bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal conductivity of high-temperature high-pressure synthesized
θ
-TaN
Authors: Liu Yizhe , Li Qinshu , Qian Yijun , Yang Yumeng , Wang Shanmin , Li Wu , Sun Bo
Published: May 2023

Recent first-principles calculation predicted that theta phase tantalum nitride (θ-TaN) single crystal has an ultrahigh thermal conductivity of ∼1000 W m−1 K−1 at room temperature, making it one of the best thermal conductors among all materials. Here, we have synthesized θ-TaN by phase change from ε-TaN powder at 1750 K and 7.8 GPa. X-ray diffraction patterns and scanning transmission electron microscopy indicate that the as-prepared θ-TaN has a hexagonal tungsten carbide structure with an average grain size of 45 nm. The room-temperature thermal conductivity of θ-TaN was measured to be 47.5 W m−1 K−1 using time-domain thermoreflectance. Temperature-dependent thermal conductivity suggests that phonon-boundary scattering dominates thermal transport. The thermal conductivity of our sample is higher than those of Si and SiC nanostructures with the same characteristic length. Our result suggests that it is probable to further increase the thermal conductivity of θ-TaN.
Near-surface wind variability over spatiotemporal scales relevant to plume tracking insects
Authors: Houle Jaleesa , van Breugel Floris
Published: May 2023

Odor plume tracking is important for many organisms, and flying insects have served as popular model systems for studying this behavior both in field and laboratory settings. The shape and statistics of the airborne odor plumes that insects follow are largely governed by the wind that advects them. Prior atmospheric studies have investigated aspects of microscale wind patterns with an emphasis on characterizing pollution dispersion, enhancing weather prediction models, and for assessing wind energy potential. Here, we aim to characterize microscale wind dynamics through the lens of short-term ecological functions by focusing on spatial and temporal scales most relevant to insects actively searching for odor sources. We collected and compared near-surface wind data across three distinct environments (sage steppe, forest, and urban) in Northern Nevada. Our findings show that near-surface wind direction variability decreases with increasing wind speeds and increases in environments with greater surface complexity. Across environments, there is a strong correlation between the variability in the wind speed (i.e., turbulence intensity) and wind direction (i.e., standard deviation in wind direction). In some environments, the standard deviation in the wind direction varied as much as 15°–75° on time scales of 1–10 min. We draw insight between our findings and previous plume tracking experiments to provide a general intuition for future field research and guidance for wind tunnel design. Our analysis suggests a hypothesis that there may be an ideal range of wind speeds and environment complexity in which insects will be most successful when tracking odor plumes over long distances.
Interlayer coupling-dependent magnetoelastic response in synthetic antiferromagnets
Authors: Hisada Yuichi , Komori Sachio , Imura Keiichiro , Taniyama Tomoyasu
Published: May 2023

In recent years, antiferromagnetic materials have been attracting increasing interest for their stability in high magnetic fields and ultrafast magnetization dynamics. Since the energy scale of an interlayer exchange coupling (IEC) in a synthetic antiferromagnet (SAF) consisting of ferromagnetic/nonmagnetic/ferromagnetic multilayers is relatively smaller than that of an exchange coupling in antiferromagnetic materials, magnetic ordering of a SAF can be potentially controlled by an electric field, which is promising for energy-saving spintronic memory devices. However, an electric field-induced magnetoelastic response of SAFs on ferroelectric materials has not been sufficiently understood due to the presence of IEC that complicates magnetization dynamics. In this study, we prepare Co/Ru/Co SAFs with various amplitude of IEC on ferroelectric Pb(Mg1/3Nb2/3)O3-PbTiO3 substrates and systematically investigate their electric field-induced magnetoelastic response. We demonstrate that the magnetoelastic response disappears at the boundary where a switching between the antiferromagnetic and ferromagnetic IEC coupling occurs. The result provides insight into the coupling of the magnetoelastic effect and IEC and is useful in designing spintronic memory devices based on SAFs.
Understanding the mechanisms of anisotropic dissolution in metal oxides by applying radiolysis simulations to liquid-phase TEM
Authors: Liu Lili , Sassi Michel , Zhang Xin , Nakouzi Elias , Kovarik Libor , Xue Sichuang , Jin Biao , Rosso Kevin M. , De Yoreo James J.
Published: May 2023

Iron-based redox-active minerals are ubiquitous in soils, sediments, and aquatic systems. Their dissolution is of great importance for microbial impacts on carbon cycling and the biogeochemistry of the lithosphere and hydrosphere. Despite its widespread significance and extensive prior study, the atomic-to-nanoscale mechanisms of dissolution remain poorly understood, particularly the interplay between acidic and reductive processes. Here, we use in situ liquid-phase-transmission electron microscopy (LP-TEM) and simulations of radiolysis to probe and control acidic versus reductive dissolution of akaganeite (β–FeOOH) nanorods. Informed by crystal structure and surface chemistry, the balance between acidic dissolution at rod tips and reductive dissolution at rod sides was systematically varied using pH buffers, background chloride anions, and electron beam dose. We find that buffers, such as bis-tris, effectively inhibited dissolution by consuming radiolytic acidic and reducing species such as superoxides and aqueous electrons. In contrast, chloride anions simultaneously suppressed dissolution at rod tips by stabilizing structural elements while promoting dissolution at rod sides through surface complexation. Dissolution behaviors were systematically varied by shifting the balance between acidic and reductive attacks. The findings show LP-TEM combined with simulations of radiolysis effects can provide a unique and versatile platform for quantitatively investigating dissolution mechanisms, with implications for understanding metal cycling in natural environments and the development of tailored nanomaterials.
Mapping potential conflicts between global agriculture and terrestrial conservation
Authors: Hoang Nguyen Tien , Taherzadeh Oliver , Ohashi Haruka , Yonekura Yusuke , Nishijima Shota , Yamabe Masaki , Matsui Tetsuya , Matsuda Hiroyuki , Moran Daniel , Kanemoto Keiichiro
Published: May 2023

Demand for food products, often from international trade, has brought agricultural land use into direct competition with biodiversity. Where these potential conflicts occur and which consumers are responsible is poorly understood. By combining conservation priority (CP) maps with agricultural trade data, we estimate current potential conservation risk hotspots driven by 197 countries across 48 agricultural products. Globally, a third of agricultural production occurs in sites of high CP (CP > 0.75, max = 1.0). While cattle, maize, rice, and soybean pose the greatest threat to very high-CP sites, other low-conservation risk products (e.g., sugar beet, pearl millet, and sunflower) currently are less likely to be grown in sites of agriculture–conservation conflict. Our analysis suggests that a commodity can cause dissimilar conservation threats in different production regions. Accordingly, some of the conservation risks posed by different countries depend on their demand and sourcing patterns of agricultural commodities. Our spatial analyses identify potential hotspots of competition between agriculture and high-conservation value sites (i.e., 0.5° resolution, or ~367 to 3,077km
2
, grid cells containing both agriculture and high-biodiversity priority habitat), thereby providing additional information that could help prioritize conservation activities and safeguard biodiversity in individual countries and globally. A web-based GIS tool at
https://agriculture.spatialfootprint.com/biodiversity/
systematically visualizes the results of our analyses.
Principles of nociceptive coding in the anterior cingulate cortex
Authors: Acuña Mario A. , Kasanetz Fernando , De Luna Paolo , Falkowska Marta , Nevian Thomas
Published: May 2023

The perception of pain is a multidimensional sensory and emotional/affective experience arising from distributed brain activity. However, the involved brain regions are not specific for pain. Thus, how the cortex distinguishes nociception from other aversive and salient sensory stimuli remains elusive. Additionally, the resulting consequences of chronic neuropathic pain on sensory processing have not been characterized. Using in vivo miniscope calcium imaging with cellular resolution in freely moving mice, we elucidated the principles of nociceptive and sensory coding in the anterior cingulate cortex, a region essential for pain processing. We found that population activity, not single-cell responses, allowed discriminating noxious from other sensory stimuli, ruling out the existence of nociception-specific neurons. Additionally, single-cell stimulus selectivity was highly dynamic over time, but stimulus representation at the population level remained stable. Peripheral nerve injury-induced chronic neuropathic pain led to dysfunctional encoding of sensory events by exacerbation of responses to innocuous stimuli and impairment of pattern separation and stimulus classification, which were restored by analgesic treatment. These findings provide a novel interpretation for altered cortical sensory processing in chronic neuropathic pain and give insights into the effects of systemic analgesic treatment in the cortex.
Meta-analytic relations between personality and cognitive ability
Authors: Stanek Kevin C. , Ones Deniz S.
Published: May 2023

Cognitive ability and personality are fundamental domains of human psychology. Despite a century of vast research, most ability–personality relations remain unestablished. Using contemporary hierarchical personality and cognitive abilities frameworks, we meta-analyze unexamined links between personality traits and cognitive abilities and offer large-scale evidence of their relations. This research quantitatively summarizes 60,690 relations between 79 personality and 97 cognitive ability constructs in 3,543 meta-analyses based on data from millions of individuals. Sets of novel relations are illuminated by distinguishing hierarchical personality and ability constructs (e.g., factors, aspects, facets). The links between personality traits and cognitive abilities are not limited to openness and its components. Some aspects and facets of neuroticism, extraversion, and conscientiousness are also considerably related to primary as well as specific abilities. Overall, the results provide an encyclopedic quantification of what is currently known about personality–ability relations, identify previously unrecognized trait pairings, and reveal knowledge gaps. The meta-analytic findings are visualized in an interactive webtool. The database of coded studies and relations is offered to the scientific community to further advance research, understanding, and applications.
Cis-inhibition suppresses basal Notch signaling during sensory organ precursor selection
Authors: Troost Tobias , Binshtok Udi , Sprinzak David , Klein Thomas
Published: May 2023

The emergence of the sensory organ precursor (SOP) from an equivalence group in
Drosophila
is a paradigm for studying single-cell fate specification through Notch-mediated lateral inhibition. Yet, it remains unclear how only a single SOP is selected from a relatively large group of cells. We show here that a critical aspect of SOP selection is controlled by cis-inhibition (CI), whereby the Notch ligands, Delta (Dl), cis-inhibit Notch receptors in the same cell. Based on the observation that the mammalian ligand Dl-like 1 cannot cis-inhibit Notch in
Drosophila
, we probe the role of CI in vivo. We develop a mathematical model for SOP selection where Dl activity is independently regulated by the ubiquitin ligases Neuralized and Mindbomb1. We show theoretically and experimentally that Mindbomb1 induces basal Notch activity, which is suppressed by CI. Our results highlight the trade-off between basal Notch activity and CI as a mechanism for singling out a SOP from a large equivalence group.
Dietary flavanols restore hippocampal-dependent memory in older adults with lower diet quality and lower habitual flavanol consumption
Authors: Brickman Adam M. , Yeung Lok-Kin , Alschuler Daniel M. , Ottaviani Javier I. , Kuhnle Gunter G. C. , Sloan Richard P. , Luttmann-Gibson Heike , Copeland Trisha , Schroeter Hagen , Sesso Howard D. , Manson JoAnn E. , Wall Melanie , Small Scott A.
Published: May 2023

Dietary flavanols are food constituents found in certain fruits and vegetables that have been linked to cognitive aging. Previous studies suggested that consumption of dietary flavanols might specifically be associated with the hippocampal-dependent memory component of cognitive aging and that memory benefits of a flavanol intervention might depend on habitual diet quality. Here, we tested these hypotheses in the context of a large-scale study of 3,562 older adults, who were randomly assigned to a 3-y intervention of cocoa extract (500 mg of cocoa flavanols per day) or a placebo [(COcoa Supplement and Multivitamin Outcomes Study) COSMOS-Web, NCT04582617]. Using the alternative Healthy Eating Index in all participants and a urine-based biomarker of flavanol intake in a subset of participants [n = 1,361], we show that habitual flavanol consumption and diet quality at baseline are positively and selectively correlated with hippocampal-dependent memory. While the prespecified primary end point testing for an intervention-related improvement in memory in all participants after 1 y was not statistically significant, the flavanol intervention restored memory among participants in lower tertiles of habitual diet quality or habitual flavanol consumption. Increases in the flavanol biomarker over the course of the trial were associated with improving memory. Collectively, our results allow dietary flavanols to be considered in the context of a depletion–repletion paradigm and suggest that low flavanol consumption can act as a driver of the hippocampal-dependent component of cognitive aging.
A null model for the distribution of fitness effects of mutations
Authors: Cotto Olivier , Day Troy
Published: May 2023

The distribution of fitness effects (DFE) of new mutations is key to our understanding of many evolutionary processes. Theoreticians have developed several models to help understand the patterns seen in empirical DFEs. Many such models reproduce the broad patterns seen in empirical DFEs but these models often rely on structural assumptions that cannot be tested empirically. Here, we investigate how much of the underlying “microscopic” biological processes involved in the mapping of new mutations to fitness can be inferred from “macroscopic” observations of the DFE. We develop a null model by generating random genotype-to-fitness maps and show that the null DFE is that with the largest possible information entropy. We further show that, subject to one simple constraint, this null DFE is a Gompertz distribution. Finally, we illustrate how the predictions of this null DFE match empirically measured DFEs from several datasets, as well as DFEs simulated from Fisher’s geometric model. This suggests that a match between models and empirical data is often not a very strong indication of the mechanisms underlying the mapping of mutation to fitness.
Isotopes illustrate vertical transport of anthropogenic Pb by reversible scavenging within Pacific Ocean particle veils
Authors: Lanning Nathan T. , Jiang Shuo , Amaral Vinicius J. , Mateos Katherine , Steffen Janelle M. , Lam Phoebe J. , Boyle Edward A. , Fitzsimmons Jessica N.
Published: May 2023

Reversible scavenging, the oceanographic process by which dissolved metals exchange onto and off sinking particles and are thereby transported to deeper depths, has been well established for the metal thorium for decades. Reversible scavenging both deepens the elemental distribution of adsorptive elements and shortens their oceanic residence times in the ocean compared to nonadsorptive metals, and scavenging ultimately removes elements from the ocean via sedimentation. Thus, it is important to understand which metals undergo reversible scavenging and under what conditions. Recently, reversible scavenging has been invoked in global biogeochemical models of a range of metals including lead, iron, copper, and zinc to fit modeled data to observations of oceanic dissolved metal distributions. Nonetheless, the effects of reversible scavenging remain difficult to visualize in ocean sections of dissolved metals and to distinguish from other processes such as biological regeneration. Here, we show that particle-rich “veils” descending from high-productivity zones in the equatorial and North Pacific provide idealized illustrations of reversible scavenging of dissolved lead (Pb). A meridional section of dissolved Pb isotope ratios across the central Pacific shows that where particle concentrations are sufficiently high, such as within particle veils, vertical transport of anthropogenic surface–dissolved Pb isotope ratios toward the deep ocean is manifested as columnar isotope anomalies. Modeling of this effect shows that reversible scavenging within particle-rich waters allows anthropogenic Pb isotope ratios from the surface to penetrate ancient deep waters on timescales sufficiently rapid to overcome horizontal mixing of deep water Pb isotope ratios along abyssal isopycnals.
Dengue virus NS5 degrades ERC1 during infection to antagonize NF-kB activation
Authors: Gonzalez Lopez Ledesma María Mora , Costa Navarro Guadalupe , Pallares Horacio M. , Paletta Ana , De Maio Federico , Iglesias Nestor G. , Gebhard Leopoldo , Oviedo Rouco Santiago , Ojeda Diego S. , de Borba Luana , Giraldo María , Rajsbaum Ricardo , Ceballos Ana , Krogan Nevan J. , Shah Priya S. , Gamarnik Andrea V.
Published: May 2023

Dengue virus (DENV) is the most important human virus transmitted by mosquitos. Dengue pathogenesis is characterized by a large induction of proinflammatory cytokines. This cytokine induction varies among the four DENV serotypes (DENV1 to 4) and poses a challenge for live DENV vaccine design. Here, we identify a viral mechanism to limit NF-κB activation and cytokine secretion by the DENV protein NS5. Using proteomics, we found that NS5 binds and degrades the host protein ERC1 to antagonize NF-κB activation, limit proinflammatory cytokine secretion, and reduce cell migration. We found that ERC1 degradation involves unique properties of the methyltransferase domain of NS5 that are not conserved among the four DENV serotypes. By obtaining chimeric DENV2 and DENV4 viruses, we map the residues in NS5 for ERC1 degradation, and generate recombinant DENVs exchanging serotype properties by single amino acid substitutions. This work uncovers a function of the viral protein NS5 to limit cytokine production, critical to dengue pathogenesis. Importantly, the information provided about the serotype-specific mechanism for counteracting the antiviral response can be applied to improve live attenuated vaccines.
Proximity to criticality predicts surface properties of biomolecular condensates
Authors: Pyo Andrew G. T. , Zhang Yaojun , Wingreen Ned S.
Published: May 2023

It has recently become appreciated that cells self-organize their interiors through the formation of biomolecular condensates. These condensates, typically formed through liquid–liquid phase separation of proteins, nucleic acids, and other biopolymers, exhibit reversible assembly/disassembly in response to changing conditions. Condensates play many functional roles, aiding in biochemical reactions, signal transduction, and sequestration of certain components. Ultimately, these functions depend on the physical properties of condensates, which are encoded in the microscopic features of the constituent biomolecules. In general, the mapping from microscopic features to macroscopic properties is complex, but it is known that near a critical point, macroscopic properties follow power laws with only a small number of parameters, making it easier to identify underlying principles. How far does this critical region extend for biomolecular condensates and what principles govern condensate properties in the critical regime? Using coarse-grained molecular-dynamics simulations of a representative class of biomolecular condensates, we found that the critical regime can be wide enough to cover the full physiological range of temperatures. Within this critical regime, we identified that polymer sequence influences surface tension predominately via shifting the critical temperature. Finally, we show that condensate surface tension over a wide range of temperatures can be calculated from the critical temperature and a single measurement of the interface width.
PRC2 direct transfer from G-quadruplex RNA to dsDNA has implications for RNA-binding chromatin modifiers
Authors: Hemphill Wayne O. , Fenske Regan , Gooding Anne R. , Cech Thomas R.
Published: May 2023

The chromatin-modifying enzyme, Polycomb Repressive Complex 2 (PRC2), deposits the H3K27me3 epigenetic mark to negatively regulate expression at numerous target genes, and this activity has been implicated in embryonic development, cell differentiation, and various cancers. A biological role for RNA binding in regulating PRC2 histone methyltransferase activity is generally accepted, but the nature and mechanism of this relationship remains an area of active investigation. Notably, many in vitro studies demonstrate that RNA inhibits PRC2 activity on nucleosomes through mutually antagonistic binding, while some in vivo studies indicate that PRC2’s RNA-binding activity is critical for facilitating its biological function(s). Here we use biochemical, biophysical, and computational approaches to interrogate PRC2’s RNA and DNA-binding kinetics. Our findings demonstrate that PRC2-polynucleotide dissociation rates are dependent on the concentration of free ligand, indicating the potential for direct transfer between nucleic acid ligands without a free-enzyme intermediate. Direct transfer explains the variation in previously reported dissociation kinetics, allows reconciliation of prior in vitro and in vivo studies, and expands the potential mechanisms of RNA-mediated PRC2 regulation. Moreover, simulations indicate that such a direct transfer mechanism could be obligatory for RNA to recruit proteins to chromatin.
Rise ofRuppiain Chesapeake Bay: Climate change–driven turnover of foundation species creates new threats and management opportunities
Authors: Hensel Marc J. S. , Patrick Christopher J. , Orth Robert J. , Wilcox David J. , Dennison William C. , Gurbisz Cassie , Hannam Michael P. , Landry J. Brooke , Moore Kenneth A. , Murphy Rebecca R. , Testa Jeremy M. , Weller Donald E. , Lefcheck Jonathan S.
Published: May 2023

Global change has converted many structurally complex and ecologically and economically valuable coastlines to bare substrate. In the structural habitats that remain, climate-tolerant and opportunistic species are increasing in response to environmental extremes and variability. The shifting of dominant foundation species identity with climate change poses a unique conservation challenge because species vary in their responses to environmental stressors and to management. Here, we combine 35 y of watershed modeling and biogeochemical water quality data with species comprehensive aerial surveys to describe causes and consequences of turnover in seagrass foundation species across 26,000 ha of habitat in the Chesapeake Bay. Repeated marine heatwaves have caused 54% retraction of the formerly dominant eelgrass (Zostera marina) since 1991, allowing 171% expansion of the temperature-tolerant widgeongrass (Ruppia maritima) that has likewise benefited from large-scale nutrient reductions. However, this phase shift in dominant seagrass identity now presents two significant shifts for management: Widgeongrass meadows are not only responsible for rapid, extensive recoveries but also for the largest crashes over the last four decades; and, while adapted to high temperatures, are much more susceptible than eelgrass to nutrient pulses driven by springtime runoff. Thus, by selecting for rapid post-disturbance recolonization but low resistance to punctuated freshwater flow disturbance, climate change could threaten the Chesapeake Bay seagrass’ ability to provide consistent fishery habitat and sustain functioning over time. We demonstrate that understanding the dynamics of the next generation of foundation species is a critical management priority, because shifts from relatively stable habitat to high interannual variability can have far-reaching consequences across marine and terrestrial ecosystems.
Electron heating in kinetic-Alfvén-wave turbulence
Authors: Zhou Muni , Liu Zhuo , Loureiro Nuno F.
Published: May 2023

We report analytical and numerical investigations of subion-scale turbulence in low-beta plasmas using a rigorous reduced kinetic model. We show that efficient electron heating occurs and is primarily due to Landau damping of kinetic Alfvén waves, as opposed to Ohmic dissipation. This collisionless damping is facilitated by the local weakening of advective nonlinearities and the ensuing unimpeded phase mixing near intermittent current sheets, where free energy concentrates. The linearly damped energy of electromagnetic fluctuations at each scale explains the steepening of their energy spectrum with respect to a fluid model where such damping is excluded (i.e., a model that imposes an isothermal electron closure). The use of a Hermite polynomial representation to express the velocity-space dependence of the electron distribution function enables us to obtain an analytical, lowest-order solution for the Hermite moments of the distribution, which is borne out by numerical simulations.
Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection
Authors: Guenthoer Jamie , Lilly Michelle , Starr Tyler N. , Dadonaite Bernadeta , Lovendahl Klaus N. , Croft Jacob T. , Stoddard Caitlin I. , Chohan Vrasha , Ding Shilei , Ruiz Felicitas , Kopp Mackenzie S. , Finzi Andrés , Bloom Jesse D. , Chu Helen Y. , Lee Kelly K. , Overbaugh Julie
Published: May 2023

The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor-binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are unique in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.
The retrotransposon R2 maintains
Drosophila
ribosomal DNA repeats
Authors: Nelson Jonathan O. , Slicko Alyssa , Yamashita Yukiko M.
Published: May 2023

Ribosomal DNA (rDNA) loci contain hundreds of tandemly repeated copies of ribosomal RNA genes needed to support cellular viability. This repetitiveness makes it highly susceptible to copy number (CN) loss due to intrachromatid recombination between rDNA copies, threatening multigenerational maintenance of rDNA. How this threat is counteracted to avoid extinction of the lineage has remained unclear. Here, we show that the rDNA-specific retrotransposon R2 is essential for restorative rDNA CN expansion to maintain rDNA loci in the Drosophila male germline. The depletion of R2 led to defective rDNA CN maintenance, causing a decline in fecundity over generations and eventual extinction. We find that double-stranded DNA breaks created by the R2 endonuclease, a feature of R2’s rDNA-specific retrotransposition, initiate the process of rDNA CN recovery, which relies on homology-dependent repair of the DNA break at rDNA copies. This study reveals that an active retrotransposon provides an essential function for its host, contrary to transposable elements’ reputation as entirely selfish. These findings suggest that benefiting host fitness can be an effective selective advantage for transposable elements to offset their threat to the host, which may contribute to retrotransposons’ widespread success throughout taxa.
Theory of chromatin organization maintained by active loop extrusion
Authors: Chan Brian , Rubinstein Michael
Published: May 2023

The active loop extrusion hypothesis proposes that chromatin threads through the cohesin protein complex into progressively larger loops until reaching specific boundary elements. We build upon this hypothesis and develop an analytical theory for active loop extrusion which predicts that loop formation probability is a nonmonotonic function of loop length and describes chromatin contact probabilities. We validate our model with Monte Carlo and hybrid Molecular Dynamics–Monte Carlo simulations and demonstrate that our theory recapitulates experimental chromatin conformation capture data. Our results support active loop extrusion as a mechanism for chromatin organization and provide an analytical description of chromatin organization that may be used to specifically modify chromatin contact probabilities.
Structural insights into the assembly of the agrin/LRP4/MuSK signaling complex
Authors: Xie Tian , Xu Guangjun , Liu Yun , Quade Bradley , Lin Weichun , Bai Xiao-chen
Published: May 2023

MuSK is a receptor tyrosine kinase (RTK) that plays essential roles in the formation and maintenance of the neuromuscular junction. Distinct from most members of RTK family, MuSK activation requires not only its cognate ligand agrin but also its coreceptor
s
LRP4. However, how agrin and LRP4 coactivate MuSK remains unclear. Here, we report the cryo-EM structure of the extracellular ternary complex of agrin/LRP4/MuSK in a stoichiometry of 1:1:1. This structure reveals that arc-shaped LRP4 simultaneously recruits both agrin and MuSK to its central cavity, thereby promoting a direct interaction between agrin and MuSK. Our cryo-EM analyses therefore uncover the assembly mechanism of agrin/LRP4/MuSK signaling complex and reveal how MuSK receptor is activated by concurrent binding of agrin and LRP4.
Direct visualization of proton beam irradiation effects in liquids by MRI
Authors: Gantz Sebastian , Karsch Leonhard , Pawelke Jörg , Schieferecke Juliane , Schellhammer Sonja , Smeets Julien , van der Kraaij Erik , Hoffmann Aswin
Published: May 2023

The main advantage proton beams offer over photon beams in radiation therapy of cancer patients is the dose maximum at their finite range, yielding a reduction in the dose deposited in healthy tissues surrounding the tumor. Since no direct method exists to measure the beam’s range during dose delivery, safety margins around the tumor are applied, compromising the dose conformality and reducing the targeting accuracy. Here, we demonstrate that online MRI can visualize the proton beam and reveal its range during irradiation of liquid-filled phantoms. A clear dependence on beam energy and current was found. These results stimulate research into novel MRI-detectable beam signatures and already find application in the geometric quality assurance for magnetic resonance-integrated proton therapy systems currently under development.
Structure of the priming arabinosyltransferase AftA required for AG biosynthesis ofMycobacterium tuberculosis
Authors: Gong Yicheng , Wei Chuancun , Wang Jun , Mu Nengjiang , Lu Qinhong , Wu Chengyao , Yan Ning , Yang Huifang , Zhao Yao , Yang Xiuna , Gurcha Sudagar S. , Veerapen Natacha , Batt Sarah M. , Hao Zhiqiang , Da Lintai , Besra Gurdyal S. , Rao Zihe , Zhang Lu
Published: May 2023

Arabinogalactan (AG) is an essential cell wall component in mycobacterial species, including the deadly human pathogenMycobacterium tuberculosis. It plays a pivotal role in forming the rigid mycolyl–AG–peptidoglycan core for in vitro growth. AftA is a membrane-bound arabinosyltransferase and a key enzyme involved in AG biosynthesis which bridges the assembly of the arabinan chain to the galactan chain. It is known that AftA catalyzes the transfer of the first arabinofuranosyl residue from the donor decaprenyl-monophosphoryl-arabinose to the mature galactan chain (i.e., priming); however, the priming mechanism remains elusive. Herein, we report the cryo-EM structure ofMtbAftA. The detergent-embedded AftA assembles as a dimer with an interface maintained by both the transmembrane domain (TMD) and the soluble C-terminal domain (CTD) in the periplasm. The structure shows a conserved glycosyltransferase-C fold and two cavities converging at the active site. A metal ion participates in the interaction of TMD and CTD of each AftA molecule. Structural analyses combined with functional mutagenesis suggests a priming mechanism catalyzed by AftA inMtbAG biosynthesis. Our data further provide a unique perspective into anti-TB drug discovery.
HIV-1 usurps transcription start site heterogeneity of host RNA polymerase II to maximize replication fitness
Authors: Nikolaitchik Olga A. , Islam Saiful , Kitzrow Jonathan P. , Duchon Alice , Cheng Zetao , Liu Yang , Rawson Jonathan M. O. , Shao Wei , Nikolaitchik Maria , Kearney Mary F. , Maldarelli Frank , Musier-Forsyth Karin , Pathak Vinay K. , Hu Wei-Shau
Published: May 2023

HIV-1 relies on host RNA polymeraseII (Pol II) to transcribe its genome and uses multiple transcription start sites (TSS), including three consecutive guanosines located near the U3-R junction, to generate transcripts containing three, two, and one guanosine at the 5′ end, referred to as 3G, 2G, and 1G RNA, respectively. The 1G RNA is preferentially selected for packaging, indicating that these 99.9% identical RNAs exhibit functional differences and highlighting the importance of TSS selection. Here, we demonstrate that TSS selection is regulated by sequences between the CATA/TATA box and the beginning of R. Furthermore, we have generated two HIV-1 mutants with distinct 2-nucleotide modifications that predominantly express 3G RNA or 1G RNA. Both mutants can generate infectious viruses and undergo multiple rounds of replication in T cells. However, both mutants exhibit replication defects compared to the wild-type virus. The 3G-RNA-expressing mutant displays an RNA genome–packaging defect and delayed replication kinetics, whereas the 1G-RNA-expressing mutant exhibits reduced Gag expression and a replication fitness defect. Additionally, reversion of the latter mutant is frequently observed, consistent with sequence correction by plus-strand DNA transfer during reverse transcription. These findings demonstrate that HIV-1 maximizes its replication fitness by usurping the TSS heterogeneity of host RNA Pol II to generate unspliced RNAs with different specialized roles in viral replication. The three consecutive guanosines at the junction of U3 and R may also maintain HIV-1 genome integrity during reverse transcription. These studies reveal the intricate regulation of HIV-1 RNA and complex replication strategy.
Evidential meanings in native and learner Japanese and English
Authors: Filipović Luna , Brown Mika , Engelhardt Paul E.
Published: May 2023

Evidentiality is a linguistic category that comprises forms and meanings related to the source of information in utterances, the use of which may impact judgments about the degree of certainty expressed by a speaker. The main dichotomy is first-hand (direct) vs. second-hand (indirect) evidence. This distinction is grammaticalised in Japanese only, though certain related meanings can be expressed in English lexically or constructionally. The relevant forms in both languages also function as indirectness-for-politeness markers. We used a judgments elicitation task and found that statements with Japanese evidentials (both first- and second-hand) and with English markers of uncertainty lead to judgments of lower certainty than the statements without the evidential forms and meanings for the majority, but not for all speakers. In addition, monolingual and bilingual usage in both languages has parallels such that these two typologically distinct languages appear closer and certainty judgments by their speakers similar.
Translation and mountaineering, a first case study
Authors: Saroldi Anna
Published: May 2023

This article argues for a dialogue between translation and mountaineering studies and provides examples of how the two could successfully interact. It contributes to literary translator studies and translation history by bringing to the fore the careers of translators and mountaineers Janet Adam Smith and Nea Morin and by establishing links between their collaborative translation andcordée féminine, arguing that they played an active role as agents of both the literary and the mountaineering fields. Moreover, it provides instances of how the awareness of translation processes can expand and deepen the analysis of gendered dynamics in mountaineering non-fiction. Finally, it shows how mountaineering studies can benefit from translation studies in order to become more aware of its dissemination processes and international dynamics, and how translation studies can benefit from mountaineering studies to more fully comprehend and capture the depth of its involvement, dependence, and interaction with the non-literary world.
Boron-induced magneto-optical Kerr spectra and dielectric tensors in ferrimagnetic (Mn4N)B antiperovskite thin films
Authors: Sakaguchi Hotaka , Isogami Shinji , Niimi Makoto , Ishibashi Takayuki
Published: May 2023

Boron-induced electronic states were investigated via a combination of polar magneto-optical Kerr effect (p-MOKE) spectroscopy and spectroscopic ellipsometry for one of the antiperovskite nitrides, Mn4N. The boron content in the Mn4N film varied from 0 to 4.3 at.%, for which the crystal structure was maintained. The amplitude of p-MOKE spectra and the diagonal and off-diagonal dielectric tensors decreased with increasing boron content, which is in agreement with the magnetic properties such as magnetic anisotropy and saturation magnetization. These results were related to the lattice expansion and displacement of the charge density in the Mn4N by boron doping. However, the peak energy of the Lorentz oscillator in the diagonal elements of dielectric tensors suggests that a dominant inter-band transition was independent of boron content.
RCS reduction using embedded meta-structure absorber in X-band
Authors: Saikia Sanghamitra , Bhattacharyya Nidhi Saxena
Published: May 2023

One approach for lowering radar cross section (RCS) is by reducing reflection, which can be achieved by use of absorbers. Embedded meta-structure absorbers (MSAs) are void of metallic resonating structures, which minimize out-of-band reflections thus reducing the chance of detection by radar systems. Here, an X-band MSA is developed by embedding ionic deep eutectic solvent gel as subwavelength cuboidal resonant structures in flexible silicone rubber. The material properties and structural geometry of the gel combines to enhance the

−
10

dB absorption bandwidth to more than

80
%

. The fabricated Gel-Si MSA is sufficiently flexible with an overall thickness of

∼
0.0775

λ
0

.

10

dB RCS reduction is evaluated in the range over the X-band. The RCS properties are insensitive to polarization angles up to

±

90
∘

and incident angle up to

±

40
∘

.
Enhanced surface insulation for SiO2/epoxy resin composites through co-modification of nanofiller with silane coupling agent and plasma
Authors: Cheng Xian , He Guangyuan , Sun Zhengwei , Wang Yizhi , Geng Shuo , Lian Haoyu
Published: May 2023

To enhance the surface insulation properties of SiO2/epoxy resin composites, the SiO2 filler is co-modified with a chemical method and dielectric barrier discharge plasma in this work. The effects on the micro-structures, electrical parameters and surface insulation properties of the materials are studied. The results show that chemical modification using the silane coupling agent (KH550) can effectively introduce organo-functional groups into SiO2 filler. On the other hand, plasma modification shows little effect on the organo-functional group but significantly increases the dispersity of the nanoparticles, therefore reducing filler conglobation in epoxy resin composite. The composite samples with SiO2 doping concentration of 1 wt.%, 2 wt.%, 3 wt.%, 5 wt.% and 7 wt.% are prepared and characterized. It is found that the synergy of chemical and plasma methods could significantly improve the surface insulation of composite samples. Through doping 2 wt.% of the co-modified SiO2 filler, the direct current flashover voltage of the composites in dry air at atmospheric pressure can be increased to 1.53 times of the pure epoxy. The enhanced surface insulation properties are explained by the trap effect and the change of electrical parameters through the co-modification process.
Impact fault detection for marine current turbines blade via MEGK-means and PCA under variable marine conditions
Authors: Xie Tao , Zhang Weidong , Li Feng , Ahmed Zahoor
Published: May 2023

The advancement of the marine current turbine (MCT) technology has the potential to aid China in achieving its carbon peak and carbon neutrality goals. The performance of MCTs is influenced by fluctuating water velocities and erratic turbulence. The blades of MCTs are susceptible to cracking due to prolonged exposure to seawater. Unpredictable changes in marine currents contribute to unstable working environments. This study presents multiple envelope geometrical K-means to categorize stator current readings and develop fault detection models. It first constructs an envelope geometric feature matrix by using the extracted modulus signal. Then, the matrix is used to select the initial center for clustering, and a multi-scale principal component analysis is performed under each working condition to decrease data dimensionality. Finally, T
2 and squared prediction error (SPE) serve as the projection of the sample vector on the principal element space and the remaining subspace, respectively, and can be utilized to monitor fault cases. The experimental findings demonstrate that the proposed method has excellent recognition capabilities and detection accuracy for the impact faults of MCTs under variable working conditions.
A performance-enhanced DVL/SINS integrated navigation system based on data-driven approach
Authors: Jin Kaidi , Chai Hongzhou , Su Chuhan , Xiang Minzhi
Published: May 2023

With the aid of Doppler velocity logger (DVL), strapdown inertial navigation systems (SINSs) can provide continuous and accurate navigation parameters for unmanned underwater vehicles (UUVs). However, owing to the complex underwater environment, partial DVL beams may fail to be reflected by the seafloor, resulting in DVL measurement outage. In this study, a novel data-driven approach enhancing DVL/SINS integrated navigation system is proposed to improve the robustness and accuracy of UUV navigation with limited DVL beams. First, to make full use of the available beam, the velocities of DVL beams are used to assist the SINS navigation instead of the 3D velocity of DVL. Subsequently, a virtual beam predictor based on multi-output least-squares support vector regression (MLS-SVR) is built to run in parallel with the DVL/SINS integrated system. Specifically, when the DVL operates normally, all four beams can be applied for integrated navigation and stored as the training dataset. Once partial beams are missing, the available beams and the outputs of SINS and pressure sensors can train the MLS-SVR model along with the corresponding missing beams in the training set. Subsequently, the missing beams can be predicted by the trained model for integrated navigation together with the available beams. UUV sea trials indicate that the proposed system can accurately predict unavailable beams and improve the positioning accuracy of the DVL/SINS integrated navigation system.
Direct visualization of nanoparticle morphology in thermally sintered nanoparticle ink traces and the relationship among nanoparticle morphology, incomplete polymer removal, and trace conductivity
Authors: Chandel Ghansham Rajendrasingh , Sun Jiayue , Etha Sai Ankit , Zhao Beihan , Sivasankar Vishal Sankar , Nikfarjam Shakiba , Wang Mei , Hines Daniel R , Dasgupta Abhijit , Woehl Taylor , Das Siddhartha
Published: May 2023

A key challenge encountered by printed electronics is that the conductivity of sintered metal nanoparticle (NP) traces is always several times smaller than the bulk metal conductivity. Identifying the relative roles of the voids and the residual polymers on NP surfaces in sintered NP traces, in determining such reduced conductivity, is essential. In this paper, we employ a combination of electron microscopy imaging and detailed simulations to quantify the relative roles of such voids and residual polymers in the conductivity of sintered traces of a commercial (Novacentrix) silver nanoparticle-based ink. High resolution transmission electron microscopy imaging revealed details of the morphology of the inks before and after being sintered at 150 °C. Prior to sintering, NPs were randomly close packed into aggregates with nanometer thick polymer layers in the interstices. The 2D porosity in the aggregates prior to sintering was near 20%. After heating at 150 °C, NPs sintered together into dense aggregates (nanoaggregates or NAgs) with sizes ranging from 100 to 500 nm and the 2D porosity decreased to near 10%. Within the NAgs, the NPs were mostly connected via sintered metal bridges, while the outer surfaces of the NAgs were coated with a nanometer thick layer of polymer. Motivated by these experimental results, we developed a computational model for calculating the effective conductivity of the ink deposit represented by a prototypical NAg consisting of NPs connected by metallic bonds and having a polymer layer on its outer surface placed in a surrounding medium. The calculations reveal that a NAg that is 35%–40% covered by a nanometer thick polymeric layer has a similar conductivity compared to prior experimental measurements. The findings also demonstrate that the conductivity is less influenced by the polymer layer thickness or the absolute value of the NAg dimensions. Most importantly, we are able to infer that the reduced value of the conductivity of the sintered traces is less dependent on the void fraction and is primarily attributed to the incomplete removal of the polymeric material even after sintering.