bluuebunny/crossref_metadata_2025_split huggingface dataset:
Winter Precipitation Changes in California Under Global Warming: Contributions of CO2, Uniform SST Warming, and SST Change Patterns
Authors: Dong Lu , Leung L. Ruby 
Published: February 2021

AbstractClimate models project a wetting winter over California, distinct from the drying in all other Mediterranean climate regions under warming. Dynamic effect via an eastward extension of the westerly jet stream over the North Pacific is the root cause for the wetting California. Utilizing four sets of prescribed‐SST (sea surface temperature) simulations, the relative effects of direct CO2 radiative forcing, uniform SST warming, and SST change patterns are investigated. The wetting winter is dominated by uniform SST warming mainly through its effect on the jet extension. As a fundamental response to the enhanced upper‐tropospheric warming in the tropics, the jet extension in coupled simulations is well reproduced under uniform SST warming and robust among models. An El Niño‐like SST warming pattern has a secondary contribution to the jet extension via atmospheric teleconnection, but with large inter‐model spread. Relative to the SST forcing, the direct CO2 radiative effect is negligible.
Changing Lengths of the Four Seasons by Global Warming
Authors: Wang Jiamin , Guan Yuping , Wu Lixin , Guan Xiaodan , Cai Wenju , Huang Jianping , Dong Wenjie , Zhang Banglin 
Published: February 2021

AbstractHow long will the four seasons be by 2100? Increasing evidence suggests that the length of a single season or in regional scales has changed under global warming, but a hemispherical‐scale response of the four seasons in the past and future remains unknown. We find that summer in the Northern Hemisphere midlatitudes has lengthened, whereas winter has shortened, owing to shifts in their onsets and withdrawals, accompanied by shorter spring and autumn. Such changes in lengths and onsets can be mainly attributed to greenhouse‐warming. Even if the current warming rate does not accelerate, changes in seasons will still be exacerbated in the future. Under the business‐as‐usual scenario, summer is projected to last nearly half a year, but winter less than 2 months by 2100. The changing seasonal clock signifies disturbed agriculture seasons and rhythm of species activities, more frequent heat waves, storms and wildfires, amounting to increased risks to humanity.
Physical Origin of Short Scale Plasma Structures in the Auroral F Region
Authors: Bisai N. , Sen A. 
Published: February 2021

AbstractThe drift instability in the auroral F region of the ionosphere is known to create long scale finger like plasma structures in the presence of a density inhomogeneity and an ambient electric field. These structures elongate mainly along the density inhomogeneity direction. In situ measurements as well as scattering experiments have also revealed the existence of small scale structures in this region. The authors propose that such structures are created due to the breakup of the long scale structures on account of their differential stretching from sheared electric fields. Using heuristic physical arguments and dimensional analysis the authors derive a general criterion for the onset of such breakups. The analytic results are validated from numerical simulations of the full set of basic nonlinear equations describing the instability and should prove useful in the prediction and interpretation of the spread F in the high latitude region.
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions
Authors: Krainer Georg , Welsh Timothy J. , Joseph Jerelle A. , Espinosa Jorge R. , Wittmann Sina , de Csilléry Ella , Sridhar Akshay , Toprakcioglu Zenon , Gudiškytė Giedre , Czekalska Magdalena A. , Arter William E. , Guillén-Boixet Jordina , Franzmann Titus M. , Qamar Seema , George-Hyslop Peter St , Hyman Anthony A. , Collepardo-Guevara Rosana , Alberti Simon , Knowles Tuomas P. J. 
Published: February 2021

AbstractLiquid–liquid phase separation of proteins underpins the formation of membraneless compartments in living cells. Elucidating the molecular driving forces underlying protein phase transitions is therefore a key objective for understanding biological function and malfunction. Here we show that cellular proteins, which form condensates at low salt concentrations, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations. By bringing together experiments and simulations, we demonstrate that this reentrant phase transition in the high-salt regime is driven by hydrophobic and non-ionic interactions, and is mechanistically distinct from the low-salt regime, where condensates are additionally stabilized by electrostatic forces. Our work thus sheds light on the cooperation of hydrophobic and non-ionic interactions as general driving forces in the condensation process, with important implications for aberrant function, druggability, and material properties of biomolecular condensates.
Inference and analysis of cell-cell communication using CellChat
Authors: Jin Suoqin , Guerrero-Juarez Christian F. , Zhang Lihua , Chang Ivan , Ramos Raul , Kuan Chen-Hsiang , Myung Peggy , Plikus Maksim V. , Nie Qing 
Published: February 2021

AbstractUnderstanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build cell-cell communication atlases in diverse tissues.
Population-specific causal disease effect sizes in functionally important regions impacted by selection
Authors: Shi Huwenbo , Gazal Steven , Kanai Masahiro , Koch Evan M. , Schoech Armin P. , Siewert Katherine M. , Kim Samuel S. , Luo Yang , Amariuta Tiffany , Huang Hailiang , Okada Yukinori , Raychaudhuri Soumya , Sunyaev Shamil R. , Price Alkes L. 
Published: February 2021

AbstractMany diseases exhibit population-specific causal effect sizes with trans-ethnic genetic correlations significantly less than 1, limiting trans-ethnic polygenic risk prediction. We develop a new method, S-LDXR, for stratifying squared trans-ethnic genetic correlation across genomic annotations, and apply S-LDXR to genome-wide summary statistics for 31 diseases and complex traits in East Asians (average N = 90K) and Europeans (average N = 267K) with an average trans-ethnic genetic correlation of 0.85. We determine that squared trans-ethnic genetic correlation is 0.82× (s.e. 0.01) depleted in the top quintile of background selection statistic, implying more population-specific causal effect sizes. Accordingly, causal effect sizes are more population-specific in functionally important regions, including conserved and regulatory regions. In regions surrounding specifically expressed genes, causal effect sizes are most population-specific for skin and immune genes, and least population-specific for brain genes. Our results could potentially be explained by stronger gene-environment interaction at loci impacted by selection, particularly positive selection.
Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome
Authors: Chen Congying , Zhou Yunyan , Fu Hao , Xiong Xinwei , Fang Shaoming , Jiang Hui , Wu Jinyuan , Yang Hui , Gao Jun , Huang Lusheng 
Published: February 2021

AbstractGut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.
Van der Waals engineering of ferroelectric heterostructures for long-retention memory
Authors: Wang Xiaowei , Zhu Chao , Deng Ya , Duan Ruihuan , Chen Jieqiong , Zeng Qingsheng , Zhou Jiadong , Fu Qundong , You Lu , Liu Song , Edgar James H. , Yu Peng , Liu Zheng 
Published: February 2021

AbstractThe limited memory retention for a ferroelectric field-effect transistor has prevented the commercialization of its nonvolatile memory potential using the commercially available ferroelectrics. Here, we show a long-retention ferroelectric transistor memory cell featuring a metal-ferroelectric-metal-insulator-semiconductor architecture built from all van der Waals single crystals. Our device exhibits 17 mV dec−1 operation, a memory window larger than 3.8 V, and program/erase ratio greater than 107. Thanks to the trap-free interfaces and the minimized depolarization effects via van der Waals engineering, more than 104 cycles endurance, a 10-year memory retention and sub-5 μs program/erase speed are achieved. A single pulse as short as 100 ns is enough for polarization reversal, and a 4-bit/cell operation of a van der Waals ferroelectric transistor is demonstrated under a 100 ns pulse train. These device characteristics suggest that van der Waals engineering is a promising direction to improve ferroelectronic memory performance and reliability for future applications.
Active-site loop variations adjust activity and selectivity of the cumene dioxygenase
Authors: Heinemann Peter M. , Armbruster Daniel , Hauer Bernhard 
Published: February 2021

AbstractActive-site loops play essential roles in various catalytically important enzyme properties like activity, selectivity, and substrate scope. However, their high flexibility and diversity makes them challenging to incorporate into rational enzyme engineering strategies. Here, we report the engineering of hot-spots in loops of the cumene dioxygenase fromPseudomonas fluorescensIP01 with high impact on activity, regio- and enantioselectivity. Libraries based on alanine scan, sequence alignments, and deletions along with a novel insertion approach result in up to 16-fold increases in activity and the formation of novel products and enantiomers. CAVER analysis suggests possible increases in the active pocket volume and formation of new active-site tunnels, suggesting additional degrees of freedom of the substrate in the pocket. The combination of identified hot-spots with the Linker In Loop Insertion approach proves to be a valuable addition to future loop engineering approaches for enhanced biocatalysts.
Tuning nonlinear damping in graphene nanoresonators by parametric–direct internal resonance
Authors: Keşkekler Ata , Shoshani Oriel , Lee Martin , van der Zant Herre S. J. , Steeneken Peter G. , Alijani Farbod 
Published: February 2021

AbstractMechanical sources of nonlinear damping play a central role in modern physics, from solid-state physics to thermodynamics. The microscopic theory of mechanical dissipation suggests that nonlinear damping of a resonant mode can be strongly enhanced when it is coupled to a vibration mode that is close to twice its resonance frequency. To date, no experimental evidence of this enhancement has been realized. In this letter, we experimentally show that nanoresonators driven into parametric-direct internal resonance provide supporting evidence for the microscopic theory of nonlinear dissipation. By regulating the drive level, we tune the parametric resonance of a graphene nanodrum over a range of 40–70 MHz to reach successive two-to-one internal resonances, leading to a nearly two-fold increase of the nonlinear damping. Our study opens up a route towards utilizing modal interactions and parametric resonance to realize resonators with engineered nonlinear dissipation over wide frequency range.
Telomeres reforged with non-telomeric sequences in mouse embryonic stem cells
Authors: Kim Chuna , Sung Sanghyun , Kim Jong-Seo , Lee Hyunji , Jung Yoonseok , Shin Sanghee , Kim Eunkyeong , Seo Jenny J. , Kim Jun , Kim Daeun , Niida Hiroyuki , Kim V. Narry , Park Daechan , Lee Junho 
Published: February 2021

AbstractTelomeres are part of a highly refined system for maintaining the stability of linear chromosomes. Most telomeres rely on simple repetitive sequences and telomerase enzymes to protect chromosomal ends; however, in some species or telomerase-defective situations, an alternative lengthening of telomeres (ALT) mechanism is used. ALT mainly utilises recombination-based replication mechanisms and the constituents of ALT-based telomeres vary depending on models. Here we show that mouse telomeres can exploit non-telomeric, unique sequences in addition to telomeric repeats. We establish that a specific subtelomeric element, the mouse template for ALT (mTALT), is used for repairing telomeric DNA damage as well as for composing portions of telomeres in ALT-dependent mouse embryonic stem cells. Epigenomic and proteomic analyses before and after ALT activation reveal a high level of non-coding mTALT transcripts despite the heterochromatic nature of mTALT-based telomeres. After ALT activation, the increased HMGN1, a non-histone chromosomal protein, contributes to the maintenance of telomere stability by regulating telomeric transcription. These findings provide a molecular basis to study the evolution of new structures in telomeres.
Depth-dependent peridotite-melt interaction and the origin of variable silica in the cratonic mantle
Authors: Tomlinson Emma L. , Kamber Balz S. 
Published: February 2021

AbstractPeridotites from the thick roots of Archaean cratons are known for their compositional diversity, whose origin remains debated. We report thermodynamic modelling results for reactions between peridotite and ascending mantle melts. Reaction between highly magnesian melt (komatiite) and peridotite leads to orthopyroxene crystallisation, yielding silica-rich harzburgite. By contrast, shallow basalt-peridotite reaction leads to olivine enrichment, producing magnesium-rich dunites that cannot be generated by simple melting. Komatiite is spatially and temporally associated with basalt within Archaean terranes indicating that modest-degree melting co-existed with advanced melting. We envisage a relatively cool mantle that experienced episodic hot upwellings, the two settings could have coexisted if roots of nascent cratons became locally strongly extended. Alternatively, deep refractory silica-rich residues could have been detached from shallower dunitic lithosphere prior to cratonic amalgamation. Regardless, the distinct Archaean melting-reaction environments collectively produced skewed and multi-modal olivine distributions in the cratonic lithosphere and bimodal mafic-ultramafic volcanism at surface.
Correlating Josephson supercurrents and Shiba states in quantum spins unconventionally coupled to superconductors
Authors: Küster Felix , Montero Ana M. , Guimarães Filipe S. M. , Brinker Sascha , Lounis Samir , Parkin Stuart S. P. , Sessi Paolo 
Published: February 2021

AbstractLocal spins coupled to superconductors give rise to several emerging phenomena directly linked to the competition between Cooper pair formation and magnetic exchange. These effects are generally scrutinized using a spectroscopic approach which relies on detecting the in-gap bound modes arising from Cooper pair breaking, the so-called Yu-Shiba-Rusinov (YSR) states. However, the impact of local magnetic impurities on the superconducting order parameter remains largely unexplored. Here, we use scanning Josephson spectroscopy to directly visualize the effect of magnetic perturbations on Cooper pair tunneling between superconducting electrodes at the atomic scale. By increasing the magnetic impurity orbital occupation by adding one electron at a time, we reveal the existence of a direct correlation between Josephson supercurrent suppression and YSR states. Moreover, in the metallic regime, we detect zero bias anomalies which break the existing framework based on competing Kondo and Cooper pair singlet formation mechanisms. Based on first-principle calculations, these results are rationalized in terms of unconventional spin-excitations induced by the finite magnetic anisotropy energy. Our findings have far reaching implications for phenomena that rely on the interplay between quantum spins and superconductivity.
Mapping ticks and tick-borne pathogens in China
Authors: Zhao Guo-Ping , Wang Yi-Xing , Fan Zheng-Wei , Ji Yang , Liu Ming-jin , Zhang Wen-Hui , Li Xin-Lou , Zhou Shi-Xia , Li Hao , Liang Song , Liu Wei , Yang Yang , Fang Li-Qun 
Published: February 2021

AbstractUnderstanding ecological niches of major tick species and prevalent tick-borne pathogens is crucial for efficient surveillance and control of tick-borne diseases. Here we provide an up-to-date review on the spatial distributions of ticks and tick-borne pathogens in China. We map at the county level 124 tick species, 103 tick-borne agents, and human cases infected with 29 species (subspecies) of tick-borne pathogens that were reported in China during 1950−2018.Haemaphysalis longicornisis found to harbor the highest variety of tick-borne agents, followed byIxodes persulcatus,Dermacentor nutalliandRhipicephalus microplus. Using a machine learning algorithm, we assess ecoclimatic and socioenvironmental drivers for the distributions of 19 predominant vector ticks and two tick-borne pathogens associated with the highest disease burden. The model-predicted suitable habitats for the 19 tick species are 14‒476% larger in size than the geographic areas where these species were detected, indicating severe under-detection. Tick species harboring pathogens of imminent threats to public health should be prioritized for more active field surveillance.
Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface
Authors: Ding Xinqiang , Lin Xingcheng , Zhang Bin 
Published: February 2021

AbstractThe three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30 nm fiber.
Bedside functional monitoring of the dynamic brain connectivity in human neonates
Authors: Baranger Jerome , Demene Charlie , Frerot Alice , Faure Flora , Delanoë Catherine , Serroune Hicham , Houdouin Alexandre , Mairesse Jerome , Biran Valerie , Baud Olivier , Tanter Mickael 
Published: February 2021

AbstractClinicians have long been interested in functional brain monitoring, as reversible functional losses often precedes observable irreversible structural insults. By characterizing neonatal functional cerebral networks, resting-state functional connectivity is envisioned to provide early markers of cognitive impairments. Here we present a pioneering bedside deep brain resting-state functional connectivity imaging at 250-μm resolution on human neonates using functional ultrasound. Signal correlations between cerebral regions unveil interhemispheric connectivity in very preterm newborns. Furthermore, fine-grain correlations between homologous pixels are consistent with white/grey matter organization. Finally, dynamic resting-state connectivity reveals a significant occurrence decrease of thalamo-cortical networks for very preterm neonates as compared to control term newborns. The same method also shows abnormal patterns in a congenital seizure disorder case compared with the control group. These results pave the way to infants’ brain continuous monitoring and may enable the identification of abnormal brain development at the bedside.
Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism
Authors: Jensen Benjamin A. H. , Holm Jacob B. , Larsen Ida S. , von Burg Nicole , Derer Stefanie , Sonne Si B. , Pærregaard Simone I. , Damgaard Mads V. , Indrelid Stine A. , Rivollier Aymeric , Agrinier Anne-Laure , Sulek Karolina , Arnoldussen Yke J. , Fjære Even , Marette André , Angell Inga L. , Rudi Knut , Treebak Jonas T. , Madsen Lise , Åkesson Caroline Piercey , Agace William , Sina Christian , Kleiveland Charlotte R. , Kristiansen Karsten , Lea Tor E. 
Published: February 2021

AbstractInteractions between host and gut microbial communities are modulated by diets and play pivotal roles in immunological homeostasis and health. We show that exchanging the protein source in a high fat, high sugar, westernized diet from casein to whole-cell lysates of the non-commensal bacterium Methylococcus capsulatus Bath is sufficient to reverse western diet-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22 °C) and at thermoneutrality (T30 °C). Concomitant with microbiota changes, mice fed the Methylococcus-based western diet exhibit improved glucose regulation, reduced body and liver fat, and diminished hepatic immune infiltration. Intake of the Methylococcu-based diet markedly boosts Parabacteroides abundances in a manner depending on adaptive immunity, and upregulates triple positive (Foxp3+RORγt+IL-17+) regulatory T cells in the small and large intestine. Collectively, these data point to the potential for leveraging the use of McB lysates to improve immunometabolic homeostasis.