bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective de novo drug design with deep interactome learning
Authors: Atz Kenneth , Cotos Leandro , Isert Clemens , Håkansson Maria , Focht Dorota , Hilleke Mattis , Nippa David F. , Iff Michael , Ledergerber Jann , Schiebroek Carl C. G. , Romeo Valentina , Hiss Jan A. , Merk Daniel , Schneider Petra , Kuhn Bernd , Grether Uwe , Schneider Gisbert 
Published: April 2024

Abstract
De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the “zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.
Double cross-linked 3D layered PBI proton exchange membranes for stable fuel cell performance above 200 °C
Authors: Zhang Liang , Liu Mengjiao , Zhu Danyi , Tang Mingyuan , Zhu Taizhong , Gao Congjie , Huang Fei , Xue Lixin 
Published: April 2024

AbstractPhosphoric acid doped proton exchange membranes often experience performance degradation above 200 °C due to membrane creeping and phosphoric acid evaporation, migration, dehydration, and condensation. To address these issues, here we present gel-state polybenzimidazole membranes with double cross-linked three-dimensional layered structures via a polyphosphoric acid sol-gel process, enabling stable operation above 200 °C. These membranes, featuring proton-conducting cross-linking phosphate bridges and branched polybenzimidazole networks, effectively anchor and retain phosphoric acid molecules, prevent 96% of its dehydration and condensation, improve creep resistance, and maintain excellent proton conductivity stability. The resulting membrane, with superior through-plane proton conductivity of 0.348 S cm−1, delivers outstanding peak power densities ranging from 1.20–1.48 W cm−2 in fuel cells operated at 200-240 °C and a low voltage decay rate of only 0.27 mV h−1 over a 250-hour period at 220 °C, opening up possibilities for their direct integration with methanol steam reforming systems.
Catalytic role of in-situ formed C-N species for enhanced Li2CO3 decomposition
Authors: Zhang Fangli , Zhang Wenchao , Yuwono Jodie A. , Wexler David , Fan Yameng , Zou Jinshuo , Liang Gemeng , Sun Liang , Guo Zaiping 
Published: April 2024

AbstractSluggish kinetics of the CO2 reduction/evolution reactions lead to the accumulation of Li2CO3 residuals and thus possible catalyst deactivation, which hinders the long-term cycling stability of Li-CO2 batteries. Apart from catalyst design, constructing a fluorinated solid-electrolyte interphase is a conventional strategy to minimize parasitic reactions and prolong cycle life. However, the catalytic effects of solid-electrolyte interphase components have been overlooked and remain unclear. Herein, we systematically regulate the compositions of solid-electrolyte interphase via tuning electrolyte solvation structures, anion coordination, and binding free energy between Li ion and anion. The cells exhibit distinct improvement in cycling performance with increasing content of C-N species in solid-electrolyte interphase layers. The enhancement originates from a catalytic effect towards accelerating the Li2CO3 formation/decomposition kinetics. Theoretical analysis reveals that C-N species provide strong adsorption sites and promote charge transfer from interface to *CO22− during discharge, and from Li2CO3 to C-N species during charge, thereby building a bidirectional fast-reacting bridge for CO2 reduction/evolution reactions. This finding enables us to design a C-N rich solid-electrolyte interphase via dual-salt electrolytes, improving cycle life of Li-CO2 batteries to twice that using traditional electrolytes. Our work provides an insight into interfacial design by tuning of catalytic properties towards CO2 reduction/evolution reactions.
Phosphorylation of the F-BAR protein Hof1 drives septin ring splitting in budding yeast
Authors: Varela Salgado Maritzaida , Adriaans Ingrid E. , Touati Sandra A. , Ibanes Sandy , Lai-Kee-Him Joséphine , Ancelin Aurélie , Cipelletti Luca , Picas Laura , Piatti Simonetta 
Published: April 2024

AbstractA double septin ring accompanies cytokinesis in yeasts and mammalian cells. In budding yeast, reorganisation of the septin collar at the bud neck into a dynamic double ring is essential for actomyosin ring constriction and cytokinesis. Septin reorganisation requires the Mitotic Exit Network (MEN), a kinase cascade essential for cytokinesis. However, the effectors of MEN in this process are unknown. Here we identify the F-BAR protein Hof1 as a critical target of MEN in septin remodelling. Phospho-mimicking HOF1 mutant alleles overcome the inability of MEN mutants to undergo septin reorganisation by decreasing Hof1 binding to septins and facilitating its translocation to the actomyosin ring. Hof1-mediated septin rearrangement requires its F-BAR domain, suggesting that it may involve a local membrane remodelling that leads to septin reorganisation. In vitro Hof1 can induce the formation of intertwined septin bundles, while a phosphomimetic Hof1 protein has impaired septin-bundling activity. Altogether, our data indicate that Hof1 modulates septin architecture in distinct ways depending on its phosphorylation status.
Highly efficient anion exchange membrane water electrolyzers via chromium-doped amorphous electrocatalysts
Authors: Li Sicheng , Liu Tong , Zhang Wei , Wang Mingzhen , Zhang Huijuan , Qin Chunlan , Zhang Lingling , Chen Yudan , Jiang Shuaiwei , Liu Dong , Liu Xiaokang , Wang Huijuan , Luo Qiquan , Ding Tao , Yao Tao 
Published: April 2024

AbstractIn-depth comprehension and modulation of the electronic structure of the active metal sites is crucial to enhance their intrinsic activity of electrocatalytic oxygen evolution reaction (OER) toward anion exchange membrane water electrolyzers (AEMWEs). Here, we elaborate a series of amorphous metal oxide catalysts (FeCrOx, CoCrOx and NiCrOx) with high performance AEMWEs by high-valent chromium dopant. We discover that the positive effect of the transition from low to high valence of the Co site on the adsorption energy of the intermediate and the lower oxidation barrier is the key factor for its increased activity by synchrotron radiation in-situ techniques. Particularly, the CoCrOx anode catalyst achieves the high current density of 1.5 A cm−2 at 2.1 V and maintains for over 120 h with attenuation less than 4.9 mV h−1 in AEMWE testing. Such exceptional performance demonstrates a promising prospect for industrial application and providing general guidelines for the design of high-efficiency AEMWEs systems.
Selective lipid recruitment by an archaeal DPANN symbiont from its host
Authors: Ding Su , Hamm Joshua N. , Bale Nicole J. , Sinninghe Damsté Jaap S. , Spang Anja 
Published: April 2024

AbstractThe symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus – Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e., nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.
Clinical associations with a polygenic predisposition to benign lower white blood cell counts
Authors: Mosley Jonathan D. , Shelley John P. , Dickson Alyson L. , Zanussi Jacy , Daniel Laura L. , Zheng Neil S. , Bastarache Lisa , Wei Wei-Qi , Shi Mingjian , Jarvik Gail P. , Rosenthal Elisabeth A. , Khan Atlas , Sherafati Alborz , Kullo Iftikhar J. , Walunas Theresa L. , Glessner Joseph , Hakonarson Hakon , Cox Nancy J. , Roden Dan M. , Frangakis Stephan G. , Vanderwerff Brett , Stein C. Michael , Van Driest Sara L. , Borinstein Scott C. , Shu Xiao-Ou , Zawistowski Matthew , Chung Cecilia P. , Kawai Vivian K. 
Published: April 2024

AbstractPolygenic variation unrelated to disease contributes to interindividual variation in baseline white blood cell (WBC) counts, but its clinical significance is uncharacterized. We investigated the clinical consequences of a genetic predisposition toward lower WBC counts among 89,559 biobank participants from tertiary care centers using a polygenic score for WBC count (PGSWBC) comprising single nucleotide polymorphisms not associated with disease. A predisposition to lower WBC counts was associated with a decreased risk of identifying pathology on a bone marrow biopsy performed for a low WBC count (odds-ratio = 0.55 per standard deviation increase in PGSWBC [95%CI, 0.30−0.94], p = 0.04), an increased risk of leukopenia (a low WBC count) when treated with a chemotherapeutic (n = 1724, hazard ratio [HR] = 0.78 [0.69−0.88], p = 4.0 × 10−5) or immunosuppressant (n = 354, HR = 0.61 [0.38–0.99], p = 0.04). A predisposition to benign lower WBC counts was associated with an increased risk of discontinuing azathioprine treatment (n = 1,466, HR = 0.62 [0.44−0.87], p = 0.006). Collectively, these findings suggest that there are genetically predisposed individuals who are susceptible to escalations or alterations in clinical care that may be harmful or of little benefit.
An approach to identify gene-environment interactions and reveal new biological insight in complex traits
Authors: Zhu Xiaofeng , Yang Yihe , Lorincz-Comi Noah , Li Gen , Bentley Amy R. , de Vries Paul S. , Brown Michael , Morrison Alanna C. , Rotimi Charles N. , Gauderman W. James , Rao Dabeeru C. , Aschard Hugues ,   the CHARGE Gene-lifestyle Interactions Working Group
Published: April 2024

AbstractThere is a long-standing debate about the magnitude of the contribution of gene-environment interactions to phenotypic variations of complex traits owing to the low statistical power and few reported interactions to date. To address this issue, the Gene-Lifestyle Interactions Working Group within the Cohorts for Heart and Aging Research in Genetic Epidemiology Consortium has been spearheading efforts to investigate G × E in large and diverse samples through meta-analysis. Here, we present a powerful new approach to screen for interactions across the genome, an approach that shares substantial similarity to the Mendelian randomization framework. We identify and confirm 5 loci (6 independent signals) interacted with either cigarette smoking or alcohol consumption for serum lipids, and empirically demonstrate that interaction and mediation are the major contributors to genetic effect size heterogeneity across populations. The estimated lower bound of the interaction and environmentally mediated heritability is significant (P < 0.02) for low-density lipoprotein cholesterol and triglycerides in Cross-Population data. Our study improves the understanding of the genetic architecture and environmental contributions to complex traits.
An organic proton cage that is ultra-resistant to hydroxide-promoted degradation
Authors: Radford Chase L. , Saatkamp Torben , Bennet Andrew J. , Holdcroft Steven 
Published: April 2024

AbstractAlkaline polymer membrane electrochemical energy conversion devices offer the prospect of using non-platinum group catalysts. However, their cationic functionalities are currently not sufficiently stable for vapor-phase applications, such as fuel cells. Herein, we report 1,6-diazabicyclo[4.4.4]tetradecan-1,6-ium (in-DBD), a cationic proton cage, that is orders of magnitude more resistant to hydroxide-promoted degradation than state-of-the-art organic cations under ultra-dry conditions and elevated temperature, and the first organic cation-hydroxide to persist at critically low hydration levels ( < 10% RH at 80 °C). This high stability against hydroxide-promoted degradation is due to the unique combination of endohedral protection and intra-bridgehead hydrogen bonding that prevents the removal of the inter-cavity proton and lowers the susceptibility to Hofmann elimination. We anticipate this discovery will facilitate a step-change in the advancement of materials and electrochemical devices utilizing anion-exchange membranes based on in-DBD that will enable stable operation under extreme alkaline conditions.
High-throughput approach to explore cold metals for electronic and thermoelectric devices
Authors: Zhang Ligong , Liu Fei 
Published: April 2024

AbstractCold metals with an energy gap around the Fermi level have been shown a great potential for reducing the power dissipation of transistors and diodes. However, only a limited number of 2D cold metals have been studied. In this work, we explored 3D cold metals through a systematic material search and found 252 types in the database. We performed first-principles calculations to investigate the conductance and work functions of 30 cold metals for material selection. Additionally, we studied the thermoelectric properties of four typical cold metals, which possess much larger Seebeck coefficients and figure-of-merits than conventional metals, by one and two orders of magnitude, respectively. Specifically, we constructed a monolayer MoS2transistor with a cold metal contact of ZrRuSb. Our quantum transport simulations indicate that cold metal contacted MoS2FETs exhibit a subthreshold swing smaller than 60 mV decade−1over four decades, and on-state currents over 1 mA μm−1are achieved at a supply voltage of 0.5 V. Our research provides a theoretical foundation and material basis for exploring 3D cold metals in developing electronic and thermoelectric devices.
An Allee-based distributed algorithm for microbial whole-cell sensors
Authors: Cravo Fabricio , Függer Matthias , Nowak Thomas 
Published: April 2024

AbstractReliable detection of substances present at potentially low concentrations is a problem common to many biomedical applications. Complementary to well-established enzyme-, antibody-antigen-, and sequencing-based approaches, so-called microbial whole-cell sensors, i.e., synthetically engineered microbial cells that sense and report substances, have been proposed as alternatives. Typically these cells operate independently: a cell reports an analyte upon local detection.In this work, we analyze a distributed algorithm for microbial whole-cell sensors, where cells communicate to coordinate if an analyte has been detected. The algorithm, inspired by the Allee effect in biological populations, causes cells to alternate between a logical 0 and 1 state in response to reacting with the particle of interest. When the cells in the logical 1 state exceed a threshold, the algorithm converts the remaining cells to the logical 1 state, representing an easily-detectable output signal. We validate the algorithm through mathematical analysis and simulations, demonstrating that it works correctly even in noisy cellular environments.
In situ observation of mass ejections caused by magnetic reconnections in the ionosphere of Mars
Authors: Ye Yudong , Xu Xiaojun , Lee Lou-Chuang , Yu Jiang , Wang Jing , Zhu Bei , Chang Qing , Xu Jiaying , Xu Qi , Zhou Zilu 
Published: April 2024

AbstractExplosive mass ejections triggered by magnetic activities are common on our Sun and other stars in the Universe. However, there is a lack of evidence for such explosive phenomena in magnetized or partially magnetized planets with atmospheres. Here we present direct evidence for explosive mass ejections from the Martian ionosphere, resulting from magnetic reconnections between strong crustal field regions with open magnetic fields. A plasma density cavity with signatures of magnetic reconnection that is directly evident for an eruptive mass ejection caught in the act indicates that a considerable amount of ionospheric mass has been rapidly ejected into space. Although Martian mass loss associated with magnetic reconnection has been reported previously, our results demonstrate that explosive mass ejections can occur even on partially magnetized planets without global magnetic fields. In this scenario, we suggest that strong localized magnetic fields extending above the exobase are needed.
Irreversible entropy transport enhanced by fermionic superfluidity
Authors: Fabritius Philipp , Mohan Jeffrey , Talebi Mohsen , Wili Simon , Zwerger Wilhelm , Huang Meng-Zi , Esslinger Tilman 
Published: April 2024

AbstractThe nature of particle and entropy flow between two superfluids is often understood in terms of reversible flow carried by an entropy-free, macroscopic wavefunction. While this wavefunction is responsible for many intriguing properties of superfluids and superconductors, its interplay with excitations in non-equilibrium situations is less understood. Here we observe large concurrent flows of both particles and entropy through a ballistic channel connecting two strongly interacting fermionic superfluids. Both currents respond nonlinearly to chemical potential and temperature biases. We find that the entropy transported per particle is much larger than the prediction of superfluid hydrodynamics in the linear regime and largely independent of changes in the channel’s geometry. By contrast, the timescales of advective and diffusive entropy transport vary significantly with the channel geometry. In our setting, superfluidity counterintuitively increases the speed of entropy transport. Moreover, we develop a phenomenological model describing the nonlinear dynamics within the framework of generalized gradient dynamics. Our approach for measuring entropy currents may help elucidate mechanisms of heat transfer in superfluids and superconducting devices.
Comprehensive mass spectrometric metabolomic profiling of a chemically diverse collection of plants of the Celastraceae family
Authors: Quiros-Guerrero Luis-Manuel , Allard Pierre-Marie , Nothias Louis-Felix , David Bruno , Grondin Antonio , Wolfender Jean-Luc 
Published: April 2024

AbstractNatural products exhibit interesting structural features and significant biological activities. The discovery of new bioactive molecules is a complex process that requires high-quality metabolite profiling data to properly target the isolation of compounds of interest and enable their complete structural characterization. The same metabolite profiling data can also be used to better understand chemotaxonomic links between species. This Data Descriptor details a dataset resulting from the untargeted liquid chromatography-mass spectrometry metabolite profiling of 76 natural extracts of the Celastraceae family. The spectral annotation results and related chemical and taxonomic metadata are shared, along with proposed examples of data reuse. This data can be further studied by researchers exploring the chemical diversity of natural products. This can serve as a reference sample set for deep metabolome investigation of this chemically rich plant family.
A Prolonged Artificial Nighttime-light Dataset of China (1984-2020)
Authors: Zhang Lixian , Ren Zhehao , Chen Bin , Gong Peng , Xu Bing , Fu Haohuan 
Published: April 2024

AbstractNighttime light remote sensing has been an increasingly important proxy for human activities. Despite an urgent need for long-term products and pilot explorations in synthesizing them, the publicly available long-term products are limited. A Night-Time Light convolutional LSTM network is proposed and applied the network to produce a 1-km annual Prolonged Artificial Nighttime-light DAtaset of China (PANDA-China) from 1984 to 2020. Assessments between modeled and original images show that on average the RMSE reaches 0.73, the coefficient of determination (R2) reaches 0.95, and the linear slope is 0.99 at the pixel level, indicating a high confidence in the quality of generated data products. Quantitative and visual comparisons witness PANDA-China’s superiority against other NTL datasets in its significantly longer NTL dynamics, higher temporal consistency, and better correlations with socioeconomics (built-up areas, gross domestic product, population) characterizing the most relevant indicator in different development phases. The PANDA-China product provides an unprecedented opportunity to trace nighttime light dynamics in the past four decades.