bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated single-cell analysis revealed immune dynamics during Ad5-nCoV immunization
Authors: Cao Qiqi , Wu Shipo , Xiao Chuanle , Chen Shuzhen , Chi Xiangyang , Cui Xiuliang , Tang Hao , Su Wenru , Zheng Yingfeng , Zhong Jiayong , Li Zhaomin , Li Fang , Chen Haijia , Hou Lihua , Wang Hongyang , Wen Wen 
Published: August 2021

AbstractCoronavirus disease 2019 (COVID-19), driven by SARS-CoV-2, is a severe infectious disease that has become a global health threat. Vaccines are among the most effective public health tools for combating COVID-19. Immune status is critical for evaluating the safety and response to the vaccine, however, the evolution of the immune response during immunization remains poorly understood. Single-cell RNA sequencing (scRNA-seq) represents a powerful tool for dissecting multicellular behavior and discovering therapeutic antibodies. Herein, by performing scRNA/V(D)J-seq on peripheral blood mononuclear cells from four COVID-19 vaccine trial participants longitudinally during immunization, we revealed enhanced cellular immunity with concerted and cell type-specific IFN responses as well as boosted humoral immunity with SARS-CoV-2-specific antibodies. Based on the CDR3 sequence and germline enrichment, we were able to identify several potential binding antibodies. We synthesized, expressed and tested 21 clones from the identified lineages. Among them, one monoclonal antibody (P3V6-1) exhibited relatively high affinity with the extracellular domain of Spike protein, which might be a promising therapeutic reagent for COVID-19. Overall, our findings provide insights for assessing vaccine through the novel scRNA/V(D)J-seq approach, which might facilitate the development of more potent, durable and safe prophylactic vaccines.
Principles of seed banks and the emergence of complexity from dormancy
Authors: Lennon Jay T. , den Hollander Frank , Wilke-Berenguer Maite , Blath Jochen 
Published: August 2021

AbstractAcross the tree of life, populations have evolved the capacity to contend with suboptimal conditions by engaging in dormancy, whereby individuals enter a reversible state of reduced metabolic activity. The resulting seed banks are complex, storing information and imparting memory that gives rise to multi-scale structures and networks spanning collections of cells to entire ecosystems. We outline the fundamental attributes and emergent phenomena associated with dormancy and seed banks, with the vision for a unifying and mathematically based framework that can address problems in the life sciences, ranging from global change to cancer biology.
The evolution of hematopoietic cells under cancer therapy
Authors: Pich Oriol , Cortes-Bullich Albert , Muiños Ferran , Pratcorona Marta , Gonzalez-Perez Abel , Lopez-Bigas Nuria 
Published: August 2021

AbstractChemotherapies may increase mutagenesis of healthy cells and change the selective pressures in tissues, thus influencing their evolution. However, their contributions to the mutation burden and clonal expansions of healthy somatic tissues are not clear. Here, exploiting the mutational footprint of some chemotherapies, we explore their influence on the evolution of hematopoietic cells. Cells of Acute Myeloid Leukemia (AML) secondary to treatment with platinum-based drugs show the mutational footprint of these drugs, indicating that non-malignant blood cells receive chemotherapy mutations. No trace of the 5-fluorouracil (5FU) mutational signature is found in AMLs secondary to exposure to 5FU, suggesting that cells establishing the leukemia could be quiescent during treatment. Using the platinum-based mutational signature as a barcode, we determine that the clonal expansion originating the secondary AMLs begins after the start of the cytotoxic treatment. Its absence in clonal hematopoiesis cases is consistent with the start of the clonal expansion predating the exposure to platinum-based drugs.
Warm temperature triggers JOX and ST2A-mediated jasmonate catabolism to promote plant growth
Authors: Zhu Tingting , Herrfurth Cornelia , Xin Mingming , Savchenko Tatyana , Feussner Ivo , Goossens Alain , De Smet Ive 
Published: August 2021

AbstractPlants respond to warm temperature by increased elongation growth of organs to enhance cooling capacity. Phytohormones, such as auxin and brassinosteroids, regulate this growth process. However, our view on the players involved in warm temperature-mediated growth remains fragmentary. Here, we show that warm temperature leads to an increased expression of JOXs and ST2A, genes controlling jasmonate catabolism. This leads to an elevated 12HSO4-JA level and consequently to a reduced level of bioactive jasmonates. Ultimately this results in more JAZ proteins, which facilitates plant growth under warm temperature conditions. Taken together, understanding the conserved role of jasmonate signalling during thermomorphogenesis contributes to ensuring food security under a changing climate.
Biomimetic chameleon soft robot with artificial crypsis and disruptive coloration skin
Authors: Kim Hyeonseok , Choi Joonhwa , Kim Kyun Kyu , Won Phillip , Hong Sukjoon , Ko Seung Hwan 
Published: August 2021

AbstractDevelopment of an artificial camouflage at a complete device level remains a vastly challenging task, especially under the aim of achieving more advanced and natural camouflage characteristics via high-resolution camouflage patterns. Our strategy is to integrate a thermochromic liquid crystal layer with the vertically stacked, patterned silver nanowire heaters in a multilayer structure to overcome the limitations of the conventional lateral pixelated scheme through the superposition of the heater-induced temperature profiles. At the same time, the weaknesses of thermochromic camouflage schemes are resolved in this study by utilizing the temperature-dependent resistance of the silver nanowire network as the process variable of the active control system. Combined with the active control system and sensing units, the complete device chameleon model successfully retrieves the local background color and matches its surface color instantaneously with natural transition characteristics to be a competent option for a next-generation artificial camouflage.
The developing mouse coronal suture at single-cell resolution
Authors: Farmer D’Juan T. , Mlcochova Hana , Zhou Yan , Koelling Nils , Wang Guanlin , Ashley Neil , Bugacov Helena , Chen Hung-Jhen , Parvez Riana , Tseng Kuo-Chang , Merrill Amy E. , Maxson Robert E. , Wilkie Andrew O. M. , Crump J. Gage , Twigg Stephen R. F. 
Published: August 2021

AbstractSutures separate the flat bones of the skull and enable coordinated growth of the brain and overlying cranium. The coronal suture is most commonly fused in monogenic craniosynostosis, yet the unique aspects of its development remain incompletely understood. To uncover the cellular diversity within the murine embryonic coronal suture, we generated single-cell transcriptomes and performed extensive expression validation. We find distinct pre-osteoblast signatures between the bone fronts and periosteum, a ligament-like population above the suture that persists into adulthood, and a chondrogenic-like population in the dura mater underlying the suture. Lineage tracing reveals an embryonic Six2+ osteoprogenitor population that contributes to the postnatal suture mesenchyme, with these progenitors being preferentially affected in a Twist1+/−; Tcf12+/− mouse model of Saethre-Chotzen Syndrome. This single-cell atlas provides a resource for understanding the development of the coronal suture and the mechanisms for its loss in craniosynostosis.
Seismicity at the Castor gas reservoir driven by pore pressure diffusion and asperities loading
Authors: Cesca Simone , Stich Daniel , Grigoli Francesco , Vuan Alessandro , López-Comino José Ángel , Niemz Peter , Blanch Estefanía , Dahm Torsten , Ellsworth William L. 
Published: August 2021

AbstractThe 2013 seismic sequence at the Castor injection platform offshore Spain, including three earthquakes of magnitude 4.1, occurred during the initial filling of a planned Underground Gas Storage facility. The Castor sequence is one of the most important cases of induced seismicity in Europe and a rare example of seismicity induced by gas injection into a depleted oil field. Here we use advanced seismological techniques applied to an enhanced waveform dataset, to resolve the geometry of the faults, develop a greatly enlarged seismicity catalog and record details of the rupture kinematics. The sequence occurred by progressive fault failure and unlocking, with seismicity initially migrating away from the injection points, triggered by pore pressure diffusion, and then back again, breaking larger asperities loaded to higher stress and producing the largest earthquakes. Seismicity occurred almost exclusively on a secondary fault, located below the reservoir, dipping opposite from the reservoir bounding fault.
CRISPR/Cas9-engineered inducible gametocyte producer lines as a valuable tool for Plasmodium falciparum malaria transmission research
Authors: Boltryk Sylwia D. , Passecker Armin , Alder Arne , Carrington Eilidh , van de Vegte-Bolmer Marga , van Gemert Geert-Jan , van der Starre Alex , Beck Hans-Peter , Sauerwein Robert W. , Kooij Taco W. A. , Brancucci Nicolas M. B. , Proellochs Nicholas I. , Gilberger Tim-Wolf , Voss Till S. 
Published: August 2021

AbstractThe malaria parasite Plasmodium falciparum replicates inside erythrocytes in the blood of infected humans. During each replication cycle, a small proportion of parasites commits to sexual development and differentiates into gametocytes, which are essential for parasite transmission via the mosquito vector. Detailed molecular investigation of gametocyte biology and transmission has been hampered by difficulties in generating large numbers of these highly specialised cells. Here, we engineer P. falciparum NF54 inducible gametocyte producer (iGP) lines for the routine mass production of synchronous gametocytes via conditional overexpression of the sexual commitment factor GDV1. NF54/iGP lines consistently achieve sexual commitment rates of 75% and produce viable gametocytes that are transmissible by mosquitoes. We also demonstrate that further genetic engineering of NF54/iGP parasites is a valuable tool for the targeted exploration of gametocyte biology. In summary, we believe the iGP approach developed here will greatly expedite basic and applied malaria transmission stage research.
Sondheimer oscillations as a probe of non-ohmic flow in WP2 crystals
Authors: van Delft Maarten R. , Wang Yaxian , Putzke Carsten , Oswald Jacopo , Varnavides Georgios , Garcia Christina A. C. , Guo Chunyu , Schmid Heinz , Süss Vicky , Borrmann Horst , Diaz Jonas , Sun Yan , Felser Claudia , Gotsmann Bernd , Narang Prineha , Moll Philip J. W. 
Published: August 2021

AbstractAs conductors in electronic applications shrink, microscopic conduction processes lead to strong deviations from Ohm’s law. Depending on the length scales of momentum conserving (lMC) and relaxing (lMR) electron scattering, and the device size (d), current flows may shift from ohmic to ballistic to hydrodynamic regimes. So far, an in situ methodology to obtain these parameters within a micro/nanodevice is critically lacking. In this context, we exploit Sondheimer oscillations, semi-classical magnetoresistance oscillations due to helical electronic motion, as a method to obtain lMR even when lMR ≫ d. We extract lMR from the Sondheimer amplitude in WP2, at temperatures up to T ~ 40 K, a range most relevant for hydrodynamic transport phenomena. Our data on μm-sized devices are in excellent agreement with experimental reports of the bulk lMR and confirm that WP2 can be microfabricated without degradation. These results conclusively establish Sondheimer oscillations as a quantitative probe of lMR in micro-devices.
A microRNA panel compared to environmental and polygenic scores for colorectal cancer risk prediction
Authors: Raut Janhavi R. , Schöttker Ben , Holleczek Bernd , Guo Feng , Bhardwaj Megha , Miah Kaya , Schrotz-King Petra , Brenner Hermann 
Published: August 2021

AbstractCirculating microRNAs (miRNAs) could improve colorectal cancer (CRC) risk prediction. Here, we derive a blood-based miRNA panel and evaluate its ability to predict CRC occurrence in a population-based cohort of adults aged 50–75 years. Forty-one miRNAs are preselected from independent studies and measured by quantitative-real-time-polymerase-chain-reaction in serum collected at baseline of 198 participants who develop CRC during 14 years of follow-up and 178 randomly selected controls. A 7-miRNA score is derived by logistic regression. Its predictive ability, quantified by the optimism-corrected area-under-the-receiver-operating-characteristic-curve (AUC) using .632+ bootstrap is 0.794. Predictive ability is compared to that of an environmental risk score (ERS) based on known risk factors and a polygenic risk score (PRS) based on 140 previously identified single-nucleotide-polymorphisms. In participants with all scores available, optimism-corrected-AUC is 0.802 for the 7-miRNA score, while AUC (95% CI) is 0.557 (0.498–0.616) for the ERS and 0.622 (0.564–0.681) for the PRS.
Real space electron delocalization, resonance, and aromaticity in chemistry
Authors: Reuter Leonard , Lüchow Arne 
Published: August 2021

AbstractChemists explaining a molecule’s stability and reactivity often refer to the concepts of delocalization, resonance, and aromaticity. Resonance is commonly discussed within valence bond theory as the stabilizing effect of mixing different Lewis structures. Yet, most computational chemists work with delocalized molecular orbitals, which are also usually employed to explain the concept of aromaticity, a ring delocalization in cyclic planar systems which abide certain number rules. However, all three concepts lack a real space definition, that is not reliant on orbitals or specific wave function expansions. Here, we outline a redefinition from first principles: delocalization means that likely electron arrangements are connected via paths of high probability density in the many-electron real space. In this picture, resonance is the consideration of additional electron arrangements, which offer alternative paths. Most notably, the famous 4n + 2 Hückel rule is generalized and derived from nothing but the antisymmetry of fermionic wave functions.
Abrupt hippocampal remapping signals resolution of memory interference
Authors: Wanjia Guo , Favila Serra E. , Kim Ghootae , Molitor Robert J. , Kuhl Brice A. 
Published: August 2021

AbstractRemapping refers to a decorrelation of hippocampal representations of similar spatial environments. While it has been speculated that remapping may contribute to the resolution of episodic memory interference in humans, direct evidence is surprisingly limited. We tested this idea using high-resolution, pattern-based fMRI analyses. Here we show that activity patterns in human CA3/dentate gyrus exhibit an abrupt, temporally-specific decorrelation of highly similar memory representations that is precisely coupled with behavioral expressions of successful learning. The magnitude of this learning-related decorrelation was predicted by the amount of pattern overlap during initial stages of learning, with greater initial overlap leading to stronger decorrelation. Finally, we show that remapped activity patterns carry relatively more information about learned episodic associations compared to competing associations, further validating the learning-related significance of remapping. Collectively, these findings establish a critical link between hippocampal remapping and episodic memory interference and provide insight into why remapping occurs.
Graded bulk-heterojunction enables 17% binary organic solar cells via nonhalogenated open air coating
Authors: Zhang Ying , Liu Kuan , Huang Jiaming , Xia Xinxin , Cao Jiupeng , Zhao Guangming , Fong Patrick W. K. , Zhu Ye , Yan Feng , Yang Yang , Lu Xinhui , Li Gang 
Published: August 2021

AbstractGraded bulk-heterojunction (G-BHJ) with well-defined vertical phase separation has potential to surpass classical BHJ in organic solar cells (OSCs). In this work, an effective G-BHJ strategy via nonhalogenated solvent sequential deposition is demonstrated using nonfullerene acceptor (NFA) OSCs. Spin-coated G-BHJ OSCs deliver an outstanding 17.48% power conversion efficiency (PCE). Depth-profiling X-ray photoelectron spectroscopy (DP-XPS) and angle-dependent grazing incidence X-ray diffraction (GI-XRD) techniques enable the visualization of polymer/NFA composition and crystallinity gradient distributions, which benefit charge transport, and enable outstanding thick OSC PCEs (16.25% for 300 nm, 14.37% for 500 nm), which are among the highest reported. Moreover, the nonhalogenated solvent enabled G-BHJ OSC via open-air blade coating and achieved a record 16.77% PCE. The blade-coated G-BHJ has drastically different D-A crystallization kinetics, which suppresses the excessive aggregation induced unfavorable phase separation in BHJ. All these make G-BHJ a feasible and promising strategy towards highly efficient, eco- and manufacture friendly OSCs.
Evidence for ligand- and solvent-induced disproportionation of uranium(IV)
Authors: Du Jingzhen , Douair Iskander , Lu Erli , Seed John A. , Tuna Floriana , Wooles Ashley J. , Maron Laurent , Liddle Stephen T. 
Published: August 2021

AbstractDisproportionation, where a chemical element converts its oxidation state to two different ones, one higher and one lower, underpins the fundamental chemistry of metal ions. The overwhelming majority of uranium disproportionations involve uranium(III) and (V), with a singular example of uranium(IV) to uranium(V/III) disproportionation known, involving a nitride to imido/triflate transformation. Here, we report a conceptually opposite disproportionation of uranium(IV)-imido complexes to uranium(V)-nitride/uranium(III)-amide mixtures. This is facilitated by benzene, but not toluene, since benzene engages in a redox reaction with the uranium(III)-amide product to give uranium(IV)-amide and reduced arene. These disproportionations occur with potassium, rubidium, and cesium counter cations, but not lithium or sodium, reflecting the stability of the corresponding alkali metal-arene by-products. This reveals an exceptional level of ligand- and solvent-control over a key thermodynamic property of uranium, and is complementary to isolobal uranium(V)-oxo disproportionations, suggesting a potentially wider prevalence possibly with broad implications for the chemistry of uranium.
NEK1-mediated retromer trafficking promotes blood–brain barrier integrity by regulating glucose metabolism and RIPK1 activation
Authors: Wang Huibing , Qi Weiwei , Zou Chengyu , Xie Zhangdan , Zhang Mengmeng , Naito Masanori Gomi , Mifflin Lauren , Liu Zhen , Najafov Ayaz , Pan Heling , Shan Bing , Li Ying , Zhu Zheng-Jiang , Yuan Junying 
Published: August 2021

AbstractLoss-of-function mutations in NEK1 gene, which encodes a serine/threonine kinase, are involved in human developmental disorders and ALS. Here we show that NEK1 regulates retromer-mediated endosomal trafficking by phosphorylating VPS26B. NEK1 deficiency disrupts endosomal trafficking of plasma membrane proteins and cerebral proteome homeostasis to promote mitochondrial and lysosomal dysfunction and aggregation of α-synuclein. The metabolic and proteomic defects of NEK1 deficiency disrupts the integrity of blood–brain barrier (BBB) by promoting lysosomal degradation of A20, a key modulator of RIPK1, thus sensitizing cerebrovascular endothelial cells to RIPK1-dependent apoptosis and necroptosis. Genetic inactivation of RIPK1 or metabolic rescue with ketogenic diet can prevent postnatal lethality and BBB damage in NEK1 deficient mice. Inhibition of RIPK1 reduces neuroinflammation and aggregation of α-synuclein in the brains of NEK1 deficient mice. Our study identifies a molecular mechanism by which retromer trafficking and metabolism regulates cerebrovascular integrity, cerebral proteome homeostasis and RIPK1-mediated neuroinflammation.
Defining the molecular mechanisms of the mitochondrial permeability transition through genetic manipulation of F-ATP synthase
Authors: Carrer Andrea , Tommasin Ludovica , Šileikytė Justina , Ciscato Francesco , Filadi Riccardo , Urbani Andrea , Forte Michael , Rasola Andrea , Szabò Ildikò , Carraro Michela , Bernardi Paolo 
Published: August 2021

AbstractF-ATP synthase is a leading candidate as the mitochondrial permeability transition pore (PTP) but the mechanism(s) leading to channel formation remain undefined. Here, to shed light on the structural requirements for PTP formation, we test cells ablated for g, OSCP and b subunits, and ρ0 cells lacking subunits a and A6L. Δg cells (that also lack subunit e) do not show PTP channel opening in intact cells or patch-clamped mitoplasts unless atractylate is added. Δb and ΔOSCP cells display currents insensitive to cyclosporin A but inhibited by bongkrekate, suggesting that the adenine nucleotide translocator (ANT) can contribute to channel formation in the absence of an assembled F-ATP synthase. Mitoplasts from ρ0 mitochondria display PTP currents indistinguishable from their wild-type counterparts. In this work, we show that peripheral stalk subunits are essential to turn the F-ATP synthase into the PTP and that the ANT provides mitochondria with a distinct permeability pathway.
The structural dynamics of macropinosome formation and PI3-kinase-mediated sealing revealed by lattice light sheet microscopy
Authors: Quinn Shayne E. , Huang Lu , Kerkvliet Jason G. , Swanson Joel A. , Smith Steve , Hoppe Adam D. , Anderson Robert B. , Thiex Natalie W. , Scott Brandon L. 
Published: August 2021

AbstractMacropinosomes are formed by shaping actin-rich plasma membrane ruffles into large intracellular organelles in a phosphatidylinositol 3-kinase (PI3K)-coordinated manner. Here, we utilize lattice lightsheet microscopy and image visualization methods to map the three-dimensional structure and dynamics of macropinosome formation relative to PI3K activity. We show that multiple ruffling morphologies produce macropinosomes and that the majority form through collisions of adjacent PI3K-rich ruffles. By combining multiple volumetric representations of the plasma membrane structure and PI3K products, we show that PI3K activity begins early throughout the entire ruffle volume and continues to increase until peak activity concentrates at the base of the ruffle after the macropinosome closes. Additionally, areas of the plasma membrane rich in ruffling had increased PI3K activity and produced many macropinosomes of various sizes. Pharmacologic inhibition of PI3K activity had little effect on the rate and morphology of membrane ruffling, demonstrating that early production of 3′-phosphoinositides within ruffles plays a minor role in regulating their morphology. However, 3′-phosphoinositides are critical for the fusogenic activity that seals ruffles into macropinosomes. Taken together, these data indicate that local PI3K activity is amplified in ruffles and serves as a priming mechanism for closure and sealing of ruffles into macropinosomes.