins Jermaine L. , Mathews David H. , Wedekind Joseph E. 
Published: January 2022

AbstractRiboswitches are structured non-coding RNAs often located upstream of essential genes in bacterial messenger RNAs. Such RNAs regulate expression of downstream genes by recognizing a specific cellular effector. Although nearly 50 riboswitch classes are known, only a handful recognize multiple effectors. Here, we report the 2.60-Å resolution co-crystal structure of a class I type I preQ1-sensing riboswitch that reveals two effectors stacked atop one another in a single binding pocket. These effectors bind with positive cooperativity in vitro and both molecules are necessary for gene regulation in bacterial cells. Stacked effector recognition appears to be a hallmark of the largest subgroup of preQ1 riboswitches, including those from pathogens such as Neisseria gonorrhoeae. We postulate that binding to stacked effectors arose in the RNA World to closely position two substrates for RNA-mediated catalysis. These findings expand known effector recognition capabilities of riboswitches and have implications for antimicrobial development.
Phosphoglycolate phosphatase homologs act as glycerol-3-phosphate phosphatase to control stress and healthspan in C. elegans
Authors: Possik Elite , Schmitt Clémence , Al-Mass Anfal , Bai Ying , Côté Laurence , Morin Johanne , Erb Heidi , Oppong Abel , Kahloan Wahab , Parker J. Alex , Madiraju S. R. Murthy , Prentki Marc 
Published: January 2022

AbstractMetabolic stress due to nutrient excess and lipid accumulation is at the root of many age-associated disorders and the identification of therapeutic targets that mimic the beneficial effects of calorie restriction has clinical importance. Here, using C. elegans as a model organism, we study the roles of a recently discovered enzyme at the heart of metabolism in mammalian cells, glycerol-3-phosphate phosphatase (G3PP) (gene name Pgp) that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol. We identify three Pgp homologues in C. elegans (pgph) and demonstrate in vivo that their protein products have G3PP activity, essential for glycerol synthesis. We demonstrate that PGPH/G3PP regulates the adaptation to various stresses, in particular hyperosmolarity and glucotoxicity. Enhanced G3PP activity reduces fat accumulation, promotes healthy aging and acts as a calorie restriction mimetic at normal food intake without altering fertility. Thus, PGP/G3PP can be considered as a target for age-related metabolic disorders.
Observation of ballistic upstream modes at fractional quantum Hall edges of graphene
Authors: Kumar Ravi , Srivastav Saurabh Kumar , Spånslätt Christian , Watanabe K. , Taniguchi T. , Gefen Yuval , Mirlin Alexander D. , Das Anindya 
Published: January 2022

AbstractThe presence of “upstream” modes, moving against the direction of charge current flow in the fractional quantum Hall (FQH) phases, is critical for the emergence of renormalized modes with exotic quantum statistics. Detection of excess noise at the edge is a smoking gun for the presence of upstream modes. Here, we report noise measurements at the edges of FQH states realized in dual graphite-gated bilayer graphene devices. A noiseless dc current is injected at one of the edge contacts, and the noise generated at contacts at length, L = 4 μm and 10 μm away along the upstream direction is studied. For integer and particle-like FQH states, no detectable noise is measured. By contrast, for “hole-conjugate” FQH states, we detect a strong noise proportional to the injected current, unambiguously proving the existence of upstream modes. The noise magnitude remains independent of length, which matches our theoretical analysis demonstrating the ballistic nature of upstream energy transport, quite distinct from the diffusive propagation reported earlier in GaAs-based systems.
Determinants of synapse diversity revealed by super-resolution quantal transmission and active zone imaging
Authors: Newman Zachary L. , Bakshinskaya Dariya , Schultz Ryan , Kenny Samuel J. , Moon Seonah , Aghi Krisha , Stanley Cherise , Marnani Nadia , Li Rachel , Bleier Julia , Xu Ke , Isacoff Ehud Y. 
Published: January 2022

AbstractNeural circuit function depends on the pattern of synaptic connections between neurons and the strength of those connections. Synaptic strength is determined by both postsynaptic sensitivity to neurotransmitter and the presynaptic probability of action potential evoked transmitter release (Pr). Whereas morphology and neurotransmitter receptor number indicate postsynaptic sensitivity, presynaptic indicators and the mechanism that sets Pr remain to be defined. To address this, we developed QuaSOR, a super-resolution method for determining Pr from quantal synaptic transmission imaging at hundreds of glutamatergic synapses at a time. We mapped the Pr onto super-resolution 3D molecular reconstructions of the presynaptic active zones (AZs) of the same synapses at the Drosophila larval neuromuscular junction (NMJ). We find that Pr varies greatly between synapses made by a single axon, quantify the contribution of key AZ proteins to Pr diversity and find that one of these, Complexin, suppresses spontaneous and evoked transmission differentially, thereby generating a spatial and quantitative mismatch between release modes. Transmission is thus regulated by the balance and nanoscale distribution of release-enhancing and suppressing presynaptic proteins to generate high signal-to-noise evoked transmission.
Multi-mode excitation drives disorder during the ultrafast melting of a C4-symmetry-broken phase
Authors: Perez-Salinas Daniel , Johnson Allan S. , Prabhakaran Dharmalingam , Wall Simon 
Published: January 2022

AbstractSpontaneous C4-symmetry breaking phases are ubiquitous in layered quantum materials, and often compete with other phases such as superconductivity. Preferential suppression of the symmetry broken phases by light has been used to explain non-equilibrium light induced superconductivity, metallicity, and the creation of metastable states. Key to understanding how these phases emerge is understanding how C4 symmetry is restored. A leading approach is based on time-dependent Ginzburg-Landau theory, which explains the coherence response seen in many systems. However, we show that, for the case of the single layered manganite La0.5Sr1.5MnO4, the theory fails. Instead, we find an ultrafast inhomogeneous disordering transition in which the mean-field order parameter no longer reflects the atomic-scale state of the system. Our results suggest that disorder may be common to light-induced phase transitions, and methods beyond the mean-field are necessary for understanding and manipulating photoinduced phases.
Design principles for site-selective hydroxylation by a Rieske oxygenase
Authors: Liu Jianxin , Tian Jiayi , Perry Christopher , Lukowski April L. , Doukov Tzanko I. , Narayan Alison R. H. , Bridwell-Rabb Jennifer 
Published: January 2022

AbstractRieske oxygenases exploit the reactivity of iron to perform chemically challenging C–H bond functionalization reactions. Thus far, only a handful of Rieske oxygenases have been structurally characterized and remarkably little information exists regarding how these enzymes use a common architecture and set of metallocenters to facilitate a diverse range of reactions. Herein, we detail how two Rieske oxygenases SxtT and GxtA use different protein regions to influence the site-selectivity of their catalyzed monohydroxylation reactions. We present high resolution crystal structures of SxtT and GxtA with the native β-saxitoxinol and saxitoxin substrates bound in addition to a Xenon-pressurized structure of GxtA that reveals the location of a substrate access tunnel to the active site. Ultimately, this structural information allowed for the identification of six residues distributed between three regions of SxtT that together control the selectivity of the C–H hydroxylation event. Substitution of these residues produces a SxtT variant that is fully adapted to exhibit the non-native site-selectivity and substrate scope of GxtA. Importantly, we also found that these selectivity regions are conserved in other structurally characterized Rieske oxygenases, providing a framework for predictively repurposing and manipulating Rieske oxygenases as biocatalysts.
Conformal elasticity of mechanism-based metamaterials
Authors: Czajkowski Michael , Coulais Corentin , van Hecke Martin , Rocklin D. Zeb 
Published: January 2022

AbstractDeformations of conventional solids are described via elasticity, a classical field theory whose form is constrained by translational and rotational symmetries. However, flexible metamaterials often contain an additional approximate symmetry due to the presence of a designer soft strain pathway. Here we show that low energy deformations of designer dilational metamaterials will be governed by a scalar field theory, conformal elasticity, in which the nonuniform, nonlinear deformations observed under generic loads correspond with the well-studied—conformal—maps. We validate this approach using experiments and finite element simulations and further show that such systems obey a holographic bulk-boundary principle, which enables an analytic method to predict and control nonuniform, nonlinear deformations. This work both presents a unique method of precise deformation control and demonstrates a general principle in which mechanisms can generate special classes of soft deformations.
An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch
Authors: Yadav Rajeev , Widom Julia R. , Chauvier Adrien , Walter Nils G. 
Published: January 2022

AbstractThe archetypical transcriptional crcB fluoride riboswitch from Bacillus cereus is an intricately structured non-coding RNA element enhancing gene expression in response to toxic levels of fluoride. Here, we used single molecule FRET to uncover three dynamically interconverting conformations appearing along the transcription process: two distinct undocked states and one pseudoknotted docked state. We find that the fluoride anion specifically snap-locks the magnesium-induced, dynamically docked state. The long-range, nesting, single base pair A40-U48 acts as the main linchpin, rather than the multiple base pairs comprising the pseudoknot. We observe that the proximally paused RNA polymerase further fine-tunes the free energy to promote riboswitch docking. Finally, we show that fluoride binding at short transcript lengths is an early step toward partitioning folding into the docked conformation. These results reveal how the anionic fluoride ion cooperates with the magnesium-associated RNA to govern regulation of downstream genes needed for fluoride detoxification of the cell.
Spin mapping of intralayer antiferromagnetism and field-induced spin reorientation in monolayer CrTe2
Authors: Xian Jing-Jing , Wang Cong , Nie Jin-Hua , Li Rui , Han Mengjiao , Lin Junhao , Zhang Wen-Hao , Liu Zhen-Yu , Zhang Zhi-Mo , Miao Mao-Peng , Yi Yangfan , Wu Shiwei , Chen Xiaodie , Han Junbo , Xia Zhengcai , Ji Wei , Fu Ying-Shuang 
Published: January 2022

AbstractIntrinsic antiferromagnetism in van der Waals (vdW) monolayer (ML) crystals enriches our understanding of two-dimensional (2D) magnetic orders and presents several advantages over ferromagnetism in spintronic applications. However, studies of 2D intrinsic antiferromagnetism are sparse, owing to the lack of net magnetisation. Here, by combining spin-polarised scanning tunnelling microscopy and first-principles calculations, we investigate the magnetism of vdW ML CrTe2, which has been successfully grown through molecular-beam epitaxy. We observe a stable antiferromagnetic (AFM) order at the atomic scale in the ML crystal, whose bulk is ferromagnetic, and correlate its imaged zigzag spin texture with the atomic lattice structure. The AFM order exhibits an intriguing noncollinear spin reorientation under magnetic fields, consistent with its calculated moderate magnetic anisotropy. The findings of this study demonstrate the intricacy of 2D vdW magnetic materials and pave the way for their in-depth analysis.
Evolution of microscopic heterogeneity and dynamics in choline chloride-based deep eutectic solvents
Authors: Spittle Stephanie , Poe Derrick , Doherty Brian , Kolodziej Charles , Heroux Luke , Haque Md Ashraful , Squire Henry , Cosby Tyler , Zhang Yong , Fraenza Carla , Bhattacharyya Sahana , Tyagi Madhusudan , Peng Jing , Elgammal Ramez A. , Zawodzinski Thomas , Tuckerman Mark , Greenbaum Steve , Gurkan Burcu , Burda Clemens , Dadmun Mark , Maginn Edward J. , Sangoro Joshua 
Published: January 2022

AbstractDeep eutectic solvents (DESs) are an emerging class of non-aqueous solvents that are potentially scalable, easy to prepare and functionalize for many applications ranging from biomass processing to energy storage technologies. Predictive understanding of the fundamental correlations between local structure and macroscopic properties is needed to exploit the large design space and tunability of DESs for specific applications. Here, we employ a range of computational and experimental techniques that span length-scales from molecular to macroscopic and timescales from picoseconds to seconds to study the evolution of structure and dynamics in model DESs, namely Glyceline and Ethaline, starting from the parent compounds. We show that systematic addition of choline chloride leads to microscopic heterogeneities that alter the primary structural relaxation in glycerol and ethylene glycol and result in new dynamic modes that are strongly correlated to the macroscopic properties of the DES formed.
Electron-momentum dependence of electron-phonon coupling underlies dramatic phonon renormalization in YNi2B2C
Authors: Kurzhals Philipp , Kremer Geoffroy , Jaouen Thomas , Nicholson Christopher W. , Heid Rolf , Nagel Peter , Castellan John-Paul , Ivanov Alexandre , Muntwiler Matthias , Rumo Maxime , Salzmann Bjoern , Strocov Vladimir N. , Reznik Dmitry , Monney Claude , Weber Frank 
Published: January 2022

AbstractElectron-phonon coupling, i.e., the scattering of lattice vibrations by electrons and vice versa, is ubiquitous in solids and can lead to emergent ground states such as superconductivity and charge-density wave order. A broad spectral phonon line shape is often interpreted as a marker of strong electron-phonon coupling associated with Fermi surface nesting, i.e., parallel sections of the Fermi surface connected by the phonon momentum. Alternatively broad phonons are known to arise from strong atomic lattice anharmonicity. Here, we show that strong phonon broadening can occur in the absence of both Fermi surface nesting and lattice anharmonicity, if electron-phonon coupling is strongly enhanced for specific values of electron-momentum, k. We use inelastic neutron scattering, soft x-ray angle-resolved photoemission spectroscopy measurements and ab-initio lattice dynamical and electronic band structure calculations to demonstrate this scenario in the highly anisotropic tetragonal electron-phonon superconductor YNi2B2C. This new scenario likely applies to a wide range of compounds.