bluuebunny/crossref_metadata_2025 huggingface dataset:
The Forecast Skill of the Summer Precipitation Over Tibetan Plateau Improved by the Adoption of a 3D Sub‐Grid Terrain Solar Radiative Effect Scheme in a Convection‐Permitting Model
Authors: Cai Shuxin , Huang Anning , Zhu Kefeng , Guo Weidong , Wu Yang , Gu Chunlei
Published: June 2023

We have successfully incorporated a 3‐dimensional sub‐grid terrain solar radiative effect (3D STSRE) parameterization scheme into a convection‐permitting Weather Research and Forecasting model (WRF_CPM) in this study. Impacts of 3D STSRE scheme on the ability of WRF_CPM in forecasting the precipitation in summer over the Tibetan Plateau (TP) and nearby regions with complex terrain have been systematically addressed by conducting experiments without and with the 3D STSRE scheme. Results show that the application of 3D STSRE scheme can obviously mitigate the overestimation of surface solar radiation (SSR) and rainfall over TP and nearby regions, especially over the areas with much more rugged terrain (i.e., southern TP) in the WRF_CPM without 3D STSRE scheme. Further mechanism analyses indicate that the decreased surface heating induced by the reduction of SSR reduces the intensity of the thermal‐low pressure over the TP, which leads to the diminished strength of southwesterly winds and thereafter the weaker convergence of moisture flux over the southern TP. Moreover, the weakened surface thermal forcing makes the local atmosphere more stable, suppressing the vertical water vapor transport and local convection. These effects greatly alleviate the overestimation of precipitation over the southern TP produced by the WRF_CPM without the 3D STSRE scheme.
Contrasting Responses of Surface Heat Fluxes to Tropical Deforestation
Authors: Chen Hung‐Chen , Lo Min‐Hui
Published: June 2023

Deforestation alters the exchange of heat, moisture, and momentum between the Earth's surface and the atmosphere, which can significantly affect the surface energy balance and water budget. However, changes in surface heat fluxes in response to deforestation are diverse among multi‐model simulations. This study explores factors that might cause different changes in surface heat fluxes due to tropical deforestation with NCAR Community Land Model. The results show that the changes in surface heat fluxes are related to the mean‐state flux partitioning conditions over the deforested areas. Deforestation tends to decrease both surface heat fluxes under conditions with smaller evaporative fractions (EFs), and tends to decrease the latent heat fluxes and increase the sensible heat fluxes under conditions with greater EFs. A similar relation can be found in the Land Use Model Intercomparison Project, which indicates that the varying simulated flux partitioning conditions might contribute to the diverse changes in surface heat fluxes among models.
The Phase Response of a Rough Rectangular Facet for Radar Sounder Simulations of Both Coherent and Incoherent Scattering
Authors: Gerekos C. , Haynes M. S. , Schroeder D. M. , Blankenship D. D.
Published: June 2023

With radar sounders, coherent backscattering simulations from global planetary digital elevation models (DEMs) typically display a deficit in diffuse clutter, which is mainly due to the implicit assumption that roughness at scales below the resolution of the DEM is absent. Indeed, while polynomial approximations of the phase evolution across the facet allow for fast and mathematically rigorous simulators, the coarse resolution of these planetary DEMs leads to a potentially significant portion of the backscattering response being neglected. In this paper, we derive the analytical phase response of a rough rectangular facet characterized by Gaussian roughness and a Gaussian isotropic correlation function under the linear phase approximation. Formulae for the coherent and incoherent power scattered by such an object are obtained for arbitrary bistatic scattering angles. Validation is done both in isolation and after inclusion in different Stratton‐Chu simulators. In order to illustrate the different uses of such a formulation, we reproduce two lunar radargrams acquired by the Lunar Radar Sounder instrument with a Stratton‐Chu simulator incorporating the proposed rough facet phase integral, and we show that the original radargrams are significantly better‐reproduced than with state‐of‐the‐art methods, at a similar computational cost. We also show how the rough facet integral formulation can be used in isolation to better characterize subglacial water bodies on Earth.
Spain’s Seafaring Sports See Fewer Calm Days
Authors: Cartier Kimberly
Published: June 2023

Knowing the best days for calm or active water activities can strengthen the local economy and help tourists optimize their trips.
Tiny Martian Moon May Be a Chip Off the Old Block
Authors: Barbuzano Javier
Published: June 2023

A close approach to Deimos reveals that its surface does not look like that of an asteroid, hinting at a Martian origin.
Interplanetary Hydrogen Properties Observed From Mars
Authors: Mayyasi M. , Quémerais E. , Koutroumpa D. , Baliukin I. , Titova A. , Izmodenov V. , Clarke J. , Deighan J. , Schneider N. , Curry S.
Published: June 2023

Observations of the Lyman‐α emissions from Interplanetary Hydrogen (IPH) atoms are made from Mars' orbit using a high spectral resolution instrument in echelle configuration. The measurements can uniquely be used to resolve IPH from planetary H emissions and to subsequently determine the brightness, velocity, and thermal broadening of the IPH flow along the instrument line of sight. Planned observations conducted during special IPH campaigns as well as serendipitous observations made of the planetary limb and a comet sighting, both upwind and downwind of the bulk IPH flow direction, are analyzed to determine these properties and to examine the variability of IPH brightness with solar activity through the declining phase of Solar Cycle 24. The results show that the IPH brightness trends with solar irradiance, the flow is fainter downwind than upwind, the IPH brightness is variable and non‐negligible compared with planetary emissions, and that deriving thermal properties of IPH requires higher spectral resolution than is presently available. A heliospheric interface model was used to simulate and further interpret the derived IPH properties. These results can improve the theoretical understanding of solar system dynamics, between the solar wind and the local interstellar medium, by providing empirical constraints to simulations of the global heliosphere from the inner boundary region near 1.6 AU and can guide the development of future interplanetary missions.
Characteristics and Mechanisms of Typhoon‐Induced Decomposition of Organic Matter and Its Implication for Climate Change
Authors: Lao Qibin , Chen Fajin , Jin Guangzhe , Lu Xuan , Chen Chunqing , Zhou Xin , Zhu Qingmei
Published: June 2023

We recently reported that decomposition (as a carbon source) of organic matter (OM) is the dominant process in coastal waters after typhoons, which is contrary to phytoplankton blooms (as a carbon sink) in previous studies. However, the characteristics and mechanisms of typhoon‐induced decomposition and the question whether the decomposition mainly decompose particulate OM (POM) or dissolved OM (DOM) are still unclear. To address these issues, physicochemical parameters and multiple isotopes in the northern South China Sea were investigated before and after Typhoon Merbok (2017). After the typhoon, the chlorophyll‐a (Chl‐a) level decreased (25%), whereas the upwelled bottom/sedimentary OM (SOM) increased in the nearshore due to the severe disturbance caused by the typhoon. In contrast, the Chl‐a level increased (over 3 times) offshore. Nevertheless, a positive apparent oxygen utilization value occurred in both nearshore and offshore, suggesting that decomposition of OM was the dominant biogeochemical process regardless of whether phytoplankton blooms occurred after the typhoon. The decomposed POM in the nearshore was mainly from the SOM, while the offshore was primarily from locally produced fresh phytoplankton. The decomposition of OM contributed to 66% of the total oxygen consumption in the nearshore, while it contributed to 36% (dominated by the decomposition of POM, accounting for 25%) in the offshore. This study suggests that typhoon‐induced decomposition might be dominated by POM, which is not conducive to the storage of OM in sediments. It means that the capacity of sediments as a carbon sink will be weakened under global warming (increasing typhoon events).
Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils
Authors: Liu Shengwei , Zeng Jiaxiong , Yu Huang , Wang Cheng , Yang Yunfeng , Wang Jianjun , He Zhili , Yan Qingyun
Published: June 2023

Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world’s largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.
Internet addiction and residual depressive symptoms among clinically stable adolescents with major psychiatric disorders during the COVID-19 pandemic: a network analysis perspective
Authors: Cai Hong , Zhao Yan-Jie , He Fan , Li Shu-Ying , Li Zong-Lei , Zhang Wu-Yang , Zhang Yao , Cheung Teris , Ng Chee H. , Sha Sha , Xiang Yu-Tao
Published: June 2023

To assess the inter-relationships between residual depressive symptoms (RDS) and Internet addiction (IA) using network analysis among clinically stable adolescents with major psychiatric disorders during the COVID-19 pandemic. RDS and IA were assessed using the Patient Health Questionnaire-9 (PHQ-9) and the Internet Addiction Test (IAT), respectively. Central symptoms and bridge symptoms in the network model were examined. A total of 1,454 adolescents met the study criteria and were included in the analyses. The prevalence of IA was 31.2% (95% CI: 28.8%-33.6%). In the network analysis, the nodes IAT15 (“Preoccupation with the Internet”), PHQ2 (“Sad mood”), and PHQ1 (“Anhedonia”) were the most central symptoms in the IA-RDS network model. Bridge symptoms included IAT10 (“Sooth disturbing about your Internet use”), PHQ9 (“Suicide ideation”), and IAT3 (“Prefer the excitement online to the time with others”). Additionally, PHQ2 (“Sad mood”) was the main node linking “Anhedonia” to other IA clusters. Internet addiction was common among clinically stable adolescents with major psychiatric disorders during the COVID-19 pandemic. Core and bridge symptoms identified in this study could be prioritized as targets for the prevention and treatment of IA in this population.
SLC43A2 and NFκB signaling pathway regulate methionine/cystine restriction-induced ferroptosis in esophageal squamous cell carcinoma via a feedback loop
Authors: Peng Hao , Yan Yuyu , He Min , Li Jinxia , Wang Lianghai , Jia Wei , Yang Lan , Jiang Jinfang , Chen Yunzhao , Li Feng , Yuan Xianglin , Pang Lijuan
Published: June 2023

Studies have indicated dietary restriction of methionine/cystine provided a therapeutic benefit in diseases such as cancer. However, the molecular and cellular mechanisms that underlie the interaction between methionine/cystine restriction (MCR) and effects on esophageal squamous cell carcinoma (ESCC) have remained elusive. Here, we discovered the dietary restriction of methionine/cystine has a large effect on cellular methionine metabolism as assayed in a ECA109 derived xenograft model. RNA-seq and enrichment analysis suggested the blocked tumor progression was affected by ferroptosis, together with the NFκB signaling pathway activation in ESCC. Consistently, GSH content and GPX4 expression were downregulated by MCR both in vivo and in vitro. The contents of Fe2+ and MDA were negatively correlated with supplementary methionine in a dose-dependent way. Mechanistically, MCR and silent of SLC43A2, a methionine transporter, diminished phosphorylation of IKKα/β and p65. Blocked NFκB signaling pathway further decreased the expression of SLC43A2 and GPX4 in both mRNA and protein level, which in turn downregulated the methionine intake and stimulated ferroptosis, respectively. ESCC progression was inhibited by enhanced ferroptosis and apoptosis and impaired cell proliferation. In this study, we proposed a novel feedback regulation mechanism underlie the correlation between dietary restriction of methionine/cystine and ESCC progression. MCR blocked cancer progression via stimulating ferroptosis through the positive feedback loop between SLC43A2 and NFκB signaling pathways. Our results provided the theoretical basis and new targets for ferroptosis-based clinical antitumor treatments for ESCC patients.
On the role of history-dependent adsorbate distribution and metastable states in switchable mesoporous metal-organic frameworks
Authors: Walenszus Francesco , Bon Volodymyr , Evans Jack D. , Krause Simon , Getzschmann Jürgen , Kaskel Stefan , Dvoyashkin Muslim
Published: June 2023

A unique feature of metal-organic frameworks (MOFs) in contrast to rigid nanoporous materials is their structural switchabilty offering a wide range of functionality for sustainable energy storage, separation and sensing applications. This has initiated a series of experimental and theoretical studies predominantly aiming at understanding the thermodynamic conditions to transform and release gas, but the nature of sorption-induced switching transitions remains poorly understood. Here we report experimental evidence for fluid metastability and history-dependent states during sorption triggering the structural change of the framework and leading to the counterintuitive phenomenon of negative gas adsorption (NGA) in flexible MOFs. Preparation of two isoreticular MOFs differing by structural flexibility and performing direct in situ diffusion studies aided by in situ X-ray diffraction, scanning electron microscopy and computational modelling, allowed assessment of n-butane molecular dynamics, phase state, and the framework response to obtain a microscopic picture for each step of the sorption process.
Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat
Authors: Wei Jing , Fontaine Laurent , Valiente Nicolas , Dörsch Peter , Hessen Dag O. , Eiler Alexander
Published: June 2023

Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.
Extreme fast charging of commercial Li-ion batteries via combined thermal switching and self-heating approaches
Authors: Zeng Yuqiang , Zhang Buyi , Fu Yanbao , Shen Fengyu , Zheng Qiye , Chalise Divya , Miao Ruijiao , Kaur Sumanjeet , Lubner Sean D. , Tucker Michael C. , Battaglia Vincent , Dames Chris , Prasher Ravi S.
Published: June 2023

The mass adoption of electric vehicles is hindered by the inadequate extreme fast charging (XFC) performance (i.e., less than 15 min charging time to reach 80% state of charge) of commercial high-specific-energy (i.e., >200 Wh/kg) lithium-ion batteries (LIBs). Here, to enable the XFC of commercial LIBs, we propose the regulation of the battery’s self-generated heat via active thermal switching. We demonstrate that retaining the heat during XFC with the switch OFF boosts the cell’s kinetics while dissipating the heat after XFC with the switch ON reduces detrimental reactions in the battery. Without modifying cell materials or structures, the proposed XFC approach enables reliable battery operation by applying <15 min of charge and 1 h of discharge. These results are almost identical regarding operativity for the same battery type tested applying a 1 h of charge and 1 h of discharge, thus, meeting the XFC targets set by the United States Department of Energy. Finally, we also demonstrate the feasibility of integrating the XFC approach in a commercial battery thermal management system.
Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants
Authors: Gonzalez-Reiche Ana S. , Alshammary Hala , Schaefer Sarah , Patel Gopi , Polanco Jose , Carreño Juan Manuel , Amoako Angela A. , Rooker Aria , Cognigni Christian , Floda Daniel , van de Guchte Adriana , Khalil Zain , Farrugia Keith , Assad Nima , Zhang Jian , Alburquerque Bremy ,   PARIS/PSP study group, Kleiner Giulio , Andre Dalles , Beach Katherine F. , Bermúdez-González Maria C. , Cai Gianna , Lyttle Neko , Mulder Lubbertus C. F. , Oostenink Annika , Salimbangon Ashley Beathrese T. , Singh Gagandeep , van Kesteren Morgan , Monahan Brian , Mauldin Jacob , Awawda Mahmoud , Sominsky Levy A. , Gleason Charles , Srivastava Komal , Sebra Robert , Ramirez Juan David , Banu Radhika , Shrestha Paras , Krammer Florian , Paniz-Mondolfi Alberto , Sordillo Emilia Mia , Simon Viviana , van Bakel Harm
Published: June 2023

Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
Direct observation of coherence transfer and rotational-to-vibrational energy exchange in optically centrifuged CO2 super-rotors
Authors: Chen Timothy Y. , Steinmetz Scott A. , Patterson Brian D. , Jasper Ahren W. , Kliewer Christopher J.
Published: June 2023

Optical centrifuges are laser-based molecular traps that can rotationally accelerate molecules to energies rivalling or exceeding molecular bond energies. Here we report time and frequency-resolved ultrafast coherent Raman measurements of optically centrifuged CO2 at 380 Torr spun to energies beyond its bond dissociation energy of 5.5 eV (Jmax = 364, Erot = 6.14 eV, Erot/kB = 71, 200 K). The entire rotational ladder from J = 24 to J = 364 was resolved simultaneously which enabled a more accurate measurement of the centrifugal distortion constants for CO2. Remarkably, coherence transfer was directly observed, and time-resolved, during the field-free relaxation of the trap as rotational energy flowed into bending-mode vibrational excitation. Vibrationally excited CO2 (ν2 > 3) was observed in the time-resolved spectra to populate after 3 mean collision times as a result of rotational-to-vibrational (R-V) energy transfer. Trajectory simulations show an optimal range of J for R-V energy transfer. Dephasing rates for molecules rotating up to 5.5 times during one collision were quantified. Very slow decays of the vibrational hot band rotational coherences suggest that they are sustained by coherence transfer and line mixing.
Non-line-of-sight imaging with arbitrary illumination and detection pattern
Authors: Liu Xintong , Wang Jianyu , Xiao Leping , Shi Zuoqiang , Fu Xing , Qiu Lingyun
Published: June 2023

Non-line-of-sight (NLOS) imaging aims at reconstructing targets obscured from the direct line of sight. Existing NLOS imaging algorithms require dense measurements at regular grid points in a large area of the relay surface, which severely hinders their availability to variable relay scenarios in practical applications such as robotic vision, autonomous driving, rescue operations and remote sensing. In this work, we propose a Bayesian framework for NLOS imaging without specific requirements on the spatial pattern of illumination and detection points. By introducing virtual confocal signals, we design a confocal complemented signal-object collaborative regularization (CC-SOCR) algorithm for high-quality reconstructions. Our approach is capable of reconstructing both the albedo and surface normal of the hidden objects with fine details under general relay settings. Moreover, with a regular relay surface, coarse rather than dense measurements are enough for our approach such that the acquisition time can be reduced significantly. As demonstrated in multiple experiments, the proposed framework substantially extends the application range of NLOS imaging.
Monolithically-grained perovskite solar cell with Mortise-Tenon structure for charge extraction balance
Authors: Wang Fangfang , Li Mubai , Tian Qiushuang , Sun Riming , Ma Hongzhuang , Wang Hongze , Chang Jingxi , Li Zihao , Chen Haoyu , Cao Jiupeng , Wang Aifei , Dong Jingjin , Liu You , Zhao Jinzheng , Chu Ying , Yan Suhao , Wu Zichao , Liu Jiaxin , Li Ya , Chen Xianglin , Gao Ping , Sun Yue , Liu Tingting , Liu Wenbo , Li Renzhi , Wang Jianpu , Cheng Yi-bing , Liu Xiaogang , Huang Wei , Qin Tianshi
Published: June 2023

Although the power conversion efficiency values of perovskite solar cells continue to be refreshed, it is still far from the theoretical Shockley-Queisser limit. Two major issues need to be addressed, including disorder crystallization of perovskite and unbalanced interface charge extraction, which limit further improvements in device efficiency. Herein, we develop a thermally polymerized additive as the polymer template in the perovskite film, which can form monolithic perovskite grain and a unique “Mortise-Tenon” structure after spin-coating hole-transport layer. Importantly, the suppressed non-radiative recombination and balanced interface charge extraction benefit from high-quality perovskite crystals and Mortise-Tenon structure, resulting in enhanced open-circuit voltage and fill-factor of the device. The PSCs achieve certified efficiency of 24.55% and maintain >95% initial efficiency over 1100 h in accordance with the ISOS-L-2 protocol, as well as excellent endurance according to the ISOS-D-3 accelerated aging test.
Multi-compartmental MOF microreactors derived from Pickering double emulsions for chemo-enzymatic cascade catalysis
Authors: Tian Danping , Hao Ruipeng , Zhang Xiaoming , Shi Hu , Wang Yuwei , Liang Linfeng , Liu Haichao , Yang Hengquan
Published: June 2023

Bioinspired multi-compartment architectures are desired in synthetic biology and metabolic engineering, as credited by their cell-like structures and intrinsic ability of assembling catalytic species for spatiotemporal control over cascade reactions like in living systems. Herein, we describe a general Pickering double emulsion-directed interfacial synthesis method for the fabrication of multicompartmental MOF microreactors. This approach employs multiple liquid–liquid interfaces as a controllable platform for the self-completing growth of dense MOF layers, enabling the microreactor with tailor-made inner architectures and selective permeability. Importantly, simultaneous encapsulation of incompatible functionalities, including hydrophilic enzyme and hydrophobic molecular catalyst, can be realized in a single MOF microreactor for operating chemo-enzymatic cascade reactions. As exemplified by the Grubb’ catalyst/CALB lipase driven olefin metathesis/ transesterification cascade reaction and glucose oxidase (GOx)/Fe-porphyrin catalyzed oxidation reaction, the multicompartmental microreactor exhibits 2.24–5.81 folds enhancement in cascade reaction efficiency in comparison to the homogeneous counterparts or physical mixture of individual analogues, due to the restrained mutual inactivation and substrate channelling effects. Our study prompts further design of multicompartment systems and the development of artificial cells capable of complex cellular transformations.
Systematic literature review reveals suboptimal use of chemical probes in cell-based biomedical research
Authors: Sterling Jayden , Baker Jennifer R. , McCluskey Adam , Munoz Lenka
Published: June 2023

Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical probes, we conducted a systematic review of 662 publications, understood here as primary research articles, employing eight different chemical probes in cell-based research. We summarised (i) concentration(s) at which chemical probes were used in cell-based assays, (ii) inclusion of structurally matched target-inactive control compounds and (iii) orthogonal chemical probes. Here, we show that only 4% of analysed eligible publications used chemical probes within the recommended concentration range and included inactive compounds as well as orthogonal chemical probes. These findings indicate that the best practice with chemical probes is yet to be implemented in biomedical research. To achieve this, we propose ‘the rule of two’: At least two chemical probes (either orthogonal target-engaging probes, and/or a pair of a chemical probe and matched target-inactive compound) to be employed at recommended concentrations in every study.
Multi-state data storage in a two-dimensional stripy antiferromagnet implemented by magnetoelectric effect
Authors: Gu Pingfan , Wang Cong , Su Dan , Dong Zehao , Wang Qiuyuan , Han Zheng , Watanabe Kenji , Taniguchi Takashi , Ji Wei , Sun Young , Ye Yu
Published: June 2023

A promising approach to the next generation of low-power, functional, and energy-efficient electronics relies on novel materials with coupled magnetic and electric degrees of freedom. In particular, stripy antiferromagnets often exhibit broken crystal and magnetic symmetries, which may bring about the magnetoelectric (ME) effect and enable the manipulation of intriguing properties and functionalities by electrical means. The demand for expanding the boundaries of data storage and processing technologies has led to the development of spintronics toward two-dimensional (2D) platforms. This work reports the ME effect in the 2D stripy antiferromagnetic insulator CrOCl down to a single layer. By measuring the tunneling resistance of CrOCl on the parameter space of temperature, magnetic field, and applied voltage, we verified the ME coupling down to the 2D limit and probed its mechanism. Utilizing the multi-stable states and ME coupling at magnetic phase transitions, we realize multi-state data storage in the tunneling devices. Our work not only advances the fundamental understanding of spin-charge coupling, but also demonstrates the great potential of 2D antiferromagnetic materials to deliver devices and circuits beyond the traditional binary operations.
Bacteriophage targeting microbiota alleviates non-alcoholic fatty liver disease induced by high alcohol-producing Klebsiella pneumoniae
Authors: Gan Lin , Feng Yanling , Du Bing , Fu Hanyu , Tian Ziyan , Xue Guanhua , Yan Chao , Cui Xiaohu , Zhang Rui , Cui Jinghua , zhao Hanqing , Feng Junxia , Xu Ziying , Fan Zheng , Fu Tongtong , Du Shuheng , Liu Shiyu , Zhang Qun , Yu Zihui , Sun Ying , Yuan Jing
Published: June 2023

Our previous studies have shown that high alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) in the intestinal microbiome could be one of the causes of non-alcoholic fatty liver disease (NAFLD). Considering antimicrobial resistance of K. pneumoniae and dysbacteriosis caused by antibiotics, phage therapy might have potential in treatment of HiAlc Kpn-induced NAFLD, because of the specificity targeting the bacteria. Here, we clarified the effectiveness of phage therapy in male mice with HiAlc Kpn-induced steatohepatitis. Comprehensive investigations including transcriptomes and metabolomes revealed that treatment with HiAlc Kpn-specific phage was able to alleviate steatohepatitis caused by HiAlc Kpn, including hepatic dysfunction and expression of cytokines and lipogenic genes. In contrast, such treatment did not cause significantly pathological changes, either in functions of liver and kidney, or in components of gut microbiota. In addition to reducing alcohol attack, phage therapy also regulated inflammation, and lipid and carbohydrate metabolism. Our data suggest that phage therapy targeting gut microbiota is an alternative to antibiotics, with potential efficacy and safety, at least in HiAlc Kpn-caused NAFLD.
Improvement of cryo-EM maps by simultaneous local and non-local deep learning
Authors: He Jiahua , Li Tao , Huang Sheng-You
Published: June 2023

Cryo-EM has emerged as the most important technique for structure determination of macromolecular complexes. However, raw cryo-EM maps often exhibit loss of contrast at high resolution and heterogeneity over the entire map. As such, various post-processing methods have been proposed to improve cryo-EM maps. Nevertheless, it is still challenging to improve both the quality and interpretability of EM maps. Addressing the challenge, we present a three-dimensional Swin-Conv-UNet-based deep learning framework to improve cryo-EM maps, named EMReady, by not only implementing both local and non-local modeling modules in a multiscale UNet architecture but also simultaneously minimizing the local smooth L1 distance and maximizing the non-local structural similarity between processed experimental and simulated target maps in the loss function. EMReady was extensively evaluated on diverse test sets of 110 primary cryo-EM maps and 25 pairs of half-maps at 3.0–6.0 Å resolutions, and compared with five state-of-the-art map post-processing methods. It is shown that EMReady can not only robustly enhance the quality of cryo-EM maps in terms of map-model correlations, but also improve the interpretability of the maps in automatic de novo model building.
Intrinsic TGF-β signaling attenuates proximal tubule mitochondrial injury and inflammation in chronic kidney disease
Authors: Kayhan Merve , Vouillamoz Judith , Rodriguez Daymé Gonzalez , Bugarski Milica , Mitamura Yasutaka , Gschwend Julia , Schneider Christoph , Hall Andrew , Legouis David , Akdis Cezmi A. , Peter Leary , Rehrauer Hubert , Gewin Leslie , Wenger Roland H. , Khodo Stellor Nlandu
Published: June 2023

Excessive TGF-β signaling and mitochondrial dysfunction fuel chronic kidney disease (CKD) progression. However, inhibiting TGF-β failed to impede CKD in humans. The proximal tubule (PT), the most vulnerable renal segment, is packed with giant mitochondria and injured PT is pivotal in CKD progression. How TGF-β signaling affects PT mitochondria in CKD remained unknown. Here, we combine spatial transcriptomics and bulk RNAseq with biochemical analyses to depict the role of TGF-β signaling on PT mitochondrial homeostasis and tubulo-interstitial interactions in CKD. Male mice carrying specific deletion of Tgfbr2 in the PT have increased mitochondrial injury and exacerbated Th1 immune response in the aristolochic acid model of CKD, partly, through impaired complex I expression and mitochondrial quality control associated with a metabolic rewiring toward aerobic glycolysis in the PT cells. Injured S3T2 PT cells are identified as the main mediators of the maladaptive macrophage/dendritic cell activation in the absence of Tgfbr2. snRNAseq database analyses confirm decreased TGF-β receptors and a metabolic deregulation in the PT of CKD patients. This study describes the role of TGF-β signaling in PT mitochondrial homeostasis and inflammation in CKD, suggesting potential therapeutic targets that might be used to mitigate CKD progression.
Yijung-tang improves thermogenesis and reduces inflammation associated with gut microbiota in hypothyroid rats
Authors: Khakisahneh Saeid , Zhang Xue-Ying , Han Song-Yi , Song Eun-Ji , Nam Young-Do , Kim Hojun
Published: June 2023

Currently, considerable attention is focused on exploring the potential relationship between herbal medicine (HM) and the gut microbiome in terms of thermoregulation, which is an important aspect of human health, in modern system biology. However, our knowledge of the mechanisms of HM in thermoregulation is inadequate. Here, we demonstrate that the canonical herbal formula, Yijung-tang (YJT), protects against hypothermia, hyperinflammation, and intestinal microbiota dysbiosis in PTU-induced hypothyroid rats. Notably, these properties were associated with alterations in the gut microbiota and signaling crosstalk between the thermoregulatory and inflammatory mediators in the small intestine and brown adipose tissue (BAT). In contrast to the conventional drug L-thyroxine for curing hypothyroidism, YJT has an efficacy for attenuating systematic inflammatory responses, related with depression in intestinal TLR4 and Nod2/Pglyrp1 signaling pathways. Our findings suggest that YJT could promote BAT thermogenesis and prevent systemic inflammation in PTU-induced hypothyroid rats, which was associated with its prebiotic effect on modulating of the gut microbiota and gene expression with relevance in the enteroendocrine function and innate immune systems. These findings may strengthen the rationale of the microbiota–gut–BAT axis for a paradigm shift to enable holobiont-centric medicine.
Extracellular vesicles of the Gram-positive gut symbiont Bifidobacterium longum induce immune-modulatory, anti-inflammatory effects
Authors: Mandelbaum Noa , Zhang Lihan , Carasso Shaqed , Ziv Tamar , Lifshiz-Simon Sapir , Davidovich Irina , Luz Ishai , Berinstein Elliot , Gefen Tal , Cooks Tomer , Talmon Yeshayahu , Balskus Emily P. , Geva-Zatorsky Naama
Published: June 2023

The gut microbiota is now well known to affect the host’s immune system. One way of bacterial communication with host cells is via the secretion of vesicles, small membrane structures containing various cargo. Research on vesicles secreted by Gram-positive gut bacteria, their mechanisms of interaction with the host and their immune-modulatory effects are still relatively scarce. Here we characterized the size, protein content, and immune-modulatory effects of extracellular vesicles (EVs) secreted by a newly sequenced Gram-positive human gut symbiont strain - Bifidobacterium longum AO44. We found that B. longum EVs exert anti-inflammatory effects, inducing IL-10 secretion from both splenocytes and dendritic cells (DC)-CD4+ T cells co-cultures. Furthermore, the EVs protein content showed enrichment in ABC transporters, quorum sensing proteins, and extracellular solute-binding proteins, which were previously shown to have a prominent function in the anti-inflammatory effect of other strains of B. longum. This study underlines the importance of bacterial vesicles in facilitating the gut bacterial immune-modulatory effects on the host and sheds light on bacterial vesicles as future therapeutics.
Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities
Authors: Hutchison Evan R. , Kasahara Kazuyuki , Zhang Qijun , Vivas Eugenio I. , Cross Tzu-Wen L. , Rey Federico E.
Published: June 2023

Dietary fiber consumption has been linked with improved cardiometabolic health, however, human studies have reported large interindividual variations in the observed benefits. We tested whether the effects of dietary fiber on atherosclerosis are influenced by the gut microbiome. We colonized germ-free ApoE−/− mice with fecal samples from three human donors (DonA, DonB, and DonC) and fed them diets supplemented with either a mix of 5 fermentable fibers (FF) or non-fermentable cellulose control (CC) diet. We found that DonA-colonized mice had reduced atherosclerosis burden with FF feeding compared to their CC-fed counterparts, whereas the type of fiber did not affect atherosclerosis in mice colonized with microbiota from the other donors. Microbial shifts associated with FF feeding in DonA mice were characterized by higher relative abundances of butyrate-producing taxa, higher butyrate levels, and enrichment of genes involved in synthesis of B vitamins. Our results suggest that atheroprotection in response to FF is not universal and is influenced by the gut microbiome.
Topological graph-based analysis of solid-state ion migration
Authors: Shen Jimmy-Xuan , Li Haoming Howard , Rutt Ann , Horton Matthew K. , Persson Kristin A.
Published: June 2023

To accelerate the development of ion conducting materials, we present a general graph-theoretic analysis framework for ion migration in any crystalline structure. The nodes of the graph represent metastable sites of the migrating ion and the edges represent discrete migration events between adjacent sites. Starting from a collection of possible metastable migration sites, the framework assigns a weight to the edges by calculating the individual migration energy barriers between those sites. Connected pathways in the periodic simulation cell corresponding to macroscopic ion migration are identified by searching for the lowest-cost cycle in the periodic migration graph. To exemplify the utility of the framework, we present the automatic analyses of Li migration in different polymorphs of VO(PO4), with the resulting identification of two distinct crystal structures with simple migration pathways demonstrating overall <300 meV migration barriers.
Giant multiphononic effects in a perovskite oxide
Authors: Cazorla Claudio , Stengel Massimiliano , Íñiguez Jorge , Rurali Riccardo
Published: June 2023

Perovskite oxides offer tremendous potential for applications in information storage and energy conversion, owing to a subtle interplay between their spin, charge, orbital and lattice degrees of freedom. Here, we further expand the possible range of perovskite oxides operation towards the fields of thermal management and thermal computing by exploiting an exceptional synergy between different ferroic orders. We propose dynamical control of the heat flow in a distinctive family of perovskite oxides obtained via the application of small electric (~10 kV/cm) and/or magnetic (~1 T) fields. Based on first-principles simulations, we predict a relative heat conductivity variation of ~100% in SrMnO3 thin films near room temperature resulting from a phase transition that involves huge changes in both the magnetization and electric polarization. The disclosed giant multiphononic effects are fundamentally caused by anharmonic spin-phonon couplings that strongly influence the mean lifetime of phonons.
Perfect Crystals: microgravity capillary counterdiffusion crystallization of human manganese superoxide dismutase for neutron crystallography
Authors: Lutz William E. , Azadmanesh Jahaun , Lovelace Jeffrey J. , Kolar Carol , Coates Leighton , Weiss Kevin L. , Borgstahl Gloria E. O.
Published: June 2023

The NASA mission Perfect Crystals used the microgravity environment on the International Space Station (ISS) to grow crystals of human manganese superoxide dismutase (MnSOD)—an oxidoreductase critical for mitochondrial vitality and human health. The mission’s overarching aim is to perform neutron protein crystallography (NPC) on MnSOD to directly visualize proton positions and derive a chemical understanding of the concerted proton electron transfers performed by the enzyme. Large crystals that are perfect enough to diffract neutrons to sufficient resolution are essential for NPC. This combination, large and perfect, is hard to achieve on Earth due to gravity-induced convective mixing. Capillary counterdiffusion methods were developed that provided a gradient of conditions for crystal growth along with a built-in time delay that prevented premature crystallization before stowage on the ISS. Here, we report a highly successful and versatile crystallization system to grow a plethora of crystals for high-resolution NPC.
Impact of timing and combination of different BNT162b2 and ChAdOx1-S COVID-19 basic and booster vaccinations on humoral immunogenicity and reactogenicity in adults
Authors: Dedroogh Simon , Schmiedl Sven , Thürmann Petra A. , Graf Katharina , Appelbaum Sebastian , Koß Reinhard , Theis Christian , Zia Zewarudin , Tebbenjohanns Jürgen , Thal Serge C. , Dedroogh Michael
Published: June 2023

In this single-center observational study with 1,206 participants, we prospectively evaluated SARS-CoV-2-antibodies (anti-S RBD) and vaccine-related adverse drug reactions (ADR) after basic and booster immunization with BNT162b2- and ChAdOx1-S-vaccines in four vaccination protocols: Homologous BNT162b2-schedule with second vaccination at either three or six weeks, homologous ChAdOx1-S-vaccination or heterologous ChAdOx1-S/BNT162b2-schedule, each at 12 weeks. All participants received a BNT162b2 booster. Blood samples for anti-S RBD analysis were obtained multiple times over a period of four weeks to six months after basic vaccination, immediately before, and up to three months after booster vaccination. After basic vaccination, the homologous ChAdOx1-S-group showed the lowest anti-S RBD levels over six months, while the heterologous BNT162b2-ChAdOx1-S-group demonstrated the highest anti-S levels, but failed to reach level of significance compared with the homologous BNT162b2-groups. Antibody levels were higher after an extended vaccination interval with BNT162b2. A BNT162b2 booster increased anti-S-levels 11- to 91-fold in all groups, with the homologous ChAdOx1-S-cohort demonstrated the highest increase in antibody levels. No severe or serious ADR were observed. The findings suggest that a heterologous vaccination schedule or prolonged vaccination interval induces robust humoral immunogenicity with good tolerability. Extending the time to boost-immunization is key to both improving antibody induction and reducing ADR rate.
Exploring the cytotoxicity on human lung cancer cells and DNA binding stratagem of camptothecin functionalised silver nanoparticles through multi-spectroscopic, and calorimetric approach
Authors: Raj Aparna , Thomas Riju K. , Vidya L. , Aparna V. M. , Neelima S. , Sudarsanakumar C.
Published: June 2023

The influence of nanoparticles inside the human body and their interactions with biological macromolecules need to be explored/studied prior to specific applications. The objective of this study is to find the potential of camptothecin functionalised silver nanoparticles (CMT-AgNPs) in biomedical applications. This article primarily investigates the binding stratagem of CMT-AgNPs with calf thymus DNA (ctDNA) through a series of spectroscopic and calorimetric methods and then analyses the anticancer activity and cytotoxicity of CMT-AgNPs. The nanoparticles were synthesized using a simple one pot method and characterized using UV–Visible, fourier transform infrared (FTIR) spectroscopy, X-ray diffraction and high-resolution transmission electron microscopy (HRTEM). The average size of CMT-AgNPs is 10 ± 2 nm. A group of experimental techniques such as UV–Visible spectrophotometry, fluorescence dye displacement assay, circular dichroism (CD) and viscosity analysis unravelled the typical groove binding mode of CMT-AgNPs with ctDNA. The CD measurement evidenced the minor conformational alterations of double helical structure of ctDNA in the presence of CMT-AgNPs. The information deduced from the isothermal titration calorimetry (ITC) experiment is that the binding was exothermic and spontaneous in nature. Moreover, all the thermodynamic binding parameters were extracted from the ITC data. The binding constants obtained from UV absorption experiments, fluorescence dye displacement studies and ITC were consistently in the order of 104 Mol−1. All these results validated the formation of CMT-AgNPs–ctDNA complex and the results unambiguously confirm the typical groove binding mode of CMT-AgNPs. An exhaustive in vitro MTT assay by CMT-AgNPs and CMT against A549, HT29, HeLa and L929 cell lines revealed the capability of CMT-AgNPs as a potential anticancer agent.
Reverse transcriptase recombinase polymerase amplification for detection of tomato spotted wilt orthotospovirus from crude plant extracts
Authors: Iturralde Martinez Juan Francisco , Rosa Cristina
Published: June 2023

Virus detection in early stages of infection could prove useful for identification and isolation of foci of inoculum before its spread to the rest of susceptible individuals via vectoring insects. However, the low number of viruses present at the beginning of infection renders their detection and identification difficult and requires the use of highly sensitive laboratory techniques that are often incompatible with a field application. To obviate this challenge, utilized Recombinase Polymerase Amplification, an isothermal amplification technique that makes millions of copies of a predefined region in the genome, to detect tomato spotted wilt orthotospovirus in real time and at the end point. The reaction occurs isothermically and can be used directly from crude plant extracts without nucleic acid extraction. Notably, a positive result can be seen with the naked eye as a flocculus made of newly synthesized DNA and metallic beads. The objective of the procedure is to create a portable and affordable system that can isolate and identify viruses in the field, from infected plants and suspected insect vectors, and can be used by scientists and extension managers for making informed decisions for viral management. Results can be obtained in situ without the need of sending the samples to a specialized lab.