bluuebunny/crossref_metadata_2025_split huggingface dataset:
Momentum-selective orbital hybridisation
Authors: Yang Xiaosheng , Jugovac Matteo , Zamborlini Giovanni , Feyer Vitaliy , Koller Georg , Puschnig Peter , Soubatch Serguei , Ramsey Michael G. , Tautz F. Stefan 
Published: September 2022

AbstractWhen a molecule interacts chemically with a metal surface, the orbitals of the molecule hybridise with metal states to form the new eigenstates of the coupled system. Spatial overlap and energy matching are determining parameters of the hybridisation. However, since every molecular orbital does not only have a characteristic spatial shape, but also a specific momentum distribution, one may additionally expect a momentum matching condition; after all, each hybridising wave function of the metal has a defined wave vector, too. Here, we report photoemission orbital tomography measurements of hybrid orbitals that emerge from molecular orbitals at a molecule-on-metal interface. We find that in the hybrid orbitals only those partial waves of the original orbital survive which match the metal band structure. Moreover, we find that the conversion of the metal’s surface state into a hybrid interface state is also governed by momentum matching constraints. Our experiments demonstrate the possibility to measure hybridisation momentum-selectively, thereby enabling deep insights into the complicated interplay of bulk states, surface states, and molecular orbitals in the formation of the electronic interface structure at molecule-on-metal hybrid interfaces.
Evolution of tropical land temperature across the last glacial termination
Authors: Løland M. H. , Krüger Y. , Fernandez A. , Buckingham F. , Carolin S. A. , Sodemann H. , Adkins J. F. , Cobb K. M. , Meckler A. N. 
Published: September 2022

AbstractThe tropical West Pacific hosts the warmest part of the surface ocean and has a considerable impact on the global climate system. Reconstructions of past temperature in this region can elucidate climate connections between the tropics and poles and the sensitivity of tropical temperature to greenhouse forcing. However, existing data are equivocal and reliable information from terrestrial archives is particularly sparse. Here we constrain the magnitude and timing of land temperature change in the tropical West Pacific across the last deglaciation using an exceptionally precise paleothermometer applied to a well-dated stalagmite from Northern Borneo. We show that the cave temperature increased by 4.4 ± 0.3 °C (2 SEM) from the Last Glacial Maximum to the Holocene, amounting to 3.6 ± 0.3 °C (2 SEM) when correcting for sea-level induced cave altitude change. The warming closely follows atmospheric CO2 and Southern Hemisphere warming. This contrasts with hydroclimate, as reflected by drip water δ18O, which responds to Northern Hemisphere cooling events in the form of prominent drying, while temperature was rising. Our results thus show a close response of tropical temperature to greenhouse forcing, independent of shifts in the tropical circulation patterns.
Mapping autophagosome contents identifies interleukin-7 receptor-α as a key cargo modulating CD4+ T cell proliferation
Authors: Zhou Dingxi , Borsa Mariana , Puleston Daniel J. , Zellner Susanne , Capera Jesusa , Sanderson Sharon , Schifferer Martina , Hester Svenja S. , Ge Xin , Fischer Roman , Jostins Luke , Behrends Christian , Alsaleh Ghada , Simon Anna Katharina 
Published: September 2022

AbstractCD4+ T cells are pivotal cells playing roles in the orchestration of humoral and cytotoxic immune responses. It is known that CD4+ T cell proliferation relies on autophagy, but identification of the autophagosomal cargo involved is missing. Here we create a transgenic mouse model, to enable direct mapping of the proteinaceous content of autophagosomes in primary cells by LC3 proximity labelling. Interleukin-7 receptor-α, a cytokine receptor mostly found in naïve and memory T cells, is reproducibly detected in autophagosomes of activated CD4+ T cells. Consistently, CD4+ T cells lacking autophagy show increased interleukin-7 receptor-α surface expression, while no defect in internalisation is observed. Mechanistically, excessive surface interleukin-7 receptor-α sequestrates the common gamma chain, impairing the interleukin-2 receptor assembly and downstream signalling crucial for T cell proliferation. This study shows that key autophagy substrates can be reliably identified in this mouse model and help mechanistically unravel autophagy’s contribution to healthy physiology and disease.
Proton-driven alternating access in a spinster lipid transporter
Authors: Dastvan Reza , Rasouli Ali , Dehghani-Ghahnaviyeh Sepehr , Gies Samantha , Tajkhorshid Emad 
Published: September 2022

AbstractSpinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60TM2:Arg289TM7) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange.
Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation
Authors: Arroyo María , Hastert Florian D. , Zhadan Andreas , Schelter Florian , Zimbelmann Susanne , Rausch Cathia , Ludwig Anne K. , Carell Thomas , Cardoso M. Cristina 
Published: September 2022

AbstractOxidation of the epigenetic DNA mark 5-methylcytosine by Tet dioxygenases is an established route to diversify the epigenetic information, modulate gene expression and overall cellular (patho-)physiology. Here, we demonstrate that Tet1 and its short isoform Tet1s exhibit distinct nuclear localization during DNA replication resulting in aberrant cytosine modification levels in human and mouse cells. We show that Tet1 is tethered away from heterochromatin via its zinc finger domain, which is missing in Tet1s allowing its targeting to these regions. We find that Tet1s interacts with and is ubiquitinated by CRL4(VprBP). The ubiquitinated Tet1s is then recognized by Uhrf1 and recruited to late replicating heterochromatin. This leads to spreading of 5-methylcytosine oxidation to heterochromatin regions, LINE 1 activation and chromatin decondensation. In summary, we elucidate a dual regulation mechanism of Tet1, contributing to the understanding of how epigenetic information can be diversified by spatio-temporal directed Tet1 catalytic activity.
Marine phosphate availability and the chemical origins of life on Earth
Authors: Brady Matthew P. , Tostevin Rosalie , Tosca Nicholas J. 
Published: September 2022

AbstractPrebiotic systems chemistry suggests that high phosphate concentrations were necessary to synthesise molecular building blocks and sustain primitive cellular systems. However, current understanding of mineral solubility predicts negligible phosphate concentrations for most natural waters, yet the role of Fe2+, ubiquitous on early Earth, is poorly quantified. Here we determine the solubility of Fe(II)-phosphate in synthetic seawater as a function of pH and ionic strength, integrate these observations into a thermodynamic model that predicts phosphate concentrations across a range of aquatic conditions, and validate these predictions against modern anoxic sediment pore waters. Experiments and models show that Fe2+ significantly increases the solubility of all phosphate minerals in anoxic systems, suggesting that Hadean and Archean seawater featured phosphate concentrations ~103–104 times higher than currently estimated. This suggests that seawater readily met the phosphorus requirements of emergent cellular systems and early microbial life, perhaps fueling primary production during the advent of oxygenic photosynthesis.
Microspectroscopic visualization of how biochar lifts the soil organic carbon ceiling
Authors: Weng Zhe , Van Zwieten Lukas , Tavakkoli Ehsan , Rose Michael T. , Singh Bhupinder Pal , Joseph Stephen , Macdonald Lynne M. , Kimber Stephen , Morris Stephen , Rose Terry J. , Archanjo Braulio S. , Tang Caixian , Franks Ashley E. , Diao Hui , Schweizer Steffen , Tobin Mark J. , Klein Annaleise R. , Vongsvivut Jitraporn , Chang Shery L. Y. , Kopittke Peter M. , Cowie Annette 
Published: September 2022

AbstractThe soil carbon (C) saturation concept suggests an upper limit to the storage of soil organic carbon (SOC). It is set by the mechanisms that protect soil organic matter from mineralization. Biochar has the capacity to protect new C, including rhizodeposits and microbial necromass. However, the decadal-scale mechanisms by which biochar influences the molecular diversity, spatial heterogeneity, and temporal changes in SOC persistence, remain unresolved. Here we show that the soil C storage ceiling of a Ferralsol under subtropical pasture was raised by a second application of Eucalyptus saligna biochar 8.2 years after the first application—the first application raised the soil C storage ceiling by 9.3 Mg new C ha−1 and the second application raised this by another 2.3 Mg new C ha−1. Linking direct visual evidence from one-, two-, and three-dimensional analyses with SOC quantification, we found high spatial heterogeneity of C functional groups that resulted in the retention of rhizodeposits and microbial necromass in microaggregates (53–250 µm) and the mineral fraction (<53 µm). Microbial C-use efficiency was concomitantly increased by lowering specific enzyme activities, contributing to the decreased mineralization of native SOC by 18%. We suggest that the SOC ceiling can be lifted using biochar in (sub)tropical grasslands globally.
Earlier ice loss accelerates lake warming in the Northern Hemisphere
Authors: Li Xinyu , Peng Shushi , Xi Yi , Woolway R. Iestyn , Liu Gang 
Published: September 2022

AbstractHow lake temperatures across large geographic regions are responding to widespread alterations in ice phenology (i.e., the timing of seasonal ice formation and loss) remains unclear. Here, we analyse satellite data and global-scale simulations to investigate the contribution of long-term variations in the seasonality of lake ice to surface water temperature trends across the Northern Hemisphere. Our analysis suggests a widespread excess lake surface warming during the months of ice-off which is, on average, 1.4 times that calculated during the open-water season. This excess warming is influenced predominantly by an 8-day advancement in the average timing of ice break-up from 1979 to 2020. Until the permanent loss of lake ice in the future, excess lake warming may be further amplified due to projected future alterations in lake ice phenology. Excess lake warming will likely alter within-lake physical and biogeochemical processes with numerous implications for lake ecosystems.
Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells
Authors: Adamik Juraj , Munson Paul V. , Hartmann Felix J. , Combes Alexis J. , Pierre Philippe , Krummel Matthew F. , Bendall Sean C. , Argüello Rafael J. , Butterfield Lisa H. 
Published: September 2022

AbstractCellular metabolism underpins immune cell functionality, yet our understanding of metabolic influences in human dendritic cell biology and their ability to orchestrate immune responses is poorly developed. Here, we map single-cell metabolic states and immune profiles of inflammatory and tolerogenic monocytic dendritic cells using recently developed multiparametric approaches. Single-cell metabolic pathway activation scores reveal simultaneous engagement of multiple metabolic pathways in distinct monocytic dendritic cell differentiation stages. GM-CSF/IL4-induce rapid reprogramming of glycolytic monocytes and transient co-activation of mitochondrial pathways followed by TLR4-dependent maturation of dendritic cells. Skewing of the mTOR:AMPK phosphorylation balance and upregulation of OXPHOS, glycolytic and fatty acid oxidation metabolism underpin metabolic hyperactivity and an immunosuppressive phenotype of tolerogenic dendritic cells, which exhibit maturation-resistance and a de-differentiated immune phenotype marked by unique immunoregulatory receptor signatures. This single-cell dataset provides important insights into metabolic pathways impacting the immune profiles of human dendritic cells.
Spatiotemporal control of signal-driven enzymatic reaction in artificial cell-like polymersomes
Authors: Seo Hanjin , Lee Hyomin 
Published: September 2022

AbstractLiving cells can spatiotemporally control biochemical reactions to dynamically assemble membraneless organelles and remodel cytoskeleton. Herein, we present a microfluidic approach to prepare semi-permeable polymersomes comprising of amphiphilic triblock copolymer to achieve external signal-driven complex coacervation as well as biophysical reconstitution of cytoskeleton within the polymersomes. We also show that the microfluidic synthesis of polymersomes enables precise control over size, efficient encapsulation of enzymes as well as regulation of substrates without the use of biopores. Moreover, we demonstrate that the resulting triblock copolymer-based membrane in polymersomes is size-selective, allowing phosphoenol pyruvate to readily diffuse through the membrane and induce enzymatic reaction and successive coacervation or actin polymerization in the presence of pyruvate kinase and adenosine diphosphate inside the polymersomes. We envision that the Pluronic-based polymersomes presented in this work will shed light in the design of in vitro enzymatic reactions in artificial cell-like vesicles.
Chimeric natural products derived from medermycin and the nature-inspired construction of their polycyclic skeletons
Authors: Yin Shupeng , Liu Zhi , Shen Jingjing , Xia Yuwei , Wang Weihong , Gui Pengyan , Jia Qian , Kachanuban Konthorn , Zhu Weiming , Fu Peng 
Published: September 2022

AbstractMedermycin, produced by Streptomyces species, represents a family of antibiotics with significant activity against Gram-positive pathogens. The biosynthesis of this family of natural products has been studied, and new skeletons related to medermycin have rarely been reported until recently. Herein, we report eight chimeric medermycin-type natural products with unusual polycyclic skeletons. The formation of these compounds features some key nonenzymatic steps, which inspired us to construct complex polycyclic skeletons via three efficient one-step reactions under mild conditions. This strategy was further developed to efficiently synthesize analogues for biological activity studies. The synthetic compounds, chimedermycins L and M, and sekgranaticin B, show potent antibacterial activity against Staphylococcus aureus, methicillin-resistant Staphylococcus aureus, and methicillin-resistant Staphylococcus epidermidis. This work paves the way for understanding the nonenzymatic formation of complex natural products and using it to synthesize natural product derivatives.
Wireless charging-mediated angiogenesis and nerve repair by adaptable microporous hydrogels from conductive building blocks
Authors: Hsu Ru-Siou , Li Ssu-Ju , Fang Jen-Hung , Lee I-Chi , Chu Li-An , Lo Yu-Chun , Lu Yu-Jen , Chen You-Yin , Hu Shang-Hsiu 
Published: September 2022

AbstractTraumatic brain injury causes inflammation and glial scarring that impede brain tissue repair, so stimulating angiogenesis and recovery of brain function remain challenging. Here we present an adaptable conductive microporous hydrogel consisting of gold nanoyarn balls-coated injectable building blocks possessing interconnected pores to improve angiogenesis and recovery of brain function in traumatic brain injury. We show that following minimally invasive implantation, the adaptable hydrogel is able to fill defects with complex shapes and regulate the traumatic brain injury environment in a mouse model. We find that placement of this injectable hydrogel at peri-trauma regions enhances mature brain-derived neurotrophic factor by 180% and improves angiogenesis by 250% in vivo within 2 weeks after electromagnetized stimulation, and that these effects facilitate neuron survival and motor function recovery by 50%. We use blood oxygenation level-dependent functional neuroimaging to reveal the successful restoration of functional brain connectivity in the corticostriatal and corticolimbic circuits.
Fabrication of Salvinia-inspired surfaces for hydrodynamic drag reduction by capillary-force-induced clustering
Authors: Kim Minsu , Yoo Seunghoon , Jeong Hoon Eui , Kwak Moon Kyu 
Published: September 2022

AbstractFor decades, bioinspired functional materials have been attracting the interest of many researchers for their remarkable characteristics. In particular, some plant leaves are well known for their inherent superhydrophobic nature. Salvinia molesta, a free-floating aquatic fern, has egg-beater-shaped hierarchical trichomes on its surface of leaves. Due to the unique structure and complex wettability of the hairs, this plant has the ability to maintain a stable thick air layer upon the structure when it is submerged underwater. Often referred to as the “Salvinia Effect,” this property is expected to be suitable for use in hydrodynamic drag reduction. However, due to the complex shape of the trichome, currently applied fabrication methods are using a three-dimensional printing system, which is not applicable to mass production because of its severely limited productivity. In this work, artificial Salvinia leaf inspired by S. molesta was fabricated using a conventional soft lithography method assisted with capillary-force-induced clustering of micropillar array. The fabrication method suggested in this work proposes a promising strategy for the manufacturing of Salvinia-inspired hydrodynamic drag reduction surfaces.
All-fluorescence white organic light-emitting diodes with record-beating power efficiencies over 130 lm W‒1 and small roll-offs
Authors: Liu Hao , Fu Yan , Tang Ben Zhong , Zhao Zujin 
Published: September 2022

AbstractImproving power efficiency (PE) and reducing roll-off are of significant importance for the commercialization of white organic light-emitting diodes (WOLEDs) in consideration of energy conservation. Herein, record-beating PE of 130.7 lm W−1 and outstanding external quantum efficiency (EQE) of 31.1% are achieved in all-fluorescence two-color WOLEDs based on a simple sandwich configuration of emitting layer consisting of sky-blue and orange delayed fluorescence materials. By introducing a red fluorescence dopant, all-fluorescence three-color WOLEDs with high color rendering index are constructed based on an interlayer sensitization configuration, furnishing ultrahigh PE of 110.7 lm W−1 and EQE of 30.8%. More importantly, both two-color and three-color WOLEDs maintain excellent PEs at operating luminance with smaller roll-offs than the reported state-of-the-art WOLEDs, and further device optimization realizes outstanding comprehensive performances of low driving voltages, large luminance, high PEs and long operational lifetimes. The underlying mechanisms of the impressive device performances are elucidated by host-tuning effect and electron-trapping effect, providing useful guidance for the development of energy-conserving all-fluorescence WOLEDs.
Learning two-phase microstructure evolution using neural operators and autoencoder architectures
Authors: Oommen Vivek , Shukla Khemraj , Goswami Somdatta , Dingreville Rémi , Karniadakis George Em 
Published: September 2022

AbstractPhase-field modeling is an effective but computationally expensive method for capturing the mesoscale morphological and microstructure evolution in materials. Hence, fast and generalizable surrogate models are needed to alleviate the cost of computationally taxing processes such as in optimization and design of materials. The intrinsic discontinuous nature of the physical phenomena incurred by the presence of sharp phase boundaries makes the training of the surrogate model cumbersome. We develop a framework that integrates a convolutional autoencoder architecture with a deep neural operator (DeepONet) to learn the dynamic evolution of a two-phase mixture and accelerate time-to-solution in predicting the microstructure evolution. We utilize the convolutional autoencoder to provide a compact representation of the microstructure data in a low-dimensional latent space. After DeepONet is trained in the latent space, it can be used to replace the high-fidelity phase-field numerical solver in interpolation tasks or to accelerate the numerical solver in extrapolation tasks.
Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations
Authors: Tumpa Katarina , Šatović Zlatko , Liber Zlatko , Vidaković Antonio , Idžojtić Marilena , Ježić Marin , Ćurković-Perica Mirna , Poljak Igor 
Published: September 2022

AbstractGene flow between cultivated and wild gene pools is common in the contact zone between agricultural lands and natural habitats and can be used to study the development of adaptations and selection of novel varieties. This is likely the case in the northern Adriatic region, where centuries-old cultivated orchards of sweet chestnut (Castanea sativa Mill.) are planted within the natural distribution area of the species. Thus, we investigated the population structure of several orchards of sweet chestnuts. Furthermore, the genetic background of three toponymous clonal varieties was explored. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this research, and both grafted and non-grafted individuals were included in this study. Five closely related clones were identified, which represent a singular, polyclonal marron variety, found in all three cultivation areas. Furthermore, many hybrids, a result of breeding between cultivated and wild chestnuts, have been found. Analyzed semi-wild orchards defined by a diverse genetic structure, represent a hotspot for further selection and could result in creation of locally adapted, high-yielding varieties.