bluuebunny/crossref_metadata_2025_split huggingface dataset:
Climatic Drivers for the Variation of Gross Primary Productivity Across Terrestrial Ecosystems in the United States
Authors: Chen Yan , Wang Guiling , Seth Anji 
Published: August 2024

AbstractTemperature and water stress are important factors limiting the gross primary productivity (GPP) in terrestrial ecosystems, yet the extent of their influence across ecosystems remains uncertain. This study examines how surface air temperature, soil water availability (SWA) and vapor pressure deficit (VPD) influence ecosystem light use efficiency (LUE), a critical metric for assessing GPP, across different ecosystems and climatic zones at 80 flux tower sites based on in situ measurements and data assimilation products. Results indicate that LUE increases with temperature in spring, with higher correlation coefficients in colder regions (0.79–0.82) than in warmer regions (0.68–0.78). LUE reaches a plateau earlier in the season in warmer regions. LUE variations in summer are mainly driven by SWA, exhibiting a positive correlation indicative of a water‐limited regime. The relationship between the daily LUE and daytime temperature shows a clear seasonal hysteresis at many sites, with a higher LUE in spring than in fall under the same temperature, likely resulting from younger leaves being more efficient in photosynthesis. Drought stress influences LUE through SWA in all ranges of water availability; VPD variation under moderate conditions does not have a clear influence on LUE, but extremely high VPD (exceeding the threshold of 1.6 kPa, often observed during extreme drought‐heat events) causes a dramatic reduction of LUE. Our findings provide insight into how ecosystem productivities respond to climate variability and how they may change under the influence of more frequent and severe heat and drought events projected for the future.
Machine Learning‐Based Hydrofacies Classification: Effects of Noise and Regularization
Authors: Oladeji Emmanuel , Parsekian Andrew , Grana Dario 
Published: August 2024

AbstractThis study utilizes an unsupervised ML approach, the expectation‐maximization (EM) algorithm using Gaussian Mixture Models (GMM), to integrate near‐surface geophysics measurements for hydrofacies classification. We examined the impact of noise and noise estimation on classification across two synthetic models with varying lateral heterogeneity, simulating and inverting resistivity and seismic data with noise levels ranging from minimal to very high. The algorithm proved robust in accurately reconstructing hydrofacies when noise was correctly estimated or not significantly underestimated, showing minimal misclassification in shallow hydrofacies. However, severe underestimation of noise during inversion led to increased misclassifications and artifact‐laden hydrofacies models, especially in shallow regions. Higher lateral heterogeneity lessened the negative impact of noise, slightly improving algorithm performance when noise was correctly estimated. We also explored the influence of geophysical measurement uncertainties on classification uncertainty through hydrofacies probability maps, noting the greatest impact when noise was underestimated. Additionally, we investigated the effect of the regularization trade‐off parameter on the hydrofacies classification and show how the performance of the algorithm can be evaluated in the absence of ground truth data using the average silhouette score of the classification with data obtained from a basement complex field site. We found that moderate regularization (λ = 200) yielded the best hydrofacies model, as indicated by the highest average silhouette score. Our findings underscore the effectiveness of unsupervised ML for facies classification and emphasizes the critical role of accurate noise characterization in geophysical data processing for enhancing the integration of subsurface heterogeneity information into hydrological models.
A dual inhibitor of PIP5K1C and PIKfyve prevents SARS-CoV-2 entry into cells
Authors: Seo Yuri , Jang Yejin , Lee Seon-gyeong , Rhlee Joon Ho , Kong Sukyeong , Vo Thi Tuyet Hanh , Kim Myung hun , Lee Myoung Kyu , Kim Byungil , Hong Sung You , Kim Meehyein , Lee Joo-Yong , Myung Kyungjae 
Published: August 2024

AbstractThe SARS-CoV-2 pandemic has had an unprecedented impact on global public health and the economy. Although vaccines and antivirals have provided effective protection and treatment, the development of new small molecule-based antiviral candidates is imperative to improve clinical outcomes against SARS-CoV-2. In this study, we identified UNI418, a dual PIKfyve and PIP5K1C inhibitor, as a new chemical agent that inhibits SARS-CoV-2 entry into host cells. UNI418 inhibited the proteolytic activation of cathepsins, which is regulated by PIKfyve, resulting in the inhibition of cathepsin L-dependent proteolytic cleavage of the SARS-CoV-2 spike protein into its mature form, a critical step for viral endosomal escape. We also demonstrated that UNI418 prevented ACE2-mediated endocytosis of the virus via PIP5K1C inhibition. Our results identified PIKfyve and PIP5K1C as potential antiviral targets and UNI418 as a putative therapeutic compound against SARS-CoV-2.
Astrocytic 5-HT1A receptor mediates age-dependent hippocampal LTD and fear memory extinction in male mice
Authors: Wu Qian-Yun , Lin Lian-Hong , Lu Kun , Deng Si-Fu , Li Wei-Min , Xu Yuan , Zhang Bin , Liu Ji-Hong 
Published: August 2024

AbstractNMDA receptor-dependent long-term depression (LTD) in the hippocampus is a well-known form of synaptic plasticity that has been linked to different cognitive functions. Although the underlying mechanisms remain unclear, this form of LTD cannot be induced by low-frequency stimulation (LFS) in adult mice. In this study, we found that LFS-induced LTD was not easily induced in adult animals and was age dependent. Interestingly, the level of the 5-HT1A receptor was correspondingly increased and exhibited an inverse correlation with the magnitude of LFS-LTD during development. Knockout or pharmacological inhibition of the 5-HT1A receptor reversed impaired LFS-LTD in adult mice (P60), while activation or inhibition of this receptor disturbed or enhanced LFS-LTD in adolescent mice (P21), respectively. Furthermore, the astrocytic 5-HT1A receptor in the hippocampus predominantly mediated age-dependent LFS-LTD through enhancing GABAergic neurotransmission. Finally, fear memory extinction differed among the above conditions. These observations enrich our knowledge of LTD at the cellular level and suggest a therapeutic approach for LTD-related psychiatric disorders.
Tailored antisense oligonucleotides designed to correct aberrant splicing reveal actionable groups of mutations for rare genetic disorders
Authors: Wai Htoo A. , Svobodova Eliska , Herrera Natalia Romero , Douglas Andrew G. L. , Holloway John W. , Baralle Francisco E. , Baralle Marco , Baralle Diana 
Published: August 2024

AbstractEffective translation of rare disease diagnosis knowledge into therapeutic applications is achievable within a reasonable timeframe; where mutations are amenable to current antisense oligonucleotide technology. In our study, we identified five distinct types of abnormal splice-causing mutations in patients with rare genetic disorders and developed a tailored antisense oligonucleotide for each mutation type using phosphorodiamidate morpholino oligomers with or without octa-guanidine dendrimers and 2′-O-methoxyethyl phosphorothioate. We observed variations in treatment effects and efficiencies, influenced by both the chosen chemistry and the specific nature of the aberrant splicing patterns targeted for correction. Our study demonstrated the successful correction of all five different types of aberrant splicing. Our findings reveal that effective correction of aberrant splicing can depend on altering the chemical composition of oligonucleotides and suggest a fast, efficient, and feasible approach for developing personalized therapeutic interventions for genetic disorders within short time frames.
Towards mixed physical node reservoir computing: light-emitting synaptic reservoir system with dual photoelectric output
Authors: Lian Minrui , Gao Changsong , Lin Zhenyuan , Shan Liuting , Chen Cong , Zou Yi , Cheng Enping , Liu Changfei , Guo Tailiang , Chen Wei , Chen Huipeng 
Published: August 2024

AbstractMemristor-based physical reservoir computing holds significant potential for efficiently processing complex spatiotemporal data, which is crucial for advancing artificial intelligence. However, owing to the single physical node mapping characteristic of traditional memristor reservoir computing, it inevitably induces high repeatability of eigenvalues to a certain extent and significantly limits the efficiency and performance of memristor-based reservoir computing for complex tasks. Hence, this work firstly reports an artificial light-emitting synaptic (LES) device with dual photoelectric output for reservoir computing, and a reservoir system with mixed physical nodes is proposed. The system effectively transforms the input signal into two eigenvalue outputs using a mixed physical node reservoir comprising distinct physical quantities, namely optical output with nonlinear optical effects and electrical output with memory characteristics. Unlike previously reported memristor-based reservoir systems, which pursue rich reservoir states in one physical dimension, our mixed physical node reservoir system can obtain reservoir states in two physical dimensions with one input without increasing the number and types of devices. The recognition rate of the artificial light-emitting synaptic reservoir system can achieve 97.22% in MNIST recognition. Furthermore, the recognition task of multichannel images can be realized through the nonlinear mapping of the photoelectric dual reservoir, resulting in a recognition accuracy of 99.25%. The mixed physical node reservoir computing proposed in this work is promising for implementing the development of photoelectric mixed neural networks and material-algorithm collaborative design.
Upconversion-based chiral nanoprobe for highly selective dual-mode sensing and bioimaging of hydrogen sulfide in vitro and in vivo
Authors: Lu Yang , Zhao Xu , Yan Dongmei , Mi Yingqian , Sun Peng , Yan Xu , Liu Xiaomin , Lu Geyu 
Published: August 2024

AbstractChiral assemblies have become one of the most active research areas due to their versatility, playing an increasingly important role in bio-detection, imaging and therapy. In this work, chiral UCNPs/CuxOS@ZIF nanoprobes are prepared by encapsulating upconversion nanoparticles (UCNPs) and CuxOS nanoparticles (NPs) into zeolitic imidazolate framework-8 (ZIF-8). The novel excited-state energy distribution-modulated upconversion nanostructure (NaYbF4@NaYF4: Yb, Er) is selected as the fluorescence source and energy donor for highly efficient fluorescence resonance energy transfer (FRET). CuxOS NP is employed as chiral source and energy acceptor to quench upconversion luminescence (UCL) and provide circular dichroism (CD) signal. Utilizing the natural adsorption and sorting advantages of ZIF-8, the designed nanoprobe can isolate the influence of other common disruptors, thus achieve ultra-sensitive and highly selective UCL/CD dual-mode quantification of H2S in aqueous solution and in living cells. Notably, the nanoprobe is also capable of in vivo intra-tumoral H2S tracking. Our work highlights the multifunctional properties of chiral nanocomposites in sensing and opens a new vision and idea for the preparation and application of chiral nanomaterials in biomedical and biological analysis.
Anisotropic phonon dynamics in Dirac semimetal PtTe2 thin films enabled by helicity-dependent ultrafast light excitation
Authors: Li Ziyang , Chen Yequan , Song Anke , Zhang Jinzhong , Zhang Rong , Zhang Zongzhi , Wang Xuefeng 
Published: August 2024

AbstractCoherent phonons have aroused considerable attention in condensed matter physics owing to their extraordinary capacity of reflecting and controlling the physical properties of matter. However, the investigation on the interaction between coherent phonons and other microscopic particles on the ultrafast timescale within topological systems continues to be an active and unresolved area. Here, we show the energy transfer of coherent optical phonons (COP) in Dirac semimetal PtTe2 thin films using ultrafast optical pump-probe spectroscopy. Specifically, the helicity-dependent light-driven anisotropic COP signals disclose their direct connection with the light-excited anisotropic spin-polarized electrons via an angular momentum transfer. Furthermore, we observe the notable decreases in the COP oscillation frequency and the decay rate with increasing temperatures due to the anharmonic phonon-phonon scattering and electron-phonon scattering in the COP dissipation process, respectively. Our work paves the way for uncovering the coherent phonons in Dirac semimetals for the potential applications in optoelectronics and opto-spintronics.
Opioid use disorder risk alleles in self-reported assigned African American/Afro-Caribbean and European biogeographical genetic ancestry groups and in males and females
Authors: Sprague Jon E. , Freiermuth Caroline E. , Lambert Joshua , Braun Robert , Frey Jennifer A. , Bachmann Daniel J. , Bischof Jason J. , Beaumont Lauren , Lyons Michael S. , Pantalon Michael V. , Punches Brittany E. , Ancona Rachel , Kisor David F. 
Published: August 2024

AbstractThe influence of genetic variants related to opioid use disorder (OUD) was evaluated using multiple logistic regression analysis in self-reported assigned African American/Afro-Caribbean and European biogeographical ancestry groups (BGAGs) and by sex. From a sample size of 1301 adult patients (>18 years of age) seen in emergency departments of three medical centers in Ohio, six variants were found to be associated with OUD. Two of the variants, rs2740574 (CYP3A4) and rs324029 (DRD3), were included in the analysis having met criteria of at least five subjects for each BGAG, variant carrier status, and OUD status combinations. Variant carriers in the African/Afro-Caribbean BGAG had slightly lower predicted probabilities of OUD. Variant carriers in the European BGAG had slightly higher predicted probabilities of OUD. Relative to sex, all the six variants met evaluation criteria (five subjects for all sex, variant, and OUD status combinations). No statistically significant interactions were found between a given variant, BGAGs and sex. Findings suggest variant testing relative to OUD risk can be applied across BGAGs and sex, however, studies in larger populations are needed.
M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops
Authors: Lin Hongda , Cui Zheng , E Tiange , Xu Hailing , Wang Di , Wang Ping , Ruan Xuelei , Liu Libo , Xue Yixue 
Published: August 2024

AbstractGlioma is the most common primary brain tumor, and targeting glioma stem cells (GSCs) has become a key aspect of glioma treatment. In this study, we discovered a molecular network in which circRNA forms an R-loop structure with its parental gene to regulate the biological behavior of GSCs. Genes with abnormal expression in GSCs were screened using RNA-seq and circRNA microarray analyses. The study results showed that high expression of YTHDC1 in GSCs promoted the transportation of N6-methyladenosine (m6A)-modified circPOLR2B from the nucleus to the cytoplasm. Decreased circPOLR2B levels in the nucleus resulted in fewer R-loop structures formed with its parental gene POLR2B. This reduction in R-loop structures relieved the inhibitory effect on POLR2B transcription and upregulated PBX1 expression through alternative polyadenylation (APA) action, thereby promoting the malignant biological behavior of GSCs. Knockdown of YTHDC1, POLR2B, and PBX1 reduced xenograft tumor volume and prolonged the survival of nude mice. The YTHDC1/circPOLR2B/POLR2B/PBX1 axis plays a regulatory role in the biological behavior of GSCs, offering potential targets and novel strategies for the treatment of glioma.
Systemic mechanisms of necrotic cell debris clearance
Authors: Schuermans Sara , Kestens Caine , Marques Pedro Elias 
Published: August 2024

AbstractNecrosis is an overarching term that describes cell death modalities caused by (extreme) adverse conditions in which cells lose structural integrity. A guaranteed consequence of necrosis is the production of necrotic cell remnants, or debris. Necrotic cell debris is a strong trigger of inflammation, and although inflammatory responses are required for tissue healing, necrotic debris may lead to uncontrolled immune responses and collateral damage. Besides local phagocytosis by recruited leukocytes, there is accumulating evidence that extracellular mechanisms are also involved in necrotic debris clearance. In this review, we focused on systemic clearance mechanisms present in the bloodstream and vasculature that often cooperate to drive the clearance of cell debris. We reviewed the contribution and cooperation of extracellular DNases, the actin-scavenger system, the fibrinolytic system and reticuloendothelial cells in performing clearance of necrotic debris. Moreover, associations of the (mis)functioning of these clearance systems with a variety of diseases were provided, illustrating the importance of the mechanisms of clearance of dead cells in the organism.
Achieving net zero greenhouse gas emissions critical to limit climate tipping risks
Authors: Möller Tessa , Högner Annika Ernest , Schleussner Carl-Friedrich , Bien Samuel , Kitzmann Niklas H. , Lamboll Robin D. , Rogelj Joeri , Donges Jonathan F. , Rockström Johan , Wunderling Nico 
Published: August 2024

AbstractUnder current emission trajectories, temporarily overshooting the Paris global warming limit of 1.5 °C is a distinct possibility. Permanently exceeding this limit would substantially increase the probability of triggering climate tipping elements. Here, we investigate the tipping risks associated with several policy-relevant future emission scenarios, using a stylised Earth system model of four interconnected climate tipping elements. We show that following current policies this century would commit to a 45% tipping risk by 2300 (median, 10–90% range: 23–71%), even if temperatures are brought back to below 1.5 °C. We find that tipping risk by 2300 increases with every additional 0.1 °C of overshoot above 1.5 °C and strongly accelerates for peak warming above 2.0 °C. Achieving and maintaining at least net zero greenhouse gas emissions by 2100 is paramount to minimise tipping risk in the long term. Our results underscore that stringent emission reductions in the current decade are critical for planetary stability.
Anchoring PdOx clusters on defective alumina for improved catalytic methane oxidation
Authors: Yu Xiang , Genz Nina S. , Mendes Rafael G. , Ye Xinwei , Meirer Florian , Nachtegaal Maarten , Monai Matteo , Weckhuysen Bert M. 
Published: August 2024

AbstractEvolution of the Pd active centers in size and spatial distribution leads to an irreversible deactivation in many high-temperature catalytic processes. This research demonstrates the use of a defective alumina (Al2O3-x) as catalyst support to anchor Pd atoms and suppress the growth of Pd clusters in catalytic methane oxidation. A combination of operando spectroscopy and density functional theory (DFT) calculations provide insights into the evolution of Pd species and reveals distinct catalytic methane oxidation mechanisms on Pd single atoms, clusters, and nanoparticles (NPs). Among these Pd species, the cluster active centers are found to be the most favorable participants in methane oxidation due to their high dispersion, high content of Pd2+ oxidation state, and resistance to deactivation by carbonates, bicarbonates, and water. The Pd/Al2O3-x catalyst shows increased stability with respect to a Pd/Al2O3 counterpart during simulated aging in alternating reducing and oxidizing conditions due to stronger interactions with the support. This study demonstrates that defect engineering of non-reducible supports can constrain the evolution of active centers, which holds promising potential for widespread utilization across diverse industrial catalytic processes, including various hydrogenation and oxidation reactions.
Neural representational geometries reflect behavioral differences in monkeys and recurrent neural networks
Authors: Fascianelli Valeria , Battista Aldo , Stefanini Fabio , Tsujimoto Satoshi , Genovesio Aldo , Fusi Stefano 
Published: August 2024

AbstractAnimals likely use a variety of strategies to solve laboratory tasks. Traditionally, combined analysis of behavioral and neural recording data across subjects employing different strategies may obscure important signals and give confusing results. Hence, it is essential to develop techniques that can infer strategy at the single-subject level. We analyzed an experiment in which two male monkeys performed a visually cued rule-based task. The analysis of their performance shows no indication that they used a different strategy. However, when we examined the geometry of stimulus representations in the state space of the neural activities recorded in dorsolateral prefrontal cortex, we found striking differences between the two monkeys. Our purely neural results induced us to reanalyze the behavior. The new analysis showed that the differences in representational geometry are associated with differences in the reaction times, revealing behavioral differences we were unaware of. All these analyses suggest that the monkeys are using different strategies. Finally, using recurrent neural network models trained to perform the same task, we show that these strategies correlate with the amount of training, suggesting a possible explanation for the observed neural and behavioral differences.
Yu-Shiba-Rusinov bands in a self-assembled kagome lattice of magnetic molecules
Authors: Farinacci Laëtitia , Reecht Gaël , von Oppen Felix , Franke Katharina J. 
Published: August 2024

AbstractKagome lattices constitute versatile platforms for studying paradigmatic correlated phases. While molecular self-assembly of kagome structures on metallic substrates is promising, it is challenging to realize pristine kagome properties because of hybridization with the bulk degrees of freedom and modified electron-electron interactions. We suggest that a superconducting substrate offers an compelling platform for realizing a magnetic kagome lattice. Exchange coupling induces kagome-derived bands at the interface, which are protected from the bulk by the superconducting energy gap. We realize a magnetic kagome lattice on a superconductor by depositing Fe-porphin-chloride molecules on Pb(111) and using temperature-activated de-chlorination and self-assembly. This allows us to control the formation of smaller kagome precursors and long-range ordered kagome islands. Using scanning tunneling microscopy and spectroscopy at 1.6 K, we identify Yu-Shiba-Rusinov states inside the superconducting energy gap and track their hybridization from the precursors to larger islands, where the kagome lattice induces extended YSR bands. These YSR-derived kagome bands inside the superconducting energy gap allow for long-range coupling and induced pairing correlations, motivating further studies to resolve possible spin-liquid or Kondo-lattice-type behavior.